1-BIN-301, 2-AIN-501 Methods in Bioinformatics, 2021/22

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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
>RKM3_YEAST
MSVTFKDDVHRILKFVANCNGRFEDSKCDIRESPLGGLGVFAKTDIAEGESILTLNKSSI
FSASNSSIANLLCDSSIDGMLALNIAFIYETTVFRNSSHWYPFLRTIRIRDDEGHLNLPP
SFWHADAKRLLKGTSFDTLFDSLAPEEEIMEGFEIAVDLAHKWNDEFGLEIPKGFLDVSE
ENHEEDYNLKLEKFISVAYTLSSRGFEIDAYHETALVPIADLFNHHVSDPDLKFVSLYDV
CDKCGEPDMCKHLIAEEYLEAENLDKNMPKVASMETRVIDEDLIKSLENDLEKEYSNVTA
NIEDDDGGIENPDECVDLVLKNDVAQGQEIFNSYGELSNVFLLARYGFTVPENQYDIVHL
GPDFMKILKKEEKYQEKVKWWSQVGHGLFSAWYAQMRQEDEEDEDGQAKSDNLSDDIESE
EEEEEEEGDDSLESWLSQLYIDSSGEPSPSTWALANLLTLTAVQWESLFSKKATPHISDS
IVNEEKLPFLAKKDNPHSKKLLSNLLKEKQLPCIKGDNSSKITSATKSMLQNARTLVQSE
HNILDRCLKRLS

Lokálne zarovnanie

########################################
# Program: water
# Rundate: Thu 14 Oct 2021 15:08:56
# Commandline: water
#    -auto
#    -stdout
#    -asequence emboss_water-I20211014-150851-0938-20653107-p2m.asequence
#    -bsequence emboss_water-I20211014-150851-0938-20653107-p2m.bsequence
#    -datafile EBLOSUM62
#    -gapopen 10.0
#    -gapextend 0.5
#    -aformat3 pair
#    -sprotein1
#    -sprotein2
# Align_format: pair
# Report_file: stdout
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: MCA_00027_1
# 2: RKM3_YEAST
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 588
# Identity:     170/588 (28.9%)
# Similarity:   270/588 (45.9%)
# Gaps:         116/588 (19.7%)
# Score: 611.0
# 
#
#=======================================

MCA_00027_1       29 IRESPLGGIGVFARKKIPKSSLILMVPKNVILSPSNCSISNLLDEADFDG     78
                     ||||||||:||||:..|.:...||.:.|:.|.|.||.||:|||.::..||
RKM3_YEAST        30 IRESPLGGLGVFAKTDIAEGESILTLNKSSIFSASNSSIANLLCDSSIDG     79

MCA_00027_1       79 MLGLALAYMYERSLGPDSL-WYEFIQTI---DHDSLISENPRFWPPEDEE    124
                     ||.|.:|::||.::..:|. ||.|::||   |.:..::..|.||..:.:.
RKM3_YEAST        80 MLALNIAFIYETTVFRNSSHWYPFLRTIRIRDDEGHLNLPPSFWHADAKR    129

MCA_00027_1      125 LLVGTELYYHTL---KVEDDDIAEVFKFDV------------------LP    153
                     ||.||.  :.||   ...:::|.|.|:..|                  |.
RKM3_YEAST       130 LLKGTS--FDTLFDSLAPEEEIMEGFEIAVDLAHKWNDEFGLEIPKGFLD    177

MCA_00027_1      154 FLERNHLFEGQPQYR-TLEYYRDCLVAVASRAFDVDVYHGLALVPGACLF    202
                     ..|.||    :..|. .||.:......::||.|::|.||..||||.|.||
RKM3_YEAST       178 VSEENH----EEDYNLKLEKFISVAYTLSSRGFEIDAYHETALVPIADLF    223

MCA_00027_1      203 NHSI-DESVHFEVVSQVCPLCGSPDFCDHLANRLGNHSESDEEEEEEEVD    251
                     ||.: |..:.|..:..||..||.||.|.||.        ::|..|.|.:|
RKM3_YEAST       224 NHHVSDPDLKFVSLYDVCDKCGEPDMCKHLI--------AEEYLEAENLD    265

MCA_00027_1      252 ELNEDGFSSGFDYSDSESDSDGFEDIEEEEEEDGIIGSEETTIPISEDSD    301
                     :....                              :.|.||.: |.||..
RKM3_YEAST       266 KNMPK------------------------------VASMETRV-IDEDLI    284

