Query 028706
Match_columns 205
No_of_seqs 167 out of 1392
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 15:43:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028706.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028706hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02227 sigpep_I_bact signal 100.0 1.3E-37 2.9E-42 251.3 15.5 133 46-188 2-163 (163)
2 KOG0171 Mitochondrial inner me 100.0 1.7E-35 3.8E-40 235.9 11.0 141 46-195 15-166 (176)
3 PRK10861 signal peptidase I; P 100.0 1.3E-33 2.9E-38 249.5 16.6 140 39-188 57-305 (324)
4 KOG1568 Mitochondrial inner me 100.0 5.8E-34 1.3E-38 226.8 10.9 156 44-203 9-167 (174)
5 PRK13838 conjugal transfer pil 99.9 1.3E-22 2.8E-27 166.1 14.4 93 91-184 36-172 (176)
6 TIGR02771 TraF_Ti conjugative 99.9 8.1E-22 1.8E-26 160.7 12.1 80 104-184 45-169 (171)
7 PRK13884 conjugal transfer pep 99.9 2.8E-21 6E-26 158.5 13.8 81 104-184 49-176 (178)
8 TIGR02754 sod_Ni_protease nick 99.9 1.6E-21 3.4E-26 142.3 9.5 89 68-182 2-90 (90)
9 PF10502 Peptidase_S26: Signal 99.8 2.7E-22 6E-27 158.2 2.3 92 89-184 9-137 (138)
10 cd06530 S26_SPase_I The S26 Ty 99.8 5.6E-20 1.2E-24 132.4 9.4 84 66-180 2-85 (85)
11 TIGR02228 sigpep_I_arch signal 99.8 2.9E-18 6.4E-23 138.2 12.1 87 67-182 34-120 (158)
12 COG0681 LepB Signal peptidase 99.6 1.6E-14 3.5E-19 115.0 11.9 127 42-180 7-144 (166)
13 COG4959 TraF Type IV secretory 99.5 3.2E-14 6.9E-19 113.0 4.4 88 94-184 45-169 (173)
14 cd06462 Peptidase_S24_S26 The 99.2 1.6E-10 3.6E-15 81.6 9.0 83 66-180 2-84 (84)
15 PF00717 Peptidase_S24: Peptid 99.2 7.4E-11 1.6E-15 81.4 6.6 56 68-138 1-56 (70)
16 KOG3342 Signal peptidase I [In 99.1 3.1E-10 6.7E-15 90.3 9.5 122 33-182 11-145 (180)
17 cd06529 S24_LexA-like Peptidas 98.9 1.6E-08 3.5E-13 71.2 8.7 61 66-159 2-62 (81)
18 COG2932 Predicted transcriptio 98.8 3.5E-08 7.6E-13 82.7 10.1 86 65-186 124-212 (214)
19 PRK10276 DNA polymerase V subu 98.5 8.2E-07 1.8E-11 69.8 10.2 85 64-185 51-136 (139)
20 PRK00215 LexA repressor; Valid 98.4 2.3E-06 5.1E-11 71.0 10.5 86 63-185 117-203 (205)
21 TIGR00498 lexA SOS regulatory 98.4 4.1E-06 8.9E-11 69.2 11.2 88 63-187 110-198 (199)
22 PRK12423 LexA repressor; Provi 98.3 4.6E-06 1E-10 69.5 10.4 84 65-184 115-199 (202)
23 COG1974 LexA SOS-response tran 97.6 0.0012 2.6E-08 55.3 11.3 89 63-187 111-200 (201)
24 COG4068 Uncharacterized protei 92.8 0.055 1.2E-06 36.6 1.2 28 8-35 8-38 (64)
25 TIGR02594 conserved hypothetic 86.9 2.6 5.7E-05 32.7 6.4 40 105-161 73-112 (129)
26 PF09889 DUF2116: Uncharacteri 86.0 0.7 1.5E-05 31.3 2.3 27 9-35 4-33 (59)
27 COG0681 LepB Signal peptidase 77.8 2.5 5.4E-05 33.0 3.1 13 105-117 84-96 (166)
28 PF05257 CHAP: CHAP domain; I 69.1 11 0.00024 28.3 4.7 35 104-138 61-96 (124)
29 PRK00364 groES co-chaperonin G 64.6 29 0.00063 25.4 6.0 86 91-180 7-94 (95)
30 COG0234 GroS Co-chaperonin Gro 61.7 45 0.00097 24.8 6.5 68 90-158 6-88 (96)
31 COG0361 InfA Translation initi 61.6 6.9 0.00015 27.8 2.1 20 90-112 49-68 (75)
32 TIGR00008 infA translation ini 58.1 11 0.00024 26.2 2.6 19 91-112 48-66 (68)
33 PF07423 DUF1510: Protein of u 51.5 17 0.00036 30.9 3.2 26 36-61 9-34 (217)
34 cd00320 cpn10 Chaperonin 10 Kd 51.0 58 0.0013 23.7 5.7 85 91-179 6-92 (93)
35 cd04456 S1_IF1A_like S1_IF1A_l 48.7 18 0.0004 25.6 2.6 21 91-113 42-62 (78)
36 cd04712 BAH_DCM_I BAH, or Brom 48.2 1.3E+02 0.0027 23.3 7.7 16 173-188 88-103 (130)
37 COG0093 RplN Ribosomal protein 47.8 1.3E+02 0.0028 23.3 7.6 15 160-174 91-105 (122)
38 PF00166 Cpn10: Chaperonin 10 47.0 31 0.00068 25.0 3.7 87 90-180 5-93 (93)
39 PRK15136 multidrug efflux syst 45.2 43 0.00093 30.5 5.1 14 104-117 81-94 (390)
40 PRK12442 translation initiatio 44.7 24 0.00052 25.8 2.7 19 91-112 50-68 (87)
41 cd05793 S1_IF1A S1_IF1A: Trans 44.1 23 0.00049 25.1 2.5 19 91-112 42-60 (77)
42 cd04714 BAH_BAHCC1 BAH, or Bro 44.1 42 0.00092 25.4 4.2 29 105-133 3-31 (121)
43 PF10377 ATG11: Autophagy-rela 42.8 1.3E+02 0.0028 23.3 6.8 58 105-183 42-99 (129)
44 smart00652 eIF1a eukaryotic tr 42.7 24 0.00053 25.3 2.5 19 91-112 47-65 (83)
45 PF01176 eIF-1a: Translation i 42.0 24 0.00053 23.8 2.3 11 105-115 41-51 (65)
46 PF14085 DUF4265: Domain of un 39.8 89 0.0019 23.6 5.4 46 91-138 11-57 (117)
47 PF06890 Phage_Mu_Gp45: Bacter 39.7 1.4E+02 0.003 24.2 6.7 38 100-139 69-109 (162)
48 PRK14533 groES co-chaperonin G 38.7 1.5E+02 0.0033 21.5 6.9 81 91-180 7-89 (91)
49 PRK04012 translation initiatio 37.6 32 0.00069 25.6 2.5 19 91-112 63-81 (100)
50 cd04717 BAH_polybromo BAH, or 36.5 67 0.0014 24.1 4.2 28 105-132 3-30 (121)
51 PF00278 Orn_DAP_Arg_deC: Pyri 35.8 62 0.0013 23.5 3.9 24 91-116 70-93 (116)
52 cd04720 BAH_Orc1p_Yeast BAH, o 35.7 1.8E+02 0.0039 23.7 6.9 39 91-131 39-77 (179)
53 PTZ00414 10 kDa heat shock pro 34.5 1.9E+02 0.0042 21.5 7.2 22 91-114 16-37 (100)
54 TIGR02219 phage_NlpC_fam putat 34.1 81 0.0018 24.2 4.4 26 105-130 76-101 (134)
55 PF10000 ACT_3: ACT domain; I 33.8 23 0.00049 24.8 1.1 18 72-99 12-29 (72)
56 COG1097 RRP4 RNA-binding prote 32.5 1.4E+02 0.0029 25.9 5.8 75 69-159 104-194 (239)
57 PF15057 DUF4537: Domain of un 30.2 71 0.0015 24.5 3.5 26 105-130 55-80 (124)
58 COG3602 Uncharacterized protei 29.6 32 0.00069 26.6 1.4 37 72-118 12-48 (134)
59 PF01426 BAH: BAH domain; Int 29.1 65 0.0014 23.4 3.0 27 106-132 3-29 (119)
60 PF07039 DUF1325: SGF29 tudor- 26.3 1.7E+02 0.0036 22.6 5.0 51 107-157 1-60 (130)
61 COG4640 Predicted membrane pro 25.5 37 0.0008 31.6 1.3 28 150-177 268-296 (465)
62 smart00439 BAH Bromo adjacent 24.9 1.1E+02 0.0025 22.0 3.7 17 170-186 70-86 (120)
63 PRK11578 macrolide transporter 24.6 1.8E+02 0.0039 25.9 5.6 14 124-137 71-84 (370)
64 PF15057 DUF4537: Domain of un 24.4 80 0.0017 24.2 2.8 34 70-114 48-81 (124)
65 KOG4146 Ubiquitin-like protein 24.4 83 0.0018 23.4 2.7 37 67-117 56-97 (101)
66 KOG3503 H/ACA snoRNP complex, 23.9 74 0.0016 21.5 2.2 26 179-204 12-37 (64)
67 cd05792 S1_eIF1AD_like S1_eIF1 23.4 65 0.0014 22.9 2.0 10 106-115 39-48 (78)
68 TIGR00523 eIF-1A eukaryotic/ar 21.4 97 0.0021 23.0 2.6 9 106-114 58-66 (99)
69 COG1188 Ribosome-associated he 21.1 2E+02 0.0042 21.6 4.2 29 104-135 47-75 (100)
No 1
>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type. A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes.
Probab=100.00 E-value=1.3e-37 Score=251.27 Aligned_cols=133 Identities=35% Similarity=0.559 Sum_probs=119.3
Q ss_pred HHHHHHHHHHHHHhhheeeEEEEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceE
Q 028706 46 TKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHV 125 (205)
Q Consensus 46 ~~~~~~~~lv~~~i~~~~~~~~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~v 125 (205)
+..++++++++++++.+++..+.|+|+||+|||++ ||+|+++|..+...++++||+|+|+.|.++++.++
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 45566777888899999999999999999999999 99999999987667899999999999887788999
Q ss_pred EEEeeeCCCeeecc------------C-----------------CCCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCE
Q 028706 126 KRIIGLPGDWIGTP------------M-----------------TNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLV 176 (205)
Q Consensus 126 KRViglpGD~V~i~------------~-----------------~~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~I 176 (205)
|||+|+|||+|++. + ...+.+||+|+|||+|||+.+|.|||+||+|++++|
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 99999999999871 0 012468999999999999999999999999999999
Q ss_pred eEEEEEEEeCCC
Q 028706 177 KGRVTHILWPPQ 188 (205)
Q Consensus 177 iGkv~~~i~P~~ 188 (205)
+|||++++||++
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=1.7e-35 Score=235.91 Aligned_cols=141 Identities=35% Similarity=0.622 Sum_probs=125.3
Q ss_pred HHHHHHHHHHHHHhhheeeEEEEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceE
Q 028706 46 TKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHV 125 (205)
Q Consensus 46 ~~~~~~~~lv~~~i~~~~~~~~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~v 125 (205)
....+..+++++.+..++.++..++|.||+||+++. ||+++.+|+++.++.+++||||++..|.++.+.++
T Consensus 15 ~~~~~~~~~f~h~t~~yl~e~~~~~gpSM~PTl~~~---------gd~l~aEkls~~f~~~~~gDIVi~~sP~~~~~~~c 85 (176)
T KOG0171|consen 15 FCSEIAYAAFTHVTHEYLGEFVMCSGPSMEPTLHDG---------GDVLLAEKLSYRFRKPQVGDIVIAKSPPDPKEHIC 85 (176)
T ss_pred hHHHHHHHHHHHHHHHHhcceeeccCCCcCceecCC---------CcEEehhhhhHhhcCCCCCCEEEEeCCCCchhhhh
Confidence 444555666778888899999999999999999996 88888899999999999999999999999999999
Q ss_pred EEEeeeCCCeeeccC-----------CCCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEEeCCCCccccc
Q 028706 126 KRIIGLPGDWIGTPM-----------TNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVE 194 (205)
Q Consensus 126 KRViglpGD~V~i~~-----------~~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i~P~~~~~~~~ 194 (205)
|||+|+|||.|.+.. ...++.||+||+||+|||.++|.|||+|||||...|+||+++++||++++....
