Query 030852
Match_columns 170
No_of_seqs 116 out of 1183
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 05:33:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030852.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030852hhsearch_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 4.6E-38 9.9E-43 243.9 15.7 133 11-153 2-163 (163)
2 KOG0171 Mitochondrial inner me 100.0 6.7E-36 1.4E-40 229.0 11.5 140 12-160 16-166 (176)
3 KOG1568 Mitochondrial inner me 100.0 6.8E-36 1.5E-40 228.6 10.5 162 3-168 3-167 (174)
4 PRK10861 signal peptidase I; P 100.0 6.6E-34 1.4E-38 241.2 16.7 140 5-154 58-306 (324)
5 PRK13838 conjugal transfer pil 99.9 3.2E-23 6.9E-28 162.9 14.6 92 57-149 37-172 (176)
6 TIGR02771 TraF_Ti conjugative 99.9 4.3E-22 9.3E-27 155.9 12.5 80 69-149 45-169 (171)
7 PRK13884 conjugal transfer pep 99.9 3.1E-21 6.7E-26 151.9 14.2 81 69-149 49-176 (178)
8 TIGR02754 sod_Ni_protease nick 99.9 1.4E-21 3E-26 137.1 9.4 89 32-146 1-89 (90)
9 PF10502 Peptidase_S26: Signal 99.8 2.5E-22 5.3E-27 152.2 2.7 89 57-149 12-137 (138)
10 cd06530 S26_SPase_I The S26 Ty 99.8 1.9E-20 4E-25 129.7 9.2 84 31-145 2-85 (85)
11 TIGR02228 sigpep_I_arch signal 99.8 5.9E-18 1.3E-22 131.0 12.3 85 33-146 35-119 (158)
12 COG0681 LepB Signal peptidase 99.6 3E-15 6.6E-20 114.5 11.6 127 7-145 7-144 (166)
13 COG4959 TraF Type IV secretory 99.4 3.6E-13 7.9E-18 102.8 7.0 86 60-148 46-168 (173)
14 PF00717 Peptidase_S24: Peptid 99.2 2.7E-11 5.8E-16 80.4 6.9 57 33-104 1-57 (70)
15 cd06462 Peptidase_S24_S26 The 99.2 6.5E-11 1.4E-15 80.5 8.9 83 31-145 2-84 (84)
16 KOG3342 Signal peptidase I [In 98.9 1.7E-08 3.7E-13 77.2 10.1 88 31-146 50-144 (180)
17 cd06529 S24_LexA-like Peptidas 98.9 1.8E-08 3.8E-13 68.3 8.8 61 31-124 2-62 (81)
18 COG2932 Predicted transcriptio 98.8 5.5E-08 1.2E-12 78.2 10.3 89 30-151 124-212 (214)
19 PRK10276 DNA polymerase V subu 98.7 3.5E-07 7.6E-12 69.1 10.6 85 29-150 51-136 (139)
20 TIGR00498 lexA SOS regulatory 98.6 1.1E-06 2.4E-11 69.7 11.3 88 28-152 110-198 (199)
21 PRK00215 LexA repressor; Valid 98.5 1.7E-06 3.7E-11 68.9 11.1 86 28-150 117-203 (205)
22 PRK12423 LexA repressor; Provi 98.4 3.4E-06 7.3E-11 67.5 10.7 85 30-150 115-200 (202)
23 COG1974 LexA SOS-response tran 98.0 0.00017 3.7E-09 58.0 11.5 88 29-152 112-200 (201)
24 TIGR02594 conserved hypothetic 86.7 3.1 6.6E-05 31.0 6.4 41 70-127 73-113 (129)
25 PRK00364 groES co-chaperonin G 83.0 5.1 0.00011 28.3 5.8 87 55-145 6-94 (95)
26 cd00320 cpn10 Chaperonin 10 Kd 80.3 7.7 0.00017 27.2 5.9 86 55-144 5-92 (93)
27 COG0681 LepB Signal peptidase 77.2 3.2 7E-05 31.0 3.5 13 70-82 84-96 (166)
28 PF00166 Cpn10: Chaperonin 10 74.5 4.8 0.0001 28.1 3.5 87 55-145 5-93 (93)
29 COG0234 GroS Co-chaperonin Gro 72.0 23 0.0005 25.2 6.5 68 54-122 5-87 (96)
30 PF05257 CHAP: CHAP domain; I 68.8 14 0.0003 26.6 5.0 36 69-104 61-97 (124)
31 cd04712 BAH_DCM_I BAH, or Brom 64.8 55 0.0012 24.3 7.8 77 70-152 5-102 (130)
32 PRK14533 groES co-chaperonin G 60.9 41 0.00088 23.6 5.9 82 55-145 6-89 (91)
33 smart00439 BAH Bromo adjacent 55.5 68 0.0015 22.3 8.2 16 135-150 70-85 (120)
34 COG0093 RplN Ribosomal protein 54.5 45 0.00098 24.7 5.4 33 107-140 74-106 (122)
35 TIGR00008 infA translation ini 50.1 16 0.00035 24.3 2.3 19 56-77 48-66 (68)
36 COG0361 InfA Translation initi 48.9 18 0.00038 24.7 2.4 19 56-77 50-68 (75)
37 PF10000 ACT_3: ACT domain; I 48.5 12 0.00026 25.1 1.5 35 37-82 12-47 (72)
38 PTZ00414 10 kDa heat shock pro 47.5 1E+02 0.0022 22.0 7.2 38 56-97 16-53 (100)
39 TIGR03673 rpl14p_arch 50S ribo 47.1 1.2E+02 0.0026 22.8 7.4 34 106-140 83-116 (131)
40 TIGR01067 rplN_bact ribosomal 46.6 1.2E+02 0.0025 22.4 7.4 31 109-140 76-106 (122)
41 PF00238 Ribosomal_L14: Riboso 46.4 81 0.0018 23.2 5.9 30 109-139 76-105 (122)
42 PF15057 DUF4537: Domain of un 45.4 32 0.0007 25.3 3.6 53 69-121 54-113 (124)
43 PF01176 eIF-1a: Translation i 45.1 18 0.00039 23.5 2.0 12 70-81 41-52 (65)
44 cd04370 BAH BAH, or Bromo Adja 44.6 56 0.0012 22.6 4.7 72 70-151 3-89 (123)
45 cd04456 S1_IF1A_like S1_IF1A_l 44.3 22 0.00047 24.2 2.3 10 71-80 39-48 (78)
46 COG4929 Uncharacterized membra 44.2 24 0.00052 28.2 2.8 26 56-81 35-60 (190)
47 CHL00057 rpl14 ribosomal prote 43.2 1.3E+02 0.0029 22.2 7.3 32 108-140 75-106 (122)
48 cd04720 BAH_Orc1p_Yeast BAH, o 42.7 1.1E+02 0.0025 23.8 6.5 89 56-158 39-150 (179)
49 PF14085 DUF4265: Domain of un 42.6 84 0.0018 22.7 5.4 46 56-103 11-57 (117)
50 cd04714 BAH_BAHCC1 BAH, or Bro 42.2 39 0.00084 24.6 3.6 79 70-160 3-94 (121)
51 cd05793 S1_IF1A S1_IF1A: Trans 41.8 24 0.00052 23.9 2.2 10 71-80 39-48 (77)
52 PRK12442 translation initiatio 41.7 27 0.00059 24.4 2.5 19 56-77 50-68 (87)
53 smart00652 eIF1a eukaryotic tr 39.6 27 0.00058 24.0 2.2 10 71-80 44-53 (83)
54 COG3602 Uncharacterized protei 39.0 18 0.00039 26.8 1.3 37 37-83 12-48 (134)
55 cd04721 BAH_plant_1 BAH, or Br 38.7 83 0.0018 23.3 4.9 77 70-160 7-97 (130)
56 PF10377 ATG11: Autophagy-rela 37.6 1.3E+02 0.0028 22.3 5.8 34 86-119 89-122 (129)
57 PF06890 Phage_Mu_Gp45: Bacter 37.6 1.9E+02 0.0042 22.4 7.1 36 68-105 72-110 (162)
58 COG1934 Uncharacterized protei 37.5 2E+02 0.0044 22.6 8.0 56 21-84 22-77 (173)
59 cd04760 BAH_Dnmt1_I BAH, or Br 35.9 67 0.0014 23.9 4.0 22 132-153 66-87 (124)
60 TIGR02219 phage_NlpC_fam putat 35.8 91 0.002 22.9 4.8 13 69-81 75-87 (134)
61 smart00002 PLP Myelin proteoli 35.0 9.5 0.00021 24.9 -0.6 20 126-145 22-41 (60)
62 PF01426 BAH: BAH domain; Int 34.4 50 0.0011 23.0 3.0 26 71-96 3-28 (119)
63 PRK04012 translation initiatio 33.3 38 0.00083 24.2 2.2 10 71-80 60-69 (100)
64 cd04717 BAH_polybromo BAH, or 33.2 63 0.0014 23.2 3.5 69 70-148 3-84 (121)
65 PRK05483 rplN 50S ribosomal pr 31.1 2.2E+02 0.0047 21.0 7.2 31 109-140 76-106 (122)
66 KOG4146 Ubiquitin-like protein 31.1 66 0.0014 22.9 3.0 26 56-81 66-96 (101)
67 PF00278 Orn_DAP_Arg_deC: Pyri 30.6 69 0.0015 22.3 3.3 25 56-82 70-94 (116)
68 COG5131 URM1 Ubiquitin-like pr 29.9 65 0.0014 22.8 2.9 26 56-81 61-91 (96)
69 COG1097 RRP4 RNA-binding prote 28.8 1.3E+02 0.0029 24.9 5.0 75 35-125 105-195 (239)
70 PF01568 Molydop_binding: Moly 28.7 1.4E+02 0.0029 20.5 4.5 27 57-83 30-56 (110)
71 PTZ00054 60S ribosomal protein 28.4 2.7E+02 0.0058 21.2 7.2 34 106-140 91-124 (139)
72 PF09285 Elong-fact-P_C: Elong 27.7 1.6E+02 0.0034 18.8 4.2 39 36-92 18-56 (56)
73 PF05382 Amidase_5: Bacterioph 24.7 1.2E+02 0.0025 23.1 3.7 38 33-82 50-87 (145)
74 PRK01191 rpl24p 50S ribosomal 24.7 1.4E+02 0.0031 22.0 4.1 25 70-96 45-69 (120)
75 PF11337 DUF3139: Protein of u 24.4 1.2E+02 0.0027 20.4 3.5 17 1-17 1-17 (85)
76 PF07039 DUF1325: SGF29 tudor- 24.3 99 0.0021 23.0 3.2 51 72-122 1-60 (130)
77 PF10222 DUF2152: Uncharacteri 23.9 89 0.0019 29.4 3.5 67 57-133 52-118 (604)
78 PF07423 DUF1510: Protein of u 23.9 1E+02 0.0022 25.2 3.4 15 110-124 163-179 (217)
79 PTZ00194 60S ribosomal protein 23.7 1.8E+02 0.0038 22.3 4.5 17 70-86 46-62 (143)
80 cd04709 BAH_MTA BAH, or Bromo 23.7 2.3E+02 0.005 21.9 5.3 24 128-151 85-108 (164)
81 PRK15095 FKBP-type peptidyl-pr 23.5 2.3E+02 0.005 21.5 5.2 35 70-106 92-126 (156)
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=4.6e-38 Score=243.94 Aligned_cols=133 Identities=36% Similarity=0.532 Sum_probs=119.9
Q ss_pred HHHHHHHHHHHHHHHheeeEEEEEcCCCccccccCCCcCCCCCCCCcEEEEEceeccCCCCccccEEEEecCCCCCcceE
Q 030852 11 TKNCFTFGLIGLTISDRYASIVPVRGSSMSPTFNLTTDSFMGSLSDDYVLVEKFCLQKYKFSHGDVIVFCSPSNHKEKHV 90 (170)
Q Consensus 11 ~~~~~~~~~v~~~i~~~~~~~~~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~~GDiV~f~~p~~~~~~~v 90 (170)
+..++++++++++++.++++.+.|+|+||+|||+. ||+++++|+.+...++++||+|+|+.|.++++.++
T Consensus 2 ~~~~~~~~~~~~~i~~~~~~~~~v~g~SM~Ptl~~----------Gd~vlv~k~~~~~~~~~rGDiVvf~~~~~~~~~~i 71 (163)
T TIGR02227 2 ILSLLIAILLALLIRTFVFFPYKIPGGSMEPTLKE----------GDRILVNKFAYGTSDPKRGDIVVFKDPDDNKNIYV 71 (163)
T ss_pred HHHHHHHHHHHHHHHhhEEEEEEECCcccccchhC----------CCEEEEEEeEcCCCCCCCCcEEEEecCCCCCceeE
Confidence 45566677778899999999999999999999999 99999999876667999999999999987788999
Q ss_pred EEEEeeCCCeEEecCC-----------------------------CCeEEecCCeEEEeeCCCCCCCCCCccccccCCCE
Q 030852 91 KRIIGLPGDWIGTPMT-----------------------------NDVMKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLI 141 (170)
Q Consensus 91 KRVia~~Gd~v~i~~~-----------------------------~~~~~vp~~~~~v~Gdn~~~s~DSR~~G~V~~~~I 141 (170)
|||+|+|||+|.++++ ..+.+||+|||||+|||+++|.|||+||+|++++|
T Consensus 72 KRVig~pGd~v~i~~~~l~vNg~~~~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~~fvlGDnr~~S~DSR~~G~V~~~~I 151 (163)
T TIGR02227 72 KRVIGLPGDKVEFRDGKLYINGKKIDEPYLKPNGSLDTSGFNTTDFKPVTVPPGHYFVLGDNRDNSLDSRYFGFVPIDDI 151 (163)
T ss_pred EEEEecCCCEEEEECCEEEECCEECcccccccccccccccccccccCceEECCCCEEEECCCCCCCcccCCcCcCCHHHe
Confidence 9999999999998541 12358999999999999999999999999999999
Q ss_pred EEEEEEEEeCCC
Q 030852 142 KGWVTHILWPPQ 153 (170)
Q Consensus 142 iGkv~~~~~p~~ 153 (170)
+|||.+++||++
T Consensus 152 ~Gk~~~~~~p~~ 163 (163)
T TIGR02227 152 IGKVSFVFYPFD 163 (163)
T ss_pred EEEEEEEECCCC
Confidence 999999999985
No 2
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.7e-36 Score=228.97 Aligned_cols=140 Identities=35% Similarity=0.617 Sum_probs=123.9
Q ss_pred HHHHHHHHHHHHHHheeeEEEEEcCCCccccccCCCcCCCCCCCCcEEEEEceeccCCCCccccEEEEecCCCCCcceEE
Q 030852 12 KNCFTFGLIGLTISDRYASIVPVRGSSMSPTFNLTTDSFMGSLSDDYVLVEKFCLQKYKFSHGDVIVFCSPSNHKEKHVK 91 (170)
Q Consensus 12 ~~~~~~~~v~~~i~~~~~~~~~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~~GDiV~f~~p~~~~~~~vK 91 (170)
.....-.++++....|++++...+|.||+||++++ ||+++..|+.+.++.+++||||++.+|.++++.+||
T Consensus 16 ~~~~~~~~f~h~t~~yl~e~~~~~gpSM~PTl~~~---------gd~l~aEkls~~f~~~~~gDIVi~~sP~~~~~~~cK 86 (176)
T KOG0171|consen 16 CSEIAYAAFTHVTHEYLGEFVMCSGPSMEPTLHDG---------GDVLLAEKLSYRFRKPQVGDIVIAKSPPDPKEHICK 86 (176)
T ss_pred HHHHHHHHHHHHHHHHhcceeeccCCCcCceecCC---------CcEEehhhhhHhhcCCCCCCEEEEeCCCCchhhhhh
Confidence 33444455566777799999999999999999996 899988999999999999999999999999999999
Q ss_pred EEEeeCCCeEEecCC-----------CCeEEecCCeEEEeeCCCCCCCCCCccccccCCCEEEEEEEEEeCCCCccccCc
Q 030852 92 RIIGLPGDWIGTPMT-----------NDVMKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLIKGWVTHILWPPQRVRHIER 160 (170)
Q Consensus 92 RVia~~Gd~v~i~~~-----------~~~~~vp~~~~~v~Gdn~~~s~DSR~~G~V~~~~IiGkv~~~~~p~~~~~~~~~ 160 (170)
||+|+|||.+.+... ..++.||+||+||+|||.++|.|||+|||+|.+.|+||+.+++||.+++..+.-
T Consensus 87 RIva~eGD~v~v~~~~~~~n~~~e~~~~~i~VP~GhVfv~GDN~~nS~DSr~yGplP~glI~gRvv~r~Wp~s~~~~~~~ 166 (176)
T KOG0171|consen 87 RIVAMEGDLVEVHDGPLVVNDLVEKFSTPIRVPEGHVFVEGDNRNNSLDSRNYGPLPMGLIQGRVVFRIWPPSRVSGLIL 166 (176)
T ss_pred eeeccCCceEEEecCCcccchhhhhccceeeccCceEEEecCCCCCcccccccCCCchhheeeeEEEEecCchhcceeee
Confidence 999999998777542 234799999999999999999999999999999999999999999999876543
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=6.8e-36 Score=228.56 Aligned_cols=162 Identities=37% Similarity=0.621 Sum_probs=140.5
Q ss_pred hhHHHHHHHHHHHHHHH--HHHHHHheeeEEEEEcCCCccccccCCCcCCCCCCCCcEEEEEceeccCCCCccccEEEEe
Q 030852 3 AQNFLWSFTKNCFTFGL--IGLTISDRYASIVPVRGSSMSPTFNLTTDSFMGSLSDDYVLVEKFCLQKYKFSHGDVIVFC 80 (170)
Q Consensus 3 ~~~~~~~~~~~~~~~~~--v~~~i~~~~~~~~~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~~GDiV~f~ 80 (170)
.+..++.|.+.++.++. +.+.+...++....|.|.||.|++++.+... ..|+|+++|+........+||+|+|.
