Query 021373
Match_columns 313
No_of_seqs 266 out of 1512
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 02:27:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021373.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021373hhsearch_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 6.9E-41 1.5E-45 292.6 19.1 153 152-311 2-162 (163)
2 PRK10861 signal peptidase I; P 100.0 2.6E-36 5.7E-41 289.4 19.6 155 151-312 63-305 (324)
3 KOG0171 Mitochondrial inner me 100.0 4.2E-33 9E-38 241.6 11.6 140 155-311 18-158 (176)
4 PRK13838 conjugal transfer pil 99.9 4.7E-27 1E-31 208.5 15.2 117 190-308 39-172 (176)
5 TIGR02771 TraF_Ti conjugative 99.9 1.9E-25 4.1E-30 197.4 17.2 132 167-308 21-169 (171)
6 PRK13884 conjugal transfer pep 99.9 3.9E-25 8.6E-30 196.5 17.0 108 200-307 49-175 (178)
7 KOG1568 Mitochondrial inner me 99.9 2.6E-25 5.5E-30 192.9 10.1 120 164-310 25-150 (174)
8 PF10502 Peptidase_S26: Signal 99.9 8.4E-26 1.8E-30 193.1 1.4 108 201-308 21-137 (138)
9 TIGR02754 sod_Ni_protease nick 99.8 3.1E-19 6.7E-24 140.7 10.1 88 174-305 2-89 (90)
10 cd06530 S26_SPase_I The S26 Ty 99.8 4.5E-18 9.7E-23 132.3 9.9 84 172-304 2-85 (85)
11 COG4959 TraF Type IV secretory 99.7 7.6E-18 1.7E-22 145.2 10.6 108 201-308 53-169 (173)
12 COG0681 LepB Signal peptidase 99.6 7.4E-15 1.6E-19 126.2 12.5 135 149-304 8-144 (166)
13 TIGR02228 sigpep_I_arch signal 99.5 6.4E-14 1.4E-18 122.6 12.8 85 174-305 35-119 (158)
14 PF00717 Peptidase_S24: Peptid 99.2 2.6E-11 5.6E-16 90.5 6.5 57 174-242 1-57 (70)
15 cd06462 Peptidase_S24_S26 The 99.0 3.7E-09 8.1E-14 80.5 9.6 53 172-236 2-54 (84)
16 cd06529 S24_LexA-like Peptidas 98.5 2.9E-07 6.2E-12 70.1 7.3 56 173-242 3-58 (81)
17 COG2932 Predicted transcriptio 98.3 1.6E-06 3.4E-11 78.8 6.5 58 172-242 125-182 (214)
18 PRK10276 DNA polymerase V subu 98.1 5.1E-05 1.1E-09 64.7 10.9 48 172-233 53-101 (139)
19 PRK12423 LexA repressor; Provi 97.9 9.3E-05 2E-09 66.9 10.6 49 172-234 116-165 (202)
20 KOG3342 Signal peptidase I [In 97.9 1.8E-05 4E-10 68.9 5.0 53 172-234 50-102 (180)
21 PRK00215 LexA repressor; Valid 97.9 0.00012 2.6E-09 65.8 10.4 56 171-241 119-175 (205)
22 TIGR00498 lexA SOS regulatory 97.8 0.00019 4.2E-09 64.2 9.8 57 170-241 111-168 (199)
23 COG1974 LexA SOS-response tran 96.5 0.034 7.4E-07 50.8 10.9 55 172-240 114-169 (201)
24 COG0681 LepB Signal peptidase 89.1 0.55 1.2E-05 40.0 4.2 29 224-252 137-165 (166)
25 PLN02705 beta-amylase 54.7 36 0.00079 36.3 6.8 17 78-94 31-47 (681)
26 PF05257 CHAP: CHAP domain; I 49.2 35 0.00077 27.8 4.8 37 200-243 61-98 (124)
27 cd04712 BAH_DCM_I BAH, or Brom 48.6 1.2E+02 0.0025 25.7 8.0 95 201-311 5-102 (130)
28 PLN02705 beta-amylase 45.6 41 0.00088 36.0 5.5 13 228-240 247-259 (681)
29 COG2932 Predicted transcriptio 44.2 1.8E+02 0.0039 26.0 9.1 40 270-310 173-212 (214)
30 PRK00215 LexA repressor; Valid 43.3 1.8E+02 0.0039 25.8 8.8 34 273-309 170-203 (205)
31 PF06890 Phage_Mu_Gp45: Bacter 42.5 90 0.0019 27.7 6.5 41 193-242 66-109 (162)
32 smart00439 BAH Bromo adjacent 40.9 1.8E+02 0.0039 22.9 8.2 30 271-310 57-86 (120)
33 TIGR00008 infA translation ini 38.3 31 0.00066 26.4 2.5 11 186-196 47-57 (68)
34 TIGR02594 conserved hypothetic 37.7 78 0.0017 26.7 5.2 13 200-212 72-84 (129)
35 COG1097 RRP4 RNA-binding prote 37.3 56 0.0012 30.9 4.6 20 176-195 105-124 (239)
36 PF00238 Ribosomal_L14: Riboso 37.1 1.1E+02 0.0024 25.7 6.0 27 271-298 79-105 (122)
37 TIGR00498 lexA SOS regulatory 36.8 2.9E+02 0.0064 24.2 9.6 36 272-310 162-197 (199)
38 COG0361 InfA Translation initi 36.5 35 0.00076 26.6 2.6 22 184-208 47-68 (75)
39 TIGR01067 rplN_bact ribosomal 35.9 2.4E+02 0.0053 23.8 7.9 23 171-193 20-42 (122)
40 COG0093 RplN Ribosomal protein 32.4 3E+02 0.0066 23.4 7.7 15 285-299 92-106 (122)
41 cd04456 S1_IF1A_like S1_IF1A_l 31.6 43 0.00093 26.0 2.5 11 202-212 39-49 (78)
42 PF01176 eIF-1a: Translation i 31.5 33 0.00071 25.4 1.7 29 184-212 22-52 (65)
43 COG4079 Uncharacterized protei 31.3 83 0.0018 30.1 4.7 32 223-254 248-283 (293)
44 smart00652 eIF1a eukaryotic tr 30.8 41 0.00088 26.4 2.2 11 202-212 44-54 (83)
45 PF11101 DUF2884: Protein of u 30.1 61 0.0013 30.0 3.6 25 230-254 17-42 (229)
46 cd05793 S1_IF1A S1_IF1A: Trans 29.8 44 0.00096 25.8 2.3 10 202-211 39-48 (77)
47 cd04370 BAH BAH, or Bromo Adja 27.8 1.3E+02 0.0029 23.5 4.9 86 202-310 4-89 (123)
48 PRK10626 hypothetical protein; 27.7 64 0.0014 30.5 3.3 23 231-254 41-64 (239)
49 CHL00057 rpl14 ribosomal prote 27.6 2.5E+02 0.0054 23.7 6.6 23 171-193 20-42 (122)
50 PF10000 ACT_3: ACT domain; I 26.9 33 0.00071 26.3 1.1 18 178-195 12-29 (72)
51 PRK12442 translation initiatio 25.7 67 0.0015 25.7 2.6 8 204-211 49-56 (87)
52 PRK04012 translation initiatio 23.7 66 0.0014 26.3 2.3 9 203-211 61-69 (100)
53 PRK05483 rplN 50S ribosomal pr 23.5 4.5E+02 0.0097 22.2 7.4 15 285-299 92-106 (122)
54 COG3602 Uncharacterized protei 23.4 47 0.001 28.2 1.4 16 179-194 13-28 (134)
55 PRK09919 anti-adapter protein 22.4 83 0.0018 26.5 2.7 21 234-254 40-60 (114)
56 PF00278 Orn_DAP_Arg_deC: Pyri 21.7 1.4E+02 0.0031 23.5 4.0 31 182-214 65-95 (116)
57 KOG4146 Ubiquitin-like protein 21.3 1.2E+02 0.0027 24.7 3.4 37 173-213 56-97 (101)
58 PF14085 DUF4265: Domain of un 20.7 3.1E+02 0.0068 22.6 5.9 46 187-241 11-57 (117)
59 PF00498 FHA: FHA domain; Int 20.5 3.2E+02 0.0069 19.3 5.3 33 238-280 32-68 (68)
60 PF04790 Sarcoglycan_1: Sarcog 20.2 7E+02 0.015 23.7 8.8 32 151-182 17-48 (264)
61 cd04709 BAH_MTA BAH, or Bromo 20.1 1.5E+02 0.0032 26.3 4.0 23 286-308 84-106 (164)
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=6.9e-41 Score=292.58 Aligned_cols=153 Identities=37% Similarity=0.555 Sum_probs=136.5
Q ss_pred HHHHHHHHHHHHHHHHceeEeEEECCCCcccCCCCCCEEEEEeeeccCCCCCCCcEEEEeCCccccccccCCCccEEEEE
Q 021373 152 AKTVLAALVISLAFRSFVAEPRYIPSLSMYPTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRV 231 (313)
Q Consensus 152 ~~~lvv~ili~lll~~fv~~~~~V~g~SMePTL~~GD~VlV~K~~~~~~~p~rGDIVVF~~P~~~~~~~~~~~~~lVKRV 231 (313)
+..++++++++++++.|+++.+.|+|+||+|||+.||+|+++|..+....+++||+|+|+.|.+ .++.+||||
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 3466677788889999999999999999999999999999999988778999999999998764 567899999
Q ss_pred EeeCCCEEEEeCCEEEECCEEccccccccCCC--------CCCCCEEecCCcEEEecCCCCCCCCCCCCCccCCCCeEEE
Q 021373 232 VAKEGDVVEVREGKLIVNGVVRNEDYILEAPS--------YNMTPITVPENSVFVMGDNRNNSYDSHGAPPCQEYHRKIS 303 (313)
Q Consensus 232 iGlPGD~V~I~~g~lyINGk~l~e~y~~~~~~--------~~~~~~~VP~g~yfVLGDNr~~S~DSRyfG~Vp~~~I~Gk 303 (313)
+|+|||+|+++++.+||||+.+.++|...... ....+++||+|||||||||+++|+||||||+|++++|+||
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 99999999999999999999999987654311 2234679999999999999999999999999999999999
Q ss_pred EEEEeecC
Q 021373 304 ISLLASAK 311 (313)
Q Consensus 304 V~~~~~~~ 311 (313)
|.+++|+.
