CB-aln-dp: Rozdiel medzi revíziami

Verzia zo dňa a času 08:27, 22. október 2015

Sekvencie a zarovnania k cvičeniu pre biológov: programy water a needle

Proteínové sekvencie

>sp|P50520|VPS34_SCHPO Phosphatidylinositol 3-kinase vps34 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=vps34 PE=2 SV=2
MDRLVFSYCPSSKVTARFLVKFCFIEYQDSQEPCICTIQLFSGNESGSLMQKCFVSKIPN
KSLLPTELSKISTHEWLDFGVTVSELSLNAKFVVSAWKPSFNDEEVYEFVGCTTYRLFDE
NNLLRQGLQKIPLQTSKEIKKYSPTSLELEQVKEINRLDGLLLKLQLGDVPSVNWLDDIS
FGKIKDFRSKHMSLVTIPILYLDFLQFSFPVVFQRSYYPKSENRVYYSSFDLELNLDSPA
ELKHRRLVRSQRNGPLDKDLKPNSKIRKELESILSYPPSEELSLEEKDLIWKFRFYLTRN
KKAMTKFLKSVVWTDSSEVNQALSLLDSWTEIDIDDALELLSPSFVHPKVRAYAVSRLET
ASNEELLLYLLQLVQALRYDNPISSDERFQPSPLALFLVNRAISSPSIGNDLYWYLVVEI
EDEPVSKLFSSVMFLFQKELSKSVEGRLIRETLSAQAKFVEKLLRISKSVQSFRGTRLKK
IEYLKVLLEDHKYHLLDFHALPLPLDPSVNIVGIIPDACTVFKSTMQPLRLLFKCQDGSK
YPIIFKNGDDLRQDQLVIQILTLMDKLLKKEKLDLHLKPYRILATGPTHGAVQFVPSKTL
ATILAEYHGSVLAYLRENNPDDGLNSANYGIDPVAMDNYVRSCAGYCVITYLLGVGDRHL
DNLLITKDGHFFHADFGYILGRDPKLFSPAMKLSKEMVEGMGGYNSPFYQQFKSYCYTTF
TALRKSSNLILNLFSLMVDANIPDIKFDKEKVVYKVKERFCLQMSESDAIKYFEQLINDS
VSALFPQIIDRMHNLAQYMRS

>tr|B1AKP8|B1AKP8_HUMAN FK506 binding protein 12-rapamycin associated protein 1 OS=Homo sapiens GN=FRAP1 PE=4 SV=1
MNFEAVLHYKHQNQARDEKKKLRHASGANITNATTAATTAATATTTASTEGSNSESEAES
TENSPTPSPLQKKVTEDLSKTLLMYTVPAVQGFFRSISLSRGNNLQDTLRVLTLWFDYGH
WPDVNEALVEGVKAIQIDTWLQVIPQLIARIDTPRPLVGRLIHQLLTDIGRYHPQALIYP
LTVASKSTTTARHNAANKILKNMCEHSNTLVQQAMMVSEELIRVAILWHEMWHEGLEEAS
RLYFGERNVKGMFEVLEPLHAMMERGPQTLKETSFNQAYGRDLMEAQEWCRKYMKSGNVK
DLTQAWDLYYHVFRRISKQLPQLTSLELQYVSPKLLMCRDLELAVPGTYDPNQPIIRIQS
IAPSLQVITSKQRPRKLTLMGSNGHEFVFLLKGHEDLRQDERVMQLFGLVNTLLANDPTS
LRKNLSIQRYAVIPLSTNSGLIGWVPHCDTLHALIRDYREKKKILLNIEHRIMLRMAPDY
DHLTLMQKVEVFEHAVNNTAGDDLAKLLWLKSPSSEVWFDRRTNYTRSLAVMSMVGYILG
LGDRHPSNLMLDRLSGKILHIDFGDCFEVAMTREKFPEKIPFRLTRMLTNAMEVTGLDGN
YRITCHTVMEVLREHKDSVMAVLEAFVYDPLLNWRLMDTNTKGNKRSRTRTDSYSAGQSV
EILDGVELGEPAHKKTGTTVPESIHSFIGDGLVKPEALNKKAIQIINRVRDKLTGRDFSH
DDTLDVPTQVELLIKQATSHENLCQCYIGWCPFW

