Query 030863
Match_columns 170
No_of_seqs 197 out of 1179
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 05:43:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030863.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030863hhsearch_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 1.9E-39 4E-44 249.7 15.1 133 11-153 2-163 (163)
2 KOG0171 Mitochondrial inner me 100.0 2.4E-38 5.2E-43 239.5 11.7 141 10-159 14-165 (176)
3 KOG1568 Mitochondrial inner me 100.0 8E-38 1.7E-42 236.2 10.3 161 4-168 4-167 (174)
4 PRK10861 signal peptidase I; P 100.0 5.2E-35 1.1E-39 245.5 16.4 139 6-154 59-306 (324)
5 PRK13838 conjugal transfer pil 99.9 9.6E-25 2.1E-29 169.9 14.2 93 56-149 36-172 (176)
6 PRK13884 conjugal transfer pep 99.9 8.8E-23 1.9E-27 159.2 13.6 81 69-149 49-176 (178)
7 TIGR02771 TraF_Ti conjugative 99.9 7.9E-23 1.7E-27 158.5 12.1 80 69-149 45-169 (171)
8 TIGR02754 sod_Ni_protease nick 99.9 9.8E-23 2.1E-27 141.9 9.4 89 33-147 2-90 (90)
9 PF10502 Peptidase_S26: Signal 99.9 1.1E-23 2.4E-28 158.1 3.0 89 57-149 12-137 (138)
10 cd06530 S26_SPase_I The S26 Ty 99.8 5.2E-21 1.1E-25 131.5 8.8 84 31-145 2-85 (85)
11 TIGR02228 sigpep_I_arch signal 99.8 7.3E-19 1.6E-23 134.7 12.2 85 34-147 36-120 (158)
12 COG0681 LepB Signal peptidase 99.6 1.8E-15 3.9E-20 115.1 11.4 130 4-145 4-144 (166)
13 COG4959 TraF Type IV secretory 99.6 3.8E-15 8.3E-20 112.2 6.5 89 58-149 44-169 (173)
14 cd06462 Peptidase_S24_S26 The 99.3 5E-11 1.1E-15 80.5 8.9 83 31-145 2-84 (84)
15 PF00717 Peptidase_S24: Peptid 99.2 1.8E-11 3.8E-16 80.6 5.8 56 33-103 1-56 (70)
16 KOG3342 Signal peptidase I [In 99.1 1.5E-09 3.3E-14 81.9 9.4 89 31-147 50-145 (180)
17 cd06529 S24_LexA-like Peptidas 98.9 9.7E-09 2.1E-13 69.1 8.5 61 31-124 2-62 (81)
18 COG2932 Predicted transcriptio 98.9 1.5E-08 3.3E-13 80.8 10.0 89 30-151 124-212 (214)
19 PRK10276 DNA polymerase V subu 98.6 6.7E-07 1.4E-11 66.9 10.3 85 29-150 51-136 (139)
20 TIGR00498 lexA SOS regulatory 98.5 1.8E-06 3.9E-11 67.9 11.1 88 28-152 110-198 (199)
21 PRK00215 LexA repressor; Valid 98.5 2.2E-06 4.7E-11 67.8 10.9 86 28-150 117-203 (205)
22 PRK12423 LexA repressor; Provi 98.4 2.6E-06 5.6E-11 67.6 10.3 85 30-150 115-200 (202)
23 COG1974 LexA SOS-response tran 97.8 0.00035 7.7E-09 55.6 11.3 89 28-152 111-200 (201)
24 TIGR02594 conserved hypothetic 86.6 3.8 8.3E-05 30.2 6.8 54 70-143 73-126 (129)
25 COG0681 LepB Signal peptidase 80.7 2 4.3E-05 32.0 3.2 13 70-82 84-96 (166)
26 PF05257 CHAP: CHAP domain; I 69.7 12 0.00026 26.6 4.9 35 69-103 61-96 (124)
27 COG0093 RplN Ribosomal protein 69.5 37 0.0008 24.9 7.1 26 114-140 81-106 (122)
28 COG0234 GroS Co-chaperonin Gro 67.4 35 0.00077 24.0 6.5 68 55-123 6-88 (96)
29 cd04712 BAH_DCM_I BAH, or Brom 60.5 65 0.0014 23.6 8.0 78 69-153 4-103 (130)