T Consensus 86 KRIva~eGD~v~v~~~~~~~n~~~e~~~~~i~VP~GhVfv~GDN~~nS~DSr~yGplP~glI~gRvv~r~Wp~s~~~~~~ 165 (176)
T KOG0171|consen 86 KRIVAMEGDLVEVHDGPLVVNDLVEKFSTPIRVPEGHVFVEGDNRNNSLDSRNYGPLPMGLIQGRVVFRIWPPSRVSGLI 165 (176)
T ss_pred heeeccCCceEEEecCCcccchhhhhccceeeccCceEEEecCCCCCcccccccCCCchhheeeeEEEEecCchhcceee
Confidence 999999999776611 123579999999999999999999999999999999999999999999988765
Q ss_pred c
Q 028706 195 R 195 (205)
Q Consensus 195 ~ 195 (205)
-
T Consensus 166 ~ 166 (176)
T KOG0171|consen 166 L 166 (176)
T ss_pred e
Confidence 3
No 3
>PRK10861 signal peptidase I; Provisional
Probab=100.00 E-value=1.3e-33 Score=249.46 Aligned_cols=140 Identities=29% Similarity=0.388 Sum_probs=124.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhheeeEEEEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeecc------------CCCC
Q 028706 39 HNFLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQ------------KYKF 106 (205)
Q Consensus 39 ~~~~~~~~~~~~~~~lv~~~i~~~~~~~~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~------------~~~~ 106 (205)
...+..++..++++++++++++.|+++++.|+|+||+|||.. ||+|+++|+.|. ...+
T Consensus 57 ~~~~~~~~~~~~~~l~i~~~ir~fv~~~~~Ips~SM~PTL~~----------GD~IlVnK~~yg~~~p~~~~~~~~~~~p 126 (324)
T PRK10861 57 KPGWLETGASVFPVLAIVLIVRSFIYEPFQIPSGSMMPTLLI----------GDFILVEKFAYGIKDPITQTTLIETGHP 126 (324)
T ss_pred cchHHHHHHHHHHHHhHHHHHHhhEEEEEEECCCcCcCcccC----------CCEEEEEEeecCccCccccccccccCCC
Confidence 344677777888888899999999999999999999999999 999999999875 2578
Q ss_pred CcceEEEEecCCCCCcceEEEEeeeCCCeeecc---------C-------------------------------------
Q 028706 107 SHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTP---------M------------------------------------- 140 (205)
Q Consensus 107 ~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~---------~------------------------------------- 140 (205)
+|||||+|+.|.+++..+||||+|+|||+|++. .
T Consensus 127 ~RGDIVVF~~P~~~~~~yIKRVIGlPGD~I~~~~~~~~l~iNg~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~ 206 (324)
T PRK10861 127 KRGDIVVFKYPEDPKLDYIKRVVGLPGDKVTYDPVSKEVTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEAT 206 (324)
T ss_pred CCCCEEEEecCCCCCCcEEEEeeecCCcEEEEEeCCCEEEEcCccccccccccccccccccccccccccccccccccccc
Confidence 999999999999888999999999999999861 0
Q ss_pred ------------------C---------------------------------CCeEEecCCeEEEeeCCCCCCCCCCccc
Q 028706 141 ------------------T---------------------------------NDVVKVPNGHCWVEGDNPSSSLDSRSFG 169 (205)
Q Consensus 141 ------------------~---------------------------------~~~~~vp~g~~~v~GDN~~~S~DSR~~G 169 (205)
. ..+++||+|+||++|||+++|.||||||
T Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~E~l~~~~h~i~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~yf~mgdnr~~S~DSRy~G 286 (324)
T PRK10861 207 SGFFQVPLNETKENGIRLSERKETLGDVTHRILTVPGAQDQVGMYYQQPGQPLATWVVPPGQYFMMGDNRDNSADSRYWG 286 (324)
T ss_pred cccccccccccccccccceeEEEecCCccceeeecCCcccccccccccCCCcCceEEECCCeEEEeCCCCCCCcccCccc
Confidence 0 0133899999999999999999999999
Q ss_pred ccCCCCEeEEEEEEEeCCC
Q 028706 170 PIPLGLVKGRVTHILWPPQ 188 (205)
Q Consensus 170 ~V~~~~IiGkv~~~i~P~~ 188 (205)
+||+++|+|||..++|+++
T Consensus 287 ~Vp~~~i~G~a~~i~~s~d 305 (324)
T PRK10861 287 FVPEANLVGKATAIWMSFE 305 (324)
T ss_pred ccCHHHcEEEEEEEEEEcC
Confidence 9999999999999999986
No 4
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=5.8e-34 Score=226.82 Aligned_cols=156 Identities=40% Similarity=0.693 Sum_probs=134.3
Q ss_pred HHHHHHHHHHH--HHHHhhheeeEEEEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCC
Q 028706 44 SLTKNCFTFGL--IGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHK 121 (205)
Q Consensus 44 ~~~~~~~~~~l--v~~~i~~~~~~~~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~ 121 (205)
.+.+.++.++. +.+.+...+.....|.|.||.|||++. .+++..|.||++|+......+.+||||+|.+|.+++
T Consensus 9 ~~~ksl~~s~~~~v~~t~~DrV~~va~v~G~smqPtlnP~----~~~~~~d~Vll~k~~v~n~~~~rGDiVvl~sP~~p~ 84 (174)
T KOG1568|consen 9 VFEKSLTGSLKWHVLLTFSDRVVHVAQVYGSSMQPTLNPT----MNTNEKDTVLLRKWNVKNRKVSRGDIVVLKSPNDPD 84 (174)
T ss_pred HHHhceeeeeeeheeeeeeeeEEEEeEEecCcCCCccCCC----cccccccEEEEEeeccccceeccCCEEEEeCCCChh
Confidence 34444444444 445566678899999999999999993 455556999999998765568899999999999999
Q ss_pred cceEEEEeeeCCCeeec-cCCCCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEEeCCCCcccccccCCCC
Q 028706 122 EKHVKRIIGLPGDWIGT-PMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVERKNHQK 200 (205)
Q Consensus 122 ~~~vKRViglpGD~V~i-~~~~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i~P~~~~~~~~~~~~~~ 200 (205)
+.+||||+|+|||.+.. ++....+.||+|||||+|||...|+|||.||||+...|.|+|++++||+.||+.+.+-.|..
T Consensus 85 ~~~iKRv~alegd~~~t~~~k~~~v~vpkghcWVegDn~~hs~DSntFGPVS~gli~grai~ilwpP~R~~~~~~~~~~~ 164 (174)
T KOG1568|consen 85 KVIIKRVAALEGDIMVTEDEKEEPVVVPKGHCWVEGDNQKHSYDSNTFGPVSTGLIVGRAIYILWPPVRWQRLDKESPGR 164 (174)
T ss_pred heeeeeeecccccEeccCCCCCCceecCCCcEEEecCCcccccccCccCCcchhheeeeEEEEEcChHHhhhhcccCCcc
Confidence 99999999999999876 67778899999999999999999999999999999999999999999999999999877766
Q ss_pred CCC
Q 028706 201 RHS 203 (205)
Q Consensus 201 ~~~ 203 (205)
|..
