Query 019676
Match_columns 337
No_of_seqs 177 out of 1533
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 03:39:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019676.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019676hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02227 sigpep_I_bact signal 100.0 1.4E-39 3.1E-44 287.5 19.1 154 152-312 2-163 (163)
2 PRK10861 signal peptidase I; P 100.0 8.5E-35 1.8E-39 282.3 19.3 155 151-312 63-305 (324)
3 KOG0171 Mitochondrial inner me 100.0 1.7E-32 3.8E-37 240.9 12.1 154 156-326 19-173 (176)
4 PRK13838 conjugal transfer pil 99.9 3.1E-25 6.7E-30 199.3 16.9 117 190-308 39-172 (176)
5 KOG1568 Mitochondrial inner me 99.9 2.4E-26 5.2E-31 201.9 9.2 130 163-319 24-159 (174)
6 PRK13884 conjugal transfer pep 99.9 3.6E-24 7.8E-29 192.6 18.7 109 200-308 49-176 (178)
7 TIGR02771 TraF_Ti conjugative 99.9 3.8E-24 8.3E-29 191.3 16.4 133 166-308 20-169 (171)
8 PF10502 Peptidase_S26: Signal 99.9 9.2E-25 2E-29 188.8 1.7 108 201-308 21-137 (138)
9 TIGR02754 sod_Ni_protease nick 99.8 1.6E-18 3.4E-23 138.2 9.9 89 174-306 2-90 (90)
10 cd06530 S26_SPase_I The S26 Ty 99.7 3.4E-17 7.3E-22 128.8 9.6 84 172-304 2-85 (85)
11 COG4959 TraF Type IV secretory 99.7 1.3E-16 2.8E-21 139.5 11.2 117 189-308 44-169 (173)
12 TIGR02228 sigpep_I_arch signal 99.6 3.8E-14 8.2E-19 125.6 12.7 115 144-305 2-119 (158)
13 COG0681 LepB Signal peptidase 99.5 2.4E-13 5.2E-18 118.1 12.2 143 149-314 8-152 (166)
14 PF00717 Peptidase_S24: Peptid 99.1 1.3E-10 2.8E-15 87.7 6.6 56 174-242 1-57 (70)
15 cd06462 Peptidase_S24_S26 The 98.9 9E-09 1.9E-13 79.2 9.3 53 172-236 2-54 (84)
16 COG2932 Predicted transcriptio 98.5 4.4E-07 9.5E-12 83.3 9.8 58 171-241 124-181 (214)
17 cd06529 S24_LexA-like Peptidas 98.5 4.7E-07 1E-11 69.6 6.9 57 172-242 2-58 (81)
18 KOG3342 Signal peptidase I [In 98.4 9.1E-07 2E-11 78.0 8.3 90 172-305 50-144 (180)
19 PRK10276 DNA polymerase V subu 98.3 8.7E-06 1.9E-10 70.3 10.5 51 169-233 50-101 (139)
20 TIGR00498 lexA SOS regulatory 98.1 3.4E-05 7.3E-10 69.9 10.8 52 169-234 110-162 (199)
21 PRK00215 LexA repressor; Valid 98.1 2.9E-05 6.4E-10 70.6 10.1 53 168-234 116-169 (205)
22 PRK12423 LexA repressor; Provi 98.0 4.9E-05 1.1E-09 69.6 10.2 50 171-234 115-165 (202)
23 COG1974 LexA SOS-response tran 97.3 0.0023 4.9E-08 59.2 11.1 52 169-233 111-163 (201)
24 COG0681 LepB Signal peptidase 75.8 4.2 9.2E-05 34.8 4.3 29 224-252 137-165 (166)
25 COG0093 RplN Ribosomal protein 47.6 1.3E+02 0.0028 25.9 7.9 26 273-299 81-106 (122)
26 PF04790 Sarcoglycan_1: Sarcog 36.8 2.4E+02 0.0052 27.3 9.0 32 151-182 17-48 (264)
27 PLN02705 beta-amylase 36.1 93 0.002 33.8 6.5 17 78-94 31-47 (681)
28 PF06890 Phage_Mu_Gp45: Bacter 35.5 1.2E+02 0.0027 27.2 6.4 45 189-242 62-109 (162)
29 COG1097 RRP4 RNA-binding prote 35.4 76 0.0016 30.4 5.2 21 176-196 105-125 (239)
30 PF00238 Ribosomal_L14: Riboso 34.1 1.3E+02 0.0028 25.7 6.0 28 270-298 78-105 (122)
31 PF05257 CHAP: CHAP domain; I 32.8 93 0.002 25.6 4.9 36 200-242 61-97 (124)
32 COG0361 InfA Translation initi 29.2 55 0.0012 25.9 2.7 12 185-196 48-59 (75)
33 CHL00057 rpl14 ribosomal prote 28.2 3.7E+02 0.008 23.1 7.8 28 271-299 79-106 (122)
34 TIGR00008 infA translation ini 27.7 57 0.0012 25.3 2.5 10 203-212 46-55 (68)
35 TIGR01067 rplN_bact ribosomal 26.5 4.1E+02 0.0089 22.7 8.1 28 271-299 79-106 (122)
36 PLN02867 Probable galacturonos 24.2 1.1E+02 0.0023 32.8 4.5 21 107-128 10-30 (535)
37 cd04456 S1_IF1A_like S1_IF1A_l 24.1 68 0.0015 25.3 2.4 11 202-212 39-49 (78)
38 PF01176 eIF-1a: Translation i 24.1 51 0.0011 24.8 1.6 39 174-212 11-52 (65)
39 COG4079 Uncharacterized protei 23.1 1.4E+02 0.0031 28.9 4.7 31 223-253 248-282 (293)
40 TIGR02594 conserved hypothetic 22.4 2.1E+02 0.0046 24.4 5.3 12 201-212 73-84 (129)
41 cd05793 S1_IF1A S1_IF1A: Trans 22.3 72 0.0016 25.1 2.2 11 202-212 39-49 (77)
42 smart00652 eIF1a eukaryotic tr 22.3 72 0.0016 25.4 2.2 11 202-212 44-54 (83)
43 PRK11578 macrolide transporter 21.4 2E+02 0.0042 28.4 5.6 24 227-250 71-94 (370)
No 1
>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type. A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes.
Probab=100.00 E-value=1.4e-39 Score=287.45 Aligned_cols=154 Identities=40% Similarity=0.711 Sum_probs=136.7
Q ss_pred HHHHHHHHHHHHHHHHheeeeEEEcCCCccccccCCCEEEEEeeecccCCCCCCcEEEEeCCccccccccCCCccEEEEE
Q 019676 152 AKTVLAALVISLAFRSFVAEPRYIPSLSMYPTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRV 231 (337)
Q Consensus 152 ~~~llv~lii~lll~~~i~~~~~V~gdSMePTL~~GD~VLVdk~~~~~~~pkrGDIVVf~~P~~~~~~gy~~~~~~VKRV 231 (337)
+..++++++++++++.++++.+.|.|+||+|||++||++++++..+....+++||+|+|+.|.. .+..+||||
T Consensus 2 ~~~~~~~~~~~~~i~~~~~~~~~v~g~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~~~~-------~~~~~iKRV 74 (163)
T TIGR02227 2 ILSLLIAILLALLIRTFVFFPYKIPGGSMEPTLKEGDRILVNKFAYGTSDPKRGDIVVFKDPDD-------NKNIYVKRV 74 (163)
T ss_pred HHHHHHHHHHHHHHHhhEEEEEEECCcccccchhCCCEEEEEEeEcCCCCCCCCcEEEEecCCC-------CCceeEEEE
Confidence 3566777788889999999999999999999999999999999987667899999999998753 567899999
Q ss_pred EeeCCCEEEEeCCEEEECCEEccccccccCC--------CCCCCCEEecCCcEEEEcCCCCCCCCCCccCcccCCCeeEE
Q 019676 232 VAKEGDVVEVREGKLIVNGVVRNEDYILEAP--------SYNMTPITVPENSVFVMGDNRNNSYDSHVWGPLPAKNIIGR 303 (337)
Q Consensus 232 ialPGDtV~i~dg~lyVNG~~~~e~~~~~~p--------~~~~~~~~VP~g~yfVLGDNr~~S~DSRyfGpVp~~~IiGk 303 (337)
+|+|||+|+++++.+||||+.+++.|..... .......+||+|||||||||+++|+||||||+|++++|+||
T Consensus 75 ig~pGd~v~i~~~~l~vNg~~~~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~~fvlGDnr~~S~DSR~~G~V~~~~I~Gk 154 (163)
T TIGR02227 75 IGLPGDKVEFRDGKLYINGKKIDEPYLKPNGSLDTSGFNTTDFKPVTVPPGHYFVLGDNRDNSLDSRYFGFVPIDDIIGK 154 (163)
T ss_pred EecCCCEEEEECCEEEECCEECcccccccccccccccccccccCceEECCCCEEEECCCCCCCcccCCcCcCCHHHeEEE
Confidence 9999999999999999999999988764321 12344679999999999999999999999999999999999
Q ss_pred EEEEEcCCC
Q 019676 304 SVFRYWPPQ 312 (337)
Q Consensus 304 v~~~lwP~~ 312 (337)
|++++||++
T Consensus 155 ~~~~~~p~~ 163 (163)
T TIGR02227 155 VSFVFYPFD 163 (163)
T ss_pred EEEEECCCC
Confidence 999999985
No 2
>PRK10861 signal peptidase I; Provisional
Probab=100.00 E-value=8.5e-35 Score=282.32 Aligned_cols=155 Identities=35% Similarity=0.538 Sum_probs=129.9
Q ss_pred HHHHHHHHHHHHHHHHHheeeeEEEcCCCccccccCCCEEEEEeeeccc------------CCCCCCcEEEEeCCccccc
Q 019676 151 DAKTVLAALVISLAFRSFVAEPRYIPSLSMYPTFDVGDRIVAEKVTYYF------------RKPCSNDIVIFKSPPVLQE 218 (337)
Q Consensus 151 ~~~~llv~lii~lll~~~i~~~~~V~gdSMePTL~~GD~VLVdk~~~~~------------~~pkrGDIVVf~~P~~~~~ 218 (337)
++..++++++++++++.|+++++.|+|.||+|||..||+|+|+|.+|.. ..|+|||||||+.|..