MCA_00027_1      302 KKTSNEQKSEEQEAEKYQYEEDDEDEADYDEPQDTCDIVTIKSVHKGNEV    351
                     |...|:.:.|.....    ...::|:...:.|.:..|:|....|.:|.|:
RKM3_YEAST       285 KSLENDLEKEYSNVT----ANIEDDDGGIENPDECVDLVLKNDVAQGQEI    330

MCA_00027_1      352 FNTYGELSNHHLASRYGFAIWDNKYETVGLSPEIRQYI-SENNLMERQEW    400
                     ||:||||||..|.:||||.:.:|:|:.|.|.|:..:.: .|....|:.:|
RKM3_YEAST       331 FNSYGELSNVFLLARYGFTVPENQYDIVHLGPDFMKILKKEEKYQEKVKW    380

MCA_00027_1      401 WSIYFYEALFGIRKDEWAEIEESEDEDDEG------------SEDSEEEN    438
                     ||    :...|:....:|::.:.::||::|            ||:.|||.
RKM3_YEAST       381 WS----QVGHGLFSAWYAQMRQEDEEDEDGQAKSDNLSDDIESEEEEEEE    426

MCA_00027_1      439 SIPPSPESISWEDEAYLTNSGAPSEGLSKLIRILSMSDSDFEALKSQFER    488
                     ....|.|  ||..:.|:.:||.||.....|..:|:::...:|:|      
RKM3_YEAST       427 EGDDSLE--SWLSQLYIDSSGEPSPSTWALANLLTLTAVQWESL------    468

MCA_00027_1      489 DVFTSKLLPS-STLVFNEKSLILLKALVNLRLQRYKDGMLTSSQI-----    532
                       |:.|..|. |..:.||:.|..|....|...::....:|...|:     
RKM3_YEAST       469 --FSKKATPHISDSIVNEEKLPFLAKKDNPHSKKLLSNLLKEKQLPCIKG    516

MCA_00027_1      533 --KDLITKLSDNQKKNSRQILALTIKGTEKIVLEKSMQ    568
                       ...||..:.:..:|:|     |:..:|..:|::.::
RKM3_YEAST       517 DNSSKITSATKSMLQNAR-----TLVQSEHNILDRCLK    549

Globálne zarovnanie

########################################
# Program: needle
# Rundate: Thu 14 Oct 2021 15:13:34
# Commandline: needle
#    -auto
#    -stdout
#    -asequence emboss_needle-I20211014-151332-0965-44565643-p2m.asequence
#    -bsequence emboss_needle-I20211014-151332-0965-44565643-p2m.bsequence
#    -datafile EBLOSUM62
#    -gapopen 10.0
#    -gapextend 0.5
#    -endweight
#    -endopen 10.0
#    -endextend 0.5
#    -aformat3 pair
#    -sprotein1
#    -sprotein2
# Align_format: pair
# Report_file: stdout
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: MCA_00027_1
# 2: RKM3_YEAST
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 650
# Identity:     178/650 (27.4%)
# Similarity:   282/650 (43.4%)
# Gaps:         153/650 (23.5%)
# Score: 588.5
# 
#
#=======================================

MCA_00027_1        1 MEDSL---MERYQSFV----GWMLDNKIQFSSLLTIRESPLGGIGVFARK     43
                     |..:.   :.|...||    |...|:|..      ||||||||:||||:.
RKM3_YEAST         1 MSVTFKDDVHRILKFVANCNGRFEDSKCD------IRESPLGGLGVFAKT     44

MCA_00027_1       44 KIPKSSLILMVPKNVILSPSNCSISNLLDEADFDGMLGLALAYMYERSLG     93
                     .|.:...||.:.|:.|.|.||.||:|||.::..||||.|.:|::||.::.
RKM3_YEAST        45 DIAEGESILTLNKSSIFSASNSSIANLLCDSSIDGMLALNIAFIYETTVF     94

MCA_00027_1       94 PDSL-WYEFIQTI---DHDSLISENPRFWPPEDEELLVGTELYYHTL---    136
                     .:|. ||.|::||   |.:..::..|.||..:.:.||.||.  :.||   
RKM3_YEAST        95 RNSSHWYPFLRTIRIRDDEGHLNLPPSFWHADAKRLLKGTS--FDTLFDS    142

MCA_00027_1      137 KVEDDDIAEVFKFDV------------------LPFLERNHLFEGQPQYR    168
                     ...:::|.|.|:..|                  |...|.||    :..|.
RKM3_YEAST       143 LAPEEEIMEGFEIAVDLAHKWNDEFGLEIPKGFLDVSEENH----EEDYN    188