T Consensus 165 ~~~ 167 (174)
T KOG1568|consen 165 RVP 167 (174)
T ss_pred ccc
Confidence 653
No 5
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=99.89 E-value=1.3e-22 Score=166.12 Aligned_cols=93 Identities=23% Similarity=0.379 Sum_probs=75.4
Q ss_pred CCeEEEEeeeccCCCCCcceEEEEecCCCC-------------------CcceEEEEeeeCCCeeecc-----------C
Q 028706 91 DDHVLMEKFCLQKYKFSHGDVIVFCSPSNH-------------------KEKHVKRIIGLPGDWIGTP-----------M 140 (205)
Q Consensus 91 GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~-------------------~~~~vKRViglpGD~V~i~-----------~ 140 (205)
.+.+.++++.+...++++||+|+|+.|.++ ...++|||+|+|||+|++. +
T Consensus 36 S~pig~y~~~~~~~~~~rGDiVvf~~P~~~~~~~a~~r~yl~~g~~p~~~~~~iKRViglpGD~V~i~~~v~iNg~~~~~ 115 (176)
T PRK13838 36 SEPLGLWRIEALDRPVAVGDLVFICPPETAAFREARERGYLRRGLCPGGFAPLIKTVAALAGQRVEIGGSVSIDGRPLPS 115 (176)
T ss_pred CCEEEEEEEeccCCCCCCCcEEEEECCchhhhhhhhhcccccccccccCCCceEEEEEEeCCcEEEECCEEEECCEEccc
Confidence 466777777654568999999999987643 1359999999999999871 0
Q ss_pred C--------------CCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEE
Q 028706 141 T--------------NDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHIL 184 (205)
Q Consensus 141 ~--------------~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i 184 (205)
. ....+||+|+|||+|||+ +|+||||||+|++++|+|+|..++
T Consensus 116 ~~~~~~~~~g~~l~~~~~~~vp~g~~fvlgd~~-~S~DSRy~G~V~~~~I~G~a~pi~ 172 (176)
T PRK13838 116 SSVRRRDGEGRPLTPFPGGVVPPGHLFLHSSFA-GSYDSRYFGPVPASGLLGLARPVL 172 (176)
T ss_pred cccccccccCCcCCCCCccCcCCCeEEEECCCC-CCCcccccCcccHHHeEEEEEEEE
Confidence 0 113579999999999985 899999999999999999998764
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=99.87 E-value=8.1e-22 Score=160.71 Aligned_cols=80 Identities=38% Similarity=0.659 Sum_probs=67.6
Q ss_pred CCCCcceEEEEecCCCCC-------------------cceEEEEeeeCCCeeecc------------C------------
Q 028706 104 YKFSHGDVIVFCSPSNHK-------------------EKHVKRIIGLPGDWIGTP------------M------------ 140 (205)
Q Consensus 104 ~~~~rGDIVvf~~p~~~~-------------------~~~vKRViglpGD~V~i~------------~------------ 140 (205)
.++++||+|+|+.|.++. ..++|||+|+|||+|++. +
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 389999999999875432 279999999999999881 0
Q ss_pred --CCCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEE
Q 028706 141 --TNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHIL 184 (205)
Q Consensus 141 --~~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i 184 (205)
...+.+||+| ||++|||+.+|+||||||+|++++|+|||..++
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 0125789999 999999999999999999999999999998653
No 7
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=99.87 E-value=2.8e-21 Score=158.50 Aligned_cols=81 Identities=21% Similarity=0.433 Sum_probs=67.7
Q ss_pred CCCCcceEEEEecCCCC-------------------CcceEEEEeeeCCCeeecc------------C------------
Q 028706 104 YKFSHGDVIVFCSPSNH-------------------KEKHVKRIIGLPGDWIGTP------------M------------ 140 (205)
Q Consensus 104 ~~~~rGDIVvf~~p~~~-------------------~~~~vKRViglpGD~V~i~------------~------------ 140 (205)
.++++||+|+|+.|... ...++|||+|+|||+|++. +
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 37899999999977521 1379999999999999871 0
Q ss_pred ----CCCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEE
Q 028706 141 ----TNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHIL 184 (205)
Q Consensus 141 ----~~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i 184 (205)
....++||+|+||++|||+.+|+||||||+|++++|+|+|..++
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 01135899999999999999999999999999999999998764
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=1.6e-21 Score=142.32 Aligned_cols=89 Identities=33% Similarity=0.514 Sum_probs=78.5
Q ss_pred EEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCCeEEe
Q 028706 68 PVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKV 147 (205)
Q Consensus 68 ~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~~~~v 147 (205)
.|.|+||+|||.+ ||+|++++.......+++||+|+|+.|.+++..++||++++++
T Consensus 2 ~V~g~SM~P~l~~----------GD~vlv~~~~~~~~~~~~Gdivv~~~~~~~~~~~vkRv~~~~~-------------- 57 (90)
T TIGR02754 2 KVTGVSMSPTLPP----------GDRIIVVPWLKIFRVPPIGNVVVVRHPLQPYGLIIKRLAAVDD-------------- 57 (90)
T ss_pred EeeCCCccCccCC----------CCEEEEEEccccCCCCCCCeEEEEecCCCCcceEEEEeeEEcC--------------
Confidence 6899999999999 9999999854433455789999999987677899999999874
Q ss_pred cCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEE
Q 028706 148 PNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTH 182 (205)
Q Consensus 148 p~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~ 182 (205)
+++|++|||+..|.|||++|+|+...|+|+|++
T Consensus 58 --~~~~l~~dN~~~~~d~~~~g~v~~~~I~G~v~~ 90 (90)
T TIGR02754 58 --NGLFLLGDNPKASTDSRQLGPVPRSLLLGKVLW 90 (90)
T ss_pred --CeEEEeCCCCCCCCcccccCCCcHHHEEEEEEC
Confidence 589999999999999999999999999999964
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=2.7e-22 Score=158.16 Aligned_cols=92 Identities=33% Similarity=0.621 Sum_probs=32.7
Q ss_pred CCCCeEEEEeeeccCCCCCcceEEEEecCCC------------CCcceEEEEeeeCCCeeecc-----------------
Q 028706 89 LSDDHVLMEKFCLQKYKFSHGDVIVFCSPSN------------HKEKHVKRIIGLPGDWIGTP----------------- 139 (205)
Q Consensus 89 ~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~------------~~~~~vKRViglpGD~V~i~----------------- 139 (205)
++.-+.++.+.. .+++||+|+|+.|.. .+..++|||+|+|||+|++.
T Consensus 9 lP~g~Y~~~~~~----~~~rGd~V~f~~p~~~~~~~~~~gy~~~~~~~iKrV~a~pGD~V~v~~~~v~iNG~~~~~~~~~ 84 (138)
T PF10502_consen 9 LPVGIYLIDPSD----KIERGDLVVFCPPAEVAFFAAERGYLPEGQPLIKRVAAVPGDTVEVTDGGVYINGRPVGEPLAT 84 (138)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cccccccccccc----cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence 334555565544 589999999999862 24689999999999999981
Q ss_pred --------CCCCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEE
Q 028706 140 --------MTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHIL 184 (205)
Q Consensus 140 --------~~~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i 184 (205)
......+||+|+|||+|||+.+|+||||||+|++++|+|+|..++
T Consensus 85 d~~g~~l~~~~~~~~vp~g~~~v~gd~~~~S~DSRy~G~V~~~~I~g~~~pl~ 137 (138)
T PF10502_consen 85 DSDGRPLPQFSGSGTVPEGEYFVLGDNRPNSFDSRYFGPVPRSQIIGKARPLW 137 (138)
T ss_dssp ----S-T----TEEE--TTEEEEE-SBTTS--SHHHH--EEGGGEEEEEEEEE
T ss_pred ccccccccccCCceEeCCCEEEEecCCCCCccccCEecccCHHHEEEEEEEEE
Confidence 112578999999999999999999999999999999999998875
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=99.82 E-value=5.6e-20 Score=132.41 Aligned_cols=84 Identities=44% Similarity=0.698 Sum_probs=75.7
Q ss_pred EEEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCCeE
Q 028706 66 IVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVV 145 (205)
Q Consensus 66 ~~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~~~ 145 (205)
.+.|.|+||+|++.. ||++++++.......+++||+|+|+.+.+++..++|||++
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 9999999877433368999999999986556899999997
Q ss_pred EecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEE
Q 028706 146 KVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRV 180 (205)
Q Consensus 146 ~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv 180 (205)
||++|||+.+|.|||+||+++.++|+|++
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=99.78 E-value=2.9e-18 Score=138.15 Aligned_cols=87 Identities=30% Similarity=0.356 Sum_probs=70.6
Q ss_pred EEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCCeEE
Q 028706 67 VPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVK 146 (205)
Q Consensus 67 ~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~~~~ 146 (205)
+.|.|+||+||+++ ||++++++... .++++||+|+|+.|.++ +.++|||+++.++.
T Consensus 34 v~V~g~SM~Ptl~~----------GD~vlv~~~~~--~~~~~GDIVvf~~~~~~-~~iihRVi~v~~~~----------- 89 (158)
T TIGR02228 34 VVVLSGSMEPTFNT----------GDLILVTGADP--NDIQVGDVITYKSPGFN-TPVTHRVIEINNSG----------- 89 (158)
T ss_pred EEEcCCCCcCCccC----------CCEEEEEeccc--CCCCCCCEEEEEECCCC-ccEEEEEEEEECCC-----------
Confidence 34999999999999 99999998543 48999999999997643 78999999997641
Q ss_pred ecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEE
Q 028706 147 VPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTH 182 (205)
Q Consensus 147 vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~ 182 (205)
.+-.|++.|||+ ...| .++|+.++|+||+..
T Consensus 90 -g~~~~~tkGDnN-~~~D---~~~v~~~~IiG~v~~ 120 (158)
T TIGR02228 90 -GELGFITKGDNN-PAPD---GEPVPSENVIGKYLG 120 (158)
T ss_pred -CcEEEEEEecCC-CCCC---cccCCHHHEEEEEEE
Confidence 012488889997 4445 689999999999983
No 12
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=99.59 E-value=1.6e-14 Score=115.03 Aligned_cols=127 Identities=30% Similarity=0.315 Sum_probs=99.7
Q ss_pred HHHHHHHHHHHHHHHHHh--hheeeEEEEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCC
Q 028706 42 LWSLTKNCFTFGLIGLTV--SDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSN 119 (205)
Q Consensus 42 ~~~~~~~~~~~~lv~~~i--~~~~~~~~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~ 119 (205)
...++..++.++++++++ ..++++++.|+|+||+|||+. ||+|+++|.++....+..+|++ ..|..
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 345556666666667776 899999999999999999999 9999999999887778888888 55666
Q ss_pred CCcceEEEEeeeCCCeeeccCCCC--eEEecCCeEEEeeCCC-------CCCCCCCcccccCCCCEeEEE
Q 028706 120 HKEKHVKRIIGLPGDWIGTPMTND--VVKVPNGHCWVEGDNP-------SSSLDSRSFGPIPLGLVKGRV 180 (205)
Q Consensus 120 ~~~~~vKRViglpGD~V~i~~~~~--~~~vp~g~~~v~GDN~-------~~S~DSR~~G~V~~~~IiGkv 180 (205)
....++||+++.+||.|.+..... ...+|++..++.++|. ..+.+++.++.......+.++
T Consensus 75 ~~~~~~kr~~~~~GD~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 144 (166)
T COG0681 75 VEGDLIKRVIGLRGDIVVFKDDRLYVVPIIPRVYGLVEKDNGKHLVDVIVNANSSRVFGIITKKDYIKRV 144 (166)
T ss_pred CCcceEEEeccCCCCEEEEECCEEEeecccCcchhhhhcccccccccccccccCccccccccccccccce
Confidence 788999999999999998854322 3455666666665443 466777778877778888877
No 13
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.47 E-value=3.2e-14 Score=112.99 Aligned_cols=88 Identities=28% Similarity=0.478 Sum_probs=72.1
Q ss_pred EEEEeeeccCCCCCcceEEEEecCCC------------CCcceEEEEeeeCCCeeec-----------------------
Q 028706 94 VLMEKFCLQKYKFSHGDVIVFCSPSN------------HKEKHVKRIIGLPGDWIGT----------------------- 138 (205)
Q Consensus 94 Vlv~k~~~~~~~~~rGDIVvf~~p~~------------~~~~~vKRViglpGD~V~i----------------------- 138 (205)
.-++|.+ .++.+||+|+++.|.. ....++|||.|+|||+|.+
T Consensus 45 yrv~k~~---~Pvt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq~Vci~~~~I~I~G~~v~~sl~~D~~GR 121 (173)
T COG4959 45 YRVSKLS---APVTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQHVCITSQGIAIDGKPVAASLPVDRVGR 121 (173)
T ss_pred EEecccC---CCcccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCCCcEEEecceEEECCEEeeeeccccccCC
Confidence 3444443 4569999999999863 3467899999999999987
Q ss_pred --cCCCCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEE
Q 028706 139 --PMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHIL 184 (205)
Q Consensus 139 --~~~~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i 184 (205)
+....+-.+-++++|+++|....|+|||||||||.++|+|.+..++
T Consensus 122 ~lp~~~gcR~l~~~el~lL~~~~~~SfDsRYfGpipas~vig~aRPvw 169 (173)
T COG4959 122 ALPRWQGCRYLAPSELLLLTDRSSTSFDSRYFGPIPASQVIGVARPVW 169 (173)
T ss_pred cCCcccCCceecCCeEEEEeccCCcccccceecccCHHHcceeeeeee
Confidence 1233445588899999999999999999999999999999998873
No 14
>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=99.19 E-value=1.6e-10 Score=81.57 Aligned_cols=83 Identities=48% Similarity=0.753 Sum_probs=65.1
Q ss_pred EEEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCCeE
Q 028706 66 IVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVV 145 (205)
Q Consensus 66 ~~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~~~ 145 (205)
.+.|.|+||+|++.. ||.+++++.. ..++.||+|++..+. +..++||+...++
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 9999999865 238999999999853 4899999998875
Q ss_pred EecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEE
Q 028706 146 KVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRV 180 (205)
Q Consensus 146 ~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv 180 (205)
++++++.+||+ +..+.+..+. .+..++|++
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 35899999994 5555554333 566677763
No 15
>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=99.17 E-value=7.4e-11 Score=81.37 Aligned_cols=56 Identities=34% Similarity=0.520 Sum_probs=44.7
Q ss_pred EEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeec
Q 028706 68 PVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGT 138 (205)
Q Consensus 68 ~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i 138 (205)
+|.|+||+|+|.+ ||+|++++.. .++.||+|+|..+.+. ..++||+++.+|+.+.+
T Consensus 1 ~V~GdSM~P~i~~----------Gd~v~v~~~~----~~~~gdivv~~~~~~~-~~~iKrv~~~~~~~~~~ 56 (70)
T PF00717_consen 1 RVEGDSMEPTIKD----------GDIVLVDPSS----EPKDGDIVVVKIDGDE-ELYIKRVVGEPGGIILI 56 (70)
T ss_dssp EEESSTTGGTSST----------TEEEEEEETS-------TTSEEEEEETTEE-SEEEEEEEEETTEEEEE
T ss_pred CeECcCcccCeeC----------CCEEEEEEcC----CCccCeEEEEEECCce-eeEEEEEEEeCCCEEEE
Confidence 5899999999999 9999999876 8899999999985321 38999999999875443
No 16
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.14 E-value=3.1e-10 Score=90.25 Aligned_cols=122 Identities=22% Similarity=0.312 Sum_probs=83.4
Q ss_pred ccchhhhHHHHHHHHHHHHHHHHHHHhhheee------EEEEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCC
Q 028706 33 ISNMAAHNFLWSLTKNCFTFGLIGLTVSDRYA------SIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKF 106 (205)
Q Consensus 33 ~~~~~~~~~~~~~~~~~~~~~lv~~~i~~~~~------~~~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~ 106 (205)
.++|+.+..+.+.+-...++..+.++-..+.+ .++.|-++||||.++. ||.++...... ...