T Consensus 63 ~~~~~~~~l~i~~~ir~fv~~~~~Ips~SM~PTL~~GD~IlVnK~~yg~~~p~~~~~~~~~~~p~RGDIVVF~~P~~--- 139 (324)
T PRK10861 63 TGASVFPVLAIVLIVRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPITQTTLIETGHPKRGDIVVFKYPED--- 139 (324)
T ss_pred HHHHHHHHHhHHHHHHhhEEEEEEECCCcCcCcccCCCEEEEEEeecCccCccccccccccCCCCCCCEEEEecCCC---
Confidence 4456677778888899999999999999999999999999999998763 5689999999998763
Q ss_pred cccCCCccEEEEEEeeCCCEEEEe--CCEEEECCEEcccc----------------------------------------
Q 019676 219 VGYTDDDVFIKRVVAKEGDVVEVR--EGKLIVNGVVRNED---------------------------------------- 256 (337)
Q Consensus 219 ~gy~~~~~~VKRVialPGDtV~i~--dg~lyVNG~~~~e~---------------------------------------- 256 (337)
++..+||||+|+|||+|+++ ++.+||||+.+...
T Consensus 140 ----~~~~yIKRVIGlPGD~I~~~~~~~~l~iNg~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 215 (324)
T PRK10861 140 ----PKLDYIKRVVGLPGDKVTYDPVSKEVTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFQVPLN 215 (324)
T ss_pred ----CCCcEEEEeeecCCcEEEEEeCCCEEEEcCcccccccccccccccccccccccccccccccccccccccccccccc
Confidence 56789999999999999998 89999999742110
Q ss_pred -----------ccc----------cCCC-------------CCCCCEEecCCcEEEEcCCCCCCCCCCccCcccCCCeeE
Q 019676 257 -----------YIL----------EAPS-------------YNMTPITVPENSVFVMGDNRNNSYDSHVWGPLPAKNIIG 302 (337)
Q Consensus 257 -----------~~~----------~~p~-------------~~~~~~~VP~g~yfVLGDNr~~S~DSRyfGpVp~~~IiG 302 (337)
|.. ..+. .....++||+|+|||||||+++|+||||||+||+++|+|
T Consensus 216 ~~~~~~~~~~~~~E~l~~~~h~i~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~yf~mgdnr~~S~DSRy~G~Vp~~~i~G 295 (324)
T PRK10861 216 ETKENGIRLSERKETLGDVTHRILTVPGAQDQVGMYYQQPGQPLATWVVPPGQYFMMGDNRDNSADSRYWGFVPEANLVG 295 (324)
T ss_pred ccccccccceeEEEecCCccceeeecCCcccccccccccCCCcCceEEECCCeEEEeCCCCCCCcccCcccccCHHHcEE
Confidence 000 0000 012456999999999999999999999999999999999
Q ss_pred EEEEEEcCCC
Q 019676 303 RSVFRYWPPQ 312 (337)
Q Consensus 303 kv~~~lwP~~ 312 (337)
||.++||+++
T Consensus 296 ~a~~i~~s~d 305 (324)
T PRK10861 296 KATAIWMSFE 305 (324)
T ss_pred EEEEEEEEcC
Confidence 9999999986
No 3
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=99.98 E-value=1.7e-32 Score=240.89 Aligned_cols=154 Identities=47% Similarity=0.715 Sum_probs=131.6
Q ss_pred HHHHHHHHHHHHheeeeEEEcCCCccccccCC-CEEEEEeeecccCCCCCCcEEEEeCCccccccccCCCccEEEEEEee
Q 019676 156 LAALVISLAFRSFVAEPRYIPSLSMYPTFDVG-DRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAK 234 (337)
Q Consensus 156 lv~lii~lll~~~i~~~~~V~gdSMePTL~~G-D~VLVdk~~~~~~~pkrGDIVVf~~P~~~~~~gy~~~~~~VKRVial 234 (337)
+.-.++......++.+...+.|.||+|||+++ |+++.+++++.++.+++||||++..|.+ .++.++|||+|+
T Consensus 19 ~~~~~f~h~t~~yl~e~~~~~gpSM~PTl~~~gd~l~aEkls~~f~~~~~gDIVi~~sP~~-------~~~~~cKRIva~ 91 (176)
T KOG0171|consen 19 IAYAAFTHVTHEYLGEFVMCSGPSMEPTLHDGGDVLLAEKLSYRFRKPQVGDIVIAKSPPD-------PKEHICKRIVAM 91 (176)
T ss_pred HHHHHHHHHHHHHhcceeeccCCCcCceecCCCcEEehhhhhHhhcCCCCCCEEEEeCCCC-------chhhhhheeecc
Confidence 33344445556699999999999999999985 5555699999999999999999999986 666799999999
Q ss_pred CCCEEEEeCCEEEECCEEccccccccCCCCCCCCEEecCCcEEEEcCCCCCCCCCCccCcccCCCeeEEEEEEEcCCCCC
Q 019676 235 EGDVVEVREGKLIVNGVVRNEDYILEAPSYNMTPITVPENSVFVMGDNRNNSYDSHVWGPLPAKNIIGRSVFRYWPPQRI 314 (337)
Q Consensus 235 PGDtV~i~dg~lyVNG~~~~e~~~~~~p~~~~~~~~VP~g~yfVLGDNr~~S~DSRyfGpVp~~~IiGkv~~~lwP~~r~ 314 (337)
+||-+++.++++.+|+.. +.+ ...++||+||+||+|||+++|+|||+|||||...|+||+++++||.++.
T Consensus 92 eGD~v~v~~~~~~~n~~~--e~~--------~~~i~VP~GhVfv~GDN~~nS~DSr~yGplP~glI~gRvv~r~Wp~s~~ 161 (176)
T KOG0171|consen 92 EGDLVEVHDGPLVVNDLV--EKF--------STPIRVPEGHVFVEGDNRNNSLDSRNYGPLPMGLIQGRVVFRIWPPSRV 161 (176)
T ss_pred CCceEEEecCCcccchhh--hhc--------cceeeccCceEEEecCCCCCcccccccCCCchhheeeeEEEEecCchhc
Confidence 999999998888877544 222 1467999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCcccc
Q 019676 315 GSTVPEGGCAVD 326 (337)
Q Consensus 315 g~~~~~~~~~~~ 326 (337)
+.+.....|...
