Query psy1431
Match_columns 1043
No_of_seqs 604 out of 2255
Neff 7.5
Searched_HMMs 46136
Date Fri Aug 16 16:35:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1431.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1431hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0045|consensus 100.0 5.2E-69 1.1E-73 637.6 35.1 555 337-1037 20-608 (612)
2 smart00230 CysPc Calpain-like 100.0 2.8E-60 6.1E-65 533.3 25.0 292 335-650 6-317 (318)
3 cd00044 CysPc Calpains, domain 100.0 3.7E-56 7.9E-61 501.7 23.4 283 336-642 5-315 (315)
4 PF00648 Peptidase_C2: Calpain 100.0 6.9E-55 1.5E-59 488.9 14.7 275 343-641 1-295 (298)
5 smart00230 CysPc Calpain-like 100.0 2.3E-36 5E-41 339.8 15.5 174 47-230 5-183 (318)
6 cd00044 CysPc Calpains, domain 100.0 1.9E-35 4E-40 333.5 14.5 173 47-229 3-190 (315)
7 PF00648 Peptidase_C2: Calpain 100.0 7.5E-35 1.6E-39 326.9 8.7 164 56-229 1-169 (298)
8 KOG0045|consensus 100.0 6.7E-33 1.4E-37 329.8 13.4 172 48-229 18-198 (612)
9 smart00720 calpain_III calpain 99.9 1.5E-24 3.3E-29 216.7 14.0 128 913-1040 1-143 (143)
10 cd00214 Calpain_III Calpain, s 99.9 2.3E-24 5E-29 216.7 14.1 130 913-1042 3-150 (150)
11 PF01067 Calpain_III: Calpain 99.9 1.3E-22 2.9E-27 203.7 10.3 128 913-1040 2-147 (147)
12 cd00214 Calpain_III Calpain, s 99.7 3.6E-17 7.7E-22 164.6 14.0 139 651-812 6-150 (150)
13 smart00720 calpain_III calpain 99.7 1.3E-16 2.9E-21 159.4 13.8 134 651-809 4-142 (143)
14 PF01067 Calpain_III: Calpain 99.6 1.8E-15 3.9E-20 151.9 12.3 137 650-809 4-146 (147)
15 cd02680 MIT_calpain7_2 MIT: do 96.5 0.0027 5.9E-08 55.6 4.0 38 252-289 1-38 (75)
16 cd02684 MIT_2 MIT: domain cont 92.6 0.18 3.8E-06 44.6 4.4 39 254-292 3-41 (75)
17 cd02678 MIT_VPS4 MIT: domain c 91.2 0.32 6.9E-06 43.0 4.6 38 254-291 3-40 (75)
18 PF04212 MIT: MIT (microtubule 89.6 0.58 1.3E-05 40.4 4.7 38 254-291 2-39 (69)
19 cd02656 MIT MIT: domain contai 89.6 0.54 1.2E-05 41.4 4.6 39 254-292 3-41 (75)
20 smart00745 MIT Microtubule Int 88.6 0.7 1.5E-05 40.8 4.6 41 253-293 4-44 (77)
21 cd02677 MIT_SNX15 MIT: domain 82.5 1.6 3.5E-05 38.5 3.8 39 254-292 3-41 (75)
22 cd02683 MIT_1 MIT: domain cont 82.1 2.1 4.5E-05 38.0 4.4 39 254-292 3-41 (77)
23 cd02681 MIT_calpain7_1 MIT: do 81.2 2.5 5.3E-05 37.5 4.4 37 254-290 3-39 (76)
24 cd02679 MIT_spastin MIT: domai 77.2 3.9 8.4E-05 36.5 4.4 39 253-291 4-42 (79)
25 COG4870 Cysteine protease [Pos 70.0 5.9 0.00013 45.0 4.7 43 562-634 263-318 (372)
26 cd02682 MIT_AAA_Arch MIT: doma 62.6 13 0.00028 32.8 4.4 37 255-291 4-40 (75)
27 KOG0739|consensus 62.2 9.2 0.0002 42.4 4.2 36 253-288 6-41 (439)
28 PF09087 Cyc-maltodext_N: Cycl 50.3 9.9 0.00021 34.7 1.7 67 831-897 15-85 (88)
29 cd02619 Peptidase_C1 C1 Peptid 43.6 23 0.0005 37.4 3.7 44 562-635 170-218 (223)
30 PF13181 TPR_8: Tetratricopept 37.4 62 0.0014 22.9 4.1 29 259-287 3-31 (34)
31 PF00515 TPR_1: Tetratricopept 36.1 69 0.0015 22.7 4.1 29 258-286 2-30 (34)
32 cd02859 AMPKbeta_GBD_like AMP- 34.8 43 0.00094 29.7 3.4 26 433-461 44-69 (79)
33 cd02859 AMPKbeta_GBD_like AMP- 30.9 56 0.0012 29.0 3.4 25 147-174 45-69 (79)
34 PF07719 TPR_2: Tetratricopept 27.3 1.2E+02 0.0026 21.2 4.1 29 259-287 3-31 (34)
35 PF00112 Peptidase_C1: Papain 24.2 89 0.0019 32.8 4.2 40 562-631 164-206 (219)
36 PF08969 USP8_dimer: USP8 dime 20.3 1.7E+02 0.0036 27.9 4.8 40 253-293 34-73 (115)
37 cd02248 Peptidase_C1A Peptidas 20.2 1.4E+02 0.003 31.4 4.6 39 562-630 157-198 (210)
No 1
>KOG0045|consensus
Probab=100.00 E-value=5.2e-69 Score=637.60 Aligned_cols=555 Identities=22% Similarity=0.294 Sum_probs=409.5
Q ss_pred hhcCCCCccCCCCCCCCCc-----ccCC---CCceeeCCccccCCCeEeeCCCCCcCCcccCCCCChHHHHHHHHHhccc
Q psy1431 337 KFQYAVPFTDKEGPLILSP-----KQKR---DFVAWVRPSEFCSEPKMVAGEFVDYFSIKQTIVSDCSFVASLAVSALYE 408 (1043)
Q Consensus 337 ~~~~~~~f~D~~~~~~l~~-----~q~~---~~~~W~Rp~e~~~~p~~~~~~~~~~~dI~Qg~lgDC~~vaaL~~la~~~ 408 (1043)
|...+.+|.|+.||+.-++ .+.. ..+.|+||+|++.+|.++. +++++.||+||.+||||||||+|++|.++
T Consensus 20 cl~~~~~F~D~~FP~~~~Sl~~~~~~p~~~~~~i~W~RP~ei~~~p~~i~-~~~~~~di~Qg~lgdCw~laA~a~la~~~ 98 (612)
T KOG0045|consen 20 CLPAKSLFVDALFPAADSSLFYKLSTPLAQFSDIVWKRPQEICANPRLIV-DGPSRFDVKQGLLGDCWFLAACAALALRP 98 (612)
T ss_pred HhhcCCcccccCCCCCCccccccccCCCcccccceecCcccccCCCCeec-CCCCcceeEEeeecchHHHHHHHHhhcCH
Confidence 4456778889888774211 1112 5899999999999999998 69999999999999999999999999987
Q ss_pred ccccccceeEeeecCCCCCCCcccCCceEEEEEeecCceEEeeecccccccCCCceEEeecCCCCchhHHHHHHHhhhhc
Q psy1431 409 RRFGKRLVTSIIYPRNRNKEPVYNPFGKYMVKLHLNGITRKVIIDDQLPMARFNQLLCSYSQNKNELWVSILEKAYMKVM 488 (1043)
Q Consensus 409 ~~~~~~ll~~~i~P~~~~~~p~~~~~G~Y~vrl~~nG~wr~VvIDD~lP~~~~g~~l~~~s~~~~e~W~~LlEKAyaKl~ 488 (1043)
+ |+.++| |+++.+ .+++.|+|+||||++|+|+.|+|||+||+. +|+++|++++..+|+|++||||||||++
T Consensus 99 ~-----ll~~vi-p~~~~~--~~~yaGif~f~~w~~G~W~~VvIDD~LP~~-~~~~~~~~s~~~~efW~aLlEKAyaKl~ 169 (612)
T KOG0045|consen 99 E-----LLDKVI-PQDQSF--QENYAGIFHFRFWQNGEWVEVVIDDRLPTS-NGGLLFSHSSGKNEFWAALLEKAYAKLL 169 (612)
T ss_pred H-----HHHhcc-CCCccc--ccccceEEEEEEEeCCeEEEEEeeeecceE-cCCEEEEeecCCceeHHHHHHHHHHHHh
Confidence 5 677777 766654 358999999999999999999999999998 6778899888889999999999999999
Q ss_pred CCCCCCCCccc---cccccCCccccccccCCcccccCChhHHHHHHHHHHhcCCccccCccccccccccCcc-ccc---c
Q psy1431 489 GGYDFPGSNST---LHALNGLDTGAARAIRPNDARILTQTSVFENLFTRLHSRAMFWLPWCKREICLRMKKR-ERS---R 561 (1043)
Q Consensus 489 G~Y~~~g~~~~---L~~LTG~ipe~~i~l~~~~~~~~~~~~lw~~l~~~~~~g~li~~~~~~~~~~l~~~~~-~~~---~ 561 (1043)
|+|+.++|+.. |.+|||+++|. +.++.... ...++++..+..++++|.++ +|++..+.....+ +.. +
T Consensus 170 GsY~~l~gg~~~~a~~~lTG~~~e~-~~l~~~~~--~~~~~l~~~~~~~~~~~~~l---~c~~~~~~~~~~~~~~~~~~g 243 (612)
T KOG0045|consen 170 GSYEALHGGSTIDALVDLTGGVTEP-FDLNKTPK--SFKNNLVWALLKSAHRGSLL---LCSIESKDPTEEEEEAKLRNG 243 (612)
T ss_pred CcccCCCCCchhhHHHhccCCccce-eEcccCcc--hhHHHHHHHHHHhhhccCce---eeeccccccchhHHHHHhhcC
Confidence 99998877655 88999999999 99986432 11226677788888988765 4443221111111 111 1
Q ss_pred -ccCceeeEee---ccc----eEEEEeeCCCCcCccCCCCCCCCCCCCCHHHHHHcCCCCCCCCCCCCceEEEecccccc
Q psy1431 562 -VDTMQSSVSW---SQG----LRLLQLKNPWSNVRWRGNYSELDRLHWTPELKRALNFDPNSASMFDNGIFWIDYESILR 633 (1043)
Q Consensus 562 -v~~HaYaV~~---v~~----~rll~LrNPWg~~eW~G~wsd~s~~~W~~~~~~~l~~~~~~~~~~~dG~FWm~~edf~~ 633 (1043)
+++|||+|++ +++ .+|++||||||+.+|+|.||+.+ .+|....+..+.... ....+||+|||+|+||++
T Consensus 244 L~~~HaYsit~~~~~~~~~~~~~lirlrNPwg~~~W~G~wsd~~-~~W~~v~~~~~~~~~--~~~~~dGeFWms~~dF~~ 320 (612)
T KOG0045|consen 244 LVKGHAYAITDVREVQGRGGKHRLIRLRNPWGESEWNGPWSDGS-EEWHLVDKSKLSELG--RQPLDDGEFWMSFDDFLR 320 (612)
T ss_pred ccccccEEEEEEEEeecccccceeEEecCCcCCceeccccccCC-cchhhhCHHHHhhcc--cccccCCCeeeeHHHHHh
Confidence 9999999765 466 99999999999999999999887 699844333332111 123799999999999999
Q ss_pred cccEEEEeccCCCCC--------ceeeeeeeeec--ccccCCCCCcccCcccccccccccceEEEEEeeCCCCCcCCCCC
Q psy1431 634 FYDVFYMNWNPGLFS--------HTFCVHQELTF--EKKNGNSTNCVKTAKQLSIVVFDYVTFKPVIIRNSSLDYFGQWP 703 (1043)
Q Consensus 634 ~F~~~~i~w~p~~f~--------~~~~~h~~~~W--~~~~~~~gg~~~~~~~~~~~~~~NPQf~l~~~~~~~~~~~~~~~ 703 (1043)
+|+.++||+....+. ....+++. | .... ..|||.+..++| ..||||.+.+..++.
T Consensus 321 ~F~~~~vC~~~~~~~~~~~~~~~~~~~~~~~--w~~~~~~-t~ggc~~~~~tF----~~npq~~~~~~~~~~-------- 385 (612)
T KOG0045|consen 321 EFDSLTVCRLRPDWLESRNQLQWVKLSLDGE--WELARGV-TAGGCRNSVDTF----DRNPQYILAVRKPTK-------- 385 (612)
T ss_pred hCCeEeecCCCcchhhhhheeeeeeeecCCc--cceeecc-cCCCCccCcccc----cCCceEEEEecCCCc--------
Confidence 999999998877654 22345555 9 3333 348998887787 999999999987321
Q ss_pred CCCCCCCCccEEEEEeeccccccccccCCceeeEEEEEEeCCee-eecCCCCCCccccccccCceEEEEEEecCCCCccE
Q psy1431 704 PSTPAASPKRNFWILLTRHITQLEDFKQNREYITVLVYKNEGKR-VYYPYDPPPYLDGVRINSPHYLCKIILNENSSRKY 782 (1043)
Q Consensus 704 ~~~~~~~~~~~VwilL~rh~~~~~~~~~~~~~I~l~V~~~~g~r-v~~~~~~~~~~~g~~~ns~~~l~r~~l~p~~~~~Y 782 (1043)
.....|+.++++|+++...++.+...|+++||+++.++ .++.........+.++|.|++..++++|| +.|
T Consensus 386 ------~~~~~v~~~~q~~~~~~~~~~~~~~~ig~~i~~v~~~~~~~~~~~~~~~~~~~~i~~r~v~~~~~~P~---~~y 456 (612)
T KOG0045|consen 386 ------SLCAVVLALFQKTRRGERSFGANILDIGFHIYEVPLEGKYFVLDNAPIASSSSFINNREVSVRFRLPP---GTY 456 (612)
T ss_pred ------cceEEEEEeecccccccccccceeeecceEEEEecCCCCceEecccchhcccccccceeEEEEecCCC---cce
Confidence 12356777888898888777778888999999998652 22322233455678999999999999775 999
Q ss_pred EEEeccccCccccceEEEEeecCCccccccCCcccccchhhhhhccccccchhccccccccCCCCCCCCCCCCCccccCC
Q psy1431 783 TLVVSQYEKMHTIYYTLRAYATCPFRLEKIENPYQFKEEVRIEIWSTYDLMFMFTSENAWRMRPSNDPPPYLDGVRINSP 862 (1043)
Q Consensus 783 tlVpst~~~~~~~~F~LriyS~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~g~~~~s~ 862 (1043)
.+||||++++++++|+|||||+..+..++-
T Consensus 457 ~~~pst~~~~~~~~f~lrvfs~~~~~~~~~-------------------------------------------------- 486 (612)
T KOG0045|consen 457 VIVPSTFEPGEEGEFLLRVFSNVKVKSEED-------------------------------------------------- 486 (612)
T ss_pred eecccCCCCCCCccEEEEEeecccccCccc--------------------------------------------------
Confidence 999999999999999999999988776530
Q ss_pred CcceeeeeccCCCCceeEEEeeccccceeeeEEEEEecCcceEeecCCCCceeEEEEceeecCCCCCCCCCCCCCCCCCc
Q psy1431 863 HYLCKIILNENSSRKYTLVVSQYEKMHTIYYTLRAYATCPFRLEKIENPYQFKEEISGEWKGLTAGGCPNYPATYPNNPR 942 (1043)
Q Consensus 863 ~~~~~~~~~~~~~~~~~lv~s~~~~~~~~~ftL~~~s~~~~~l~~~~~~~~~~~~i~G~W~~~tAGG~~n~~~ty~~NPq 942 (1043)
..|++ ..........-|++-+.|.|.+.-..+...+-
T Consensus 487 ------------------------------~~i~~-------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 523 (612)
T KOG0045|consen 487 ------------------------------MEISL-------------DETKRSTNIIVMKGFSLGECGDKWKLSSTLVN 523 (612)
T ss_pred ------------------------------eEEee-------------cccccceeeeeecceehhhhchhhhccccccc
Confidence 00000 00011223334447777777776655555555
Q ss_pred EEEEecCCCCCCceEEEEEcCCCceeeeEEEEEEeCCCCCcCCCcccccCCCcccceEEEEeecCCCccEEEEeccCCCC
Q psy1431 943 YQVTLDSRQSMDNTLLVFLKGPKQYSLGVKISCVRLDDETATAPFKTKDSGAYRSGFVAVEMDNLPSGTYEIMPSTFSPQ 1022 (1043)
Q Consensus 943 y~l~l~~~~~~~~~l~i~l~~~~~~~ig~~v~~~~~~~~~~~~~~~~~~sg~yr~g~~~~~~~~L~~G~Y~IVPSTf~p~ 1022 (1043)
.++....... +.+.+..+ + .+-.........+.......++.|...+.+..+....|+.....++|+...
