Query 030087
Match_columns 183
No_of_seqs 186 out of 1173
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 08:19:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030087.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030087hhsearch_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 2.2E-37 4.7E-42 244.0 14.9 135 7-149 1-163 (163)
2 KOG0171 Mitochondrial inner me 100.0 6.8E-35 1.5E-39 226.9 10.6 136 18-158 23-168 (176)
3 KOG1568 Mitochondrial inner me 100.0 2.6E-33 5.7E-38 217.6 13.2 133 24-161 27-164 (174)
4 PRK10861 signal peptidase I; P 100.0 1.1E-32 2.5E-37 237.5 16.2 127 19-150 73-306 (324)
5 PRK13838 conjugal transfer pil 99.9 1.9E-22 4.2E-27 161.0 13.3 91 49-145 39-172 (176)
6 PRK13884 conjugal transfer pep 99.9 4E-22 8.6E-27 159.5 13.5 104 26-145 27-176 (178)
7 TIGR02771 TraF_Ti conjugative 99.9 3.7E-22 8E-27 158.7 13.2 105 25-145 21-169 (171)
8 TIGR02754 sod_Ni_protease nick 99.9 1.2E-21 2.5E-26 139.6 10.2 89 32-143 2-90 (90)
9 PF10502 Peptidase_S26: Signal 99.8 2.9E-22 6.2E-27 154.2 2.3 81 61-145 21-137 (138)
10 cd06530 S26_SPase_I The S26 Ty 99.8 1.1E-19 2.3E-24 127.9 9.2 84 30-141 2-85 (85)
11 TIGR02228 sigpep_I_arch signal 99.7 3.3E-17 7.1E-22 128.8 12.8 86 32-143 35-120 (158)
12 COG0681 LepB Signal peptidase 99.6 4.9E-14 1.1E-18 109.5 11.8 129 5-141 8-144 (166)
13 COG4959 TraF Type IV secretory 99.5 1.5E-14 3.3E-19 112.0 6.7 90 48-145 44-169 (173)
14 PF00717 Peptidase_S24: Peptid 99.3 2E-11 4.4E-16 82.2 7.3 57 32-95 1-57 (70)
15 cd06462 Peptidase_S24_S26 The 99.2 9.9E-11 2.2E-15 80.8 9.2 83 30-141 2-84 (84)
16 cd06529 S24_LexA-like Peptidas 99.0 6.8E-09 1.5E-13 71.4 9.0 62 30-117 2-63 (81)
17 COG2932 Predicted transcriptio 98.9 2E-08 4.4E-13 82.0 10.8 90 29-148 124-213 (214)
18 KOG3342 Signal peptidase I [In 98.9 1.8E-08 4E-13 78.3 9.2 90 30-144 50-146 (180)
19 PRK10276 DNA polymerase V subu 98.7 2.1E-07 4.5E-12 71.4 11.2 86 28-147 51-137 (139)
20 PRK00215 LexA repressor; Valid 98.6 5.7E-07 1.2E-11 72.8 11.4 87 27-147 117-204 (205)
21 TIGR00498 lexA SOS regulatory 98.6 8.3E-07 1.8E-11 71.5 11.8 88 27-148 110-198 (199)
22 PRK12423 LexA repressor; Provi 98.6 6.8E-07 1.5E-11 72.6 11.3 86 29-147 115-201 (202)
23 COG1974 LexA SOS-response tran 97.8 0.00047 1E-08 56.3 11.8 89 27-148 111-200 (201)
24 PRK00364 groES co-chaperonin G 86.6 5.2 0.00011 28.7 7.3 92 42-141 3-94 (95)
25 COG0234 GroS Co-chaperonin Gro 82.1 6.8 0.00015 28.4 6.2 74 42-115 3-88 (96)
26 PRK14533 groES co-chaperonin G 80.9 12 0.00025 26.8 7.1 86 42-141 3-89 (91)
27 PTZ00414 10 kDa heat shock pro 79.9 15 0.00032 26.8 7.4 27 40-69 10-36 (100)
28 cd00320 cpn10 Chaperonin 10 Kd 78.7 12 0.00025 26.7 6.5 91 42-140 2-92 (93)
29 TIGR02594 conserved hypothetic 77.1 14 0.00031 27.8 7.0 40 60-117 72-111 (129)
30 COG0681 LepB Signal peptidase 72.7 5.1 0.00011 30.4 3.6 13 61-73 84-96 (166)
31 PF00166 Cpn10: Chaperonin 10 71.7 8.7 0.00019 27.2 4.4 91 43-141 3-93 (93)
32 PF09935 DUF2167: Protein of u 67.2 1.2 2.6E-05 37.4 -1.0 73 101-182 16-89 (239)
33 COG0093 RplN Ribosomal protein 56.7 83 0.0018 23.7 7.4 26 106-136 81-106 (122)
34 PF05257 CHAP: CHAP domain; I 56.0 48 0.001 24.1 6.0 37 60-96 61-98 (124)
35 cd04714 BAH_BAHCC1 BAH, or Bro 55.5 29 0.00062 25.7 4.7 28 61-88 3-30 (121)
36 TIGR00008 infA translation ini 52.1 16 0.00036 24.7 2.6 20 45-68 47-66 (68)
37 PF10000 ACT_3: ACT domain; I 51.3 9.3 0.0002 26.1 1.3 18 36-54 12-29 (72)
38 COG0361 InfA Translation initi 50.5 18 0.00039 25.0 2.7 22 42-68 47-68 (75)
39 PF14118 YfzA: YfzA-like prote 50.1 13 0.00029 26.7 2.0 35 4-48 10-44 (94)
40 cd04717 BAH_polybromo BAH, or 48.4 41 0.00089 24.6 4.6 26 62-87 4-29 (121)
41 PF00238 Ribosomal_L14: Riboso 48.4 65 0.0014 24.1 5.7 87 28-135 19-105 (122)
42 PF01176 eIF-1a: Translation i 43.9 25 0.00053 23.2 2.5 12 61-72 41-52 (65)
43 COG3602 Uncharacterized protei 42.5 16 0.00035 27.5 1.6 17 36-53 12-28 (134)
44 cd04456 S1_IF1A_like S1_IF1A_l 42.1 28 0.0006 24.0 2.6 10 62-71 39-48 (78)
45 cd04709 BAH_MTA BAH, or Bromo 41.7 1E+02 0.0022 24.3 6.1 25 123-147 84-108 (164)
46 cd05793 S1_IF1A S1_IF1A: Trans 40.0 29 0.00063 23.9 2.4 10 62-71 39-48 (77)
47 smart00652 eIF1a eukaryotic tr 39.3 30 0.00065 24.1 2.5 10 62-71 44-53 (83)
48 CHL00057 rpl14 ribosomal prote 38.7 1.7E+02 0.0037 22.0 7.9 85 28-136 19-106 (122)
49 cd04721 BAH_plant_1 BAH, or Br 36.8 98 0.0021 23.3 5.1 27 60-88 6-32 (130)
50 TIGR01067 rplN_bact ribosomal 35.7 1.9E+02 0.0041 21.7 7.9 85 28-136 19-106 (122)
51 smart00002 PLP Myelin proteoli 34.6 10 0.00022 25.1 -0.5 19 123-141 23-41 (60)
52 COG1097 RRP4 RNA-binding prote 34.5 69 0.0015 27.0 4.3 77 34-117 105-195 (239)
53 PF06890 Phage_Mu_Gp45: Bacter 33.4 2.3E+02 0.0051 22.3 6.9 37 58-96 71-110 (162)
54 PRK04012 translation initiatio 33.2 42 0.00091 24.3 2.5 11 62-72 60-70 (100)
55 PRK12442 translation initiatio 32.6 52 0.0011 23.4 2.8 19 46-68 50-68 (87)
56 PF01426 BAH: BAH domain; Int 31.8 50 0.0011 23.4 2.8 27 62-88 3-29 (119)
57 PF07039 DUF1325: SGF29 tudor- 31.2 1.1E+02 0.0025 23.0 4.7 52 63-114 1-60 (130)
58 smart00439 BAH Bromo adjacent 30.9 95 0.0021 21.9 4.1 17 131-147 70-86 (120)
59 cd04760 BAH_Dnmt1_I BAH, or Br 28.7 2.6E+02 0.0056 21.1 7.2 24 126-149 64-87 (124)
60 PF10377 ATG11: Autophagy-rela 28.3 2.6E+02 0.0056 21.0 7.0 34 77-111 89-122 (129)
61 PF14085 DUF4265: Domain of un 28.1 2.3E+02 0.005 20.7 5.8 40 46-88 11-50 (117)
62 PF13124 DUF3963: Protein of u 27.6 1.1E+02 0.0023 18.3 3.0 17 3-19 15-31 (40)
63 cd04712 BAH_DCM_I BAH, or Brom 26.8 2.7E+02 0.0059 20.8 8.5 79 60-149 4-103 (130)
64 cd06555 ASCH_PF0470_like ASC-1 26.6 1.9E+02 0.004 21.3 5.0 28 59-87 29-56 (109)
65 cd05792 S1_eIF1AD_like S1_eIF1 25.7 61 0.0013 22.5 2.1 11 62-72 39-49 (78)
66 KOG4146 Ubiquitin-like protein 23.3 1.6E+02 0.0036 21.3 4.0 37 31-72 56-96 (101)
67 PF15057 DUF4537: Domain of un 22.6 1.3E+02 0.0027 22.5 3.5 28 60-87 54-81 (124)
68 PHA02141 hypothetical protein 22.4 84 0.0018 22.4 2.3 22 2-23 6-27 (105)
69 PF09285 Elong-fact-P_C: Elong 21.2 2.2E+02 0.0048 18.4 4.0 38 36-83 19-56 (56)
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=2.2e-37 Score=244.00 Aligned_cols=135 Identities=26% Similarity=0.438 Sum_probs=115.7
Q ss_pred HHHHHHHHHHHHHHHhhhceeEEEEEEeCCCCcccccCCCcEEEEEecCCCCCCCCCcCeEEEEecCCCCCccEEEEEEE
Q 030087 7 WFRYIANKLEYSVSISWKGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAA 86 (183)
Q Consensus 7 wl~~~~~~i~i~v~i~~~~~~~~~~~V~g~SM~PtL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~~~~vKRVia 86 (183)
|+..++.++++++ +++.|+++.+.|+|+||+|||+ .||+|+++|+.+ ...++++||+|+|+.|.+.++.++|||+|
T Consensus 1 ~~~~~~~~~~~~~--~i~~~~~~~~~v~g~SM~Ptl~-~Gd~vlv~k~~~-~~~~~~rGDiVvf~~~~~~~~~~iKRVig 76 (163)
T TIGR02227 1 LILSLLIAILLAL--LIRTFVFFPYKIPGGSMEPTLK-EGDRILVNKFAY-GTSDPKRGDIVVFKDPDDNKNIYVKRVIG 76 (163)
T ss_pred CHHHHHHHHHHHH--HHHhhEEEEEEECCcccccchh-CCCEEEEEEeEc-CCCCCCCCcEEEEecCCCCCceeEEEEEe
Confidence 4555555554444 4588999999999999999999 899999999865 35789999999999987777899999999
Q ss_pred EcCceEEecCCC----------------------------CCcccccCCeEEEEeCCCCCCCCCCCCCCccccccCCCeE
Q 030087 87 IEGYEMVSTDEK----------------------------DEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIV 138 (183)
Q Consensus 87 ~pGD~V~~~~~~----------------------------~~~~~vp~g~~~vlGDn~~~~~~~S~DSR~~G~V~~~~I~ 138 (183)
+|||+|+++++. ..+++||+|+||++|||+. +|.|||+||+|++++|+
T Consensus 77 ~pGd~v~i~~~~l~vNg~~~~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~~fvlGDnr~----~S~DSR~~G~V~~~~I~ 152 (163)
T TIGR02227 77 LPGDKVEFRDGKLYINGKKIDEPYLKPNGSLDTSGFNTTDFKPVTVPPGHYFVLGDNRD----NSLDSRYFGFVPIDDII 152 (163)
T ss_pred cCCCEEEEECCEEEECCEECcccccccccccccccccccccCceEECCCCEEEECCCCC----CCcccCCcCcCCHHHeE
Confidence 999999986530 1235899999999999998 89999999999999999
Q ss_pred EEEEEEEecCC
Q 030087 139 GRAIYCLRTAV 149 (183)
Q Consensus 139 Gkv~~~~~p~~ 149 (183)
||+.+++||++
T Consensus 153 Gk~~~~~~p~~ 163 (163)
T TIGR02227 153 GKVSFVFYPFD 163 (163)
T ss_pred EEEEEEECCCC
Confidence 99999999974
No 2
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.8e-35 Score=226.87 Aligned_cols=136 Identities=26% Similarity=0.399 Sum_probs=119.3
Q ss_pred HHHHhhhceeEEEEEEeCCCCcccccCCCcEEEEEecCCCCCCCCCcCeEEEEecCCCCCccEEEEEEEEcCceEEecCC
Q 030087 18 SVSISWKGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDE 97 (183)
Q Consensus 18 ~v~i~~~~~~~~~~~V~g~SM~PtL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~~~~vKRVia~pGD~V~~~~~ 97 (183)
+++.+...|++++..++|.||+|||++.||+++.+|+++ .++.+++||||++..|.++.+.++|||+|++||.+.+.++
T Consensus 23 ~f~h~t~~yl~e~~~~~gpSM~PTl~~~gd~l~aEkls~-~f~~~~~gDIVi~~sP~~~~~~~cKRIva~eGD~v~v~~~ 101 (176)
T KOG0171|consen 23 AFTHVTHEYLGEFVMCSGPSMEPTLHDGGDVLLAEKLSY-RFRKPQVGDIVIAKSPPDPKEHICKRIVAMEGDLVEVHDG 101 (176)
T ss_pred HHHHHHHHHhcceeeccCCCcCceecCCCcEEehhhhhH-hhcCCCCCCEEEEeCCCCchhhhhheeeccCCceEEEecC
Confidence 344445679999999999999999997778787799987 5788999999999999999999999999999997776543
Q ss_pred C----------CCcccccCCeEEEEeCCCCCCCCCCCCCCccccccCCCeEEEEEEEEecCCCCCCcccCC
Q 030087 98 K----------DEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNSN 158 (183)
Q Consensus 98 ~----------~~~~~vp~g~~~vlGDn~~~~~~~S~DSR~~G~V~~~~I~Gkv~~~~~p~~~~~~~~~~~ 158 (183)
. ..+++||+||+||+|||++ +|.|||+|||+|...|+||+++++||+++.+...-..