T Consensus 162 ~~~~~~~~~~~~ 173 (176)
T KOG0171|consen 162 SGLILHWINNTF 173 (176)
T ss_pred ceeeecccchhh
Confidence 998888777654
No 4
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=99.93 E-value=3.1e-25 Score=199.27 Aligned_cols=117 Identities=23% Similarity=0.314 Sum_probs=92.2
Q ss_pred EEEEeeecccCCCCCCcEEEEeCCcccc-----ccccCC-------CccEEEEEEeeCCCEEEEeCCEEEECCEEccccc
Q 019676 190 IVAEKVTYYFRKPCSNDIVIFKSPPVLQ-----EVGYTD-------DDVFIKRVVAKEGDVVEVREGKLIVNGVVRNEDY 257 (337)
Q Consensus 190 VLVdk~~~~~~~pkrGDIVVf~~P~~~~-----~~gy~~-------~~~~VKRVialPGDtV~i~dg~lyVNG~~~~e~~ 257 (337)
+.+.++.+....+++||+|+|+.|...+ +++|.+ ...++|||+|+|||+|++++ .+||||+.+.+.+
T Consensus 39 ig~y~~~~~~~~~~rGDiVvf~~P~~~~~~~a~~r~yl~~g~~p~~~~~~iKRViglpGD~V~i~~-~v~iNg~~~~~~~ 117 (176)
T PRK13838 39 LGLWRIEALDRPVAVGDLVFICPPETAAFREARERGYLRRGLCPGGFAPLIKTVAALAGQRVEIGG-SVSIDGRPLPSSS 117 (176)
T ss_pred EEEEEEeccCCCCCCCcEEEEECCchhhhhhhhhcccccccccccCCCceEEEEEEeCCcEEEECC-EEEECCEEccccc
Confidence 6777766555789999999999876421 234421 23599999999999999985 8999999999887
Q ss_pred cccCCCC-----CCCCEEecCCcEEEEcCCCCCCCCCCccCcccCCCeeEEEEEEE
Q 019676 258 ILEAPSY-----NMTPITVPENSVFVMGDNRNNSYDSHVWGPLPAKNIIGRSVFRY 308 (337)
Q Consensus 258 ~~~~p~~-----~~~~~~VP~g~yfVLGDNr~~S~DSRyfGpVp~~~IiGkv~~~l 308 (337)
....... .....+||+|+||||||| ++|+||||||+|++++|+|+|..+|
T Consensus 118 ~~~~~~~g~~l~~~~~~~vp~g~~fvlgd~-~~S~DSRy~G~V~~~~I~G~a~pi~ 172 (176)
T PRK13838 118 VRRRDGEGRPLTPFPGGVVPPGHLFLHSSF-AGSYDSRYFGPVPASGLLGLARPVL 172 (176)
T ss_pred cccccccCCcCCCCCccCcCCCeEEEECCC-CCCCcccccCcccHHHeEEEEEEEE
Confidence 6533211 223468999999999998 5899999999999999999998754
No 5
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=99.93 E-value=2.4e-26 Score=201.93 Aligned_cols=130 Identities=36% Similarity=0.590 Sum_probs=112.6
Q ss_pred HHHHHheeeeEEEcCCCccccccCC------CEEEEEeeecccCCCCCCcEEEEeCCccccccccCCCccEEEEEEeeCC
Q 019676 163 LAFRSFVAEPRYIPSLSMYPTFDVG------DRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAKEG 236 (337)
Q Consensus 163 lll~~~i~~~~~V~gdSMePTL~~G------D~VLVdk~~~~~~~pkrGDIVVf~~P~~~~~~gy~~~~~~VKRVialPG 236 (337)
+-+...+.....|.|.||.|+|+++ |+|++.|..-..+...|||||+|..|.+ .++++||||+|++|
T Consensus 24 ~t~~DrV~~va~v~G~smqPtlnP~~~~~~~d~Vll~k~~v~n~~~~rGDiVvl~sP~~-------p~~~~iKRv~aleg 96 (174)
T KOG1568|consen 24 LTFSDRVVHVAQVYGSSMQPTLNPTMNTNEKDTVLLRKWNVKNRKVSRGDIVVLKSPND-------PDKVIIKRVAALEG 96 (174)
T ss_pred eeeeeeEEEEeEEecCcCCCccCCCcccccccEEEEEeeccccceeccCCEEEEeCCCC-------hhheeeeeeecccc
Confidence 3344556778889999999999975 8999999875545688999999999985 78899999999999
Q ss_pred CEEEEeCCEEEECCEEccccccccCCCCCCCCEEecCCcEEEEcCCCCCCCCCCccCcccCCCeeEEEEEEEcCCCCCCC
Q 019676 237 DVVEVREGKLIVNGVVRNEDYILEAPSYNMTPITVPENSVFVMGDNRNNSYDSHVWGPLPAKNIIGRSVFRYWPPQRIGS 316 (337)
Q Consensus 237 DtV~i~dg~lyVNG~~~~e~~~~~~p~~~~~~~~VP~g~yfVLGDNr~~S~DSRyfGpVp~~~IiGkv~~~lwP~~r~g~ 316 (337)
|.+... .+....+.||+|||||.|||...|+|||.||||+...|+|||++++||+.|+++
T Consensus 97 d~~~t~--------------------~~k~~~v~vpkghcWVegDn~~hs~DSntFGPVS~gli~grai~ilwpP~R~~~ 156 (174)
T KOG1568|consen 97 DIMVTE--------------------DEKEEPVVVPKGHCWVEGDNQKHSYDSNTFGPVSTGLIVGRAIYILWPPVRWQR 156 (174)
T ss_pred cEeccC--------------------CCCCCceecCCCcEEEecCCcccccccCccCCcchhheeeeEEEEEcChHHhhh
Confidence 988753 234557899999999999999999999999999999999999999999999887
Q ss_pred CCC
Q 019676 317 TVP 319 (337)
Q Consensus 317 ~~~ 319 (337)
+..
T Consensus 157 ~~~ 159 (174)
T KOG1568|consen 157 LDK 159 (174)
T ss_pred hcc
Confidence 763
No 6
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=99.92 E-value=3.6e-24 Score=192.63 Aligned_cols=109 Identities=26% Similarity=0.387 Sum_probs=88.0
Q ss_pred CCCCCCcEEEEeCCccc-----cccccCCC-------ccEEEEEEeeCCCEEEEeCCEEEECCEEccccccc--cC----
Q 019676 200 RKPCSNDIVIFKSPPVL-----QEVGYTDD-------DVFIKRVVAKEGDVVEVREGKLIVNGVVRNEDYIL--EA---- 261 (337)
Q Consensus 200 ~~pkrGDIVVf~~P~~~-----~~~gy~~~-------~~~VKRVialPGDtV~i~dg~lyVNG~~~~e~~~~--~~---- 261 (337)
..+++||+|+|+.|... .+++|.+. ..++|||+|+|||+|+++++.+||||+.+.+.... +.
T Consensus 49 ~~~~~Gd~V~f~~p~~~~~~~a~~rgyl~~g~~p~~~~~liKRVva~pGD~V~~~~~~l~VNG~~v~~~~~~~~d~~g~~ 128 (178)
T PRK13884 49 APVEKGAYVLFCPPQRGVFDDAKERGYIGAGFCPGGYGYMMKRVLAAKGDAVSVTDDGVRVNGELLPLSKPILADGAGRP 128 (178)
T ss_pred CCCCCCCEEEEeCCchHHHHHHHhCCccccCcCCCCCCceEEEEEeeCCcEEEEECCEEEECCEEccccccccccccCCc
Confidence 36899999999987631 34566322 36999999999999999999999999998654322 21
Q ss_pred -CCCCCCCEEecCCcEEEEcCCCCCCCCCCccCcccCCCeeEEEEEEE
Q 019676 262 -PSYNMTPITVPENSVFVMGDNRNNSYDSHVWGPLPAKNIIGRSVFRY 308 (337)
Q Consensus 262 -p~~~~~~~~VP~g~yfVLGDNr~~S~DSRyfGpVp~~~IiGkv~~~l 308 (337)
+.+....++||+|+|||||||+++|+||||||+|++++|+|++..++
T Consensus 129 l~~~~~~~~~lp~g~~fvlgd~~~~S~DSRYfG~V~~~~I~G~~~Pl~ 176 (178)
T PRK13884 129 LPRYQANSYTLGESELLLMSDVSATSFDGRYFGPINRSQIKTVIRPVI 176 (178)
T ss_pred ccccCCCceEECCCEEEEECCCCCCCCcccccCcccHHHEEEEEEEeE
Confidence 22334456999999999999999999999999999999999998764
No 7
>TIGR02771 TraF_Ti conjugative transfer signal peptidase TraF. This protein is found in apparent operons encoding elements of conjugative transfer systems. This family is homologous to a broader family of signal (leader) peptidases such as lepB. This family is present in both Ti-type and I-type conjugative systems.
Probab=99.92 E-value=3.8e-24 Score=191.33 Aligned_cols=133 Identities=26% Similarity=0.377 Sum_probs=98.5
Q ss_pred HHheeeeEEEcCCCccccccCCCEEEEEeeecccCCCCCCcEEEEeCCccc-----cccccCCC-------ccEEEEEEe
Q 019676 166 RSFVAEPRYIPSLSMYPTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVL-----QEVGYTDD-------DVFIKRVVA 233 (337)
Q Consensus 166 ~~~i~~~~~V~gdSMePTL~~GD~VLVdk~~~~~~~pkrGDIVVf~~P~~~-----~~~gy~~~-------~~~VKRVia 233 (337)
..|........++||.. |-+. +.+ ...++|||+|+|+.|... ..++|.+. ..+||||+|
T Consensus 20 ~~~~~~~~~N~T~S~P~----g~Y~-~~~----~~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRVig 90 (171)
T TIGR02771 20 GLYCVGARINTTKSLPL----GLYW-TTS----SKPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVLG 90 (171)
T ss_pred hcceeeEEEECCCCCcc----eEEE-eCC----CCCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEEE
Confidence 33444445566777754 3333 322 247999999999987532 12344222 279999999
Q ss_pred eCCCEEEEeCCEEEECCEEccccccccC-----CCCCCCCEEecCCcEEEEcCCCCCCCCCCccCcccCCCeeEEEEEEE
Q 019676 234 KEGDVVEVREGKLIVNGVVRNEDYILEA-----PSYNMTPITVPENSVFVMGDNRNNSYDSHVWGPLPAKNIIGRSVFRY 308 (337)
Q Consensus 234 lPGDtV~i~dg~lyVNG~~~~e~~~~~~-----p~~~~~~~~VP~g~yfVLGDNr~~S~DSRyfGpVp~~~IiGkv~~~l 308 (337)
+|||+|+++++.+||||+.+.+.+.... +.......+||+| ||+||||+++|+||||||+|++++|+|||..+|
T Consensus 91 lpGD~V~i~~~~v~INg~~~~~~~~~~~~~~g~~l~~~~~~~vp~g-yf~lgdn~~~S~DSRy~G~V~~~~IiGk~~pl~ 169 (171)
T TIGR02771 91 LPGDRVTVRADVVAINGQLLPYSKPLATDSSGRPLPPFPEGVIPPG-FFVVHDTSPTSFDSRYFGPISREQVIGRVKPLF 169 (171)
T ss_pred eCCCEEEEECCEEEECCEEcccccccccccCCCccccCCCcEECCC-EEEECCCCCCCCcccccceecHHHeEEEEEEeE
Confidence 9999999999999999999877654321 1112236899999 999999999999999999999999999998654
No 8
>PF10502 Peptidase_S26: Signal peptidase, peptidase S26 ; InterPro: IPR019533 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents a conserved region found in the S26A family of serine endopeptidases, which function in the processing of newly-synthesised secreted proteins. Peptidase S26 removes the hydrophobic, N-terminal signal peptides as proteins are translocated across membranes. ; PDB: 3S04_B 1KN9_C 1B12_D 3IIQ_B 1T7D_A.