T Consensus 524 ~k~s~~~~~~----~~~~~~~~----~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 593 (612)
T KOG0045|consen 524 TKVSRSSEFI----LTVEVVSP----L--DIEGESTLVVDIPIAIESKGSGDVAPLLNVIRLRIADPEIAYSFDSTSCCA 593 (612)
T ss_pred cccchhhcee----eeeccccc----E--EEeccccccccccceeeccCCcccccceeeeeeeccChhheeecccccccc
Confidence 5544333321 34444444 2 222221111123334556788899999998888889999999999999999
Q ss_pred CccCeEEEEEeCCce
Q psy1431 1023 QEGPFFLELKSSCSI 1037 (1043)
Q Consensus 1023 ~~g~F~L~V~S~~~~ 1037 (1043)
++|++.++.+.+.+.
T Consensus 594 ~~~~~~~~~~~~~~~ 608 (612)
T KOG0045|consen 594 TEGPLVLDELFDLSS 608 (612)
T ss_pred ccCcchhhhhhcCCC
Confidence 999999988776544
No 2
>smart00230 CysPc Calpain-like thiol protease family. Calpain-like thiol protease family (peptidase family C2). Calcium activated neutral protease (large subunit).
Probab=100.00 E-value=2.8e-60 Score=533.28 Aligned_cols=292 Identities=29% Similarity=0.502 Sum_probs=241.7
Q ss_pred hhhhcCCCCccCCCCCCCCC-----cccCCCCceeeCCccccCCCeEeeCCCCCcCCcccCCCCChHHHHHHHHHhcccc
Q psy1431 335 AEKFQYAVPFTDKEGPLILS-----PKQKRDFVAWVRPSEFCSEPKMVAGEFVDYFSIKQTIVSDCSFVASLAVSALYER 409 (1043)
Q Consensus 335 ~~~~~~~~~f~D~~~~~~l~-----~~q~~~~~~W~Rp~e~~~~p~~~~~~~~~~~dI~Qg~lgDC~~vaaL~~la~~~~ 409 (1043)
..|...+.+|+|++|++.-. +.+ ...+.|+||.|++++|+++. +++++.||+||.+|||||||||++||+++.
T Consensus 6 ~~c~~~~~~f~D~~Fpp~~~sl~~~~~~-~~~~~W~Rp~e~~~~~~~~~-~~i~~~di~QG~lgDC~~lsal~~la~~~~ 83 (318)
T smart00230 6 QYCKESGTLFEDPLFPANNGSLFFSQRQ-RKFVVWKRPHEIFENPPFIV-GGASRTDICQGVLGDCWLLAALASLTLREK 83 (318)
T ss_pred HHHHHcCCCccCCCCCCCcCccccCCCC-CCCcEEECcHHHcCCCEEEe-CCCChhhccCcccccHHHHHHHHHHHhCHH
Confidence 45667888999999988532 222 35789999999999999987 588999999999999999999999999875
Q ss_pred cccccceeEeeecCCCCCCCcccCCceEEEEEeecCceEEeeecccccccCCCceEEeecCCCCchhHHHHHHHhhhhcC
Q psy1431 410 RFGKRLVTSIIYPRNRNKEPVYNPFGKYMVKLHLNGITRKVIIDDQLPMARFNQLLCSYSQNKNELWVSILEKAYMKVMG 489 (1043)
Q Consensus 410 ~~~~~ll~~~i~P~~~~~~p~~~~~G~Y~vrl~~nG~wr~VvIDD~lP~~~~g~~l~~~s~~~~e~W~~LlEKAyaKl~G 489 (1043)
++.+++ |+++... .++.|+|+||||+||+|+.|+|||+||+.. |.++|+++++++|+|++||||||||+||
T Consensus 84 -----~i~~if-~~~~~~~--~~~~G~y~vrl~~~G~w~~V~VDd~lP~~~-~~~~~~~~~~~~e~W~~LLEKAyAK~~G 154 (318)
T smart00230 84 -----LLDRVI-PHDQEFS--ENYAGIFHFRFWRFGKWVDVVIDDRLPTYN-GELVFMHSNSRNEFWSALLEKAYAKLNG 154 (318)
T ss_pred -----HHhheE-eCCcccc--cccCCEEEEEEEECCEEEEEEecCCCeeeC-CceEEEEeCCCCcchhHHHHHHHHHHcC
Confidence 566655 5543322 478999999999999999999999999985 4599999999999999999999999999
Q ss_pred CCCCCCCccc---cccccCCccccccccCCcccccCChhHHHHHHHHHHhcCCccccCccccccccccCcccc--cc-cc
Q psy1431 490 GYDFPGSNST---LHALNGLDTGAARAIRPNDARILTQTSVFENLFTRLHSRAMFWLPWCKREICLRMKKRER--SR-VD 563 (1043)
Q Consensus 490 ~Y~~~g~~~~---L~~LTG~ipe~~i~l~~~~~~~~~~~~lw~~l~~~~~~g~li~~~~~~~~~~l~~~~~~~--~~-v~ 563 (1043)
||++++|+.. |++||||+|+. +.++.. ..+.+++|+.|.+++++|++| +|++..-....+++. .+ ++
T Consensus 155 sY~~i~gg~~~~al~~LTG~~~~~-i~l~~~---~~~~~~~w~~l~~~~~~g~lv---~~~t~~~~~~~~~~~~~~GLv~ 227 (318)
T smart00230 155 CYEALKGGSTTEALEDLTGGVAES-IDLKEA---SKDPDNLFEDLFKAFERGSLM---GCSIGAGTAVEEEEQKDCGLVK 227 (318)
T ss_pred CCcccCCCCHHHHHHHhcCCCeEE-EEcccc---cCCHHHHHHHHHHHHhCCCeE---EEEcCCCCcchhhhhhhcCccc
Confidence 9999877765 99999999999 998853 236899999999999999765 444331100111111 12 99
Q ss_pred CceeeEeec---cceE--EEEeeCCCCcCccCCCCCCCCCCCCC---HHHHHHcCCCCCCCCCCCCceEEEecccccccc
Q psy1431 564 TMQSSVSWS---QGLR--LLQLKNPWSNVRWRGNYSELDRLHWT---PELKRALNFDPNSASMFDNGIFWIDYESILRFY 635 (1043)
Q Consensus 564 ~HaYaV~~v---~~~r--ll~LrNPWg~~eW~G~wsd~s~~~W~---~~~~~~l~~~~~~~~~~~dG~FWm~~edf~~~F 635 (1043)
+|||+|+++ ++.+ ||+||||||+.||+|+||+.| .+|+ +++++.|+++ ..+||+|||+|+||++||
T Consensus 228 ~HaYsVl~v~~~~~~~~~Ll~lrNPWg~~eW~G~wsd~s-~~W~~~~~~~~~~l~~~-----~~~dG~FWM~~~df~~~F 301 (318)
T smart00230 228 GHAYSVTDVREVQGRRQELLRLRNPWGQVEWNGPWSDDS-PEWRSVSASEKKNLGLT-----FDDDGEFWMSFEDFLRHF 301 (318)
T ss_pred CccEEEEEEEEEecCCeEEEEEECCCCCCCcCCCCCCCC-ccccccCHHHHHHhCCC-----CCCCCEEEEEhHHHHhhC
Confidence 999998765 4545 999999999999999999987 6999 8999999884 459999999999999999
Q ss_pred cEEEEe-ccCCCCCce
Q psy1431 636 DVFYMN-WNPGLFSHT 650 (1043)
Q Consensus 636 ~~~~i~-w~p~~f~~~ 650 (1043)
++++|| |+|+.|.++
T Consensus 302 ~~~~vc~~~~~~~~~r 317 (318)
T smart00230 302 DKVEICNLNPDSLEER 317 (318)
T ss_pred CeEEEeccCCcccccc
Confidence 999995 999988764
No 3
>cd00044 CysPc Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.
Probab=100.00 E-value=3.7e-56 Score=501.74 Aligned_cols=283 Identities=33% Similarity=0.509 Sum_probs=232.8
Q ss_pred hhhcCCCCccCCCCCCCC---------CcccCCCCceeeCCccccCC-----CeEeeCCCCCcCCcccCCCCChHHHHHH
Q psy1431 336 EKFQYAVPFTDKEGPLIL---------SPKQKRDFVAWVRPSEFCSE-----PKMVAGEFVDYFSIKQTIVSDCSFVASL 401 (1043)
Q Consensus 336 ~~~~~~~~f~D~~~~~~l---------~~~q~~~~~~W~Rp~e~~~~-----p~~~~~~~~~~~dI~Qg~lgDC~~vaaL 401 (1043)
.|...+.+|+|++||+.. +..+....+.|+||.|++.. |.++. +++++.||+||.+|||||||||
T Consensus 5 ~c~~~~~~f~D~~Fpp~~~s~~~~~~~~~~~~~~~~~W~Rp~~~~~~~~~~~~~~~~-~~~~~~dI~QG~lgDC~~lsaL 83 (315)
T cd00044 5 ICLLSGVLFEDPDFPPNDSSLGFDDSLSNGQPKKVIEWKRPSEIFADDGNSNPRLFV-NGASPSDVCQGILGDCWFLAAL 83 (315)
T ss_pred HHHHcCCCccCCCCCCCccccccccccccccCcCcceEECcHHHhCcccCCCCEEEe-CCCChhhcccCcccchHHHHHH
Confidence 445567788888887742 24466788999999999987 88876 6899999999999999999999
Q ss_pred HHHhcccccccccceeEeeecCCCCCCCcccCCceEEEEEeecCceEEeeecccccccCCCceEEeecCCCCchhHHHHH
Q psy1431 402 AVSALYERRFGKRLVTSIIYPRNRNKEPVYNPFGKYMVKLHLNGITRKVIIDDQLPMARFNQLLCSYSQNKNELWVSILE 481 (1043)
Q Consensus 402 ~~la~~~~~~~~~ll~~~i~P~~~~~~p~~~~~G~Y~vrl~~nG~wr~VvIDD~lP~~~~g~~l~~~s~~~~e~W~~LlE 481 (1043)
++||+++. +|.++|.+... . ..++.|+|+||||+||+|+.|+|||+||+..++ ++|+++.+.+|+|++|||
T Consensus 84 ~~la~~~~-----~i~~lf~~~~~-~--~~~~~G~y~v~l~~~G~w~~V~VDD~lP~~~~~-~~~~~s~~~~e~W~~LlE 154 (315)
T cd00044 84 AALAERPE-----LLKRVIPPDQS-F--EENYAGIYHFRFWKNGEWVEVVIDDRLPTSNGG-LLFMHSRDRNELWVALLE 154 (315)
T ss_pred HHHHcCHH-----HHhheEcCCcc-c--ccCcCcEEEEEEEECCEEEEEEecCCCeecCCc-eEEEEECCCCeEcHHHHH
Confidence 99999875 67777744321 1 136899999999999999999999999998655 999999889999999999
Q ss_pred HHhhhhcCCCCC-CCCccc--cccccCCccccccccCCcccccCChhHHHHHHHHHHhcCCccccCccccccccccCccc
Q psy1431 482 KAYMKVMGGYDF-PGSNST--LHALNGLDTGAARAIRPNDARILTQTSVFENLFTRLHSRAMFWLPWCKREICLRMKKRE 558 (1043)
Q Consensus 482 KAyaKl~G~Y~~-~g~~~~--L~~LTG~ipe~~i~l~~~~~~~~~~~~lw~~l~~~~~~g~li~~~~~~~~~~l~~~~~~ 558 (1043)
|||||+||||++ .||++. |++||||+++. +.++.... ....+.+|+.|.++.+.|.+| +|++. ..+..+
T Consensus 155 KAyAK~~GsY~~i~gg~~~~al~~LTG~~~~~-i~~~~~~~-~~~~~~~~~~l~~~~~~~~lv---~~~t~---~~~~~~ 226 (315)
T cd00044 155 KAYAKLHGSYEALVGGNTAEALEDLTGGPTER-IDLKSADA-SSGDNDLFALLLSFLQGGSLI---GCSTG---SRSEEE 226 (315)
T ss_pred HHHHhhcCCccccCCCCHHHHHHHhhCCCcEE-EEcccccc-ccCHHHHHHHHHHHhhCCCEE---EEEcC---CCCcch
Confidence 999999999997 688877 99999999999 99885321 135789999999999999765 44433 222221
Q ss_pred ---ccc-ccCceeeEeec---c--ceEEEEeeCCCCcCccCCCCCCCCCCCCC--HHHHHHcCCCCCCCCCCCCceEEEe
Q psy1431 559 ---RSR-VDTMQSSVSWS---Q--GLRLLQLKNPWSNVRWRGNYSELDRLHWT--PELKRALNFDPNSASMFDNGIFWID 627 (1043)
Q Consensus 559 ---~~~-v~~HaYaV~~v---~--~~rll~LrNPWg~~eW~G~wsd~s~~~W~--~~~~~~l~~~~~~~~~~~dG~FWm~ 627 (1043)
..+ +.+|||+|+++ + +.|||+||||||+.+|+|+||+.|+ .|. +.+++.+.. ...+||+|||+
T Consensus 227 ~~~~~Gl~~~HaY~Vl~~~~~~~~~~~lv~lrNPWg~~~w~G~ws~~~~-~w~~~~~~~~~~~~-----~~~~dG~Fwm~ 300 (315)
T cd00044 227 ARTANGLVKGHAYSVLDVREVQEEGLRLLRLRNPWGVGEWWGGWSDDSS-EWWVIDAERKKLLL-----SGKDDGEFWMS 300 (315)
T ss_pred hhccCCcccCcceEEeEEEEEccCceEEEEecCCccCCCccCCCCCCCc-hhccChHHHHHhcC-----CCCCCCEEEEE
Confidence 222 99999997664 5 8999999999999999999999984 773 566666654 36799999999
Q ss_pred cccccccccEEEEec
Q psy1431 628 YESILRFYDVFYMNW 642 (1043)
Q Consensus 628 ~edf~~~F~~~~i~w 642 (1043)
|+||+++|+.+++||
T Consensus 301 ~~df~~~F~~~~vc~ 315 (315)
T cd00044 301 FEDFLRNFDGLYVCN 315 (315)
T ss_pred hHHhheeeCeEEEeC
Confidence 999999999999997
No 4