T Consensus 3 ~~~~~~~~~ksl~~s~~~~v~~t~~DrV~~va~v~G~smqPtlnP~~~~~----~~d~Vll~k~~v~n~~~~rGDiVvl~ 78 (174)
T KOG1568|consen 3 RRYIFKVFEKSLTGSLKWHVLLTFSDRVVHVAQVYGSSMQPTLNPTMNTN----EKDTVLLRKWNVKNRKVSRGDIVVLK 78 (174)
T ss_pred HHHHHHHHHhceeeeeeeheeeeeeeeEEEEeEEecCcCCCccCCCcccc----cccEEEEEeeccccceeccCCEEEEe
Confidence 34455566666666655 5677888899999999999999999964333 24999999998665568899999999
Q ss_pred cCCCCCcceEEEEEeeCCCeEEe-cCCCCeEEecCCeEEEeeCCCCCCCCCCccccccCCCEEEEEEEEEeCCCCccccC
Q 030852 81 SPSNHKEKHVKRIIGLPGDWIGT-PMTNDVMKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLIKGWVTHILWPPQRVRHIE 159 (170)
Q Consensus 81 ~p~~~~~~~vKRVia~~Gd~v~i-~~~~~~~~vp~~~~~v~Gdn~~~s~DSR~~G~V~~~~IiGkv~~~~~p~~~~~~~~ 159 (170)
+|+++++.+||||+|+|||++.. .+.+..+.+|+|||||+|||...|+|||.||||+.+.|+|+|++++||+.||++++
T Consensus 79 sP~~p~~~~iKRv~alegd~~~t~~~k~~~v~vpkghcWVegDn~~hs~DSntFGPVS~gli~grai~ilwpP~R~~~~~ 158 (174)
T KOG1568|consen 79 SPNDPDKVIIKRVAALEGDIMVTEDEKEEPVVVPKGHCWVEGDNQKHSYDSNTFGPVSTGLIVGRAIYILWPPVRWQRLD 158 (174)
T ss_pred CCCChhheeeeeeecccccEeccCCCCCCceecCCCcEEEecCCcccccccCccCCcchhheeeeEEEEEcChHHhhhhc
Confidence 99999999999999999999886 44678899999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCC
Q 030852 160 RKNHENILS 168 (170)
Q Consensus 160 ~~~~~~~~~ 168 (170)
+..|.-|++
T Consensus 159 ~~~~~~~~~ 167 (174)
T KOG1568|consen 159 KESPGRRVP 167 (174)
T ss_pred ccCCccccc
Confidence 988877764
No 4
>PRK10861 signal peptidase I; Provisional
Probab=100.00 E-value=6.6e-34 Score=241.18 Aligned_cols=140 Identities=29% Similarity=0.414 Sum_probs=124.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHheeeEEEEEcCCCccccccCCCcCCCCCCCCcEEEEEceeccC------------CCCc
Q 030852 5 NFLWSFTKNCFTFGLIGLTISDRYASIVPVRGSSMSPTFNLTTDSFMGSLSDDYVLVEKFCLQK------------YKFS 72 (170)
Q Consensus 5 ~~~~~~~~~~~~~~~v~~~i~~~~~~~~~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~------------~~~~ 72 (170)
..+..+++.++.+++++++++.|+++++.|+|+||+|||+. ||+++++|+.+.. ..++
T Consensus 58 ~~~~~~~~~~~~~l~i~~~ir~fv~~~~~Ips~SM~PTL~~----------GD~IlVnK~~yg~~~p~~~~~~~~~~~p~ 127 (324)
T PRK10861 58 PGWLETGASVFPVLAIVLIVRSFIYEPFQIPSGSMMPTLLI----------GDFILVEKFAYGIKDPITQTTLIETGHPK 127 (324)
T ss_pred chHHHHHHHHHHHHhHHHHHHhhEEEEEEECCCcCcCcccC----------CCEEEEEEeecCccCccccccccccCCCC
Confidence 34677778888888889999999999999999999999999 9999999998752 5789
Q ss_pred cccEEEEecCCCCCcceEEEEEeeCCCeEEec--------CC--------------------------------------
Q 030852 73 HGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTP--------MT-------------------------------------- 106 (170)
Q Consensus 73 ~GDiV~f~~p~~~~~~~vKRVia~~Gd~v~i~--------~~-------------------------------------- 106 (170)
|||||+|+.|.++++.+||||+|+|||+|.++ +.
T Consensus 128 RGDIVVF~~P~~~~~~yIKRVIGlPGD~I~~~~~~~~l~iNg~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~ 207 (324)
T PRK10861 128 RGDIVVFKYPEDPKLDYIKRVVGLPGDKVTYDPVSKEVTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATS 207 (324)
T ss_pred CCCEEEEecCCCCCCcEEEEeeecCCcEEEEEeCCCEEEEcCcccccccccccccccccccccccccccccccccccccc
Confidence 99999999999888999999999999999984 10
Q ss_pred -----------------------------------C----------------CeEEecCCeEEEeeCCCCCCCCCCcccc
Q 030852 107 -----------------------------------N----------------DVMKVPNGHCWVEGDNPSSSLDSRSFGP 135 (170)
Q Consensus 107 -----------------------------------~----------------~~~~vp~~~~~v~Gdn~~~s~DSR~~G~ 135 (170)
. ..++||+|+||++|||+++|.||||||+
T Consensus 208 ~~~~~~~~~~~~~~~~~~~~~E~l~~~~h~i~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~yf~mgdnr~~S~DSRy~G~ 287 (324)
T PRK10861 208 GFFQVPLNETKENGIRLSERKETLGDVTHRILTVPGAQDQVGMYYQQPGQPLATWVVPPGQYFMMGDNRDNSADSRYWGF 287 (324)
T ss_pred ccccccccccccccccceeEEEecCCccceeeecCCcccccccccccCCCcCceEEECCCeEEEeCCCCCCCcccCcccc
Confidence 0 1238999999999999999999999999
Q ss_pred ccCCCEEEEEEEEEeCCCC
Q 030852 136 IPLGLIKGWVTHILWPPQR 154 (170)
Q Consensus 136 V~~~~IiGkv~~~~~p~~~ 154 (170)
||.++|+|+|.+++|++++
T Consensus 288 Vp~~~i~G~a~~i~~s~d~ 306 (324)
T PRK10861 288 VPEANLVGKATAIWMSFEK 306 (324)
T ss_pred cCHHHcEEEEEEEEEEcCC
Confidence 9999999999999999874
No 5
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=99.91 E-value=3.2e-23 Score=162.89 Aligned_cols=92 Identities=23% Similarity=0.374 Sum_probs=73.3
Q ss_pred cEEEEEceeccCCCCccccEEEEecCCCC-------------------CcceEEEEEeeCCCeEEecCC-----------
Q 030852 57 DYVLVEKFCLQKYKFSHGDVIVFCSPSNH-------------------KEKHVKRIIGLPGDWIGTPMT----------- 106 (170)
Q Consensus 57 d~vlv~k~~~~~~~~~~GDiV~f~~p~~~-------------------~~~~vKRVia~~Gd~v~i~~~----------- 106 (170)
+.+.+.++.+...++++||+|+|+.|.++ ...++|||+|+|||+|.+.+.
T Consensus 37 ~pig~y~~~~~~~~~~rGDiVvf~~P~~~~~~~a~~r~yl~~g~~p~~~~~~iKRViglpGD~V~i~~~v~iNg~~~~~~ 116 (176)
T PRK13838 37 EPLGLWRIEALDRPVAVGDLVFICPPETAAFREARERGYLRRGLCPGGFAPLIKTVAALAGQRVEIGGSVSIDGRPLPSS 116 (176)
T ss_pred CEEEEEEEeccCCCCCCCcEEEEECCchhhhhhhhhcccccccccccCCCceEEEEEEeCCcEEEECCEEEECCEEcccc
Confidence 44445555443468999999999988643 135999999999999998530
Q ss_pred --------------CCeEEecCCeEEEeeCCCCCCCCCCccccccCCCEEEEEEEEE
Q 030852 107 --------------NDVMKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLIKGWVTHIL 149 (170)
Q Consensus 107 --------------~~~~~vp~~~~~v~Gdn~~~s~DSR~~G~V~~~~IiGkv~~~~ 149 (170)
....+||+|+|||+||| ++|+||||||+|++++|+|+|..++
T Consensus 117 ~~~~~~~~g~~l~~~~~~~vp~g~~fvlgd~-~~S~DSRy~G~V~~~~I~G~a~pi~ 172 (176)
T PRK13838 117 SVRRRDGEGRPLTPFPGGVVPPGHLFLHSSF-AGSYDSRYFGPVPASGLLGLARPVL 172 (176)
T ss_pred ccccccccCCcCCCCCccCcCCCeEEEECCC-CCCCcccccCcccHHHeEEEEEEEE
Confidence 01347999999999998 5899999999999999999998664
No 6
>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=4.3e-22 Score=155.86 Aligned_cols=80 Identities=35% Similarity=0.628 Sum_probs=68.6
Q ss_pred CCCccccEEEEecCCCCC-------------------cceEEEEEeeCCCeEEecCC-----------------------
Q 030852 69 YKFSHGDVIVFCSPSNHK-------------------EKHVKRIIGLPGDWIGTPMT----------------------- 106 (170)
Q Consensus 69 ~~~~~GDiV~f~~p~~~~-------------------~~~vKRVia~~Gd~v~i~~~----------------------- 106 (170)
.++++||+|+|+.|.++. ..++|||+|+|||+|+++++
T Consensus 45 ~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRViglpGD~V~i~~~~v~INg~~~~~~~~~~~~~~g~~ 124 (171)
T TIGR02771 45 KPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVLGLPGDRVTVRADVVAINGQLLPYSKPLATDSSGRP 124 (171)
T ss_pred CCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEEEeCCCEEEEECCEEEECCEEcccccccccccCCCc
Confidence 389999999999986432 27999999999999999541
Q ss_pred ---CCeEEecCCeEEEeeCCCCCCCCCCccccccCCCEEEEEEEEE
Q 030852 107 ---NDVMKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLIKGWVTHIL 149 (170)
Q Consensus 107 ---~~~~~vp~~~~~v~Gdn~~~s~DSR~~G~V~~~~IiGkv~~~~ 149 (170)
..+.+||+| ||++|||+++|+||||||+|+.++|+|||...+
T Consensus 125 l~~~~~~~vp~g-yf~lgdn~~~S~DSRy~G~V~~~~IiGk~~pl~ 169 (171)
T TIGR02771 125 LPPFPEGVIPPG-FFVVHDTSPTSFDSRYFGPISREQVIGRVKPLF 169 (171)
T ss_pred cccCCCcEECCC-EEEECCCCCCCCcccccceecHHHeEEEEEEeE
Confidence 125789999 999999999999999999999999999998643
No 7
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=99.87 E-value=3.1e-21 Score=151.88 Aligned_cols=81 Identities=22% Similarity=0.414 Sum_probs=68.5
Q ss_pred CCCccccEEEEecCCCC-------------------CcceEEEEEeeCCCeEEecCC-----------------------
Q 030852 69 YKFSHGDVIVFCSPSNH-------------------KEKHVKRIIGLPGDWIGTPMT----------------------- 106 (170)
Q Consensus 69 ~~~~~GDiV~f~~p~~~-------------------~~~~vKRVia~~Gd~v~i~~~----------------------- 106 (170)
.++++||+|+|+.|... ...++|||+|+|||+|.+.++
T Consensus 49 ~~~~~Gd~V~f~~p~~~~~~~a~~rgyl~~g~~p~~~~~liKRVva~pGD~V~~~~~~l~VNG~~v~~~~~~~~d~~g~~ 128 (178)
T PRK13884 49 APVEKGAYVLFCPPQRGVFDDAKERGYIGAGFCPGGYGYMMKRVLAAKGDAVSVTDDGVRVNGELLPLSKPILADGAGRP 128 (178)
T ss_pred CCCCCCCEEEEeCCchHHHHHHHhCCccccCcCCCCCCceEEEEEeeCCcEEEEECCEEEECCEEccccccccccccCCc
Confidence 38999999999987621 137999999999999999541
Q ss_pred -----CCeEEecCCeEEEeeCCCCCCCCCCccccccCCCEEEEEEEEE
Q 030852 107 -----NDVMKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLIKGWVTHIL 149 (170)
Q Consensus 107 -----~~~~~vp~~~~~v~Gdn~~~s~DSR~~G~V~~~~IiGkv~~~~ 149 (170)
...++||+|+||++|||+++|+||||||+|++++|+|+|..++
T Consensus 129 l~~~~~~~~~lp~g~~fvlgd~~~~S~DSRYfG~V~~~~I~G~~~Pl~ 176 (178)
T PRK13884 129 LPRYQANSYTLGESELLLMSDVSATSFDGRYFGPINRSQIKTVIRPVI 176 (178)
T ss_pred ccccCCCceEECCCEEEEECCCCCCCCcccccCcccHHHEEEEEEEeE
Confidence 0124899999999999999999999999999999999997654
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=99.86 E-value=1.4e-21 Score=137.11 Aligned_cols=89 Identities=33% Similarity=0.458 Sum_probs=78.6
Q ss_pred EEEcCCCccccccCCCcCCCCCCCCcEEEEEceeccCCCCccccEEEEecCCCCCcceEEEEEeeCCCeEEecCCCCeEE
Q 030852 32 VPVRGSSMSPTFNLTTDSFMGSLSDDYVLVEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVMK 111 (170)
Q Consensus 32 ~~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~~GDiV~f~~p~~~~~~~vKRVia~~Gd~v~i~~~~~~~~ 111 (170)
+.|.|+||+|+|.+ ||+|++++.......+++||+|+|+.|.++++.++||++++++
T Consensus 1 ~~V~g~SM~P~l~~----------GD~vlv~~~~~~~~~~~~Gdivv~~~~~~~~~~~vkRv~~~~~------------- 57 (90)
T TIGR02754 1 AKVTGVSMSPTLPP----------GDRIIVVPWLKIFRVPPIGNVVVVRHPLQPYGLIIKRLAAVDD------------- 57 (90)
T ss_pred CEeeCCCccCccCC----------CCEEEEEEccccCCCCCCCeEEEEecCCCCcceEEEEeeEEcC-------------
Confidence 36899999999999 9999999864433456789999999987677899999999865
Q ss_pred ecCCeEEEeeCCCCCCCCCCccccccCCCEEEEEE
Q 030852 112 VPNGHCWVEGDNPSSSLDSRSFGPIPLGLIKGWVT 146 (170)
Q Consensus 112 vp~~~~~v~Gdn~~~s~DSR~~G~V~~~~IiGkv~ 146 (170)
+++|+.|||+..|.|||++|+|+..+|+|+|+
T Consensus 58 ---~~~~l~~dN~~~~~d~~~~g~v~~~~I~G~v~ 89 (90)
T TIGR02754 58 ---NGLFLLGDNPKASTDSRQLGPVPRSLLLGKVL 89 (90)
T ss_pred ---CeEEEeCCCCCCCCcccccCCCcHHHEEEEEE
Confidence 58999999999999999999999999999985
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=2.5e-22 Score=152.16 Aligned_cols=89 Identities=34% Similarity=0.620 Sum_probs=32.4
Q ss_pred cEEEEEceeccCCCCccccEEEEecCCC------------CCcceEEEEEeeCCCeEEecCC------------------
Q 030852 57 DYVLVEKFCLQKYKFSHGDVIVFCSPSN------------HKEKHVKRIIGLPGDWIGTPMT------------------ 106 (170)
Q Consensus 57 d~vlv~k~~~~~~~~~~GDiV~f~~p~~------------~~~~~vKRVia~~Gd~v~i~~~------------------ 106 (170)
-+.++.+.. .+++||+|+|+.|.. .+..++|||+|+|||+|.+++.