Lokálne zarovnanie

########################################
# Program: water
# Rundate: Thu 11 Oct 2012 09:37:58
# Commandline: water
#    -asequence ggg1
#    -bsequence ggg2
#    -outfile ggg12.w
# Align_format: srspair
# Report_file: ggg12.w
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: VPS34_SCHPO
# 2: B1AKP8_HUMAN
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 645
# Identity:     124/645 (19.2%)
# Similarity:   221/645 (34.3%)
# Gaps:         211/645 (32.7%)
# Score: 226.0
# 
#
#=======================================

VPS34_SCHPO      235 NLDSPAELKHRRLVRSQRNGPLDKDLKPNSKIRKELESILSYPPSEELSL    284
                     |.:|.||        |..|.|....|:  .|:.::|...|          
B1AKP8_HUMAN      53 NSESEAE--------STENSPTPSPLQ--KKVTEDLSKTL----------     82

VPS34_SCHPO      285 EEKDLIWKFRFYLTRNKKAMTKFLKSVVWTDSSEVNQALSLLDSWTEI--    332
                                 |.....|:..|.:|:..:..:.:...|.:|..|.:.  
B1AKP8_HUMAN      83 ------------LMYTVPAVQGFFRSISLSRGNNLQDTLRVLTLWFDYGH    120

VPS34_SCHPO      333 --DIDDALELLSPSFVHPKVRAYAVSRLETASNEELLLYLLQLVQAL--R    378
                       |:::||           |......:::|         .||::..|  |
B1AKP8_HUMAN     121 WPDVNEAL-----------VEGVKAIQIDT---------WLQVIPQLIAR    150

VPS34_SCHPO      379 YDNP-----------ISSDERFQPS----PLAL-----------------    396
                     .|.|           ::...|:.|.    ||.:                 
B1AKP8_HUMAN     151 IDTPRPLVGRLIHQLLTDIGRYHPQALIYPLTVASKSTTTARHNAANKIL    200

VPS34_SCHPO      397 --------FLVNRA--ISSPSIGNDLYWYLVVEIEDEPVSKLF---SSVM    433
                             .||.:|  :|...|...:.|:.:.....|..|:|:   .:|.
B1AKP8_HUMAN     201 KNMCEHSNTLVQQAMMVSEELIRVAILWHEMWHEGLEEASRLYFGERNVK    250

VPS34_SCHPO      434 FLFQ----------------KELS-----------------KSVEGRLIR    450
                     .:|:                ||.|                 |.::...::
B1AKP8_HUMAN     251 GMFEVLEPLHAMMERGPQTLKETSFNQAYGRDLMEAQEWCRKYMKSGNVK    300

VPS34_SCHPO      451 ETLSAQAKFVEKLLRISKSVQSFRGTRLKKIEYLKVLLEDHKYHLLDFHA    500
                     :...|...:.....||||.:.......|:.:....::..|.:.      |
B1AKP8_HUMAN     301 DLTQAWDLYYHVFRRISKQLPQLTSLELQYVSPKLLMCRDLEL------A    344

VPS34_SCHPO      501 LPLPLDPSVNIVGI--IPDACTVFKSTMQPLRLLFKCQDGSKYPIIFKNG    548
                     :|...||:..|:.|  |..:..|..|..:|.:|.....:|.::..:.|..
B1AKP8_HUMAN     345 VPGTYDPNQPIIRIQSIAPSLQVITSKQRPRKLTLMGSNGHEFVFLLKGH    394

VPS34_SCHPO      549 DDLRQDQLVIQILTLMDKLLKKE----KLDLHLKPYRILATGPTHGAVQF    594
                     :|||||:.|:|:..|::.||..:    :.:|.::.|.::......|.:.:
B1AKP8_HUMAN     395 EDLRQDERVMQLFGLVNTLLANDPTSLRKNLSIQRYAVIPLSTNSGLIGW    444