Probab=99.89 E-value=9.2e-25 Score=188.85 Aligned_cols=108 Identities=39% Similarity=0.608 Sum_probs=33.0
Q ss_pred CCCCCcEEEEeCCccc----cccccCC-CccEEEEEEeeCCCEEEEeCCEEEECCEEccccccccCCCCC----CCCEEe
Q 019676 201 KPCSNDIVIFKSPPVL----QEVGYTD-DDVFIKRVVAKEGDVVEVREGKLIVNGVVRNEDYILEAPSYN----MTPITV 271 (337)
Q Consensus 201 ~pkrGDIVVf~~P~~~----~~~gy~~-~~~~VKRVialPGDtV~i~dg~lyVNG~~~~e~~~~~~p~~~----~~~~~V 271 (337)
.+++||+|+|+.|... .+++|.+ +..++|||+|+|||+|+++++.++|||+.+.+.+..+..+.. ....+|
T Consensus 21 ~~~rGd~V~f~~p~~~~~~~~~~gy~~~~~~~iKrV~a~pGD~V~v~~~~v~iNG~~~~~~~~~d~~g~~l~~~~~~~~v 100 (138)
T PF10502_consen 21 KIERGDLVVFCPPAEVAFFAAERGYLPEGQPLIKRVAAVPGDTVEVTDGGVYINGRPVGEPLATDSDGRPLPQFSGSGTV 100 (138)
T ss_dssp --------------------------------------------------------------------S-T----TEEE-
T ss_pred ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccCCceEe
Confidence 4899999999998742 3456643 458999999999999999999999999988887665443322 246899
Q ss_pred cCCcEEEEcCCCCCCCCCCccCcccCCCeeEEEEEEE
Q 019676 272 PENSVFVMGDNRNNSYDSHVWGPLPAKNIIGRSVFRY 308 (337)
Q Consensus 272 P~g~yfVLGDNr~~S~DSRyfGpVp~~~IiGkv~~~l 308 (337)
|+|+|||||||+.+|+||||||+|++++|+|+|..+|
T Consensus 101 p~g~~~v~gd~~~~S~DSRy~G~V~~~~I~g~~~pl~ 137 (138)
T PF10502_consen 101 PEGEYFVLGDNRPNSFDSRYFGPVPRSQIIGKARPLW 137 (138)
T ss_dssp -TTEEEEE-SBTTS--SHHHH--EEGGGEEEEEEEEE
T ss_pred CCCEEEEecCCCCCccccCEecccCHHHEEEEEEEEE
Confidence 9999999999999999999999999999999998876
No 9
>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease. Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see Pfam model pfam00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad.
Probab=99.77 E-value=1.6e-18 Score=138.23 Aligned_cols=89 Identities=33% Similarity=0.597 Sum_probs=75.2
Q ss_pred EEcCCCccccccCCCEEEEEeeecccCCCCCCcEEEEeCCccccccccCCCccEEEEEEeeCCCEEEEeCCEEEECCEEc
Q 019676 174 YIPSLSMYPTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAKEGDVVEVREGKLIVNGVVR 253 (337)
Q Consensus 174 ~V~gdSMePTL~~GD~VLVdk~~~~~~~pkrGDIVVf~~P~~~~~~gy~~~~~~VKRVialPGDtV~i~dg~lyVNG~~~ 253 (337)
.|.|+||+|+|++||+|+|++.......+++||+|+|+.+.. ++..++|||++++
T Consensus 2 ~V~g~SM~P~l~~GD~vlv~~~~~~~~~~~~Gdivv~~~~~~-------~~~~~vkRv~~~~------------------ 56 (90)
T TIGR02754 2 KVTGVSMSPTLPPGDRIIVVPWLKIFRVPPIGNVVVVRHPLQ-------PYGLIIKRLAAVD------------------ 56 (90)
T ss_pred EeeCCCccCccCCCCEEEEEEccccCCCCCCCeEEEEecCCC-------CcceEEEEeeEEc------------------
Confidence 579999999999999999998543334456799999997642 4678999999864
Q ss_pred cccccccCCCCCCCCEEecCCcEEEEcCCCCCCCCCCccCcccCCCeeEEEEE
Q 019676 254 NEDYILEAPSYNMTPITVPENSVFVMGDNRNNSYDSHVWGPLPAKNIIGRSVF 306 (337)
Q Consensus 254 ~e~~~~~~p~~~~~~~~VP~g~yfVLGDNr~~S~DSRyfGpVp~~~IiGkv~~ 306 (337)
+++||++|||+..++|||++|+|+..+|+|||+|
T Consensus 57 -------------------~~~~~l~~dN~~~~~d~~~~g~v~~~~I~G~v~~ 90 (90)
T TIGR02754 57 -------------------DNGLFLLGDNPKASTDSRQLGPVPRSLLLGKVLW 90 (90)
T ss_pred -------------------CCeEEEeCCCCCCCCcccccCCCcHHHEEEEEEC
Confidence 4568999999999999999999999999999864
No 10
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa
Probab=99.72 E-value=3.4e-17 Score=128.77 Aligned_cols=84 Identities=48% Similarity=0.877 Sum_probs=74.0
Q ss_pred eEEEcCCCccccccCCCEEEEEeeecccCCCCCCcEEEEeCCccccccccCCCccEEEEEEeeCCCEEEEeCCEEEECCE
Q 019676 172 PRYIPSLSMYPTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAKEGDVVEVREGKLIVNGV 251 (337)
Q Consensus 172 ~~~V~gdSMePTL~~GD~VLVdk~~~~~~~pkrGDIVVf~~P~~~~~~gy~~~~~~VKRVialPGDtV~i~dg~lyVNG~ 251 (337)
.+.|.|+||+|+++.||++++++.......+++||+|+|+.+.. .+..++|||++
T Consensus 2 ~~~v~g~SM~P~i~~gd~v~v~~~~~~~~~~~~GDiv~~~~~~~-------~~~~~vkRv~~------------------ 56 (85)
T cd06530 2 PVVVPGGSMEPTLQPGDLVLVNKLSYGFREPKRGDVVVFKSPGD-------PGKPIIKRVIG------------------ 56 (85)
T ss_pred eeEEcCCCCcCcccCCCEEEEEEeecccCCCCCCCEEEEeCCCC-------CCCEEEEEEEE------------------
Confidence 47899999999999999999998764334689999999998641 25789999987
Q ss_pred EccccccccCCCCCCCCEEecCCcEEEEcCCCCCCCCCCccCcccCCCeeEEE
Q 019676 252 VRNEDYILEAPSYNMTPITVPENSVFVMGDNRNNSYDSHVWGPLPAKNIIGRS 304 (337)
Q Consensus 252 ~~~e~~~~~~p~~~~~~~~VP~g~yfVLGDNr~~S~DSRyfGpVp~~~IiGkv 304 (337)
||+.|||..+|+|||+||+|+.++|+|++
T Consensus 57 ------------------------~~~~gDn~~ns~d~~~~g~~~~~~i~G~~ 85 (85)
T cd06530 57 ------------------------YFVLGDNRNNSLDSRYWGPVPEDDIVGKV 85 (85)
T ss_pred ------------------------EEEeeCCCCCCCccCCcCCCcHHHeEEeC
Confidence 89999999899999999999999999985
No 11
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.69 E-value=1.3e-16 Score=139.50 Aligned_cols=117 Identities=19% Similarity=0.314 Sum_probs=93.7
Q ss_pred EEEEEeeecccCCCCCCcEEEEeCCcc----ccccccCC-CccEEEEEEeeCCCEEEEeCCEEEECCEEccccccccCCC
Q 019676 189 RIVAEKVTYYFRKPCSNDIVIFKSPPV----LQEVGYTD-DDVFIKRVVAKEGDVVEVREGKLIVNGVVRNEDYILEAPS 263 (337)
Q Consensus 189 ~VLVdk~~~~~~~pkrGDIVVf~~P~~----~~~~gy~~-~~~~VKRVialPGDtV~i~dg~lyVNG~~~~e~~~~~~p~ 263 (337)
+..++|.. .-+.+||+|+++.|+. .++|||.+ ...++|||.|+|||+|++.++.+.|||+.+......+..+
T Consensus 44 lyrv~k~~---~Pvt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq~Vci~~~~I~I~G~~v~~sl~~D~~G 120 (173)
T COG4959 44 LYRVSKLS---APVTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQHVCITSQGIAIDGKPVAASLPVDRVG 120 (173)
T ss_pred EEEecccC---CCcccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCCCcEEEecceEEECCEEeeeeccccccC
Confidence 34555533 2348999999999984 25689855 4569999999999999999999999999987666555433
Q ss_pred CC----CCCEEecCCcEEEEcCCCCCCCCCCccCcccCCCeeEEEEEEE
Q 019676 264 YN----MTPITVPENSVFVMGDNRNNSYDSHVWGPLPAKNIIGRSVFRY 308 (337)
Q Consensus 264 ~~----~~~~~VP~g~yfVLGDNr~~S~DSRyfGpVp~~~IiGkv~~~l 308 (337)
+. .....+.++|+|+|+|..+.|||||||||||.++|+|.+..+|
T Consensus 121 R~lp~~~gcR~l~~~el~lL~~~~~~SfDsRYfGpipas~vig~aRPvw 169 (173)
T COG4959 121 RALPRWQGCRYLAPSELLLLTDRSSTSFDSRYFGPIPASQVIGVARPVW 169 (173)
T ss_pred CcCCcccCCceecCCeEEEEeccCCcccccceecccCHHHcceeeeeee
Confidence 22 2234599999999999999999999999999999999998754
No 12
>TIGR02228 sigpep_I_arch signal peptidase I, archaeal type. This model represents signal peptidase I from most archaea, a subunit of the eukaryotic endoplasmic reticulum signal peptidase I complex, and an apparent signal peptidase I from a small number of bacteria. It is related to but does not overlap in hits with TIGR02227, the bacterial and mitochondrial signal peptidase I.