T Consensus 102 ~~~~n~~~e~~~~~i~VP~GhVfv~GDN~~----nS~DSr~yGplP~glI~gRvv~r~Wp~s~~~~~~~~~ 168 (176)
T KOG0171|consen 102 PLVVNDLVEKFSTPIRVPEGHVFVEGDNRN----NSLDSRNYGPLPMGLIQGRVVFRIWPPSRVSGLILHW 168 (176)
T ss_pred CcccchhhhhccceeeccCceEEEecCCCC----CcccccccCCCchhheeeeEEEEecCchhcceeeecc
Confidence 2 2457999999999999999 9999999999999999999999999999998776444
No 3
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=2.6e-33 Score=217.65 Aligned_cols=133 Identities=39% Similarity=0.647 Sum_probs=119.9
Q ss_pred hceeEEEEEEeCCCCcccccCC-----CcEEEEEecCCCCCCCCCcCeEEEEecCCCCCccEEEEEEEEcCceEEecCCC
Q 030087 24 KGKLTYLYGNKGDQMAPVMGGL-----GGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEK 98 (183)
Q Consensus 24 ~~~~~~~~~V~g~SM~PtL~~~-----GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~~~~vKRVia~pGD~V~~~~~~ 98 (183)
...+.....|.|.||.|||+|. .|+||+.|+... ...+.|||+|+|..|.++++.+||||+|++||.+...+..
T Consensus 27 ~DrV~~va~v~G~smqPtlnP~~~~~~~d~Vll~k~~v~-n~~~~rGDiVvl~sP~~p~~~~iKRv~alegd~~~t~~~k 105 (174)
T KOG1568|consen 27 SDRVVHVAQVYGSSMQPTLNPTMNTNEKDTVLLRKWNVK-NRKVSRGDIVVLKSPNDPDKVIIKRVAALEGDIMVTEDEK 105 (174)
T ss_pred eeeEEEEeEEecCcCCCccCCCcccccccEEEEEeeccc-cceeccCCEEEEeCCCChhheeeeeeecccccEeccCCCC
Confidence 3567788999999999999973 399999998652 3568999999999999999999999999999999998888
Q ss_pred CCcccccCCeEEEEeCCCCCCCCCCCCCCccccccCCCeEEEEEEEEecCCCCCCcccCCCCC
Q 030087 99 DEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNSNDSM 161 (183)
Q Consensus 99 ~~~~~vp~g~~~vlGDn~~~~~~~S~DSR~~G~V~~~~I~Gkv~~~~~p~~~~~~~~~~~~~~ 161 (183)
.+++.||+|||||+|||.. .|+|||.||||+...|.|||+.++||+.|++.+.+.-.+.
T Consensus 106 ~~~v~vpkghcWVegDn~~----hs~DSntFGPVS~gli~grai~ilwpP~R~~~~~~~~~~~ 164 (174)
T KOG1568|consen 106 EEPVVVPKGHCWVEGDNQK----HSYDSNTFGPVSTGLIVGRAIYILWPPVRWQRLDKESPGR 164 (174)
T ss_pred CCceecCCCcEEEecCCcc----cccccCccCCcchhheeeeEEEEEcChHHhhhhcccCCcc
Confidence 8999999999999999998 9999999999999999999999999999999887655443
No 4
>PRK10861 signal peptidase I; Provisional
Probab=100.00 E-value=1.1e-32 Score=237.46 Aligned_cols=127 Identities=22% Similarity=0.352 Sum_probs=110.5
Q ss_pred HHHhhhceeEEEEEEeCCCCcccccCCCcEEEEEecCCCC-----------CCCCCcCeEEEEecCCCCCccEEEEEEEE
Q 030087 19 VSISWKGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAAD-----------PKRVSVGDVVVMKDPEKSDNYIVRRLAAI 87 (183)
Q Consensus 19 v~i~~~~~~~~~~~V~g~SM~PtL~~~GD~Vlv~k~~~~~-----------~~~~~rGDIVvf~~p~~~~~~~vKRVia~ 87 (183)
++++++.|+++++.|+|.||+|||. .||+|+++|++|.. ...++|||||+|+.|.+++..+||||+|+
T Consensus 73 i~~~ir~fv~~~~~Ips~SM~PTL~-~GD~IlVnK~~yg~~~p~~~~~~~~~~~p~RGDIVVF~~P~~~~~~yIKRVIGl 151 (324)
T PRK10861 73 IVLIVRSFIYEPFQIPSGSMMPTLL-IGDFILVEKFAYGIKDPITQTTLIETGHPKRGDIVVFKYPEDPKLDYIKRVVGL 151 (324)
T ss_pred HHHHHHhhEEEEEEECCCcCcCccc-CCCEEEEEEeecCccCccccccccccCCCCCCCEEEEecCCCCCCcEEEEeeec
Confidence 3445589999999999999999999 89999999998631 35799999999999988888999999999
Q ss_pred cCceEEec--------CCC-------------------------------------------------------------
Q 030087 88 EGYEMVST--------DEK------------------------------------------------------------- 98 (183)
Q Consensus 88 pGD~V~~~--------~~~------------------------------------------------------------- 98 (183)
|||+|+++ ++.
T Consensus 152 PGD~I~~~~~~~~l~iNg~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~l 231 (324)
T PRK10861 152 PGDKVTYDPVSKEVTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFQVPLNETKENGIRLSERKETL 231 (324)
T ss_pred CCcEEEEEeCCCEEEEcCccccccccccccccccccccccccccccccccccccccccccccccccccccccceeEEEec
Confidence 99999984 110
Q ss_pred ---------------------------CCcccccCCeEEEEeCCCCCCCCCCCCCCccccccCCCeEEEEEEEEecCCC
Q 030087 99 ---------------------------DEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVD 150 (183)
Q Consensus 99 ---------------------------~~~~~vp~g~~~vlGDn~~~~~~~S~DSR~~G~V~~~~I~Gkv~~~~~p~~~ 150 (183)
..+++||+|+||++|||++ +|+||||||+||.++|+|+|.+++++++.
T Consensus 232 ~~~~h~i~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~yf~mgdnr~----~S~DSRy~G~Vp~~~i~G~a~~i~~s~d~ 306 (324)
T PRK10861 232 GDVTHRILTVPGAQDQVGMYYQQPGQPLATWVVPPGQYFMMGDNRD----NSADSRYWGFVPEANLVGKATAIWMSFEK 306 (324)
T ss_pred CCccceeeecCCcccccccccccCCCcCceEEECCCeEEEeCCCCC----CCcccCcccccCHHHcEEEEEEEEEEcCC
Confidence 0123789999999999999 99999999999999999999999999863
No 5
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=99.89 E-value=1.9e-22 Score=160.98 Aligned_cols=91 Identities=26% Similarity=0.357 Sum_probs=71.8
Q ss_pred EEEEecCCCCCCCCCcCeEEEEecCCCC-------------------CccEEEEEEEEcCceEEecCC------------
Q 030087 49 LLVRKLPAADPKRVSVGDVVVMKDPEKS-------------------DNYIVRRLAAIEGYEMVSTDE------------ 97 (183)
Q Consensus 49 Vlv~k~~~~~~~~~~rGDIVvf~~p~~~-------------------~~~~vKRVia~pGD~V~~~~~------------ 97 (183)
+.+.++.+ ...++++||+|+|+.|... ...++|||+|+|||+|++.+.
T Consensus 39 ig~y~~~~-~~~~~~rGDiVvf~~P~~~~~~~a~~r~yl~~g~~p~~~~~~iKRViglpGD~V~i~~~v~iNg~~~~~~~ 117 (176)
T PRK13838 39 LGLWRIEA-LDRPVAVGDLVFICPPETAAFREARERGYLRRGLCPGGFAPLIKTVAALAGQRVEIGGSVSIDGRPLPSSS 117 (176)
T ss_pred EEEEEEec-cCCCCCCCcEEEEECCchhhhhhhhhcccccccccccCCCceEEEEEEeCCcEEEECCEEEECCEEccccc
Confidence 44444432 2468999999999987643 135999999999999998631
Q ss_pred ------C------CCcccccCCeEEEEeCCCCCCCCCCCCCCccccccCCCeEEEEEEEE
Q 030087 98 ------K------DEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCL 145 (183)
Q Consensus 98 ------~------~~~~~vp~g~~~vlGDn~~~~~~~S~DSR~~G~V~~~~I~Gkv~~~~ 145 (183)
. ....+||+|+|||+|||. +|+||||||+|++++|+|++.+++
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 0 113479999999999984 699999999999999999998774
No 6
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=99.88 E-value=4e-22 Score=159.48 Aligned_cols=104 Identities=20% Similarity=0.310 Sum_probs=79.7
Q ss_pred eeEEEEEEeCCCCcccccCCCcEEEEEecCCCCCCCCCcCeEEEEecCCCC-------------------CccEEEEEEE
Q 030087 26 KLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKS-------------------DNYIVRRLAA 86 (183)
Q Consensus 26 ~~~~~~~V~g~SM~PtL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~-------------------~~~~vKRVia 86 (183)
+........++||- .|=+.+ .. ..+++||+|+|+.|... ...++|||+|
T Consensus 27 ~~~~~~~N~T~S~P-----~glY~~-~~------~~~~~Gd~V~f~~p~~~~~~~a~~rgyl~~g~~p~~~~~liKRVva 94 (178)
T PRK13884 27 YAAGARVNTTKSIP-----VGLYWT-SS------APVEKGAYVLFCPPQRGVFDDAKERGYIGAGFCPGGYGYMMKRVLA 94 (178)
T ss_pred HhCcEEEECCCCCc-----ceEEEE-eC------CCCCCCCEEEEeCCchHHHHHHHhCCccccCcCCCCCCceEEEEEe
Confidence 34445566666765 443333 22 47999999999987631 1379999999
Q ss_pred EcCceEEecCC---------------------C------CCcccccCCeEEEEeCCCCCCCCCCCCCCccccccCCCeEE
Q 030087 87 IEGYEMVSTDE---------------------K------DEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVG 139 (183)
Q Consensus 87 ~pGD~V~~~~~---------------------~------~~~~~vp~g~~~vlGDn~~~~~~~S~DSR~~G~V~~~~I~G 139 (183)
+|||+|++.++ . ...++||+|+||++|||+. +|+||||||+|++++|+|
T Consensus 95 ~pGD~V~~~~~~l~VNG~~v~~~~~~~~d~~g~~l~~~~~~~~~lp~g~~fvlgd~~~----~S~DSRYfG~V~~~~I~G 170 (178)
T PRK13884 95 AKGDAVSVTDDGVRVNGELLPLSKPILADGAGRPLPRYQANSYTLGESELLLMSDVSA----TSFDGRYFGPINRSQIKT 170 (178)
T ss_pred eCCcEEEEECCEEEECCEEccccccccccccCCcccccCCCceEECCCEEEEECCCCC----CCCcccccCcccHHHEEE
Confidence 99999998642 0 0124899999999999998 899999999999999999
Q ss_pred EEEEEE
Q 030087 140 RAIYCL 145 (183)
Q Consensus 140 kv~~~~ 145 (183)
++.+++
T Consensus 171 ~~~Pl~ 176 (178)
T PRK13884 171 VIRPVI 176 (178)
T ss_pred EEEEeE
Confidence 998764
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=99.88 E-value=3.7e-22 Score=158.73 Aligned_cols=105 Identities=22% Similarity=0.294 Sum_probs=82.1
Q ss_pred ceeEEEEEEeCCCCcccccCCCcEEEEEecCCCCCCCCCcCeEEEEecCCCCC-------------------ccEEEEEE
Q 030087 25 GKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSD-------------------NYIVRRLA 85 (183)
Q Consensus 25 ~~~~~~~~V~g~SM~PtL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~-------------------~~~vKRVi 85 (183)
.|........++||. .|-+. +.+ ...++|||+|+|+.|..+. ..++|||+
T Consensus 21 ~~~~~~~~N~T~S~P-----~g~Y~-~~~-----~~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRVi 89 (171)
T TIGR02771 21 LYCVGARINTTKSLP-----LGLYW-TTS-----SKPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVL 89 (171)
T ss_pred cceeeEEEECCCCCc-----ceEEE-eCC-----CCCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEE
Confidence 445555667777776 45444 322 2589999999999876432 27999999
Q ss_pred EEcCceEEecCC-------------------------CCCcccccCCeEEEEeCCCCCCCCCCCCCCccccccCCCeEEE
Q 030087 86 AIEGYEMVSTDE-------------------------KDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGR 140 (183)
Q Consensus 86 a~pGD~V~~~~~-------------------------~~~~~~vp~g~~~vlGDn~~~~~~~S~DSR~~G~V~~~~I~Gk 140 (183)
|+|||+|+++++ ...+++||+| ||++|||+. +|+||||||+|++++|+||
T Consensus 90 glpGD~V~i~~~~v~INg~~~~~~~~~~~~~~g~~l~~~~~~~vp~g-yf~lgdn~~----~S~DSRy~G~V~~~~IiGk 164 (171)
T TIGR02771 90 GLPGDRVTVRADVVAINGQLLPYSKPLATDSSGRPLPPFPEGVIPPG-FFVVHDTSP----TSFDSRYFGPISREQVIGR 164 (171)
T ss_pred EeCCCEEEEECCEEEECCEEcccccccccccCCCccccCCCcEECCC-EEEECCCCC----CCCcccccceecHHHeEEE
Confidence 999999998642 0125789999 999999999 9999999999999999999
Q ss_pred EEEEE
Q 030087 141 AIYCL 145 (183)
Q Consensus 141 v~~~~ 145 (183)
+.+++
T Consensus 165 ~~pl~ 169 (171)
T TIGR02771 165 VKPLF 169 (171)
T ss_pred EEEeE
Confidence 99764
No 8
>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=99.87 E-value=1.2e-21 Score=139.63 Aligned_cols=89 Identities=29% Similarity=0.561 Sum_probs=77.2
Q ss_pred EEeCCCCcccccCCCcEEEEEecCCCCCCCCCcCeEEEEecCCCCCccEEEEEEEEcCceEEecCCCCCcccccCCeEEE
Q 030087 32 GNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWV 111 (183)
Q Consensus 32 ~V~g~SM~PtL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~~~~vKRVia~pGD~V~~~~~~~~~~~vp~g~~~v 111 (183)
.|.|+||+|||+ +||+|+++++.. ....+++||+|+|+.|.+++..++||+++++ ++++|+
T Consensus 2 ~V~g~SM~P~l~-~GD~vlv~~~~~-~~~~~~~Gdivv~~~~~~~~~~~vkRv~~~~-----------------~~~~~l 62 (90)
T TIGR02754 2 KVTGVSMSPTLP-PGDRIIVVPWLK-IFRVPPIGNVVVVRHPLQPYGLIIKRLAAVD-----------------DNGLFL 62 (90)
T ss_pred EeeCCCccCccC-CCCEEEEEEccc-cCCCCCCCeEEEEecCCCCcceEEEEeeEEc-----------------CCeEEE
Confidence 689999999999 899999998532 1244567999999998766789999999985 458999
Q ss_pred EeCCCCCCCCCCCCCCccccccCCCeEEEEEE
Q 030087 112 LADNENMKPKEANDSRTFGPVPMRNIVGRAIY 143 (183)