T Consensus 155 ~~~~~~p~ 162 (163)
T TIGR02227 155 VSFVFYPF 162 (163)
T ss_pred EEEEECCC
Confidence 99999985
No 2
>PRK10861 signal peptidase I; Provisional
Probab=100.00 E-value=2.6e-36 Score=289.36 Aligned_cols=155 Identities=33% Similarity=0.404 Sum_probs=130.0
Q ss_pred HHHHHHHHHHHHHHHHHceeEeEEECCCCcccCCCCCCEEEEEeeeccC------------CCCCCCcEEEEeCCccccc
Q 021373 151 DAKTVLAALVISLAFRSFVAEPRYIPSLSMYPTFDVGDRIVAEKVTYYF------------RKPCSNDIVIFKSPPVLQE 218 (313)
Q Consensus 151 ~~~~lvv~ili~lll~~fv~~~~~V~g~SMePTL~~GD~VlV~K~~~~~------------~~p~rGDIVVF~~P~~~~~ 218 (313)
++..++++++++++++.|+++++.|+|+||+|||..||+|+|+|++|++ ..|+|||||||+.|.+
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 3456677778888999999999999999999999999999999999864 5789999999999875
Q ss_pred cccCCCccEEEEEEeeCCCEEEEe--CCEEEECCEEcccc----------------------------------------
Q 021373 219 VGYTDDDVFIKRVVAKEGDVVEVR--EGKLIVNGVVRNED---------------------------------------- 256 (313)
Q Consensus 219 ~~~~~~~~lVKRViGlPGD~V~I~--~g~lyINGk~l~e~---------------------------------------- 256 (313)
++..+||||||+|||+|+++ ++.+||||+.+...
T Consensus 140 ----~~~~yIKRVIGlPGD~I~~~~~~~~l~iNg~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 215 (324)
T PRK10861 140 ----PKLDYIKRVVGLPGDKVTYDPVSKEVTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFQVPLN 215 (324)
T ss_pred ----CCCcEEEEeeecCCcEEEEEeCCCEEEEcCcccccccccccccccccccccccccccccccccccccccccccccc
Confidence 67789999999999999998 89999999742110
Q ss_pred -----------cccc----------CCC-------------CCCCCEEecCCcEEEecCCCCCCCCCCCCCccCCCCeEE
Q 021373 257 -----------YILE----------APS-------------YNMTPITVPENSVFVMGDNRNNSYDSHGAPPCQEYHRKI 302 (313)
Q Consensus 257 -----------y~~~----------~~~-------------~~~~~~~VP~g~yfVLGDNr~~S~DSRyfG~Vp~~~I~G 302 (313)
|... .+. ....+++||+|+|||||||+++|+||||||+||+++|+|
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 0000 000 013467999999999999999999999999999999999
Q ss_pred EEEEEeecCC
Q 021373 303 SISLLASAKD 312 (313)
Q Consensus 303 kV~~~~~~~~ 312 (313)
+|...++|-+
T Consensus 296 ~a~~i~~s~d 305 (324)
T PRK10861 296 KATAIWMSFE 305 (324)
T ss_pred EEEEEEEEcC
Confidence 9999998853
No 3
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=4.2e-33 Score=241.64 Aligned_cols=140 Identities=42% Similarity=0.576 Sum_probs=120.6
Q ss_pred HHHHHHHHHHHHHceeEeEEECCCCcccCCCC-CCEEEEEeeeccCCCCCCCcEEEEeCCccccccccCCCccEEEEEEe
Q 021373 155 VLAALVISLAFRSFVAEPRYIPSLSMYPTFDV-GDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVA 233 (313)
Q Consensus 155 lvv~ili~lll~~fv~~~~~V~g~SMePTL~~-GD~VlV~K~~~~~~~p~rGDIVVF~~P~~~~~~~~~~~~~lVKRViG 233 (313)
.+.-.|+......|+.++..++|.||+|||++ ||+++.+|+.+.++++++||||++..|.+ .++.+||||+|
T Consensus 18 ~~~~~~f~h~t~~yl~e~~~~~gpSM~PTl~~~gd~l~aEkls~~f~~~~~gDIVi~~sP~~-------~~~~~cKRIva 90 (176)
T KOG0171|consen 18 EIAYAAFTHVTHEYLGEFVMCSGPSMEPTLHDGGDVLLAEKLSYRFRKPQVGDIVIAKSPPD-------PKEHICKRIVA 90 (176)
T ss_pred HHHHHHHHHHHHHHhcceeeccCCCcCceecCCCcEEehhhhhHhhcCCCCCCEEEEeCCCC-------chhhhhheeec
Confidence 33444556666679999999999999998887 56666699999999999999999999986 67889999999
Q ss_pred eCCCEEEEeCCEEEECCEEccccccccCCCCCCCCEEecCCcEEEecCCCCCCCCCCCCCccCCCCeEEEEEEEeecC
Q 021373 234 KEGDVVEVREGKLIVNGVVRNEDYILEAPSYNMTPITVPENSVFVMGDNRNNSYDSHGAPPCQEYHRKISISLLASAK 311 (313)
Q Consensus 234 lPGD~V~I~~g~lyINGk~l~e~y~~~~~~~~~~~~~VP~g~yfVLGDNr~~S~DSRyfG~Vp~~~I~GkV~~~~~~~ 311 (313)
++||.|++.++.+.+|+.. |.+. .++.||+||+||+|||+.+|+|||+|||||..+|+||+++|+|+.
T Consensus 91 ~eGD~v~v~~~~~~~n~~~--e~~~--------~~i~VP~GhVfv~GDN~~nS~DSr~yGplP~glI~gRvv~r~Wp~ 158 (176)
T KOG0171|consen 91 MEGDLVEVHDGPLVVNDLV--EKFS--------TPIRVPEGHVFVEGDNRNNSLDSRNYGPLPMGLIQGRVVFRIWPP 158 (176)
T ss_pred cCCceEEEecCCcccchhh--hhcc--------ceeeccCceEEEecCCCCCcccccccCCCchhheeeeEEEEecCc
Confidence 9999999998888877643 2111 456899999999999999999999999999999999999999974
No 4
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=99.95 E-value=4.7e-27 Score=208.55 Aligned_cols=117 Identities=19% Similarity=0.154 Sum_probs=92.9
Q ss_pred EEEEeeeccCCCCCCCcEEEEeCCccccc-----ccc-CC------CccEEEEEEeeCCCEEEEeCCEEEECCEEccccc
Q 021373 190 IVAEKVTYYFRKPCSNDIVIFKSPPVLQE-----VGY-TD------DDVFIKRVVAKEGDVVEVREGKLIVNGVVRNEDY 257 (313)
Q Consensus 190 VlV~K~~~~~~~p~rGDIVVF~~P~~~~~-----~~~-~~------~~~lVKRViGlPGD~V~I~~g~lyINGk~l~e~y 257 (313)
+.++++.+....+++||+|+|+.|...+. .+| .. ...+||||+|+|||+|++++ .+||||+.+.++|
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 78888776567899999999998865321 111 11 24699999999999999985 8999999999987
Q ss_pred cccCCCC-----CCCCEEecCCcEEEecCCCCCCCCCCCCCccCCCCeEEEEEEEe
Q 021373 258 ILEAPSY-----NMTPITVPENSVFVMGDNRNNSYDSHGAPPCQEYHRKISISLLA 308 (313)
Q Consensus 258 ~~~~~~~-----~~~~~~VP~g~yfVLGDNr~~S~DSRyfG~Vp~~~I~GkV~~~~ 308 (313)
....... .....+||+|+|||||||. +|+||||||+|++++|+|+|...+
T Consensus 118 ~~~~~~~g~~l~~~~~~~vp~g~~fvlgd~~-~S~DSRy~G~V~~~~I~G~a~pi~ 172 (176)
T PRK13838 118 VRRRDGEGRPLTPFPGGVVPPGHLFLHSSFA-GSYDSRYFGPVPASGLLGLARPVL 172 (176)
T ss_pred cccccccCCcCCCCCccCcCCCeEEEECCCC-CCCcccccCcccHHHeEEEEEEEE
Confidence 6543221 1234589999999999985 899999999999999999998654
No 5
>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=99.94 E-value=1.9e-25 Score=197.43 Aligned_cols=132 Identities=22% Similarity=0.228 Sum_probs=97.1
Q ss_pred HceeEeEEECCCCcccCCCCCCEEEEEeeeccCCCCCCCcEEEEeCCccccc-----cc-cCCC------ccEEEEEEee
Q 021373 167 SFVAEPRYIPSLSMYPTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQE-----VG-YTDD------DVFIKRVVAK 234 (313)
Q Consensus 167 ~fv~~~~~V~g~SMePTL~~GD~VlV~K~~~~~~~p~rGDIVVF~~P~~~~~-----~~-~~~~------~~lVKRViGl 234 (313)
.|......-.++||-. |-+. +.+. ..++|||+|+|+.|.+... .+ +..+ ..+||||+|+
T Consensus 21 ~~~~~~~~N~T~S~P~----g~Y~-~~~~----~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRVigl 91 (171)
T TIGR02771 21 LYCVGARINTTKSLPL----GLYW-TTSS----KPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVLGL 91 (171)
T ss_pred cceeeEEEECCCCCcc----eEEE-eCCC----CCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEEEe
Confidence 3444444555666664 3333 3221 5899999999998864221 11 1122 3799999999
Q ss_pred CCCEEEEeCCEEEECCEEccccccccCC--C---CCCCCEEecCCcEEEecCCCCCCCCCCCCCccCCCCeEEEEEEEe
Q 021373 235 EGDVVEVREGKLIVNGVVRNEDYILEAP--S---YNMTPITVPENSVFVMGDNRNNSYDSHGAPPCQEYHRKISISLLA 308 (313)
Q Consensus 235 PGD~V~I~~g~lyINGk~l~e~y~~~~~--~---~~~~~~~VP~g~yfVLGDNr~~S~DSRyfG~Vp~~~I~GkV~~~~ 308 (313)
|||+|+++++.++|||+.+.+.+..... + ....+.+||+| ||+||||+.+|+||||||+|++++|+|||...+
T Consensus 92 pGD~V~i~~~~v~INg~~~~~~~~~~~~~~g~~l~~~~~~~vp~g-yf~lgdn~~~S~DSRy~G~V~~~~IiGk~~pl~ 169 (171)
T TIGR02771 92 PGDRVTVRADVVAINGQLLPYSKPLATDSSGRPLPPFPEGVIPPG-FFVVHDTSPTSFDSRYFGPISREQVIGRVKPLF 169 (171)
T ss_pred CCCEEEEECCEEEECCEEcccccccccccCCCccccCCCcEECCC-EEEECCCCCCCCcccccceecHHHeEEEEEEeE
Confidence 9999999999999999998876544221 1 12246799999 999999999999999999999999999998543
No 6
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=99.93 E-value=3.9e-25 Score=196.52 Aligned_cols=108 Identities=26% Similarity=0.342 Sum_probs=85.0
Q ss_pred CCCCCCcEEEEeCCccc-----ccccc------CCC-ccEEEEEEeeCCCEEEEeCCEEEECCEEccccccccCC--C--
Q 021373 200 RKPCSNDIVIFKSPPVL-----QEVGY------TDD-DVFIKRVVAKEGDVVEVREGKLIVNGVVRNEDYILEAP--S-- 263 (313)
Q Consensus 200 ~~p~rGDIVVF~~P~~~-----~~~~~------~~~-~~lVKRViGlPGD~V~I~~g~lyINGk~l~e~y~~~~~--~-- 263 (313)
..+++||+|+|+.|+.. .+.+| +++ ..+||||+|+|||+|+++++.+||||+.+.+....... +
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 47899999999987642 11122 122 37999999999999999999999999998654322211 1
Q ss_pred ---CCCCCEEecCCcEEEecCCCCCCCCCCCCCccCCCCeEEEEEEE
Q 021373 264 ---YNMTPITVPENSVFVMGDNRNNSYDSHGAPPCQEYHRKISISLL 307 (313)
Q Consensus 264 ---~~~~~~~VP~g~yfVLGDNr~~S~DSRyfG~Vp~~~I~GkV~~~ 307 (313)
.....++||+|+|||||||+++|+||||||+|++++|+|+|.-.