>PF00648 Peptidase_C2: Calpain family cysteine protease This is family C2 in the peptidase classification. ; InterPro: IPR001300 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C2 (calpain family, clan CA). A type example is calpain, which is an intracellular protease involved in many important cellular functions that are regulated by calcium []. The protein is a complex of 2 polypeptide chains (light and heavy), with three known forms in mammals [, ]: a highly calcium-sensitive (i.e., micro-molar range) form known as mu-calpain, mu-CANP or calpain I; a form sensitive to calcium in the milli-molar range, known as m-calpain, m-CANP or calpain II; and a third form, known as p94, which is found in skeletal muscle only []. All forms have identical light but different heavy chains. Both mu- and m-calpain are heterodimers containing an identical 28kDa subunit and an 80kDa subunit that shares 55-65% sequence homology between the two proteases [, ]. The crystallographic structure of m-calpain reveals six "domains" in the 80kDa subunit: A 19-amino acid NH2-terminal sequence; Active site domain IIa; Active site domain IIb. Domain 2 shows low levels of sequence similarity to papain; although the catalytic His has not been located by biochemical means, it is likely that calpain and papain are related []. Domain III; An 18-amino acid extended sequence linking domain III to domain IV; Domain IV, which resembles the penta EF-hand family of polypeptides, binds calcium and regulates activity []. />]. Ca2+-binding causes a rearrangement of the protein backbone, the net effect of which is that a Trp side chain, which acts as a wedge between catalytic domains IIa and IIb in the apo state, moves away from the active site cleft allowing for the proper formation of the catalytic triad []. Calpain-like mRNAs have been identified in other organisms including bacteria, but the molecules encoded by these mRNAs have not been isolated, so little is known about their properties. How calpain activity is regulated in these organisms cells is still unclear In metazoans, the activity of calpain is controlled by a single proteinase inhibitor, calpastatin (IPR001259 from INTERPRO). The calpastatin gene can produce eight or more calpastatin polypeptides ranging from 17 to 85 kDa by use of different promoters and alternative splicing events. The physiological significance of these different calpastatins is unclear, although all bind to three different places on the calpain molecule; binding to at least two of the sites is Ca2+ dependent. The calpains ostensibly participate in a variety of cellular processes including remodelling of cytoskeletal/membrane attachments, different signal transduction pathways, and apoptosis. Deregulated calpain activity following loss of Ca2+ homeostasis results in tissue damage in response to events such as myocardial infarcts, stroke, and brain trauma []. Calpains are a family of cytosolic cysteine proteinases (see PDOC00126 from PROSITEDOC). Members of the calpain family are believed to function in various biological processes, including integrin-mediated cell migration, cytoskeletal remodeling, cell differentiation and apoptosis [, ]. The calpain family includes numerous members from C. elegans to mammals and with homologues in yeast and bacteria. The best characterised members are the m- and mu-calpains, both proteins are heterodimer composed of a large catalytic subunit and a small regulatory subunit. The large subunit comprises four domains (dI-dIV) while the small subunit has two domains (dV-dVI). Domain dI is a short region cleaved by autolysis, dII is the catalytic core, dIII is a C2-like domain, dIV consists of five calcium binding EF-hand motifs []. The crystal structure of calpain has been solved [, ]. The catalytic region consists of two distinct structural domains (dIIa and dIIb). dIIa contains a central helix flanked on three faces by a cluster of alpha-helices and is entirely unrelated to the corresponding domain in the typical thiol proteinases. The fold of dIIb is similar to the corresponding domain in other cysteine proteinases and contains two three-stranded anti-parallel beta-sheets. The catalytic triad residues (C,H,N) are located in dIIa and dIIb. The activation of the domain is dependent on the binding of two calcium atoms in two non EF-hand calcium binding sites located in the catalytic core, one close to the Cys active site in dIIa and one at the end of dIIb. Calcium-binding induced conformational changes in the catalytic domain which align the active site [][]. The profile covers the whole catalytic domain.; GO: 0004198 calcium-dependent cysteine-type endopeptidase activity, 0006508 proteolysis, 0005622 intracellular; PDB: 2NQA_A 1KFU_L 1KFX_L 1QXP_B 2R9C_A 1TL9_A 2G8E_A 1KXR_B 2G8J_A 2NQG_A ....
Probab=100.00 E-value=6.9e-55 Score=488.86 Aligned_cols=275 Identities=33% Similarity=0.579 Sum_probs=203.2
Q ss_pred CccCCCCCCC---CCc-ccCCCCceeeCCccccCCCeEeeCCCCCcCCcccCCCCChHHHHHHHHHhcccccccccceeE
Q psy1431 343 PFTDKEGPLI---LSP-KQKRDFVAWVRPSEFCSEPKMVAGEFVDYFSIKQTIVSDCSFVASLAVSALYERRFGKRLVTS 418 (1043)
Q Consensus 343 ~f~D~~~~~~---l~~-~q~~~~~~W~Rp~e~~~~p~~~~~~~~~~~dI~Qg~lgDC~~vaaL~~la~~~~~~~~~ll~~ 418 (1043)
.|+|++||+. |.. .+....+.|+||+|++.+|+++. +++.+.||.||.+|||||||||+++|.+++ +|.+
T Consensus 1 ~f~D~~Fpp~~~Sl~~~~~~~~~~~W~R~~e~~~~~~~~~-~~~~~~di~QG~lgDc~llaaL~~la~~~~-----~i~~ 74 (298)
T PF00648_consen 1 LFEDPEFPPNDSSLGFDDQKPKNVEWKRPSEICENPQFFI-DGISPSDIRQGSLGDCWLLAALAALAEHPD-----LIKK 74 (298)
T ss_dssp ----TTS-SSHHHHTSSTTSTTT-EEE-HHHHSSS-BSSS-SSSSGGGEBE-SSSSHHHHHHHHHHTTSHH-----HHHH
T ss_pred CccCCCCccCccccccCCCCCCcceeEechhcCCCCeEEE-CCCccccccccccCChhHHHHHHHHHhccc-----cccc
Confidence 3889999884 322 22347789999999999999876 688999999999999999999999999875 5555
Q ss_pred eeecCCCCCCCcccCCceEEEEEeecCceEEeeecccccccCCCceEEeecCCCCchhHHHHHHHhhhhcCCCCC-CCCc
Q psy1431 419 IIYPRNRNKEPVYNPFGKYMVKLHLNGITRKVIIDDQLPMARFNQLLCSYSQNKNELWVSILEKAYMKVMGGYDF-PGSN 497 (1043)
Q Consensus 419 ~i~P~~~~~~p~~~~~G~Y~vrl~~nG~wr~VvIDD~lP~~~~g~~l~~~s~~~~e~W~~LlEKAyaKl~G~Y~~-~g~~ 497 (1043)
+| |.++... .++.|+|.||||++|+|++|+|||+||+ .+|+++|+++++++|+|++||||||||++|||+. .||+
T Consensus 75 i~-~~~~~~~--~~~~G~y~v~l~~~G~w~~V~VDd~lP~-~~g~~~f~~s~~~~elW~~LlEKAyAKl~GsY~~l~gg~ 150 (298)
T PF00648_consen 75 IF-PVNQSFN--ENYNGIYTVRLFKNGEWREVTVDDRLPC-KNGKPLFARSSDPNELWPSLLEKAYAKLHGSYSALEGGN 150 (298)
T ss_dssp HS--SS--SS--TT-SSEEEEEEEETTEEEEEEEES-EEE-ETTEESSSBESSTTB-HHHHHHHHHHHHTTSSGGGSSBS
T ss_pred cc-ccccccc--cccCceeeEeeccCCeeeeeccchhhhc-cccceeeeccCCcccchhhhhhchhhhccccccccCCCC
Confidence 55 5443322 2357999999999999999999999999 6899999998899999999999999999999996 4555
Q ss_pred cc--cccccCCccccccccCCcccccCChhHHHHHHHHHHhcCCccccCccccccccccCccc--ccc-ccCceeeEeec
Q psy1431 498 ST--LHALNGLDTGAARAIRPNDARILTQTSVFENLFTRLHSRAMFWLPWCKREICLRMKKRE--RSR-VDTMQSSVSWS 572 (1043)
Q Consensus 498 ~~--L~~LTG~ipe~~i~l~~~~~~~~~~~~lw~~l~~~~~~g~li~~~~~~~~~~l~~~~~~--~~~-v~~HaYaV~~v 572 (1043)
+. |++|||++++. +.++.. ...+++|+.+....+++.++ +|.+........++ ..+ +++|||+|+++
T Consensus 151 ~~~al~~LTG~~~~~-~~l~~~----~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~gl~~~HaY~Vl~~ 222 (298)
T PF00648_consen 151 PSEALQDLTGGPPES-IDLRDD----SSDDELWELWKKLLKSGSLV---GCSTGSSTPFDSEEYEKNGLVPGHAYAVLDV 222 (298)
T ss_dssp HHHHHHHHHSSEEEE-EEGGG------T--THHHHHHHHHHCT-EE---EEE--SSSGGGTTSBCTTSBBTTS-EEEEEE
T ss_pred hhhhhHhhcCCccee-eecccc----chhhhHHHHHHHHHHhcccc---ccccccccccccccccccCcccceeEEEEEE
Confidence 55 99999999999 888742 22467888888888888754 22221110111111 122 99999998765
Q ss_pred ---cc----eEEEEeeCCCCcCccCCCCCCCCCCCCC---HHHHHHcCCCCCCCCCCCCceEEEecccccccccEEEEe
Q psy1431 573 ---QG----LRLLQLKNPWSNVRWRGNYSELDRLHWT---PELKRALNFDPNSASMFDNGIFWIDYESILRFYDVFYMN 641 (1043)
Q Consensus 573 ---~~----~rll~LrNPWg~~eW~G~wsd~s~~~W~---~~~~~~l~~~~~~~~~~~dG~FWm~~edf~~~F~~~~i~ 641 (1043)
++ .|||+||||||..+|+|+||+.+ .+|+ +++++.++. ...+||+|||+|+||++||+.|+||
T Consensus 223 ~~~~~~~~~~~lv~LrNPwg~~~w~G~ws~~s-~~W~~~~~~~~~~~~~-----~~~~dg~FWM~~~df~~~F~~i~vc 295 (298)
T PF00648_consen 223 REVNGNGEGHRLVKLRNPWGSTEWKGDWSDDS-PEWTEIHPSLRKRLNQ-----SSSDDGTFWMSFEDFLKYFSSIYVC 295 (298)
T ss_dssp EEEEETTEEEEEEEEE-TTSS---SSTTSTTS-GGGGGS-HHHHHHHTT-----TSSSSSEEEEEHHHHHHHSEEEEEE
T ss_pred EeeccccceeEEEEEcCCCccccccccccccc-cccccCCHHHHhhccc-----ccccCccHhHhHHHHHhhCCceEEE
Confidence 33 89999999999999999999987 6999 788888876 3568999999999999999999998
No 5
>smart00230 CysPc Calpain-like thiol protease family. Calpain-like thiol protease family (peptidase family C2). Calcium activated neutral protease (large subunit).