T Consensus 12 g~Y~~~~~~----~~~rGd~V~f~~p~~~~~~~~~~gy~~~~~~~iKrV~a~pGD~V~v~~~~v~iNG~~~~~~~~~d~~ 87 (138)
T PF10502_consen 12 GIYLIDPSD----KIERGDLVVFCPPAEVAFFAAERGYLPEGQPLIKRVAAVPGDTVEVTDGGVYINGRPVGEPLATDSD 87 (138)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred ccccccccc----ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence 334455444 589999999999862 3568999999999999999652
Q ss_pred -------CCeEEecCCeEEEeeCCCCCCCCCCccccccCCCEEEEEEEEE
Q 030852 107 -------NDVMKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLIKGWVTHIL 149 (170)
Q Consensus 107 -------~~~~~vp~~~~~v~Gdn~~~s~DSR~~G~V~~~~IiGkv~~~~ 149 (170)
....+||+|+||++|||..+|+||||||+|+.++|+|+|..++
T Consensus 88 g~~l~~~~~~~~vp~g~~~v~gd~~~~S~DSRy~G~V~~~~I~g~~~pl~ 137 (138)
T PF10502_consen 88 GRPLPQFSGSGTVPEGEYFVLGDNRPNSFDSRYFGPVPRSQIIGKARPLW 137 (138)
T ss_dssp -S-T----TEEE--TTEEEEE-SBTTS--SHHHH--EEGGGEEEEEEEEE
T ss_pred cccccccCCceEeCCCEEEEecCCCCCccccCEecccCHHHEEEEEEEEE
Confidence 2468999999999999999999999999999999999998764
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=99.84 E-value=1.9e-20 Score=129.74 Aligned_cols=84 Identities=45% Similarity=0.653 Sum_probs=76.3
Q ss_pred EEEEcCCCccccccCCCcCCCCCCCCcEEEEEceeccCCCCccccEEEEecCCCCCcceEEEEEeeCCCeEEecCCCCeE
Q 030852 31 IVPVRGSSMSPTFNLTTDSFMGSLSDDYVLVEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVM 110 (170)
Q Consensus 31 ~~~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~~GDiV~f~~p~~~~~~~vKRVia~~Gd~v~i~~~~~~~ 110 (170)
.+.+.|+||+|++.. ||++++++......++++||+|+|+.|..+++.++|||++
T Consensus 2 ~~~v~g~SM~P~i~~----------gd~v~v~~~~~~~~~~~~GDiv~~~~~~~~~~~~vkRv~~--------------- 56 (85)
T cd06530 2 PVVVPGGSMEPTLQP----------GDLVLVNKLSYGFREPKRGDVVVFKSPGDPGKPIIKRVIG--------------- 56 (85)
T ss_pred eeEEcCCCCcCcccC----------CCEEEEEEeecccCCCCCCCEEEEeCCCCCCCEEEEEEEE---------------
Confidence 578999999999999 9999999877433469999999999987657899999999
Q ss_pred EecCCeEEEeeCCCCCCCCCCccccccCCCEEEEE
Q 030852 111 KVPNGHCWVEGDNPSSSLDSRSFGPIPLGLIKGWV 145 (170)
Q Consensus 111 ~vp~~~~~v~Gdn~~~s~DSR~~G~V~~~~IiGkv 145 (170)
||+.|||.++|.|||+||+++.++|+|++
T Consensus 57 ------~~~~gDn~~ns~d~~~~g~~~~~~i~G~~ 85 (85)
T cd06530 57 ------YFVLGDNRNNSLDSRYWGPVPEDDIVGKV 85 (85)
T ss_pred ------EEEeeCCCCCCCccCCcCCCcHHHeEEeC
Confidence 99999999999999999999999999985
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=99.77 E-value=5.9e-18 Score=130.97 Aligned_cols=85 Identities=29% Similarity=0.340 Sum_probs=69.9
Q ss_pred EEcCCCccccccCCCcCCCCCCCCcEEEEEceeccCCCCccccEEEEecCCCCCcceEEEEEeeCCCeEEecCCCCeEEe
Q 030852 33 PVRGSSMSPTFNLTTDSFMGSLSDDYVLVEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVMKV 112 (170)
Q Consensus 33 ~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~~GDiV~f~~p~~~~~~~vKRVia~~Gd~v~i~~~~~~~~v 112 (170)
.|.|+||+||+++ ||++++++... .++++||+|+|+.|.++ +.++|||+++.++.
T Consensus 35 ~V~g~SM~Ptl~~----------GD~vlv~~~~~--~~~~~GDIVvf~~~~~~-~~iihRVi~v~~~~------------ 89 (158)
T TIGR02228 35 VVLSGSMEPTFNT----------GDLILVTGADP--NDIQVGDVITYKSPGFN-TPVTHRVIEINNSG------------ 89 (158)
T ss_pred EEcCCCCcCCccC----------CCEEEEEeccc--CCCCCCCEEEEEECCCC-ccEEEEEEEEECCC------------
Confidence 3999999999999 99999998543 48999999999998643 78999999997641
Q ss_pred cCCeEEEeeCCCCCCCCCCccccccCCCEEEEEE
Q 030852 113 PNGHCWVEGDNPSSSLDSRSFGPIPLGLIKGWVT 146 (170)
Q Consensus 113 p~~~~~v~Gdn~~~s~DSR~~G~V~~~~IiGkv~ 146 (170)
-+..+++.|||+ ...| .++|+.++|+|++.
T Consensus 90 g~~~~~tkGDnN-~~~D---~~~v~~~~IiG~v~ 119 (158)
T TIGR02228 90 GELGFITKGDNN-PAPD---GEPVPSENVIGKYL 119 (158)
T ss_pred CcEEEEEEecCC-CCCC---cccCCHHHEEEEEE
Confidence 001488889997 4445 68999999999998
No 12
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=99.64 E-value=3e-15 Score=114.51 Aligned_cols=127 Identities=29% Similarity=0.288 Sum_probs=104.7
Q ss_pred HHHHHHHHHHHHHHHHHH--HheeeEEEEEcCCCccccccCCCcCCCCCCCCcEEEEEceeccCCCCccccEEEEecCCC
Q 030852 7 LWSFTKNCFTFGLIGLTI--SDRYASIVPVRGSSMSPTFNLTTDSFMGSLSDDYVLVEKFCLQKYKFSHGDVIVFCSPSN 84 (170)
Q Consensus 7 ~~~~~~~~~~~~~v~~~i--~~~~~~~~~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~~GDiV~f~~p~~ 84 (170)
...++..++.++++++++ +.++++.+.|+|+||+||++. ||+++++|+.+....+..++++ ..|..
T Consensus 7 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~V~s~SM~Ptl~~----------GD~v~v~k~~~~~~~~~~~~~~--~~~~~ 74 (166)
T COG0681 7 FLELISSLLIAIILALIIGVRTFVFEPVVVPSGSMEPTLNV----------GDRVLVKKFSYGFGKLKVPDII--VLPAV 74 (166)
T ss_pred HHHHHHHHHHHHHHhheeeeEEEEEEEEEECCCcccccccc----------CCEEEEEeccccccCCccceee--ecCCC
Confidence 447777888888888888 899999999999999999999 9999999999887788999888 55666
Q ss_pred CCcceEEEEEeeCCCeEEecCCCCe--EEecCCeEEEeeCC-------CCCCCCCCccccccCCCEEEEE
Q 030852 85 HKEKHVKRIIGLPGDWIGTPMTNDV--MKVPNGHCWVEGDN-------PSSSLDSRSFGPIPLGLIKGWV 145 (170)
Q Consensus 85 ~~~~~vKRVia~~Gd~v~i~~~~~~--~~vp~~~~~v~Gdn-------~~~s~DSR~~G~V~~~~IiGkv 145 (170)
.+..++||+++.+||.+.+++...+ ..+|++..++.++| ...+.+++.++.......+.++
T Consensus 75 ~~~~~~kr~~~~~GD~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 144 (166)
T COG0681 75 VEGDLIKRVIGLRGDIVVFKDDRLYVVPIIPRVYGLVEKDNGKHLVDVIVNANSSRVFGIITKKDYIKRV 144 (166)
T ss_pred CCcceEEEeccCCCCEEEEECCEEEeecccCcchhhhhcccccccccccccccCccccccccccccccce
Confidence 7889999999999999999875544 56667666666544 3467778888877788888777
No 13
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.43 E-value=3.6e-13 Score=102.81 Aligned_cols=86 Identities=28% Similarity=0.487 Sum_probs=70.2
Q ss_pred EEEceeccCCCCccccEEEEecCCC------------CCcceEEEEEeeCCCeEEecCC---------------------
Q 030852 60 LVEKFCLQKYKFSHGDVIVFCSPSN------------HKEKHVKRIIGLPGDWIGTPMT--------------------- 106 (170)
Q Consensus 60 lv~k~~~~~~~~~~GDiV~f~~p~~------------~~~~~vKRVia~~Gd~v~i~~~--------------------- 106 (170)
.++|.. .++++||+|+++.|.. ....++|||.|+|||+|.+..+
T Consensus 46 rv~k~~---~Pvt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq~Vci~~~~I~I~G~~v~~sl~~D~~GR~ 122 (173)
T COG4959 46 RVSKLS---APVTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQHVCITSQGIAIDGKPVAASLPVDRVGRA 122 (173)
T ss_pred EecccC---CCcccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCCCcEEEecceEEECCEEeeeeccccccCCc
Confidence 355544 3669999999999973 3568999999999999998431
Q ss_pred ----CCeEEecCCeEEEeeCCCCCCCCCCccccccCCCEEEEEEEE
Q 030852 107 ----NDVMKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLIKGWVTHI 148 (170)
Q Consensus 107 ----~~~~~vp~~~~~v~Gdn~~~s~DSR~~G~V~~~~IiGkv~~~ 148 (170)
...-.+-++++++++|..+.|+|||||||||.++|+|.+..+
T Consensus 123 lp~~~gcR~l~~~el~lL~~~~~~SfDsRYfGpipas~vig~aRPv 168 (173)
T COG4959 123 LPRWQGCRYLAPSELLLLTDRSSTSFDSRYFGPIPASQVIGVARPV 168 (173)
T ss_pred CCcccCCceecCCeEEEEeccCCcccccceecccCHHHcceeeeee
Confidence 122247789999999999999999999999999999999765
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=99.24 E-value=2.7e-11 Score=80.39 Aligned_cols=57 Identities=35% Similarity=0.514 Sum_probs=46.4
Q ss_pred EEcCCCccccccCCCcCCCCCCCCcEEEEEceeccCCCCccccEEEEecCCCCCcceEEEEEeeCCCeEEec
Q 030852 33 PVRGSSMSPTFNLTTDSFMGSLSDDYVLVEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTP 104 (170)
Q Consensus 33 ~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~~GDiV~f~~p~~~~~~~vKRVia~~Gd~v~i~ 104 (170)
+|.|+||+|+++. ||++++++.. .++.||+|++..+.+. ..++||+.+.+|+.+.+.
T Consensus 1 ~V~GdSM~P~i~~----------Gd~v~v~~~~----~~~~gdivv~~~~~~~-~~~iKrv~~~~~~~~~~~ 57 (70)
T PF00717_consen 1 RVEGDSMEPTIKD----------GDIVLVDPSS----EPKDGDIVVVKIDGDE-ELYIKRVVGEPGGIILIS 57 (70)
T ss_dssp EEESSTTGGTSST----------TEEEEEEETS-------TTSEEEEEETTEE-SEEEEEEEEETTEEEEE-
T ss_pred CeECcCcccCeeC----------CCEEEEEEcC----CCccCeEEEEEECCce-eeEEEEEEEeCCCEEEEe
Confidence 5899999999999 9999999876 8999999999996422 389999999999877664
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=99.24 E-value=6.5e-11 Score=80.45 Aligned_cols=83 Identities=51% Similarity=0.756 Sum_probs=65.4
Q ss_pred EEEEcCCCccccccCCCcCCCCCCCCcEEEEEceeccCCCCccccEEEEecCCCCCcceEEEEEeeCCCeEEecCCCCeE
Q 030852 31 IVPVRGSSMSPTFNLTTDSFMGSLSDDYVLVEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVM 110 (170)
Q Consensus 31 ~~~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~~GDiV~f~~p~~~~~~~vKRVia~~Gd~v~i~~~~~~~ 110 (170)
.+.+.|+||+|++.. ||++++++.. ..++.||+|+++.+. +..++||+...++
T Consensus 2 ~~~v~g~SM~P~i~~----------gd~v~i~~~~---~~~~~G~iv~~~~~~--~~~~ikrl~~~~~------------ 54 (84)
T cd06462 2 ALRVEGDSMEPTIPD----------GDLVLVDKSS---YEPKRGDIVVFRLPG--GELTVKRVIGLPG------------ 54 (84)
T ss_pred eeEEcCCCccCcccC----------CCEEEEEecC---CCCcCCEEEEEEcCC--CcEEEEEEEEECC------------
Confidence 468999999999999 9999999866 248999999999953 4899999999876
Q ss_pred EecCCeEEEeeCCCCCCCCCCccccccCCCEEEEE
Q 030852 111 KVPNGHCWVEGDNPSSSLDSRSFGPIPLGLIKGWV 145 (170)
Q Consensus 111 ~vp~~~~~v~Gdn~~~s~DSR~~G~V~~~~IiGkv 145 (170)
++++++.+||. ++.+.+..+. ....++|++
T Consensus 55 ---~~~~~l~~~N~-~~~~~~~~~~-~~~~i~g~v 84 (84)
T cd06462 55 ---EGHYFLLGDNP-NSPDSRIDGP-PELDIVGVV 84 (84)
T ss_pred ---CCEEEEECCCC-CCCcccccCC-CHHHEEEeC
Confidence 36899999994 5555544333 556677663
No 16
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.90 E-value=1.7e-08 Score=77.24 Aligned_cols=88 Identities=28% Similarity=0.380 Sum_probs=65.1
Q ss_pred EEEEcCCCccccccCCCcCCCCCCCCcEEEEEceeccCCCCccccEEEEecCCCCCcceEEEEEeeCCCeEEecCCCCeE
Q 030852 31 IVPVRGSSMSPTFNLTTDSFMGSLSDDYVLVEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVM 110 (170)
Q Consensus 31 ~~~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~~GDiV~f~~p~~~~~~~vKRVia~~Gd~v~i~~~~~~~ 110 (170)
++.|-++||||.++. ||.+++..... ...+.||||+|+.+. ..-.+++||+.+-+..
T Consensus 50 iVVVLSgSMePaF~R----------GDlLfL~N~~~--~p~~vGdivVf~veg-R~IPiVHRviK~he~~---------- 106 (180)
T KOG3342|consen 50 IVVVLSGSMEPAFHR----------GDLLFLTNRNE--DPIRVGDIVVFKVEG-REIPIVHRVIKQHEKS---------- 106 (180)
T ss_pred EEEEEcCCcCccccc----------ccEEEEecCCC--CcceeccEEEEEECC-ccCchhHHHHHHhccc----------
Confidence 478999999999999 99999875443 377899999999964 4667999999764310
Q ss_pred EecCC--eEEEeeCCCCCCCCCCc-c----ccccCCCEEEEEE
Q 030852 111 KVPNG--HCWVEGDNPSSSLDSRS-F----GPIPLGLIKGWVT 146 (170)
Q Consensus 111 ~vp~~--~~~v~Gdn~~~s~DSR~-~----G~V~~~~IiGkv~ 146 (170)
+| ++...|||+ ..|-|. | --..+++|.|+|.