T Consensus 129 l~~~~~~~~~lp~g~~fvlgd~~~~S~DSRYfG~V~~~~I~G~~~Pl 175 (178)
T PRK13884 129 LPRYQANSYTLGESELLLMSDVSATSFDGRYFGPINRSQIKTVIRPV 175 (178)
T ss_pred ccccCCCceEECCCEEEEECCCCCCCCcccccCcccHHHEEEEEEEe
Confidence 22234699999999999999999999999999999999999754
No 7
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=99.92 E-value=2.6e-25 Score=192.90 Aligned_cols=120 Identities=32% Similarity=0.399 Sum_probs=104.9
Q ss_pred HHHHceeEeEEECCCCcccCCCCC------CEEEEEeeeccCCCCCCCcEEEEeCCccccccccCCCccEEEEEEeeCCC
Q 021373 164 AFRSFVAEPRYIPSLSMYPTFDVG------DRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAKEGD 237 (313)
Q Consensus 164 ll~~fv~~~~~V~g~SMePTL~~G------D~VlV~K~~~~~~~p~rGDIVVF~~P~~~~~~~~~~~~~lVKRViGlPGD 237 (313)
.+...+.....|.|.||.|||+.+ |+|+++|+.-..+.+.|||+|+|.+|.+ .++++||||+|++||
T Consensus 25 t~~DrV~~va~v~G~smqPtlnP~~~~~~~d~Vll~k~~v~n~~~~rGDiVvl~sP~~-------p~~~~iKRv~alegd 97 (174)
T KOG1568|consen 25 TFSDRVVHVAQVYGSSMQPTLNPTMNTNEKDTVLLRKWNVKNRKVSRGDIVVLKSPND-------PDKVIIKRVAALEGD 97 (174)
T ss_pred eeeeeEEEEeEEecCcCCCccCCCcccccccEEEEEeeccccceeccCCEEEEeCCCC-------hhheeeeeeeccccc
Confidence 344456778889999999999974 9999999875545688999999999987 889999999999999
Q ss_pred EEEEeCCEEEECCEEccccccccCCCCCCCCEEecCCcEEEecCCCCCCCCCCCCCccCCCCeEEEEEEEeec
Q 021373 238 VVEVREGKLIVNGVVRNEDYILEAPSYNMTPITVPENSVFVMGDNRNNSYDSHGAPPCQEYHRKISISLLASA 310 (313)
Q Consensus 238 ~V~I~~g~lyINGk~l~e~y~~~~~~~~~~~~~VP~g~yfVLGDNr~~S~DSRyfG~Vp~~~I~GkV~~~~~~ 310 (313)
++.-. .+....+.||+|||||.|||...|+|||.||||+...|.|||++..|+
T Consensus 98 ~~~t~--------------------~~k~~~v~vpkghcWVegDn~~hs~DSntFGPVS~gli~grai~ilwp 150 (174)
T KOG1568|consen 98 IMVTE--------------------DEKEEPVVVPKGHCWVEGDNQKHSYDSNTFGPVSTGLIVGRAIYILWP 150 (174)
T ss_pred EeccC--------------------CCCCCceecCCCcEEEecCCcccccccCccCCcchhheeeeEEEEEcC
Confidence 88742 244566799999999999999999999999999999999999999996
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=99.91 E-value=8.4e-26 Score=193.06 Aligned_cols=108 Identities=34% Similarity=0.455 Sum_probs=32.7
Q ss_pred CCCCCcEEEEeCCcccccc----cc-CCCccEEEEEEeeCCCEEEEeCCEEEECCEEccccccccCCCCCC----CCEEe
Q 021373 201 KPCSNDIVIFKSPPVLQEV----GY-TDDDVFIKRVVAKEGDVVEVREGKLIVNGVVRNEDYILEAPSYNM----TPITV 271 (313)
Q Consensus 201 ~p~rGDIVVF~~P~~~~~~----~~-~~~~~lVKRViGlPGD~V~I~~g~lyINGk~l~e~y~~~~~~~~~----~~~~V 271 (313)
.+++||+|+|+.|...... +| ..+..++|||+|+|||+|+++++.++|||+.+.+.+..+..+..+ ..++|
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 4899999999999754321 22 456699999999999999999999999999888776654433322 46799
Q ss_pred cCCcEEEecCCCCCCCCCCCCCccCCCCeEEEEEEEe
Q 021373 272 PENSVFVMGDNRNNSYDSHGAPPCQEYHRKISISLLA 308 (313)
Q Consensus 272 P~g~yfVLGDNr~~S~DSRyfG~Vp~~~I~GkV~~~~ 308 (313)
|+|+|||||||+.+|+||||||+|++++|+|+|...+
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 9999999999999999999999999999999998754
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=99.80 E-value=3.1e-19 Score=140.72 Aligned_cols=88 Identities=30% Similarity=0.436 Sum_probs=76.0
Q ss_pred EECCCCcccCCCCCCEEEEEeeeccCCCCCCCcEEEEeCCccccccccCCCccEEEEEEeeCCCEEEEeCCEEEECCEEc
Q 021373 174 YIPSLSMYPTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAKEGDVVEVREGKLIVNGVVR 253 (313)
Q Consensus 174 ~V~g~SMePTL~~GD~VlV~K~~~~~~~p~rGDIVVF~~P~~~~~~~~~~~~~lVKRViGlPGD~V~I~~g~lyINGk~l 253 (313)
.|.|+||+|||++||+|+|++.......+++||+|+|+.+.+ ++..++|||++++
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 589999999999999999998543334556899999998753 4689999999874
Q ss_pred cccccccCCCCCCCCEEecCCcEEEecCCCCCCCCCCCCCccCCCCeEEEEE
Q 021373 254 NEDYILEAPSYNMTPITVPENSVFVMGDNRNNSYDSHGAPPCQEYHRKISIS 305 (313)
Q Consensus 254 ~e~y~~~~~~~~~~~~~VP~g~yfVLGDNr~~S~DSRyfG~Vp~~~I~GkV~ 305 (313)
++++|++|||+..|.|||++|+|+..+|+|+|+
T Consensus 57 -------------------~~~~~l~~dN~~~~~d~~~~g~v~~~~I~G~v~ 89 (90)
T TIGR02754 57 -------------------DNGLFLLGDNPKASTDSRQLGPVPRSLLLGKVL 89 (90)
T ss_pred -------------------CCeEEEeCCCCCCCCcccccCCCcHHHEEEEEE
Confidence 356899999999999999999999999999986
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=99.76 E-value=4.5e-18 Score=132.31 Aligned_cols=84 Identities=43% Similarity=0.637 Sum_probs=74.9
Q ss_pred eEEECCCCcccCCCCCCEEEEEeeeccCCCCCCCcEEEEeCCccccccccCCCccEEEEEEeeCCCEEEEeCCEEEECCE
Q 021373 172 PRYIPSLSMYPTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAKEGDVVEVREGKLIVNGV 251 (313)
Q Consensus 172 ~~~V~g~SMePTL~~GD~VlV~K~~~~~~~p~rGDIVVF~~P~~~~~~~~~~~~~lVKRViGlPGD~V~I~~g~lyINGk 251 (313)
.+.|.|+||+|++..||+|++++....+..+++||+|+|+.+.. .+..++|||++
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 47899999999999999999998764434689999999998652 35789999998
Q ss_pred EccccccccCCCCCCCCEEecCCcEEEecCCCCCCCCCCCCCccCCCCeEEEE
Q 021373 252 VRNEDYILEAPSYNMTPITVPENSVFVMGDNRNNSYDSHGAPPCQEYHRKISI 304 (313)
Q Consensus 252 ~l~e~y~~~~~~~~~~~~~VP~g~yfVLGDNr~~S~DSRyfG~Vp~~~I~GkV 304 (313)
||+.|||..+|.|||+||+|+.++|+|++
T Consensus 57 ------------------------~~~~gDn~~ns~d~~~~g~~~~~~i~G~~ 85 (85)
T cd06530 57 ------------------------YFVLGDNRNNSLDSRYWGPVPEDDIVGKV 85 (85)
T ss_pred ------------------------EEEeeCCCCCCCccCCcCCCcHHHeEEeC
Confidence 99999999899999999999999999985
No 11
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.75 E-value=7.6e-18 Score=145.24 Aligned_cols=108 Identities=15% Similarity=0.182 Sum_probs=88.3
Q ss_pred CCCCCcEEEEeCCccc----ccccc-CCCccEEEEEEeeCCCEEEEeCCEEEECCEEccccccccCCCCCCC----CEEe
Q 021373 201 KPCSNDIVIFKSPPVL----QEVGY-TDDDVFIKRVVAKEGDVVEVREGKLIVNGVVRNEDYILEAPSYNMT----PITV 271 (313)
Q Consensus 201 ~p~rGDIVVF~~P~~~----~~~~~-~~~~~lVKRViGlPGD~V~I~~g~lyINGk~l~e~y~~~~~~~~~~----~~~V 271 (313)
.+++||+|+++.|... ++.+| +....++|||.|+|||+|++.++.|.|||+.+......+..+..+. .-.+
T Consensus 53 Pvt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq~Vci~~~~I~I~G~~v~~sl~~D~~GR~lp~~~gcR~l 132 (173)
T COG4959 53 PVTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQHVCITSQGIAIDGKPVAASLPVDRVGRALPRWQGCRYL 132 (173)
T ss_pred CcccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCCCcEEEecceEEECCEEeeeeccccccCCcCCcccCCcee
Confidence 4599999999999753 22344 5567899999999999999999999999999876555444443322 2248
Q ss_pred cCCcEEEecCCCCCCCCCCCCCccCCCCeEEEEEEEe
Q 021373 272 PENSVFVMGDNRNNSYDSHGAPPCQEYHRKISISLLA 308 (313)
Q Consensus 272 P~g~yfVLGDNr~~S~DSRyfG~Vp~~~I~GkV~~~~ 308 (313)
.++|+|+|+|..+.||||||||+||.++|+|.+.-.+
T Consensus 133 ~~~el~lL~~~~~~SfDsRYfGpipas~vig~aRPvw 169 (173)
T COG4959 133 APSELLLLTDRSSTSFDSRYFGPIPASQVIGVARPVW 169 (173)
T ss_pred cCCeEEEEeccCCcccccceecccCHHHcceeeeeee
Confidence 9999999999999999999999999999999987654
No 12
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=99.61 E-value=7.4e-15 Score=126.23 Aligned_cols=135 Identities=28% Similarity=0.373 Sum_probs=98.2
Q ss_pred HHHHHHHHHHHHHHHHH--HHceeEeEEECCCCcccCCCCCCEEEEEeeeccCCCCCCCcEEEEeCCccccccccCCCcc
Q 021373 149 SDDAKTVLAALVISLAF--RSFVAEPRYIPSLSMYPTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDV 226 (313)
Q Consensus 149 ~~~~~~lvv~ili~lll--~~fv~~~~~V~g~SMePTL~~GD~VlV~K~~~~~~~p~rGDIVVF~~P~~~~~~~~~~~~~ 226 (313)
..++..++.++++++++ +.|+++.+.|+|+||+|||+.||+|+++|..+....+..+|++.+. . ..+..