Q Consensus 112 lGDn~~~~~~~S~DSR~~G~V~~~~I~Gkv~~ 143 (183)
+|||+. .|.|||++|+|+..+|+|+|++
T Consensus 63 ~~dN~~----~~~d~~~~g~v~~~~I~G~v~~ 90 (90)
T TIGR02754 63 LGDNPK----ASTDSRQLGPVPRSLLLGKVLW 90 (90)
T ss_pred eCCCCC----CCCcccccCCCcHHHEEEEEEC
Confidence 999998 8999999999999999999863
No 9
>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=99.85 E-value=2.9e-22 Score=154.20 Aligned_cols=81 Identities=33% Similarity=0.525 Sum_probs=32.2
Q ss_pred CCCcCeEEEEecCCC------------CCccEEEEEEEEcCceEEecCC------------------------CCCcccc
Q 030087 61 RVSVGDVVVMKDPEK------------SDNYIVRRLAAIEGYEMVSTDE------------------------KDEPFVL 104 (183)
Q Consensus 61 ~~~rGDIVvf~~p~~------------~~~~~vKRVia~pGD~V~~~~~------------------------~~~~~~v 104 (183)
.+++||+|+|+.|.. .+..++|||+|+|||+|+++++ ...+++|
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 489999999999863 2457999999999999998753 0135789
Q ss_pred cCCeEEEEeCCCCCCCCCCCCCCccccccCCCeEEEEEEEE
Q 030087 105 DKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCL 145 (183)
Q Consensus 105 p~g~~~vlGDn~~~~~~~S~DSR~~G~V~~~~I~Gkv~~~~ 145 (183)
|+|+||++|||+. +|+||||||+|++++|+|++.+++
T Consensus 101 p~g~~~v~gd~~~----~S~DSRy~G~V~~~~I~g~~~pl~ 137 (138)
T PF10502_consen 101 PEGEYFVLGDNRP----NSFDSRYFGPVPRSQIIGKARPLW 137 (138)
T ss_dssp -TTEEEEE-SBTT----S--SHHHH--EEGGGEEEEEEEEE
T ss_pred CCCEEEEecCCCC----CccccCEecccCHHHEEEEEEEEE
Confidence 9999999999998 899999999999999999999875
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=99.81 E-value=1.1e-19 Score=127.89 Aligned_cols=84 Identities=38% Similarity=0.600 Sum_probs=74.3
Q ss_pred EEEEeCCCCcccccCCCcEEEEEecCCCCCCCCCcCeEEEEecCCCCCccEEEEEEEEcCceEEecCCCCCcccccCCeE
Q 030087 30 LYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDEC 109 (183)
Q Consensus 30 ~~~V~g~SM~PtL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~~~~vKRVia~pGD~V~~~~~~~~~~~vp~g~~ 109 (183)
++.|.|+||+|+++ .||++++++... ....+++||+|+|+.+...+..++|||++ |
T Consensus 2 ~~~v~g~SM~P~i~-~gd~v~v~~~~~-~~~~~~~GDiv~~~~~~~~~~~~vkRv~~----------------------~ 57 (85)
T cd06530 2 PVVVPGGSMEPTLQ-PGDLVLVNKLSY-GFREPKRGDVVVFKSPGDPGKPIIKRVIG----------------------Y 57 (85)
T ss_pred eeEEcCCCCcCccc-CCCEEEEEEeec-ccCCCCCCCEEEEeCCCCCCCEEEEEEEE----------------------E
Confidence 57899999999999 899999998642 12369999999999987656789999997 9
Q ss_pred EEEeCCCCCCCCCCCCCCccccccCCCeEEEE
Q 030087 110 WVLADNENMKPKEANDSRTFGPVPMRNIVGRA 141 (183)
Q Consensus 110 ~vlGDn~~~~~~~S~DSR~~G~V~~~~I~Gkv 141 (183)
|+.|||+. +|.|||+||+++.++|+|++
T Consensus 58 ~~~gDn~~----ns~d~~~~g~~~~~~i~G~~ 85 (85)
T cd06530 58 FVLGDNRN----NSLDSRYWGPVPEDDIVGKV 85 (85)
T ss_pred EEeeCCCC----CCCccCCcCCCcHHHeEEeC
Confidence 99999987 89999999999999999985
No 11
>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=99.74 E-value=3.3e-17 Score=128.82 Aligned_cols=86 Identities=27% Similarity=0.398 Sum_probs=70.2
Q ss_pred EEeCCCCcccccCCCcEEEEEecCCCCCCCCCcCeEEEEecCCCCCccEEEEEEEEcCceEEecCCCCCcccccCCeEEE
Q 030087 32 GNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWV 111 (183)
Q Consensus 32 ~V~g~SM~PtL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~~~~vKRVia~pGD~V~~~~~~~~~~~vp~g~~~v 111 (183)
.|.|+||+|||+ .||.+++++.. ..++++||+|+|++|..+ +.++|||+++.++. .+-.|+.
T Consensus 35 ~V~g~SM~Ptl~-~GD~vlv~~~~---~~~~~~GDIVvf~~~~~~-~~iihRVi~v~~~~-------------g~~~~~t 96 (158)
T TIGR02228 35 VVLSGSMEPTFN-TGDLILVTGAD---PNDIQVGDVITYKSPGFN-TPVTHRVIEINNSG-------------GELGFIT 96 (158)
T ss_pred EEcCCCCcCCcc-CCCEEEEEecc---cCCCCCCCEEEEEECCCC-ccEEEEEEEEECCC-------------CcEEEEE
Confidence 499999999999 89999999953 368999999999997654 78999999997430 0113777
Q ss_pred EeCCCCCCCCCCCCCCccccccCCCeEEEEEE
Q 030087 112 LADNENMKPKEANDSRTFGPVPMRNIVGRAIY 143 (183)
Q Consensus 112 lGDn~~~~~~~S~DSR~~G~V~~~~I~Gkv~~ 143 (183)
.|||+. ..| .++|+.++|+|++..
T Consensus 97 kGDnN~-----~~D---~~~v~~~~IiG~v~~ 120 (158)
T TIGR02228 97 KGDNNP-----APD---GEPVPSENVIGKYLG 120 (158)
T ss_pred EecCCC-----CCC---cccCCHHHEEEEEEE
Confidence 799986 456 689999999999983
No 12
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=99.56 E-value=4.9e-14 Score=109.54 Aligned_cols=129 Identities=18% Similarity=0.233 Sum_probs=95.9
Q ss_pred HHHHHHHHHHHHHHHHHhhhceeEEEEEEeCCCCcccccCCCcEEEEEecCCCCCCCCCcCeEEEEecCCCCCccEEEEE
Q 030087 5 STWFRYIANKLEYSVSISWKGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRL 84 (183)
Q Consensus 5 ~~wl~~~~~~i~i~v~i~~~~~~~~~~~V~g~SM~PtL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~~~~vKRV 84 (183)
..|+..++.++++++++.++.|+++++.|+|.||+|||+ .||+|+++|.++ ....+..++++ ..|......++||+
T Consensus 8 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~V~s~SM~Ptl~-~GD~v~v~k~~~-~~~~~~~~~~~--~~~~~~~~~~~kr~ 83 (166)
T COG0681 8 LELISSLLIAIILALIIGVRTFVFEPVVVPSGSMEPTLN-VGDRVLVKKFSY-GFGKLKVPDII--VLPAVVEGDLIKRV 83 (166)
T ss_pred HHHHHHHHHHHHHhheeeeEEEEEEEEEECCCccccccc-cCCEEEEEeccc-cccCCccceee--ecCCCCCcceEEEe
Confidence 367777777666665544479999999999999999999 899999999986 35567888887 44445567899999
Q ss_pred EEEcCceEEecCCCCC-cccccCCeEEEEe-------CCCCCCCCCCCCCCccccccCCCeEEEE
Q 030087 85 AAIEGYEMVSTDEKDE-PFVLDKDECWVLA-------DNENMKPKEANDSRTFGPVPMRNIVGRA 141 (183)
Q Consensus 85 ia~pGD~V~~~~~~~~-~~~vp~g~~~vlG-------Dn~~~~~~~S~DSR~~G~V~~~~I~Gkv 141 (183)
++.+||.+.++++... ...+|++..++.+ +... .+.+++.++.......+.++
T Consensus 84 ~~~~GD~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~ 144 (166)
T COG0681 84 IGLRGDIVVFKDDRLYVVPIIPRVYGLVEKDNGKHLVDVIV----NANSSRVFGIITKKDYIKRV 144 (166)
T ss_pred ccCCCCEEEEECCEEEeecccCcchhhhhcccccccccccc----cccCccccccccccccccce
Confidence 9999999999874322 2344555555444 3334 57777878777777777777
No 13
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.53 E-value=1.5e-14 Score=111.98 Aligned_cols=90 Identities=28% Similarity=0.417 Sum_probs=72.7
Q ss_pred EEEEEecCCCCCCCCCcCeEEEEecCCC------------CCccEEEEEEEEcCceEEecCC-----------------C
Q 030087 48 TLLVRKLPAADPKRVSVGDVVVMKDPEK------------SDNYIVRRLAAIEGYEMVSTDE-----------------K 98 (183)
Q Consensus 48 ~Vlv~k~~~~~~~~~~rGDIVvf~~p~~------------~~~~~vKRVia~pGD~V~~~~~-----------------~ 98 (183)
..-++|.+ ..+++||+|++++|.+ ...+++|||.|+|||+|++.+. .
T Consensus 44 lyrv~k~~----~Pvt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq~Vci~~~~I~I~G~~v~~sl~~D~~ 119 (173)
T COG4959 44 LYRVSKLS----APVTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQHVCITSQGIAIDGKPVAASLPVDRV 119 (173)
T ss_pred EEEecccC----CCcccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCCCcEEEecceEEECCEEeeeecccccc
Confidence 56667653 3569999999999874 2357999999999999998641 0
Q ss_pred -------CCcccccCCeEEEEeCCCCCCCCCCCCCCccccccCCCeEEEEEEEE
Q 030087 99 -------DEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCL 145 (183)
Q Consensus 99 -------~~~~~vp~g~~~vlGDn~~~~~~~S~DSR~~G~V~~~~I~Gkv~~~~ 145 (183)
.....+-++++|+++|... .|+|||||||||.++|+|.+.+++
T Consensus 120 GR~lp~~~gcR~l~~~el~lL~~~~~----~SfDsRYfGpipas~vig~aRPvw 169 (173)
T COG4959 120 GRALPRWQGCRYLAPSELLLLTDRSS----TSFDSRYFGPIPASQVIGVARPVW 169 (173)
T ss_pred CCcCCcccCCceecCCeEEEEeccCC----cccccceecccCHHHcceeeeeee
Confidence 1223588899999999888 899999999999999999998774
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=99.27 E-value=2e-11 Score=82.22 Aligned_cols=57 Identities=25% Similarity=0.365 Sum_probs=45.3
Q ss_pred EEeCCCCcccccCCCcEEEEEecCCCCCCCCCcCeEEEEecCCCCCccEEEEEEEEcCceEEec
Q 030087 32 GNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVST 95 (183)
Q Consensus 32 ~V~g~SM~PtL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~~~~vKRVia~pGD~V~~~ 95 (183)
+|.|+||+|+|+ +||+|++++. ..++.||+|+|..+... ..++||+++.+|+.+.+.
T Consensus 1 ~V~GdSM~P~i~-~Gd~v~v~~~-----~~~~~gdivv~~~~~~~-~~~iKrv~~~~~~~~~~~ 57 (70)
T PF00717_consen 1 RVEGDSMEPTIK-DGDIVLVDPS-----SEPKDGDIVVVKIDGDE-ELYIKRVVGEPGGIILIS 57 (70)
T ss_dssp EEESSTTGGTSS-TTEEEEEEET-----S---TTSEEEEEETTEE-SEEEEEEEEETTEEEEE-
T ss_pred CeECcCcccCee-CCCEEEEEEc-----CCCccCeEEEEEECCce-eeEEEEEEEeCCCEEEEe
Confidence 589999999999 8999999986 47999999999985442 389999999998866554
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=99.22 E-value=9.9e-11 Score=80.77 Aligned_cols=83 Identities=35% Similarity=0.559 Sum_probs=63.4
Q ss_pred EEEEeCCCCcccccCCCcEEEEEecCCCCCCCCCcCeEEEEecCCCCCccEEEEEEEEcCceEEecCCCCCcccccCCeE
Q 030087 30 LYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDEC 109 (183)
Q Consensus 30 ~~~V~g~SM~PtL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~~~~vKRVia~pGD~V~~~~~~~~~~~vp~g~~ 109 (183)
.+.+.|+||+|+|+ .||.+++++.. ..++.||+|++..+. +..++||+...++ ++++
T Consensus 2 ~~~v~g~SM~P~i~-~gd~v~i~~~~----~~~~~G~iv~~~~~~--~~~~ikrl~~~~~----------------~~~~ 58 (84)
T cd06462 2 ALRVEGDSMEPTIP-DGDLVLVDKSS----YEPKRGDIVVFRLPG--GELTVKRVIGLPG----------------EGHY 58 (84)
T ss_pred eeEEcCCCccCccc-CCCEEEEEecC----CCCcCCEEEEEEcCC--CcEEEEEEEEECC----------------CCEE
Confidence 47899999999999 89999999852 248999999999854 4789999998864 3689
Q ss_pred EEEeCCCCCCCCCCCCCCccccccCCCeEEEE
Q 030087 110 WVLADNENMKPKEANDSRTFGPVPMRNIVGRA 141 (183)
Q Consensus 110 ~vlGDn~~~~~~~S~DSR~~G~V~~~~I~Gkv 141 (183)
++.+||++ +.+.+..+. ....++|++
T Consensus 59 ~l~~~N~~-----~~~~~~~~~-~~~~i~g~v 84 (84)
T cd06462 59 FLLGDNPN-----SPDSRIDGP-PELDIVGVV 84 (84)
T ss_pred EEECCCCC-----CCcccccCC-CHHHEEEeC
Confidence 99999954 444443322 455666653
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=98.95 E-value=6.8e-09 Score=71.42 Aligned_cols=62 Identities=29% Similarity=0.390 Sum_probs=52.4
Q ss_pred EEEEeCCCCcccccCCCcEEEEEecCCCCCCCCCcCeEEEEecCCCCCccEEEEEEEEcCceEEecCCCCCcccccCCeE
Q 030087 30 LYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDEC 109 (183)
Q Consensus 30 ~~~V~g~SM~PtL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~~~~vKRVia~pGD~V~~~~~~~~~~~vp~g~~ 109 (183)
.+++.|+||+|+++ +||.+++++. ..++.||++++..+. ..++||+...++ +.+
T Consensus 2 ~~~v~g~sM~p~i~-~gd~lii~~~-----~~~~~g~i~~~~~~~---~~~ikr~~~~~~-----------------~~~ 55 (81)
T cd06529 2 ALRVKGDSMEPTIP-DGDLVLVDPS-----DTPRDGDIVVARLDG---ELTVKRLQRRGG-----------------GRL 55 (81)
T ss_pred EEEEECCCcCCccC-CCCEEEEcCC-----CCCCCCCEEEEEECC---EEEEEEEEECCC-----------------CcE
Confidence 47899999999999 8999999985 358999999999843 689999998753 478
Q ss_pred EEEeCCCC
Q 030087 110 WVLADNEN 117 (183)
Q Consensus 110 ~vlGDn~~ 117 (183)
++.++|+.