VPS34_SCHPO      595 VP-SKTLATILAEYHG-----------------------------SVLAY    614
                     || ..||..::.:|..                             .|..:
B1AKP8_HUMAN     445 VPHCDTLHALIRDYREKKKILLNIEHRIMLRMAPDYDHLTLMQKVEVFEH    494

VPS34_SCHPO      615 LRENNPDDGLNSANYGIDP---VAMD---NYVRSCAGYCVITYLLGVGDR    658
                     ...|...|.|....:...|   |..|   ||.||.|...::.|:||:|||
B1AKP8_HUMAN     495 AVNNTAGDDLAKLLWLKSPSSEVWFDRRTNYTRSLAVMSMVGYILGLGDR    544

VPS34_SCHPO      659 HLDNLLITK-DGHFFHADFG--------------YILGRDPKLFSPAMKL    693
                     |..||::.: .|...|.|||              .|..|..::.:.||: 
B1AKP8_HUMAN     545 HPSNLMLDRLSGKILHIDFGDCFEVAMTREKFPEKIPFRLTRMLTNAME-    593

VPS34_SCHPO      694 SKEMVEGMGGYNSPFYQQFKSYCYTTFTALRKSSNLILNLFSLMV    738
                         |.|:.|       .::..|:|....||:..:.::.:....|
B1AKP8_HUMAN     594 ----VTGLDG-------NYRITCHTVMEVLREHKDSVMAVLEAFV    627

Globálne zarovnanie

########################################
# Program: needle
# Rundate: Thu 11 Oct 2012 09:40:40
# Commandline: needle
#    -asequence ggg1
#    -bsequence ggg2
#    -endweight
#    -outfile ggg12.n2
# Align_format: srspair
# Report_file: ggg12.n2
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: VPS34_SCHPO
# 2: B1AKP8_HUMAN
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 948
# Identity:     167/948 (17.6%)
# Similarity:   292/948 (30.8%)
# Gaps:         341/948 (36.0%)
# Score: 130.5
# 
#
#=======================================

VPS34_SCHPO        1 MD-RLVFSYCPSSKVTARFLVKFCFIEYQDSQEPCICTIQLFSGNESGSL     49
                     |: ..|..|                 ::|:            ...:....
B1AKP8_HUMAN       1 MNFEAVLHY-----------------KHQN------------QARDEKKK     21

VPS34_SCHPO       50 MQKCFVSKIPNKSLLPTELSKISTHEWLDFGVTVSELSLNAKFVVSAWKP     99
                     ::....:.|.|.:...|..:..:|                     :|...
B1AKP8_HUMAN      22 LRHASGANITNATTAATTAATATT---------------------TASTE     50

VPS34_SCHPO      100 SFNDEEVYEFVGCTTYRLFDENNLLRQGLQ-KIPLQTSKEIKKYSPTSLE    148
                     ..|.|...|..         ||:.....|| |:....||.:..|:..:::
B1AKP8_HUMAN      51 GSNSESEAEST---------ENSPTPSPLQKKVTEDLSKTLLMYTVPAVQ     91

VPS34_SCHPO      149 ----LEQVKEINRLDGLLLKLQLGDVPSVNWLDDISFGKIKDFRSKHMSL    194
                         ...:...|.|...|..|.|       |.|   :|...|...   :|
B1AKP8_HUMAN      92 GFFRSISLSRGNNLQDTLRVLTL-------WFD---YGHWPDVNE---AL    128

VPS34_SCHPO      195 VT-IPILYLDFLQFSFPVVFQRSYYPKSENRVYYSSFDLELNLDSP----    239
                     |. :..:.:|......|.:..|                    :|:|    
B1AKP8_HUMAN     129 VEGVKAIQIDTWLQVIPQLIAR--------------------IDTPRPLV    158

VPS34_SCHPO      240 AELKHRRLVRSQRNGPLDKDLKPNSKIRKELESILSYPPSEELSLEEKDL    289
                     ..|.|:.|....|..|                ..|.||    |::..|..
B1AKP8_HUMAN     159 GRLIHQLLTDIGRYHP----------------QALIYP----LTVASKST    188