30 PF10377 ATG11: Autophagy-rela 57.8 27 0.0006 25.7 4.9 35 86-120 89-123 (129)
31 PRK00364 groES co-chaperonin G 54.9 69 0.0015 22.2 6.9 86 56-145 7-94 (95)
32 COG0361 InfA Translation initi 54.4 14 0.00029 24.9 2.5 19 56-77 50-68 (75)
33 PF00238 Ribosomal_L14: Riboso 52.8 52 0.0011 24.0 5.6 28 111-139 78-105 (122)
34 cd04714 BAH_BAHCC1 BAH, or Bro 50.5 24 0.00053 25.4 3.6 29 70-98 3-31 (121)
35 TIGR00008 infA translation ini 49.2 19 0.00042 23.7 2.6 19 56-77 48-66 (68)
36 cd04720 BAH_Orc1p_Yeast BAH, o 49.2 73 0.0016 24.7 6.3 79 56-146 39-140 (179)
37 PF01176 eIF-1a: Translation i 47.6 20 0.00042 23.0 2.4 12 70-81 41-52 (65)
38 TIGR01067 rplN_bact ribosomal 47.1 1.1E+02 0.0024 22.3 7.4 39 112-152 79-117 (122)
39 cd04456 S1_IF1A_like S1_IF1A_l 46.5 22 0.00048 23.9 2.6 10 71-80 39-48 (78)
40 PF15057 DUF4537: Domain of un 46.5 27 0.00059 25.5 3.3 52 69-120 54-112 (124)
41 cd05793 S1_IF1A S1_IF1A: Trans 45.1 23 0.0005 23.7 2.5 10 71-80 39-48 (77)
42 PF10000 ACT_3: ACT domain; I 44.0 13 0.00029 24.6 1.2 18 37-64 12-29 (72)
43 PF01426 BAH: BAH domain; Int 43.9 26 0.00057 24.3 2.8 28 70-97 2-29 (119)
44 COG1097 RRP4 RNA-binding prote 43.9 65 0.0014 26.4 5.4 74 35-124 105-194 (239)
45 smart00652 eIF1a eukaryotic tr 43.2 26 0.00055 23.8 2.5 10 71-80 44-53 (83)
46 PF00278 Orn_DAP_Arg_deC: Pyri 43.2 31 0.00068 23.9 3.1 25 56-82 70-94 (116)
47 PRK12442 translation initiatio 42.1 29 0.00063 24.0 2.7 10 71-80 47-56 (87)
48 cd04717 BAH_polybromo BAH, or 41.6 39 0.00084 24.1 3.5 28 70-97 3-30 (121)
49 PF00166 Cpn10: Chaperonin 10 40.8 73 0.0016 21.8 4.6 86 56-145 6-93 (93)
50 smart00002 PLP Myelin proteoli 40.6 7.1 0.00015 25.1 -0.5 20 126-145 22-41 (60)
51 cd04709 BAH_MTA BAH, or Bromo 39.2 41 0.0009 25.9 3.4 23 128-150 85-107 (164)
52 COG3602 Uncharacterized protei 37.3 21 0.00045 26.1 1.4 17 37-63 12-28 (134)
53 PF06890 Phage_Mu_Gp45: Bacter 37.1 1.7E+02 0.0038 22.4 6.6 39 64-104 68-109 (162)
54 PRK04012 translation initiatio 37.1 35 0.00077 24.1 2.5 10 71-80 60-69 (100)
55 cd00320 cpn10 Chaperonin 10 Kd 36.4 1.4E+02 0.0031 20.5 6.6 40 56-99 6-45 (93)
56 smart00439 BAH Bromo adjacent 36.4 66 0.0014 22.2 4.0 17 135-151 70-86 (120)
57 TIGR02219 phage_NlpC_fam putat 36.3 79 0.0017 23.1 4.5 13 69-81 75-87 (134)
58 PRK14533 groES co-chaperonin G 36.0 1.5E+02 0.0032 20.5 7.3 81 56-145 7-89 (91)
59 PF01568 Molydop_binding: Moly 35.4 98 0.0021 21.0 4.7 48 57-120 30-77 (110)
60 PRK05483 rplN 50S ribosomal pr 34.7 1.8E+02 0.0039 21.2 6.8 28 112-140 79-106 (122)
61 PRK11578 macrolide transporter 34.7 1.1E+02 0.0025 25.9 5.8 15 89-103 71-85 (370)
62 PF07039 DUF1325: SGF29 tudor- 33.1 1.1E+02 0.0024 22.4 4.8 51 72-122 1-60 (130)