T Consensus 11 ~k~mn~Rq~l~Q~ln~~mivssA~MiwK~l~vvt~seSPiVVVLSgSMePaF~R----------GDlLfL~N~~~--~p~ 78 (180)
T KOG3342|consen 11 LKRMNIRQLLYQVLNFAMIVSSAYMIWKGLMVVTGSESPIVVVLSGSMEPAFHR----------GDLLFLTNRNE--DPI 78 (180)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhheeeeCCCCCEEEEEcCCcCccccc----------ccEEEEecCCC--Ccc
Confidence 44577777766665444444333333333322 3788999999999999 99999975543 367
Q ss_pred CcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCCeEEecCC--eEEEeeCCCCCCCCCCc-c----cccCCCCEeEE
Q 028706 107 SHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNG--HCWVEGDNPSSSLDSRS-F----GPIPLGLVKGR 179 (205)
Q Consensus 107 ~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~~~~vp~g--~~~v~GDN~~~S~DSR~-~----G~V~~~~IiGk 179 (205)
+.||||+|+.+. .+..++|||+-+-+.. +| ++.+.|||+. .|.|. | --..+++|+|+
T Consensus 79 ~vGdivVf~veg-R~IPiVHRviK~he~~-------------~~~~~~LTKGDNN~--~dD~~Ly~~gq~~L~r~~Ivg~ 142 (180)
T KOG3342|consen 79 RVGDIVVFKVEG-REIPIVHRVIKQHEKS-------------NGHIKFLTKGDNNA--VDDRGLYAQGQNWLERKDIVGR 142 (180)
T ss_pred eeccEEEEEECC-ccCchhHHHHHHhccc-------------CCcEEEEecCCCCc--ccchhcccccccceeccceeeE
Confidence 899999999854 4678999999765421 23 4778899963 34442 2 13788999999
Q ss_pred EEE
Q 028706 180 VTH 182 (205)
Q Consensus 180 v~~ 182 (205)
|.-
T Consensus 143 ~~G 145 (180)
T KOG3342|consen 143 VRG 145 (180)
T ss_pred Eee
Confidence 965
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=98.87 E-value=1.6e-08 Score=71.20 Aligned_cols=61 Identities=34% Similarity=0.446 Sum_probs=52.9
Q ss_pred EEEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCCeE
Q 028706 66 IVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVV 145 (205)
Q Consensus 66 ~~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~~~ 145 (205)
...|.|+||+|+++. ||.+++++.. .++.||++++..+ +..++||+...++
T Consensus 2 ~~~v~g~sM~p~i~~----------gd~lii~~~~----~~~~g~i~~~~~~---~~~~ikr~~~~~~------------ 52 (81)
T cd06529 2 ALRVKGDSMEPTIPD----------GDLVLVDPSD----TPRDGDIVVARLD---GELTVKRLQRRGG------------ 52 (81)
T ss_pred EEEEECCCcCCccCC----------CCEEEEcCCC----CCCCCCEEEEEEC---CEEEEEEEEECCC------------
Confidence 468999999999999 9999999765 6899999999984 4789999998874
Q ss_pred EecCCeEEEeeCCC
Q 028706 146 KVPNGHCWVEGDNP 159 (205)
Q Consensus 146 ~vp~g~~~v~GDN~ 159 (205)
+.+++.++|+
T Consensus 53 ----~~~~L~s~N~ 62 (81)
T cd06529 53 ----GRLRLISDNP 62 (81)
T ss_pred ----CcEEEEeCCC
Confidence 3788889996
No 18
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=98.81 E-value=3.5e-08 Score=82.65 Aligned_cols=86 Identities=26% Similarity=0.305 Sum_probs=65.1
Q ss_pred EEEEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCCe
Q 028706 65 SIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDV 144 (205)
Q Consensus 65 ~~~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~~ 144 (205)
....|.|+||+|++.+ ||.++|+.-. ...+||.|++..- .++.+|||+...+|
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 5689999999999999 9999998776 6678996666542 46899999998875
Q ss_pred EEecCCeEEEeeCCCCCCCCCCcccccCCC---CEeEEEEEEEeC
Q 028706 145 VKVPNGHCWVEGDNPSSSLDSRSFGPIPLG---LVKGRVTHILWP 186 (205)
Q Consensus 145 ~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~---~IiGkv~~~i~P 186 (205)
|.+.+..+|+....|-- ...+ .|||+|++..-+
T Consensus 177 -----~~~~l~S~N~~~~~~~~----~~~~~~v~iIgrVv~~~~~ 212 (214)
T COG2932 177 -----GLLRLVSLNPDYYPDEI----FSEDDDVEIIGRVVWVSRL 212 (214)
T ss_pred -----CeEEEEeCCCCCCcccc----cCccceEEEEEEEEEEeee
Confidence 56779999985433332 2233 489999887543
No 19
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=98.55 E-value=8.2e-07 Score=69.82 Aligned_cols=85 Identities=22% Similarity=0.201 Sum_probs=60.4
Q ss_pred eEEEEEcCCCCc-cccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCC
Q 028706 64 ASIVPVRGSSMS-PTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTN 142 (205)
Q Consensus 64 ~~~~~V~g~SM~-Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~ 142 (205)
.....|.|+||. |++.+ ||++++++-. .++.||+|++.. .++..+||+.-.
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 455899999998 68999 9999999754 678999999987 467899998742
Q ss_pred CeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEEe
Q 028706 143 DVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILW 185 (205)
Q Consensus 143 ~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i~ 185 (205)
+++++..+|+.. .....-.-..=.|+|+|++++-
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 247788888631 1111111112269999988763
No 20
>PRK00215 LexA repressor; Validated
Probab=98.43 E-value=2.3e-06 Score=70.95 Aligned_cols=86 Identities=26% Similarity=0.350 Sum_probs=63.4
Q ss_pred eeEEEEEcCCCCc-cccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCC
Q 028706 63 YASIVPVRGSSMS-PTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMT 141 (205)
Q Consensus 63 ~~~~~~V~g~SM~-Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~ 141 (205)
-.....|.|+||. |++.+ ||++++++.. .++.||+|++.. +++..+||+.-.
T Consensus 117 ~~~~~~V~GdSM~~~~i~~----------Gd~v~v~~~~----~~~~G~ivv~~~---~~~~~vKrl~~~---------- 169 (205)
T PRK00215 117 EDFLLRVRGDSMIDAGILD----------GDLVIVRKQQ----TARNGQIVVALI---DDEATVKRFRRE---------- 169 (205)
T ss_pred CeEEEEEccCCCCCCCcCC----------CCEEEEeCCC----CCCCCCEEEEEE---CCEEEEEEEEEe----------
Confidence 4556889999995 79999 9999998743 678999999987 358899999754
Q ss_pred CCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEEe
Q 028706 142 NDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILW 185 (205)
Q Consensus 142 ~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i~ 185 (205)
.|.+++..||+.. +.....+ ..-.|+|+|+..+-
T Consensus 170 -------~~~~~L~s~Np~y--~~~~~~~-~~~~IiG~Vv~~~r 203 (205)
T PRK00215 170 -------GGHIRLEPENPAY--EPIIVDP-DRVTIEGKVVGLIR 203 (205)
T ss_pred -------CCEEEEEcCCCCC--CCEEeCC-CcEEEEEEEEEEEE
Confidence 2478888898742 2221111 13589999988763
No 21
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=98.40 E-value=4.1e-06 Score=69.16 Aligned_cols=88 Identities=16% Similarity=0.165 Sum_probs=65.5
Q ss_pred eeEEEEEcCCCCc-cccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCC
Q 028706 63 YASIVPVRGSSMS-PTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMT 141 (205)
Q Consensus 63 ~~~~~~V~g~SM~-Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~ 141 (205)
-...+.|.|+||. |++.+ ||++++++.. .++.||+|++.. .+...+||+.-.
T Consensus 110 ~~f~~~V~GdSM~~~~i~~----------Gd~v~v~~~~----~~~~G~ivvv~~---~~~~~vKrl~~~---------- 162 (199)
T TIGR00498 110 AVFLLKVMGDSMVDAGICD----------GDLLIVRSQK----DARNGEIVAAMI---DGEVTVKRFYKD---------- 162 (199)
T ss_pred CEEEEEecCCCCCCCCCCC----------CCEEEEecCC----CCCCCCEEEEEE---CCEEEEEEEEEE----------
Confidence 4567899999996 58999 9999998653 788999999998 567899998743
Q ss_pred CCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEEeCC
Q 028706 142 NDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPP 187 (205)
Q Consensus 142 ~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i~P~ 187 (205)
.+.+++..+|+... ..... -..=.|+|+|+.++..+
T Consensus 163 -------~~~i~L~s~N~~y~--~i~~~-~~~~~IiG~Vv~~~r~~ 198 (199)
T TIGR00498 163 -------GTKVELKPENPEFD--PIVLN-AEDVTILGKVVGVIRNF 198 (199)
T ss_pred -------CCEEEEEcCCCCCc--CCcCC-CCcEEEEEEEEEEEEec
Confidence 24788889987421 11111 01358999999887643
No 22
>PRK12423 LexA repressor; Provisional
Probab=98.34 E-value=4.6e-06 Score=69.47 Aligned_cols=84 Identities=18% Similarity=0.165 Sum_probs=62.3
Q ss_pred EEEEEcCCCCc-cccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCC
Q 028706 65 SIVPVRGSSMS-PTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTND 143 (205)
Q Consensus 65 ~~~~V~g~SM~-Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~ 143 (205)
....|.|+||. |+|.+ ||+|+|++-. .++.||+|++.. .++..+||+.-..