Probab=100.00 E-value=2.3e-36 Score=339.79 Aligned_cols=174 Identities=27% Similarity=0.427 Sum_probs=150.3
Q ss_pred hHhhhcCCCCccCCCCCCCCCCC----CCCCCceEeccccccCCCeeecCCccCccCcccCCCCCchHHHHHHHHhhhhh
Q psy1431 47 LAEKFQYAVPFTDKEGPLILSPK----QKRDFVAWVRPSEFCSEPKMVAGEFVDYFSIKQTIVSDCSFVASLAVSALYER 122 (1043)
Q Consensus 47 ~~~~~~~~~~f~D~~fp~~l~~~----~~~~~~~W~Rp~e~~~~~~~~~~~~~~~~di~Qg~lgDC~~laal~~la~~~~ 122 (1043)
.+.|++.+.+|+|++|||...+. .....+.|+||.|++.+|.++.++ +++.||+||.+|||||||||++||++++
T Consensus 5 ~~~c~~~~~~f~D~~Fpp~~~sl~~~~~~~~~~~W~Rp~e~~~~~~~~~~~-i~~~di~QG~lgDC~~lsal~~la~~~~ 83 (318)
T smart00230 5 RQYCKESGTLFEDPLFPANNGSLFFSQRQRKFVVWKRPHEIFENPPFIVGG-ASRTDICQGVLGDCWLLAALASLTLREK 83 (318)
T ss_pred HHHHHHcCCCccCCCCCCCcCccccCCCCCCCcEEECcHHHcCCCEEEeCC-CChhhccCcccccHHHHHHHHHHHhCHH
Confidence 46789999999999999954321 122479999999999999998876 8899999999999999999999999998
Q ss_pred hccCceEEEEeecCCCCCCCcccCCceEEEEeeeCCcEEEEEEcCCCccccCCceEEeecCCCCchhHHHHHHHhhhhcC
Q psy1431 123 RFGKRLVTSIIYPRNRNKEPVYNPFGKYMVKLHLNGITRKVIIDDQLPMARFNQLLCSYSQNKNELWVSILEKAYMKVMG 202 (1043)
Q Consensus 123 ~~~~~l~~~~i~p~~~~~~~~~n~~G~y~v~l~~~G~w~~V~VDD~lP~~~~g~~~~~~s~~~~elW~~LlEKAyaK~~G 202 (1043)
.+.+ |+|+++... .|+.|+|+||||+||+|+.|+|||+||+.. |.++++++++++|+|++||||||||++|
T Consensus 84 ~i~~------if~~~~~~~--~~~~G~y~vrl~~~G~w~~V~VDd~lP~~~-~~~~~~~~~~~~e~W~~LLEKAyAK~~G 154 (318)
T smart00230 84 LLDR------VIPHDQEFS--ENYAGIFHFRFWRFGKWVDVVIDDRLPTYN-GELVFMHSNSRNEFWSALLEKAYAKLNG 154 (318)
T ss_pred HHhh------eEeCCcccc--cccCCEEEEEEEECCEEEEEEecCCCeeeC-CceEEEEeCCCCcchhHHHHHHHHHHcC
Confidence 7765 556543322 567899999999999999999999999986 5599999999999999999999999999
Q ss_pred CcCC-CCCCcccccccccccceeEEEecC
Q psy1431 203 GYDF-PGSNSPGIRRSFTTVDCLRIEFNP 230 (1043)
Q Consensus 203 ~Y~~-~g~~~~~~l~~lTG~~~~~idl~~ 230 (1043)
||+. .||...++|++|||++++.|+++.
T Consensus 155 sY~~i~gg~~~~al~~LTG~~~~~i~l~~ 183 (318)
T smart00230 155 CYEALKGGSTTEALEDLTGGVAESIDLKE 183 (318)
T ss_pred CCcccCCCCHHHHHHHhcCCCeEEEEccc
Confidence 9995 566777999999999999999863
No 6
>cd00044 CysPc Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.
Probab=100.00 E-value=1.9e-35 Score=333.51 Aligned_cols=173 Identities=32% Similarity=0.485 Sum_probs=150.9
Q ss_pred hHhhhcCCCCccCCCCCCCCC---------CCCCCCCceEeccccccCC-----CeeecCCccCccCcccCCCCCchHHH
Q psy1431 47 LAEKFQYAVPFTDKEGPLILS---------PKQKRDFVAWVRPSEFCSE-----PKMVAGEFVDYFSIKQTIVSDCSFVA 112 (1043)
Q Consensus 47 ~~~~~~~~~~f~D~~fp~~l~---------~~~~~~~~~W~Rp~e~~~~-----~~~~~~~~~~~~di~Qg~lgDC~~la 112 (1043)
++.|.+.+.+|+|++|||... ..+....+.|+||.|++.+ |.++.++ +++.||+||.+|||||||
T Consensus 3 ~~~c~~~~~~f~D~~Fpp~~~s~~~~~~~~~~~~~~~~~W~Rp~~~~~~~~~~~~~~~~~~-~~~~dI~QG~lgDC~~ls 81 (315)
T cd00044 3 LQICLLSGVLFEDPDFPPNDSSLGFDDSLSNGQPKKVIEWKRPSEIFADDGNSNPRLFVNG-ASPSDVCQGILGDCWFLA 81 (315)
T ss_pred HHHHHHcCCCccCCCCCCCccccccccccccccCcCcceEECcHHHhCcccCCCCEEEeCC-CChhhcccCcccchHHHH
Confidence 467889999999999999532 3345667999999999987 8888776 899999999999999999
Q ss_pred HHHHHhhhhhhccCceEEEEeecCCCCCCCcccCCceEEEEeeeCCcEEEEEEcCCCccccCCceEEeecCCCCchhHHH
Q psy1431 113 SLAVSALYERRFGKRLVTSIIYPRNRNKEPVYNPFGKYMVKLHLNGITRKVIIDDQLPMARFNQLLCSYSQNKNELWVSI 192 (1043)
Q Consensus 113 al~~la~~~~~~~~~l~~~~i~p~~~~~~~~~n~~G~y~v~l~~~G~w~~V~VDD~lP~~~~g~~~~~~s~~~~elW~~L 192 (1043)
||++||++++.+.+ +++...... .++.|+|+||||+||+|+.|+|||+||+..++ ++|+++.+.+|+|++|
T Consensus 82 aL~~la~~~~~i~~------lf~~~~~~~--~~~~G~y~v~l~~~G~w~~V~VDD~lP~~~~~-~~~~~s~~~~e~W~~L 152 (315)
T cd00044 82 ALAALAERPELLKR------VIPPDQSFE--ENYAGIYHFRFWKNGEWVEVVIDDRLPTSNGG-LLFMHSRDRNELWVAL 152 (315)
T ss_pred HHHHHHcCHHHHhh------eEcCCcccc--cCcCcEEEEEEEECCEEEEEEecCCCeecCCc-eEEEEECCCCeEcHHH
Confidence 99999999997776 333322111 47789999999999999999999999998755 9999998889999999
Q ss_pred HHHHhhhhcCCcCC-CCCCcccccccccccceeEEEec
Q psy1431 193 LEKAYMKVMGGYDF-PGSNSPGIRRSFTTVDCLRIEFN 229 (1043)
Q Consensus 193 lEKAyaK~~G~Y~~-~g~~~~~~l~~lTG~~~~~idl~ 229 (1043)
|||||||+||||+. .||++.++|++|||++++.|+++
T Consensus 153 lEKAyAK~~GsY~~i~gg~~~~al~~LTG~~~~~i~~~ 190 (315)
T cd00044 153 LEKAYAKLHGSYEALVGGNTAEALEDLTGGPTERIDLK 190 (315)
T ss_pred HHHHHHhhcCCccccCCCCHHHHHHHhhCCCcEEEEcc
Confidence 99999999999995 99999999999999999999985
No 7
>PF00648 Peptidase_C2: Calpain family cysteine protease This is family C2 in the peptidase classification. ; InterPro: IPR001300 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C2 (calpain family, clan CA). A type example is calpain, which is an intracellular protease involved in many important cellular functions that are regulated by calcium []. The protein is a complex of 2 polypeptide chains (light and heavy), with three known forms in mammals [, ]: a highly calcium-sensitive (i.e., micro-molar range) form known as mu-calpain, mu-CANP or calpain I; a form sensitive to calcium in the milli-molar range, known as m-calpain, m-CANP or calpain II; and a third form, known as p94, which is found in skeletal muscle only []. All forms have identical light but different heavy chains. Both mu- and m-calpain are heterodimers containing an identical 28kDa subunit and an 80kDa subunit that shares 55-65% sequence homology between the two proteases [, ]. The crystallographic structure of m-calpain reveals six "domains" in the 80kDa subunit: A 19-amino acid NH2-terminal sequence; Active site domain IIa; Active site domain IIb. Domain 2 shows low levels of sequence similarity to papain; although the catalytic His has not been located by biochemical means, it is likely that calpain and papain are related []. Domain III; An 18-amino acid extended sequence linking domain III to domain IV; Domain IV, which resembles the penta EF-hand family of polypeptides, binds calcium and regulates activity []. />]. Ca2+-binding causes a rearrangement of the protein backbone, the net effect of which is that a Trp side chain, which acts as a wedge between catalytic domains IIa and IIb in the apo state, moves away from the active site cleft allowing for the proper formation of the catalytic triad []. Calpain-like mRNAs have been identified in other organisms including bacteria, but the molecules encoded by these mRNAs have not been isolated, so little is known about their properties. How calpain activity is regulated in these organisms cells is still unclear In metazoans, the activity of calpain is controlled by a single proteinase inhibitor, calpastatin (IPR001259 from INTERPRO). The calpastatin gene can produce eight or more calpastatin polypeptides ranging from 17 to 85 kDa by use of different promoters and alternative splicing events. The physiological significance of these different calpastatins is unclear, although all bind to three different places on the calpain molecule; binding to at least two of the sites is Ca2+ dependent. The calpains ostensibly participate in a variety of cellular processes including remodelling of cytoskeletal/membrane attachments, different signal transduction pathways, and apoptosis. Deregulated calpain activity following loss of Ca2+ homeostasis results in tissue damage in response to events such as myocardial infarcts, stroke, and brain trauma []. Calpains are a family of cytosolic cysteine proteinases (see PDOC00126 from PROSITEDOC). Members of the calpain family are believed to function in various biological processes, including integrin-mediated cell migration, cytoskeletal remodeling, cell differentiation and apoptosis [, ]. The calpain family includes numerous members from C. elegans to mammals and with homologues in yeast and bacteria. The best characterised members are the m- and mu-calpains, both proteins are heterodimer composed of a large catalytic subunit and a small regulatory subunit. The large subunit comprises four domains (dI-dIV) while the small subunit has two domains (dV-dVI). Domain dI is a short region cleaved by autolysis, dII is the catalytic core, dIII is a C2-like domain, dIV consists of five calcium binding EF-hand motifs []. The crystal structure of calpain has been solved [, ]. The catalytic region consists of two distinct structural domains (dIIa and dIIb). dIIa contains a central helix flanked on three faces by a cluster of alpha-helices and is entirely unrelated to the corresponding domain in the typical thiol proteinases. The fold of dIIb is similar to the corresponding domain in other cysteine proteinases and contains two three-stranded anti-parallel beta-sheets. The catalytic triad residues (C,H,N) are located in dIIa and dIIb. The activation of the domain is dependent on the binding of two calcium atoms in two non EF-hand calcium binding sites located in the catalytic core, one close to the Cys active site in dIIa and one at the end of dIIb. Calcium-binding induced conformational changes in the catalytic domain which align the active site [][]. The profile covers the whole catalytic domain.; GO: 0004198 calcium-dependent cysteine-type endopeptidase activity, 0006508 proteolysis, 0005622 intracellular; PDB: 2NQA_A 1KFU_L 1KFX_L 1QXP_B 2R9C_A 1TL9_A 2G8E_A 1KXR_B 2G8J_A 2NQG_A ....
Probab=100.00 E-value=7.5e-35 Score=326.85 Aligned_cols=164 Identities=35% Similarity=0.511 Sum_probs=130.3
Q ss_pred CccCCCCCCCC---CC-CCCCCCceEeccccccCCCeeecCCccCccCcccCCCCCchHHHHHHHHhhhhhhccCceEEE
Q psy1431 56 PFTDKEGPLIL---SP-KQKRDFVAWVRPSEFCSEPKMVAGEFVDYFSIKQTIVSDCSFVASLAVSALYERRFGKRLVTS 131 (1043)
Q Consensus 56 ~f~D~~fp~~l---~~-~~~~~~~~W~Rp~e~~~~~~~~~~~~~~~~di~Qg~lgDC~~laal~~la~~~~~~~~~l~~~ 131 (1043)
.|+||+|||.. .. ......+.|+||+|++.+|+++.++ +++.||+||.+|||||||||++||++++.+.+
T Consensus 1 ~f~D~~Fpp~~~Sl~~~~~~~~~~~W~R~~e~~~~~~~~~~~-~~~~di~QG~lgDc~llaaL~~la~~~~~i~~----- 74 (298)
T PF00648_consen 1 LFEDPEFPPNDSSLGFDDQKPKNVEWKRPSEICENPQFFIDG-ISPSDIRQGSLGDCWLLAALAALAEHPDLIKK----- 74 (298)
T ss_dssp ----TTS-SSHHHHTSSTTSTTT-EEE-HHHHSSS-BSSSSS-SSGGGEBE-SSSSHHHHHHHHHHTTSHHHHHH-----
T ss_pred CccCCCCccCccccccCCCCCCcceeEechhcCCCCeEEECC-CccccccccccCChhHHHHHHHHHhccccccc-----
Confidence 49999999952 21 2234668999999999999988765 78999999999999999999999999998876
Q ss_pred EeecCCCCCCCcccCCceEEEEeeeCCcEEEEEEcCCCccccCCceEEeecCCCCchhHHHHHHHhhhhcCCcC-CCCCC
Q psy1431 132 IIYPRNRNKEPVYNPFGKYMVKLHLNGITRKVIIDDQLPMARFNQLLCSYSQNKNELWVSILEKAYMKVMGGYD-FPGSN 210 (1043)
Q Consensus 132 ~i~p~~~~~~~~~n~~G~y~v~l~~~G~w~~V~VDD~lP~~~~g~~~~~~s~~~~elW~~LlEKAyaK~~G~Y~-~~g~~ 210 (1043)
++|.++...+ +..|+|+||||++|+|++|+|||+||+ .+|+++|+++++++|+|++||||||||++|||+ +.||+
T Consensus 75 -i~~~~~~~~~--~~~G~y~v~l~~~G~w~~V~VDd~lP~-~~g~~~f~~s~~~~elW~~LlEKAyAKl~GsY~~l~gg~ 150 (298)
T PF00648_consen 75 -IFPVNQSFNE--NYNGIYTVRLFKNGEWREVTVDDRLPC-KNGKPLFARSSDPNELWPSLLEKAYAKLHGSYSALEGGN 150 (298)
T ss_dssp -HS-SS--SST--T-SSEEEEEEEETTEEEEEEEES-EEE-ETTEESSSBESSTTB-HHHHHHHHHHHHTTSSGGGSSBS
T ss_pred -cccccccccc--ccCceeeEeeccCCeeeeeccchhhhc-cccceeeeccCCcccchhhhhhchhhhccccccccCCCC
Confidence 4454433222 235999999999999999999999999 569999999889999999999999999999999 58999
Q ss_pred cccccccccccceeEEEec
Q psy1431 211 SPGIRRSFTTVDCLRIEFN 229 (1043)
Q Consensus 211 ~~~~l~~lTG~~~~~idl~ 229 (1043)
+.++|.+|||++++.|+++
T Consensus 151 ~~~al~~LTG~~~~~~~l~ 169 (298)
T PF00648_consen 151 PSEALQDLTGGPPESIDLR 169 (298)
T ss_dssp HHHHHHHHHSSEEEEEEGG
T ss_pred hhhhhHhhcCCcceeeecc
Confidence 9999999999999999974
No 8
>KOG0045|consensus
Probab=99.98 E-value=6.7e-33 Score=329.82 Aligned_cols=172 Identities=30% Similarity=0.490 Sum_probs=150.3
Q ss_pred HhhhcCCCCccCCCCCCCCCC-----CCCC---CCceEeccccccCCCeeecCCccCccCcccCCCCCchHHHHHHHHhh
Q psy1431 48 AEKFQYAVPFTDKEGPLILSP-----KQKR---DFVAWVRPSEFCSEPKMVAGEFVDYFSIKQTIVSDCSFVASLAVSAL 119 (1043)
Q Consensus 48 ~~~~~~~~~f~D~~fp~~l~~-----~~~~---~~~~W~Rp~e~~~~~~~~~~~~~~~~di~Qg~lgDC~~laal~~la~ 119 (1043)
..|...+..|+|+.||+.-++ .+.. ..+.|+||+|++.+|.++.++ +++.||+||.+||||||||+|+||.