Probab=99.56 E-value=3.8e-14 Score=125.56 Aligned_cols=115 Identities=24% Similarity=0.326 Sum_probs=80.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHheee--e-EEEcCCCccccccCCCEEEEEeeecccCCCCCCcEEEEeCCccccccc
Q 019676 144 WLNITSDDAKTVLAALVISLAFRSFVAE--P-RYIPSLSMYPTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVG 220 (337)
Q Consensus 144 Wl~~l~~~~~~llv~lii~lll~~~i~~--~-~~V~gdSMePTL~~GD~VLVdk~~~~~~~pkrGDIVVf~~P~~~~~~g 220 (337)
|++.+..++..++++++++..+...... + +.|.|+||+|||++||.+++++... .++++||+|+|+.+.
T Consensus 2 ~~~~ii~~~~~~~l~~~~~~~l~~~~~~~~p~v~V~g~SM~Ptl~~GD~vlv~~~~~--~~~~~GDIVvf~~~~------ 73 (158)
T TIGR02228 2 KISNVIYFILIILLVILLLYGLVSKASGPDPVVVVLSGSMEPTFNTGDLILVTGADP--NDIQVGDVITYKSPG------ 73 (158)
T ss_pred hhHHHHHHHHHHHHHHHHHHHheeeccCCCcEEEEcCCCCcCCccCCCEEEEEeccc--CCCCCCCEEEEEECC------
Confidence 5555544444444444443333322221 2 3389999999999999999998542 579999999999753
Q ss_pred cCCCccEEEEEEeeCCCEEEEeCCEEEECCEEccccccccCCCCCCCCEEecCCcEEEEcCCCCCCCCCCccCcccCCCe
Q 019676 221 YTDDDVFIKRVVAKEGDVVEVREGKLIVNGVVRNEDYILEAPSYNMTPITVPENSVFVMGDNRNNSYDSHVWGPLPAKNI 300 (337)
Q Consensus 221 y~~~~~~VKRVialPGDtV~i~dg~lyVNG~~~~e~~~~~~p~~~~~~~~VP~g~yfVLGDNr~~S~DSRyfGpVp~~~I 300 (337)
+...++|||+++.++ + .+..|++.|||+ ...| .++|+.++|
T Consensus 74 --~~~~iihRVi~v~~~-----~----------------------------g~~~~~tkGDnN-~~~D---~~~v~~~~I 114 (158)
T TIGR02228 74 --FNTPVTHRVIEINNS-----G----------------------------GELGFITKGDNN-PAPD---GEPVPSENV 114 (158)
T ss_pred --CCccEEEEEEEEECC-----C----------------------------CcEEEEEEecCC-CCCC---cccCCHHHE
Confidence 237899999998643 0 012377779996 5556 689999999
Q ss_pred eEEEE
Q 019676 301 IGRSV 305 (337)
Q Consensus 301 iGkv~ 305 (337)
+|++.
T Consensus 115 iG~v~ 119 (158)
T TIGR02228 115 IGKYL 119 (158)
T ss_pred EEEEE
Confidence 99997
No 13
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=99.50 E-value=2.4e-13 Score=118.08 Aligned_cols=143 Identities=31% Similarity=0.455 Sum_probs=104.0
Q ss_pred HHHHHHHHHHHHHHHHH--HHheeeeEEEcCCCccccccCCCEEEEEeeecccCCCCCCcEEEEeCCccccccccCCCcc
Q 019676 149 SDDAKTVLAALVISLAF--RSFVAEPRYIPSLSMYPTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDV 226 (337)
Q Consensus 149 ~~~~~~llv~lii~lll--~~~i~~~~~V~gdSMePTL~~GD~VLVdk~~~~~~~pkrGDIVVf~~P~~~~~~gy~~~~~ 226 (337)
..++..+++++++++++ +.++++.+.|+|+||+|||+.||+|+++|..+....+..++++.+.. .....
T Consensus 8 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~V~s~SM~Ptl~~GD~v~v~k~~~~~~~~~~~~~~~~~~---------~~~~~ 78 (166)
T COG0681 8 LELISSLLIAIILALIIGVRTFVFEPVVVPSGSMEPTLNVGDRVLVKKFSYGFGKLKVPDIIVLPA---------VVEGD 78 (166)
T ss_pred HHHHHHHHHHHHHhheeeeEEEEEEEEEECCCccccccccCCEEEEEeccccccCCccceeeecCC---------CCCcc
Confidence 34556667777777777 89999999999999999999999999999998888888888883332 36778
Q ss_pred EEEEEEeeCCCEEEEeCCEEEECCEEccccccccCCCCCCCCEEecCCcEEEEcCCCCCCCCCCccCcccCCCeeEEEEE
Q 019676 227 FIKRVVAKEGDVVEVREGKLIVNGVVRNEDYILEAPSYNMTPITVPENSVFVMGDNRNNSYDSHVWGPLPAKNIIGRSVF 306 (337)
Q Consensus 227 ~VKRVialPGDtV~i~dg~lyVNG~~~~e~~~~~~p~~~~~~~~VP~g~yfVLGDNr~~S~DSRyfGpVp~~~IiGkv~~ 306 (337)
++||+++++||.+.++++..|+ +..+.+.+. .+..++.++.++....+.+++.++......++.++
T Consensus 79 ~~kr~~~~~GD~i~~~~~~~~~-~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-- 144 (166)
T COG0681 79 LIKRVIGLRGDIVVFKDDRLYV-VPIIPRVYG-----------LVEKDNGKHLVDVIVNANSSRVFGIITKKDYIKRV-- 144 (166)
T ss_pred eEEEeccCCCCEEEEECCEEEe-ecccCcchh-----------hhhcccccccccccccccCccccccccccccccce--
Confidence 9999999999999999999887 222222111 11111111455555677888888887778888777
Q ss_pred EEcCCCCC
Q 019676 307 RYWPPQRI 314 (337)
Q Consensus 307 ~lwP~~r~ 314 (337)
.+-|.+++
T Consensus 145 ~~~~gd~~ 152 (166)
T COG0681 145 IGLPGDNI 152 (166)
T ss_pred EEeeccce
Confidence 34444443
No 14
>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification. ; InterPro: IPR019759 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ].; PDB: 1KCA_H 3BDN_A 1F39_A 1JHH_A 1JHE_B 3JSP_A 1JHF_B 1JHC_A 3JSO_B 1B12_D ....
Probab=99.13 E-value=1.3e-10 Score=87.68 Aligned_cols=56 Identities=32% Similarity=0.564 Sum_probs=46.2
Q ss_pred EEcCCCccccccCCCEEEEEeeecccCCCCCCcEEEEeCCccccccccCCC-ccEEEEEEeeCCCEEEEe
Q 019676 174 YIPSLSMYPTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDD-DVFIKRVVAKEGDVVEVR 242 (337)
Q Consensus 174 ~V~gdSMePTL~~GD~VLVdk~~~~~~~pkrGDIVVf~~P~~~~~~gy~~~-~~~VKRVialPGDtV~i~ 242 (337)
+|.|+||+|+|++||+|+|++.. .++.||+|+|..+. + ..++|||.+.+|+.+.+.
T Consensus 1 ~V~GdSM~P~i~~Gd~v~v~~~~----~~~~gdivv~~~~~---------~~~~~iKrv~~~~~~~~~~~ 57 (70)
T PF00717_consen 1 RVEGDSMEPTIKDGDIVLVDPSS----EPKDGDIVVVKIDG---------DEELYIKRVVGEPGGIILIS 57 (70)
T ss_dssp EEESSTTGGTSSTTEEEEEEETS-------TTSEEEEEETT---------EESEEEEEEEEETTEEEEE-
T ss_pred CeECcCcccCeeCCCEEEEEEcC----CCccCeEEEEEECC---------ceeeEEEEEEEeCCCEEEEe
Confidence 57899999999999999999864 78899999999742 2 289999999999999987
No 15
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=98.91 E-value=9e-09 Score=79.25 Aligned_cols=53 Identities=32% Similarity=0.544 Sum_probs=44.3
Q ss_pred eEEEcCCCccccccCCCEEEEEeeecccCCCCCCcEEEEeCCccccccccCCCccEEEEEEeeCC
Q 019676 172 PRYIPSLSMYPTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAKEG 236 (337)
Q Consensus 172 ~~~V~gdSMePTL~~GD~VLVdk~~~~~~~pkrGDIVVf~~P~~~~~~gy~~~~~~VKRVialPG 236 (337)
.+.|.|+||+|++..||++++++.. ..++.||+|++..+ ++..++||+...++
T Consensus 2 ~~~v~g~SM~P~i~~gd~v~i~~~~---~~~~~G~iv~~~~~---------~~~~~ikrl~~~~~ 54 (84)
T cd06462 2 ALRVEGDSMEPTIPDGDLVLVDKSS---YEPKRGDIVVFRLP---------GGELTVKRVIGLPG 54 (84)
T ss_pred eeEEcCCCccCcccCCCEEEEEecC---CCCcCCEEEEEEcC---------CCcEEEEEEEEECC
Confidence 4678999999999999999999865 24889999999963 23789999997654
No 16
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=98.54 E-value=4.4e-07 Score=83.33 Aligned_cols=58 Identities=17% Similarity=0.368 Sum_probs=46.4
Q ss_pred eeEEEcCCCccccccCCCEEEEEeeecccCCCCCCcEEEEeCCccccccccCCCccEEEEEEeeCCCEEEE
Q 019676 171 EPRYIPSLSMYPTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAKEGDVVEV 241 (337)
Q Consensus 171 ~~~~V~gdSMePTL~~GD~VLVdk~~~~~~~pkrGDIVVf~~P~~~~~~gy~~~~~~VKRVialPGDtV~i 241 (337)
..++|.||||+|++.+||.++|+... ...+||.|++.. .++..+|||++..+|..+.+
T Consensus 124 ~~i~V~GDSMeP~~~~Gd~ilVd~~~----~~~~gd~v~v~~---------~g~~~~VK~l~~~~~~~~~l 181 (214)
T COG2932 124 FALRVTGDSMEPTYEDGDTLLVDPGV----NTRRGDRVYVET---------DGGELYVKKLQREPGGLLRL 181 (214)
T ss_pred EEEEEeCCcccccccCCCEEEECCCC----ceeeCCEEEEEE---------eCCeEEEEEEEEecCCeEEE
Confidence 56899999999999999999999864 455788666654 26789999999888776643
No 17
>cd06529 S24_LexA-like Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the
Probab=98.47 E-value=4.7e-07 Score=69.63 Aligned_cols=57 Identities=25% Similarity=0.397 Sum_probs=48.2
Q ss_pred eEEEcCCCccccccCCCEEEEEeeecccCCCCCCcEEEEeCCccccccccCCCccEEEEEEeeCCCEEEEe
Q 019676 172 PRYIPSLSMYPTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAKEGDVVEVR 242 (337)
Q Consensus 172 ~~~V~gdSMePTL~~GD~VLVdk~~~~~~~pkrGDIVVf~~P~~~~~~gy~~~~~~VKRVialPGDtV~i~ 242 (337)
.++|.|+||+|+++.||++++++.. .++.||+|++.. ++..++||+...+++.+.+.