T Consensus 115 f~l~V~GdSM~~~~i~~----------Gd~viv~~~~----~~~~Gdivv~~~---~~~~~vKrl~~~~----------- 166 (202)
T PRK12423 115 YLLQVQGDSMIDDGILD----------GDLVGVHRSP----EARDGQIVVARL---DGEVTIKRLERSG----------- 166 (202)
T ss_pred EEEEEecCcCCCCCcCC----------CCEEEEeCCC----cCCCCCEEEEEE---CCEEEEEEEEEeC-----------
Confidence 45899999997 79999 9999999753 778999999987 4678999987542
Q ss_pred eEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEE
Q 028706 144 VVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHIL 184 (205)
Q Consensus 144 ~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i 184 (205)
+.+++..+|+.. +...+-+-..=.|+|+|+..+
T Consensus 167 ------~~~~L~s~N~~y--~~i~~~~~~~~~I~Gvv~g~~ 199 (202)
T PRK12423 167 ------DRIRLLPRNPAY--APIVVAPDQDFAIEGVFCGLI 199 (202)
T ss_pred ------CEEEEEcCCCCC--CCEEcCCCCcEEEEEEEEEEE
Confidence 368888888632 222221112347999998876
No 23
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=97.57 E-value=0.0012 Score=55.34 Aligned_cols=89 Identities=19% Similarity=0.214 Sum_probs=65.5
Q ss_pred eeEEEEEcCCCCc-cccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCC
Q 028706 63 YASIVPVRGSSMS-PTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMT 141 (205)
Q Consensus 63 ~~~~~~V~g~SM~-Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~ 141 (205)
-.....|.|+||. +.+.+ ||.|+|++-. ..+.||||+...+. ++.-+||..-..
T Consensus 111 ~~f~L~V~GdSM~~~gi~d----------GDlvvV~~~~----~a~~GdiVvA~i~g--~e~TvKrl~~~g--------- 165 (201)
T COG1974 111 ATFFLRVSGDSMIDAGILD----------GDLVVVDPTE----DAENGDIVVALIDG--EEATVKRLYRDG--------- 165 (201)
T ss_pred ceEEEEecCCccccCcCCC----------CCEEEEcCCC----CCCCCCEEEEEcCC--CcEEEEEEEEeC---------
Confidence 3556899999997 56666 9999999765 88999999999853 568899987543
Q ss_pred CCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEEEeCC
Q 028706 142 NDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPP 187 (205)
Q Consensus 142 ~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~i~P~ 187 (205)
+.++++--|+.. ....+..- .-.|+|+|+.++|+.
T Consensus 166 --------~~i~L~p~Np~~--~~i~~~~~-~~~I~G~vvgv~r~~ 200 (201)
T COG1974 166 --------NQILLKPENPAY--PPIPVDAD-SVTILGKVVGVIRDI 200 (201)
T ss_pred --------CEEEEEeCCCCC--CCcccCcc-ceEEEEEEEEEEecC
Confidence 367777777632 22222111 457999999999974
No 24
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=92.77 E-value=0.055 Score=36.58 Aligned_cols=28 Identities=21% Similarity=0.476 Sum_probs=22.5
Q ss_pred ccccccccc---cCCCCCCCccccccccccc
Q 028706 8 QKTCMNCKT---LNPQLPLQPCRCILGEISN 35 (205)
Q Consensus 8 ~~~~~~~~~---~~~~~~~~~~r~~~~~~~~ 35 (205)
.+-|-+|++ ++.|++++.|+++++..++
T Consensus 8 H~HC~VCg~aIp~de~~CSe~C~eil~ker~ 38 (64)
T COG4068 8 HRHCVVCGKAIPPDEQVCSEECGEILNKERK 38 (64)
T ss_pred CccccccCCcCCCccchHHHHHHHHHHHHHH
Confidence 467999998 7779999999987776654
No 25
>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=86.94 E-value=2.6 Score=32.70 Aligned_cols=40 Identities=25% Similarity=0.233 Sum_probs=29.9
Q ss_pred CCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCCeEEecCCeEEEeeCCCCC
Q 028706 105 KFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPSS 161 (205)
Q Consensus 105 ~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~~~~vp~g~~~v~GDN~~~ 161 (205)
.+++||+|+|+.. +.-+|.-+++...+ .|.++++|-|-.+
T Consensus 73 ~p~~GDiv~f~~~---~~~HVGi~~g~~~~--------------~g~i~~lgGNq~~ 112 (129)
T TIGR02594 73 KPAYGCIAVKRRG---GGGHVGFVVGKDKQ--------------TGTIIVLGGNQGD 112 (129)
T ss_pred CCCccEEEEEECC---CCCEEEEEEeEcCC--------------CCEEEEeeCCCCC
Confidence 6899999999863 34578888876654 4688999888643
No 26
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=85.97 E-value=0.7 Score=31.33 Aligned_cols=27 Identities=19% Similarity=0.312 Sum_probs=18.0
Q ss_pred cccccccc---cCCCCCCCccccccccccc
Q 028706 9 KTCMNCKT---LNPQLPLQPCRCILGEISN 35 (205)
Q Consensus 9 ~~~~~~~~---~~~~~~~~~~r~~~~~~~~ 35 (205)
+-|-+|++ .+....+..||+.....++
T Consensus 4 kHC~~CG~~Ip~~~~fCS~~C~~~~~k~qk 33 (59)
T PF09889_consen 4 KHCPVCGKPIPPDESFCSPKCREEYRKRQK 33 (59)
T ss_pred CcCCcCCCcCCcchhhhCHHHHHHHHHHHH
Confidence 56889987 4446777788875555443
No 27
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=77.77 E-value=2.5 Score=33.01 Aligned_cols=13 Identities=31% Similarity=0.414 Sum_probs=10.7
Q ss_pred CCCcceEEEEecC
Q 028706 105 KFSHGDVIVFCSP 117 (205)
Q Consensus 105 ~~~rGDIVvf~~p 117 (205)
...+||+|+|+.+
T Consensus 84 ~~~~GD~i~~~~~ 96 (166)
T COG0681 84 IGLRGDIVVFKDD 96 (166)
T ss_pred ccCCCCEEEEECC
Confidence 4578999999983
No 28
>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=69.10 E-value=11 Score=28.27 Aligned_cols=35 Identities=26% Similarity=0.252 Sum_probs=21.4
Q ss_pred CCCCcceEEEEecCCCCCcceEEEEeee-CCCeeec
Q 028706 104 YKFSHGDVIVFCSPSNHKEKHVKRIIGL-PGDWIGT 138 (205)
Q Consensus 104 ~~~~rGDIVvf~~p~~~~~~~vKRVigl-pGD~V~i 138 (205)
..|+.||||+|.......--+|--|.++ .+++|.+
T Consensus 61 ~~P~~Gdivv~~~~~~~~~GHVaIV~~v~~~~~i~v 96 (124)
T PF05257_consen 61 STPQPGDIVVWDSGSGGGYGHVAIVESVNDGGTITV 96 (124)
T ss_dssp S---TTEEEEEEECTTTTT-EEEEEEEE-TTSEEEE
T ss_pred cccccceEEEeccCCCCCCCeEEEEEEECCCCEEEE
Confidence 5899999999953332344488888888 6665544
No 29
>PRK00364 groES co-chaperonin GroES; Reviewed
Probab=64.56 E-value=29 Score=25.43 Aligned_cols=86 Identities=12% Similarity=0.103 Sum_probs=41.2
Q ss_pred CCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCCeEEecCCeEEEeeCCCC--CCCCCCcc
Q 028706 91 DDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPS--SSLDSRSF 168 (205)
Q Consensus 91 GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~~~~vp~g~~~v~GDN~~--~S~DSR~~ 168 (205)
||+||+.+.... +-..|-|++=.. ...+.....|+|+.-....-.-...+..|..|...+..+... --.|...|
T Consensus 7 ~drVLV~~~~~e--~~T~gGI~Lp~~--a~~k~~~G~VvaVG~G~~~~~G~~~~~~vk~GD~Vlf~~~~g~ev~~~~~~y 82 (95)
T PRK00364 7 GDRVLVKRLEEE--EKTAGGIVLPDS--AKEKPQEGEVVAVGPGRRLDNGERVPLDVKVGDKVLFGKYAGTEVKIDGEEY 82 (95)
T ss_pred CCEEEEEEcccC--ccccceEEcCcc--ccCCcceEEEEEECCCeECCCCCEeecccCCCCEEEEcCCCCeEEEECCEEE
Confidence 899999876522 344566665322 134456667776653321110011122333333333332221 11244445
Q ss_pred cccCCCCEeEEE
Q 028706 169 GPIPLGLVKGRV 180 (205)
Q Consensus 169 G~V~~~~IiGkv 180 (205)
=.++.++|+|++
T Consensus 83 ~iv~~~DIlavi 94 (95)
T PRK00364 83 LILRESDILAIV 94 (95)
T ss_pred EEEEHHHEEEEe
Confidence 567777777764
No 30
>COG0234 GroS Co-chaperonin GroES (HSP10) [Posttranslational modification, protein turnover, chaperones]
Probab=61.74 E-value=45 Score=24.81 Aligned_cols=68 Identities=16% Similarity=0.178 Sum_probs=36.9
Q ss_pred CCCeEEEEeeecc-------------CCCCCcceEEEEecCC-CCCcceEEEEeeeCCCeeec-cCCCCeEEecCCeEEE
Q 028706 90 SDDHVLMEKFCLQ-------------KYKFSHGDVIVFCSPS-NHKEKHVKRIIGLPGDWIGT-PMTNDVVKVPNGHCWV 154 (205)
Q Consensus 90 ~GD~Vlv~k~~~~-------------~~~~~rGDIVvf~~p~-~~~~~~vKRViglpGD~V~i-~~~~~~~~vp~g~~~v 154 (205)
.||+|++.+.... ..++++|.||+.-.-. +.+. -....-=..||+|-+ .+...++++-..+|.+
T Consensus 6 L~DRVlVk~~e~EekT~gGIvlpdsakeK~~~g~VvAVG~G~~~~~g-~~~~~~VkvGD~Vlf~ky~G~evk~dgeeyli 84 (96)
T COG0234 6 LGDRVLVKRVEEEEKTAGGIVLPDSAKEKPQEGEVVAVGPGRRDENG-ELVPLDVKVGDRVLFGKYAGTEVKIDGEEYLI 84 (96)
T ss_pred cCCEEEEEEchhhccccCcEEecCccccCCcceEEEEEccceecCCC-CEeccccccCCEEEECccCCcEEEECCEEEEE
Confidence 3899999877522 2456777777765311 1111 111111224677666 4555666666667776
Q ss_pred eeCC
Q 028706 155 EGDN 158 (205)
Q Consensus 155 ~GDN 158 (205)
+.+.