T Consensus 107 ---~~~~~~LTKGDNN--~~dD~~Ly~~gq~~L~r~~Ivg~~~ 144 (180)
T KOG3342|consen 107 ---NGHIKFLTKGDNN--AVDDRGLYAQGQNWLERKDIVGRVR 144 (180)
T ss_pred ---CCcEEEEecCCCC--cccchhcccccccceeccceeeEEe
Confidence 23 466779985 445553 1 1277899999985
No 17
>cd06529 S24_LexA-like Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the
Probab=98.88 E-value=1.8e-08 Score=68.26 Aligned_cols=61 Identities=34% Similarity=0.413 Sum_probs=52.7
Q ss_pred EEEEcCCCccccccCCCcCCCCCCCCcEEEEEceeccCCCCccccEEEEecCCCCCcceEEEEEeeCCCeEEecCCCCeE
Q 030852 31 IVPVRGSSMSPTFNLTTDSFMGSLSDDYVLVEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVM 110 (170)
Q Consensus 31 ~~~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~~GDiV~f~~p~~~~~~~vKRVia~~Gd~v~i~~~~~~~ 110 (170)
...+.|+||+|+++. ||++++++.. .++.||+++++.+ ++..+||+...+++
T Consensus 2 ~~~v~g~sM~p~i~~----------gd~lii~~~~----~~~~g~i~~~~~~---~~~~ikr~~~~~~~----------- 53 (81)
T cd06529 2 ALRVKGDSMEPTIPD----------GDLVLVDPSD----TPRDGDIVVARLD---GELTVKRLQRRGGG----------- 53 (81)
T ss_pred EEEEECCCcCCccCC----------CCEEEEcCCC----CCCCCCEEEEEEC---CEEEEEEEEECCCC-----------
Confidence 468999999999999 9999999866 6899999999994 47899999988753
Q ss_pred EecCCeEEEeeCCC
Q 030852 111 KVPNGHCWVEGDNP 124 (170)
Q Consensus 111 ~vp~~~~~v~Gdn~ 124 (170)
.+++.++|.
T Consensus 54 -----~~~L~s~N~ 62 (81)
T cd06529 54 -----RLRLISDNP 62 (81)
T ss_pred -----cEEEEeCCC
Confidence 778888885
No 18
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=98.79 E-value=5.5e-08 Score=78.18 Aligned_cols=89 Identities=27% Similarity=0.249 Sum_probs=64.7
Q ss_pred EEEEEcCCCccccccCCCcCCCCCCCCcEEEEEceeccCCCCccccEEEEecCCCCCcceEEEEEeeCCCeEEecCCCCe
Q 030852 30 SIVPVRGSSMSPTFNLTTDSFMGSLSDDYVLVEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDV 109 (170)
Q Consensus 30 ~~~~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~~GDiV~f~~p~~~~~~~vKRVia~~Gd~v~i~~~~~~ 109 (170)
....|.|+||+|++++ ||+++|+.-. ...+||.|++..- .++.++||+...+|
T Consensus 124 ~~i~V~GDSMeP~~~~----------Gd~ilVd~~~----~~~~gd~v~v~~~--g~~~~VK~l~~~~~----------- 176 (214)
T COG2932 124 FALRVTGDSMEPTYED----------GDTLLVDPGV----NTRRGDRVYVETD--GGELYVKKLQREPG----------- 176 (214)
T ss_pred EEEEEeCCcccccccC----------CCEEEECCCC----ceeeCCEEEEEEe--CCeEEEEEEEEecC-----------
Confidence 4689999999999999 9999999876 6678996666652 46899999999877
Q ss_pred EEecCCeEEEeeCCCCCCCCCCccccccCCCEEEEEEEEEeC
Q 030852 110 MKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLIKGWVTHILWP 151 (170)
Q Consensus 110 ~~vp~~~~~v~Gdn~~~s~DSR~~G~V~~~~IiGkv~~~~~p 151 (170)
|.+.+.++|+....|-- +..=..=.|||+|++..-+
T Consensus 177 -----~~~~l~S~N~~~~~~~~-~~~~~~v~iIgrVv~~~~~ 212 (214)
T COG2932 177 -----GLLRLVSLNPDYYPDEI-FSEDDDVEIIGRVVWVSRL 212 (214)
T ss_pred -----CeEEEEeCCCCCCcccc-cCccceEEEEEEEEEEeee
Confidence 46668899984432222 1111112489999876543
No 19
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=98.66 E-value=3.5e-07 Score=69.05 Aligned_cols=85 Identities=22% Similarity=0.199 Sum_probs=60.1
Q ss_pred eEEEEEcCCCcc-ccccCCCcCCCCCCCCcEEEEEceeccCCCCccccEEEEecCCCCCcceEEEEEeeCCCeEEecCCC
Q 030852 29 ASIVPVRGSSMS-PTFNLTTDSFMGSLSDDYVLVEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTN 107 (170)
Q Consensus 29 ~~~~~v~~~SM~-Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~~GDiV~f~~p~~~~~~~vKRVia~~Gd~v~i~~~~ 107 (170)
....+|.|+||+ |++.. ||++++++-. .++.||+|++.. +++..+||+...
T Consensus 51 ~f~l~V~GdSM~~~~I~~----------GD~liVd~~~----~~~~Gdivv~~~---~g~~~vKrl~~~----------- 102 (139)
T PRK10276 51 TYFVKASGDSMIDAGISD----------GDLLIVDSAI----TASHGDIVIAAV---DGEFTVKKLQLR----------- 102 (139)
T ss_pred EEEEEEecCCCCCCCCCC----------CCEEEEECCC----CCCCCCEEEEEE---CCEEEEEEEEEC-----------
Confidence 455899999997 68999 9999999754 678999999987 457789998742
Q ss_pred CeEEecCCeEEEeeCCCCCCCCCCccccccCCCEEEEEEEEEe
Q 030852 108 DVMKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLIKGWVTHILW 150 (170)
Q Consensus 108 ~~~~vp~~~~~v~Gdn~~~s~DSR~~G~V~~~~IiGkv~~~~~ 150 (170)
+++++..+|+.. .....-.-..-.|+|+|++.+-
T Consensus 103 -------~~~~L~s~N~~y--~~i~i~~~~~~~IiG~V~~~~~ 136 (139)
T PRK10276 103 -------PTVQLIPMNSAY--SPITISSEDTLDVFGVVTHIVK 136 (139)
T ss_pred -------CcEEEEcCCCCC--CCEEcCCCCcEEEEEEEEEEEE
Confidence 246777777521 1111111112379999998764
No 20
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=98.56 E-value=1.1e-06 Score=69.67 Aligned_cols=88 Identities=20% Similarity=0.189 Sum_probs=65.5
Q ss_pred eeEEEEEcCCCcc-ccccCCCcCCCCCCCCcEEEEEceeccCCCCccccEEEEecCCCCCcceEEEEEeeCCCeEEecCC
Q 030852 28 YASIVPVRGSSMS-PTFNLTTDSFMGSLSDDYVLVEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMT 106 (170)
Q Consensus 28 ~~~~~~v~~~SM~-Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~~GDiV~f~~p~~~~~~~vKRVia~~Gd~v~i~~~ 106 (170)
-...+.|.|+||+ |.+.. ||++++++.. .++.||+|++.. +++..+||+.-. |
T Consensus 110 ~~f~~~V~GdSM~~~~i~~----------Gd~v~v~~~~----~~~~G~ivvv~~---~~~~~vKrl~~~-~-------- 163 (199)
T TIGR00498 110 AVFLLKVMGDSMVDAGICD----------GDLLIVRSQK----DARNGEIVAAMI---DGEVTVKRFYKD-G-------- 163 (199)
T ss_pred CEEEEEecCCCCCCCCCCC----------CCEEEEecCC----CCCCCCEEEEEE---CCEEEEEEEEEE-C--------
Confidence 4567899999996 57999 9999999754 889999999998 567899998754 3
Q ss_pred CCeEEecCCeEEEeeCCCCCCCCCCccccccCCCEEEEEEEEEeCC
Q 030852 107 NDVMKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLIKGWVTHILWPP 152 (170)
Q Consensus 107 ~~~~~vp~~~~~v~Gdn~~~s~DSR~~G~V~~~~IiGkv~~~~~p~ 152 (170)
+.+++..+|+.. ....... ..=.|+|+|+..+..+
T Consensus 164 --------~~i~L~s~N~~y--~~i~~~~-~~~~IiG~Vv~~~r~~ 198 (199)
T TIGR00498 164 --------TKVELKPENPEF--DPIVLNA-EDVTILGKVVGVIRNF 198 (199)
T ss_pred --------CEEEEEcCCCCC--cCCcCCC-CcEEEEEEEEEEEEec
Confidence 478888888732 1111110 1348999999887643
No 21
>PRK00215 LexA repressor; Validated
Probab=98.50 E-value=1.7e-06 Score=68.88 Aligned_cols=86 Identities=29% Similarity=0.339 Sum_probs=63.2
Q ss_pred eeEEEEEcCCCcc-ccccCCCcCCCCCCCCcEEEEEceeccCCCCccccEEEEecCCCCCcceEEEEEeeCCCeEEecCC
Q 030852 28 YASIVPVRGSSMS-PTFNLTTDSFMGSLSDDYVLVEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMT 106 (170)
Q Consensus 28 ~~~~~~v~~~SM~-Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~~GDiV~f~~p~~~~~~~vKRVia~~Gd~v~i~~~ 106 (170)
-.....|.|+||+ |++.+ ||++++++-. .++.||+|++... ++..+||+.-. +
T Consensus 117 ~~~~~~V~GdSM~~~~i~~----------Gd~v~v~~~~----~~~~G~ivv~~~~---~~~~vKrl~~~-~-------- 170 (205)
T PRK00215 117 EDFLLRVRGDSMIDAGILD----------GDLVIVRKQQ----TARNGQIVVALID---DEATVKRFRRE-G-------- 170 (205)
T ss_pred CeEEEEEccCCCCCCCcCC----------CCEEEEeCCC----CCCCCCEEEEEEC---CEEEEEEEEEe-C--------
Confidence 3556889999995 79999 9999999744 6789999999883 47899999864 2
Q ss_pred CCeEEecCCeEEEeeCCCCCCCCCCccccccCCCEEEEEEEEEe
Q 030852 107 NDVMKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLIKGWVTHILW 150 (170)
Q Consensus 107 ~~~~~vp~~~~~v~Gdn~~~s~DSR~~G~V~~~~IiGkv~~~~~ 150 (170)
|.+++..+|+.. +.....+= .-.|+|+|+..+-
T Consensus 171 --------~~~~L~s~Np~y--~~~~~~~~-~~~IiG~Vv~~~r 203 (205)
T PRK00215 171 --------GHIRLEPENPAY--EPIIVDPD-RVTIEGKVVGLIR 203 (205)
T ss_pred --------CEEEEEcCCCCC--CCEEeCCC-cEEEEEEEEEEEE
Confidence 478888888732 22211110 3579999987764
No 22
>PRK12423 LexA repressor; Provisional
Probab=98.41 E-value=3.4e-06 Score=67.45 Aligned_cols=85 Identities=21% Similarity=0.200 Sum_probs=62.9
Q ss_pred EEEEEcCCCcc-ccccCCCcCCCCCCCCcEEEEEceeccCCCCccccEEEEecCCCCCcceEEEEEeeCCCeEEecCCCC
Q 030852 30 SIVPVRGSSMS-PTFNLTTDSFMGSLSDDYVLVEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTND 108 (170)
Q Consensus 30 ~~~~v~~~SM~-Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~~GDiV~f~~p~~~~~~~vKRVia~~Gd~v~i~~~~~ 108 (170)
....|.|+||. |++.. ||++++++-. .++.||+|++.. +++..+||+.-. +
T Consensus 115 f~l~V~GdSM~~~~i~~----------Gd~viv~~~~----~~~~Gdivv~~~---~~~~~vKrl~~~-~---------- 166 (202)
T PRK12423 115 YLLQVQGDSMIDDGILD----------GDLVGVHRSP----EARDGQIVVARL---DGEVTIKRLERS-G---------- 166 (202)
T ss_pred EEEEEecCcCCCCCcCC----------CCEEEEeCCC----cCCCCCEEEEEE---CCEEEEEEEEEe-C----------
Confidence 45899999997 79999 9999999754 788999999987 457899999754 2
Q ss_pred eEEecCCeEEEeeCCCCCCCCCCccccccCCCEEEEEEEEEe
Q 030852 109 VMKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLIKGWVTHILW 150 (170)
Q Consensus 109 ~~~vp~~~~~v~Gdn~~~s~DSR~~G~V~~~~IiGkv~~~~~ 150 (170)
+.+++..+|++ ++...+-+-..-.|+|+|+..+.
T Consensus 167 ------~~~~L~s~N~~--y~~i~~~~~~~~~I~Gvv~g~~r 200 (202)
T PRK12423 167 ------DRIRLLPRNPA--YAPIVVAPDQDFAIEGVFCGLIR 200 (202)
T ss_pred ------CEEEEEcCCCC--CCCEEcCCCCcEEEEEEEEEEEE
Confidence 36888888863 22222211123489999998764
No 23
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=97.95 E-value=0.00017 Score=57.96 Aligned_cols=88 Identities=22% Similarity=0.222 Sum_probs=65.7
Q ss_pred eEEEEEcCCCc-cccccCCCcCCCCCCCCcEEEEEceeccCCCCccccEEEEecCCCCCcceEEEEEeeCCCeEEecCCC
Q 030852 29 ASIVPVRGSSM-SPTFNLTTDSFMGSLSDDYVLVEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTN 107 (170)
Q Consensus 29 ~~~~~v~~~SM-~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~~GDiV~f~~p~~~~~~~vKRVia~~Gd~v~i~~~~ 107 (170)
....+|.|+|| ++.+.. ||+|+|++-. +.+.||||+..... ++.-+||..--.
T Consensus 112 ~f~L~V~GdSM~~~gi~d----------GDlvvV~~~~----~a~~GdiVvA~i~g--~e~TvKrl~~~g---------- 165 (201)
T COG1974 112 TFFLRVSGDSMIDAGILD----------GDLVVVDPTE----DAENGDIVVALIDG--EEATVKRLYRDG---------- 165 (201)
T ss_pred eEEEEecCCccccCcCCC----------CCEEEEcCCC----CCCCCCEEEEEcCC--CcEEEEEEEEeC----------
Confidence 45578999999 566666 9999999866 89999999999954 558899987642
Q ss_pred CeEEecCCeEEEeeCCCCCCCCCCccccccCCCEEEEEEEEEeCC
Q 030852 108 DVMKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLIKGWVTHILWPP 152 (170)
Q Consensus 108 ~~~~vp~~~~~v~Gdn~~~s~DSR~~G~V~~~~IiGkv~~~~~p~ 152 (170)
+.++++-.|+. +....+..- .-.|+|+|+.++|+.
T Consensus 166 -------~~i~L~p~Np~--~~~i~~~~~-~~~I~G~vvgv~r~~ 200 (201)
T COG1974 166 -------NQILLKPENPA--YPPIPVDAD-SVTILGKVVGVIRDI 200 (201)
T ss_pred -------CEEEEEeCCCC--CCCcccCcc-ceEEEEEEEEEEecC
Confidence 46888888762 223222221 457999999999874
No 24
>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=86.72 E-value=3.1 Score=31.02 Aligned_cols=41 Identities=24% Similarity=0.225 Sum_probs=30.0
Q ss_pred CCccccEEEEecCCCCCcceEEEEEeeCCCeEEecCCCCeEEecCCeEEEeeCCCCCC
Q 030852 70 KFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVMKVPNGHCWVEGDNPSSS 127 (170)
Q Consensus 70 ~~~~GDiV~f~~p~~~~~~~vKRVia~~Gd~v~i~~~~~~~~vp~~~~~v~Gdn~~~s 127 (170)
.+++||+|.|+.. +.-+|--+++...+ .|.+.++|-|.++.