T Consensus 8 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~V~s~SM~Ptl~~GD~v~v~k~~~~~~~~~~~~~~~~~--~-------~~~~~ 78 (166)
T COG0681 8 LELISSLLIAIILALIIGVRTFVFEPVVVPSGSMEPTLNVGDRVLVKKFSYGFGKLKVPDIIVLP--A-------VVEGD 78 (166)
T ss_pred HHHHHHHHHHHHHhheeeeEEEEEEEEEECCCccccccccCCEEEEEeccccccCCccceeeecC--C-------CCCcc
Confidence 45566777777777777 8999999999999999999999999999999988888889888332 2 26778
Q ss_pred EEEEEEeeCCCEEEEeCCEEEECCEEccccccccCCCCCCCCEEecCCcEEEecCCCCCCCCCCCCCccCCCCeEEEE
Q 021373 227 FIKRVVAKEGDVVEVREGKLIVNGVVRNEDYILEAPSYNMTPITVPENSVFVMGDNRNNSYDSHGAPPCQEYHRKISI 304 (313)
Q Consensus 227 lVKRViGlPGD~V~I~~g~lyINGk~l~e~y~~~~~~~~~~~~~VP~g~yfVLGDNr~~S~DSRyfG~Vp~~~I~GkV 304 (313)
++||+++++||.|.++++..|+ +..+.+.+. .+..++.++.++....+.++|.++.......+.++
T Consensus 79 ~~kr~~~~~GD~i~~~~~~~~~-~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 144 (166)
T COG0681 79 LIKRVIGLRGDIVVFKDDRLYV-VPIIPRVYG-----------LVEKDNGKHLVDVIVNANSSRVFGIITKKDYIKRV 144 (166)
T ss_pred eEEEeccCCCCEEEEECCEEEe-ecccCcchh-----------hhhcccccccccccccccCccccccccccccccce
Confidence 9999999999999999999988 332322221 11111222445555566666666665555555555
No 13
>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=99.55 E-value=6.4e-14 Score=122.61 Aligned_cols=85 Identities=26% Similarity=0.310 Sum_probs=68.3
Q ss_pred EECCCCcccCCCCCCEEEEEeeeccCCCCCCCcEEEEeCCccccccccCCCccEEEEEEeeCCCEEEEeCCEEEECCEEc
Q 021373 174 YIPSLSMYPTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAKEGDVVEVREGKLIVNGVVR 253 (313)
Q Consensus 174 ~V~g~SMePTL~~GD~VlV~K~~~~~~~p~rGDIVVF~~P~~~~~~~~~~~~~lVKRViGlPGD~V~I~~g~lyINGk~l 253 (313)
.|.|+||+||+++||.+++++... .++++||+|+|+.|. +...++|||+++.++ + |
T Consensus 35 ~V~g~SM~Ptl~~GD~vlv~~~~~--~~~~~GDIVvf~~~~--------~~~~iihRVi~v~~~-----~------g--- 90 (158)
T TIGR02228 35 VVLSGSMEPTFNTGDLILVTGADP--NDIQVGDVITYKSPG--------FNTPVTHRVIEINNS-----G------G--- 90 (158)
T ss_pred EEcCCCCcCCccCCCEEEEEeccc--CCCCCCCEEEEEECC--------CCccEEEEEEEEECC-----C------C---
Confidence 399999999999999999998542 589999999999864 237899999998643 0 0
Q ss_pred cccccccCCCCCCCCEEecCCcEEEecCCCCCCCCCCCCCccCCCCeEEEEE
Q 021373 254 NEDYILEAPSYNMTPITVPENSVFVMGDNRNNSYDSHGAPPCQEYHRKISIS 305 (313)
Q Consensus 254 ~e~y~~~~~~~~~~~~~VP~g~yfVLGDNr~~S~DSRyfG~Vp~~~I~GkV~ 305 (313)
+-.|+..|||. ...| .++|..++|+|++.
T Consensus 91 -------------------~~~~~tkGDnN-~~~D---~~~v~~~~IiG~v~ 119 (158)
T TIGR02228 91 -------------------ELGFITKGDNN-PAPD---GEPVPSENVIGKYL 119 (158)
T ss_pred -------------------cEEEEEEecCC-CCCC---cccCCHHHEEEEEE
Confidence 01366779997 4556 68999999999998
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=99.22 E-value=2.6e-11 Score=90.45 Aligned_cols=57 Identities=30% Similarity=0.526 Sum_probs=46.6
Q ss_pred EECCCCcccCCCCCCEEEEEeeeccCCCCCCCcEEEEeCCccccccccCCCccEEEEEEeeCCCEEEEe
Q 021373 174 YIPSLSMYPTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAKEGDVVEVR 242 (313)
Q Consensus 174 ~V~g~SMePTL~~GD~VlV~K~~~~~~~p~rGDIVVF~~P~~~~~~~~~~~~~lVKRViGlPGD~V~I~ 242 (313)
+|.|+||+|+|++||+|++++.. .++.||+|+|..+.. +..++|||++.+|+.+.+.
T Consensus 1 ~V~GdSM~P~i~~Gd~v~v~~~~----~~~~gdivv~~~~~~--------~~~~iKrv~~~~~~~~~~~ 57 (70)
T PF00717_consen 1 RVEGDSMEPTIKDGDIVLVDPSS----EPKDGDIVVVKIDGD--------EELYIKRVVGEPGGIILIS 57 (70)
T ss_dssp EEESSTTGGTSSTTEEEEEEETS-------TTSEEEEEETTE--------ESEEEEEEEEETTEEEEE-
T ss_pred CeECcCcccCeeCCCEEEEEEcC----CCccCeEEEEEECCc--------eeeEEEEEEEeCCCEEEEe
Confidence 58899999999999999999864 889999999997431 1389999999999999987
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=98.99 E-value=3.7e-09 Score=80.50 Aligned_cols=53 Identities=32% Similarity=0.544 Sum_probs=44.9
Q ss_pred eEEECCCCcccCCCCCCEEEEEeeeccCCCCCCCcEEEEeCCccccccccCCCccEEEEEEeeCC
Q 021373 172 PRYIPSLSMYPTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAKEG 236 (313)
Q Consensus 172 ~~~V~g~SMePTL~~GD~VlV~K~~~~~~~p~rGDIVVF~~P~~~~~~~~~~~~~lVKRViGlPG 236 (313)
.+.|.|+||+|++..||.|++++.. ..++.||+|++..+ ++..++||+...++
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 3679999999999999999999864 24889999999973 23799999998876
No 16
>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=98.54 E-value=2.9e-07 Score=70.05 Aligned_cols=56 Identities=25% Similarity=0.402 Sum_probs=48.6
Q ss_pred EEECCCCcccCCCCCCEEEEEeeeccCCCCCCCcEEEEeCCccccccccCCCccEEEEEEeeCCCEEEEe
Q 021373 173 RYIPSLSMYPTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAKEGDVVEVR 242 (313)
Q Consensus 173 ~~V~g~SMePTL~~GD~VlV~K~~~~~~~p~rGDIVVF~~P~~~~~~~~~~~~~lVKRViGlPGD~V~I~ 242 (313)
++|.|+||+|+++.||.|++++.. .++.||+|++.. +++.++||+...+++.+.+.
T Consensus 3 ~~v~g~sM~p~i~~gd~lii~~~~----~~~~g~i~~~~~----------~~~~~ikr~~~~~~~~~~L~ 58 (81)
T cd06529 3 LRVKGDSMEPTIPDGDLVLVDPSD----TPRDGDIVVARL----------DGELTVKRLQRRGGGRLRLI 58 (81)
T ss_pred EEEECCCcCCccCCCCEEEEcCCC----CCCCCCEEEEEE----------CCEEEEEEEEECCCCcEEEE
Confidence 689999999999999999999764 589999999997 45789999999987766664
No 17
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=98.28 E-value=1.6e-06 Score=78.77 Aligned_cols=58 Identities=17% Similarity=0.375 Sum_probs=46.8
Q ss_pred eEEECCCCcccCCCCCCEEEEEeeeccCCCCCCCcEEEEeCCccccccccCCCccEEEEEEeeCCCEEEEe
Q 021373 172 PRYIPSLSMYPTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAKEGDVVEVR 242 (313)
Q Consensus 172 ~~~V~g~SMePTL~~GD~VlV~K~~~~~~~p~rGDIVVF~~P~~~~~~~~~~~~~lVKRViGlPGD~V~I~ 242 (313)
.+.|.|+||+|++++||.|+|+.-. ...+||.|++..- +++.+|||+...+|-.+.+.