T Consensus 2 ~~~v~g~sM~p~i~~gd~lii~~~~----~~~~g~i~~~~~----------~~~~~ikr~~~~~~~~~~L~ 58 (81)
T cd06529 2 ALRVKGDSMEPTIPDGDLVLVDPSD----TPRDGDIVVARL----------DGELTVKRLQRRGGGRLRLI 58 (81)
T ss_pred EEEEECCCcCCccCCCCEEEEcCCC----CCCCCCEEEEEE----------CCEEEEEEEEECCCCcEEEE
Confidence 4688999999999999999999854 488999999996 45789999998886665554
No 18
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.43 E-value=9.1e-07 Score=78.02 Aligned_cols=90 Identities=27% Similarity=0.333 Sum_probs=62.9
Q ss_pred eEEEcCCCccccccCCCEEEEEeeecccCCCCCCcEEEEeCCccccccccCCCccEEEEEEeeCCCEEEEeCCEEEECCE
Q 019676 172 PRYIPSLSMYPTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAKEGDVVEVREGKLIVNGV 251 (337)
Q Consensus 172 ~~~V~gdSMePTL~~GD~VLVdk~~~~~~~pkrGDIVVf~~P~~~~~~gy~~~~~~VKRVialPGDtV~i~dg~lyVNG~ 251 (337)
++.|-+.||||.++.||+++...... .-++.||||||+.++ ..-..|+||+.+-+. .+
T Consensus 50 iVVVLSgSMePaF~RGDlLfL~N~~~--~p~~vGdivVf~veg--------R~IPiVHRviK~he~----~~-------- 107 (180)
T KOG3342|consen 50 IVVVLSGSMEPAFHRGDLLFLTNRNE--DPIRVGDIVVFKVEG--------REIPIVHRVIKQHEK----SN-------- 107 (180)
T ss_pred EEEEEcCCcCcccccccEEEEecCCC--CcceeccEEEEEECC--------ccCchhHHHHHHhcc----cC--------
Confidence 67889999999999999999875331 235789999999864 455799999876432 00
Q ss_pred EccccccccCCCCCCCCEEecCCcEEEEcCCCCCCCCCCc-c----CcccCCCeeEEEE
Q 019676 252 VRNEDYILEAPSYNMTPITVPENSVFVMGDNRNNSYDSHV-W----GPLPAKNIIGRSV 305 (337)
Q Consensus 252 ~~~e~~~~~~p~~~~~~~~VP~g~yfVLGDNr~~S~DSRy-f----GpVp~~~IiGkv~ 305 (337)
.+-+++.-||| |-.|.|. | =...+++|+|+|.
T Consensus 108 --------------------~~~~~LTKGDN--N~~dD~~Ly~~gq~~L~r~~Ivg~~~ 144 (180)
T KOG3342|consen 108 --------------------GHIKFLTKGDN--NAVDDRGLYAQGQNWLERKDIVGRVR 144 (180)
T ss_pred --------------------CcEEEEecCCC--CcccchhcccccccceeccceeeEEe
Confidence 01124555888 4455552 2 2578899999985
No 19
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=98.26 E-value=8.7e-06 Score=70.31 Aligned_cols=51 Identities=20% Similarity=0.222 Sum_probs=41.9
Q ss_pred eeeeEEEcCCCcc-ccccCCCEEEEEeeecccCCCCCCcEEEEeCCccccccccCCCccEEEEEEe
Q 019676 169 VAEPRYIPSLSMY-PTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVA 233 (337)
Q Consensus 169 i~~~~~V~gdSMe-PTL~~GD~VLVdk~~~~~~~pkrGDIVVf~~P~~~~~~gy~~~~~~VKRVia 233 (337)
-...++|.|+||. |++++||+++|++.. .++.||+|++.. ++...+||+..
T Consensus 50 ~~f~l~V~GdSM~~~~I~~GD~liVd~~~----~~~~Gdivv~~~----------~g~~~vKrl~~ 101 (139)
T PRK10276 50 ATYFVKASGDSMIDAGISDGDLLIVDSAI----TASHGDIVIAAV----------DGEFTVKKLQL 101 (139)
T ss_pred CEEEEEEecCCCCCCCCCCCCEEEEECCC----CCCCCCEEEEEE----------CCEEEEEEEEE
Confidence 3456889999997 699999999999743 577899999885 56678999874
No 20
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=98.07 E-value=3.4e-05 Score=69.87 Aligned_cols=52 Identities=19% Similarity=0.166 Sum_probs=43.2
Q ss_pred eeeeEEEcCCCcc-ccccCCCEEEEEeeecccCCCCCCcEEEEeCCccccccccCCCccEEEEEEee
Q 019676 169 VAEPRYIPSLSMY-PTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAK 234 (337)
Q Consensus 169 i~~~~~V~gdSMe-PTL~~GD~VLVdk~~~~~~~pkrGDIVVf~~P~~~~~~gy~~~~~~VKRVial 234 (337)
-...++|.|+||. |.+.+||+++|++. ..++.||+|++.. ++...|||+.-.
T Consensus 110 ~~f~~~V~GdSM~~~~i~~Gd~v~v~~~----~~~~~G~ivvv~~----------~~~~~vKrl~~~ 162 (199)
T TIGR00498 110 AVFLLKVMGDSMVDAGICDGDLLIVRSQ----KDARNGEIVAAMI----------DGEVTVKRFYKD 162 (199)
T ss_pred CEEEEEecCCCCCCCCCCCCCEEEEecC----CCCCCCCEEEEEE----------CCEEEEEEEEEE
Confidence 4567899999995 68999999999974 3688999999995 567899998744
No 21
>PRK00215 LexA repressor; Validated
Probab=98.06 E-value=2.9e-05 Score=70.56 Aligned_cols=53 Identities=21% Similarity=0.140 Sum_probs=43.1
Q ss_pred heeeeEEEcCCCcc-ccccCCCEEEEEeeecccCCCCCCcEEEEeCCccccccccCCCccEEEEEEee
Q 019676 168 FVAEPRYIPSLSMY-PTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAK 234 (337)
Q Consensus 168 ~i~~~~~V~gdSMe-PTL~~GD~VLVdk~~~~~~~pkrGDIVVf~~P~~~~~~gy~~~~~~VKRVial 234 (337)
--...+.|.|+||. |++++||+|+|++.. .++.||+|++.. ++...|||+.-.
T Consensus 116 ~~~~~~~V~GdSM~~~~i~~Gd~v~v~~~~----~~~~G~ivv~~~----------~~~~~vKrl~~~ 169 (205)
T PRK00215 116 GEDFLLRVRGDSMIDAGILDGDLVIVRKQQ----TARNGQIVVALI----------DDEATVKRFRRE 169 (205)
T ss_pred CCeEEEEEccCCCCCCCcCCCCEEEEeCCC----CCCCCCEEEEEE----------CCEEEEEEEEEe
Confidence 34556889999995 799999999999743 567899999985 457899999754
No 22
>PRK12423 LexA repressor; Provisional
Probab=97.98 E-value=4.9e-05 Score=69.59 Aligned_cols=50 Identities=22% Similarity=0.193 Sum_probs=41.6
Q ss_pred eeEEEcCCCcc-ccccCCCEEEEEeeecccCCCCCCcEEEEeCCccccccccCCCccEEEEEEee
Q 019676 171 EPRYIPSLSMY-PTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAK 234 (337)
Q Consensus 171 ~~~~V~gdSMe-PTL~~GD~VLVdk~~~~~~~pkrGDIVVf~~P~~~~~~gy~~~~~~VKRVial 234 (337)
..+.|.|+||. |++.+||+|+|++. ..++.||+|++.. ++...+||+.-.