T Consensus 18 ~~cl~~~~~F~D~~FP~~~~Sl~~~~~~p~~~~~~i~W~RP~ei~~~p~~i~~~-~~~~di~Qg~lgdCw~laA~a~la~ 96 (612)
T KOG0045|consen 18 RDCLPAKSLFVDALFPAADSSLFYKLSTPLAQFSDIVWKRPQEICANPRLIVDG-PSRFDVKQGLLGDCWFLAACAALAL 96 (612)
T ss_pred HHHhhcCCcccccCCCCCCccccccccCCCcccccceecCcccccCCCCeecCC-CCcceeEEeeecchHHHHHHHHhhc
Confidence 358889999999999985322 1122 579999999999999999987 8999999999999999999999999
Q ss_pred hhhhccCceEEEEeecCCCCCCCcccCCceEEEEeeeCCcEEEEEEcCCCccccCCceEEeecCCCCchhHHHHHHHhhh
Q psy1431 120 YERRFGKRLVTSIIYPRNRNKEPVYNPFGKYMVKLHLNGITRKVIIDDQLPMARFNQLLCSYSQNKNELWVSILEKAYMK 199 (1043)
Q Consensus 120 ~~~~~~~~l~~~~i~p~~~~~~~~~n~~G~y~v~l~~~G~w~~V~VDD~lP~~~~g~~~~~~s~~~~elW~~LlEKAyaK 199 (1043)
+++++.+ +.|+++... ++..|+|+||||.+|+|+.|+|||+||+.. |+++++++++.+|+|++||||||||
T Consensus 97 ~~~ll~~------vip~~~~~~--~~yaGif~f~~w~~G~W~~VvIDD~LP~~~-~~~~~~~s~~~~efW~aLlEKAyaK 167 (612)
T KOG0045|consen 97 RPELLDK------VIPQDQSFQ--ENYAGIFHFRFWQNGEWVEVVIDDRLPTSN-GGLLFSHSSGKNEFWAALLEKAYAK 167 (612)
T ss_pred CHHHHHh------ccCCCcccc--cccceEEEEEEEeCCeEEEEEeeeecceEc-CCEEEEeecCCceeHHHHHHHHHHH
Confidence 9998887 667665544 455699999999999999999999999987 7778888888899999999999999
Q ss_pred hcCCcCC-CCCCcccccccccccceeEEEec
Q psy1431 200 VMGGYDF-PGSNSPGIRRSFTTVDCLRIEFN 229 (1043)
Q Consensus 200 ~~G~Y~~-~g~~~~~~l~~lTG~~~~~idl~ 229 (1043)
++|||+. .||...++|.||||+.++.++|+
T Consensus 168 l~GsY~~l~gg~~~~a~~~lTG~~~e~~~l~ 198 (612)
T KOG0045|consen 168 LLGSYEALHGGSTIDALVDLTGGVTEPFDLN 198 (612)
T ss_pred HhCcccCCCCCchhhHHHhccCCccceeEcc
Confidence 9999995 67777799999999999998874
No 9
>smart00720 calpain_III calpain_III.
Probab=99.92 E-value=1.5e-24 Score=216.70 Aligned_cols=128 Identities=35% Similarity=0.609 Sum_probs=105.3
Q ss_pred ceeEEEEceee-cCCCCCCCCCCCCCCCCCcEEEEecCCCCCCceEEEEEc----------CCCceeeeEEEEEEeCCC-
Q psy1431 913 QFKEEISGEWK-GLTAGGCPNYPATYPNNPRYQVTLDSRQSMDNTLLVFLK----------GPKQYSLGVKISCVRLDD- 980 (1043)
Q Consensus 913 ~~~~~i~G~W~-~~tAGG~~n~~~ty~~NPqy~l~l~~~~~~~~~l~i~l~----------~~~~~~ig~~v~~~~~~~- 980 (1043)
++.++++|+|+ +.|||||+|+++||++||||.|++.++++....++|+|. +.+.++|||+|++++...
T Consensus 1 w~~~~~~G~W~~~~tAGG~~~~~~tf~~NPqy~l~v~~~~~~~~~v~i~L~q~~~r~~~~~~~~~~~iGf~v~~~~~~~~ 80 (143)
T smart00720 1 WHTKSVQGSWTRGQTAGGCRNYPATFWTNPQFRITLEEPDDDDCTVLIALMQKNRRRLRRKGADFLTIGFAVYKVPKELH 80 (143)
T ss_pred CcEEEEeCeEECCCccCCccccccccccCCeEEEEecCCCCCceEEEEEecccCcccccccCCccceEeEEEEEeccccc
Confidence 35689999997 999999999977999999999999988742212788883 234679999999997542
Q ss_pred ---CCcCCCcccccCCCcccceEEEEeecCCCccEEEEeccCCCCCccCeEEEEEeCCceeEE
Q psy1431 981 ---ETATAPFKTKDSGAYRSGFVAVEMDNLPSGTYEIMPSTFSPQQEGPFFLELKSSCSITIS 1040 (1043)
Q Consensus 981 ---~~~~~~~~~~~sg~yr~g~~~~~~~~L~~G~Y~IVPSTf~p~~~g~F~L~V~S~~~~~l~ 1040 (1043)
........++.++.|++++++.....|+||.|+||||||+|+++|+|.|||+|+.+++|+
T Consensus 81 ~~~~~~~~~~~~~~s~~y~~~r~v~~~~~L~~G~Y~iVPsT~~p~~~g~F~LrV~s~~~~~l~ 143 (143)
T smart00720 81 LRRDFFLSNAPRASSGDYINGREVSERFRLPPGEYVIVPSTFEPNQEGDFLLRVFSEGPFKLT 143 (143)
T ss_pred cchhhhhccCccccccccccCeEEEEEEEcCCCCEEEEEeecCCCCccCEEEEEEecCccccC
Confidence 112222445688999999998888899999999999999999999999999999998863
No 10
>cd00214 Calpain_III Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains.
Probab=99.91 E-value=2.3e-24 Score=216.68 Aligned_cols=130 Identities=28% Similarity=0.463 Sum_probs=103.9
Q ss_pred ceeEEEEceeec-CCCCCCCCCCCCCCCCCcEEEEecCCCCC--CceEEEEEcC----------CCceeeeEEEEEEeCC
Q psy1431 913 QFKEEISGEWKG-LTAGGCPNYPATYPNNPRYQVTLDSRQSM--DNTLLVFLKG----------PKQYSLGVKISCVRLD 979 (1043)
Q Consensus 913 ~~~~~i~G~W~~-~tAGG~~n~~~ty~~NPqy~l~l~~~~~~--~~~l~i~l~~----------~~~~~ig~~v~~~~~~ 979 (1043)
|+.++++|+|+. .|||||.|+++||++||||.|.|.++++. ...++|.|.. .+.++|||+||+++..
T Consensus 3 W~~~~~~G~W~~g~tAGGc~~~~~tf~~NPQf~l~v~~~~~~~~~~~v~i~L~q~~~r~~~~~~~~~~~IGf~v~~~~~~ 82 (150)
T cd00214 3 WHTKSFNGEWRRGQTAGGCRNNPDTFWTNPQFRIRVPEPDDDEGKCTVLIALMQKNRRHLRKKGLDLLTIGFHVYKVPGE 82 (150)
T ss_pred ceEEEEeCeEeCCcccCCCCCcccccccCceEEEEecCCCCCCCccEEEEEeccCCcchhcccCCCcceEEEEEEEeCCc
Confidence 567999999976 99999999988999999999999988531 0128888853 3467999999999753
Q ss_pred CCCcCCC-----cccccCCCcccceEEEEeecCCCccEEEEeccCCCCCccCeEEEEEeCCceeEEec
Q psy1431 980 DETATAP-----FKTKDSGAYRSGFVAVEMDNLPSGTYEIMPSTFSPQQEGPFFLELKSSCSITISRI 1042 (1043)
Q Consensus 980 ~~~~~~~-----~~~~~sg~yr~g~~~~~~~~L~~G~Y~IVPSTf~p~~~g~F~L~V~S~~~~~l~~i 1042 (1043)
...+... ..++.++.|.+.+++.....|+||.|+||||||+|+++|+|.|||+|+.++.+++|
T Consensus 83 ~~~~~~~~~~~~~~~~~s~~~~~~rev~~~~~L~pG~YvIIPsT~~p~~~g~F~LrVfs~~~~~~~~~ 150 (150)
T cd00214 83 NRHLRRDFFLHKAPRARSSTFINTREVSLRFRLPPGEYVIVPSTFEPGEEGEFLLRVFSEKSIKSSEL 150 (150)
T ss_pred CcccChhhhhccCcccccCccccccEEEEEEEcCCCCEEEEeeecCCCCcccEEEEEEecCCCccccC
Confidence 2222221 12346777888777666667999999999999999999999999999999998875
No 11
>PF01067 Calpain_III: Calpain large subunit, domain III; InterPro: IPR022682 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C2 (calpain family, clan CA). A type example is calpain, which is an intracellular protease involved in many important cellular functions that are regulated by calcium []. The protein is a complex of 2 polypeptide chains (light and heavy), with three known forms in mammals [, ]: a highly calcium-sensitive (i.e., micro-molar range) form known as mu-calpain, mu-CANP or calpain I; a form sensitive to calcium in the milli-molar range, known as m-calpain, m-CANP or calpain II; and a third form, known as p94, which is found in skeletal muscle only []. All forms have identical light but different heavy chains. Both mu- and m-calpain are heterodimers containing an identical 28kDa subunit and an 80kDa subunit that shares 55-65% sequence homology between the two proteases [, ]. The crystallographic structure of m-calpain reveals six "domains" in the 80kDa subunit: A 19-amino acid NH2-terminal sequence; Active site domain IIa; Active site domain IIb. Domain 2 shows low levels of sequence similarity to papain; although the catalytic His has not been located by biochemical means, it is likely that calpain and papain are related []. Domain III; An 18-amino acid extended sequence linking domain III to domain IV; Domain IV, which resembles the penta EF-hand family of polypeptides, binds calcium and regulates activity []. />]. Ca2+-binding causes a rearrangement of the protein backbone, the net effect of which is that a Trp side chain, which acts as a wedge between catalytic domains IIa and IIb in the apo state, moves away from the active site cleft allowing for the proper formation of the catalytic triad []. Calpain-like mRNAs have been identified in other organisms including bacteria, but the molecules encoded by these mRNAs have not been isolated, so little is known about their properties. How calpain activity is regulated in these organisms cells is still unclear In metazoans, the activity of calpain is controlled by a single proteinase inhibitor, calpastatin (IPR001259 from INTERPRO). The calpastatin gene can produce eight or more calpastatin polypeptides ranging from 17 to 85 kDa by use of different promoters and alternative splicing events. The physiological significance of these different calpastatins is unclear, although all bind to three different places on the calpain molecule; binding to at least two of the sites is Ca2+ dependent. The calpains ostensibly participate in a variety of cellular processes including remodelling of cytoskeletal/membrane attachments, different signal transduction pathways, and apoptosis. Deregulated calpain activity following loss of Ca2+ homeostasis results in tissue damage in response to events such as myocardial infarcts, stroke, and brain trauma []. This entry represents domain III. It is found in association with PF00648 from PFAM. The function of the domain III and I are currently unknown. Domain II is a cysteine protease and domain IV is a calcium binding domain. Calpains are believed to participate in intracellular signaling pathways mediated by calcium ions. ; PDB: 1QXP_B 2QFE_A 1DF0_A 1U5I_A 3DF0_A 3BOW_A 1KFU_L 1KFX_L.
Probab=99.88 E-value=1.3e-22 Score=203.72 Aligned_cols=128 Identities=34% Similarity=0.547 Sum_probs=95.0
Q ss_pred ceeEEEEcee-ecCCCCCCCCCCCCCCCCCcEEEEecCCCCCC--ceEEEEEcC----------CCceeeeEEEEEEeCC
Q psy1431 913 QFKEEISGEW-KGLTAGGCPNYPATYPNNPRYQVTLDSRQSMD--NTLLVFLKG----------PKQYSLGVKISCVRLD 979 (1043)
Q Consensus 913 ~~~~~i~G~W-~~~tAGG~~n~~~ty~~NPqy~l~l~~~~~~~--~~l~i~l~~----------~~~~~ig~~v~~~~~~ 979 (1043)
|+..+++|+| ++.|||||.+++.+|++||||.|+|.++++.. ..++|.|.. .+..+|||+|+++...
T Consensus 2 W~~~~~~G~W~~~~taGG~~~~~~s~~~NPQy~l~v~~~~~~~~~~~v~i~L~q~~~~~~~~~~~~~~~Ig~~v~~~~~~ 81 (147)
T PF01067_consen 2 WHTVTIEGEWVTGNTAGGCPNNPYSWWNNPQYRLTVSEPTEESNKCTVVISLMQKDRRRKRDVGEKDLPIGFYVFKVQSQ 81 (147)
T ss_dssp EEEEEEEEEE-TTTS---STT-TTTGGGS-EEEEEESSGCCCSSBEEEEEEEEECSGCCGCSTTTTTSEEEEEEEEETTT
T ss_pred eeEEEEeCEEeCCCcCCCCcccccccccCcEEEEEEcCCCCCcceeEEEEEEEecCcchhhcccccceEEeEEEEeeecc
Confidence 4679999999 99999999999999999999999999988641 116666641 2457899999999222
Q ss_pred CCCcCC-----CcccccCCCcccceEEEEeecCCCccEEEEeccCCCCCccCeEEEEEeCCceeEE
Q psy1431 980 DETATA-----PFKTKDSGAYRSGFVAVEMDNLPSGTYEIMPSTFSPQQEGPFFLELKSSCSITIS 1040 (1043)
Q Consensus 980 ~~~~~~-----~~~~~~sg~yr~g~~~~~~~~L~~G~Y~IVPSTf~p~~~g~F~L~V~S~~~~~l~ 1040 (1043)
..++.. ...+..++.|++++++.....|+||+|+||||||+|+++|+|.|+|+|+.+++|.