T Consensus 125 ~i~V~GDSMeP~~~~Gd~ilVd~~~----~~~~gd~v~v~~~---------g~~~~VK~l~~~~~~~~~l~ 182 (214)
T COG2932 125 ALRVTGDSMEPTYEDGDTLLVDPGV----NTRRGDRVYVETD---------GGELYVKKLQREPGGLLRLV 182 (214)
T ss_pred EEEEeCCcccccccCCCEEEECCCC----ceeeCCEEEEEEe---------CCeEEEEEEEEecCCeEEEE
Confidence 4789999999999999999998753 5667886665541 56899999999988877543
No 18
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=98.05 E-value=5.1e-05 Score=64.73 Aligned_cols=48 Identities=21% Similarity=0.250 Sum_probs=40.3
Q ss_pred eEEECCCCcc-cCCCCCCEEEEEeeeccCCCCCCCcEEEEeCCccccccccCCCccEEEEEEe
Q 021373 172 PRYIPSLSMY-PTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVA 233 (313)
Q Consensus 172 ~~~V~g~SMe-PTL~~GD~VlV~K~~~~~~~p~rGDIVVF~~P~~~~~~~~~~~~~lVKRViG 233 (313)
.++|.|+||. |++.+||+++|++-. .++.||+|++.. ++...+||+.-
T Consensus 53 ~l~V~GdSM~~~~I~~GD~liVd~~~----~~~~Gdivv~~~----------~g~~~vKrl~~ 101 (139)
T PRK10276 53 FVKASGDSMIDAGISDGDLLIVDSAI----TASHGDIVIAAV----------DGEFTVKKLQL 101 (139)
T ss_pred EEEEecCCCCCCCCCCCCEEEEECCC----CCCCCCEEEEEE----------CCEEEEEEEEE
Confidence 4789999997 699999999999753 578899999875 56788999874
No 19
>PRK12423 LexA repressor; Provisional
Probab=97.92 E-value=9.3e-05 Score=66.91 Aligned_cols=49 Identities=22% Similarity=0.215 Sum_probs=41.2
Q ss_pred eEEECCCCcc-cCCCCCCEEEEEeeeccCCCCCCCcEEEEeCCccccccccCCCccEEEEEEee
Q 021373 172 PRYIPSLSMY-PTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAK 234 (313)
Q Consensus 172 ~~~V~g~SMe-PTL~~GD~VlV~K~~~~~~~p~rGDIVVF~~P~~~~~~~~~~~~~lVKRViGl 234 (313)
.+.|.|+||. |+|.+||+|+|++. ..++.||+|++.. ++..++||+.-.
T Consensus 116 ~l~V~GdSM~~~~i~~Gd~viv~~~----~~~~~Gdivv~~~----------~~~~~vKrl~~~ 165 (202)
T PRK12423 116 LLQVQGDSMIDDGILDGDLVGVHRS----PEARDGQIVVARL----------DGEVTIKRLERS 165 (202)
T ss_pred EEEEecCcCCCCCcCCCCEEEEeCC----CcCCCCCEEEEEE----------CCEEEEEEEEEe
Confidence 3789999997 79999999999974 3678899999986 567899998754
No 20
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=97.87 E-value=1.8e-05 Score=68.92 Aligned_cols=53 Identities=26% Similarity=0.300 Sum_probs=41.8
Q ss_pred eEEECCCCcccCCCCCCEEEEEeeeccCCCCCCCcEEEEeCCccccccccCCCccEEEEEEee
Q 021373 172 PRYIPSLSMYPTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAK 234 (313)
Q Consensus 172 ~~~V~g~SMePTL~~GD~VlV~K~~~~~~~p~rGDIVVF~~P~~~~~~~~~~~~~lVKRViGl 234 (313)
.+.|-++||||.++.||.++...... ...+.||||||+.+. .+...|+||+-+
T Consensus 50 iVVVLSgSMePaF~RGDlLfL~N~~~--~p~~vGdivVf~veg--------R~IPiVHRviK~ 102 (180)
T KOG3342|consen 50 IVVVLSGSMEPAFHRGDLLFLTNRNE--DPIRVGDIVVFKVEG--------REIPIVHRVIKQ 102 (180)
T ss_pred EEEEEcCCcCcccccccEEEEecCCC--CcceeccEEEEEECC--------ccCchhHHHHHH
Confidence 57788999999999999999975431 346789999999864 456788888754
No 21
>PRK00215 LexA repressor; Validated
Probab=97.87 E-value=0.00012 Score=65.77 Aligned_cols=56 Identities=21% Similarity=0.245 Sum_probs=43.8
Q ss_pred EeEEECCCCcc-cCCCCCCEEEEEeeeccCCCCCCCcEEEEeCCccccccccCCCccEEEEEEeeCCCEEEE
Q 021373 171 EPRYIPSLSMY-PTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAKEGDVVEV 241 (313)
Q Consensus 171 ~~~~V~g~SMe-PTL~~GD~VlV~K~~~~~~~p~rGDIVVF~~P~~~~~~~~~~~~~lVKRViGlPGD~V~I 241 (313)
..++|.|+||. |++.+||+|+|++. ..++.||+|++.. ++..+|||+.-. ++.+.+
T Consensus 119 ~~~~V~GdSM~~~~i~~Gd~v~v~~~----~~~~~G~ivv~~~----------~~~~~vKrl~~~-~~~~~L 175 (205)
T PRK00215 119 FLLRVRGDSMIDAGILDGDLVIVRKQ----QTARNGQIVVALI----------DDEATVKRFRRE-GGHIRL 175 (205)
T ss_pred EEEEEccCCCCCCCcCCCCEEEEeCC----CCCCCCCEEEEEE----------CCEEEEEEEEEe-CCEEEE
Confidence 34789999995 79999999999874 3678899999986 457899999755 333433
No 22
>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=97.76 E-value=0.00019 Score=64.17 Aligned_cols=57 Identities=23% Similarity=0.231 Sum_probs=44.8
Q ss_pred eEeEEECCCCcc-cCCCCCCEEEEEeeeccCCCCCCCcEEEEeCCccccccccCCCccEEEEEEeeCCCEEEE
Q 021373 170 AEPRYIPSLSMY-PTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAKEGDVVEV 241 (313)
Q Consensus 170 ~~~~~V~g~SMe-PTL~~GD~VlV~K~~~~~~~p~rGDIVVF~~P~~~~~~~~~~~~~lVKRViGlPGD~V~I 241 (313)
...++|.|+||. |++.+||+|++++. ..++.||+|++.. ++...|||+.-. |+.+.+
T Consensus 111 ~f~~~V~GdSM~~~~i~~Gd~v~v~~~----~~~~~G~ivvv~~----------~~~~~vKrl~~~-~~~i~L 168 (199)
T TIGR00498 111 VFLLKVMGDSMVDAGICDGDLLIVRSQ----KDARNGEIVAAMI----------DGEVTVKRFYKD-GTKVEL 168 (199)
T ss_pred EEEEEecCCCCCCCCCCCCCEEEEecC----CCCCCCCEEEEEE----------CCEEEEEEEEEE-CCEEEE
Confidence 345889999996 68999999999865 3788999999986 567899998744 443433
No 23
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=96.47 E-value=0.034 Score=50.81 Aligned_cols=55 Identities=20% Similarity=0.241 Sum_probs=42.2
Q ss_pred eEEECCCCcc-cCCCCCCEEEEEeeeccCCCCCCCcEEEEeCCccccccccCCCccEEEEEEeeCCCEEE
Q 021373 172 PRYIPSLSMY-PTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAKEGDVVE 240 (313)
Q Consensus 172 ~~~V~g~SMe-PTL~~GD~VlV~K~~~~~~~p~rGDIVVF~~P~~~~~~~~~~~~~lVKRViGlPGD~V~ 240 (313)
..+|.|+||. +.+.+||.|+|++. ...+.||||+.... ++...+||..-- |+.|.
T Consensus 114 ~L~V~GdSM~~~gi~dGDlvvV~~~----~~a~~GdiVvA~i~---------g~e~TvKrl~~~-g~~i~ 169 (201)
T COG1974 114 FLRVSGDSMIDAGILDGDLVVVDPT----EDAENGDIVVALID---------GEEATVKRLYRD-GNQIL 169 (201)
T ss_pred EEEecCCccccCcCCCCCEEEEcCC----CCCCCCCEEEEEcC---------CCcEEEEEEEEe-CCEEE
Confidence 3789999997 57888999999976 47889999999973 344788887644 33343
No 24
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=89.09 E-value=0.55 Score=39.95 Aligned_cols=29 Identities=31% Similarity=0.487 Sum_probs=23.6
Q ss_pred CccEEEEEEeeCCCEEEEeCCEEEECCEE
Q 021373 224 DDVFIKRVVAKEGDVVEVREGKLIVNGVV 252 (313)
Q Consensus 224 ~~~lVKRViGlPGD~V~I~~g~lyINGk~ 252 (313)
...++||+++++||.+...+..++++|+.
T Consensus 137 ~~~~~~~~~~~~gd~~~~~~~~~~~~g~~ 165 (166)
T COG0681 137 KKDYIKRVIGLPGDNILYTDDDLPINGKP 165 (166)
T ss_pred ccccccceEEeeccceeeccCceeecCCC
Confidence 35689999999999999985448888764
No 25
>PLN02705 beta-amylase
Probab=54.68 E-value=36 Score=36.30 Aligned_cols=17 Identities=12% Similarity=0.319 Sum_probs=10.4
Q ss_pred CCCCCCCCCCccccccc
Q 021373 78 FQHQNPRPLNPKNLLYR 94 (313)
Q Consensus 78 ~~~~~~~~~~~~~~~~~ 94 (313)
.+|+-|++-+|..+..+
T Consensus 31 ~~~~~~~~~~~~~~~~~ 47 (681)
T PLN02705 31 RNRNQPQSRRPRGFAAT 47 (681)
T ss_pred CCCCCCccCCCcchhhh
Confidence 56666777777555443
No 26
>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=49.24 E-value=35 Score=27.77 Aligned_cols=37 Identities=24% Similarity=0.318 Sum_probs=23.3
Q ss_pred CCCCCCcEEEEeCCccccccccCCCccEEEEEEee-CCCEEEEeC
Q 021373 200 RKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAK-EGDVVEVRE 243 (313)
Q Consensus 200 ~~p~rGDIVVF~~P~~~~~~~~~~~~~lVKRViGl-PGD~V~I~~ 243 (313)
..|+.||||+|..... ...=.|--|.++ .+++|.+.+
T Consensus 61 ~~P~~Gdivv~~~~~~-------~~~GHVaIV~~v~~~~~i~v~e 98 (124)
T PF05257_consen 61 STPQPGDIVVWDSGSG-------GGYGHVAIVESVNDGGTITVIE 98 (124)
T ss_dssp S---TTEEEEEEECTT-------TTT-EEEEEEEE-TTSEEEEEE
T ss_pred cccccceEEEeccCCC-------CCCCeEEEEEEECCCCEEEEEE
Confidence 5899999999952111 233467888888 888888764
No 27
>cd04712 BAH_DCM_I BAH, or Bromo Adjacent Homology domain, as present in DNA (Cytosine-5)-methyltransferases (DCM) 1. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=48.62 E-value=1.2e+02 Score=25.71 Aligned_cols=95 Identities=11% Similarity=-0.041 Sum_probs=44.1
Q ss_pred CCCCCcEEEEeCCccccccc-c--CCCccEEEEEEeeCCCEEEEeCCEEEECCEEccccccccCCCCCCCCEEecCCcEE
Q 021373 201 KPCSNDIVIFKSPPVLQEVG-Y--TDDDVFIKRVVAKEGDVVEVREGKLIVNGVVRNEDYILEAPSYNMTPITVPENSVF 277 (313)
Q Consensus 201 ~p~rGDIVVF~~P~~~~~~~-~--~~~~~lVKRViGlPGD~V~I~~g~lyINGk~l~e~y~~~~~~~~~~~~~VP~g~yf 277 (313)
.++.||+|.++.+....... . .....+|-||.-+.-+. ++..++.|+-+-.+ ......-.-.+.|+|
T Consensus 5 ~i~vGD~V~v~~d~~~~~~~~~~~~~~~~~i~~V~~~~e~~----~g~~~~h~~W~yrp------~eTv~g~~~~~~ElF 74 (130)
T cd04712 5 TIRVGDVVSVERDDADSTTKWNDDHRWLPLVQFVEYMKKGS----DGSKMFHGRWLYRG------CDTVLGNYANERELF 74 (130)
T ss_pred EEeCCCEEEEcCCCCCccccccccccccceEEEEEEeeecC----CCceEEEEEEEEcc------hhccccccCCCceEE
Confidence 46679999888754310000 0 00134677776553221 33334433322110 111000034567777
Q ss_pred EecCCCCCCCCCCCCCccCCCCeEEEEEEEeecC
Q 021373 278 VMGDNRNNSYDSHGAPPCQEYHRKISISLLASAK 311 (313)
Q Consensus 278 VLGDNr~~S~DSRyfG~Vp~~~I~GkV~~~~~~~ 311 (313)
+...-...+.++. ...|+|++...+.+.