T Consensus 56 ~L~s~N~~ 63 (81)
T cd06529 56 RLISDNPA 63 (81)
T ss_pred EEEeCCCC
Confidence 88888875
No 17
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=98.88 E-value=2e-08 Score=82.02 Aligned_cols=90 Identities=22% Similarity=0.285 Sum_probs=64.6
Q ss_pred EEEEEeCCCCcccccCCCcEEEEEecCCCCCCCCCcCeEEEEecCCCCCccEEEEEEEEcCceEEecCCCCCcccccCCe
Q 030087 29 YLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDE 108 (183)
Q Consensus 29 ~~~~V~g~SM~PtL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~~~~vKRVia~pGD~V~~~~~~~~~~~vp~g~ 108 (183)
..+.|.|+||+|++. +||.++|+.- .+..+||.|++..- .++.++||+...+ .|.
T Consensus 124 ~~i~V~GDSMeP~~~-~Gd~ilVd~~-----~~~~~gd~v~v~~~--g~~~~VK~l~~~~-----------------~~~ 178 (214)
T COG2932 124 FALRVTGDSMEPTYE-DGDTLLVDPG-----VNTRRGDRVYVETD--GGELYVKKLQREP-----------------GGL 178 (214)
T ss_pred EEEEEeCCccccccc-CCCEEEECCC-----CceeeCCEEEEEEe--CCeEEEEEEEEec-----------------CCe
Confidence 678999999999999 8999999985 46777886655542 3578999999875 457
Q ss_pred EEEEeCCCCCCCCCCCCCCccccccCCCeEEEEEEEEecC
Q 030087 109 CWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTA 148 (183)
Q Consensus 109 ~~vlGDn~~~~~~~S~DSR~~G~V~~~~I~Gkv~~~~~p~ 148 (183)
+.+.++|+.+ .+.+.+..=..=+|||+|++....+
T Consensus 179 ~~l~S~N~~~-----~~~~~~~~~~~v~iIgrVv~~~~~~ 213 (214)
T COG2932 179 LRLVSLNPDY-----YPDEIFSEDDDVEIIGRVVWVSRLL 213 (214)
T ss_pred EEEEeCCCCC-----CcccccCccceEEEEEEEEEEeeec
Confidence 7789999873 1222221111125899999887653
No 18
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.86 E-value=1.8e-08 Score=78.28 Aligned_cols=90 Identities=23% Similarity=0.307 Sum_probs=68.5
Q ss_pred EEEEeCCCCcccccCCCcEEEEEecCCCCCCCCCcCeEEEEecCCCCCccEEEEEEEEcCceEEecCCCCCcccccCCe-
Q 030087 30 LYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDE- 108 (183)
Q Consensus 30 ~~~V~g~SM~PtL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~~~~vKRVia~pGD~V~~~~~~~~~~~vp~g~- 108 (183)
+..|-+.||+|.++ .||.++..... ....+.||||+|+.+.. ..+++|||+..-+. .+|+
T Consensus 50 iVVVLSgSMePaF~-RGDlLfL~N~~---~~p~~vGdivVf~vegR-~IPiVHRviK~he~--------------~~~~~ 110 (180)
T KOG3342|consen 50 IVVVLSGSMEPAFH-RGDLLFLTNRN---EDPIRVGDIVVFKVEGR-EIPIVHRVIKQHEK--------------SNGHI 110 (180)
T ss_pred EEEEEcCCcCcccc-cccEEEEecCC---CCcceeccEEEEEECCc-cCchhHHHHHHhcc--------------cCCcE
Confidence 58899999999999 89999988652 36788999999998644 46899999977542 2444
Q ss_pred -EEEEeCCCCCCCCCCCCCCc-c----ccccCCCeEEEEEEE
Q 030087 109 -CWVLADNENMKPKEANDSRT-F----GPVPMRNIVGRAIYC 144 (183)
Q Consensus 109 -~~vlGDn~~~~~~~S~DSR~-~----G~V~~~~I~Gkv~~~ 144 (183)
+...|||+. .|.|. | -...++.|+|+|.--
T Consensus 111 ~~LTKGDNN~------~dD~~Ly~~gq~~L~r~~Ivg~~~G~ 146 (180)
T KOG3342|consen 111 KFLTKGDNNA------VDDRGLYAQGQNWLERKDIVGRVRGY 146 (180)
T ss_pred EEEecCCCCc------ccchhcccccccceeccceeeEEeec
Confidence 455599975 56563 2 247889999998753
No 19
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=98.72 E-value=2.1e-07 Score=71.42 Aligned_cols=86 Identities=20% Similarity=0.294 Sum_probs=61.6
Q ss_pred EEEEEEeCCCCc-ccccCCCcEEEEEecCCCCCCCCCcCeEEEEecCCCCCccEEEEEEEEcCceEEecCCCCCcccccC
Q 030087 28 TYLYGNKGDQMA-PVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDK 106 (183)
Q Consensus 28 ~~~~~V~g~SM~-PtL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~~~~vKRVia~pGD~V~~~~~~~~~~~vp~ 106 (183)
.+..+|.|+||. |+|+ +||++++++- .+++.||+|++.. .++..+||+...
T Consensus 51 ~f~l~V~GdSM~~~~I~-~GD~liVd~~-----~~~~~Gdivv~~~---~g~~~vKrl~~~------------------- 102 (139)
T PRK10276 51 TYFVKASGDSMIDAGIS-DGDLLIVDSA-----ITASHGDIVIAAV---DGEFTVKKLQLR------------------- 102 (139)
T ss_pred EEEEEEecCCCCCCCCC-CCCEEEEECC-----CCCCCCCEEEEEE---CCEEEEEEEEEC-------------------
Confidence 456899999998 6899 8999999974 3578899999976 356789998742
Q ss_pred CeEEEEeCCCCCCCCCCCCCCccccccCCCeEEEEEEEEec
Q 030087 107 DECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRT 147 (183)
Q Consensus 107 g~~~vlGDn~~~~~~~S~DSR~~G~V~~~~I~Gkv~~~~~p 147 (183)
+++++..+|+.+ ....+-.-..=.|+|+|++.++.
T Consensus 103 ~~~~L~s~N~~y------~~i~i~~~~~~~IiG~V~~~~~~ 137 (139)
T PRK10276 103 PTVQLIPMNSAY------SPITISSEDTLDVFGVVTHIVKA 137 (139)
T ss_pred CcEEEEcCCCCC------CCEEcCCCCcEEEEEEEEEEEEe
Confidence 257788888752 11111111122799999988764
No 20
>PRK00215 LexA repressor; Validated
Probab=98.62 E-value=5.7e-07 Score=72.78 Aligned_cols=87 Identities=22% Similarity=0.289 Sum_probs=64.1
Q ss_pred eEEEEEEeCCCCc-ccccCCCcEEEEEecCCCCCCCCCcCeEEEEecCCCCCccEEEEEEEEcCceEEecCCCCCccccc
Q 030087 27 LTYLYGNKGDQMA-PVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLD 105 (183)
Q Consensus 27 ~~~~~~V~g~SM~-PtL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~~~~vKRVia~pGD~V~~~~~~~~~~~vp 105 (183)
-.+.++|.|+||. |++. +||++++++- ..++.||+|++... ++..+||+.-.
T Consensus 117 ~~~~~~V~GdSM~~~~i~-~Gd~v~v~~~-----~~~~~G~ivv~~~~---~~~~vKrl~~~------------------ 169 (205)
T PRK00215 117 EDFLLRVRGDSMIDAGIL-DGDLVIVRKQ-----QTARNGQIVVALID---DEATVKRFRRE------------------ 169 (205)
T ss_pred CeEEEEEccCCCCCCCcC-CCCEEEEeCC-----CCCCCCCEEEEEEC---CEEEEEEEEEe------------------
Confidence 3566899999995 7999 8999999874 35788999999873 36899999853
Q ss_pred CCeEEEEeCCCCCCCCCCCCCCccccccCCCeEEEEEEEEec
Q 030087 106 KDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRT 147 (183)
Q Consensus 106 ~g~~~vlGDn~~~~~~~S~DSR~~G~V~~~~I~Gkv~~~~~p 147 (183)
.|.+++..+|+.+ +...+.. ..=.|+|+|+..++.
T Consensus 170 ~~~~~L~s~Np~y------~~~~~~~-~~~~IiG~Vv~~~r~ 204 (205)
T PRK00215 170 GGHIRLEPENPAY------EPIIVDP-DRVTIEGKVVGLIRN 204 (205)
T ss_pred CCEEEEEcCCCCC------CCEEeCC-CcEEEEEEEEEEEEc
Confidence 2478888999863 2221111 024799999988763
No 21
>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=98.60 E-value=8.3e-07 Score=71.53 Aligned_cols=88 Identities=22% Similarity=0.282 Sum_probs=65.7
Q ss_pred eEEEEEEeCCCCc-ccccCCCcEEEEEecCCCCCCCCCcCeEEEEecCCCCCccEEEEEEEEcCceEEecCCCCCccccc
Q 030087 27 LTYLYGNKGDQMA-PVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLD 105 (183)
Q Consensus 27 ~~~~~~V~g~SM~-PtL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~~~~vKRVia~pGD~V~~~~~~~~~~~vp 105 (183)
-.+.++|.|+||. |.+. +||++++++. ..++.||+|++.. .++..+||+.-.
T Consensus 110 ~~f~~~V~GdSM~~~~i~-~Gd~v~v~~~-----~~~~~G~ivvv~~---~~~~~vKrl~~~------------------ 162 (199)
T TIGR00498 110 AVFLLKVMGDSMVDAGIC-DGDLLIVRSQ-----KDARNGEIVAAMI---DGEVTVKRFYKD------------------ 162 (199)
T ss_pred CEEEEEecCCCCCCCCCC-CCCEEEEecC-----CCCCCCCEEEEEE---CCEEEEEEEEEE------------------
Confidence 4567999999996 6899 8999999874 4788899999997 456899998753
Q ss_pred CCeEEEEeCCCCCCCCCCCCCCccccccCCCeEEEEEEEEecC
Q 030087 106 KDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTA 148 (183)
Q Consensus 106 ~g~~~vlGDn~~~~~~~S~DSR~~G~V~~~~I~Gkv~~~~~p~ 148 (183)
.+.+++..+|+.+.+..-.+ ..=.|+|+|+..++.+
T Consensus 163 ~~~i~L~s~N~~y~~i~~~~-------~~~~IiG~Vv~~~r~~ 198 (199)
T TIGR00498 163 GTKVELKPENPEFDPIVLNA-------EDVTILGKVVGVIRNF 198 (199)
T ss_pred CCEEEEEcCCCCCcCCcCCC-------CcEEEEEEEEEEEEec
Confidence 24788889998632111111 1248999999988754
No 22
>PRK12423 LexA repressor; Provisional
Probab=98.60 E-value=6.8e-07 Score=72.65 Aligned_cols=86 Identities=22% Similarity=0.227 Sum_probs=63.7
Q ss_pred EEEEEeCCCCc-ccccCCCcEEEEEecCCCCCCCCCcCeEEEEecCCCCCccEEEEEEEEcCceEEecCCCCCcccccCC
Q 030087 29 YLYGNKGDQMA-PVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKD 107 (183)
Q Consensus 29 ~~~~V~g~SM~-PtL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~~~~vKRVia~pGD~V~~~~~~~~~~~vp~g 107 (183)
+...|.|+||. |+|. +||+|+|++- ..++.||+|++.. .++..+||+.-. .+
T Consensus 115 f~l~V~GdSM~~~~i~-~Gd~viv~~~-----~~~~~Gdivv~~~---~~~~~vKrl~~~------------------~~ 167 (202)
T PRK12423 115 YLLQVQGDSMIDDGIL-DGDLVGVHRS-----PEARDGQIVVARL---DGEVTIKRLERS------------------GD 167 (202)
T ss_pred EEEEEecCcCCCCCcC-CCCEEEEeCC-----CcCCCCCEEEEEE---CCEEEEEEEEEe------------------CC
Confidence 46899999997 7999 8999999974 4678899999987 346899999753 24
Q ss_pred eEEEEeCCCCCCCCCCCCCCccccccCCCeEEEEEEEEec
Q 030087 108 ECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRT 147 (183)
Q Consensus 108 ~~~vlGDn~~~~~~~S~DSR~~G~V~~~~I~Gkv~~~~~p 147 (183)
.+++..+|+.+ +...+-+-..=.|+|+++..++.