T Consensus 85 l~e~ 88 (96)
T COG0234 85 LSES 88 (96)
T ss_pred echH
Confidence 6544
No 31
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=61.61 E-value=6.9 Score=27.79 Aligned_cols=20 Identities=25% Similarity=0.416 Sum_probs=13.4
Q ss_pred CCCeEEEEeeeccCCCCCcceEE
Q 028706 90 SDDHVLMEKFCLQKYKFSHGDVI 112 (205)
Q Consensus 90 ~GD~Vlv~k~~~~~~~~~rGDIV 112 (205)
+||+|+|..+.+ .+++|||+
T Consensus 49 ~GD~V~Ve~~~~---d~~kg~I~ 68 (75)
T COG0361 49 PGDVVLVELSPY---DLTKGRIV 68 (75)
T ss_pred CCCEEEEEeccc---ccccccEE
Confidence 377777776663 46777765
No 32
>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=58.12 E-value=11 Score=26.22 Aligned_cols=19 Identities=21% Similarity=0.305 Sum_probs=11.3
Q ss_pred CCeEEEEeeeccCCCCCcceEE
Q 028706 91 DDHVLMEKFCLQKYKFSHGDVI 112 (205)
Q Consensus 91 GD~Vlv~k~~~~~~~~~rGDIV 112 (205)
||+|.|....| ++.+||||
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 45666665
No 33
>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=51.48 E-value=17 Score=30.93 Aligned_cols=26 Identities=8% Similarity=0.004 Sum_probs=14.4
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHhhh
Q 028706 36 MAAHNFLWSLTKNCFTFGLIGLTVSD 61 (205)
Q Consensus 36 ~~~~~~~~~~~~~~~~~~lv~~~i~~ 61 (205)
.++.+.++++++.++++|+++++...
T Consensus 9 rRK~N~iLNiaI~IV~lLIiiva~~l 34 (217)
T PF07423_consen 9 RRKTNKILNIAIGIVSLLIIIVAYQL 34 (217)
T ss_pred hhhhhhhHHHHHHHHHHHHHHHhhhh
Confidence 34555667776666665544444433
No 34
>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=50.99 E-value=58 Score=23.67 Aligned_cols=85 Identities=12% Similarity=0.105 Sum_probs=41.0
Q ss_pred CCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCCeEEecCCeEEEeeCCCC--CCCCCCcc
Q 028706 91 DDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPS--SSLDSRSF 168 (205)
Q Consensus 91 GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~~~~vp~g~~~v~GDN~~--~S~DSR~~ 168 (205)
||+|++.+.... +-..|-|++=... ..+.....|+|+.-....-.-...+..+..|...+..+... --.|...|
T Consensus 6 ~DrVLV~~~~~e--~~T~~GI~Lp~~~--~~k~~~g~VvAVG~g~~~~~g~~~~~~vk~GD~Vl~~~~~g~~v~~~~~~y 81 (93)
T cd00320 6 GDRVLVKRIEAE--EKTKGGIILPDSA--KEKPQEGKVVAVGPGRRNENGERVPLSVKVGDKVLFPKYAGTEVKLDGEEY 81 (93)
T ss_pred CCEEEEEEcccc--ceecceEEeCCCc--CCCceEEEEEEECCCeECCCCCCccccccCCCEEEECCCCceEEEECCEEE
Confidence 899999877532 3345666653332 24556677776654422111111122333333333332221 11233344
Q ss_pred cccCCCCEeEE
Q 028706 169 GPIPLGLVKGR 179 (205)
Q Consensus 169 G~V~~~~IiGk 179 (205)
=.++.++|+|+
T Consensus 82 ~i~~~~DIla~ 92 (93)
T cd00320 82 LILRESDILAV 92 (93)
T ss_pred EEEEHHHEEEE
Confidence 56667777765
No 35
>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=48.67 E-value=18 Score=25.63 Aligned_cols=21 Identities=14% Similarity=0.254 Sum_probs=10.5
Q ss_pred CCeEEEEeeeccCCCCCcceEEE
Q 028706 91 DDHVLMEKFCLQKYKFSHGDVIV 113 (205)
Q Consensus 91 GD~Vlv~k~~~~~~~~~rGDIVv 113 (205)
||+|+++...+. +..+||||-
T Consensus 42 GD~VlV~~~~~~--~~~kg~Iv~ 62 (78)
T cd04456 42 GDFLIVDPIEEG--EDVKADIIF 62 (78)
T ss_pred CCEEEEEecccC--CCceEEEEE
Confidence 566665554431 345555553
No 36
>cd04712 BAH_DCM_I BAH, or Bromo Adjacent Homology domain, as present in DNA (Cytosine-5)-methyltransferases (DCM) 1. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=48.18 E-value=1.3e+02 Score=23.27 Aligned_cols=16 Identities=13% Similarity=-0.174 Sum_probs=12.5
Q ss_pred CCCEeEEEEEEEeCCC
Q 028706 173 LGLVKGRVTHILWPPQ 188 (205)
Q Consensus 173 ~~~IiGkv~~~i~P~~ 188 (205)
.+.|.||+..-+.+..
T Consensus 88 ~~~I~~k~~V~~~~~~ 103 (130)
T cd04712 88 STEIKGVHKVDWSGTP 103 (130)
T ss_pred cceeEEEEEEEEecCc
Confidence 5599999988876643
No 37
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=47.81 E-value=1.3e+02 Score=23.29 Aligned_cols=15 Identities=27% Similarity=0.554 Sum_probs=12.0
Q ss_pred CCCCCCCcccccCCC
Q 028706 160 SSSLDSRSFGPIPLG 174 (205)
Q Consensus 160 ~~S~DSR~~G~V~~~ 174 (205)
....-+|-||||.++
T Consensus 91 g~P~GtrI~GPVaRE 105 (122)
T COG0093 91 GEPRGTRIFGPVARE 105 (122)
T ss_pred CCcccceEecchhHH
Confidence 366788999999876
No 38
>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=47.03 E-value=31 Score=24.96 Aligned_cols=87 Identities=10% Similarity=0.064 Sum_probs=45.4
Q ss_pred CCCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCCeEEecCCeEEEeeCCCC--CCCCCCc
Q 028706 90 SDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPS--SSLDSRS 167 (205)
Q Consensus 90 ~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~~~~vp~g~~~v~GDN~~--~S~DSR~ 167 (205)
.||+|++.+... ..-..|-+++=.. ........+|+++......-....-+..+..|...+..+... -..|...
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 389999988632 3455666666532 234667777887765332211111122344444444444431 2235555
Q ss_pred ccccCCCCEeEEE
Q 028706 168 FGPIPLGLVKGRV 180 (205)
Q Consensus 168 ~G~V~~~~IiGkv 180 (205)
|=.++.++|+|++
T Consensus 81 ~~~~~~~dIlavi 93 (93)
T PF00166_consen 81 YLIVREDDILAVI 93 (93)
T ss_dssp EEEEEGGGEEEEE
T ss_pred EEEEEHHHeEEEC
Confidence 6677888888763
No 39
>PRK15136 multidrug efflux system protein EmrA; Provisional
Probab=45.17 E-value=43 Score=30.47 Aligned_cols=14 Identities=36% Similarity=0.472 Sum_probs=10.3
Q ss_pred CCCCcceEEEEecC
Q 028706 104 YKFSHGDVIVFCSP 117 (205)
Q Consensus 104 ~~~~rGDIVvf~~p 117 (205)
..+++||+++--.+
T Consensus 81 d~VkkGqvL~~LD~ 94 (390)
T PRK15136 81 DFVKEGDVLVTLDP 94 (390)
T ss_pred CEECCCCEEEEECc
Confidence 47889998876554
No 40
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=44.67 E-value=24 Score=25.77 Aligned_cols=19 Identities=21% Similarity=0.301 Sum_probs=9.8
Q ss_pred CCeEEEEeeeccCCCCCcceEE
Q 028706 91 DDHVLMEKFCLQKYKFSHGDVI 112 (205)
Q Consensus 91 GD~Vlv~k~~~~~~~~~rGDIV 112 (205)
||.|.|.-..| ++.+|+||
T Consensus 50 GD~V~VE~spY---DltkGRIi 68 (87)
T PRK12442 50 GDRVTLELSPY---DLTKGRIN 68 (87)
T ss_pred CCEEEEEECcc---cCCceeEE
Confidence 55555554442 34555554
No 41
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=44.14 E-value=23 Score=25.07 Aligned_cols=19 Identities=26% Similarity=0.419 Sum_probs=9.3
Q ss_pred CCeEEEEeeeccCCCCCcceEE
Q 028706 91 DDHVLMEKFCLQKYKFSHGDVI 112 (205)
Q Consensus 91 GD~Vlv~k~~~~~~~~~rGDIV 112 (205)
||+|++....+ +..+|||+
T Consensus 42 GD~V~Ve~~~~---d~~kg~Iv 60 (77)
T cd05793 42 GDIVLVAPWDF---QDDKADII 60 (77)
T ss_pred CCEEEEEeccc---cCCEEEEE
Confidence 55555554432 34455554
No 42
>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=44.07 E-value=42 Score=25.43 Aligned_cols=29 Identities=31% Similarity=0.330 Sum_probs=21.7
Q ss_pred CCCcceEEEEecCCCCCcceEEEEeeeCC
Q 028706 105 KFSHGDVIVFCSPSNHKEKHVKRIIGLPG 133 (205)
Q Consensus 105 ~~~rGDIVvf~~p~~~~~~~vKRViglpG 133 (205)
.++.||-|.++.+..++..+|.||..+-.
T Consensus 3 ~~~vGD~V~v~~~~~~~~pyIgrI~~i~e 31 (121)
T cd04714 3 IIRVGDCVLFKSPGRPSLPYVARIESLWE 31 (121)
T ss_pred EEEcCCEEEEeCCCCCCCCEEEEEEEEEE
Confidence 35679999998876556788888877654
No 43
>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=42.85 E-value=1.3e+02 Score=23.26 Aligned_cols=58 Identities=22% Similarity=0.375 Sum_probs=31.0
Q ss_pred CCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCCeEEecCCeEEEeeCCCCCCCCCCcccccCCCCEeEEEEEE
Q 028706 105 KFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHI 183 (205)
Q Consensus 105 ~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~~~~vp~g~~~v~GDN~~~S~DSR~~G~V~~~~IiGkv~~~ 183 (205)
.++.||+|+|-.-..... .+|.- ..+.+..=+||+-.|.-.. .+ .-.+++|+|+++.+
T Consensus 42 ~f~~GDlvLflpt~~~~~--~~~~~-------------~af~~~~~~YFL~~~s~~~-~~-----~~~~~w~vgrI~~~ 99 (129)
T PF10377_consen 42 NFQVGDLVLFLPTRNHNN--KKQPW-------------AAFNVGCPHYFLHEDSIAA-NE-----LKRREWIVGRIVSI 99 (129)
T ss_pred cCCCCCEEEEEecCCCCc--cccce-------------EEeeCCCceEEEecccchh-cc-----CCCCCEEEEEEEEE
Confidence 788899999965332221 00000 0111223378887766422 11 12378899999875
No 44
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=42.65 E-value=24 Score=25.26 Aligned_cols=19 Identities=26% Similarity=0.440 Sum_probs=8.8
Q ss_pred CCeEEEEeeeccCCCCCcceEE
Q 028706 91 DDHVLMEKFCLQKYKFSHGDVI 112 (205)
Q Consensus 91 GD~Vlv~k~~~~~~~~~rGDIV 112 (205)
||+|+|+...+ ...+||||
T Consensus 47 GD~VlVe~~~~---~~~kg~Iv 65 (83)
T smart00652 47 GDIVLVDPWDF---QDVKADII 65 (83)
T ss_pred CCEEEEEecCC---CCCEEEEE
Confidence 55555554432 23455543
No 45
>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=42.05 E-value=24 Score=23.82 Aligned_cols=11 Identities=18% Similarity=0.353 Sum_probs=5.4
Q ss_pred CCCcceEEEEe
Q 028706 105 KFSHGDVIVFC 115 (205)
Q Consensus 105 ~~~rGDIVvf~ 115 (205)
-+++||+|+..