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~L~~G~YvIVPsT~~~~~~g~F~L~v~s~~~~~l~ 147 (147)
T PF01067_consen 82 QKRLPRQYFLFNKPVVSSGDYSNSREVSEEFTLPPGTYVIVPSTYEPGQEGEFTLRVFSDSPFELQ 147 (147)
T ss_dssp TSE--HHHHHTS-SSEE-SSEBSSSEEEEEEEE-SEEEEEEEEESSTT--EEEEEEEEESSSEEE-
T ss_pred cccCCcceeccccceeeccccccceEEEEEEEcCCCCEEEEEecCCCCCeeeEEEEEEECCCcccC
Confidence 222111 2346688999999998888889999999999999999999999999999999874
No 12
>cd00214 Calpain_III Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains.
Probab=99.73 E-value=3.6e-17 Score=164.62 Aligned_cols=139 Identities=16% Similarity=0.197 Sum_probs=104.1
Q ss_pred eeeeeeeecccccCCCCCcccCcccccccccccceEEEEEeeCCCCCcCCCCCCCCCCCCCccEEEEEeeccc-cccccc
Q psy1431 651 FCVHQELTFEKKNGNSTNCVKTAKQLSIVVFDYVTFKPVIIRNSSLDYFGQWPPSTPAASPKRNFWILLTRHI-TQLEDF 729 (1043)
Q Consensus 651 ~~~h~~~~W~~~~~~~gg~~~~~~~~~~~~~~NPQf~l~~~~~~~~~~~~~~~~~~~~~~~~~~VwilL~rh~-~~~~~~ 729 (1043)
..+++. |..+..+ |||.+...++ ++||||.|++..++. + ..+++|+|.|.|.. +..+..
T Consensus 6 ~~~~G~--W~~g~tA-GGc~~~~~tf----~~NPQf~l~v~~~~~-----------~--~~~~~v~i~L~q~~~r~~~~~ 65 (150)
T cd00214 6 KSFNGE--WRRGQTA-GGCRNNPDTF----WTNPQFRIRVPEPDD-----------D--EGKCTVLIALMQKNRRHLRKK 65 (150)
T ss_pred EEEeCe--EeCCccc-CCCCCccccc----ccCceEEEEecCCCC-----------C--CCccEEEEEeccCCcchhccc
Confidence 456666 9987655 9997776666 999999999987421 0 12378999776554 333333
Q ss_pred cCCceeeEEEEEEeCCeeeecC-----CCCCCccccccccCceEEEEEEecCCCCccEEEEeccccCccccceEEEEeec
Q psy1431 730 KQNREYITVLVYKNEGKRVYYP-----YDPPPYLDGVRINSPHYLCKIILNENSSRKYTLVVSQYEKMHTIYYTLRAYAT 804 (1043)
Q Consensus 730 ~~~~~~I~l~V~~~~g~rv~~~-----~~~~~~~~g~~~ns~~~l~r~~l~p~~~~~YtlVpst~~~~~~~~F~LriyS~ 804 (1043)
+.+...|||+||++++....++ .....+..+.|.+++++.+++.|+| |.|+|||||++++++|+|+|||||+
T Consensus 66 ~~~~~~IGf~v~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~rev~~~~~L~p---G~YvIIPsT~~p~~~g~F~LrVfs~ 142 (150)
T cd00214 66 GLDLLTIGFHVYKVPGENRHLRRDFFLHKAPRARSSTFINTREVSLRFRLPP---GEYVIVPSTFEPGEEGEFLLRVFSE 142 (150)
T ss_pred CCCcceEEEEEEEeCCcCcccChhhhhccCcccccCccccccEEEEEEEcCC---CCEEEEeeecCCCCcccEEEEEEec
Confidence 4556789999999976322222 1122345778999999999999987 7999999999999999999999999
Q ss_pred CCcccccc
Q psy1431 805 CPFRLEKI 812 (1043)
Q Consensus 805 ~~~~~~~l 812 (1043)
++++++++
T Consensus 143 ~~~~~~~~ 150 (150)
T cd00214 143 KSIKSSEL 150 (150)
T ss_pred CCCccccC
Confidence 99988754
No 13
>smart00720 calpain_III calpain_III.
Probab=99.70 E-value=1.3e-16 Score=159.42 Aligned_cols=134 Identities=17% Similarity=0.243 Sum_probs=102.0
Q ss_pred eeeeeeeecccccCCCCCcccCcccccccccccceEEEEEeeCCCCCcCCCCCCCCCCCCCccEEEEEeecccccc-ccc
Q psy1431 651 FCVHQELTFEKKNGNSTNCVKTAKQLSIVVFDYVTFKPVIIRNSSLDYFGQWPPSTPAASPKRNFWILLTRHITQL-EDF 729 (1043)
Q Consensus 651 ~~~h~~~~W~~~~~~~gg~~~~~~~~~~~~~~NPQf~l~~~~~~~~~~~~~~~~~~~~~~~~~~VwilL~rh~~~~-~~~ 729 (1043)
..+++. |.++..+ |||.+...++ ++||||.|++..++. ..++|+|.|.|+.++. ++.
T Consensus 4 ~~~~G~--W~~~~tA-GG~~~~~~tf----~~NPqy~l~v~~~~~---------------~~~~v~i~L~q~~~r~~~~~ 61 (143)
T smart00720 4 KSVQGS--WTRGQTA-GGCRNYPATF----WTNPQFRITLEEPDD---------------DDCTVLIALMQKNRRRLRRK 61 (143)
T ss_pred EEEeCe--EECCCcc-CCcccccccc----ccCCeEEEEecCCCC---------------CceEEEEEecccCccccccc
Confidence 456666 9966655 8998765565 999999999987321 1178999987664433 223
Q ss_pred cCCceeeEEEEEEeCCe-e---eecCCCCCCccccccccCceEEEEEEecCCCCccEEEEeccccCccccceEEEEeecC
Q psy1431 730 KQNREYITVLVYKNEGK-R---VYYPYDPPPYLDGVRINSPHYLCKIILNENSSRKYTLVVSQYEKMHTIYYTLRAYATC 805 (1043)
Q Consensus 730 ~~~~~~I~l~V~~~~g~-r---v~~~~~~~~~~~g~~~ns~~~l~r~~l~p~~~~~YtlVpst~~~~~~~~F~LriyS~~ 805 (1043)
+.....|||+||++++. + .++......+.++.|.+++++.+++.|+| |.|+|||||++++++|+|+||||++.
T Consensus 62 ~~~~~~iGf~v~~~~~~~~~~~~~~~~~~~~~~s~~y~~~r~v~~~~~L~~---G~Y~iVPsT~~p~~~g~F~LrV~s~~ 138 (143)
T smart00720 62 GADFLTIGFAVYKVPKELHLRRDFFLSNAPRASSGDYINGREVSERFRLPP---GEYVIVPSTFEPNQEGDFLLRVFSEG 138 (143)
T ss_pred CCccceEeEEEEEeccccccchhhhhccCccccccccccCeEEEEEEEcCC---CCEEEEEeecCCCCccCEEEEEEecC
Confidence 34567899999999765 2 23333333455678999999999999987 78999999999999999999999999
Q ss_pred Cccc
Q psy1431 806 PFRL 809 (1043)
Q Consensus 806 ~~~~ 809 (1043)
++.+
T Consensus 139 ~~~l 142 (143)
T smart00720 139 PFKL 142 (143)
T ss_pred cccc
Confidence 9876
No 14
>PF01067 Calpain_III: Calpain large subunit, domain III; InterPro: IPR022682 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C2 (calpain family, clan CA). A type example is calpain, which is an intracellular protease involved in many important cellular functions that are regulated by calcium []. The protein is a complex of 2 polypeptide chains (light and heavy), with three known forms in mammals [, ]: a highly calcium-sensitive (i.e., micro-molar range) form known as mu-calpain, mu-CANP or calpain I; a form sensitive to calcium in the milli-molar range, known as m-calpain, m-CANP or calpain II; and a third form, known as p94, which is found in skeletal muscle only []. All forms have identical light but different heavy chains. Both mu- and m-calpain are heterodimers containing an identical 28kDa subunit and an 80kDa subunit that shares 55-65% sequence homology between the two proteases [, ]. The crystallographic structure of m-calpain reveals six "domains" in the 80kDa subunit: A 19-amino acid NH2-terminal sequence; Active site domain IIa; Active site domain IIb. Domain 2 shows low levels of sequence similarity to papain; although the catalytic His has not been located by biochemical means, it is likely that calpain and papain are related []. Domain III; An 18-amino acid extended sequence linking domain III to domain IV; Domain IV, which resembles the penta EF-hand family of polypeptides, binds calcium and regulates activity []. />]. Ca2+-binding causes a rearrangement of the protein backbone, the net effect of which is that a Trp side chain, which acts as a wedge between catalytic domains IIa and IIb in the apo state, moves away from the active site cleft allowing for the proper formation of the catalytic triad []. Calpain-like mRNAs have been identified in other organisms including bacteria, but the molecules encoded by these mRNAs have not been isolated, so little is known about their properties. How calpain activity is regulated in these organisms cells is still unclear In metazoans, the activity of calpain is controlled by a single proteinase inhibitor, calpastatin (IPR001259 from INTERPRO). The calpastatin gene can produce eight or more calpastatin polypeptides ranging from 17 to 85 kDa by use of different promoters and alternative splicing events. The physiological significance of these different calpastatins is unclear, although all bind to three different places on the calpain molecule; binding to at least two of the sites is Ca2+ dependent. The calpains ostensibly participate in a variety of cellular processes including remodelling of cytoskeletal/membrane attachments, different signal transduction pathways, and apoptosis. Deregulated calpain activity following loss of Ca2+ homeostasis results in tissue damage in response to events such as myocardial infarcts, stroke, and brain trauma []. This entry represents domain III. It is found in association with PF00648 from PFAM. The function of the domain III and I are currently unknown. Domain II is a cysteine protease and domain IV is a calcium binding domain. Calpains are believed to participate in intracellular signaling pathways mediated by calcium ions. ; PDB: 1QXP_B 2QFE_A 1DF0_A 1U5I_A 3DF0_A 3BOW_A 1KFU_L 1KFX_L.
Probab=99.63 E-value=1.8e-15 Score=151.95 Aligned_cols=137 Identities=23% Similarity=0.328 Sum_probs=93.7
Q ss_pred eeeeeeeeecccccCCCCCcccCcccccccccccceEEEEEeeCCCCCcCCCCCCCCCCCCCccEEEEEeeccccccc-c
Q psy1431 650 TFCVHQELTFEKKNGNSTNCVKTAKQLSIVVFDYVTFKPVIIRNSSLDYFGQWPPSTPAASPKRNFWILLTRHITQLE-D 728 (1043)
Q Consensus 650 ~~~~h~~~~W~~~~~~~gg~~~~~~~~~~~~~~NPQf~l~~~~~~~~~~~~~~~~~~~~~~~~~~VwilL~rh~~~~~-~ 728 (1043)
...+++. |..+..+ |||.+...++ ++||||.|++..+.. ...++.|+|+|.++..+.. +
T Consensus 4 ~~~~~G~--W~~~~ta-GG~~~~~~s~----~~NPQy~l~v~~~~~-------------~~~~~~v~i~L~q~~~~~~~~ 63 (147)
T PF01067_consen 4 TVTIEGE--WVTGNTA-GGCPNNPYSW----WNNPQYRLTVSEPTE-------------ESNKCTVVISLMQKDRRRKRD 63 (147)
T ss_dssp EEEEEEE--E-TTTS----STT-TTTG----GGS-EEEEEESSGCC-------------CSSBEEEEEEEEECSGCCGCS
T ss_pred EEEEeCE--EeCCCcC-CCCccccccc----ccCcEEEEEEcCCCC-------------CcceeEEEEEEEecCcchhhc
Confidence 3567877 9766655 8887765555 999999999987421 1113689998887654432 2
Q ss_pred ccCCceeeEEEEEEeC--Cee---eecCCCCCCccccccccCceEEEEEEecCCCCccEEEEeccccCccccceEEEEee
Q psy1431 729 FKQNREYITVLVYKNE--GKR---VYYPYDPPPYLDGVRINSPHYLCKIILNENSSRKYTLVVSQYEKMHTIYYTLRAYA 803 (1043)
Q Consensus 729 ~~~~~~~I~l~V~~~~--g~r---v~~~~~~~~~~~g~~~ns~~~l~r~~l~p~~~~~YtlVpst~~~~~~~~F~LriyS 803 (1043)
.+....+|+|+||+.. ..+ .+.......+..+.|.+++++..++.|+| |.|+|||||++++.+++|+|||||
T Consensus 64 ~~~~~~~Ig~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~L~~---G~YvIVPsT~~~~~~g~F~L~v~s 140 (147)
T PF01067_consen 64 VGEKDLPIGFYVFKVQSQQKRLPRQYFLFNKPVVSSGDYSNSREVSEEFTLPP---GTYVIVPSTYEPGQEGEFTLRVFS 140 (147)
T ss_dssp TTTTTSEEEEEEEEETTTTSE--HHHHHTS-SSEE-SSEBSSSEEEEEEEE-S---EEEEEEEEESSTT--EEEEEEEEE
T ss_pred ccccceEEeEEEEeeecccccCCcceeccccceeeccccccceEEEEEEEcCC---CCEEEEEecCCCCCeeeEEEEEEE
Confidence 2345678999999992 111 12222234567789999999999999987 889999999999999999999999
Q ss_pred cCCccc
Q psy1431 804 TCPFRL 809 (1043)
Q Consensus 804 ~~~~~~ 809 (1043)
+.++++
T Consensus 141 ~~~~~l 146 (147)
T PF01067_consen 141 DSPFEL 146 (147)
T ss_dssp SSSEEE
T ss_pred CCCccc
Confidence 999886
No 15
>cd02680 MIT_calpain7_2 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in the nuclear thiol protease PalBH. The molecular function of the MIT domain is unclear.
Probab=96.53 E-value=0.0027 Score=55.63 Aligned_cols=38 Identities=39% Similarity=0.682 Sum_probs=35.0
Q ss_pred hhhHHHHHHHHhhHhhhhcCchHHHHHHHHHHHHhhcc
Q psy1431 252 LLSEKCHFLLSQALDADEAGLKDTAVQLYMQSIEMTKP 289 (1043)
Q Consensus 252 ~~l~~~~~l~~~a~~~~~~~~~~~a~~~y~~~~e~~~~ 289 (1043)
+++++|++|+.+|..+|+.|++++|+++|++|++.+..