T Consensus 73 ~p~~GDiv~f~~~---~~~HVGi~~g~~~~--------------~g~i~~lgGNq~~~ 113 (129)
T TIGR02594 73 KPAYGCIAVKRRG---GGGHVGFVVGKDKQ--------------TGTIIVLGGNQGDR 113 (129)
T ss_pred CCCccEEEEEECC---CCCEEEEEEeEcCC--------------CCEEEEeeCCCCCe
Confidence 6899999999863 34477777776554 36888888887553
No 25
>PRK00364 groES co-chaperonin GroES; Reviewed
Probab=82.95 E-value=5.1 Score=28.27 Aligned_cols=87 Identities=14% Similarity=0.084 Sum_probs=48.0
Q ss_pred CCcEEEEEceeccCCCCccccEEEEecCCCCCcceEEEEEeeCCCeEEecCCCCeEEecCCeEEEeeCCC--CCCCCCCc
Q 030852 55 SDDYVLVEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVMKVPNGHCWVEGDNP--SSSLDSRS 132 (170)
Q Consensus 55 ~gd~vlv~k~~~~~~~~~~GDiV~f~~p~~~~~~~vKRVia~~Gd~v~i~~~~~~~~vp~~~~~v~Gdn~--~~s~DSR~ 132 (170)
.||+|++.+... .+-..|-|++=.. ..++....+|+|+.-....-+....++.+..|...+..+.. .--.|...
T Consensus 6 l~drVLV~~~~~--e~~T~gGI~Lp~~--a~~k~~~G~VvaVG~G~~~~~G~~~~~~vk~GD~Vlf~~~~g~ev~~~~~~ 81 (95)
T PRK00364 6 LGDRVLVKRLEE--EEKTAGGIVLPDS--AKEKPQEGEVVAVGPGRRLDNGERVPLDVKVGDKVLFGKYAGTEVKIDGEE 81 (95)
T ss_pred cCCEEEEEEccc--CccccceEEcCcc--ccCCcceEEEEEECCCeECCCCCEeecccCCCCEEEEcCCCCeEEEECCEE
Confidence 499999988753 2556677776333 23456677788775433222222233445555544443322 11234445
Q ss_pred cccccCCCEEEEE
Q 030852 133 FGPIPLGLIKGWV 145 (170)
Q Consensus 133 ~G~V~~~~IiGkv 145 (170)
|=.++.++|+|++
T Consensus 82 y~iv~~~DIlavi 94 (95)
T PRK00364 82 YLILRESDILAIV 94 (95)
T ss_pred EEEEEHHHEEEEe
Confidence 6667777777764
No 26
>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=80.28 E-value=7.7 Score=27.19 Aligned_cols=86 Identities=14% Similarity=0.081 Sum_probs=48.2
Q ss_pred CCcEEEEEceeccCCCCccccEEEEecCCCCCcceEEEEEeeCCCeEEecCCCCeEEecCCeEEEeeCCCC--CCCCCCc
Q 030852 55 SDDYVLVEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVMKVPNGHCWVEGDNPS--SSLDSRS 132 (170)
Q Consensus 55 ~gd~vlv~k~~~~~~~~~~GDiV~f~~p~~~~~~~vKRVia~~Gd~v~i~~~~~~~~vp~~~~~v~Gdn~~--~s~DSR~ 132 (170)
.||+|++.+... .+-..|-|++=.+. ..+.....|+|+.-+...-+....+..+..|..-+..+..- --.|...
T Consensus 5 l~DrVLV~~~~~--e~~T~~GI~Lp~~~--~~k~~~g~VvAVG~g~~~~~g~~~~~~vk~GD~Vl~~~~~g~~v~~~~~~ 80 (93)
T cd00320 5 LGDRVLVKRIEA--EEKTKGGIILPDSA--KEKPQEGKVVAVGPGRRNENGERVPLSVKVGDKVLFPKYAGTEVKLDGEE 80 (93)
T ss_pred cCCEEEEEEccc--cceecceEEeCCCc--CCCceEEEEEEECCCeECCCCCCccccccCCCEEEECCCCceEEEECCEE
Confidence 489999988753 24556777764442 34567778888765443333333344555555444433221 1234445
Q ss_pred cccccCCCEEEE
Q 030852 133 FGPIPLGLIKGW 144 (170)
Q Consensus 133 ~G~V~~~~IiGk 144 (170)
|=.++.++|+|+
T Consensus 81 y~i~~~~DIla~ 92 (93)
T cd00320 81 YLILRESDILAV 92 (93)
T ss_pred EEEEEHHHEEEE
Confidence 556777777765
No 27
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=77.22 E-value=3.2 Score=31.00 Aligned_cols=13 Identities=31% Similarity=0.414 Sum_probs=11.0
Q ss_pred CCccccEEEEecC
Q 030852 70 KFSHGDVIVFCSP 82 (170)
Q Consensus 70 ~~~~GDiV~f~~p 82 (170)
...+||+|+|+.+
T Consensus 84 ~~~~GD~i~~~~~ 96 (166)
T COG0681 84 IGLRGDIVVFKDD 96 (166)
T ss_pred ccCCCCEEEEECC
Confidence 5688999999984
No 28
>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=74.53 E-value=4.8 Score=28.11 Aligned_cols=87 Identities=14% Similarity=0.073 Sum_probs=49.1
Q ss_pred CCcEEEEEceeccCCCCccccEEEEecCCCCCcceEEEEEeeCCCeEEecCCCCeEEecCCeEEEeeCCCC--CCCCCCc
Q 030852 55 SDDYVLVEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVMKVPNGHCWVEGDNPS--SSLDSRS 132 (170)
Q Consensus 55 ~gd~vlv~k~~~~~~~~~~GDiV~f~~p~~~~~~~vKRVia~~Gd~v~i~~~~~~~~vp~~~~~v~Gdn~~--~s~DSR~ 132 (170)
.||+|++.+... ..-..|-+++=.. ...+....+|+|+......-+...-+..+..|...+..+... --.|...
T Consensus 5 l~drVLV~~~~~--e~~T~~GiiLp~~--~~~~~~~G~VvaVG~G~~~~~g~~~~~~vk~GD~Vl~~~~~g~~v~~~~~~ 80 (93)
T PF00166_consen 5 LGDRVLVKKIEA--EEKTASGIILPES--AKEKPNQGKVVAVGPGRYNENGEEVPMDVKVGDKVLFPKYAGTEVKFDGEK 80 (93)
T ss_dssp STTEEEEEECSC--TCTCTTSCCE-CC--SSSSEEEEEEEEE-SEEETTTSSEEETSS-TTSEEEEETTTSEEEEETTEE
T ss_pred cCCEEEEEEccc--cceecceEEeccc--cccccceeEEEEcCCccccCCCcEeeeeeeeccEEeccccCceEEEECCEE
Confidence 489999998642 4566677777633 234667778888866444322222233454555544444321 2245566
Q ss_pred cccccCCCEEEEE
Q 030852 133 FGPIPLGLIKGWV 145 (170)
Q Consensus 133 ~G~V~~~~IiGkv 145 (170)
|=.++.++|+|+.
T Consensus 81 ~~~~~~~dIlavi 93 (93)
T PF00166_consen 81 YLIVREDDILAVI 93 (93)
T ss_dssp EEEEEGGGEEEEE
T ss_pred EEEEEHHHeEEEC
Confidence 7778888888763
No 29
>COG0234 GroS Co-chaperonin GroES (HSP10) [Posttranslational modification, protein turnover, chaperones]
Probab=72.00 E-value=23 Score=25.24 Aligned_cols=68 Identities=16% Similarity=0.132 Sum_probs=35.7
Q ss_pred CCCcEEEEEceecc-------------CCCCccccEEEEecCC-CCCcceEEEEEeeCCCeEEec-CCCCeEEecCCeEE
Q 030852 54 LSDDYVLVEKFCLQ-------------KYKFSHGDVIVFCSPS-NHKEKHVKRIIGLPGDWIGTP-MTNDVMKVPNGHCW 118 (170)
Q Consensus 54 ~~gd~vlv~k~~~~-------------~~~~~~GDiV~f~~p~-~~~~~~vKRVia~~Gd~v~i~-~~~~~~~vp~~~~~ 118 (170)
|.||+|++.+.... ...+++|.+|+.-.-. ..+... ...--..||+|.+. .....+++-..+|.
T Consensus 5 PL~DRVlVk~~e~EekT~gGIvlpdsakeK~~~g~VvAVG~G~~~~~g~~-~~~~VkvGD~Vlf~ky~G~evk~dgeeyl 83 (96)
T COG0234 5 PLGDRVLVKRVEEEEKTAGGIVLPDSAKEKPQEGEVVAVGPGRRDENGEL-VPLDVKVGDRVLFGKYAGTEVKIDGEEYL 83 (96)
T ss_pred ecCCEEEEEEchhhccccCcEEecCccccCCcceEEEEEccceecCCCCE-eccccccCCEEEECccCCcEEEECCEEEE
Confidence 34899999887532 2355666666665411 111111 11222346776663 34455666666666
Q ss_pred EeeC
Q 030852 119 VEGD 122 (170)
Q Consensus 119 v~Gd 122 (170)
++.+
T Consensus 84 il~e 87 (96)
T COG0234 84 ILSE 87 (96)
T ss_pred Eech
Confidence 6654
No 30
>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=68.77 E-value=14 Score=26.58 Aligned_cols=36 Identities=25% Similarity=0.221 Sum_probs=22.6
Q ss_pred CCCccccEEEEecCCCCCcceEEEEEee-CCCeEEec
Q 030852 69 YKFSHGDVIVFCSPSNHKEKHVKRIIGL-PGDWIGTP 104 (170)
Q Consensus 69 ~~~~~GDiV~f~~p~~~~~~~vKRVia~-~Gd~v~i~ 104 (170)
..|+.|||++|.......-=++--|.++ .+++|.+.
T Consensus 61 ~~P~~Gdivv~~~~~~~~~GHVaIV~~v~~~~~i~v~ 97 (124)
T PF05257_consen 61 STPQPGDIVVWDSGSGGGYGHVAIVESVNDGGTITVI 97 (124)
T ss_dssp S---TTEEEEEEECTTTTT-EEEEEEEE-TTSEEEEE
T ss_pred cccccceEEEeccCCCCCCCeEEEEEEECCCCEEEEE
Confidence 5899999999953333344488888898 77666554
No 31
>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=64.84 E-value=55 Score=24.26 Aligned_cols=77 Identities=13% Similarity=-0.080 Sum_probs=40.7
Q ss_pred CCccccEEEEecCCCC----------CcceEEEEEeeCCC---eEEec--------CCCCeEEecCCeEEEeeCCCCCCC
Q 030852 70 KFSHGDVIVFCSPSNH----------KEKHVKRIIGLPGD---WIGTP--------MTNDVMKVPNGHCWVEGDNPSSSL 128 (170)
Q Consensus 70 ~~~~GDiV~f~~p~~~----------~~~~vKRVia~~Gd---~v~i~--------~~~~~~~vp~~~~~v~Gdn~~~s~ 128 (170)
.++.||+|+++.+..+ ...+|.||..+..+ .-.++ +..-...-.+.++|+.-.-...+.
T Consensus 5 ~i~vGD~V~v~~d~~~~~~~~~~~~~~~~~i~~V~~~~e~~~g~~~~h~~W~yrp~eTv~g~~~~~~ElFLSd~c~~~~~ 84 (130)
T cd04712 5 TIRVGDVVSVERDDADSTTKWNDDHRWLPLVQFVEYMKKGSDGSKMFHGRWLYRGCDTVLGNYANERELFLTNECTCLEL 84 (130)
T ss_pred EEeCCCEEEEcCCCCCccccccccccccceEEEEEEeeecCCCceEEEEEEEEcchhccccccCCCceEEEecccccccc
Confidence 5677888888776543 24567777765433 11111 011111445566776632221211
Q ss_pred CCCccccccCCCEEEEEEEEEeCC
Q 030852 129 DSRSFGPIPLGLIKGWVTHILWPP 152 (170)
Q Consensus 129 DSR~~G~V~~~~IiGkv~~~~~p~ 152 (170)
++ + .+.|.||+..-+.+.
T Consensus 85 ~~-----~-~~~I~~k~~V~~~~~ 102 (130)
T cd04712 85 DL-----L-STEIKGVHKVDWSGT 102 (130)
T ss_pred cc-----c-cceeEEEEEEEEecC
Confidence 11 1 559999999887653
No 32
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=60.88 E-value=41 Score=23.58 Aligned_cols=82 Identities=10% Similarity=0.091 Sum_probs=42.7
Q ss_pred CCcEEEEEceeccCCCCccccEEEEecCCCCCcceEEEEEeeCCCeEEecCCCCeEEecCCeEEEeeCCCC--CCCCCCc
Q 030852 55 SDDYVLVEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVMKVPNGHCWVEGDNPS--SSLDSRS 132 (170)
Q Consensus 55 ~gd~vlv~k~~~~~~~~~~GDiV~f~~p~~~~~~~vKRVia~~Gd~v~i~~~~~~~~vp~~~~~v~Gdn~~--~s~DSR~ 132 (170)
.||+|++.+... ..=..|-|++=... ..+.....|+|+.-.. ...+..+..|.-.+.++..- --.|...
T Consensus 6 l~DRVLVk~~~~--e~~T~gGI~Lp~~a--~ek~~~G~VvavG~g~-----~~~~~~Vk~GD~Vl~~~y~g~ev~~~~~~ 76 (91)
T PRK14533 6 LGERLLIKPIKE--EKKTEGGIVLPDSA--KEKPMKAEVVAVGKLD-----DEEDFDIKVGDKVIFSKYAGTEIKIDDED 76 (91)
T ss_pred cCCEEEEEEccc--cceecccEEecccc--cCCcceEEEEEECCCC-----ccccccccCCCEEEEccCCCeEEEECCEE
Confidence 489999988753 24455777764442 2344566666664211 01233444444444433321 1133444
Q ss_pred cccccCCCEEEEE
Q 030852 133 FGPIPLGLIKGWV 145 (170)
Q Consensus 133 ~G~V~~~~IiGkv 145 (170)
|=.++.++|+|++
T Consensus 77 y~iv~e~DILa~i 89 (91)
T PRK14533 77 YIIIDVNDILAKI 89 (91)
T ss_pred EEEEEhHhEEEEe
Confidence 5566677777765
No 33
>smart00439 BAH Bromo adjacent homology domain.
Probab=55.51 E-value=68 Score=22.29 Aligned_cols=16 Identities=25% Similarity=0.250 Sum_probs=13.2
Q ss_pred cccCCCEEEEEEEEEe
Q 030852 135 PIPLGLIKGWVTHILW 150 (170)
Q Consensus 135 ~V~~~~IiGkv~~~~~ 150 (170)
-++.+.|+||+.....
T Consensus 70 ~i~~~~I~~kc~V~~~ 85 (120)
T smart00439 70 TVPLSDIIGKCNVLSK 85 (120)
T ss_pred cCChHHeeeEEEEEEc
Confidence 5899999999987643
No 34
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=54.50 E-value=45 Score=24.71 Aligned_cols=33 Identities=18% Similarity=0.363 Sum_probs=23.5
Q ss_pred CCeEEecCCeEEEeeCCCCCCCCCCccccccCCC
Q 030852 107 NDVMKVPNGHCWVEGDNPSSSLDSRSFGPIPLGL 140 (170)
Q Consensus 107 ~~~~~vp~~~~~v~Gdn~~~s~DSR~~G~V~~~~ 140 (170)
...+..-.|-+.++.++ ....-+|-||||.+|.
T Consensus 74 Gs~i~FddNA~Viin~~-g~P~GtrI~GPVaREl 106 (122)
T COG0093 74 GSYIKFDDNAAVIINPD-GEPRGTRIFGPVAREL 106 (122)
T ss_pred CCEEEeCCceEEEECCC-CCcccceEecchhHHH
Confidence 34455556777777666 3678899999998764
No 35
>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=50.14 E-value=16 Score=24.34 Aligned_cols=19 Identities=26% Similarity=0.289 Sum_probs=11.1
Q ss_pred CcEEEEEceeccCCCCccccEE
Q 030852 56 DDYVLVEKFCLQKYKFSHGDVI 77 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~~GDiV 77 (170)
||.|.+...++ ++.+|+|+
T Consensus 48 GD~V~Ve~spy---d~tkgrIi 66 (68)
T TIGR00008 48 GDKVKVELSPY---DLTRGRIT 66 (68)
T ss_pred CCEEEEEECcc---cCCcEeEE
Confidence 66666665553 55666654
No 36
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=48.94 E-value=18 Score=24.66 Aligned_cols=19 Identities=32% Similarity=0.478 Sum_probs=12.9
Q ss_pred CcEEEEEceeccCCCCccccEE
Q 030852 56 DDYVLVEKFCLQKYKFSHGDVI 77 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~~GDiV 77 (170)
||.|++...++ ++++|||+
T Consensus 50 GD~V~Ve~~~~---d~~kg~I~ 68 (75)
T COG0361 50 GDVVLVELSPY---DLTKGRIV 68 (75)
T ss_pred CCEEEEEeccc---ccccccEE
Confidence 77777776663 56777765
No 37
>PF10000 ACT_3: ACT domain; InterPro: IPR018717 This domain has no known function.; PDB: 1ZVP_C.