T Consensus 41 wI~~GD~V~V~ 51 (65)
T PF01176_consen 41 WIKRGDFVLVE 51 (65)
T ss_dssp ---TTEEEEEE
T ss_pred ecCCCCEEEEE
Confidence 35667766665
No 46
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=39.79 E-value=89 Score=23.58 Aligned_cols=46 Identities=17% Similarity=0.254 Sum_probs=29.9
Q ss_pred CCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEe-eeCCCeeec
Q 028706 91 DDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRII-GLPGDWIGT 138 (205)
Q Consensus 91 GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRVi-glpGD~V~i 138 (205)
+|...+.........+..||+|.++... +...+.+++ .-.+-|+++
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 5666676666556789999999998754 455444444 433445554
No 47
>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=39.74 E-value=1.4e+02 Score=24.22 Aligned_cols=38 Identities=18% Similarity=0.284 Sum_probs=27.3
Q ss_pred eccCCCCCcceEEEEecCCCCCcceEEE---EeeeCCCeeecc
Q 028706 100 CLQKYKFSHGDVIVFCSPSNHKEKHVKR---IIGLPGDWIGTP 139 (205)
Q Consensus 100 ~~~~~~~~rGDIVvf~~p~~~~~~~vKR---ViglpGD~V~i~ 139 (205)
.|....++.||+.+|... ....++|| ++.+.++++.+.
T Consensus 69 ~yR~~~L~~GEvalY~~~--G~~I~L~~~G~ii~~~~~~~~v~ 109 (162)
T PF06890_consen 69 RYRPKGLKPGEVALYDDE--GQKIHLKRDGRIIEVTCKTVTVN 109 (162)
T ss_pred cccccCCCCCcEEEEcCC--CCEEEEEecceEEeccCceEEEe
Confidence 344456899999999862 34566765 777888888873
No 48
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=38.66 E-value=1.5e+02 Score=21.53 Aligned_cols=81 Identities=9% Similarity=0.142 Sum_probs=40.3
Q ss_pred CCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeeeCCCeeeccCCCCeEEecCCeEEEeeCCCC--CCCCCCcc
Q 028706 91 DDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPS--SSLDSRSF 168 (205)
Q Consensus 91 GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~V~i~~~~~~~~vp~g~~~v~GDN~~--~S~DSR~~ 168 (205)
||+||+.+.... .-..|-|++=... ..+.....|+|+.... ...+..|..|...+.++... --.|...|
T Consensus 7 ~DRVLVk~~~~e--~~T~gGI~Lp~~a--~ek~~~G~VvavG~g~-----~~~~~~Vk~GD~Vl~~~y~g~ev~~~~~~y 77 (91)
T PRK14533 7 GERLLIKPIKEE--KKTEGGIVLPDSA--KEKPMKAEVVAVGKLD-----DEEDFDIKVGDKVIFSKYAGTEIKIDDEDY 77 (91)
T ss_pred CCEEEEEEcccc--ceecccEEecccc--cCCcceEEEEEECCCC-----ccccccccCCCEEEEccCCCeEEEECCEEE
Confidence 899999876522 3345666654332 2344555666554211 01133344444444443321 12334445
Q ss_pred cccCCCCEeEEE
Q 028706 169 GPIPLGLVKGRV 180 (205)
Q Consensus 169 G~V~~~~IiGkv 180 (205)
=.++.++|+|++
T Consensus 78 ~iv~e~DILa~i 89 (91)
T PRK14533 78 IIIDVNDILAKI 89 (91)
T ss_pred EEEEhHhEEEEe
Confidence 567777787764
No 49
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=37.61 E-value=32 Score=25.64 Aligned_cols=19 Identities=21% Similarity=0.396 Sum_probs=9.8
Q ss_pred CCeEEEEeeeccCCCCCcceEE
Q 028706 91 DDHVLMEKFCLQKYKFSHGDVI 112 (205)
Q Consensus 91 GD~Vlv~k~~~~~~~~~rGDIV 112 (205)
||+|+|..+.+ +..+||||
T Consensus 63 GD~VlVe~~~~---~~~kg~Iv 81 (100)
T PRK04012 63 GDVVIVAPWDF---QDEKADII 81 (100)
T ss_pred CCEEEEEeccc---CCCEEEEE
Confidence 56666555443 24455554
No 50
>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=36.47 E-value=67 Score=24.08 Aligned_cols=28 Identities=21% Similarity=0.363 Sum_probs=19.7
Q ss_pred CCCcceEEEEecCCCCCcceEEEEeeeC
Q 028706 105 KFSHGDVIVFCSPSNHKEKHVKRIIGLP 132 (205)
Q Consensus 105 ~~~rGDIVvf~~p~~~~~~~vKRViglp 132 (205)
.++.||.|.+..+.+++..+|-||..+-
T Consensus 3 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~ 30 (121)
T cd04717 3 QYRVGDCVYVANPEDPSKPIIFRIERLW 30 (121)
T ss_pred EEECCCEEEEeCCCCCCCCEEEEEeEEE
Confidence 3567888888877655667777777654
No 51
>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=35.80 E-value=62 Score=23.53 Aligned_cols=24 Identities=21% Similarity=0.292 Sum_probs=16.3
Q ss_pred CCeEEEEeeeccCCCCCcceEEEEec
Q 028706 91 DDHVLMEKFCLQKYKFSHGDVIVFCS 116 (205)
Q Consensus 91 GD~Vlv~k~~~~~~~~~rGDIVvf~~ 116 (205)
+|++.-+.... .+++.||+++|..
T Consensus 70 ~D~i~~~~~lP--~~l~~GD~l~f~~ 93 (116)
T PF00278_consen 70 GDVIARDVMLP--KELEVGDWLVFEN 93 (116)
T ss_dssp TSEEEEEEEEE--STTTTT-EEEESS
T ss_pred CceEeeeccCC--CCCCCCCEEEEec
Confidence 88776443332 2789999999976
No 52
>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=35.69 E-value=1.8e+02 Score=23.70 Aligned_cols=39 Identities=15% Similarity=0.185 Sum_probs=25.3
Q ss_pred CCeEEEEeeeccCCCCCcceEEEEecCCCCCcceEEEEeee
Q 028706 91 DDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGL 131 (205)
Q Consensus 91 GD~Vlv~k~~~~~~~~~rGDIVvf~~p~~~~~~~vKRVigl 131 (205)
++.+...+..-. ..++.||-|+++.+.. +..++..|..+
T Consensus 39 ~~~i~l~R~~d~-~~~~vGD~Vlik~~~~-~~~~V~iI~ei 77 (179)
T cd04720 39 KRKIFLARDSDG-LELSVGDTILVKDDVA-NSPSVYLIHEI 77 (179)
T ss_pred CCcEEEEEccCC-eEEeCCCEEEEeCCCC-CCCEEEEEEEE
Confidence 344555554222 4789999999998753 55666666654
No 53
>PTZ00414 10 kDa heat shock protein; Provisional
Probab=34.50 E-value=1.9e+02 Score=21.49 Aligned_cols=22 Identities=18% Similarity=0.277 Sum_probs=13.6
Q ss_pred CCeEEEEeeeccCCCCCcceEEEE
Q 028706 91 DDHVLMEKFCLQKYKFSHGDVIVF 114 (205)
Q Consensus 91 GD~Vlv~k~~~~~~~~~rGDIVvf 114 (205)
||+|++.+.... +-..|-|++=
T Consensus 16 ~dRVLVk~~~~e--~kT~gGIiLP 37 (100)
T PTZ00414 16 GQRVLVKRTLAA--KQTKAGVLIP 37 (100)
T ss_pred CCEEEEEEcccc--cccccCEEcc
Confidence 999999876522 2334555543
No 54
>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=34.15 E-value=81 Score=24.20 Aligned_cols=26 Identities=27% Similarity=0.294 Sum_probs=15.2
Q ss_pred CCCcceEEEEecCCCCCcceEEEEee
Q 028706 105 KFSHGDVIVFCSPSNHKEKHVKRIIG 130 (205)
Q Consensus 105 ~~~rGDIVvf~~p~~~~~~~vKRVig 130 (205)
++++||+|.|+.........+.-.+|
T Consensus 76 ~~qpGDlvff~~~~~~~~~HvGIy~G 101 (134)
T TIGR02219 76 AAQPGDVLVFRWRPGAAAKHAAIAAS 101 (134)
T ss_pred cCCCCCEEEEeeCCCCCCcEEEEEeC
Confidence 67899999997422122234444443
No 55
>PF10000 ACT_3: ACT domain; InterPro: IPR018717 This domain has no known function.; PDB: 1ZVP_C.
Probab=33.76 E-value=23 Score=24.77 Aligned_cols=18 Identities=39% Similarity=0.560 Sum_probs=12.2
Q ss_pred CCCccccCCCCCCCCCCCCCCeEEEEee
Q 028706 72 SSMSPTFNPTTDSFMGSLSDDHVLMEKF 99 (205)
Q Consensus 72 ~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~ 99 (205)
.||+|.|++ |++|++.--
T Consensus 12 ~~m~P~L~~----------~~yVF~t~~ 29 (72)
T PF10000_consen 12 ASMSPELNP----------GEYVFCTVP 29 (72)
T ss_dssp ST-EEEE-S----------S-EEEEEE-
T ss_pred hhCCcEeCC----------CCEEEEEec
Confidence 489999999 999999754
No 56
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=32.55 E-value=1.4e+02 Score=25.90 Aligned_cols=75 Identities=25% Similarity=0.416 Sum_probs=46.9
Q ss_pred EcCCCCccccCCCCCCCCCCCCCCeEEEEeeec-------------cCCCCCcceEEEEecCCCCCcceEEEEeeeCCCe
Q 028706 69 VRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCL-------------QKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDW 135 (205)
Q Consensus 69 V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~-------------~~~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~ 135 (205)
-....|.|.|+. ||.|+..=... ...+++.|-+|-..+ ..+-|++|.-|.-
T Consensus 104 ~~~~~~r~~l~v----------GD~v~AkV~~vd~~~~~~L~~k~~~~GkL~~G~iv~i~p------~kVpRvig~~~sm 167 (239)
T COG1097 104 NAEKDLRPFLNV----------GDLVYAKVVDVDRDGEVELTLKDEGLGKLKNGQIVKIPP------SKVPRVIGKKGSM 167 (239)
T ss_pred cccccccccccc----------CCEEEEEEEEccCCCceEEEeecCCCccccCCEEEEEch------hhcceEecCCCcH
Confidence 346789999999 99887632211 124566677776644 3566777777665
Q ss_pred eec--cCCCCeEEe-cCCeEEEeeCCC
Q 028706 136 IGT--PMTNDVVKV-PNGHCWVEGDNP 159 (205)
Q Consensus 136 V~i--~~~~~~~~v-p~g~~~v~GDN~ 159 (205)
+.. ......+.| -+|.+||-|.|.