T Consensus 168 ~~~L~s~N~~y------~~i~~~~~~~~~I~Gvv~g~~r~ 201 (202)
T PRK12423 168 RIRLLPRNPAY------APIVVAPDQDFAIEGVFCGLIRQ 201 (202)
T ss_pred EEEEEcCCCCC------CCEEcCCCCcEEEEEEEEEEEEC
Confidence 78888998763 22221111123799999988764
No 23
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=97.80 E-value=0.00047 Score=56.33 Aligned_cols=89 Identities=19% Similarity=0.227 Sum_probs=67.1
Q ss_pred eEEEEEEeCCCCcc-cccCCCcEEEEEecCCCCCCCCCcCeEEEEecCCCCCccEEEEEEEEcCceEEecCCCCCccccc
Q 030087 27 LTYLYGNKGDQMAP-VMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLD 105 (183)
Q Consensus 27 ~~~~~~V~g~SM~P-tL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~~~~vKRVia~pGD~V~~~~~~~~~~~vp 105 (183)
-.+..+|.|+||.. .+. +||.|+|++- ...+.||+|+...++ ++.-+||..--
T Consensus 111 ~~f~L~V~GdSM~~~gi~-dGDlvvV~~~-----~~a~~GdiVvA~i~g--~e~TvKrl~~~------------------ 164 (201)
T COG1974 111 ATFFLRVSGDSMIDAGIL-DGDLVVVDPT-----EDAENGDIVVALIDG--EEATVKRLYRD------------------ 164 (201)
T ss_pred ceEEEEecCCccccCcCC-CCCEEEEcCC-----CCCCCCCEEEEEcCC--CcEEEEEEEEe------------------
Confidence 46779999999975 555 7999999974 678999999999754 55889999853
Q ss_pred CCeEEEEeCCCCCCCCCCCCCCccccccCCCeEEEEEEEEecC
Q 030087 106 KDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTA 148 (183)
Q Consensus 106 ~g~~~vlGDn~~~~~~~S~DSR~~G~V~~~~I~Gkv~~~~~p~ 148 (183)
.+.+++.--|+. +.+..+..- .-.|+|+++.++|+.
T Consensus 165 g~~i~L~p~Np~------~~~i~~~~~-~~~I~G~vvgv~r~~ 200 (201)
T COG1974 165 GNQILLKPENPA------YPPIPVDAD-SVTILGKVVGVIRDI 200 (201)
T ss_pred CCEEEEEeCCCC------CCCcccCcc-ceEEEEEEEEEEecC
Confidence 247888888876 333333222 447999999999874
No 24
>PRK00364 groES co-chaperonin GroES; Reviewed
Probab=86.60 E-value=5.2 Score=28.68 Aligned_cols=92 Identities=12% Similarity=0.171 Sum_probs=46.6
Q ss_pred ccCCCcEEEEEecCCCCCCCCCcCeEEEEecCCCCCccEEEEEEEEcCceEEecCCCCCcccccCCeEEEEeCCCCCCCC
Q 030087 42 MGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWVLADNENMKPK 121 (183)
Q Consensus 42 L~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~~~~vKRVia~pGD~V~~~~~~~~~~~vp~g~~~vlGDn~~~~~~ 121 (183)
|+|-||+||+.+.. ..+-..|-|++=. ....+.....|+|+.-. ....++...+..+..|..-+..+.....
T Consensus 3 i~Pl~drVLV~~~~---~e~~T~gGI~Lp~--~a~~k~~~G~VvaVG~G-~~~~~G~~~~~~vk~GD~Vlf~~~~g~e-- 74 (95)
T PRK00364 3 LKPLGDRVLVKRLE---EEEKTAGGIVLPD--SAKEKPQEGEVVAVGPG-RRLDNGERVPLDVKVGDKVLFGKYAGTE-- 74 (95)
T ss_pred ceEcCCEEEEEEcc---cCccccceEEcCc--cccCCcceEEEEEECCC-eECCCCCEeecccCCCCEEEEcCCCCeE--
Confidence 55689999998863 2344456555522 12345567777777321 1112233334445555444443332100
Q ss_pred CCCCCCccccccCCCeEEEE
Q 030087 122 EANDSRTFGPVPMRNIVGRA 141 (183)
Q Consensus 122 ~S~DSR~~G~V~~~~I~Gkv 141 (183)
--+|...|=.++.++|+|++
T Consensus 75 v~~~~~~y~iv~~~DIlavi 94 (95)
T PRK00364 75 VKIDGEEYLILRESDILAIV 94 (95)
T ss_pred EEECCEEEEEEEHHHEEEEe
Confidence 12344445567777777764
No 25
>COG0234 GroS Co-chaperonin GroES (HSP10) [Posttranslational modification, protein turnover, chaperones]
Probab=82.12 E-value=6.8 Score=28.37 Aligned_cols=74 Identities=18% Similarity=0.297 Sum_probs=39.4
Q ss_pred ccCCCcEEEEEecCC------------CCCCCCCcCeEEEEecCCCCCccEEEEEEEEcCceEEecCCCCCcccccCCeE
Q 030087 42 MGGLGGTLLVRKLPA------------ADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDEC 109 (183)
Q Consensus 42 L~~~GD~Vlv~k~~~------------~~~~~~~rGDIVvf~~p~~~~~~~vKRVia~pGD~V~~~~~~~~~~~vp~g~~ 109 (183)
|+|-||+|++.+.-. ..-..+++|.+|++-.-...+.--....--..||+|.+.......+++...+|
T Consensus 3 ikPL~DRVlVk~~e~EekT~gGIvlpdsakeK~~~g~VvAVG~G~~~~~g~~~~~~VkvGD~Vlf~ky~G~evk~dgeey 82 (96)
T COG0234 3 IKPLGDRVLVKRVEEEEKTAGGIVLPDSAKEKPQEGEVVAVGPGRRDENGELVPLDVKVGDRVLFGKYAGTEVKIDGEEY 82 (96)
T ss_pred ceecCCEEEEEEchhhccccCcEEecCccccCCcceEEEEEccceecCCCCEeccccccCCEEEECccCCcEEEECCEEE
Confidence 456789999988631 01245666777766531111110111111234777777765555566665666
Q ss_pred EEEeCC
Q 030087 110 WVLADN 115 (183)
Q Consensus 110 ~vlGDn 115 (183)
.++.+.
T Consensus 83 lil~e~ 88 (96)
T COG0234 83 LILSES 88 (96)
T ss_pred EEechH
Confidence 666543
No 26
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=80.91 E-value=12 Score=26.80 Aligned_cols=86 Identities=13% Similarity=0.256 Sum_probs=43.7
Q ss_pred ccCCCcEEEEEecCCCCCCCCCcCeEEEEecCCCCCccEEEEEEEEc-CceEEecCCCCCcccccCCeEEEEeCCCCCCC
Q 030087 42 MGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIE-GYEMVSTDEKDEPFVLDKDECWVLADNENMKP 120 (183)
Q Consensus 42 L~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~~~~vKRVia~p-GD~V~~~~~~~~~~~vp~g~~~vlGDn~~~~~ 120 (183)
|.|-||+||+.+.. ..+-..|-|++=.. ...+.....|+|+. |.. ..+..+..|..-+.++.....
T Consensus 3 i~Pl~DRVLVk~~~---~e~~T~gGI~Lp~~--a~ek~~~G~VvavG~g~~-------~~~~~Vk~GD~Vl~~~y~g~e- 69 (91)
T PRK14533 3 VIPLGERLLIKPIK---EEKKTEGGIVLPDS--AKEKPMKAEVVAVGKLDD-------EEDFDIKVGDKVIFSKYAGTE- 69 (91)
T ss_pred ceEcCCEEEEEEcc---ccceecccEEeccc--ccCCcceEEEEEECCCCc-------cccccccCCCEEEEccCCCeE-
Confidence 45689999998863 23344455555322 22344566666663 321 123344455444444333210
Q ss_pred CCCCCCCccccccCCCeEEEE
Q 030087 121 KEANDSRTFGPVPMRNIVGRA 141 (183)
Q Consensus 121 ~~S~DSR~~G~V~~~~I~Gkv 141 (183)
--+|...|=.++.++|+|++
T Consensus 70 -v~~~~~~y~iv~e~DILa~i 89 (91)
T PRK14533 70 -IKIDDEDYIIIDVNDILAKI 89 (91)
T ss_pred -EEECCEEEEEEEhHhEEEEe
Confidence 12344445567777777764
No 27
>PTZ00414 10 kDa heat shock protein; Provisional
Probab=79.89 E-value=15 Score=26.78 Aligned_cols=27 Identities=19% Similarity=0.348 Sum_probs=17.6
Q ss_pred ccccCCCcEEEEEecCCCCCCCCCcCeEEE
Q 030087 40 PVMGGLGGTLLVRKLPAADPKRVSVGDVVV 69 (183)
Q Consensus 40 PtL~~~GD~Vlv~k~~~~~~~~~~rGDIVv 69 (183)
+.|+|-||+|++.+.. ..+-..|-|++
T Consensus 10 ~~ikPL~dRVLVk~~~---~e~kT~gGIiL 36 (100)
T PTZ00414 10 KKLQPLGQRVLVKRTL---AAKQTKAGVLI 36 (100)
T ss_pred ccceecCCEEEEEEcc---cccccccCEEc
Confidence 5677899999998863 12333455544
No 28
>cd00320 cpn10 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It forms heptameric rings with a dome-like structure, forming a lid to the large cavity of the tetradecameric cpn60 cylinder and thereby tightly regulating release and binding of proteins to the cpn60 surface.
Probab=78.68 E-value=12 Score=26.73 Aligned_cols=91 Identities=10% Similarity=0.198 Sum_probs=43.9
Q ss_pred ccCCCcEEEEEecCCCCCCCCCcCeEEEEecCCCCCccEEEEEEEEcCceEEecCCCCCcccccCCeEEEEeCCCCCCCC
Q 030087 42 MGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWVLADNENMKPK 121 (183)
Q Consensus 42 L~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~~~~vKRVia~pGD~V~~~~~~~~~~~vp~g~~~vlGDn~~~~~~ 121 (183)
|+|-+|+||+.+.. ..+-..|-|++=.. ...+.....|+|+.-... -.++...+..+..|..-+........
T Consensus 2 i~Pl~DrVLV~~~~---~e~~T~~GI~Lp~~--~~~k~~~g~VvAVG~g~~-~~~g~~~~~~vk~GD~Vl~~~~~g~~-- 73 (93)
T cd00320 2 IKPLGDRVLVKRIE---AEEKTKGGIILPDS--AKEKPQEGKVVAVGPGRR-NENGERVPLSVKVGDKVLFPKYAGTE-- 73 (93)
T ss_pred ceecCCEEEEEEcc---ccceecceEEeCCC--cCCCceEEEEEEECCCeE-CCCCCCccccccCCCEEEECCCCceE--
Confidence 44579999998863 23444555555322 224567777777732211 11222233344444433333322100
Q ss_pred CCCCCCccccccCCCeEEE
Q 030087 122 EANDSRTFGPVPMRNIVGR 140 (183)
Q Consensus 122 ~S~DSR~~G~V~~~~I~Gk 140 (183)
--.|...|=.++.++|+|+
T Consensus 74 v~~~~~~y~i~~~~DIla~ 92 (93)
T cd00320 74 VKLDGEEYLILRESDILAV 92 (93)
T ss_pred EEECCEEEEEEEHHHEEEE
Confidence 1233334445666666664
No 29
>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=77.12 E-value=14 Score=27.84 Aligned_cols=40 Identities=15% Similarity=0.121 Sum_probs=26.1
Q ss_pred CCCCcCeEEEEecCCCCCccEEEEEEEEcCceEEecCCCCCcccccCCeEEEEeCCCC
Q 030087 60 KRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWVLADNEN 117 (183)
Q Consensus 60 ~~~~rGDIVvf~~p~~~~~~~vKRVia~pGD~V~~~~~~~~~~~vp~g~~~vlGDn~~ 117 (183)
.++++||+|+|+... .--+--+++...+ .|.+.++|-|..
T Consensus 72 ~~p~~GDiv~f~~~~---~~HVGi~~g~~~~---------------~g~i~~lgGNq~ 111 (129)
T TIGR02594 72 SKPAYGCIAVKRRGG---GGHVGFVVGKDKQ---------------TGTIIVLGGNQG 111 (129)
T ss_pred CCCCccEEEEEECCC---CCEEEEEEeEcCC---------------CCEEEEeeCCCC
Confidence 468999999997532 2244555543321 358899988875
No 30
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=72.65 E-value=5.1 Score=30.42 Aligned_cols=13 Identities=46% Similarity=0.519 Sum_probs=10.7
Q ss_pred CCCcCeEEEEecC
Q 030087 61 RVSVGDVVVMKDP 73 (183)
Q Consensus 61 ~~~rGDIVvf~~p 73 (183)
...+||+|+|+.+
T Consensus 84 ~~~~GD~i~~~~~ 96 (166)
T COG0681 84 IGLRGDIVVFKDD 96 (166)
T ss_pred ccCCCCEEEEECC
Confidence 4678999999973
No 31
>PF00166 Cpn10: Chaperonin 10 Kd subunit; InterPro: IPR020818 The chaperonins are `helper' molecules required for correct folding and subsequent assembly of some proteins []. These are required for normal cell growth [], and are stress-induced, acting to stabilise or protect disassembled polypeptides under heat-shock conditions. Type I chaperonins present in eubacteria, mitochondria and chloroplasts require the concerted action of 2 proteins, chaperonin 60 (cpn60) and chaperonin 10 (cpn10) []. The 10 kDa chaperonin (cpn10 - or groES in bacteria) exists as a ring-shaped oligomer of between six to eight identical subunits, while the 60 kDa chaperonin (cpn60 - or groEL in bacteria) forms a structure comprising 2 stacked rings, each ring containing 7 identical subunits []. These ring structures assemble by self-stimulation in the presence of Mg2+-ATP. The central cavity of the cylindrical cpn60 tetradecamer provides as isolated environment for protein folding whilst cpn-10 binds to cpn-60 and synchronizes the release of the folded protein in an Mg2+-ATP dependent manner []. The binding of cpn10 to cpn60 inhibits the weak ATPase activity of cpn60. Escherichia coli GroES has also been shown to bind ATP cooperatively, and with an affinity comparable to that of GroEL []. Each GroEL subunit contains three structurally distinct domains: an apical, an intermediate and an equatorial domain. The apical domain contains the binding sites for both GroES and the unfolded protein substrate. The equatorial domain contains the ATP-binding site and most of the oligomeric contacts. The intermediate domain links the apical and equatorial domains and transfers allosteric information between them. The GroEL oligomer is a tetradecamer, cylindrically shaped, that is organised in two heptameric rings stacked back to back. Each GroEL ring contains a central cavity, known as the `Anfinsen cage', that provides an isolated environment for protein folding. The identical 10 kDa subunits of GroES form a dome-like heptameric oligomer in solution. ATP binding to GroES may be important in charging the seven subunits of the interacting GroEL ring with ATP, to facilitate cooperative ATP binding and hydrolysis for substrate protein release.; GO: 0006457 protein folding, 0005737 cytoplasm; PDB: 1PF9_Q 1AON_P 1SX4_T 1SVT_R 2C7D_P 1PCQ_O 2C7C_Q 1GRU_Q 1WNR_F 1P3H_I ....