Probab=48.51 E-value=12 Score=25.08 Aligned_cols=35 Identities=23% Similarity=0.265 Sum_probs=18.0
Q ss_pred CCccccccCCCcCCCCCCCCcEEEEEceeccCCCCcc-ccEEEEecC
Q 030852 37 SSMSPTFNLTTDSFMGSLSDDYVLVEKFCLQKYKFSH-GDVIVFCSP 82 (170)
Q Consensus 37 ~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~~-GDiV~f~~p 82 (170)
.||+|.+.+ |+||++.--. ....+.. .=+-.|+.+
T Consensus 12 ~~m~P~L~~----------~~yVF~t~~~-~~~~~~~l~pi~~frE~ 47 (72)
T PF10000_consen 12 ASMSPELNP----------GEYVFCTVPG-DLADPPGLEPIATFREA 47 (72)
T ss_dssp ST-EEEE-S----------S-EEEEEE-S--GGGGGGG--SEEEEET
T ss_pred hhCCcEeCC----------CCEEEEEecC-cccCccCCcceEEEEec
Confidence 589999999 9999987541 1112222 234566654
No 38
>PTZ00414 10 kDa heat shock protein; Provisional
Probab=47.50 E-value=1e+02 Score=22.03 Aligned_cols=38 Identities=13% Similarity=0.155 Sum_probs=21.5
Q ss_pred CcEEEEEceeccCCCCccccEEEEecCCCCCcceEEEEEeeC
Q 030852 56 DDYVLVEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLP 97 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~~GDiV~f~~p~~~~~~~vKRVia~~ 97 (170)
||+|++.+.... +=..|-|++=.+- +.+.....|+|+.
T Consensus 16 ~dRVLVk~~~~e--~kT~gGIiLP~sa--kekp~~g~VvAVG 53 (100)
T PTZ00414 16 GQRVLVKRTLAA--KQTKAGVLIPEQV--AGKVNEGTVVAVA 53 (100)
T ss_pred CCEEEEEEcccc--cccccCEEccccc--ccCCceeEEEEEC
Confidence 999999887532 4455666664432 2333444555543
No 39
>TIGR03673 rpl14p_arch 50S ribosomal protein L14P. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L24e, part of which may contact the 16S rRNA in 2 intersubunit bridges.
Probab=47.07 E-value=1.2e+02 Score=22.75 Aligned_cols=34 Identities=9% Similarity=0.108 Sum_probs=26.1
Q ss_pred CCCeEEecCCeEEEeeCCCCCCCCCCccccccCCC
Q 030852 106 TNDVMKVPNGHCWVEGDNPSSSLDSRSFGPIPLGL 140 (170)
Q Consensus 106 ~~~~~~vp~~~~~v~Gdn~~~s~DSR~~G~V~~~~ 140 (170)
+...+..-+|.+.++.++. +..-+|-||||+.|.
T Consensus 83 dGs~i~FddNa~VLin~~~-~P~GTRI~GpV~rEl 116 (131)
T TIGR03673 83 DGTRVKFEDNAVVIVTPDG-EPKGTEIKGPVAREA 116 (131)
T ss_pred CCcEEEeCCcEEEEECCCC-CEeeeEEEccchHHH
Confidence 3445666678888888765 668889999999887
No 40
>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=46.57 E-value=1.2e+02 Score=22.45 Aligned_cols=31 Identities=23% Similarity=0.494 Sum_probs=23.1
Q ss_pred eEEecCCeEEEeeCCCCCCCCCCccccccCCC
Q 030852 109 VMKVPNGHCWVEGDNPSSSLDSRSFGPIPLGL 140 (170)
Q Consensus 109 ~~~vp~~~~~v~Gdn~~~s~DSR~~G~V~~~~ 140 (170)
.+...+|.+.++.++. +-.-+|-+|||+.+.
T Consensus 76 ~i~F~~Na~VLin~~~-~p~GTrI~Gpv~~el 106 (122)
T TIGR01067 76 YIRFDDNACVLINKNK-EPRGTRIFGPVAREL 106 (122)
T ss_pred EEECCCceEEEECCCC-CEeeeEEEccchHHH
Confidence 4455567777777664 668889999999875
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=46.44 E-value=81 Score=23.19 Aligned_cols=30 Identities=23% Similarity=0.470 Sum_probs=24.1
Q ss_pred eEEecCCeEEEeeCCCCCCCCCCccccccCC
Q 030852 109 VMKVPNGHCWVEGDNPSSSLDSRSFGPIPLG 139 (170)
Q Consensus 109 ~~~vp~~~~~v~Gdn~~~s~DSR~~G~V~~~ 139 (170)
.+...+|.+.++.++. +...+|-+|||+.+
T Consensus 76 ~i~F~~Na~VLln~~~-~p~GtrI~Gpv~~e 105 (122)
T PF00238_consen 76 FIKFDDNAVVLLNKKG-NPLGTRIFGPVPRE 105 (122)
T ss_dssp EEEESSEEEEEEETTS-SBSSSSBCSEEEHH
T ss_pred EEEeCCccEEEEcCCC-CEeeeEEEeeehHH
Confidence 4455678888888885 78999999999865
No 42
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=45.36 E-value=32 Score=25.29 Aligned_cols=53 Identities=13% Similarity=0.085 Sum_probs=28.6
Q ss_pred CCCccccEEEEecCCCCCcceEEEEEe------eCCCeEEecC-CCCeEEecCCeEEEee
Q 030852 69 YKFSHGDVIVFCSPSNHKEKHVKRIIG------LPGDWIGTPM-TNDVMKVPNGHCWVEG 121 (170)
Q Consensus 69 ~~~~~GDiV~f~~p~~~~~~~vKRVia------~~Gd~v~i~~-~~~~~~vp~~~~~v~G 121 (170)
+.++.||-|+...+.....+.=..|++ ..+..+++.- +.....+|.++++-+.
T Consensus 54 ~~L~~GD~VLA~~~~~~~~Y~Pg~V~~~~~~~~~~~~~~~V~f~ng~~~~vp~~~~~~I~ 113 (124)
T PF15057_consen 54 HSLQVGDKVLAPWEPDDCRYGPGTVIAGPERRASEDKEYTVRFYNGKTAKVPRGEVIWIS 113 (124)
T ss_pred CcCCCCCEEEEecCcCCCEEeCEEEEECccccccCCceEEEEEECCCCCccchhhEEECC
Confidence 577777777777665444444456664 3444444421 2334556666655443
No 43
>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=45.11 E-value=18 Score=23.45 Aligned_cols=12 Identities=17% Similarity=0.335 Sum_probs=5.8
Q ss_pred CCccccEEEEec
Q 030852 70 KFSHGDVIVFCS 81 (170)
Q Consensus 70 ~~~~GDiV~f~~ 81 (170)
-+++||+|++..
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 456677666663
No 44
>cd04370 BAH BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.
Probab=44.57 E-value=56 Score=22.61 Aligned_cols=72 Identities=15% Similarity=0.113 Sum_probs=38.5
Q ss_pred CCccccEEEEecCCC--CCcceEEEEEeeCCC-----eEEec------CCC--CeEEecCCeEEEeeCCCCCCCCCCccc
Q 030852 70 KFSHGDVIVFCSPSN--HKEKHVKRIIGLPGD-----WIGTP------MTN--DVMKVPNGHCWVEGDNPSSSLDSRSFG 134 (170)
Q Consensus 70 ~~~~GDiV~f~~p~~--~~~~~vKRVia~~Gd-----~v~i~------~~~--~~~~vp~~~~~v~Gdn~~~s~DSR~~G 134 (170)
.++.||.|.+..+.. .....+.||..+-.+ .+.+. +.. ..-..-++++|+..+. -
T Consensus 3 ~y~vgd~V~v~~~~~~~~~~~~i~~I~~i~~~~~~~~~~~v~wf~rp~e~~~~~~~~~~~~Elf~s~~~----------~ 72 (123)
T cd04370 3 TYEVGDSVYVEPDDSIKSDPPYIARIEELWEDTNGSKQVKVRWFYRPEETPKGLSPFALRRELFLSDHL----------D 72 (123)
T ss_pred EEecCCEEEEecCCcCCCCCCEEEEEeeeeECCCCCEEEEEEEEEchhHhccccccccccceeEEecCc----------c
Confidence 345677777776543 245666677655332 11111 000 0012334566664332 2
Q ss_pred cccCCCEEEEEEEEEeC
Q 030852 135 PIPLGLIKGWVTHILWP 151 (170)
Q Consensus 135 ~V~~~~IiGkv~~~~~p 151 (170)
.++.+.|.|++.....+
T Consensus 73 ~i~v~~I~gkc~V~~~~ 89 (123)
T cd04370 73 EIPVESIIGKCKVLFVS 89 (123)
T ss_pred ccCHHHhccccEEEech
Confidence 58899999999877544
No 45
>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=44.34 E-value=22 Score=24.19 Aligned_cols=10 Identities=20% Similarity=0.531 Sum_probs=4.7
Q ss_pred CccccEEEEe
Q 030852 71 FSHGDVIVFC 80 (170)
Q Consensus 71 ~~~GDiV~f~ 80 (170)
+++||+|++.
T Consensus 39 I~~GD~VlV~ 48 (78)
T cd04456 39 IKRGDFLIVD 48 (78)
T ss_pred EcCCCEEEEE
Confidence 3445554444
No 46
>COG4929 Uncharacterized membrane-anchored protein [Function unknown]
Probab=44.21 E-value=24 Score=28.16 Aligned_cols=26 Identities=8% Similarity=0.179 Sum_probs=14.8
Q ss_pred CcEEEEEceeccCCCCccccEEEEec
Q 030852 56 DDYVLVEKFCLQKYKFSHGDVIVFCS 81 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~~GDiV~f~~ 81 (170)
|+.+++...+..-.++-+||.+..+-
T Consensus 35 G~~IiLqtaPVDPRslmrGDYmtLnY 60 (190)
T COG4929 35 GREIILQTAPVDPRSLMRGDYMTLNY 60 (190)
T ss_pred CCEEEEEeCCCChHHhhccceEEeee
Confidence 56666655444444666666666553
No 47
>CHL00057 rpl14 ribosomal protein L14
Probab=43.16 E-value=1.3e+02 Score=22.16 Aligned_cols=32 Identities=22% Similarity=0.380 Sum_probs=24.2
Q ss_pred CeEEecCCeEEEeeCCCCCCCCCCccccccCCC
Q 030852 108 DVMKVPNGHCWVEGDNPSSSLDSRSFGPIPLGL 140 (170)
Q Consensus 108 ~~~~vp~~~~~v~Gdn~~~s~DSR~~G~V~~~~ 140 (170)
..+..-+|.+.++.++. +-.-+|-+|||+.+.
T Consensus 75 ~~i~F~~Na~VLin~~~-~p~GTrI~Gpv~~el 106 (122)
T CHL00057 75 MIIRFDDNAAVVIDQEG-NPKGTRVFGPIAREL 106 (122)
T ss_pred cEEEcCCceEEEECCCC-CEeEeEEEccchHHH
Confidence 34556677888887765 678889999999775
No 48
>cd04720 BAH_Orc1p_Yeast BAH, or Bromo Adjacent Homology domain, as present in Orc1p, which again is part of the Saccharomyces cerevisiae Sir1-origin recognition complex, and as present in Sir3p. The Orc1p BAH doman functions in epigenetic silencing. 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=42.73 E-value=1.1e+02 Score=23.85 Aligned_cols=89 Identities=10% Similarity=0.052 Sum_probs=49.9
Q ss_pred CcEEEEEceeccCCCCccccEEEEecCCCCCcceEEEEEeeCC----CeEEecC----------CCCe--E-------Ee
Q 030852 56 DDYVLVEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPG----DWIGTPM----------TNDV--M-------KV 112 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~~GDiV~f~~p~~~~~~~vKRVia~~G----d~v~i~~----------~~~~--~-------~v 112 (170)
++.+...|... ...++.||-|+++.+.. +...+..|..+.- +.+.+.= .... . .+
T Consensus 39 ~~~i~l~R~~d-~~~~~vGD~Vlik~~~~-~~~~V~iI~ei~~~~~~~~v~i~v~Wy~r~~Ei~~~~~~~~~~~~~~~~~ 116 (179)
T cd04720 39 KRKIFLARDSD-GLELSVGDTILVKDDVA-NSPSVYLIHEIRLNTLNNEVELWVMWFLRWFEINPARYYKQFDPEFRSES 116 (179)
T ss_pred CCcEEEEEccC-CeEEeCCCEEEEeCCCC-CCCEEEEEEEEEeCCCCCEEEEEEEEcCCHHHcccccccccccchhcccC
Confidence 34455555421 14789999999999864 5556666665532 2233310 0000 1 22
Q ss_pred cCCeEEEeeCCCCCCCCCCccccccCCCEEEEEEEEEeCCCCcccc
Q 030852 113 PNGHCWVEGDNPSSSLDSRSFGPIPLGLIKGWVTHILWPPQRVRHI 158 (170)
Q Consensus 113 p~~~~~v~Gdn~~~s~DSR~~G~V~~~~IiGkv~~~~~p~~~~~~~ 158 (170)
.++++|+..+- -.++.+.|+|++.- -+...|..+
T Consensus 117 ~~nElflT~~~----------d~i~l~~Ii~k~~V--ls~~ef~~~ 150 (179)
T cd04720 117 NKNELYLTAEL----------SEIKLKDIIDKANV--LSESEFNDL 150 (179)
T ss_pred CCceEEEeccc----------ceEEhhheeeeEEE--ecHHHhhhh
Confidence 35677765443 25899999999953 344444433
No 49
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=42.61 E-value=84 Score=22.73 Aligned_cols=46 Identities=20% Similarity=0.286 Sum_probs=30.0
Q ss_pred CcEEEEEceeccCCCCccccEEEEecCCCCCcceEEEEEeeCC-CeEEe
Q 030852 56 DDYVLVEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPG-DWIGT 103 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~~GDiV~f~~p~~~~~~~vKRVia~~G-d~v~i 103 (170)
.|...+...+.....+..||+|.++..+ +...+.+++.-.| -|+++
T Consensus 11 ~~~y~l~n~Pf~a~glA~gDvV~~~~~~--g~~~~~~~v~~sGnsTiRv 57 (117)
T PF14085_consen 11 DDTYRLDNIPFFAYGLALGDVVRAEPDD--GELWFQKVVESSGNSTIRV 57 (117)
T ss_pred CCEEEEEecccccCCCCCCCEEEEEeCC--CeEEEEEEEecCCCEEEEE
Confidence 4566666666555799999999999864 4555555544443 45554
No 50
>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=42.24 E-value=39 Score=24.58 Aligned_cols=79 Identities=15% Similarity=0.096 Sum_probs=44.2
Q ss_pred CCccccEEEEecCCCCCcceEEEEEeeCCC---eEEecCC----------CCeEEecCCeEEEeeCCCCCCCCCCccccc
Q 030852 70 KFSHGDVIVFCSPSNHKEKHVKRIIGLPGD---WIGTPMT----------NDVMKVPNGHCWVEGDNPSSSLDSRSFGPI 136 (170)
Q Consensus 70 ~~~~GDiV~f~~p~~~~~~~vKRVia~~Gd---~v~i~~~----------~~~~~vp~~~~~v~Gdn~~~s~DSR~~G~V 136 (170)
.++.||-|.++.+..++..+|.||..+-.+ ...+.-. ...-..-++++|.. .+.--+
T Consensus 3 ~~~vGD~V~v~~~~~~~~pyIgrI~~i~e~~~g~~~~~v~WfyrPeEt~~~~~~~~~~~EvF~S----------~~~d~~ 72 (121)
T cd04714 3 IIRVGDCVLFKSPGRPSLPYVARIESLWEDPEGNMVVRVKWYYRPEETKGGRKPNHGEKELFAS----------DHQDEN 72 (121)
T ss_pred EEEcCCEEEEeCCCCCCCCEEEEEEEEEEcCCCCEEEEEEEEEcHHHccCcccccCCCCceEec----------CCcccc
Confidence 467899999998765566788888765332 1122100 00001122333332 233458
Q ss_pred cCCCEEEEEEEEEeCCCCccccCc
Q 030852 137 PLGLIKGWVTHILWPPQRVRHIER 160 (170)
Q Consensus 137 ~~~~IiGkv~~~~~p~~~~~~~~~ 160 (170)
+.+.|+||+.-. .+..+...+.