MCA_00027_1      169 -TLEYYRDCLVAVASRAFDVDVYHGLALVPGACLFNHSI-DESVHFEVVS    216
                      .||.:......::||.|::|.||..||||.|.||||.: |..:.|..:.
RKM3_YEAST       189 LKLEKFISVAYTLSSRGFEIDAYHETALVPIADLFNHHVSDPDLKFVSLY    238

MCA_00027_1      217 QVCPLCGSPDFCDHLANRLGNHSESDEEEEEEEVDELNEDGFSSGFDYSD    266
                     .||..||.||.|.||.        ::|..|.|.:|:....          
RKM3_YEAST       239 DVCDKCGEPDMCKHLI--------AEEYLEAENLDKNMPK----------    270

MCA_00027_1      267 SESDSDGFEDIEEEEEEDGIIGSEETTIPISEDSDKKTSNEQKSEEQEAE    316
                                         :.|.||.: |.||..|...|:.:.|.....
RKM3_YEAST       271 --------------------VASMETRV-IDEDLIKSLENDLEKEYSNVT    299

MCA_00027_1      317 KYQYEEDDEDEADYDEPQDTCDIVTIKSVHKGNEVFNTYGELSNHHLASR    366
                         ...::|:...:.|.:..|:|....|.:|.|:||:||||||..|.:|
RKM3_YEAST       300 ----ANIEDDDGGIENPDECVDLVLKNDVAQGQEIFNSYGELSNVFLLAR    345

MCA_00027_1      367 YGFAIWDNKYETVGLSPEIRQYI-SENNLMERQEWWSIYFYEALFGIRKD    415
                     |||.:.:|:|:.|.|.|:..:.: .|....|:.:|||    :...|:...
RKM3_YEAST       346 YGFTVPENQYDIVHLGPDFMKILKKEEKYQEKVKWWS----QVGHGLFSA    391

MCA_00027_1      416 EWAEIEESEDEDDEG------------SEDSEEENSIPPSPESISWEDEA    453
                     .:|::.:.::||::|            ||:.|||.....|.|  ||..:.
RKM3_YEAST       392 WYAQMRQEDEEDEDGQAKSDNLSDDIESEEEEEEEEGDDSLE--SWLSQL    439

MCA_00027_1      454 YLTNSGAPSEGLSKLIRILSMSDSDFEALKSQFERDVFTSKLLPS-STLV    502
                     |:.:||.||.....|..:|:::...:|:|        |:.|..|. |..:
RKM3_YEAST       440 YIDSSGEPSPSTWALANLLTLTAVQWESL--------FSKKATPHISDSI    481

MCA_00027_1      503 FNEKSLILLKALVNLRLQRYKDGMLTSSQI-------KDLITKLSDNQKK    545
                     .||:.|..|....|...::....:|...|:       ...||..:.:..:
RKM3_YEAST       482 VNEEKLPFLAKKDNPHSKKLLSNLLKEKQLPCIKGDNSSKITSATKSMLQ    531

MCA_00027_1      546 NSRQILALTIKGTEKIVLEKSMQWIAQLEKKKKRKPSNSNHKKPNSRKLK    595
                     |:|     |:..:|..:|::.:                        ::|.
RKM3_YEAST       532 NAR-----TLVQSEHNILDRCL------------------------KRLS    552

Globálne zarovnanie s nulovou penaltou medzier na koncoch sekvencie

########################################
# Program: needle
# Rundate: Thu 14 Oct 2021 15:05:37
# Commandline: needle
#    -auto
#    -stdout
#    -asequence emboss_needle-I20211014-151156-0154-17922699-p1m.asequence
#    -bsequence emboss_needle-I20211014-151156-0154-17922699-p1m.bsequence
#    -datafile EBLOSUM62
#    -gapopen 10.0
#    -gapextend 0.5
#    -endopen 10.0
#    -endextend 0.5
#    -aformat3 pair
#    -sprotein1
#    -sprotein2
# Align_format: pair
# Report_file: stdout
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: MCA_00027_1
# 2: RKM3_YEAST
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 651
# Identity:     177/651 (27.2%)
# Similarity:   282/651 (43.3%)
# Gaps:         155/651 (23.8%)
# Score: 608.0
# 
#
#=======================================

MCA_00027_1        1 ----MEDSLMERYQSFV----GWMLDNKIQFSSLLTIRESPLGGIGVFAR     42
                         .:|. :.|...||    |...|:|..      ||||||||:||||:
RKM3_YEAST         1 MSVTFKDD-VHRILKFVANCNGRFEDSKCD------IRESPLGGLGVFAK     43