T Consensus 75 LSd~c~~~~~~~~------~~~I~~k~~V~~~~~ 102 (130)
T cd04712 75 LTNECTCLELDLL------STEIKGVHKVDWSGT 102 (130)
T ss_pred Eeccccccccccc------cceeEEEEEEEEecC
Confidence 7533222222222 558999988876554
No 28
>PLN02705 beta-amylase
Probab=45.55 E-value=41 Score=35.95 Aligned_cols=13 Identities=8% Similarity=0.102 Sum_probs=7.8
Q ss_pred EEEEEeeCCCEEE
Q 021373 228 IKRVVAKEGDVVE 240 (313)
Q Consensus 228 VKRViGlPGD~V~ 240 (313)
|.=-|.+|=|+|.
T Consensus 247 VpVyVMLPLd~V~ 259 (681)
T PLN02705 247 VPVYVMLAVGIIN 259 (681)
T ss_pred eeEEEEeecceec
Confidence 4444666766664
No 29
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=44.22 E-value=1.8e+02 Score=26.04 Aligned_cols=40 Identities=5% Similarity=-0.101 Sum_probs=24.6
Q ss_pred EecCCcEEEecCCCCCCCCCCCCCccCCCCeEEEEEEEeec
Q 021373 270 TVPENSVFVMGDNRNNSYDSHGAPPCQEYHRKISISLLASA 310 (313)
Q Consensus 270 ~VP~g~yfVLGDNr~~S~DSRyfG~Vp~~~I~GkV~~~~~~ 310 (313)
..+.|.+.|+.+|++..- -+.+-.-..=.|+|+|+....+
T Consensus 173 ~~~~~~~~l~S~N~~~~~-~~~~~~~~~v~iIgrVv~~~~~ 212 (214)
T COG2932 173 REPGGLLRLVSLNPDYYP-DEIFSEDDDVEIIGRVVWVSRL 212 (214)
T ss_pred EecCCeEEEEeCCCCCCc-ccccCccceEEEEEEEEEEeee
Confidence 577888889999984322 2222111112489999987654
No 30
>PRK00215 LexA repressor; Validated
Probab=43.26 E-value=1.8e+02 Score=25.76 Aligned_cols=34 Identities=12% Similarity=0.050 Sum_probs=21.1
Q ss_pred CCcEEEecCCCCCCCCCCCCCccCCCCeEEEEEEEee
Q 021373 273 ENSVFVMGDNRNNSYDSHGAPPCQEYHRKISISLLAS 309 (313)
Q Consensus 273 ~g~yfVLGDNr~~S~DSRyfG~Vp~~~I~GkV~~~~~ 309 (313)
.|.+++..||.+ ++......= .-.|+|+|+..+.
T Consensus 170 ~~~~~L~s~Np~--y~~~~~~~~-~~~IiG~Vv~~~r 203 (205)
T PRK00215 170 GGHIRLEPENPA--YEPIIVDPD-RVTIEGKVVGLIR 203 (205)
T ss_pred CCEEEEEcCCCC--CCCEEeCCC-cEEEEEEEEEEEE
Confidence 567888888874 233222110 3579999988765
No 31
>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=42.49 E-value=90 Score=27.67 Aligned_cols=41 Identities=15% Similarity=0.333 Sum_probs=27.2
Q ss_pred EeeeccCCCCCCCcEEEEeCCccccccccCCCccEEEE---EEeeCCCEEEEe
Q 021373 193 EKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKR---VVAKEGDVVEVR 242 (313)
Q Consensus 193 ~K~~~~~~~p~rGDIVVF~~P~~~~~~~~~~~~~lVKR---ViGlPGD~V~I~ 242 (313)
+...|+...++.||+++|... +...++|| |+.+.++.+++.
T Consensus 66 ~d~~yR~~~L~~GEvalY~~~---------G~~I~L~~~G~ii~~~~~~~~v~ 109 (162)
T PF06890_consen 66 EDRRYRPKGLKPGEVALYDDE---------GQKIHLKRDGRIIEVTCKTVTVN 109 (162)
T ss_pred CCccccccCCCCCcEEEEcCC---------CCEEEEEecceEEeccCceEEEe
Confidence 344455566889999999852 34455665 666777777765
No 32
>smart00439 BAH Bromo adjacent homology domain.
Probab=40.85 E-value=1.8e+02 Score=22.91 Aligned_cols=30 Identities=13% Similarity=0.121 Sum_probs=20.1
Q ss_pred ecCCcEEEecCCCCCCCCCCCCCccCCCCeEEEEEEEeec
Q 021373 271 VPENSVFVMGDNRNNSYDSHGAPPCQEYHRKISISLLASA 310 (313)
Q Consensus 271 VP~g~yfVLGDNr~~S~DSRyfG~Vp~~~I~GkV~~~~~~ 310 (313)
.-++|+|..... -.|+.+.|+|++.....+
T Consensus 57 ~~~~Elf~s~~~----------~~i~~~~I~~kc~V~~~~ 86 (120)
T smart00439 57 FDKNEVFLSDEY----------DTVPLSDIIGKCNVLSKS 86 (120)
T ss_pred CCCcceEEEccC----------ccCChHHeeeEEEEEEcc
Confidence 346777754421 368889999998876554
No 33
>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=38.28 E-value=31 Score=26.37 Aligned_cols=11 Identities=27% Similarity=0.434 Sum_probs=4.9
Q ss_pred CCCEEEEEeee
Q 021373 186 VGDRIVAEKVT 196 (313)
Q Consensus 186 ~GD~VlV~K~~ 196 (313)
.||.|.|....
T Consensus 47 ~GD~V~Ve~sp 57 (68)
T TIGR00008 47 PGDKVKVELSP 57 (68)
T ss_pred CCCEEEEEECc
Confidence 34444444433
No 34
>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=37.69 E-value=78 Score=26.73 Aligned_cols=13 Identities=23% Similarity=0.329 Sum_probs=11.0
Q ss_pred CCCCCCcEEEEeC
Q 021373 200 RKPCSNDIVIFKS 212 (313)
Q Consensus 200 ~~p~rGDIVVF~~ 212 (313)
..++.||||+|+.
T Consensus 72 ~~p~~GDiv~f~~ 84 (129)
T TIGR02594 72 SKPAYGCIAVKRR 84 (129)
T ss_pred CCCCccEEEEEEC
Confidence 4689999999985
No 35
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=37.31 E-value=56 Score=30.87 Aligned_cols=20 Identities=30% Similarity=0.489 Sum_probs=16.3
Q ss_pred CCCCcccCCCCCCEEEEEee
Q 021373 176 PSLSMYPTFDVGDRIVAEKV 195 (313)
Q Consensus 176 ~g~SMePTL~~GD~VlV~K~ 195 (313)
....|.|.|+.||.|...-.
T Consensus 105 ~~~~~r~~l~vGD~v~AkV~ 124 (239)
T COG1097 105 AEKDLRPFLNVGDLVYAKVV 124 (239)
T ss_pred cccccccccccCCEEEEEEE
Confidence 36789999999999977543
No 36
>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=37.13 E-value=1.1e+02 Score=25.68 Aligned_cols=27 Identities=15% Similarity=0.235 Sum_probs=19.8
Q ss_pred ecCCcEEEecCCCCCCCCCCCCCccCCC
Q 021373 271 VPENSVFVMGDNRNNSYDSHGAPPCQEY 298 (313)
Q Consensus 271 VP~g~yfVLGDNr~~S~DSRyfG~Vp~~ 298 (313)
..+|.+-++.++. +-..+|-+|||+.+
T Consensus 79 F~~Na~VLln~~~-~p~GtrI~Gpv~~e 105 (122)
T PF00238_consen 79 FDDNAVVLLNKKG-NPLGTRIFGPVPRE 105 (122)
T ss_dssp ESSEEEEEEETTS-SBSSSSBCSEEEHH
T ss_pred eCCccEEEEcCCC-CEeeeEEEeeehHH
Confidence 4456666777775 67889999999865
No 37
>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=36.80 E-value=2.9e+02 Score=24.24 Aligned_cols=36 Identities=8% Similarity=-0.081 Sum_probs=21.5
Q ss_pred cCCcEEEecCCCCCCCCCCCCCccCCCCeEEEEEEEeec
Q 021373 272 PENSVFVMGDNRNNSYDSHGAPPCQEYHRKISISLLASA 310 (313)
Q Consensus 272 P~g~yfVLGDNr~~S~DSRyfG~Vp~~~I~GkV~~~~~~ 310 (313)
..+.+++..+|++. .-..... ..=.|+|+|+..+..