T Consensus 115 f~l~V~GdSM~~~~i~~Gd~viv~~~----~~~~~Gdivv~~~----------~~~~~vKrl~~~ 165 (202)
T PRK12423 115 YLLQVQGDSMIDDGILDGDLVGVHRS----PEARDGQIVVARL----------DGEVTIKRLERS 165 (202)
T ss_pred EEEEEecCcCCCCCcCCCCEEEEeCC----CcCCCCCEEEEEE----------CCEEEEEEEEEe
Confidence 35789999996 79999999999974 3677899999985 567899999754
No 23
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=97.34 E-value=0.0023 Score=59.20 Aligned_cols=52 Identities=19% Similarity=0.169 Sum_probs=42.6
Q ss_pred eeeeEEEcCCCc-cccccCCCEEEEEeeecccCCCCCCcEEEEeCCccccccccCCCccEEEEEEe
Q 019676 169 VAEPRYIPSLSM-YPTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVA 233 (337)
Q Consensus 169 i~~~~~V~gdSM-ePTL~~GD~VLVdk~~~~~~~pkrGDIVVf~~P~~~~~~gy~~~~~~VKRVia 233 (337)
-....+|.|+|| ++.+.+||+|+|++. ...+.||||+...+ ++...+||..-
T Consensus 111 ~~f~L~V~GdSM~~~gi~dGDlvvV~~~----~~a~~GdiVvA~i~---------g~e~TvKrl~~ 163 (201)
T COG1974 111 ATFFLRVSGDSMIDAGILDGDLVVVDPT----EDAENGDIVVALID---------GEEATVKRLYR 163 (201)
T ss_pred ceEEEEecCCccccCcCCCCCEEEEcCC----CCCCCCCEEEEEcC---------CCcEEEEEEEE
Confidence 345678999999 789999999999975 37889999999973 44478999874
No 24
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=75.81 E-value=4.2 Score=34.85 Aligned_cols=29 Identities=31% Similarity=0.487 Sum_probs=22.8
Q ss_pred CccEEEEEEeeCCCEEEEeCCEEEECCEE
Q 019676 224 DDVFIKRVVAKEGDVVEVREGKLIVNGVV 252 (337)
Q Consensus 224 ~~~~VKRVialPGDtV~i~dg~lyVNG~~ 252 (337)
...++||+.+++||.+...+..++++|+.
T Consensus 137 ~~~~~~~~~~~~gd~~~~~~~~~~~~g~~ 165 (166)
T COG0681 137 KKDYIKRVIGLPGDNILYTDDDLPINGKP 165 (166)
T ss_pred ccccccceEEeeccceeeccCceeecCCC
Confidence 35689999999999999885447777754
No 25
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=47.57 E-value=1.3e+02 Score=25.95 Aligned_cols=26 Identities=12% Similarity=0.488 Sum_probs=15.2
Q ss_pred CCcEEEEcCCCCCCCCCCccCcccCCC
Q 019676 273 ENSVFVMGDNRNNSYDSHVWGPLPAKN 299 (337)
Q Consensus 273 ~g~yfVLGDNr~~S~DSRyfGpVp~~~ 299 (337)
+|-+.++.++ ..-.-+|.||||.+|.
T Consensus 81 dNA~Viin~~-g~P~GtrI~GPVaREl 106 (122)
T COG0093 81 DNAAVIINPD-GEPRGTRIFGPVAREL 106 (122)
T ss_pred CceEEEECCC-CCcccceEecchhHHH
Confidence 3334444433 2556678899988763
No 26
>PF04790 Sarcoglycan_1: Sarcoglycan complex subunit protein; InterPro: IPR006875 The dystrophin glycoprotein complex (DGC) is a membrane-spanning complex that links the interior cytoskeleton to the extracellular matrix in muscle. The sarcoglycan complex is a subcomplex within the DGC and is composed of several muscle-specific, transmembrane proteins (alpha-, beta-, gamma-, delta- and zeta-sarcoglycan). The sarcoglycans are asparagine-linked glycosylated proteins with single transmembrane domains. This family contains beta, gamma and delta members [, ].; GO: 0007010 cytoskeleton organization, 0016012 sarcoglycan complex, 0016021 integral to membrane
Probab=36.84 E-value=2.4e+02 Score=27.27 Aligned_cols=32 Identities=16% Similarity=0.104 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHHHHHheeeeEEEcCCCccc
Q 019676 151 DAKTVLAALVISLAFRSFVAEPRYIPSLSMYP 182 (337)
Q Consensus 151 ~~~~llv~lii~lll~~~i~~~~~V~gdSMeP 182 (337)
++..+++.+++-+++..+++.+.++..+-|..
T Consensus 17 ~vllL~il~iiNL~LTiwIl~Vl~~~~~Gm~~ 48 (264)
T PF04790_consen 17 FVLLLFILAIINLALTIWILKVLRFSSNGMGS 48 (264)
T ss_pred HHHHHHHHHHHHHHHHhhhheeeecccCcccc
Confidence 34444455556667788999999998888875
No 27
>PLN02705 beta-amylase
Probab=36.11 E-value=93 Score=33.82 Aligned_cols=17 Identities=12% Similarity=0.319 Sum_probs=8.3
Q ss_pred cCCCCCCCCCccccccc
Q 019676 78 FQHQNPRPLNPKNLLYR 94 (337)
Q Consensus 78 ~~~~~~~~~~~~~~~~~ 94 (337)
-.|+.|++-+|..+..+
T Consensus 31 ~~~~~~~~~~~~~~~~~ 47 (681)
T PLN02705 31 RNRNQPQSRRPRGFAAT 47 (681)
T ss_pred CCCCCCccCCCcchhhh
Confidence 34455555555444433
No 28
>PF06890 Phage_Mu_Gp45: Bacteriophage Mu Gp45 protein; InterPro: IPR014462 This entry is represented by the Bacteriophage Mu, Gp45. The characteristics of the protein distribution suggest prophage matches.
Probab=35.49 E-value=1.2e+02 Score=27.22 Aligned_cols=45 Identities=16% Similarity=0.320 Sum_probs=29.0
Q ss_pred EEEEEeeecccCCCCCCcEEEEeCCccccccccCCCccEEEE---EEeeCCCEEEEe
Q 019676 189 RIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKR---VVAKEGDVVEVR 242 (337)
Q Consensus 189 ~VLVdk~~~~~~~pkrGDIVVf~~P~~~~~~gy~~~~~~VKR---VialPGDtV~i~ 242 (337)
.|.++...|+...++.|++++|... +..+.+|| ++.+.++++++.
T Consensus 62 via~~d~~yR~~~L~~GEvalY~~~---------G~~I~L~~~G~ii~~~~~~~~v~ 109 (162)
T PF06890_consen 62 VIAVEDRRYRPKGLKPGEVALYDDE---------GQKIHLKRDGRIIEVTCKTVTVN 109 (162)
T ss_pred EEEeCCccccccCCCCCcEEEEcCC---------CCEEEEEecceEEeccCceEEEe
Confidence 3444444455556789999999962 44556665 566667777765
No 29
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=35.41 E-value=76 Score=30.42 Aligned_cols=21 Identities=29% Similarity=0.466 Sum_probs=17.4
Q ss_pred cCCCccccccCCCEEEEEeee
Q 019676 176 PSLSMYPTFDVGDRIVAEKVT 196 (337)
Q Consensus 176 ~gdSMePTL~~GD~VLVdk~~ 196 (337)
....|.|.|+.||+|...-..
T Consensus 105 ~~~~~r~~l~vGD~v~AkV~~ 125 (239)
T COG1097 105 AEKDLRPFLNVGDLVYAKVVD 125 (239)
T ss_pred cccccccccccCCEEEEEEEE
Confidence 467899999999998876654
No 30
>PF00238 Ribosomal_L14: Ribosomal protein L14p/L23e; InterPro: IPR000218 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L14 is one of the proteins from the large ribosomal subunit. In eubacteria, L14 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins, which have been grouped on the basis of sequence similarities []. Based on amino-acid sequence homology, it is predicted that ribosomal protein L14 is a member of a recently identified family of structurally related RNA-binding proteins []. L14 is a protein of 119 to 137 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZR_M 4A1C_J 4A1E_J 4A1A_J 4A17_J 1VSP_I 3D5D_O 1VSA_I 3MRZ_K 3F1F_O ....
Probab=34.06 E-value=1.3e+02 Score=25.73 Aligned_cols=28 Identities=21% Similarity=0.634 Sum_probs=21.4
Q ss_pred EecCCcEEEEcCCCCCCCCCCccCcccCC
Q 019676 270 TVPENSVFVMGDNRNNSYDSHVWGPLPAK 298 (337)
Q Consensus 270 ~VP~g~yfVLGDNr~~S~DSRyfGpVp~~ 298 (337)
...+|.+.++.++. +...+|-+|||+.+
T Consensus 78 ~F~~Na~VLln~~~-~p~GtrI~Gpv~~e 105 (122)
T PF00238_consen 78 KFDDNAVVLLNKKG-NPLGTRIFGPVPRE 105 (122)
T ss_dssp EESSEEEEEEETTS-SBSSSSBCSEEEHH
T ss_pred EeCCccEEEEcCCC-CEeeeEEEeeehHH
Confidence 34566777778775 78889999999864
No 31
>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism [, ]. The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands [, ]. Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigenes putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2LRJ_A 2VPM_B 2VOB_B 2VPS_A 2K3A_A 2IO9_A 2IO8_A 2IOB_A 2IOA_B 2IO7_B ....
Probab=32.79 E-value=93 Score=25.61 Aligned_cols=36 Identities=22% Similarity=0.314 Sum_probs=22.6
Q ss_pred CCCCCCcEEEEeCCccccccccCCCccEEEEEEee-CCCEEEEe
Q 019676 200 RKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAK-EGDVVEVR 242 (337)
Q Consensus 200 ~~pkrGDIVVf~~P~~~~~~gy~~~~~~VKRVial-PGDtV~i~ 242 (337)
..|+.|||++|.... ....=.|--|.++ .+++|++.