Probab=71.68 E-value=8.7 Score=27.22 Aligned_cols=91 Identities=11% Similarity=0.175 Sum_probs=50.7
Q ss_pred cCCCcEEEEEecCCCCCCCCCcCeEEEEecCCCCCccEEEEEEEEcCceEEecCCCCCcccccCCeEEEEeCCCCCCCCC
Q 030087 43 GGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWVLADNENMKPKE 122 (183)
Q Consensus 43 ~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~~~~vKRVia~pGD~V~~~~~~~~~~~vp~g~~~vlGDn~~~~~~~ 122 (183)
.|-+|+||+.+.. ..+-..|-+++=.. ........+|+|+...... .++...+..+..|..-+..+..... -
T Consensus 3 ~Pl~drVLV~~~~---~e~~T~~GiiLp~~--~~~~~~~G~VvaVG~G~~~-~~g~~~~~~vk~GD~Vl~~~~~g~~--v 74 (93)
T PF00166_consen 3 KPLGDRVLVKKIE---AEEKTASGIILPES--AKEKPNQGKVVAVGPGRYN-ENGEEVPMDVKVGDKVLFPKYAGTE--V 74 (93)
T ss_dssp EESTTEEEEEECS---CTCTCTTSCCE-CC--SSSSEEEEEEEEE-SEEET-TTSSEEETSS-TTSEEEEETTTSEE--E
T ss_pred eecCCEEEEEEcc---ccceecceEEeccc--cccccceeEEEEcCCcccc-CCCcEeeeeeeeccEEeccccCceE--E
Confidence 3578999999963 24445565655532 2336778888888543222 3333334455556655555543210 2
Q ss_pred CCCCCccccccCCCeEEEE
Q 030087 123 ANDSRTFGPVPMRNIVGRA 141 (183)
Q Consensus 123 S~DSR~~G~V~~~~I~Gkv 141 (183)
.+|...|=.++.++|+|+.
T Consensus 75 ~~~~~~~~~~~~~dIlavi 93 (93)
T PF00166_consen 75 KFDGEKYLIVREDDILAVI 93 (93)
T ss_dssp EETTEEEEEEEGGGEEEEE
T ss_pred EECCEEEEEEEHHHeEEEC
Confidence 3455666678888888763
No 32
>PF09935 DUF2167: Protein of unknown function (DUF2167); InterPro: IPR018682 This family of various hypothetical membrane-anchored prokaryotic proteins has no known function.
Probab=67.22 E-value=1.2 Score=37.40 Aligned_cols=73 Identities=16% Similarity=0.178 Sum_probs=49.9
Q ss_pred cccccCCeEEEEeCCCCCCCCCCCCCCccccccCCCeEEEEEEEEecCCCCCC-cccCCCCCCCCCCccceeccHHHHHh
Q 030087 101 PFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHGP-VQNSNDSMRKDSPVLEVELDVDEMMK 179 (183)
Q Consensus 101 ~~~vp~g~~~vlGDn~~~~~~~S~DSR~~G~V~~~~I~Gkv~~~~~p~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 179 (183)
.+.+|+|.+|+-..+.. .-. +.+|-.|.+..+|-+++.- .-..|.. ++..+.+.++|.- +.+.|.||++|
T Consensus 16 tL~lP~g~~fL~~~~a~----~~l--~~~GN~~~~~~~Gli~P~~-~~~~W~v~~~y~~~GyVkDdd--a~~id~d~LL~ 86 (239)
T PF09935_consen 16 TLNLPAGFRFLNPEDAR----KVL--EEWGNPPSPAELGLIFPDD-DDEDWFVVFEYEDSGYVKDDD--AKNIDYDELLK 86 (239)
T ss_pred EEECCCCcEEcCHHHHH----HHH--HHhCCCCCcceEEEEeccC-CCCCEEEEEEEcCCCceecch--hhhCCHHHHHH
Confidence 45789999999665543 112 5678878777787777653 1123332 3456677788887 88999999998
Q ss_pred hcC
Q 030087 180 NHK 182 (183)
Q Consensus 180 ~~~ 182 (183)
+-|
T Consensus 87 ~~k 89 (239)
T PF09935_consen 87 SMK 89 (239)
T ss_pred HHH
Confidence 765
No 33
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=56.69 E-value=83 Score=23.70 Aligned_cols=26 Identities=23% Similarity=0.480 Sum_probs=18.2
Q ss_pred CCeEEEEeCCCCCCCCCCCCCCccccccCCC
Q 030087 106 KDECWVLADNENMKPKEANDSRTFGPVPMRN 136 (183)
Q Consensus 106 ~g~~~vlGDn~~~~~~~S~DSR~~G~V~~~~ 136 (183)
++.+-++.++. +..-+|-||||.+|.
T Consensus 81 dNA~Viin~~g-----~P~GtrI~GPVaREl 106 (122)
T COG0093 81 DNAAVIINPDG-----EPRGTRIFGPVAREL 106 (122)
T ss_pred CceEEEECCCC-----CcccceEecchhHHH
Confidence 34565555553 478899999998764
No 34
>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=56.02 E-value=48 Score=24.07 Aligned_cols=37 Identities=16% Similarity=0.212 Sum_probs=21.0
Q ss_pred CCCCcCeEEEEecCCCCCccEEEEEEEE-cCceEEecC
Q 030087 60 KRVSVGDVVVMKDPEKSDNYIVRRLAAI-EGYEMVSTD 96 (183)
Q Consensus 60 ~~~~rGDIVvf~~p~~~~~~~vKRVia~-pGD~V~~~~ 96 (183)
..|+.|||++|.......---+--|.++ .+++|.+.+
T Consensus 61 ~~P~~Gdivv~~~~~~~~~GHVaIV~~v~~~~~i~v~e 98 (124)
T PF05257_consen 61 STPQPGDIVVWDSGSGGGYGHVAIVESVNDGGTITVIE 98 (124)
T ss_dssp S---TTEEEEEEECTTTTT-EEEEEEEE-TTSEEEEEE
T ss_pred cccccceEEEeccCCCCCCCeEEEEEEECCCCEEEEEE
Confidence 6799999999953222222357777777 666665543
No 35
>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. 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=55.49 E-value=29 Score=25.69 Aligned_cols=28 Identities=29% Similarity=0.468 Sum_probs=20.9
Q ss_pred CCCcCeEEEEecCCCCCccEEEEEEEEc
Q 030087 61 RVSVGDVVVMKDPEKSDNYIVRRLAAIE 88 (183)
Q Consensus 61 ~~~rGDIVvf~~p~~~~~~~vKRVia~p 88 (183)
.++.||-|.++.++.+...+|.||..+-
T Consensus 3 ~~~vGD~V~v~~~~~~~~pyIgrI~~i~ 30 (121)
T cd04714 3 IIRVGDCVLFKSPGRPSLPYVARIESLW 30 (121)
T ss_pred EEEcCCEEEEeCCCCCCCCEEEEEEEEE
Confidence 3567899998886655667888888764
No 36
>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=52.08 E-value=16 Score=24.70 Aligned_cols=20 Identities=20% Similarity=0.328 Sum_probs=11.9
Q ss_pred CCcEEEEEecCCCCCCCCCcCeEE
Q 030087 45 LGGTLLVRKLPAADPKRVSVGDVV 68 (183)
Q Consensus 45 ~GD~Vlv~k~~~~~~~~~~rGDIV 68 (183)
.||.|.|....| ++.+|+|+
T Consensus 47 ~GD~V~Ve~spy----d~tkgrIi 66 (68)
T TIGR00008 47 PGDKVKVELSPY----DLTRGRIT 66 (68)
T ss_pred CCCEEEEEECcc----cCCcEeEE
Confidence 467777766533 45666664
No 37
>PF10000 ACT_3: ACT domain; InterPro: IPR018717 This domain has no known function.; PDB: 1ZVP_C.
Probab=51.26 E-value=9.3 Score=26.05 Aligned_cols=18 Identities=17% Similarity=0.287 Sum_probs=12.2
Q ss_pred CCCcccccCCCcEEEEEec
Q 030087 36 DQMAPVMGGLGGTLLVRKL 54 (183)
Q Consensus 36 ~SM~PtL~~~GD~Vlv~k~ 54 (183)
.||+|.|+ .|++|++.--
T Consensus 12 ~~m~P~L~-~~~yVF~t~~ 29 (72)
T PF10000_consen 12 ASMSPELN-PGEYVFCTVP 29 (72)
T ss_dssp ST-EEEE--SS-EEEEEE-
T ss_pred hhCCcEeC-CCCEEEEEec
Confidence 48999999 7999998764
No 38
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=50.53 E-value=18 Score=25.03 Aligned_cols=22 Identities=27% Similarity=0.416 Sum_probs=13.1
Q ss_pred ccCCCcEEEEEecCCCCCCCCCcCeEE
Q 030087 42 MGGLGGTLLVRKLPAADPKRVSVGDVV 68 (183)
Q Consensus 42 L~~~GD~Vlv~k~~~~~~~~~~rGDIV 68 (183)
|. .||.|+|....| ...+|||+
T Consensus 47 I~-~GD~V~Ve~~~~----d~~kg~I~ 68 (75)
T COG0361 47 IL-PGDVVLVELSPY----DLTKGRIV 68 (75)
T ss_pred eC-CCCEEEEEeccc----ccccccEE
Confidence 44 477777766543 45666664
No 39
>PF14118 YfzA: YfzA-like protein
Probab=50.14 E-value=13 Score=26.74 Aligned_cols=35 Identities=17% Similarity=0.187 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhhceeEEEEEEeCCCCcccccCCCcE
Q 030087 4 LSTWFRYIANKLEYSVSISWKGKLTYLYGNKGDQMAPVMGGLGGT 48 (183)
Q Consensus 4 ~~~wl~~~~~~i~i~v~i~~~~~~~~~~~V~g~SM~PtL~~~GD~ 48 (183)
.++|++.++..++.=++. ..+++.|+.|.++ +||.
T Consensus 10 kk~W~~~L~iF~i~QLlF---------i~~d~t~w~pnf~-~g~~ 44 (94)
T PF14118_consen 10 KKRWFITLGIFLIVQLLF---------IIFDGTGWGPNFN-EGDF 44 (94)
T ss_pred hhhHHHHHHHHHHHHHHH---------HHhhccccccccC-CCch
Confidence 367888876655433322 3467999999999 6764
No 40
>cd04717 BAH_polybromo BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. 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=48.41 E-value=41 Score=24.59 Aligned_cols=26 Identities=31% Similarity=0.552 Sum_probs=19.1
Q ss_pred CCcCeEEEEecCCCCCccEEEEEEEE
Q 030087 62 VSVGDVVVMKDPEKSDNYIVRRLAAI 87 (183)
Q Consensus 62 ~~rGDIVvf~~p~~~~~~~vKRVia~ 87 (183)
++.||.|.+.+++.+...+|-||..+
T Consensus 4 ~~vGD~V~v~~~~~~~~~~i~~I~~i 29 (121)
T cd04717 4 YRVGDCVYVANPEDPSKPIIFRIERL 29 (121)
T ss_pred EECCCEEEEeCCCCCCCCEEEEEeEE
Confidence 56688888887766566777777765
No 41
>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=48.36 E-value=65 Score=24.10 Aligned_cols=87 Identities=16% Similarity=0.205 Sum_probs=47.2
Q ss_pred EEEEEEeCCCCcccccCCCcEEEEEecCCCCCCCCCcCeEEEEecCCCCCccEEEEEEEEcCceEEecCCCCCcccccCC
Q 030087 28 TYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKD 107 (183)
Q Consensus 28 ~~~~~V~g~SM~PtL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~~~~vKRVia~pGD~V~~~~~~~~~~~vp~g 107 (183)
...+.+.+.+=.+.-. -||.|++.--.......+++|+++-.--=... +...-..|..+.++ ++
T Consensus 19 v~cI~v~~~~~~~~a~-vGD~I~vsVkk~~~~~~vkkg~v~~avIVrtk-----~~~~r~dg~~i~F~----------~N 82 (122)
T PF00238_consen 19 VKCIKVLGGKRRKYAS-VGDIIVVSVKKGRPKSKVKKGQVYKAVIVRTK-----KPIRRKDGSFIKFD----------DN 82 (122)
T ss_dssp EEEEEETSSTTTSEE--TTSEEEEEEEEE-SSSSSTTTEEEEEEEEECS-----SEEETTTSEEEEES----------SE
T ss_pred EEEEEEeCCcCccccc-cceEEEEEEeecccCccccccceEEEEEEEEe-----EEEEEeCCcEEEeC----------Cc
Confidence 3456666655555566 68887754311101346777776532100000 01112334444443 46
Q ss_pred eEEEEeCCCCCCCCCCCCCCccccccCC
Q 030087 108 ECWVLADNENMKPKEANDSRTFGPVPMR 135 (183)
Q Consensus 108 ~~~vlGDn~~~~~~~S~DSR~~G~V~~~ 135 (183)
.+-++.++. +...+|-+|||+.+
T Consensus 83 a~VLln~~~-----~p~GtrI~Gpv~~e 105 (122)
T PF00238_consen 83 AVVLLNKKG-----NPLGTRIFGPVPRE 105 (122)
T ss_dssp EEEEEETTS-----SBSSSSBCSEEEHH
T ss_pred cEEEEcCCC-----CEeeeEEEeeehHH
Confidence 777788876 48999999999865
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=43.87 E-value=25 Score=23.18 Aligned_cols=12 Identities=25% Similarity=0.509 Sum_probs=5.9
Q ss_pred CCCcCeEEEEec
Q 030087 61 RVSVGDVVVMKD 72 (183)
Q Consensus 61 ~~~rGDIVvf~~ 72 (183)
-+++||+|++..