VPS34_SCHPO      290 IWKFRFYLTRNKKAMTKFLKSVVWTDSSEVNQALSLLDSWTEIDI-----    334
                            .|....|..|.||::....::.|.||:.:.:....:.|     
B1AKP8_HUMAN     189 -------TTARHNAANKILKNMCEHSNTLVQQAMMVSEELIRVAILWHEM    231

VPS34_SCHPO      335 -DDALELLSPSFVHPKVRAYAVSRLETASNEELLLYLLQLVQALRYDNPI    383
                      .:.||..|        |.|...|     |.:.:..:|:.:.|:.     
B1AKP8_HUMAN     232 WHEGLEEAS--------RLYFGER-----NVKGMFEVLEPLHAMM-----    263

VPS34_SCHPO      384 SSDERFQPSPLALFLVNRAISSPSIGNDLYWYLVVEIEDEPVSKLFSSVM    433
                        || .|..|.....|:|     .|.||     :|.             
B1AKP8_HUMAN     264 ---ER-GPQTLKETSFNQA-----YGRDL-----MEA-------------    286

VPS34_SCHPO      434 FLFQKELSKSVEGRLIRETLSAQAKFVEKLLRISKSVQSFRGTRLKKIEY    483
                        |:...|.::...:::...|...:.....||||.:.......|:.:..
B1AKP8_HUMAN     287 ---QEWCRKYMKSGNVKDLTQAWDLYYHVFRRISKQLPQLTSLELQYVSP    333

VPS34_SCHPO      484 LKVLLEDHKYHLLDFHALPLPLDPSVNIVGI--IPDACTVFKSTMQPLRL    531
                     ..::..|.:.      |:|...||:..|:.|  |..:..|..|..:|.:|
B1AKP8_HUMAN     334 KLLMCRDLEL------AVPGTYDPNQPIIRIQSIAPSLQVITSKQRPRKL    377

VPS34_SCHPO      532 LFKCQDGSKYPIIFKNGDDLRQDQLVIQILTLMDKLLKKE----KLDLHL    577
                     .....:|.::..:.|..:|||||:.|:|:..|::.||..:    :.:|.:
B1AKP8_HUMAN     378 TLMGSNGHEFVFLLKGHEDLRQDERVMQLFGLVNTLLANDPTSLRKNLSI    427

VPS34_SCHPO      578 KPYRILATGPTHGAVQFVP-SKTLATILAEYHG-----------------    609
                     :.|.::......|.:.:|| ..||..::.:|..                 
B1AKP8_HUMAN     428 QRYAVIPLSTNSGLIGWVPHCDTLHALIRDYREKKKILLNIEHRIMLRMA    477

VPS34_SCHPO      610 ------------SVLAYLRENNPDDGLNSANYGIDP---VAMD---NYVR    641
                                 .|..:...|...|.|....:...|   |..|   ||.|
B1AKP8_HUMAN     478 PDYDHLTLMQKVEVFEHAVNNTAGDDLAKLLWLKSPSSEVWFDRRTNYTR    527

VPS34_SCHPO      642 SCAGYCVITYLLGVGDRHLDNLLITK-DGHFFHADFG-------------    677
                     |.|...::.|:||:||||..||::.: .|...|.|||             
B1AKP8_HUMAN     528 SLAVMSMVGYILGLGDRHPSNLMLDRLSGKILHIDFGDCFEVAMTREKFP    577

VPS34_SCHPO      678 -YILGRDPKLFSPAMKLSKEMVEGMGGYNSPFYQQFKSYCYTTFTALRKS    726
                      .|..|..::.:.||:     |.|:.|       .::..|:|....||:.
B1AKP8_HUMAN     578 EKIPFRLTRMLTNAME-----VTGLDG-------NYRITCHTVMEVLREH    615

VPS34_SCHPO      727 SNLILNLFSLMV----------DAN-------------------------    741
                     .:.::.:....|          |.|                         
B1AKP8_HUMAN     616 KDSVMAVLEAFVYDPLLNWRLMDTNTKGNKRSRTRTDSYSAGQSVEILDG    665