MCA_00027_1       43 KKIPKSSLILMVPKNVILSPSNCSISNLLDEADFDGMLGLALAYMYERSL     92
                     ..|.:...||.:.|:.|.|.||.||:|||.::..||||.|.:|::||.::
RKM3_YEAST        44 TDIAEGESILTLNKSSIFSASNSSIANLLCDSSIDGMLALNIAFIYETTV     93

MCA_00027_1       93 GPDSL-WYEFIQTI---DHDSLISENPRFWPPEDEELLVGTELYYHTL--    136
                     ..:|. ||.|::||   |.:..::..|.||..:.:.||.||.  :.||  
RKM3_YEAST        94 FRNSSHWYPFLRTIRIRDDEGHLNLPPSFWHADAKRLLKGTS--FDTLFD    141

MCA_00027_1      137 -KVEDDDIAEVFKFDV------------------LPFLERNHLFEGQPQY    167
                      ...:::|.|.|:..|                  |...|.||    :..|
RKM3_YEAST       142 SLAPEEEIMEGFEIAVDLAHKWNDEFGLEIPKGFLDVSEENH----EEDY    187

MCA_00027_1      168 R-TLEYYRDCLVAVASRAFDVDVYHGLALVPGACLFNHSI-DESVHFEVV    215
                     . .||.:......::||.|::|.||..||||.|.||||.: |..:.|..:
RKM3_YEAST       188 NLKLEKFISVAYTLSSRGFEIDAYHETALVPIADLFNHHVSDPDLKFVSL    237

MCA_00027_1      216 SQVCPLCGSPDFCDHLANRLGNHSESDEEEEEEEVDELNEDGFSSGFDYS    265
                     ..||..||.||.|.||.        ::|..|.|.:|:....         
RKM3_YEAST       238 YDVCDKCGEPDMCKHLI--------AEEYLEAENLDKNMPK---------    270

MCA_00027_1      266 DSESDSDGFEDIEEEEEEDGIIGSEETTIPISEDSDKKTSNEQKSEEQEA    315
                                          :.|.||.: |.||..|...|:.:.|....
RKM3_YEAST       271 ---------------------VASMETRV-IDEDLIKSLENDLEKEYSNV    298

MCA_00027_1      316 EKYQYEEDDEDEADYDEPQDTCDIVTIKSVHKGNEVFNTYGELSNHHLAS    365
                     .    ...::|:...:.|.:..|:|....|.:|.|:||:||||||..|.:
RKM3_YEAST       299 T----ANIEDDDGGIENPDECVDLVLKNDVAQGQEIFNSYGELSNVFLLA    344

MCA_00027_1      366 RYGFAIWDNKYETVGLSPEIRQYI-SENNLMERQEWWSIYFYEALFGIRK    414
                     ||||.:.:|:|:.|.|.|:..:.: .|....|:.:|||    :...|:..
RKM3_YEAST       345 RYGFTVPENQYDIVHLGPDFMKILKKEEKYQEKVKWWS----QVGHGLFS    390

MCA_00027_1      415 DEWAEIEESEDEDDEG------------SEDSEEENSIPPSPESISWEDE    452
                     ..:|::.:.::||::|            ||:.|||.....|.|  ||..:
RKM3_YEAST       391 AWYAQMRQEDEEDEDGQAKSDNLSDDIESEEEEEEEEGDDSLE--SWLSQ    438

MCA_00027_1      453 AYLTNSGAPSEGLSKLIRILSMSDSDFEALKSQFERDVFTSKLLPS-STL    501
                     .|:.:||.||.....|..:|:::...:|:|        |:.|..|. |..
RKM3_YEAST       439 LYIDSSGEPSPSTWALANLLTLTAVQWESL--------FSKKATPHISDS    480

MCA_00027_1      502 VFNEKSLILLKALVNLRLQRYKDGMLTSSQI-------KDLITKLSDNQK    544
                     :.||:.|..|....|...::....:|...|:       ...||..:.:..
RKM3_YEAST       481 IVNEEKLPFLAKKDNPHSKKLLSNLLKEKQLPCIKGDNSSKITSATKSML    530

MCA_00027_1      545 KNSRQILALTIKGTEKIVLEKSMQWIAQLEKKKKRKPSNSNHKKPNSRKL    594
                     :|:|     |:..:|..:|::.::.::                       
RKM3_YEAST       531 QNAR-----TLVQSEHNILDRCLKRLS-----------------------    552

MCA_00027_1      595 K    595
                      
RKM3_YEAST       553 -    552