T Consensus 41 wI~~GD~V~V~~ 52 (65)
T PF01176_consen 41 WIKRGDFVLVEP 52 (65)
T ss_dssp ---TTEEEEEEE
T ss_pred ecCCCCEEEEEe
Confidence 356667666664
No 43
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.46 E-value=16 Score=27.46 Aligned_cols=17 Identities=18% Similarity=0.229 Sum_probs=14.8
Q ss_pred CCCcccccCCCcEEEEEe
Q 030087 36 DQMAPVMGGLGGTLLVRK 53 (183)
Q Consensus 36 ~SM~PtL~~~GD~Vlv~k 53 (183)
.||.|.|. +||+|++.-
T Consensus 12 ~smtPeL~-~G~yVfcT~ 28 (134)
T COG3602 12 ASMTPELL-DGDYVFCTV 28 (134)
T ss_pred HhcCcccc-CCceEEEEe
Confidence 38999999 899999865
No 44
>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=42.13 E-value=28 Score=24.05 Aligned_cols=10 Identities=20% Similarity=0.654 Sum_probs=5.5
Q ss_pred CCcCeEEEEe
Q 030087 62 VSVGDVVVMK 71 (183)
Q Consensus 62 ~~rGDIVvf~ 71 (183)
+++||+|++.
T Consensus 39 I~~GD~VlV~ 48 (78)
T cd04456 39 IKRGDFLIVD 48 (78)
T ss_pred EcCCCEEEEE
Confidence 4455555554
No 45
>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=41.74 E-value=1e+02 Score=24.30 Aligned_cols=25 Identities=24% Similarity=0.247 Sum_probs=19.6
Q ss_pred CCCCCccccccCCCeEEEEEEEEec
Q 030087 123 ANDSRTFGPVPMRNIVGRAIYCLRT 147 (183)
Q Consensus 123 S~DSR~~G~V~~~~I~Gkv~~~~~p 147 (183)
=+=|++...+|.+.|.||.......
T Consensus 84 LF~S~~~d~~p~~~IrGKC~V~~~~ 108 (164)
T cd04709 84 LFLSRQVETLPATHIRGKCSVTLLN 108 (164)
T ss_pred eEEecccccccHHHeeeeEEEEEeh
Confidence 3556677899999999999876543
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=40.01 E-value=29 Score=23.87 Aligned_cols=10 Identities=30% Similarity=0.763 Sum_probs=5.0
Q ss_pred CCcCeEEEEe
Q 030087 62 VSVGDVVVMK 71 (183)
Q Consensus 62 ~~rGDIVvf~ 71 (183)
+++||+|++.
T Consensus 39 I~~GD~V~Ve 48 (77)
T cd05793 39 INEGDIVLVA 48 (77)
T ss_pred EcCCCEEEEE
Confidence 4445555554
No 47
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=39.34 E-value=30 Score=24.14 Aligned_cols=10 Identities=30% Similarity=0.753 Sum_probs=5.8
Q ss_pred CCcCeEEEEe
Q 030087 62 VSVGDVVVMK 71 (183)
Q Consensus 62 ~~rGDIVvf~ 71 (183)
+++||+|++.
T Consensus 44 I~~GD~VlVe 53 (83)
T smart00652 44 IRRGDIVLVD 53 (83)
T ss_pred EcCCCEEEEE
Confidence 4556666655
No 48
>CHL00057 rpl14 ribosomal protein L14
Probab=38.66 E-value=1.7e+02 Score=22.00 Aligned_cols=85 Identities=15% Similarity=0.202 Sum_probs=44.5
Q ss_pred EEEEEEeCCCCcccccCCCcEEEEEecCCCCCCCCCcCeEEE---EecCCCCCccEEEEEEEEcCceEEecCCCCCcccc
Q 030087 28 TYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVV---MKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVL 104 (183)
Q Consensus 28 ~~~~~V~g~SM~PtL~~~GD~Vlv~k~~~~~~~~~~rGDIVv---f~~p~~~~~~~vKRVia~pGD~V~~~~~~~~~~~v 104 (183)
...+.+.|.+..+.-. -||.+++.=-.-.....+++||++- ++.- .-++| ..|-.+.+
T Consensus 19 v~cI~v~~~~~~~~a~-vGD~IvvsVk~~~~~~k~kkg~v~kAvIVrtk-----~~~~r---~dG~~i~F---------- 79 (122)
T CHL00057 19 LMCIRVLGASNRKYAH-IGDVIIAVVKEAVPNMPLKRSEVVRAVIVRTC-----KELKR---DNGMIIRF---------- 79 (122)
T ss_pred EEEEEEeCCCCCcccc-CCCEEEEEEEeccCCCceecCCEEEEEEEEec-----cccCc---CCCcEEEc----------
Confidence 3445556666667666 6887765332110112355666541 1110 00111 12333333
Q ss_pred cCCeEEEEeCCCCCCCCCCCCCCccccccCCC
Q 030087 105 DKDECWVLADNENMKPKEANDSRTFGPVPMRN 136 (183)
Q Consensus 105 p~g~~~vlGDn~~~~~~~S~DSR~~G~V~~~~ 136 (183)
.++.+-++.++. +..=+|-+|||+.+.
T Consensus 80 ~~Na~VLin~~~-----~p~GTrI~Gpv~~el 106 (122)
T CHL00057 80 DDNAAVVIDQEG-----NPKGTRVFGPIAREL 106 (122)
T ss_pred CCceEEEECCCC-----CEeEeEEEccchHHH
Confidence 345666777665 468899999999775
No 49
>cd04721 BAH_plant_1 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. 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=36.75 E-value=98 Score=23.27 Aligned_cols=27 Identities=22% Similarity=0.268 Sum_probs=18.8
Q ss_pred CCCCcCeEEEEecCCCCCccEEEEEEEEc
Q 030087 60 KRVSVGDVVVMKDPEKSDNYIVRRLAAIE 88 (183)
Q Consensus 60 ~~~~rGDIVvf~~p~~~~~~~vKRVia~p 88 (183)
..++.||.|.+..++ +..++-+|..+-
T Consensus 6 ~~i~vGD~V~v~~~~--~~~~va~Ie~i~ 32 (130)
T cd04721 6 VTISVHDFVYVLSEE--EDRYVAYIEDLY 32 (130)
T ss_pred EEEECCCEEEEeCCC--CCcEEEEEEEEE
Confidence 347789999998654 345677776664
No 50
>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=35.75 E-value=1.9e+02 Score=21.70 Aligned_cols=85 Identities=26% Similarity=0.350 Sum_probs=46.7
Q ss_pred EEEEEEeCCCCcccccCCCcEEEEEecCCCCCCCCCcCeEEE---EecCCCCCccEEEEEEEEcCceEEecCCCCCcccc
Q 030087 28 TYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVV---MKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVL 104 (183)
Q Consensus 28 ~~~~~V~g~SM~PtL~~~GD~Vlv~k~~~~~~~~~~rGDIVv---f~~p~~~~~~~vKRVia~pGD~V~~~~~~~~~~~v 104 (183)
...+.+.|.+..+.-. -||.+++.=-.-.....+++|+++- ++. . .-++| ..|-.+.+
T Consensus 19 v~cI~v~~~~~~~~a~-iGD~I~vsVk~~~~~~~~kkg~v~~AvIVrt---k--k~~~r---~dG~~i~F---------- 79 (122)
T TIGR01067 19 VQCIKVLGGSRRRYAT-VGDVIVVVVKDAIPNGKVKKGDVVKAVIVRT---K--KGVRR---KDGSYIRF---------- 79 (122)
T ss_pred EEEEEEeCCCCCCccc-cCCEEEEEEEEcCCCCccccccEEEEEEEEe---e--cceEe---CCCCEEEC----------
Confidence 3455666777667777 7888776432110112356666642 221 0 01122 22333333
Q ss_pred cCCeEEEEeCCCCCCCCCCCCCCccccccCCC
Q 030087 105 DKDECWVLADNENMKPKEANDSRTFGPVPMRN 136 (183)
Q Consensus 105 p~g~~~vlGDn~~~~~~~S~DSR~~G~V~~~~ 136 (183)
.++.+-++.++. +..=+|-||||+++.
T Consensus 80 ~~Na~VLin~~~-----~p~GTrI~Gpv~~el 106 (122)
T TIGR01067 80 DDNACVLINKNK-----EPRGTRIFGPVAREL 106 (122)
T ss_pred CCceEEEECCCC-----CEeeeEEEccchHHH
Confidence 345666666664 468899999999775
No 51
>smart00002 PLP Myelin proteolipid protein (PLP or lipophilin).
Probab=34.60 E-value=10 Score=25.14 Aligned_cols=19 Identities=26% Similarity=0.613 Sum_probs=16.0
Q ss_pred CCCCCccccccCCCeEEEE
Q 030087 123 ANDSRTFGPVPMRNIVGRA 141 (183)
Q Consensus 123 S~DSR~~G~V~~~~I~Gkv 141 (183)
+.|-|+||.+|-++.-||+
T Consensus 23 C~D~RQyGilpwna~pgK~ 41 (60)
T smart00002 23 CVDARQYGILPWNAFPGKV 41 (60)
T ss_pred EeechhcceeecCCCCCch
Confidence 7999999999877777775
No 52
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=34.53 E-value=69 Score=26.97 Aligned_cols=77 Identities=14% Similarity=0.323 Sum_probs=43.9
Q ss_pred eCCCCcccccCCCcEEEEEecCC------------CCCCCCCcCeEEEEecCCCCCccEEEEEEEEcCceEEec-CCCCC
Q 030087 34 KGDQMAPVMGGLGGTLLVRKLPA------------ADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVST-DEKDE 100 (183)
Q Consensus 34 ~g~SM~PtL~~~GD~Vlv~k~~~------------~~~~~~~rGDIVvf~~p~~~~~~~vKRVia~pGD~V~~~-~~~~~ 100 (183)
....|.|.|+ .||.|+..=... .....++.|.+|-..+ ..+-|+++-.|--+..- ....-
T Consensus 105 ~~~~~r~~l~-vGD~v~AkV~~vd~~~~~~L~~k~~~~GkL~~G~iv~i~p------~kVpRvig~~~sm~~~l~~~~~~ 177 (239)
T COG1097 105 AEKDLRPFLN-VGDLVYAKVVDVDRDGEVELTLKDEGLGKLKNGQIVKIPP------SKVPRVIGKKGSMLNMLKEKTGC 177 (239)
T ss_pred cccccccccc-cCCEEEEEEEEccCCCceEEEeecCCCccccCCEEEEEch------hhcceEecCCCcHHHHhhhhcCe
Confidence 4689999999 899987633211 1345677788877764 24555555443222110 00011
Q ss_pred cccc-cCCeEEEEeCCCC
Q 030087 101 PFVL-DKDECWVLADNEN 117 (183)
Q Consensus 101 ~~~v-p~g~~~vlGDn~~ 117 (183)
.+.| ..|.+|+-|.|..
T Consensus 178 ~I~VG~NG~IWV~~~~~~ 195 (239)
T COG1097 178 EIIVGQNGRIWVDGENES 195 (239)
T ss_pred EEEEecCCEEEecCCCcc
Confidence 1222 2678999998873
No 53
>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=33.44 E-value=2.3e+02 Score=22.27 Aligned_cols=37 Identities=16% Similarity=0.350 Sum_probs=27.3
Q ss_pred CCCCCCcCeEEEEecCCCCCccEEEE---EEEEcCceEEecC
Q 030087 58 DPKRVSVGDVVVMKDPEKSDNYIVRR---LAAIEGYEMVSTD 96 (183)
Q Consensus 58 ~~~~~~rGDIVvf~~p~~~~~~~vKR---Via~pGD~V~~~~ 96 (183)
+.+.++.|++.+|... .....+|| ++.+.++++.+..
T Consensus 71 R~~~L~~GEvalY~~~--G~~I~L~~~G~ii~~~~~~~~v~a 110 (162)
T PF06890_consen 71 RPKGLKPGEVALYDDE--GQKIHLKRDGRIIEVTCKTVTVNA 110 (162)
T ss_pred cccCCCCCcEEEEcCC--CCEEEEEecceEEeccCceEEEec
Confidence 4567899999999852 23455665 7788889888874
No 54
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=33.24 E-value=42 Score=24.35 Aligned_cols=11 Identities=36% Similarity=0.688 Sum_probs=6.2
Q ss_pred CCcCeEEEEec
Q 030087 62 VSVGDVVVMKD 72 (183)
Q Consensus 62 ~~rGDIVvf~~ 72 (183)
+.+||+|++..
T Consensus 60 I~~GD~VlVe~ 70 (100)
T PRK04012 60 IREGDVVIVAP 70 (100)
T ss_pred ecCCCEEEEEe
Confidence 45566666553
No 55
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=32.60 E-value=52 Score=23.39 Aligned_cols=19 Identities=16% Similarity=0.333 Sum_probs=10.5
Q ss_pred CcEEEEEecCCCCCCCCCcCeEE
Q 030087 46 GGTLLVRKLPAADPKRVSVGDVV 68 (183)
Q Consensus 46 GD~Vlv~k~~~~~~~~~~rGDIV 68 (183)
||.|.|.-..| ++.+|+|+
T Consensus 50 GD~V~VE~spY----DltkGRIi 68 (87)
T PRK12442 50 GDRVTLELSPY----DLTKGRIN 68 (87)
T ss_pred CCEEEEEECcc----cCCceeEE
Confidence 66666665433 45556554
No 56
>PF01426 BAH: BAH domain; InterPro: IPR001025 The BAH (bromo-adjacent homology) family contains proteins such as eukaryotic DNA (cytosine-5) methyltransferases IPR001525 from INTERPRO, the origin recognition complex 1 (Orc1) proteins, as well as several proteins involved in transcriptional regulation. The BAH domain appears to act as a protein-protein interaction module specialised in gene silencing, as suggested for example by its interaction within yeast Orc1p with the silent information regulator Sir1p. The BAH module might therefore play an important role by linking DNA methylation, replication and transcriptional regulation [].; GO: 0003677 DNA binding; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 3SWR_A 3PTA_A 1M4Z_A 1ZBX_A ....