VPS34_SCHPO      742 --------------IPD----------IK---FDKE--KVVYKVKERFC-    761
                                   :|:          :|   .:|:  :::.:|:::.. 
B1AKP8_HUMAN     666 VELGEPAHKKTGTTVPESIHSFIGDGLVKPEALNKKAIQIINRVRDKLTG    715

VPS34_SCHPO      762 LQMSESDAI---KYFEQLINDSVSALFPQIIDRMHNLAQYMRS-----    801
                     ...|..|.:   ...|.||..:.|         ..||.|....     
B1AKP8_HUMAN     716 RDFSHDDTLDVPTQVELLIKQATS---------HENLCQCYIGWCPFW    754

Globálne zarovnanie s nulovou penaltou medzier na koncoch sekvencie

########################################
# Program: needle
# Rundate: Thu 11 Oct 2012 09:37:33
# Commandline: needle
#    -asequence ggg1
#    -bsequence ggg2
#    -outfile ggg12.n
# Align_format: srspair
# Report_file: ggg12.n
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: VPS34_SCHPO
# 2: B1AKP8_HUMAN
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 1060
# Identity:     138/1060 (13.0%)
# Similarity:   245/1060 (23.1%)
# Gaps:         565/1060 (53.3%)
# Score: 206.0
# 
#
#=======================================

VPS34_SCHPO        1 MDRLVFSYCPSSKVTARFLVKFCFIEYQDSQEPCICTIQLFSGNESGSLM     50
                                                                       
B1AKP8_HUMAN       0 --------------------------------------------------      0

VPS34_SCHPO       51 QKCFVSKIPNKSLLPTELSKISTHEWLDFGVTVSELSLNAKFVVSAWKPS    100
                                                                       
B1AKP8_HUMAN       0 --------------------------------------------------      0

VPS34_SCHPO      101 FNDEEVYEFVGCTTYRLFDENNLLRQGLQKIPLQTSKEIKKYSPTSLELE    150
                                                                       
B1AKP8_HUMAN       0 --------------------------------------------------      0

VPS34_SCHPO      151 QVKEINRLDGLLLKLQLGDVPSVNWLDDISFGKIKDFRSKHMSLVTIPIL    200
                                                                       
B1AKP8_HUMAN       0 --------------------------------------------------      0

VPS34_SCHPO      201 YLDFLQFSFPVVFQRSYYPKSENRVYYSSFDLELNLDSPAELKHRRLVRS    250
                                                      :|.::....||:...|.
B1AKP8_HUMAN       1 ---------------------------------MNFEAVLHYKHQNQARD     17

VPS34_SCHPO      251 QRNGPLDKDLK--------------------------PNSKIRKELESIL    274
                     ::     |.|:                          ..|....|.||..
B1AKP8_HUMAN      18 EK-----KKLRHASGANITNATTAATTAATATTTASTEGSNSESEAESTE     62

VPS34_SCHPO      275 SYP-PSEELSLEEKDLIWKFRFYLTRNKKAMTKFLKSVVWTDSSEVNQAL    323
                     :.| ||.......:||......|..   .|:..|.:|:..:..:.:...|
B1AKP8_HUMAN      63 NSPTPSPLQKKVTEDLSKTLLMYTV---PAVQGFFRSISLSRGNNLQDTL    109

VPS34_SCHPO      324 SLLDSWTEI----DIDDALELLSPSFVHPKVRAYAVSRLETASNEELLLY    369
                     .:|..|.:.    |:::||           |......:::|         
B1AKP8_HUMAN     110 RVLTLWFDYGHWPDVNEAL-----------VEGVKAIQIDT---------    139

VPS34_SCHPO      370 LLQLVQAL--RYDNP-----------ISSDERFQPS----PLAL------    396
                     .||::..|  |.|.|           ::...|:.|.    ||.:      
B1AKP8_HUMAN     140 WLQVIPQLIARIDTPRPLVGRLIHQLLTDIGRYHPQALIYPLTVASKSTT    189

VPS34_SCHPO      397 -------------------FLVNRA--ISSPSIGNDLYWYLVVEIEDEPV    425
                                        .||.:|  :|...|...:.|:.:.....|..
B1AKP8_HUMAN     190 TARHNAANKILKNMCEHSNTLVQQAMMVSEELIRVAILWHEMWHEGLEEA    239