63 PF14085 DUF4265: Domain of un 32.4 1.4E+02 0.003 21.3 5.1 42 56-99 11-52 (117)
64 PF11337 DUF3139: Protein of u 32.0 78 0.0017 21.2 3.5 16 1-16 1-16 (85)
65 cd04721 BAH_plant_1 BAH, or Br 31.5 1.2E+02 0.0025 22.3 4.7 28 70-99 7-34 (130)
66 PTZ00414 10 kDa heat shock pro 28.1 2.2E+02 0.0047 20.1 7.2 10 56-65 16-25 (100)
67 PF07423 DUF1510: Protein of u 28.1 73 0.0016 25.7 3.3 27 111-140 164-192 (217)
68 PF10222 DUF2152: Uncharacteri 27.9 80 0.0017 29.4 3.9 67 57-133 52-118 (604)
69 PRK01191 rpl24p 50S ribosomal 25.8 1.3E+02 0.0029 22.0 4.0 57 70-142 45-101 (120)
70 KOG4146 Ubiquitin-like protein 24.7 96 0.0021 21.8 2.9 27 56-82 66-97 (101)
71 PTZ00194 60S ribosomal protein 24.5 1.6E+02 0.0035 22.2 4.3 56 70-141 46-101 (143)
72 PF10030 DUF2272: Uncharacteri 23.9 2.1E+02 0.0046 22.4 5.1 15 69-83 92-106 (183)
73 cd06555 ASCH_PF0470_like ASC-1 23.9 1.2E+02 0.0027 21.7 3.5 27 69-96 30-56 (109)
74 cd06836 PLPDE_III_ODC_DapDC_li 23.7 84 0.0018 27.0 3.1 24 56-82 332-355 (379)
75 cd04370 BAH BAH, or Bromo Adja 23.6 1.1E+02 0.0024 20.9 3.3 72 70-151 3-89 (123)
76 PF05382 Amidase_5: Bacterioph 22.8 1.2E+02 0.0026 22.9 3.4 39 33-83 50-88 (145)
77 cd06840 PLPDE_III_Bif_AspK_Dap 22.2 93 0.002 26.6 3.1 23 56-81 323-345 (368)
78 PTZ00054 60S ribosomal protein 22.2 2.2E+02 0.0049 21.3 4.7 40 110-152 95-134 (139)
79 cd05792 S1_eIF1AD_like S1_eIF1 21.9 89 0.0019 21.0 2.3 10 71-80 39-48 (78)
80 CHL00057 rpl14 ribosomal prote 21.7 3.3E+02 0.0071 19.9 7.6 41 111-153 78-118 (122)
81 COG5131 URM1 Ubiquitin-like pr 21.4 1.1E+02 0.0025 21.3 2.8 26 56-81 61-91 (96)
82 PRK05467 Fe(II)-dependent oxyg 21.2 1.4E+02 0.003 24.2 3.7 42 56-103 130-172 (226)
83 TIGR03099 dCO2ase_PEP1 pyridox 21.1 99 0.0021 26.5 3.0 24 56-82 352-375 (398)
84 cd06839 PLPDE_III_Btrk_like Ty 20.7 1.1E+02 0.0023 26.0 3.1 24 56-82 336-359 (382)
85 COG4929 Uncharacterized membra 20.7 1.4E+02 0.0029 23.7 3.4 26 56-81 35-60 (190)
86 PF13550 Phage-tail_3: Putativ 20.6 1.3E+02 0.0029 21.8 3.3 25 69-96 138-162 (164)
87 cd03695 CysN_NodQ_II CysN_NodQ 20.5 1.9E+02 0.0041 19.0 3.8 33 69-103 25-65 (81)
88 KOG0557 Dihydrolipoamide acety 20.3 1.1E+02 0.0024 27.6 3.1 55 31-97 38-100 (470)
89 cd06843 PLPDE_III_PvsE_like Ty 20.3 1.1E+02 0.0023 26.1 3.1 24 56-82 331-354 (377)
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=1.9e-39 Score=249.66 Aligned_cols=133 Identities=35% Similarity=0.557 Sum_probs=120.0
Q ss_pred HHHHHHHHHHHHHHHhceeEEEEEcCCCcccccCCCCCCCCCCCCCcEEEEEccccccCCCccceEEEEecCCCCCCceE
Q 030863 11 TKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHV 90 (170)
Q Consensus 11 ~~~~~~~~~~~~~i~~~~~~~~~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~rGDiV~f~~p~~~~~~~v 90 (170)
+..++++++++++++.|+++.+.|+|+||+|||+. ||+++++|..+...++++||+|+|+.|.++++.++