T Consensus 73 ~~~~I~gkc~V~--~~~ey~~~~~ 94 (121)
T cd04714 73 SVQTIEHKCYVL--TFAEYERLAR 94 (121)
T ss_pred cHHHhCcccEEE--ehhHheeccc
Confidence 889999999654 4456655554
No 51
>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=41.76 E-value=24 Score=23.90 Aligned_cols=10 Identities=20% Similarity=0.740 Sum_probs=5.0
Q ss_pred CccccEEEEe
Q 030852 71 FSHGDVIVFC 80 (170)
Q Consensus 71 ~~~GDiV~f~ 80 (170)
+++||+|+++
T Consensus 39 I~~GD~V~Ve 48 (77)
T cd05793 39 INEGDIVLVA 48 (77)
T ss_pred EcCCCEEEEE
Confidence 3445555554
No 52
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=41.65 E-value=27 Score=24.43 Aligned_cols=19 Identities=21% Similarity=0.242 Sum_probs=9.2
Q ss_pred CcEEEEEceeccCCCCccccEE
Q 030852 56 DDYVLVEKFCLQKYKFSHGDVI 77 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~~GDiV 77 (170)
||.|.+.-.+| ++.+|+|+
T Consensus 50 GD~V~VE~spY---DltkGRIi 68 (87)
T PRK12442 50 GDRVTLELSPY---DLTKGRIN 68 (87)
T ss_pred CCEEEEEECcc---cCCceeEE
Confidence 55555554442 44555543
No 53
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=39.64 E-value=27 Score=24.00 Aligned_cols=10 Identities=20% Similarity=0.587 Sum_probs=5.3
Q ss_pred CccccEEEEe
Q 030852 71 FSHGDVIVFC 80 (170)
Q Consensus 71 ~~~GDiV~f~ 80 (170)
+++||+|++.
T Consensus 44 I~~GD~VlVe 53 (83)
T smart00652 44 IRRGDIVLVD 53 (83)
T ss_pred EcCCCEEEEE
Confidence 4455555554
No 54
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.99 E-value=18 Score=26.82 Aligned_cols=37 Identities=19% Similarity=0.118 Sum_probs=22.4
Q ss_pred CCccccccCCCcCCCCCCCCcEEEEEceeccCCCCccccEEEEecCC
Q 030852 37 SSMSPTFNLTTDSFMGSLSDDYVLVEKFCLQKYKFSHGDVIVFCSPS 83 (170)
Q Consensus 37 ~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~~GDiV~f~~p~ 83 (170)
.||+|.|.+ ||||+.---.....+..---+-.|+.++
T Consensus 12 ~smtPeL~~----------G~yVfcT~~~ga~~~~~lePla~FRE~E 48 (134)
T COG3602 12 ASMTPELLD----------GDYVFCTVAPGALQPKNLEPLATFRERE 48 (134)
T ss_pred HhcCccccC----------CceEEEEecCCcCCCcCCChHhhhcccc
Confidence 489999999 9999975332111122223355666654
No 55
>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=38.66 E-value=83 Score=23.29 Aligned_cols=77 Identities=16% Similarity=0.107 Sum_probs=41.2
Q ss_pred CCccccEEEEecCCCCCcceEEEEEeeCCCe---EEec------CCCC-----eEEecCCeEEEeeCCCCCCCCCCcccc
Q 030852 70 KFSHGDVIVFCSPSNHKEKHVKRIIGLPGDW---IGTP------MTND-----VMKVPNGHCWVEGDNPSSSLDSRSFGP 135 (170)
Q Consensus 70 ~~~~GDiV~f~~p~~~~~~~vKRVia~~Gd~---v~i~------~~~~-----~~~vp~~~~~v~Gdn~~~s~DSR~~G~ 135 (170)
.++.||.|.+..++ ++..+.+|..+-.|. ..+. ..+. .....++++|+.- ++-.
T Consensus 7 ~i~vGD~V~v~~~~--~~~~va~Ie~i~ed~~g~~~v~v~WF~~p~E~~~~~~~~~~~~~EvFlS~----------~~d~ 74 (130)
T cd04721 7 TISVHDFVYVLSEE--EDRYVAYIEDLYEDKKGSKMVKVRWFHTTDEVGAALSPDSVNPREIFLSP----------NLQV 74 (130)
T ss_pred EEECCCEEEEeCCC--CCcEEEEEEEEEEcCCCCEEEEEEEecCHHHhccccCCCCCCCCeEEEcC----------Cccc
Confidence 46789999998754 455676776654331 1110 0000 0112334444432 2335
Q ss_pred ccCCCEEEEEEEEEeCCCCccccCc
Q 030852 136 IPLGLIKGWVTHILWPPQRVRHIER 160 (170)
Q Consensus 136 V~~~~IiGkv~~~~~p~~~~~~~~~ 160 (170)
++.+.|+||+.- -+...|..+..
T Consensus 75 i~~~~I~gk~~V--ls~~~y~k~~~ 97 (130)
T cd04721 75 ISVECIDGLATV--LTREHYEKFQS 97 (130)
T ss_pred cchHHeeeeeEE--CCHHHHhhhhc
Confidence 899999999953 34444444443
No 56
>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=37.62 E-value=1.3e+02 Score=22.31 Aligned_cols=34 Identities=18% Similarity=0.254 Sum_probs=23.4
Q ss_pred CcceEEEEEeeCCCeEEecCCCCeEEecCCeEEE
Q 030852 86 KEKHVKRIIGLPGDWIGTPMTNDVMKVPNGHCWV 119 (170)
Q Consensus 86 ~~~~vKRVia~~Gd~v~i~~~~~~~~vp~~~~~v 119 (170)
..+++.||+.++--.+.-.....++.+|.|.-|.
T Consensus 89 ~~w~vgrI~~~e~~~v~~~~~~Npy~Lp~Gt~~y 122 (129)
T PF10377_consen 89 REWIVGRIVSIEECQVKDDKDSNPYNLPVGTKFY 122 (129)
T ss_pred CCEEEEEEEEEEEEEeccCCCCCCCcCCCCCEEE
Confidence 5678888888865544333667778888887554
No 57
>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=37.61 E-value=1.9e+02 Score=22.38 Aligned_cols=36 Identities=19% Similarity=0.300 Sum_probs=26.7
Q ss_pred CCCCccccEEEEecCCCCCcceEEE---EEeeCCCeEEecC
Q 030852 68 KYKFSHGDVIVFCSPSNHKEKHVKR---IIGLPGDWIGTPM 105 (170)
Q Consensus 68 ~~~~~~GDiV~f~~p~~~~~~~vKR---Via~~Gd~v~i~~ 105 (170)
...++.||+.+|.+- ....++|| ++.+.++++.+..
T Consensus 72 ~~~L~~GEvalY~~~--G~~I~L~~~G~ii~~~~~~~~v~a 110 (162)
T PF06890_consen 72 PKGLKPGEVALYDDE--GQKIHLKRDGRIIEVTCKTVTVNA 110 (162)
T ss_pred ccCCCCCcEEEEcCC--CCEEEEEecceEEeccCceEEEec
Confidence 346899999999973 34556665 7778888888863
No 58
>COG1934 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.47 E-value=2e+02 Score=22.55 Aligned_cols=56 Identities=7% Similarity=0.083 Sum_probs=31.1
Q ss_pred HHHHHheeeEEEEEcCCCccccccCCCcCCCCCCCCcEEEEEceeccCCCCccccEEEEecCCC
Q 030852 21 GLTISDRYASIVPVRGSSMSPTFNLTTDSFMGSLSDDYVLVEKFCLQKYKFSHGDVIVFCSPSN 84 (170)
Q Consensus 21 ~~~i~~~~~~~~~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~~GDiV~f~~p~~ 84 (170)
++.+...--++..+.+++-|--...+.-+|- |.+++..... .++-+.++++..+++
T Consensus 22 a~al~~d~~qPi~i~ad~~el~~~~~~a~ft----GNV~i~qG~~----~l~Adkv~v~~~~~~ 77 (173)
T COG1934 22 AFALKGDRDQPITIEADQQELDDKNGVATFT----GNVVVTQGTI----TLRADKVTVTRDKEG 77 (173)
T ss_pred hhhccccccCCEEEEccceeeeccCCEEEEE----ccEEEEeccc----EEEeeeEEEEccCCC
Confidence 4444444466778888777555444322232 5666665433 556566666666443
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=35.91 E-value=67 Score=23.88 Aligned_cols=22 Identities=27% Similarity=0.323 Sum_probs=17.0
Q ss_pred ccccccCCCEEEEEEEEEeCCC
Q 030852 132 SFGPIPLGLIKGWVTHILWPPQ 153 (170)
Q Consensus 132 ~~G~V~~~~IiGkv~~~~~p~~ 153 (170)
..--.+.+.|.||+...+-+++
T Consensus 66 ~c~d~~l~~I~~Kv~V~~~~p~ 87 (124)
T cd04760 66 ECEDMALSSIHGKVNVIYKAPS 87 (124)
T ss_pred ccCCcchHHheeeeEEEEeCCC
Confidence 3445778899999999887765
No 60
>TIGR02219 phage_NlpC_fam putative phage cell wall peptidase, NlpC/P60 family. Members of this family show sequence similarity to members of the NlpC/P60 family described by Pfam model pfam00877 and by Anantharaman and Aravind (PubMed:12620121). The NlpC/P60 family includes a number of characterized bacterial cell wall hydrolases. Members of this related family are all found in prophage regions of bacterial genomes.
Probab=35.81 E-value=91 Score=22.93 Aligned_cols=13 Identities=38% Similarity=0.411 Sum_probs=11.0
Q ss_pred CCCccccEEEEec
Q 030852 69 YKFSHGDVIVFCS 81 (170)
Q Consensus 69 ~~~~~GDiV~f~~ 81 (170)
.++++||+|.|..
T Consensus 75 ~~~qpGDlvff~~ 87 (134)
T TIGR02219 75 DAAQPGDVLVFRW 87 (134)
T ss_pred hcCCCCCEEEEee
Confidence 3789999999985
No 61
>smart00002 PLP Myelin proteolipid protein (PLP or lipophilin).
Probab=34.98 E-value=9.5 Score=24.87 Aligned_cols=20 Identities=30% Similarity=0.591 Sum_probs=17.1
Q ss_pred CCCCCCccccccCCCEEEEE
Q 030852 126 SSLDSRSFGPIPLGLIKGWV 145 (170)
Q Consensus 126 ~s~DSR~~G~V~~~~IiGkv 145 (170)
-+.|-|+||.+|-+..-|||
T Consensus 22 lC~D~RQyGilpwna~pgK~ 41 (60)
T smart00002 22 LCVDARQYGILPWNAFPGKV 41 (60)
T ss_pred EEeechhcceeecCCCCCch
Confidence 47899999999988877776
No 62
>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=34.39 E-value=50 Score=23.02 Aligned_cols=26 Identities=19% Similarity=0.271 Sum_probs=18.9
Q ss_pred CccccEEEEecCCCCCcceEEEEEee
Q 030852 71 FSHGDVIVFCSPSNHKEKHVKRIIGL 96 (170)
Q Consensus 71 ~~~GDiV~f~~p~~~~~~~vKRVia~ 96 (170)
++.||.|.+..+.......+.||..+
T Consensus 3 ~~vGD~V~v~~~~~~~~~~v~~I~~i 28 (119)
T PF01426_consen 3 YKVGDFVYVKPDDPPEPPYVARIEEI 28 (119)
T ss_dssp EETTSEEEEECTSTTSEEEEEEEEEE
T ss_pred EeCCCEEEEeCCCCCCCCEEEEEEEE
Confidence 56788888887665566777787766
No 63
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=33.35 E-value=38 Score=24.19 Aligned_cols=10 Identities=30% Similarity=0.757 Sum_probs=4.8
Q ss_pred CccccEEEEe
Q 030852 71 FSHGDVIVFC 80 (170)
Q Consensus 71 ~~~GDiV~f~ 80 (170)
+.+||+|++.
T Consensus 60 I~~GD~VlVe 69 (100)
T PRK04012 60 IREGDVVIVA 69 (100)
T ss_pred ecCCCEEEEE
Confidence 3445555544
No 64
>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=33.21 E-value=63 Score=23.21 Aligned_cols=69 Identities=16% Similarity=0.143 Sum_probs=39.0
Q ss_pred CCccccEEEEecCCCCCcceEEEEEeeCCC---eEEecC----------CCCeEEecCCeEEEeeCCCCCCCCCCccccc
Q 030852 70 KFSHGDVIVFCSPSNHKEKHVKRIIGLPGD---WIGTPM----------TNDVMKVPNGHCWVEGDNPSSSLDSRSFGPI 136 (170)
Q Consensus 70 ~~~~GDiV~f~~p~~~~~~~vKRVia~~Gd---~v~i~~----------~~~~~~vp~~~~~v~Gdn~~~s~DSR~~G~V 136 (170)
.++.||.|.+..+++++...+.||..+--+ ...+.- ....-..-++++|+.+. +-.+
T Consensus 3 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~~~~Wf~rP~et~~~~~~~~~~~Evfls~~----------~d~~ 72 (121)
T cd04717 3 QYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFFGCWFYRPEETFHEPTRKFYKNEVFKSPL----------YETV 72 (121)
T ss_pred EEECCCEEEEeCCCCCCCCEEEEEeEEEECCCCCEEEEEEEEeChHHccCCCccccccCceEEcCc----------cccc
Confidence 456788888888765566677777765322 111110 00111223455665433 3358
Q ss_pred cCCCEEEEEEEE
Q 030852 137 PLGLIKGWVTHI 148 (170)
Q Consensus 137 ~~~~IiGkv~~~ 148 (170)
+.+.|+||+.-.
T Consensus 73 ~~~~I~~kc~Vl 84 (121)
T cd04717 73 PVEEIVGKCAVM 84 (121)
T ss_pred cHHHhcCeeEEE
Confidence 899999999644
No 65
>PRK05483 rplN 50S ribosomal protein L14; Validated
Probab=31.09 E-value=2.2e+02 Score=21.03 Aligned_cols=31 Identities=16% Similarity=0.366 Sum_probs=22.8
Q ss_pred eEEecCCeEEEeeCCCCCCCCCCccccccCCC
Q 030852 109 VMKVPNGHCWVEGDNPSSSLDSRSFGPIPLGL 140 (170)
Q Consensus 109 ~~~vp~~~~~v~Gdn~~~s~DSR~~G~V~~~~ 140 (170)
.+..-+|.+.++.++. +..-+|-+|||+.+.
T Consensus 76 ~i~F~dNavVLin~~~-~p~GTrI~Gpv~~el 106 (122)
T PRK05483 76 YIRFDDNAAVLLNNDG-EPRGTRIFGPVAREL 106 (122)
T ss_pred EEEcCCCEEEEECCCC-CEeEeEEeccchHHH
Confidence 4455567777777664 678889999999775
No 66
>KOG4146 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=31.07 E-value=66 Score=22.93 Aligned_cols=26 Identities=35% Similarity=0.539 Sum_probs=18.4
Q ss_pred CcEEEEEceecc-----CCCCccccEEEEec
Q 030852 56 DDYVLVEKFCLQ-----KYKFSHGDVIVFCS 81 (170)
Q Consensus 56 gd~vlv~k~~~~-----~~~~~~GDiV~f~~ 81 (170)
|-.|++++.... ...++.||.|+|-+
T Consensus 66 Gii~lINd~DWEllekedy~ledgD~ivfiS 96 (101)
T KOG4146|consen 66 GIIVLINDMDWELLEKEDYPLEDGDHIVFIS 96 (101)
T ss_pred cEEEEEeccchhhhcccccCcccCCEEEEEE
Confidence 667777765432 35788899999876
No 67
>PF00278 Orn_DAP_Arg_deC: Pyridoxal-dependent decarboxylase, C-terminal sheet domain; InterPro: IPR022643 These enzymes are collectively known as group IV decarboxylases []. Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities [, ]. Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC [], to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region []. This entry represents the C-terminal region of the Orn/DAP/Arg decarboxylases.; GO: 0003824 catalytic activity; PDB: 1TWI_B 1TUF_A 3MT1_A 3N2B_C 2O0T_A 1HKW_A 1HKV_A 3VAB_A 3N2O_A 7ODC_A ....