T Consensus 1 ~~l~kai~Lv~~A~~eD~~gny~eA~~lY~~ale~~~~ 38 (75)
T cd02680 1 LDLERAHFLVTQAFDEDEKGNAEEAIELYTEAVELCIN 38 (75)
T ss_pred CCHHHHHHHHHHHHHhhHhhhHHHHHHHHHHHHHHHHH
Confidence 36789999999999999999999999999999998744
No 16
>cd02684 MIT_2 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in proteins with an n-terminal serine/threonine kinase domain. The molecular function of the MIT domain is unclear.
Probab=92.57 E-value=0.18 Score=44.60 Aligned_cols=39 Identities=33% Similarity=0.479 Sum_probs=35.0
Q ss_pred hHHHHHHHHhhHhhhhcCchHHHHHHHHHHHHhhccccc
Q psy1431 254 SEKCHFLLSQALDADEAGLKDTAVQLYMQSIEMTKPTLH 292 (1043)
Q Consensus 254 l~~~~~l~~~a~~~~~~~~~~~a~~~y~~~~e~~~~~l~ 292 (1043)
+++|..|+.+|...|..|++++|+.+|+++++.+...++
T Consensus 3 l~~Ai~lv~~Av~~D~~g~y~eA~~lY~~ale~~~~~~k 41 (75)
T cd02684 3 LEKAIALVVQAVKKDQRGDAAAALSLYCSALQYFVPALH 41 (75)
T ss_pred HHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHh
Confidence 578999999999999999999999999999999855443
No 17
>cd02678 MIT_VPS4 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in intracellular protein transport proteins of the AAA-ATPase family. The molecular function of the MIT domain is unclear.
Probab=91.24 E-value=0.32 Score=42.97 Aligned_cols=38 Identities=29% Similarity=0.435 Sum_probs=34.5
Q ss_pred hHHHHHHHHhhHhhhhcCchHHHHHHHHHHHHhhcccc
Q psy1431 254 SEKCHFLLSQALDADEAGLKDTAVQLYMQSIEMTKPTL 291 (1043)
Q Consensus 254 l~~~~~l~~~a~~~~~~~~~~~a~~~y~~~~e~~~~~l 291 (1043)
+++|..++.+|...|..|++++|+.+|+++++.+...+
T Consensus 3 ~~~A~~l~~~Av~~D~~g~y~eA~~~Y~~aie~l~~~~ 40 (75)
T cd02678 3 LQKAIELVKKAIEEDNAGNYEEALRLYQHALEYFMHAL 40 (75)
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHH
Confidence 57899999999999999999999999999999985543
No 18
>PF04212 MIT: MIT (microtubule interacting and transport) domain; InterPro: IPR007330 The MIT domain is found in vacuolar sorting proteins, spastin (probable ATPase involved in the assembly or function of nuclear protein complexes), and a sorting nexin, which may play a role in intracellular trafficking.; PDB: 2DL1_A 2JQK_A 1WR0_A 2CPT_A 2JQH_A 2V6Y_A 2JQ9_A 2K3W_A 1YXR_A 3EAB_E ....
Probab=89.58 E-value=0.58 Score=40.45 Aligned_cols=38 Identities=37% Similarity=0.517 Sum_probs=34.0
Q ss_pred hHHHHHHHHhhHhhhhcCchHHHHHHHHHHHHhhcccc
Q psy1431 254 SEKCHFLLSQALDADEAGLKDTAVQLYMQSIEMTKPTL 291 (1043)
Q Consensus 254 l~~~~~l~~~a~~~~~~~~~~~a~~~y~~~~e~~~~~l 291 (1043)
+..|..++++|+..|+.|++.+|+++|+++++.+...+
T Consensus 2 ~~~A~~~~~~Av~~D~~g~~~~A~~~Y~~ai~~l~~~~ 39 (69)
T PF04212_consen 2 LDKAIELIKKAVEADEAGNYEEALELYKEAIEYLMQAL 39 (69)
T ss_dssp HHHHHHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 56889999999999999999999999999999975443
No 19
>cd02656 MIT MIT: domain contained within Microtubule Interacting and Trafficking molecules. The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar sorting proteins and others. The molecular function of the MIT domain is unclear.
Probab=89.57 E-value=0.54 Score=41.41 Aligned_cols=39 Identities=26% Similarity=0.434 Sum_probs=35.1
Q ss_pred hHHHHHHHHhhHhhhhcCchHHHHHHHHHHHHhhccccc
Q psy1431 254 SEKCHFLLSQALDADEAGLKDTAVQLYMQSIEMTKPTLH 292 (1043)
Q Consensus 254 l~~~~~l~~~a~~~~~~~~~~~a~~~y~~~~e~~~~~l~ 292 (1043)
+++|..++++|+..|..|++++|+.+|++|++.+...+.
T Consensus 3 ~~~a~~l~~~Av~~D~~g~~~~Al~~Y~~a~e~l~~~~~ 41 (75)
T cd02656 3 LQQAKELIKQAVKEDEDGNYEEALELYKEALDYLLQALK 41 (75)
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhc
Confidence 568999999999999999999999999999999865554
No 20
>smart00745 MIT Microtubule Interacting and Trafficking molecule domain.
Probab=88.55 E-value=0.7 Score=40.85 Aligned_cols=41 Identities=37% Similarity=0.447 Sum_probs=36.1
Q ss_pred hhHHHHHHHHhhHhhhhcCchHHHHHHHHHHHHhhcccccC
Q psy1431 253 LSEKCHFLLSQALDADEAGLKDTAVQLYMQSIEMTKPTLHR 293 (1043)
Q Consensus 253 ~l~~~~~l~~~a~~~~~~~~~~~a~~~y~~~~e~~~~~l~~ 293 (1043)
.+.+|..++.+|+..|+.|++++|+.+|+++++.+...++.
T Consensus 4 ~~~~A~~li~~Av~~d~~g~~~eAl~~Y~~a~e~l~~~~~~ 44 (77)
T smart00745 4 YLSKAKELISKALKADEAGDYEEALELYKKAIEYLLEGIKV 44 (77)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhcc
Confidence 36789999999999999999999999999999998665543
No 21
>cd02677 MIT_SNX15 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in sorting nexin 15 and related proteins. The molecular function of the MIT domain is unclear.
Probab=82.48 E-value=1.6 Score=38.51 Aligned_cols=39 Identities=21% Similarity=0.357 Sum_probs=35.1
Q ss_pred hHHHHHHHHhhHhhhhcCchHHHHHHHHHHHHhhccccc
Q psy1431 254 SEKCHFLLSQALDADEAGLKDTAVQLYMQSIEMTKPTLH 292 (1043)
Q Consensus 254 l~~~~~l~~~a~~~~~~~~~~~a~~~y~~~~e~~~~~l~ 292 (1043)
+.+|..++.+|...|..+++.+|+.+|+++++.+...++
T Consensus 3 l~~A~~l~~~Ave~d~~~~y~eA~~~Y~~~i~~~~~~~k 41 (75)
T cd02677 3 LEQAAELIRLALEKEEEGDYEAAFEFYRAGVDLLLKGVQ 41 (75)
T ss_pred HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhc
Confidence 568899999999999999999999999999999866554
No 22
>cd02683 MIT_1 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in proteins with unknown function, co-occuring with an as yet undescribed domain. The molecular function of the MIT domain is unclear.
Probab=82.09 E-value=2.1 Score=38.05 Aligned_cols=39 Identities=21% Similarity=0.317 Sum_probs=34.3
Q ss_pred hHHHHHHHHhhHhhhhcCchHHHHHHHHHHHHhhccccc
Q psy1431 254 SEKCHFLLSQALDADEAGLKDTAVQLYMQSIEMTKPTLH 292 (1043)
Q Consensus 254 l~~~~~l~~~a~~~~~~~~~~~a~~~y~~~~e~~~~~l~ 292 (1043)
...|..++.+|...|..|++.+|+.+|+++++.+...++
T Consensus 3 ~~~a~~l~~~Ave~D~~g~y~eAl~~Y~~aie~l~~~lk 41 (77)
T cd02683 3 ELAAKEVLKRAVELDQEGRFQEALVCYQEGIDLLMQVLK 41 (77)
T ss_pred hHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHh
Confidence 457889999999999999999999999999999855444
No 23
>cd02681 MIT_calpain7_1 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in the nuclear thiol protease PalBH. The molecular function of the MIT domain is unclear.
Probab=81.17 E-value=2.5 Score=37.48 Aligned_cols=37 Identities=16% Similarity=0.180 Sum_probs=33.0
Q ss_pred hHHHHHHHHhhHhhhhcCchHHHHHHHHHHHHhhccc
Q psy1431 254 SEKCHFLLSQALDADEAGLKDTAVQLYMQSIEMTKPT 290 (1043)
Q Consensus 254 l~~~~~l~~~a~~~~~~~~~~~a~~~y~~~~e~~~~~ 290 (1043)
.+.|..++.+|...|..|++.+|+.+|+++++.+...
T Consensus 3 e~~Ai~~a~~Ave~D~~g~y~eA~~~Y~~aie~l~~~ 39 (76)
T cd02681 3 ERDAVQFARLAVQRDQEGRYSEAVFYYKEAAQLLIYA 39 (76)
T ss_pred HHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHH
Confidence 3578889999999999999999999999999998543
No 24
>cd02679 MIT_spastin MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in the AAA protein spastin, a probable ATPase involved in the assembly or function of nuclear protein complexes; spastins might also be involved in microtubule dynamics. The molecular function of the MIT domain is unclear.
Probab=77.17 E-value=3.9 Score=36.51 Aligned_cols=39 Identities=26% Similarity=0.302 Sum_probs=34.7
Q ss_pred hhHHHHHHHHhhHhhhhcCchHHHHHHHHHHHHhhcccc
Q psy1431 253 LSEKCHFLLSQALDADEAGLKDTAVQLYMQSIEMTKPTL 291 (1043)
Q Consensus 253 ~l~~~~~l~~~a~~~~~~~~~~~a~~~y~~~~e~~~~~l 291 (1043)
.++.|..-+++|+..||.|+.++|+.+|.++++++...+
T Consensus 4 ~~~~A~~~I~kaL~~dE~g~~e~Al~~Y~~gi~~l~eg~ 42 (79)
T cd02679 4 YYKQAFEEISKALRADEWGDKEQALAHYRKGLRELEEGI 42 (79)
T ss_pred HHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHHHHHHc
Confidence 367889999999999999999999999999999986543
No 25
>COG4870 Cysteine protease [Posttranslational modification, protein turnover, chaperones]
Probab=69.98 E-value=5.9 Score=45.04 Aligned_cols=43 Identities=28% Similarity=0.463 Sum_probs=32.3
Q ss_pred ccCceeeEeecc-------------ceEEEEeeCCCCcCccCCCCCCCCCCCCCHHHHHHcCCCCCCCCCCCCceEEEec
Q psy1431 562 VDTMQSSVSWSQ-------------GLRLLQLKNPWSNVRWRGNYSELDRLHWTPELKRALNFDPNSASMFDNGIFWIDY 628 (1043)
Q Consensus 562 v~~HaYaV~~v~-------------~~rll~LrNPWg~~eW~G~wsd~s~~~W~~~~~~~l~~~~~~~~~~~dG~FWm~~ 628 (1043)
..+||=.|...+ |.--++|||-||. .| .++|-|||++
T Consensus 263 ~~gHAv~iVGyDDs~~~n~~~~~~~g~GAfiikNSWGt-------------~w-----------------G~~GYfwisY 312 (372)
T COG4870 263 NWGHAVLIVGYDDSFDINNFKYGPPGDGAFIIKNSWGT-------------NW-----------------GENGYFWISY 312 (372)
T ss_pred cccceEEEEeccccccccccccCCCCCceEEEECcccc-------------cc-----------------ccCceEEEEe
Confidence 778998876553 2347999999994 23 3679999999
Q ss_pred cccccc
Q psy1431 629 ESILRF 634 (1043)
Q Consensus 629 edf~~~ 634 (1043)
++...-
T Consensus 313 ~ya~~g 318 (372)
T COG4870 313 YYALNG 318 (372)
T ss_pred eecccc
Confidence 987655
No 26
>cd02682 MIT_AAA_Arch MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in mostly archaebacterial AAA-ATPases. The molecular function of the MIT domain is unclear.
Probab=62.55 E-value=13 Score=32.85 Aligned_cols=37 Identities=22% Similarity=0.318 Sum_probs=32.6
Q ss_pred HHHHHHHHhhHhhhhcCchHHHHHHHHHHHHhhcccc
Q psy1431 255 EKCHFLLSQALDADEAGLKDTAVQLYMQSIEMTKPTL 291 (1043)
Q Consensus 255 ~~~~~l~~~a~~~~~~~~~~~a~~~y~~~~e~~~~~l 291 (1043)
+.|...+.+|...|..|++.+|+..|.++++.+..-+
T Consensus 4 ~~A~~~a~~AVe~D~~gr~~eAi~~Y~~aIe~L~q~~ 40 (75)
T cd02682 4 EMARKYAINAVKAEKEGNAEDAITNYKKAIEVLSQIV 40 (75)
T ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHH
Confidence 4678889999999999999999999999999975443
No 27
>KOG0739|consensus
Probab=62.22 E-value=9.2 Score=42.38 Aligned_cols=36 Identities=28% Similarity=0.376 Sum_probs=33.5
Q ss_pred hhHHHHHHHHhhHhhhhcCchHHHHHHHHHHHHhhc
Q psy1431 253 LSEKCHFLLSQALDADEAGLKDTAVQLYMQSIEMTK 288 (1043)
Q Consensus 253 ~l~~~~~l~~~a~~~~~~~~~~~a~~~y~~~~e~~~ 288 (1043)
-+++|..|+.+|.++|..+++.+|..+|+.|++.+.
T Consensus 6 ~l~kaI~lv~kA~~eD~a~nY~eA~~lY~~aleYF~ 41 (439)
T KOG0739|consen 6 FLQKAIDLVKKAIDEDNAKNYEEALRLYQNALEYFL 41 (439)
T ss_pred HHHHHHHHHHHHhhhcchhchHHHHHHHHHHHHHHH
Confidence 478999999999999999999999999999999863
No 28
>PF09087 Cyc-maltodext_N: Cyclomaltodextrinase, N-terminal; InterPro: IPR015171 This domain is found at the N terminus of cyclomaltodextrinase. The domain assumes a beta-sandwich structure composed of the eight antiparallel beta-strands. A ten residue linker is also present at the C-terminal end, which connects the N-terminal domain to a distal domain in the protein. This domain participates in oligomerisation of the protein, wherein the N-terminal domain of one subunit contacts the active centre of the other subunit, and is also required for binding of cyclodextrin to substrate []. ; PDB: 3EDK_B 3EDD_A 3EDJ_B 3EDE_A 1H3G_B 3EDF_B.