T Consensus 2 ~~~~~~~~~~~~~i~~~~~~~~~v~g~SM~Ptl~~----------Gd~vlv~k~~~~~~~~~rGDiVvf~~~~~~~~~~i 71 (163)
T TIGR02227 2 ILSLLIAILLALLIRTFVFFPYKIPGGSMEPTLKE----------GDRILVNKFAYGTSDPKRGDIVVFKDPDDNKNIYV 71 (163)
T ss_pred HHHHHHHHHHHHHHHhhEEEEEEECCcccccchhC----------CCEEEEEEeEcCCCCCCCCcEEEEecCCCCCceeE
Confidence 55677777888999999999999999999999999 99999999887667999999999999987788999
Q ss_pred EEEEEeCCCeEeccC-----------------------------CCCeEEccCCeEEEecCCCCCCCCCCccccccCCCE
Q 030863 91 KRIIGLPGDWIGTPM-----------------------------TNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLV 141 (170)
Q Consensus 91 KRVvg~~GD~v~~~~-----------------------------~~~~~~vp~g~~~v~gDn~~~S~DSR~~G~V~~~~I 141 (170)
|||+|+|||+|++.. ...+.+||+|||||+|||+++|.|||+||+|++++|
T Consensus 72 KRVig~pGd~v~i~~~~l~vNg~~~~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~~fvlGDnr~~S~DSR~~G~V~~~~I 151 (163)
T TIGR02227 72 KRVIGLPGDKVEFRDGKLYINGKKIDEPYLKPNGSLDTSGFNTTDFKPVTVPPGHYFVLGDNRDNSLDSRYFGFVPIDDI 151 (163)
T ss_pred EEEEecCCCEEEEECCEEEECCEECcccccccccccccccccccccCceEECCCCEEEECCCCCCCcccCCcCcCCHHHe
Confidence 999999999998711 012468999999999999999999999999999999
Q ss_pred eEEEEEEEeCCC
Q 030863 142 KGRVTHILWPPQ 153 (170)
Q Consensus 142 ~Gkv~~~~~P~~ 153 (170)
+|||.+++||++
T Consensus 152 ~Gk~~~~~~p~~ 163 (163)
T TIGR02227 152 IGKVSFVFYPFD 163 (163)
T ss_pred EEEEEEEECCCC
Confidence 999999999985
No 2
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.4e-38 Score=239.47 Aligned_cols=141 Identities=35% Similarity=0.622 Sum_probs=126.5
Q ss_pred HHHHHHHHHHHHHHHHhceeEEEEEcCCCcccccCCCCCCCCCCCCCcEEEEEccccccCCCccceEEEEecCCCCCCce
Q 030863 10 LTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKH 89 (170)
Q Consensus 10 ~~~~~~~~~~~~~~i~~~~~~~~~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~rGDiV~f~~p~~~~~~~ 89 (170)
+.......+++++++..|++++..++|.||+||+.++ ||+++.+|+++.++.+++||||++.+|.++++.+
T Consensus 14 ~~~~~~~~~~f~h~t~~yl~e~~~~~gpSM~PTl~~~---------gd~l~aEkls~~f~~~~~gDIVi~~sP~~~~~~~ 84 (176)
T KOG0171|consen 14 SFCSEIAYAAFTHVTHEYLGEFVMCSGPSMEPTLHDG---------GDVLLAEKLSYRFRKPQVGDIVIAKSPPDPKEHI 84 (176)
T ss_pred hhHHHHHHHHHHHHHHHHhcceeeccCCCcCceecCC---------CcEEehhhhhHhhcCCCCCCEEEEeCCCCchhhh
Confidence 3455566677788888899999999999999999996 8999999999999999999999999999999999
Q ss_pred EEEEEEeCCCeEeccC-----------CCCeEEccCCeEEEecCCCCCCCCCCccccccCCCEeEEEEEEEeCCCCcccc
Q 030863 90 VKRIIGLPGDWIGTPM-----------TNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHV 158 (170)
Q Consensus 90 vKRVvg~~GD~v~~~~-----------~~~~~~vp~g~~~v~gDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~P~~~~g~~ 158 (170)
+|||+|+|||.|++.. ...+..||+||+||+|||+++|.|||+|||+|..+|+||+++++||.++.+..