T Consensus 162 ~~~~i~L~s~N~~y--~~i~~~~-~~~~IiG~Vv~~~r~ 197 (199)
T TIGR00498 162 DGTKVELKPENPEF--DPIVLNA-EDVTILGKVVGVIRN 197 (199)
T ss_pred ECCEEEEEcCCCCC--cCCcCCC-CcEEEEEEEEEEEEe
Confidence 35678888888732 1111110 124799999987754
No 38
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=36.47 E-value=35 Score=26.59 Aligned_cols=22 Identities=27% Similarity=0.353 Sum_probs=10.1
Q ss_pred CCCCCEEEEEeeeccCCCCCCCcEE
Q 021373 184 FDVGDRIVAEKVTYYFRKPCSNDIV 208 (313)
Q Consensus 184 L~~GD~VlV~K~~~~~~~p~rGDIV 208 (313)
|.+||.|+|.-..| ...+|||+
T Consensus 47 I~~GD~V~Ve~~~~---d~~kg~I~ 68 (75)
T COG0361 47 ILPGDVVLVELSPY---DLTKGRIV 68 (75)
T ss_pred eCCCCEEEEEeccc---ccccccEE
Confidence 33455555554442 23445543
No 39
>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=35.86 E-value=2.4e+02 Score=23.75 Aligned_cols=23 Identities=26% Similarity=0.043 Sum_probs=15.0
Q ss_pred EeEEECCCCcccCCCCCCEEEEE
Q 021373 171 EPRYIPSLSMYPTFDVGDRIVAE 193 (313)
Q Consensus 171 ~~~~V~g~SMePTL~~GD~VlV~ 193 (313)
..+.|.|.+..+.-..||.+++.
T Consensus 20 ~cI~v~~~~~~~~a~iGD~I~vs 42 (122)
T TIGR01067 20 QCIKVLGGSRRRYATVGDVIVVV 42 (122)
T ss_pred EEEEEeCCCCCCccccCCEEEEE
Confidence 34455566666777778877665
No 40
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=32.41 E-value=3e+02 Score=23.38 Aligned_cols=15 Identities=7% Similarity=-0.075 Sum_probs=10.3
Q ss_pred CCCCCCCCCccCCCC
Q 021373 285 NSYDSHGAPPCQEYH 299 (313)
Q Consensus 285 ~S~DSRyfG~Vp~~~ 299 (313)
.-.-+|.||||.+|.
T Consensus 92 ~P~GtrI~GPVaREl 106 (122)
T COG0093 92 EPRGTRIFGPVAREL 106 (122)
T ss_pred CcccceEecchhHHH
Confidence 445678888887764
No 41
>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=31.61 E-value=43 Score=26.03 Aligned_cols=11 Identities=18% Similarity=0.223 Sum_probs=6.2
Q ss_pred CCCCcEEEEeC
Q 021373 202 PCSNDIVIFKS 212 (313)
Q Consensus 202 p~rGDIVVF~~ 212 (313)
+++||+|++..
T Consensus 39 I~~GD~VlV~~ 49 (78)
T cd04456 39 IKRGDFLIVDP 49 (78)
T ss_pred EcCCCEEEEEe
Confidence 44566666653
No 42
>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=31.48 E-value=33 Score=25.43 Aligned_cols=29 Identities=14% Similarity=0.014 Sum_probs=13.2
Q ss_pred CCCCCEEEEEeeec--cCCCCCCCcEEEEeC
Q 021373 184 FDVGDRIVAEKVTY--YFRKPCSNDIVIFKS 212 (313)
Q Consensus 184 L~~GD~VlV~K~~~--~~~~p~rGDIVVF~~ 212 (313)
+.+|..+++.-... ..--+++||+|++..
T Consensus 22 ~~dg~~~l~~i~gK~r~~iwI~~GD~V~V~~ 52 (65)
T PF01176_consen 22 CEDGEERLARIPGKFRKRIWIKRGDFVLVEP 52 (65)
T ss_dssp ETTSEEEEEEE-HHHHTCC---TTEEEEEEE
T ss_pred eCCCCEEEEEeccceeeeEecCCCCEEEEEe
Confidence 44555555542221 111356788887774
No 43
>COG4079 Uncharacterized protein conserved in archaea [Function unknown]
Probab=31.28 E-value=83 Score=30.06 Aligned_cols=32 Identities=22% Similarity=0.368 Sum_probs=25.8
Q ss_pred CCccEEEEEEe----eCCCEEEEeCCEEEECCEEcc
Q 021373 223 DDDVFIKRVVA----KEGDVVEVREGKLIVNGVVRN 254 (313)
Q Consensus 223 ~~~~lVKRViG----lPGD~V~I~~g~lyINGk~l~ 254 (313)
++...+++|-+ .|||.|.++++.+.|+|+.+.
T Consensus 248 Pg~~v~m~v~~~g~~~pGd~vvv~dg~mki~G~d~k 283 (293)
T COG4079 248 PGEEVVMAVEGNGEVEPGDRVVVKDGVMKIDGKDLK 283 (293)
T ss_pred CCceEEEEEccCCccCCCCEEEEecCceEeccccce
Confidence 45667777765 589999999999999998653
No 44
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=30.75 E-value=41 Score=26.44 Aligned_cols=11 Identities=27% Similarity=0.344 Sum_probs=6.5
Q ss_pred CCCCcEEEEeC
Q 021373 202 PCSNDIVIFKS 212 (313)
Q Consensus 202 p~rGDIVVF~~ 212 (313)
+++||+|++..
T Consensus 44 I~~GD~VlVe~ 54 (83)
T smart00652 44 IRRGDIVLVDP 54 (83)
T ss_pred EcCCCEEEEEe
Confidence 45666666653
No 45
>PF11101 DUF2884: Protein of unknown function (DUF2884); InterPro: IPR021307 Some members in this bacterial family of proteins are annotated as YggN which currently has no known function.
Probab=30.12 E-value=61 Score=30.02 Aligned_cols=25 Identities=28% Similarity=0.581 Sum_probs=20.3
Q ss_pred EEEeeCCCEEEEe-CCEEEECCEEcc
Q 021373 230 RVVAKEGDVVEVR-EGKLIVNGVVRN 254 (313)
Q Consensus 230 RViGlPGD~V~I~-~g~lyINGk~l~ 254 (313)
+|++..|+.+.|. +|.+||||+.+.
T Consensus 17 ~v~~~~~~~~~I~~~g~L~i~G~~v~ 42 (229)
T PF11101_consen 17 EVVQASGEKLRIDPDGNLFINGKKVS 42 (229)
T ss_pred EEEeCCCceEEEcCCCcEEECCEEcc
Confidence 4566777889995 899999999874
No 46
>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=29.77 E-value=44 Score=25.85 Aligned_cols=10 Identities=30% Similarity=0.361 Sum_probs=5.6
Q ss_pred CCCCcEEEEe
Q 021373 202 PCSNDIVIFK 211 (313)
Q Consensus 202 p~rGDIVVF~ 211 (313)
+.+||+|++.
T Consensus 39 I~~GD~V~Ve 48 (77)
T cd05793 39 INEGDIVLVA 48 (77)
T ss_pred EcCCCEEEEE
Confidence 3456666655
No 47
>cd04370 BAH BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.
Probab=27.80 E-value=1.3e+02 Score=23.53 Aligned_cols=86 Identities=12% Similarity=-0.050 Sum_probs=42.3
Q ss_pred CCCCcEEEEeCCccccccccCCCccEEEEEEeeCCCEEEEeCCEEEECCEEccccccccCCCCCCCCEEecCCcEEEecC
Q 021373 202 PCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAKEGDVVEVREGKLIVNGVVRNEDYILEAPSYNMTPITVPENSVFVMGD 281 (313)
Q Consensus 202 p~rGDIVVF~~P~~~~~~~~~~~~~lVKRViGlPGD~V~I~~g~lyINGk~l~e~y~~~~~~~~~~~~~VP~g~yfVLGD 281 (313)
++.||.|.+..+... .....+|-||..+--+. ++..++.++-.-.+.-.. . ......-++|+|+..+
T Consensus 4 y~vgd~V~v~~~~~~-----~~~~~~i~~I~~i~~~~----~~~~~~~v~wf~rp~e~~--~--~~~~~~~~~Elf~s~~ 70 (123)
T cd04370 4 YEVGDSVYVEPDDSI-----KSDPPYIARIEELWEDT----NGSKQVKVRWFYRPEETP--K--GLSPFALRRELFLSDH 70 (123)
T ss_pred EecCCEEEEecCCcC-----CCCCCEEEEEeeeeECC----CCCEEEEEEEEEchhHhc--c--ccccccccceeEEecC
Confidence 456787777764310 02457788887663321 233333333221000000 0 0000245567777433
Q ss_pred CCCCCCCCCCCCccCCCCeEEEEEEEeec
Q 021373 282 NRNNSYDSHGAPPCQEYHRKISISLLASA 310 (313)
Q Consensus 282 Nr~~S~DSRyfG~Vp~~~I~GkV~~~~~~ 310 (313)
. -.|+.+.|.|++.....+
T Consensus 71 ~----------~~i~v~~I~gkc~V~~~~ 89 (123)
T cd04370 71 L----------DEIPVESIIGKCKVLFVS 89 (123)
T ss_pred c----------cccCHHHhccccEEEech
Confidence 2 367888888888776654
No 48
>PRK10626 hypothetical protein; Provisional
Probab=27.72 E-value=64 Score=30.45 Aligned_cols=23 Identities=26% Similarity=0.537 Sum_probs=17.3
Q ss_pred EEeeCCCEEEEe-CCEEEECCEEcc
Q 021373 231 VVAKEGDVVEVR-EGKLIVNGVVRN 254 (313)
Q Consensus 231 ViGlPGD~V~I~-~g~lyINGk~l~ 254 (313)
|++..|+ +.|. +|.|||||+.+.
T Consensus 41 V~~~sg~-l~I~~dg~L~inGk~v~ 64 (239)
T PRK10626 41 VVGASGN-LVISPDGNVMRNGKQLS 64 (239)
T ss_pred EEecCCc-eEEcCCCCEEECCEEec
Confidence 4455676 6776 779999999874
No 49
>CHL00057 rpl14 ribosomal protein L14
Probab=27.63 E-value=2.5e+02 Score=23.73 Aligned_cols=23 Identities=22% Similarity=0.067 Sum_probs=14.0
Q ss_pred EeEEECCCCcccCCCCCCEEEEE
Q 021373 171 EPRYIPSLSMYPTFDVGDRIVAE 193 (313)
Q Consensus 171 ~~~~V~g~SMePTL~~GD~VlV~ 193 (313)
..+.|.+.+..+.-..||.+++.
T Consensus 20 ~cI~v~~~~~~~~a~vGD~Ivvs 42 (122)
T CHL00057 20 MCIRVLGASNRKYAHIGDVIIAV 42 (122)
T ss_pred EEEEEeCCCCCccccCCCEEEEE
Confidence 33445565566666777777664
No 50
>PF10000 ACT_3: ACT domain; InterPro: IPR018717 This domain has no known function.; PDB: 1ZVP_C.
Probab=26.88 E-value=33 Score=26.29 Aligned_cols=18 Identities=22% Similarity=0.388 Sum_probs=12.3
Q ss_pred CCcccCCCCCCEEEEEee
Q 021373 178 LSMYPTFDVGDRIVAEKV 195 (313)
Q Consensus 178 ~SMePTL~~GD~VlV~K~ 195 (313)
.||+|.|++|++|++.-.