Probab=30.55 E-value=69 Score=22.29 Aligned_cols=25 Identities=20% Similarity=0.256 Sum_probs=15.1
Q ss_pred CcEEEEEceeccCCCCccccEEEEecC
Q 030852 56 DDYVLVEKFCLQKYKFSHGDVIVFCSP 82 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~~GDiV~f~~p 82 (170)
+|++.-+..-. .+++.||+++|..-
T Consensus 70 ~D~i~~~~~lP--~~l~~GD~l~f~~~ 94 (116)
T PF00278_consen 70 GDVIARDVMLP--KELEVGDWLVFENM 94 (116)
T ss_dssp TSEEEEEEEEE--STTTTT-EEEESS-
T ss_pred CceEeeeccCC--CCCCCCCEEEEecC
Confidence 67775332221 27899999999864
No 68
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=29.94 E-value=65 Score=22.77 Aligned_cols=26 Identities=31% Similarity=0.589 Sum_probs=18.4
Q ss_pred CcEEEEEceecc-----CCCCccccEEEEec
Q 030852 56 DDYVLVEKFCLQ-----KYKFSHGDVIVFCS 81 (170)
Q Consensus 56 gd~vlv~k~~~~-----~~~~~~GDiV~f~~ 81 (170)
|-.++++..... ...++.||+|+|-+
T Consensus 61 GiI~LINd~DWeLleke~y~ledgDiIvfis 91 (96)
T COG5131 61 GIICLINDMDWELLEKERYPLEDGDIIVFIS 91 (96)
T ss_pred cEEEEEcCccHhhhhcccccCCCCCEEEEEe
Confidence 777777765433 35778888888876
No 69
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=28.83 E-value=1.3e+02 Score=24.87 Aligned_cols=75 Identities=24% Similarity=0.452 Sum_probs=43.3
Q ss_pred cCCCccccccCCCcCCCCCCCCcEEEEEceec-------------cCCCCccccEEEEecCCCCCcceEEEEEeeCCCeE
Q 030852 35 RGSSMSPTFNLTTDSFMGSLSDDYVLVEKFCL-------------QKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWI 101 (170)
Q Consensus 35 ~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~-------------~~~~~~~GDiV~f~~p~~~~~~~vKRVia~~Gd~v 101 (170)
....|.|.|+. ||+|...=... ..+.++.|-+|-+..- .+-|+++-.|.-+
T Consensus 105 ~~~~~r~~l~v----------GD~v~AkV~~vd~~~~~~L~~k~~~~GkL~~G~iv~i~p~------kVpRvig~~~sm~ 168 (239)
T COG1097 105 AEKDLRPFLNV----------GDLVYAKVVDVDRDGEVELTLKDEGLGKLKNGQIVKIPPS------KVPRVIGKKGSML 168 (239)
T ss_pred ccccccccccc----------CCEEEEEEEEccCCCceEEEeecCCCccccCCEEEEEchh------hcceEecCCCcHH
Confidence 35789999999 89986532111 1356777777766541 3445665555433
Q ss_pred Eec---CCCCeEEecCCeEEEeeCCCC
Q 030852 102 GTP---MTNDVMKVPNGHCWVEGDNPS 125 (170)
Q Consensus 102 ~i~---~~~~~~~vp~~~~~v~Gdn~~ 125 (170)
..- ....-+.=-+|.+|+-|.|.+
T Consensus 169 ~~l~~~~~~~I~VG~NG~IWV~~~~~~ 195 (239)
T COG1097 169 NMLKEKTGCEIIVGQNGRIWVDGENES 195 (239)
T ss_pred HHhhhhcCeEEEEecCCEEEecCCCcc
Confidence 221 111222234678999998873
No 70
>PF01568 Molydop_binding: Molydopterin dinucleotide binding domain; InterPro: IPR006657 A domain in this entry corresponds to the C-terminal domain IV in dimethyl sulphoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [].; GO: 0016491 oxidoreductase activity, 0030151 molybdenum ion binding, 0055114 oxidation-reduction process; PDB: 2IVF_A 1OGY_G 3ML1_A 3O5A_A 1TI2_G 1VLE_M 1VLD_U 1VLF_O 1TI4_I 1TI6_E ....
Probab=28.67 E-value=1.4e+02 Score=20.47 Aligned_cols=27 Identities=22% Similarity=0.287 Sum_probs=20.3
Q ss_pred cEEEEEceeccCCCCccccEEEEecCC
Q 030852 57 DYVLVEKFCLQKYKFSHGDVIVFCSPS 83 (170)
Q Consensus 57 d~vlv~k~~~~~~~~~~GDiV~f~~p~ 83 (170)
.++.++.-......++.||.|.+.++.
T Consensus 30 ~~v~inp~dA~~~Gi~~Gd~V~v~s~~ 56 (110)
T PF01568_consen 30 PFVEINPEDAAKLGIKDGDWVRVSSPR 56 (110)
T ss_dssp EEEEEEHHHHHHCT--TTCEEEEEETT
T ss_pred CEEEEcHHHHHHhcCcCCCEEEEEecc
Confidence 488888776666789999999999964
No 71
>PTZ00054 60S ribosomal protein L23; Provisional
Probab=28.35 E-value=2.7e+02 Score=21.16 Aligned_cols=34 Identities=9% Similarity=0.027 Sum_probs=25.6
Q ss_pred CCCeEEecCCeEEEeeCCCCCCCCCCccccccCCC
Q 030852 106 TNDVMKVPNGHCWVEGDNPSSSLDSRSFGPIPLGL 140 (170)
Q Consensus 106 ~~~~~~vp~~~~~v~Gdn~~~s~DSR~~G~V~~~~ 140 (170)
+...+..-+|.+.++.++. +..-+|-+|||+.|.
T Consensus 91 dGs~i~F~dNA~VLin~~~-~p~GTRI~GpV~rEl 124 (139)
T PTZ00054 91 DGVFIYFEDNAGVIVNPKG-EMKGSAITGPVAKEC 124 (139)
T ss_pred CCcEEEeCCcEEEEECCCC-CEeeeEEeCchhHHH
Confidence 3445666677888887664 667889999999987
No 72
>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=27.73 E-value=1.6e+02 Score=18.80 Aligned_cols=39 Identities=28% Similarity=0.285 Sum_probs=23.1
Q ss_pred CCCccccccCCCcCCCCCCCCcEEEEEceeccCCCCccccEEEEecCCCCCcceEEE
Q 030852 36 GSSMSPTFNLTTDSFMGSLSDDYVLVEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKR 92 (170)
Q Consensus 36 ~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~~GDiV~f~~p~~~~~~~vKR 92 (170)
++++.|....+ |-.+.+..| ++.||.|.++- .+..++.|
T Consensus 18 ~~~~K~A~let---------G~~i~VP~F------I~~Gd~I~VdT---~~g~Yv~R 56 (56)
T PF09285_consen 18 SSSYKPATLET---------GAEIQVPLF------IEEGDKIKVDT---RDGSYVER 56 (56)
T ss_dssp STTEEEEEETT---------S-EEEEETT--------TT-EEEEET---TTTEEEEE
T ss_pred CCCccEEEEcC---------CCEEEccce------ecCCCEEEEEC---CCCeEeCC
Confidence 34566665554 788888764 47899999987 34446555
No 73
>PF05382 Amidase_5: Bacteriophage peptidoglycan hydrolase ; InterPro: IPR008044 This entry is represented by Bacteriophage SFi21, lysin (Cell wall hydrolase; 3.5.1.28 from EC). At least one of proteins in this entry, the Pal protein from the pneumococcal bacteriophage Dp-1 (O03979 from SWISSPROT) has been shown to be an N-acetylmuramoyl-L-alanine amidase []. According to the known modular structure of this and other peptidoglycan hydrolases from the pneumococcal system, the active site should reside within this domain while a C-terminal domain binds to the choline residues of the cell wall teichoic acids [, ].
Probab=24.74 E-value=1.2e+02 Score=23.14 Aligned_cols=38 Identities=5% Similarity=0.243 Sum_probs=26.0
Q ss_pred EEcCCCccccccCCCcCCCCCCCCcEEEEEceeccCCCCccccEEEEecC
Q 030852 33 PVRGSSMSPTFNLTTDSFMGSLSDDYVLVEKFCLQKYKFSHGDVIVFCSP 82 (170)
Q Consensus 33 ~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~~GDiV~f~~p 82 (170)
...+++|...|..+ -+..+..-. ..++++|||++...+
T Consensus 50 ~~nT~tl~~~L~~~----------G~~~I~~~~--~~~~q~GDI~I~g~~ 87 (145)
T PF05382_consen 50 AGNTETLHDWLKKN----------GFKKISENV--DWNLQRGDIFIWGRR 87 (145)
T ss_pred ccCHHHHHHHHhhC----------CcEEeccCC--cccccCCCEEEEcCC
Confidence 45668888878773 355555432 137899999998665
No 74
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=24.74 E-value=1.4e+02 Score=22.03 Aligned_cols=25 Identities=12% Similarity=0.234 Sum_probs=16.7
Q ss_pred CCccccEEEEecCCCCCcceEEEEEee
Q 030852 70 KFSHGDVIVFCSPSNHKEKHVKRIIGL 96 (170)
Q Consensus 70 ~~~~GDiV~f~~p~~~~~~~vKRVia~ 96 (170)
.+++||.|.+....+.++ ..+|..+
T Consensus 45 ~IkkGD~V~VisG~~KGk--~GkV~~V 69 (120)
T PRK01191 45 PVRKGDTVKVMRGDFKGE--EGKVVEV 69 (120)
T ss_pred eEeCCCEEEEeecCCCCc--eEEEEEE
Confidence 678899888888655543 2455554
No 75
>PF11337 DUF3139: Protein of unknown function (DUF3139); InterPro: IPR021486 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=24.36 E-value=1.2e+02 Score=20.42 Aligned_cols=17 Identities=6% Similarity=-0.037 Sum_probs=7.7
Q ss_pred CchhHHHHHHHHHHHHH
Q 030852 1 MAAQNFLWSFTKNCFTF 17 (170)
Q Consensus 1 m~~~~~~~~~~~~~~~~ 17 (170)
|..+..++.++..++++
T Consensus 1 MKK~kii~iii~li~i~ 17 (85)
T PF11337_consen 1 MKKKKIILIIIILIVIS 17 (85)
T ss_pred CCchHHHHHHHHHHHHH
Confidence 55444554444444333
No 76
>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=24.30 E-value=99 Score=22.96 Aligned_cols=51 Identities=10% Similarity=0.035 Sum_probs=33.4
Q ss_pred ccccEEEEecC--CCCCcceEEEEEeeCCCe--EEecC---C--CCeEEecCCeEEEeeC
Q 030852 72 SHGDVIVFCSP--SNHKEKHVKRIIGLPGDW--IGTPM---T--NDVMKVPNGHCWVEGD 122 (170)
Q Consensus 72 ~~GDiV~f~~p--~~~~~~~vKRVia~~Gd~--v~i~~---~--~~~~~vp~~~~~v~Gd 122 (170)
+.||-|+++.+ +.++.+++-+|+...+++ ..+.+ + ...++++..++.-+=.
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 57999999886 456789999999988775 55532 1 2356666666666644
No 77
>PF10222 DUF2152: Uncharacterized conserved protein (DUF2152); InterPro: IPR018795 This entry includes mainly uncharacterised proteins, though some are described as belonging to the glycoside hydrolase family 65.
Probab=23.92 E-value=89 Score=29.39 Aligned_cols=67 Identities=12% Similarity=0.155 Sum_probs=38.8
Q ss_pred cEEEEEceeccCCCCccccEEEEecCCCCCcceEEEEEeeCCCeEEecCCCCeEEecCCeEEEeeCCCCCCCCCCcc
Q 030852 57 DYVLVEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVMKVPNGHCWVEGDNPSSSLDSRSF 133 (170)
Q Consensus 57 d~vlv~k~~~~~~~~~~GDiV~f~~p~~~~~~~vKRVia~~Gd~v~i~~~~~~~~vp~~~~~v~Gdn~~~s~DSR~~ 133 (170)
+.++-+++........+||.++...|...+...+ -.+. |+.....|..|+.|+.|.++.-+.+.++.
T Consensus 52 ~~Cl~~~l~~w~~~~~e~da~i~~~~~p~e~~~~---P~VG-------NG~iGl~V~~d~L~I~~~~R~l~~~~~f~ 118 (604)
T PF10222_consen 52 GKCLQDRLAPWYSQAEEGDAVILHPPKPQEKNYL---PFVG-------NGYIGLDVDSDNLYIKGSGRALSLPVPFH 118 (604)
T ss_pred chhHHHHHHHHHHHHhcCCEEEccCCCCCcccCC---ceec-------CCEEEEEEcCCeEEEEecCcccccccCCC
Confidence 4455555554445678899999986541111122 1111 23345667778888887666566666664
No 78
>PF07423 DUF1510: Protein of unknown function (DUF1510); InterPro: IPR009988 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=23.85 E-value=1e+02 Score=25.15 Aligned_cols=15 Identities=20% Similarity=0.592 Sum_probs=8.4
Q ss_pred EEecCCe--EEEeeCCC
Q 030852 110 MKVPNGH--CWVEGDNP 124 (170)
Q Consensus 110 ~~vp~~~--~~v~Gdn~ 124 (170)
.-||++. +|.+|.|-
T Consensus 163 tgi~~~~mi~w~ign~G 179 (217)
T PF07423_consen 163 TGISEDNMIVWFIGNNG 179 (217)
T ss_pred hCCChhheEEEhhhcCC
Confidence 3566555 56666553
No 79
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=23.74 E-value=1.8e+02 Score=22.28 Aligned_cols=17 Identities=6% Similarity=0.126 Sum_probs=11.5
Q ss_pred CCccccEEEEecCCCCC
Q 030852 70 KFSHGDVIVFCSPSNHK 86 (170)
Q Consensus 70 ~~~~GDiV~f~~p~~~~ 86 (170)
.++.||.|.+....+.+
T Consensus 46 ~IkkGD~V~Vi~Gk~KG 62 (143)
T PTZ00194 46 PVRKDDEVMVVRGHHKG 62 (143)
T ss_pred eeecCCEEEEecCCCCC
Confidence 56778877777755444
No 80
>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=23.72 E-value=2.3e+02 Score=21.92 Aligned_cols=24 Identities=25% Similarity=0.304 Sum_probs=18.7
Q ss_pred CCCCccccccCCCEEEEEEEEEeC
Q 030852 128 LDSRSFGPIPLGLIKGWVTHILWP 151 (170)
Q Consensus 128 ~DSR~~G~V~~~~IiGkv~~~~~p 151 (170)
+-|++.-.+|.+.|.||..-....
T Consensus 85 F~S~~~d~~p~~~IrGKC~V~~~~ 108 (164)
T cd04709 85 FLSRQVETLPATHIRGKCSVTLLN 108 (164)
T ss_pred EEecccccccHHHeeeeEEEEEeh
Confidence 445567889999999999877543
No 81
>PRK15095 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=23.52 E-value=2.3e+02 Score=21.49 Aligned_cols=35 Identities=17% Similarity=0.228 Sum_probs=27.9
Q ss_pred CCccccEEEEecCCCCCcceEEEEEeeCCCeEEecCC
Q 030852 70 KFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMT 106 (170)
Q Consensus 70 ~~~~GDiV~f~~p~~~~~~~vKRVia~~Gd~v~i~~~ 106 (170)
.++.|..+.+..+ ++..+.-||..+.+++|.++.+
T Consensus 92 ~~~~G~~~~~~~~--~G~~~~~~V~~i~~~~v~vD~N 126 (156)
T PRK15095 92 EPEIGAIMLFTAM--DGSEMPGVIREINGDSITVDFN 126 (156)
T ss_pred CCCCCCEEEEECC--CCCEEEEEEEEEcCCEEEEECC
Confidence 5788999888775 3566778999999999998754
Done!