T Consensus 61 ~~P~~Gdivv~~~~~-------~~~~GHVaIV~~v~~~~~i~v~ 97 (124)
T PF05257_consen 61 STPQPGDIVVWDSGS-------GGGYGHVAIVESVNDGGTITVI 97 (124)
T ss_dssp S---TTEEEEEEECT-------TTTT-EEEEEEEE-TTSEEEEE
T ss_pred cccccceEEEeccCC-------CCCCCeEEEEEEECCCCEEEEE
Confidence 579999999995211 1233368888888 88888876
No 32
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=29.16 E-value=55 Score=25.92 Aligned_cols=12 Identities=25% Similarity=0.255 Sum_probs=6.1
Q ss_pred cCCCEEEEEeee
Q 019676 185 DVGDRIVAEKVT 196 (337)
Q Consensus 185 ~~GD~VLVdk~~ 196 (337)
.+||.|+|....
T Consensus 48 ~~GD~V~Ve~~~ 59 (75)
T COG0361 48 LPGDVVLVELSP 59 (75)
T ss_pred CCCCEEEEEecc
Confidence 345555555544
No 33
>CHL00057 rpl14 ribosomal protein L14
Probab=28.16 E-value=3.7e+02 Score=23.09 Aligned_cols=28 Identities=21% Similarity=0.480 Sum_probs=17.9
Q ss_pred ecCCcEEEEcCCCCCCCCCCccCcccCCC
Q 019676 271 VPENSVFVMGDNRNNSYDSHVWGPLPAKN 299 (337)
Q Consensus 271 VP~g~yfVLGDNr~~S~DSRyfGpVp~~~ 299 (337)
.-+|.+.++.++. +-.=+|-+|||+++-
T Consensus 79 F~~Na~VLin~~~-~p~GTrI~Gpv~~el 106 (122)
T CHL00057 79 FDDNAAVVIDQEG-NPKGTRVFGPIAREL 106 (122)
T ss_pred cCCceEEEECCCC-CEeEeEEEccchHHH
Confidence 3455555555553 556678899998765
No 34
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=27.65 E-value=57 Score=25.29 Aligned_cols=10 Identities=20% Similarity=0.082 Sum_probs=4.8
Q ss_pred CCCcEEEEeC
Q 019676 203 CSNDIVIFKS 212 (337)
Q Consensus 203 krGDIVVf~~ 212 (337)
..||.|.+..
T Consensus 46 ~~GD~V~Ve~ 55 (68)
T TIGR00008 46 LPGDKVKVEL 55 (68)
T ss_pred CCCCEEEEEE
Confidence 3455555543
No 35
>TIGR01067 rplN_bact ribosomal protein L14, bacterial/organelle. This model distinguishes bacterial and most organellar examples of ribosomal protein L14 from all archaeal and eukaryotic forms.
Probab=26.53 E-value=4.1e+02 Score=22.74 Aligned_cols=28 Identities=14% Similarity=0.490 Sum_probs=17.9
Q ss_pred ecCCcEEEEcCCCCCCCCCCccCcccCCC
Q 019676 271 VPENSVFVMGDNRNNSYDSHVWGPLPAKN 299 (337)
Q Consensus 271 VP~g~yfVLGDNr~~S~DSRyfGpVp~~~ 299 (337)
..+|.+.++.++. +-.=+|-+|||+++-
T Consensus 79 F~~Na~VLin~~~-~p~GTrI~Gpv~~el 106 (122)
T TIGR01067 79 FDDNACVLINKNK-EPRGTRIFGPVAREL 106 (122)
T ss_pred CCCceEEEECCCC-CEeeeEEEccchHHH
Confidence 3455555555553 456678899998765
No 36
>PLN02867 Probable galacturonosyltransferase
Probab=24.18 E-value=1.1e+02 Score=32.76 Aligned_cols=21 Identities=33% Similarity=0.558 Sum_probs=10.5
Q ss_pred ccccccCCCCCCCCCCCCCCCC
Q 019676 107 TKSVVNTGSGGGGGGDGGGGDG 128 (337)
Q Consensus 107 ~~~~~~~~~~~~~~~sag~G~~ 128 (337)
.+.++-++ +|+|+||+|-|+.
T Consensus 10 ~~~~~~~~-~~~~~~~~~~~~~ 30 (535)
T PLN02867 10 IKKVTISN-PGSGKGSGGCAAA 30 (535)
T ss_pred eeEEEecC-CCCCCCCCcchHH
Confidence 34555444 4445555555554
No 37
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=24.14 E-value=68 Score=25.30 Aligned_cols=11 Identities=18% Similarity=0.223 Sum_probs=6.4
Q ss_pred CCCCcEEEEeC
Q 019676 202 PCSNDIVIFKS 212 (337)
Q Consensus 202 pkrGDIVVf~~ 212 (337)
+++||+|++..
T Consensus 39 I~~GD~VlV~~ 49 (78)
T cd04456 39 IKRGDFLIVDP 49 (78)
T ss_pred EcCCCEEEEEe
Confidence 45666666653
No 38
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=24.08 E-value=51 Score=24.77 Aligned_cols=39 Identities=10% Similarity=0.021 Sum_probs=17.4
Q ss_pred EEcCCCc-cccccCCCEEEEEeeecc--cCCCCCCcEEEEeC
Q 019676 174 YIPSLSM-YPTFDVGDRIVAEKVTYY--FRKPCSNDIVIFKS 212 (337)
Q Consensus 174 ~V~gdSM-ePTL~~GD~VLVdk~~~~--~~~pkrGDIVVf~~ 212 (337)
...|..+ +-.+.+|..+++.-.... .--+++||+|++..
T Consensus 11 ~~lG~~~~~V~~~dg~~~l~~i~gK~r~~iwI~~GD~V~V~~ 52 (65)
T PF01176_consen 11 EMLGNNLFEVECEDGEERLARIPGKFRKRIWIKRGDFVLVEP 52 (65)
T ss_dssp EEESSSEEEEEETTSEEEEEEE-HHHHTCC---TTEEEEEEE
T ss_pred EECCCCEEEEEeCCCCEEEEEeccceeeeEecCCCCEEEEEe
Confidence 3334443 334445555555443221 11256788887774
No 39
>COG4079 Uncharacterized protein conserved in archaea [Function unknown]
Probab=23.06 E-value=1.4e+02 Score=28.94 Aligned_cols=31 Identities=23% Similarity=0.371 Sum_probs=24.8
Q ss_pred CCccEEEEEEe----eCCCEEEEeCCEEEECCEEc
Q 019676 223 DDDVFIKRVVA----KEGDVVEVREGKLIVNGVVR 253 (337)
Q Consensus 223 ~~~~~VKRVia----lPGDtV~i~dg~lyVNG~~~ 253 (337)
++..++++|-+ .|||+|.++|+.+.|.|+.+
T Consensus 248 Pg~~v~m~v~~~g~~~pGd~vvv~dg~mki~G~d~ 282 (293)
T COG4079 248 PGEEVVMAVEGNGEVEPGDRVVVKDGVMKIDGKDL 282 (293)
T ss_pred CCceEEEEEccCCccCCCCEEEEecCceEeccccc
Confidence 44557777754 58999999999999999875
No 40
>TIGR02594 conserved hypothetical protein TIGR02594. Members of this protein family known so far are restricted to the bacteria, and for the most to the proteobacteria. The function is unknown.
Probab=22.37 E-value=2.1e+02 Score=24.45 Aligned_cols=12 Identities=25% Similarity=0.362 Sum_probs=10.2
Q ss_pred CCCCCcEEEEeC
Q 019676 201 KPCSNDIVIFKS 212 (337)
Q Consensus 201 ~pkrGDIVVf~~ 212 (337)
.++.||||+|+.
T Consensus 73 ~p~~GDiv~f~~ 84 (129)
T TIGR02594 73 KPAYGCIAVKRR 84 (129)
T ss_pred CCCccEEEEEEC
Confidence 678999999984
No 41
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=22.33 E-value=72 Score=25.07 Aligned_cols=11 Identities=27% Similarity=0.341 Sum_probs=6.1
Q ss_pred CCCCcEEEEeC
Q 019676 202 PCSNDIVIFKS 212 (337)
Q Consensus 202 pkrGDIVVf~~ 212 (337)
+++||+|++..
T Consensus 39 I~~GD~V~Ve~ 49 (77)
T cd05793 39 INEGDIVLVAP 49 (77)
T ss_pred EcCCCEEEEEe
Confidence 34566666653
No 42
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=22.28 E-value=72 Score=25.43 Aligned_cols=11 Identities=27% Similarity=0.344 Sum_probs=6.5
Q ss_pred CCCCcEEEEeC
Q 019676 202 PCSNDIVIFKS 212 (337)
Q Consensus 202 pkrGDIVVf~~ 212 (337)
+++||+|++..
T Consensus 44 I~~GD~VlVe~ 54 (83)
T smart00652 44 IRRGDIVLVDP 54 (83)
T ss_pred EcCCCEEEEEe
Confidence 45666666653
No 43
>PRK11578 macrolide transporter subunit MacA; Provisional
Probab=21.44 E-value=2e+02 Score=28.38 Aligned_cols=24 Identities=17% Similarity=0.152 Sum_probs=16.0
Q ss_pred EEEEEEeeCCCEEEEeCCEEEECC
Q 019676 227 FIKRVVAKEGDVVEVREGKLIVNG 250 (337)
Q Consensus 227 ~VKRVialPGDtV~i~dg~lyVNG 250 (337)
.|+++...+||.|.--+--+.++.
T Consensus 71 ~V~~v~v~~G~~V~kG~~L~~ld~ 94 (370)
T PRK11578 71 QLKTLSVAIGDKVKKDQLLGVIDP 94 (370)
T ss_pred EEEEEEcCCCCEEcCCCEEEEECc
Confidence 688888889998764333344554
Done!