T Consensus 12 ~~m~P~L~~~~yVF~t~~ 29 (72)
T PF10000_consen 12 ASMSPELNPGEYVFCTVP 29 (72)
T ss_dssp ST-EEEE-SS-EEEEEE-
T ss_pred hhCCcEeCCCCEEEEEec
Confidence 489999999999999754
No 51
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=25.72 E-value=67 Score=25.75 Aligned_cols=8 Identities=25% Similarity=0.409 Sum_probs=3.8
Q ss_pred CCcEEEEe
Q 021373 204 SNDIVIFK 211 (313)
Q Consensus 204 rGDIVVF~ 211 (313)
.||.|.+.
T Consensus 49 ~GD~V~VE 56 (87)
T PRK12442 49 AGDRVTLE 56 (87)
T ss_pred CCCEEEEE
Confidence 45554444
No 52
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=23.67 E-value=66 Score=26.26 Aligned_cols=9 Identities=33% Similarity=0.493 Sum_probs=4.6
Q ss_pred CCCcEEEEe
Q 021373 203 CSNDIVIFK 211 (313)
Q Consensus 203 ~rGDIVVF~ 211 (313)
.+||+|++.
T Consensus 61 ~~GD~VlVe 69 (100)
T PRK04012 61 REGDVVIVA 69 (100)
T ss_pred cCCCEEEEE
Confidence 345555554
No 53
>PRK05483 rplN 50S ribosomal protein L14; Validated
Probab=23.47 E-value=4.5e+02 Score=22.19 Aligned_cols=15 Identities=7% Similarity=-0.075 Sum_probs=9.9
Q ss_pred CCCCCCCCCccCCCC
Q 021373 285 NSYDSHGAPPCQEYH 299 (313)
Q Consensus 285 ~S~DSRyfG~Vp~~~ 299 (313)
+-.-+|-+|||+++.
T Consensus 92 ~p~GTrI~Gpv~~el 106 (122)
T PRK05483 92 EPRGTRIFGPVAREL 106 (122)
T ss_pred CEeEeEEeccchHHH
Confidence 345567788887654
No 54
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.41 E-value=47 Score=28.18 Aligned_cols=16 Identities=31% Similarity=0.389 Sum_probs=14.3
Q ss_pred CcccCCCCCCEEEEEe
Q 021373 179 SMYPTFDVGDRIVAEK 194 (313)
Q Consensus 179 SMePTL~~GD~VlV~K 194 (313)
||.|.|.+||+|+..-
T Consensus 13 smtPeL~~G~yVfcT~ 28 (134)
T COG3602 13 SMTPELLDGDYVFCTV 28 (134)
T ss_pred hcCccccCCceEEEEe
Confidence 7999999999998764
No 55
>PRK09919 anti-adapter protein IraM; Provisional
Probab=22.38 E-value=83 Score=26.47 Aligned_cols=21 Identities=10% Similarity=0.207 Sum_probs=19.1
Q ss_pred eCCCEEEEeCCEEEECCEEcc
Q 021373 234 KEGDVVEVREGKLIVNGVVRN 254 (313)
Q Consensus 234 lPGD~V~I~~g~lyINGk~l~ 254 (313)
.|||.+...+.+|.|||++++
T Consensus 40 ~pG~~i~~~~~gvliNdk~~p 60 (114)
T PRK09919 40 PPGSIITPVKSGVLLNDKPYP 60 (114)
T ss_pred CCCCEEEEcCCeEEECCcEeE
Confidence 589999999999999999865
No 56
>PF00278 Orn_DAP_Arg_deC: Pyridoxal-dependent decarboxylase, C-terminal sheet domain; InterPro: IPR022643 These enzymes are collectively known as group IV decarboxylases []. Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities [, ]. Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC [], to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region []. This entry represents the C-terminal region of the Orn/DAP/Arg decarboxylases.; GO: 0003824 catalytic activity; PDB: 1TWI_B 1TUF_A 3MT1_A 3N2B_C 2O0T_A 1HKW_A 1HKV_A 3VAB_A 3N2O_A 7ODC_A ....
Probab=21.66 E-value=1.4e+02 Score=23.54 Aligned_cols=31 Identities=26% Similarity=0.376 Sum_probs=20.3
Q ss_pred cCCCCCCEEEEEeeeccCCCCCCCcEEEEeCCc
Q 021373 182 PTFDVGDRIVAEKVTYYFRKPCSNDIVIFKSPP 214 (313)
Q Consensus 182 PTL~~GD~VlV~K~~~~~~~p~rGDIVVF~~P~ 214 (313)
||...+|++.-+..-. .+++.||+++|..-.
T Consensus 65 ptC~~~D~i~~~~~lP--~~l~~GD~l~f~~~G 95 (116)
T PF00278_consen 65 PTCDSGDVIARDVMLP--KELEVGDWLVFENMG 95 (116)
T ss_dssp SSSSTTSEEEEEEEEE--STTTTT-EEEESS-S
T ss_pred CCcCCCceEeeeccCC--CCCCCCCEEEEecCc
Confidence 6777889886433221 278999999998643
No 57
>KOG4146 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=21.33 E-value=1.2e+02 Score=24.68 Aligned_cols=37 Identities=19% Similarity=0.279 Sum_probs=26.6
Q ss_pred EEECCCCcccCCCCCCEEEEEeeeccC-----CCCCCCcEEEEeCC
Q 021373 173 RYIPSLSMYPTFDVGDRIVAEKVTYYF-----RKPCSNDIVIFKSP 213 (313)
Q Consensus 173 ~~V~g~SMePTL~~GD~VlV~K~~~~~-----~~p~rGDIVVF~~P 213 (313)
+.+.++|..| |-.+++++....+ -.++.||.|+|-+.
T Consensus 56 lFi~~gsvrp----Gii~lINd~DWEllekedy~ledgD~ivfiST 97 (101)
T KOG4146|consen 56 LFIHHGSVRP----GIIVLINDMDWELLEKEDYPLEDGDHIVFIST 97 (101)
T ss_pred eEeeCCcCcC----cEEEEEeccchhhhcccccCcccCCEEEEEEe
Confidence 5578888887 5568888766432 25678999999763
No 58
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=20.74 E-value=3.1e+02 Score=22.55 Aligned_cols=46 Identities=17% Similarity=0.416 Sum_probs=31.0
Q ss_pred CCEEEEEeeeccCCCCCCCcEEEEeCCccccccccCCCccEEEEEEeeCCC-EEEE
Q 021373 187 GDRIVAEKVTYYFRKPCSNDIVIFKSPPVLQEVGYTDDDVFIKRVVAKEGD-VVEV 241 (313)
Q Consensus 187 GD~VlV~K~~~~~~~p~rGDIVVF~~P~~~~~~~~~~~~~lVKRViGlPGD-~V~I 241 (313)
+|...+....+....+..||+|.+... ++.+.+.+++.-.|- ++++
T Consensus 11 ~~~y~l~n~Pf~a~glA~gDvV~~~~~---------~g~~~~~~~v~~sGnsTiRv 57 (117)
T PF14085_consen 11 DDTYRLDNIPFFAYGLALGDVVRAEPD---------DGELWFQKVVESSGNSTIRV 57 (117)
T ss_pred CCEEEEEecccccCCCCCCCEEEEEeC---------CCeEEEEEEEecCCCEEEEE
Confidence 566677777666678899999999963 355666666555554 4443
No 59
>PF00498 FHA: FHA domain; InterPro: IPR000253 The forkhead-associated (FHA) domain [] is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich, which sometimes contain small helical insertions between the loops connecting the strands []. To date, genes encoding FHA-containing proteins have been identified in eubacterial and eukaryotic but not archaeal genomes. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes - DNA repair, signal transduction, vesicular transport and protein degradation are just a few examples.; GO: 0005515 protein binding; PDB: 1LGQ_B 1LGP_A 2CSW_A 2PIE_A 3FM8_A 3MDB_B 3GQS_B 1UHT_A 1WLN_A 3POA_A ....
Probab=20.50 E-value=3.2e+02 Score=19.28 Aligned_cols=33 Identities=15% Similarity=0.290 Sum_probs=20.6
Q ss_pred EEEEe----CCEEEECCEEccccccccCCCCCCCCEEecCCcEEEec
Q 021373 238 VVEVR----EGKLIVNGVVRNEDYILEAPSYNMTPITVPENSVFVMG 280 (313)
Q Consensus 238 ~V~I~----~g~lyINGk~l~e~y~~~~~~~~~~~~~VP~g~yfVLG 280 (313)
.+.+. .+.++|||+.+.. ..++.|..|..+.+|
T Consensus 32 ~~~i~d~~s~ngt~vng~~l~~----------~~~~~L~~gd~i~~G 68 (68)
T PF00498_consen 32 QFYIEDLGSTNGTFVNGQRLGP----------GEPVPLKDGDIIRFG 68 (68)
T ss_dssp EEEEEESSSSS-EEETTEEESS----------TSEEEE-TTEEEEET
T ss_pred eEEEEeCCCCCcEEECCEEcCC----------CCEEECCCCCEEEcC
Confidence 45554 3789999998864 224567777777665
No 60
>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=20.18 E-value=7e+02 Score=23.74 Aligned_cols=32 Identities=16% Similarity=0.104 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHHHceeEeEEECCCCccc
Q 021373 151 DAKTVLAALVISLAFRSFVAEPRYIPSLSMYP 182 (313)
Q Consensus 151 ~~~~lvv~ili~lll~~fv~~~~~V~g~SMeP 182 (313)
++..+++.+++-+++..+++...++..+.|..
T Consensus 17 ~vllL~il~iiNL~LTiwIl~Vl~~~~~Gm~~ 48 (264)
T PF04790_consen 17 FVLLLFILAIINLALTIWILKVLRFSSNGMGS 48 (264)
T ss_pred HHHHHHHHHHHHHHHHhhhheeeecccCcccc
Confidence 33344444455566777888889998888886
No 61
>cd04709 BAH_MTA BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=20.07 E-value=1.5e+02 Score=26.27 Aligned_cols=23 Identities=13% Similarity=-0.009 Sum_probs=18.4
Q ss_pred CCCCCCCCccCCCCeEEEEEEEe
Q 021373 286 SYDSHGAPPCQEYHRKISISLLA 308 (313)
Q Consensus 286 S~DSRyfG~Vp~~~I~GkV~~~~ 308 (313)
=|=|++.-.+|.+.|.||...+.
T Consensus 84 LF~S~~~d~~p~~~IrGKC~V~~ 106 (164)
T cd04709 84 LFLSRQVETLPATHIRGKCSVTL 106 (164)
T ss_pred eEEecccccccHHHeeeeEEEEE
Confidence 34577888999999999987654
Done!