VPS34_SCHPO      426 SKLF---SSVMFLFQ----------------KELS---------------    441
                     |:|:   .:|..:|:                ||.|               
B1AKP8_HUMAN     240 SRLYFGERNVKGMFEVLEPLHAMMERGPQTLKETSFNQAYGRDLMEAQEW    289

VPS34_SCHPO      442 --KSVEGRLIRETLSAQAKFVEKLLRISKSVQSFRGTRLKKIEYLKVLLE    489
                       |.::...:::...|...:.....||||.:.......|:.:....::..
B1AKP8_HUMAN     290 CRKYMKSGNVKDLTQAWDLYYHVFRRISKQLPQLTSLELQYVSPKLLMCR    339

VPS34_SCHPO      490 DHKYHLLDFHALPLPLDPSVNIVGI--IPDACTVFKSTMQPLRLLFKCQD    537
                     |.:.      |:|...||:..|:.|  |..:..|..|..:|.:|.....:
B1AKP8_HUMAN     340 DLEL------AVPGTYDPNQPIIRIQSIAPSLQVITSKQRPRKLTLMGSN    383

VPS34_SCHPO      538 GSKYPIIFKNGDDLRQDQLVIQILTLMDKLLKKE----KLDLHLKPYRIL    583
                     |.::..:.|..:|||||:.|:|:..|::.||..:    :.:|.::.|.::
B1AKP8_HUMAN     384 GHEFVFLLKGHEDLRQDERVMQLFGLVNTLLANDPTSLRKNLSIQRYAVI    433

VPS34_SCHPO      584 ATGPTHGAVQFVP-SKTLATILAEYHG-----------------------    609
                     ......|.:.:|| ..||..::.:|..                       
B1AKP8_HUMAN     434 PLSTNSGLIGWVPHCDTLHALIRDYREKKKILLNIEHRIMLRMAPDYDHL    483

VPS34_SCHPO      610 ------SVLAYLRENNPDDGLNSANYGIDP---VAMD---NYVRSCAGYC    647
                           .|..:...|...|.|....:...|   |..|   ||.||.|...
B1AKP8_HUMAN     484 TLMQKVEVFEHAVNNTAGDDLAKLLWLKSPSSEVWFDRRTNYTRSLAVMS    533

VPS34_SCHPO      648 VITYLLGVGDRHLDNLLITK-DGHFFHADFG--------------YILGR    682
                     ::.|:||:||||..||::.: .|...|.|||              .|..|
B1AKP8_HUMAN     534 MVGYILGLGDRHPSNLMLDRLSGKILHIDFGDCFEVAMTREKFPEKIPFR    583

VPS34_SCHPO      683 DPKLFSPAMKLSKEMVEGMGGYNSPFYQQFKSYCYTTFTALRKSSNLILN    732
                     ..::.:.||:     |.|:.|       .::..|:|....||:..:.::.
B1AKP8_HUMAN     584 LTRMLTNAME-----VTGLDG-------NYRITCHTVMEVLREHKDSVMA    621

VPS34_SCHPO      733 LFSLMV----------DANIPDIKFDKEKVVYKVKERFCLQMSESDAIKY    772
                     :....|          |.|....|..:.:                     
B1AKP8_HUMAN     622 VLEAFVYDPLLNWRLMDTNTKGNKRSRTR---------------------    650

VPS34_SCHPO      773 FEQLINDSVSA-LFPQIIDRMHNLAQYMRS--------------------    801
                          .||.|| ...:|:|.: .|.:....                    
B1AKP8_HUMAN     651 -----TDSYSAGQSVEILDGV-ELGEPAHKKTGTTVPESIHSFIGDGLVK    694

VPS34_SCHPO      801 --------------------------------------------------    801
                                                                       
B1AKP8_HUMAN     695 PEALNKKAIQIINRVRDKLTGRDFSHDDTLDVPTQVELLIKQATSHENLC    744

VPS34_SCHPO      801 ----------    801
                               
B1AKP8_HUMAN     745 QCYIGWCPFW    754