Probab=31.78 E-value=50 Score=23.37 Aligned_cols=27 Identities=30% Similarity=0.372 Sum_probs=17.9
Q ss_pred CCcCeEEEEecCCCCCccEEEEEEEEc
Q 030087 62 VSVGDVVVMKDPEKSDNYIVRRLAAIE 88 (183)
Q Consensus 62 ~~rGDIVvf~~p~~~~~~~vKRVia~p 88 (183)
++.||.|.+..+......+|.||..+-
T Consensus 3 ~~vGD~V~v~~~~~~~~~~v~~I~~i~ 29 (119)
T PF01426_consen 3 YKVGDFVYVKPDDPPEPPYVARIEEIW 29 (119)
T ss_dssp EETTSEEEEECTSTTSEEEEEEEEEEE
T ss_pred EeCCCEEEEeCCCCCCCCEEEEEEEEE
Confidence 345777777766545567777777663
No 57
>PF07039 DUF1325: SGF29 tudor-like domain; InterPro: IPR010750 SAGA-associated factor 29 is involved in transcriptional regulation, probably through association with histone acetyltransferase (HAT) complexes like the TFTC-HAT or STAGA complexes. It also may be involved in MYC-mediated oncogenic transformation. It is a component of the ATAC complex, which is a complex with histone acetyltransferase activity on histones H3 and H4 []. This entry represents a domain found in yeast and human SAGA-associated factor 29 proteins that is related to the tudor domain. ; PDB: 3MP6_A 3MP1_A 3MP8_A 3MET_B 3ME9_A 3MEU_B 3MEA_A 3MEV_B 3LX7_A 3MEW_A.
Probab=31.23 E-value=1.1e+02 Score=22.99 Aligned_cols=52 Identities=15% Similarity=0.258 Sum_probs=35.2
Q ss_pred CcCeEEEEecC--CCCCccEEEEEEEEcCce--EEecCCC----CCcccccCCeEEEEeC
Q 030087 63 SVGDVVVMKDP--EKSDNYIVRRLAAIEGYE--MVSTDEK----DEPFVLDKDECWVLAD 114 (183)
Q Consensus 63 ~rGDIVvf~~p--~~~~~~~vKRVia~pGD~--V~~~~~~----~~~~~vp~g~~~vlGD 114 (183)
+.||-|+++.+ +..+.+++-+|+...++. .++.|.. ...++++..++.-+=.
T Consensus 1 q~G~~VAak~~~~~~~~~WIla~Vv~~~~~~~rYeV~D~d~~~~~~~~~~~~~~iIPLP~ 60 (130)
T PF07039_consen 1 QPGDQVAAKVKQGNEEEEWILAEVVKYNSDGNRYEVEDPDPEEEKKRYKLSRKQIIPLPK 60 (130)
T ss_dssp -TT-EEEEEECTTTTTCEEEEEEEEEEETTTTEEEEEETTTCTTTEEEEEEGGGEEEE-S
T ss_pred CCCCEEEEEcCCCCCCCCEEEEEEEEEeCCCCEEEEecCCCCCCCceEEeCHHHEEECCC
Confidence 46999999876 345689999999998775 6665432 2356777777777744
No 58
>smart00439 BAH Bromo adjacent homology domain.
Probab=30.89 E-value=95 Score=21.87 Aligned_cols=17 Identities=24% Similarity=0.579 Sum_probs=13.9
Q ss_pred cccCCCeEEEEEEEEec
Q 030087 131 PVPMRNIVGRAIYCLRT 147 (183)
Q Consensus 131 ~V~~~~I~Gkv~~~~~p 147 (183)
-++.+.|+|++.....+
T Consensus 70 ~i~~~~I~~kc~V~~~~ 86 (120)
T smart00439 70 TVPLSDIIGKCNVLSKS 86 (120)
T ss_pred cCChHHeeeEEEEEEcc
Confidence 58999999999877544
No 59
>cd04760 BAH_Dnmt1_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. 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=28.73 E-value=2.6e+02 Score=21.09 Aligned_cols=24 Identities=8% Similarity=0.151 Sum_probs=17.9
Q ss_pred CCccccccCCCeEEEEEEEEecCC
Q 030087 126 SRTFGPVPMRNIVGRAIYCLRTAV 149 (183)
Q Consensus 126 SR~~G~V~~~~I~Gkv~~~~~p~~ 149 (183)
|+..--.+.+.|.||+...+.+++
T Consensus 64 sd~c~d~~l~~I~~Kv~V~~~~p~ 87 (124)
T cd04760 64 VDECEDMALSSIHGKVNVIYKAPS 87 (124)
T ss_pred ecccCCcchHHheeeeEEEEeCCC
Confidence 333445677899999999988865
No 60
>PF10377 ATG11: Autophagy-related protein 11; InterPro: IPR019460 This family consists of proteins involved in telomere maintenance. In Schizosaccharomyces pombe (fission yeast) this protein is called Taf1 (taz1 interacting factor) and is part of the telomere cap complex. In Saccharomyces cerevisiae (baker's yeast) this protein is called ATG11 and is known to be involved in vacuolar targeting and peroxisome degradation [, ].
Probab=28.30 E-value=2.6e+02 Score=21.00 Aligned_cols=34 Identities=24% Similarity=0.470 Sum_probs=21.6
Q ss_pred CccEEEEEEEEcCceEEecCCCCCcccccCCeEEE
Q 030087 77 DNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWV 111 (183)
Q Consensus 77 ~~~~vKRVia~pGD~V~~~~~~~~~~~vp~g~~~v 111 (183)
..+++.||+.++--.+.- +....+|.+|.|..|.
T Consensus 89 ~~w~vgrI~~~e~~~v~~-~~~~Npy~Lp~Gt~~y 122 (129)
T PF10377_consen 89 REWIVGRIVSIEECQVKD-DKDSNPYNLPVGTKFY 122 (129)
T ss_pred CCEEEEEEEEEEEEEecc-CCCCCCCcCCCCCEEE
Confidence 357888888776333321 2456778888887553
No 61
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=28.07 E-value=2.3e+02 Score=20.72 Aligned_cols=40 Identities=15% Similarity=0.252 Sum_probs=24.1
Q ss_pred CcEEEEEecCCCCCCCCCcCeEEEEecCCCCCccEEEEEEEEc
Q 030087 46 GGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIE 88 (183)
Q Consensus 46 GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~~~~vKRVia~p 88 (183)
+|...+..... --..+..||+|.++..+ +.+.+.+++.-.
T Consensus 11 ~~~y~l~n~Pf-~a~glA~gDvV~~~~~~--g~~~~~~~v~~s 50 (117)
T PF14085_consen 11 DDTYRLDNIPF-FAYGLALGDVVRAEPDD--GELWFQKVVESS 50 (117)
T ss_pred CCEEEEEeccc-ccCCCCCCCEEEEEeCC--CeEEEEEEEecC
Confidence 44444544432 23679999999999754 445555554433
No 62
>PF13124 DUF3963: Protein of unknown function (DUF3963)
Probab=27.58 E-value=1.1e+02 Score=18.30 Aligned_cols=17 Identities=24% Similarity=0.473 Sum_probs=11.3
Q ss_pred cHHHHHHHHHHHHHHHH
Q 030087 3 SLSTWFRYIANKLEYSV 19 (183)
Q Consensus 3 ~~~~wl~~~~~~i~i~v 19 (183)
.+.+|+|.+-.++++.+
T Consensus 15 diqkwirnit~cfal~v 31 (40)
T PF13124_consen 15 DIQKWIRNITFCFALLV 31 (40)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 47899997766554433
No 63
>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=26.84 E-value=2.7e+02 Score=20.81 Aligned_cols=79 Identities=13% Similarity=0.032 Sum_probs=41.4
Q ss_pred CCCCcCeEEEEecCCCCC----------ccEEEEEEEEcCc---eEEec------CC--CCCcccccCCeEEEEeCCCCC
Q 030087 60 KRVSVGDVVVMKDPEKSD----------NYIVRRLAAIEGY---EMVST------DE--KDEPFVLDKDECWVLADNENM 118 (183)
Q Consensus 60 ~~~~rGDIVvf~~p~~~~----------~~~vKRVia~pGD---~V~~~------~~--~~~~~~vp~g~~~vlGDn~~~ 118 (183)
..++.||+|+++.++... ..+|-||..+.-+ .-.+. .. .... .-.+.++|+. |+.+.
T Consensus 4 ~~i~vGD~V~v~~d~~~~~~~~~~~~~~~~~i~~V~~~~e~~~g~~~~h~~W~yrp~eTv~g~-~~~~~ElFLS-d~c~~ 81 (130)
T cd04712 4 LTIRVGDVVSVERDDADSTTKWNDDHRWLPLVQFVEYMKKGSDGSKMFHGRWLYRGCDTVLGN-YANERELFLT-NECTC 81 (130)
T ss_pred CEEeCCCEEEEcCCCCCccccccccccccceEEEEEEeeecCCCceEEEEEEEEcchhccccc-cCCCceEEEe-ccccc
Confidence 456778888888755431 4577777766422 11110 00 0111 3345566664 44321
Q ss_pred CCCCCCCCCccccccCCCeEEEEEEEEecCC
Q 030087 119 KPKEANDSRTFGPVPMRNIVGRAIYCLRTAV 149 (183)
Q Consensus 119 ~~~~S~DSR~~G~V~~~~I~Gkv~~~~~p~~ 149 (183)
++.++. .+.|+||+..-+.+..
T Consensus 82 ---~~~~~~------~~~I~~k~~V~~~~~~ 103 (130)
T cd04712 82 ---LELDLL------STEIKGVHKVDWSGTP 103 (130)
T ss_pred ---cccccc------cceeEEEEEEEEecCc
Confidence 122211 5599999988876543
No 64
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=26.63 E-value=1.9e+02 Score=21.31 Aligned_cols=28 Identities=18% Similarity=0.487 Sum_probs=19.3
Q ss_pred CCCCCcCeEEEEecCCCCCccEEEEEEEE
Q 030087 59 PKRVSVGDVVVMKDPEKSDNYIVRRLAAI 87 (183)
Q Consensus 59 ~~~~~rGDIVvf~~p~~~~~~~vKRVia~ 87 (183)
.+.++.||.++|..-.+ +..+.-+|+.+
T Consensus 29 r~~ikvGD~I~f~~~~~-~~~l~v~V~~i 56 (109)
T cd06555 29 RQQIKVGDKILFNDLDT-GQQLLVKVVDI 56 (109)
T ss_pred hhcCCCCCEEEEEEcCC-CcEEEEEEEEE
Confidence 35799999999986333 44566666655
No 65
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A 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.
Probab=25.75 E-value=61 Score=22.47 Aligned_cols=11 Identities=27% Similarity=0.604 Sum_probs=7.3
Q ss_pred CCcCeEEEEec
Q 030087 62 VSVGDVVVMKD 72 (183)
Q Consensus 62 ~~rGDIVvf~~ 72 (183)
+++||+|++.+
T Consensus 39 IkrGd~VlV~p 49 (78)
T cd05792 39 IKRGDFVLVEP 49 (78)
T ss_pred EEeCCEEEEEe
Confidence 56677777754
No 66
>KOG4146 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=23.34 E-value=1.6e+02 Score=21.26 Aligned_cols=37 Identities=16% Similarity=0.215 Sum_probs=26.5
Q ss_pred EEEeCCCCcccccCCCcEEEEEecCCC----CCCCCCcCeEEEEec
Q 030087 31 YGNKGDQMAPVMGGLGGTLLVRKLPAA----DPKRVSVGDVVVMKD 72 (183)
Q Consensus 31 ~~V~g~SM~PtL~~~GD~Vlv~k~~~~----~~~~~~rGDIVvf~~ 72 (183)
+.+.++|..| |-++++++..+. ....++.||.|+|-.
T Consensus 56 lFi~~gsvrp-----Gii~lINd~DWEllekedy~ledgD~ivfiS 96 (101)
T KOG4146|consen 56 LFIHHGSVRP-----GIIVLINDMDWELLEKEDYPLEDGDHIVFIS 96 (101)
T ss_pred eEeeCCcCcC-----cEEEEEeccchhhhcccccCcccCCEEEEEE
Confidence 6677888774 666888776541 235788999999975
No 67
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=22.63 E-value=1.3e+02 Score=22.48 Aligned_cols=28 Identities=21% Similarity=0.126 Sum_probs=14.0
Q ss_pred CCCCcCeEEEEecCCCCCccEEEEEEEE
Q 030087 60 KRVSVGDVVVMKDPEKSDNYIVRRLAAI 87 (183)
Q Consensus 60 ~~~~rGDIVvf~~p~~~~~~~vKRVia~ 87 (183)
..++.||-|+...+.....+.=..|++.
T Consensus 54 ~~L~~GD~VLA~~~~~~~~Y~Pg~V~~~ 81 (124)
T PF15057_consen 54 HSLQVGDKVLAPWEPDDCRYGPGTVIAG 81 (124)
T ss_pred CcCCCCCEEEEecCcCCCEEeCEEEEEC
Confidence 3455566666655444333333555543
No 68
>PHA02141 hypothetical protein
Probab=22.36 E-value=84 Score=22.36 Aligned_cols=22 Identities=18% Similarity=0.318 Sum_probs=15.4
Q ss_pred ccHHHHHHHHHHHHHHHHHHhh
Q 030087 2 VSLSTWFRYIANKLEYSVSISW 23 (183)
Q Consensus 2 ~~~~~wl~~~~~~i~i~v~i~~ 23 (183)
+|+.+|++.-+..+++.+++++
T Consensus 6 ss~~swl~~n~ly~ii~~l~~~ 27 (105)
T PHA02141 6 SSTISWLRNNVLYMIIIGLLGW 27 (105)
T ss_pred HHHHHHHHhchHHHHHHHHHHH
Confidence 5789999977766666555544
No 69
>PF09285 Elong-fact-P_C: Elongation factor P, C-terminal; InterPro: IPR015365 These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology []. ; GO: 0043043 peptide biosynthetic process, 0005737 cytoplasm; PDB: 1YBY_A 3OYY_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H.
Probab=21.16 E-value=2.2e+02 Score=18.41 Aligned_cols=38 Identities=18% Similarity=0.299 Sum_probs=20.5
Q ss_pred CCCcccccCCCcEEEEEecCCCCCCCCCcCeEEEEecCCCCCccEEEE
Q 030087 36 DQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRR 83 (183)
Q Consensus 36 ~SM~PtL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~p~~~~~~~vKR 83 (183)
.++.|..-..|-.|.|..+ ++.||.|.+.... ..|+.|
T Consensus 19 ~~~K~A~letG~~i~VP~F-------I~~Gd~I~VdT~~---g~Yv~R 56 (56)
T PF09285_consen 19 SSYKPATLETGAEIQVPLF-------IEEGDKIKVDTRD---GSYVER 56 (56)
T ss_dssp TTEEEEEETTS-EEEEETT---------TT-EEEEETTT---TEEEEE
T ss_pred CCccEEEEcCCCEEEccce-------ecCCCEEEEECCC---CeEeCC
Confidence 4556654435666666554 6679999998632 246665
Done!