Probab=50.28 E-value=9.9 Score=34.68 Aligned_cols=67 Identities=21% Similarity=0.338 Sum_probs=39.4
Q ss_pred ccchhccccccccCCCCCCCC-CCCCC-ccccCCCc-ceeeeeccCCCCceeEEEeec-cccceeeeEEEE
Q psy1431 831 DLMFMFTSENAWRMRPSNDPP-PYLDG-VRINSPHY-LCKIILNENSSRKYTLVVSQY-EKMHTIYYTLRA 897 (1043)
Q Consensus 831 ~~~~~~~~~~~~~~~~s~~~~-~~~~g-~~~~s~~~-~~~~~~~~~~~~~~~lv~s~~-~~~~~~~ftL~~ 897 (1043)
.+++|+.+++--..+++-+-| ..+.. .++.|||| .|.+.+..-.+|.++|..++. .......|.|+.
T Consensus 15 ~LQLmvyG~nI~~~~v~i~~~gV~i~~v~~~~npNYLFv~L~i~~akpg~~~i~~~~~~~~~~~~~Y~Lk~ 85 (88)
T PF09087_consen 15 ELQLMVYGKNIASAEVSISYPGVTIKKVVKTDNPNYLFVYLDISDAKPGTFTINFKKGDKKKTTFDYELKA 85 (88)
T ss_dssp EEEEEEESTTGGGSEEEE-BTTEEEEEEEE-SSTTEEEEEEEE-T--SEEEEEEEEET-TEEEEEEEEEE-
T ss_pred cEEEEEecCCcccCEEEEeCCCeEEEEEEecCCCCEEEEEEecCCCCCcEEEEEEEcCCCceEEEEeEecc
Confidence 456777776654433332211 11222 25579999 677777766789999999987 566777787764
No 29
>cd02619 Peptidase_C1 C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel str
Probab=43.64 E-value=23 Score=37.40 Aligned_cols=44 Identities=25% Similarity=0.438 Sum_probs=35.0
Q ss_pred ccCceeeEeecc-----ceEEEEeeCCCCcCccCCCCCCCCCCCCCHHHHHHcCCCCCCCCCCCCceEEEecccccccc
Q psy1431 562 VDTMQSSVSWSQ-----GLRLLQLKNPWSNVRWRGNYSELDRLHWTPELKRALNFDPNSASMFDNGIFWIDYESILRFY 635 (1043)
Q Consensus 562 v~~HaYaV~~v~-----~~rll~LrNPWg~~eW~G~wsd~s~~~W~~~~~~~l~~~~~~~~~~~dG~FWm~~edf~~~F 635 (1043)
..+||-.|...+ +.....+||-||. .| .++|-|||+++++..++
T Consensus 170 ~~~Hav~ivGy~~~~~~~~~~~i~~NSwG~-------------~w-----------------g~~Gy~~i~~~~~~~~~ 218 (223)
T cd02619 170 LGGHAVVIVGYDDNYVEGKGAFIVKNSWGT-------------DW-----------------GDNGYGRISYEDVYEMT 218 (223)
T ss_pred cCCeEEEEEeecCCCCCCCCEEEEEeCCCC-------------cc-----------------ccCCEEEEehhhhhhhh
Confidence 788999987763 4688999999993 34 36899999999998554
No 30
>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A ....
Probab=37.43 E-value=62 Score=22.88 Aligned_cols=29 Identities=10% Similarity=0.197 Sum_probs=22.3
Q ss_pred HHHHhhHhhhhcCchHHHHHHHHHHHHhh
Q psy1431 259 FLLSQALDADEAGLKDTAVQLYMQSIEMT 287 (1043)
Q Consensus 259 ~l~~~a~~~~~~~~~~~a~~~y~~~~e~~ 287 (1043)
.+...+.-....|+.++|++.|.+++++-
T Consensus 3 ~~~~lg~~y~~~~~~~~A~~~~~~a~~~~ 31 (34)
T PF13181_consen 3 AYYNLGKIYEQLGDYEEALEYFEKALELN 31 (34)
T ss_dssp HHHHHHHHHHHTTSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence 34445555667999999999999999864
No 31
>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....
Probab=36.12 E-value=69 Score=22.73 Aligned_cols=29 Identities=14% Similarity=0.186 Sum_probs=22.6
Q ss_pred HHHHHhhHhhhhcCchHHHHHHHHHHHHh
Q psy1431 258 HFLLSQALDADEAGLKDTAVQLYMQSIEM 286 (1043)
Q Consensus 258 ~~l~~~a~~~~~~~~~~~a~~~y~~~~e~ 286 (1043)
..+.+.+.-....+++++|++.|.+|+++
T Consensus 2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~ 30 (34)
T PF00515_consen 2 EAYYNLGNAYFQLGDYEEALEYYQRALEL 30 (34)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCchHHHHHHHHHHHH
Confidence 34556666778899999999999999985
No 32
>cd02859 AMPKbeta_GBD_like AMP-activated protein kinase (AMPK) beta subunit glycogen binding domain (GBD). AMPK is a metabolic stress sensing protein that senses AMP/ATP and has recently been found to act as a glycogen sensor as well. The protein functions as a alpha-beta-gamma heterotrimer. This domain is the glycogen binding domain of the beta subunit.
Probab=34.80 E-value=43 Score=29.70 Aligned_cols=26 Identities=35% Similarity=0.465 Sum_probs=21.0
Q ss_pred CCceEEEEEeecCceEEeeecccccccCC
Q psy1431 433 PFGKYMVKLHLNGITRKVIIDDQLPMARF 461 (1043)
Q Consensus 433 ~~G~Y~vrl~~nG~wr~VvIDD~lP~~~~ 461 (1043)
+.|.|.+||.++|.|+ +|...|+..+
T Consensus 44 ~~g~y~YkF~Vdg~w~---~d~~~~~~~d 69 (79)
T cd02859 44 PPGKYQYKFIVDGEWR---HSPDLPTETD 69 (79)
T ss_pred CCCCEEEEEEECCEEE---eCCCCCccCC
Confidence 4699999999999884 5877887643
No 33
>cd02859 AMPKbeta_GBD_like AMP-activated protein kinase (AMPK) beta subunit glycogen binding domain (GBD). AMPK is a metabolic stress sensing protein that senses AMP/ATP and has recently been found to act as a glycogen sensor as well. The protein functions as a alpha-beta-gamma heterotrimer. This domain is the glycogen binding domain of the beta subunit.
Probab=30.89 E-value=56 Score=28.98 Aligned_cols=25 Identities=28% Similarity=0.288 Sum_probs=20.4
Q ss_pred CceEEEEeeeCCcEEEEEEcCCCccccC
Q psy1431 147 FGKYMVKLHLNGITRKVIIDDQLPMARF 174 (1043)
Q Consensus 147 ~G~y~v~l~~~G~w~~V~VDD~lP~~~~ 174 (1043)
.|.|..||.++|.| ++|...|+..+
T Consensus 45 ~g~y~YkF~Vdg~w---~~d~~~~~~~d 69 (79)
T cd02859 45 PGKYQYKFIVDGEW---RHSPDLPTETD 69 (79)
T ss_pred CCCEEEEEEECCEE---EeCCCCCccCC
Confidence 49999999999988 46888887643
No 34
>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....
Probab=27.32 E-value=1.2e+02 Score=21.21 Aligned_cols=29 Identities=10% Similarity=0.161 Sum_probs=20.9
Q ss_pred HHHHhhHhhhhcCchHHHHHHHHHHHHhh
Q psy1431 259 FLLSQALDADEAGLKDTAVQLYMQSIEMT 287 (1043)
Q Consensus 259 ~l~~~a~~~~~~~~~~~a~~~y~~~~e~~ 287 (1043)
.+...+.-....|++++|++.|.+++++-
T Consensus 3 ~~~~lg~~~~~~~~~~~A~~~~~~al~l~ 31 (34)
T PF07719_consen 3 AWYYLGQAYYQLGNYEEAIEYFEKALELD 31 (34)
T ss_dssp HHHHHHHHHHHTT-HHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHHHC
Confidence 34444555667899999999999998863
No 35
>PF00112 Peptidase_C1: Papain family cysteine protease This is family C1 in the peptidase classification. ; InterPro: IPR000668 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of proteins belong to the peptidase family C1, sub-family C1A (papain family, clan CA). It includes proteins classed as non-peptidase homologs. These are have either been shown experimentally to lack peptidase activity or lack one or more of the active site residues. The papain family has a wide variety of activities, including broad-range (papain) and narrow-range endo-peptidases, aminopeptidases, dipeptidyl peptidases and enzymes with both exo- and endo-peptidase activity []. Members of the papain family are widespread, found in baculovirus [], eubacteria, yeast, and practically all protozoa, plants and mammals []. The proteins are typically lysosomal or secreted, and proteolytic cleavage of the propeptide is required for enzyme activation, although bleomycin hydrolase is cytosolic in fungi and mammals []. Papain-like cysteine proteinases are essentially synthesised as inactive proenzymes (zymogens) with N-terminal propeptide regions. The activation process of these enzymes includes the removal of propeptide regions. The propeptide regions serve a variety of functions in vivo and in vitro. The pro-region is required for the proper folding of the newly synthesised enzyme, the inactivation of the peptidase domain and stabilisation of the enzyme against denaturing at neutral to alkaline pH conditions. Amino acid residues within the pro-region mediate their membrane association, and play a role in the transport of the proenzyme to lysosomes. Among the most notable features of propeptides is their ability to inhibit the activity of their cognate enzymes and that certain propeptides exhibit high selectivity for inhibition of the peptidases from which they originate []. The catalytic residues of papain are Cys-25 and His-159, other important residues being Gln-19, which helps form the 'oxyanion hole', and Asn-175, which orientates the imidazole ring of His-159. ; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 3MOR_B 3HHI_B 1S4V_A 3F75_A 1MEG_A 1PCI_C 1PPO_A 3HD3_B 1F29_A 1EWL_A ....
Probab=24.21 E-value=89 Score=32.81 Aligned_cols=40 Identities=28% Similarity=0.461 Sum_probs=29.4
Q ss_pred ccCceeeEeecc---ceEEEEeeCCCCcCccCCCCCCCCCCCCCHHHHHHcCCCCCCCCCCCCceEEEecccc
Q psy1431 562 VDTMQSSVSWSQ---GLRLLQLKNPWSNVRWRGNYSELDRLHWTPELKRALNFDPNSASMFDNGIFWIDYESI 631 (1043)
Q Consensus 562 v~~HaYaV~~v~---~~rll~LrNPWg~~eW~G~wsd~s~~~W~~~~~~~l~~~~~~~~~~~dG~FWm~~edf 631 (1043)
..+||=.|...+ +.....+||-||. .| .++|-|||+.+..
T Consensus 164 ~~~Hav~iVGy~~~~~~~~wiv~NSWG~-------------~W-----------------G~~Gy~~i~~~~~ 206 (219)
T PF00112_consen 164 SGGHAVLIVGYDDENGKGYWIVKNSWGT-------------DW-----------------GDNGYFRISYDYN 206 (219)
T ss_dssp SEEEEEEEEEEEEETTEEEEEEE-SBTT-------------TS-----------------TBTTEEEEESSSS
T ss_pred cccccccccccccccceeeEeeehhhCC-------------cc-----------------CCCeEEEEeeCCC
Confidence 567777777654 4689999999993 34 3689999999864
No 36
>PF08969 USP8_dimer: USP8 dimerisation domain; InterPro: IPR015063 This domain is predominantly found in the amino terminal region of Ubiquitin carboxyl-terminal hydrolase 8 (USP8). It has no known function. ; PDB: 2XZE_B 2A9U_A.
Probab=20.28 E-value=1.7e+02 Score=27.93 Aligned_cols=40 Identities=20% Similarity=0.329 Sum_probs=35.0
Q ss_pred hhHHHHHHHHhhHhhhhcCchHHHHHHHHHHHHhhcccccC
Q psy1431 253 LSEKCHFLLSQALDADEAGLKDTAVQLYMQSIEMTKPTLHR 293 (1043)
Q Consensus 253 ~l~~~~~l~~~a~~~~~~~~~~~a~~~y~~~~e~~~~~l~~ 293 (1043)
-+..|..|+.+|......|+.+.|..+||+.+.++ ..|..
T Consensus 34 y~rsa~~l~~~A~~~~~egd~E~AYvl~~R~~~L~-~ki~~ 73 (115)
T PF08969_consen 34 YLRSANKLLREAEEYRQEGDEEQAYVLYMRYLTLV-EKIPK 73 (115)
T ss_dssp HHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHH-CCHCC
T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH-HHhhc
Confidence 67899999999999999999999999999999998 65543
No 37
>cd02248 Peptidase_C1A Peptidase C1A subfamily (MEROPS database nomenclature); composed of cysteine peptidases (CPs) similar to papain, including the mammalian CPs (cathepsins B, C, F, H, L, K, O, S, V, X and W). Papain is an endopeptidase with specific substrate preferences, primarily for bulky hydrophobic or aromatic residues at the S2 subsite, a hydrophobic pocket in papain that accommodates the P2 sidechain of the substrate (the second residue away from the scissile bond). Most members of the papain subfamily are endopeptidases. Some exceptions to this rule can be explained by specific details of the catalytic domains like the occluding loop in cathepsin B which confers an additional carboxydipeptidyl activity and the mini-chain of cathepsin H resulting in an N-terminal exopeptidase activity. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds. Parasitic CPs act extracellularly to help invade tissues and cells, to h
Probab=20.17 E-value=1.4e+02 Score=31.37 Aligned_cols=39 Identities=21% Similarity=0.295 Sum_probs=29.7
Q ss_pred ccCceeeEeecc---ceEEEEeeCCCCcCccCCCCCCCCCCCCCHHHHHHcCCCCCCCCCCCCceEEEeccc
Q psy1431 562 VDTMQSSVSWSQ---GLRLLQLKNPWSNVRWRGNYSELDRLHWTPELKRALNFDPNSASMFDNGIFWIDYES 630 (1043)
Q Consensus 562 v~~HaYaV~~v~---~~rll~LrNPWg~~eW~G~wsd~s~~~W~~~~~~~l~~~~~~~~~~~dG~FWm~~ed 630 (1043)
..+||=.|...+ +.....+||-||. .| .++|-|||++++
T Consensus 157 ~~~Hav~iVGy~~~~~~~ywiv~NSWG~-------------~W-----------------G~~Gy~~i~~~~ 198 (210)
T cd02248 157 NLNHAVLLVGYGTENGVDYWIVKNSWGT-------------SW-----------------GEKGYIRIARGS 198 (210)
T ss_pred cCCEEEEEEEEeecCCceEEEEEcCCCC-------------cc-----------------ccCcEEEEEcCC
Confidence 557887776654 4689999999993 34 367999999987
Done!