T Consensus 168 ~~~l~~~~~~~I~VG~NG~IWV~~~~~ 194 (239)
T COG1097 168 LNMLKEKTGCEIIVGQNGRIWVDGENE 194 (239)
T ss_pred HHHhhhhcCeEEEEecCCEEEecCCCc
Confidence 543 122333444 457789999986
No 57
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=30.21 E-value=71 Score=24.48 Aligned_cols=26 Identities=12% Similarity=0.094 Sum_probs=11.8
Q ss_pred CCCcceEEEEecCCCCCcceEEEEee
Q 028706 105 KFSHGDVIVFCSPSNHKEKHVKRIIG 130 (205)
Q Consensus 105 ~~~rGDIVvf~~p~~~~~~~vKRVig 130 (205)
.++.||-|+...+.....+.=..|++
T Consensus 55 ~L~~GD~VLA~~~~~~~~Y~Pg~V~~ 80 (124)
T PF15057_consen 55 SLQVGDKVLAPWEPDDCRYGPGTVIA 80 (124)
T ss_pred cCCCCCEEEEecCcCCCEEeCEEEEE
Confidence 44555555555443333333355553
No 58
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.60 E-value=32 Score=26.61 Aligned_cols=37 Identities=16% Similarity=0.050 Sum_probs=22.7
Q ss_pred CCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEEecCC
Q 028706 72 SSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPS 118 (205)
Q Consensus 72 ~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf~~p~ 118 (205)
.||.|.|.+ ||+|++.--.....+..-.-+-.|+.++
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 379999999 9999985432111122233455676654
No 59
>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=29.12 E-value=65 Score=23.36 Aligned_cols=27 Identities=19% Similarity=0.199 Sum_probs=19.0
Q ss_pred CCcceEEEEecCCCCCcceEEEEeeeC
Q 028706 106 FSHGDVIVFCSPSNHKEKHVKRIIGLP 132 (205)
Q Consensus 106 ~~rGDIVvf~~p~~~~~~~vKRViglp 132 (205)
++.||.|.+..+..+...+|.||..+-
T Consensus 3 ~~vGD~V~v~~~~~~~~~~v~~I~~i~ 29 (119)
T PF01426_consen 3 YKVGDFVYVKPDDPPEPPYVARIEEIW 29 (119)
T ss_dssp EETTSEEEEECTSTTSEEEEEEEEEEE
T ss_pred EeCCCEEEEeCCCCCCCCEEEEEEEEE
Confidence 456888888776555677888887664
No 60
>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=26.34 E-value=1.7e+02 Score=22.65 Aligned_cols=51 Identities=12% Similarity=0.089 Sum_probs=35.3
Q ss_pred CcceEEEEecC--CCCCcceEEEEeeeCCCe--eec----cC-CCCeEEecCCeEEEeeC
Q 028706 107 SHGDVIVFCSP--SNHKEKHVKRIIGLPGDW--IGT----PM-TNDVVKVPNGHCWVEGD 157 (205)
Q Consensus 107 ~rGDIVvf~~p--~~~~~~~vKRViglpGD~--V~i----~~-~~~~~~vp~g~~~v~GD 157 (205)
+.||-|+|+.+ ...+..++-+|++.-+++ .++ ++ ....++++..++.-+=.
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 47999999876 345788999999998886 555 12 23477778888877755
No 61
>COG4640 Predicted membrane protein [Function unknown]
Probab=25.46 E-value=37 Score=31.60 Aligned_cols=28 Identities=18% Similarity=0.338 Sum_probs=16.9
Q ss_pred CeEEEeeCCC-CCCCCCCcccccCCCCEe
Q 028706 150 GHCWVEGDNP-SSSLDSRSFGPIPLGLVK 177 (205)
Q Consensus 150 g~~~v~GDN~-~~S~DSR~~G~V~~~~Ii 177 (205)
++.|+-+-+. -.-.||..|||++.+-=+
T Consensus 268 ae~fI~~kdi~kkikdskTyGP~~~ntsi 296 (465)
T COG4640 268 AEKFITIKDIGKKIKDSKTYGPYPQNTSI 296 (465)
T ss_pred cceeeccccccccccccceecCcCCCCce
Confidence 3444443332 134789999999976544
No 62
>smart00439 BAH Bromo adjacent homology domain.
Probab=24.89 E-value=1.1e+02 Score=21.99 Aligned_cols=17 Identities=18% Similarity=0.347 Sum_probs=13.5
Q ss_pred ccCCCCEeEEEEEEEeC
Q 028706 170 PIPLGLVKGRVTHILWP 186 (205)
Q Consensus 170 ~V~~~~IiGkv~~~i~P 186 (205)
-++.+.|+||+.....+
T Consensus 70 ~i~~~~I~~kc~V~~~~ 86 (120)
T smart00439 70 TVPLSDIIGKCNVLSKS 86 (120)
T ss_pred cCChHHeeeEEEEEEcc
Confidence 48999999999876543
No 63
>PRK11578 macrolide transporter subunit MacA; Provisional
Probab=24.60 E-value=1.8e+02 Score=25.95 Aligned_cols=14 Identities=21% Similarity=0.233 Sum_probs=9.7
Q ss_pred eEEEEeeeCCCeee
Q 028706 124 HVKRIIGLPGDWIG 137 (205)
Q Consensus 124 ~vKRViglpGD~V~ 137 (205)
.|+++.-.+||+|.
T Consensus 71 ~V~~v~v~~G~~V~ 84 (370)
T PRK11578 71 QLKTLSVAIGDKVK 84 (370)
T ss_pred EEEEEEcCCCCEEc
Confidence 66666667777775
No 64
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=24.45 E-value=80 Score=24.17 Aligned_cols=34 Identities=21% Similarity=0.315 Sum_probs=22.7
Q ss_pred cCCCCccccCCCCCCCCCCCCCCeEEEEeeeccCCCCCcceEEEE
Q 028706 70 RGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVF 114 (205)
Q Consensus 70 ~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~~~~~~rGDIVvf 114 (205)
.+++|.+.|.. ||.||.. +......+-+|-|+.-
T Consensus 48 ~~~~~~~~L~~----------GD~VLA~-~~~~~~~Y~Pg~V~~~ 81 (124)
T PF15057_consen 48 LSDAMRHSLQV----------GDKVLAP-WEPDDCRYGPGTVIAG 81 (124)
T ss_pred ccCcccCcCCC----------CCEEEEe-cCcCCCEEeCEEEEEC
Confidence 45788999999 9999996 3322233445555543
No 65
>KOG4146 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=24.44 E-value=83 Score=23.37 Aligned_cols=37 Identities=30% Similarity=0.469 Sum_probs=24.9
Q ss_pred EEEcCCCCccccCCCCCCCCCCCCCCeEEEEeeecc-----CCCCCcceEEEEecC
Q 028706 67 VPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQ-----KYKFSHGDVIVFCSP 117 (205)
Q Consensus 67 ~~V~g~SM~Ptl~~~~~~~~~~~~GD~Vlv~k~~~~-----~~~~~rGDIVvf~~p 117 (205)
..+.++|..| |-++++++.... ...++.||.|+|.+.
T Consensus 56 lFi~~gsvrp--------------Gii~lINd~DWEllekedy~ledgD~ivfiST 97 (101)
T KOG4146|consen 56 LFIHHGSVRP--------------GIIVLINDMDWELLEKEDYPLEDGDHIVFIST 97 (101)
T ss_pred eEeeCCcCcC--------------cEEEEEeccchhhhcccccCcccCCEEEEEEe
Confidence 5567776555 566777655421 357899999999863
No 66
>KOG3503 consensus H/ACA snoRNP complex, subunit NOP10 [RNA processing and modification]
Probab=23.87 E-value=74 Score=21.54 Aligned_cols=26 Identities=19% Similarity=0.124 Sum_probs=17.0
Q ss_pred EEEEEEeCCCCcccccccCCCCCCCC
Q 028706 179 RVTHILWPPQRVRHVERKNHQKRHSP 204 (205)
Q Consensus 179 kv~~~i~P~~~~~~~~~~~~~~~~~~ 204 (205)
+-+|.+--....|...--.|++||||
T Consensus 12 ~rvYTlKk~~p~G~~T~saHPARFSP 37 (64)
T KOG3503|consen 12 KRVYTLKKVSPSGEQTLSAHPARFSP 37 (64)
T ss_pred cEEEEEeecCCCCceecccCccccCc
Confidence 33455544555666667788889887
No 67
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=23.41 E-value=65 Score=22.92 Aligned_cols=10 Identities=20% Similarity=0.504 Sum_probs=5.4
Q ss_pred CCcceEEEEe
Q 028706 106 FSHGDVIVFC 115 (205)
Q Consensus 106 ~~rGDIVvf~ 115 (205)
+++||+|+..
T Consensus 39 IkrGd~VlV~ 48 (78)
T cd05792 39 IKRGDFVLVE 48 (78)
T ss_pred EEeCCEEEEE
Confidence 3556665554
No 68
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=21.35 E-value=97 Score=22.99 Aligned_cols=9 Identities=33% Similarity=0.822 Sum_probs=4.5
Q ss_pred CCcceEEEE
Q 028706 106 FSHGDVIVF 114 (205)
Q Consensus 106 ~~rGDIVvf 114 (205)
+.+||+|+.
T Consensus 58 I~~GD~VlV 66 (99)
T TIGR00523 58 IREGDVVIV 66 (99)
T ss_pred ecCCCEEEE
Confidence 344555555
No 69
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=21.07 E-value=2e+02 Score=21.58 Aligned_cols=29 Identities=10% Similarity=0.237 Sum_probs=23.6
Q ss_pred CCCCcceEEEEecCCCCCcceEEEEeeeCCCe
Q 028706 104 YKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDW 135 (205)
Q Consensus 104 ~~~~rGDIVvf~~p~~~~~~~vKRViglpGD~ 135 (205)
..++.||++.++. ....+.-+|.+++..+
T Consensus 47 ~~VK~GD~l~i~~---~~~~~~v~Vl~~~~~r 75 (100)
T COG1188 47 KEVKVGDILTIRF---GNKEFTVKVLALGEQR 75 (100)
T ss_pred cccCCCCEEEEEe---CCcEEEEEEEeccccc
Confidence 5789999999998 5667888898888643
Done!