T Consensus 85 cKRIva~eGD~v~v~~~~~~~n~~~e~~~~~i~VP~GhVfv~GDN~~nS~DSr~yGplP~glI~gRvv~r~Wp~s~~~~~ 164 (176)
T KOG0171|consen 85 CKRIVAMEGDLVEVHDGPLVVNDLVEKFSTPIRVPEGHVFVEGDNRNNSLDSRNYGPLPMGLIQGRVVFRIWPPSRVSGL 164 (176)
T ss_pred hheeeccCCceEEEecCCcccchhhhhccceeeccCceEEEecCCCCCcccccccCCCchhheeeeEEEEecCchhccee
Confidence 9999999999777621 12357999999999999999999999999999999999999999999988776
Q ss_pred c
Q 030863 159 E 159 (170)
Q Consensus 159 ~ 159 (170)
.
T Consensus 165 ~ 165 (176)
T KOG0171|consen 165 I 165 (176)
T ss_pred e
Confidence 5
No 3
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=8e-38 Score=236.24 Aligned_cols=161 Identities=39% Similarity=0.668 Sum_probs=140.6
Q ss_pred hHHHHHHHHHHHHHHH--HHHHHHhceeEEEEEcCCCcccccCCCCCCCCCCCCCcEEEEEccccccCCCccceEEEEec
Q 030863 4 HNFLWSLTKNCFTFGL--IGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCS 81 (170)
Q Consensus 4 ~~~~~~~~~~~~~~~~--~~~~i~~~~~~~~~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~rGDiV~f~~ 81 (170)
+.-++.+.+.++.++. +.+.+...+.....|.|.||.||+++. .++.+.|+||++|+......+.+||+|+|.+
T Consensus 4 ~~~~~~~~ksl~~s~~~~v~~t~~DrV~~va~v~G~smqPtlnP~----~~~~~~d~Vll~k~~v~n~~~~rGDiVvl~s 79 (174)
T KOG1568|consen 4 RYIFKVFEKSLTGSLKWHVLLTFSDRVVHVAQVYGSSMQPTLNPT----MNTNEKDTVLLRKWNVKNRKVSRGDIVVLKS 79 (174)
T ss_pred HHHHHHHHhceeeeeeeheeeeeeeeEEEEeEEecCcCCCccCCC----cccccccEEEEEeeccccceeccCCEEEEeC
Confidence 3344555555555555 456677788999999999999999993 3444569999999987656789999999999
Q ss_pred CCCCCCceEEEEEEeCCCeEec-cCCCCeEEccCCeEEEecCCCCCCCCCCccccccCCCEeEEEEEEEeCCCCcccccc
Q 030863 82 PSNHKEKHVKRIIGLPGDWIGT-PMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQRVRHVER 160 (170)
Q Consensus 82 p~~~~~~~vKRVvg~~GD~v~~-~~~~~~~~vp~g~~~v~gDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~P~~~~g~~~~ 160 (170)
|.++++.+||||+|+|||++.. ++....+.||+|||||+|||...|+|||.||||+..+|.|||++++||+.|++.+++
T Consensus 80 P~~p~~~~iKRv~alegd~~~t~~~k~~~v~vpkghcWVegDn~~hs~DSntFGPVS~gli~grai~ilwpP~R~~~~~~ 159 (174)
T KOG1568|consen 80 PNDPDKVIIKRVAALEGDIMVTEDEKEEPVVVPKGHCWVEGDNQKHSYDSNTFGPVSTGLIVGRAIYILWPPVRWQRLDK 159 (174)
T ss_pred CCChhheeeeeeecccccEeccCCCCCCceecCCCcEEEecCCcccccccCccCCcchhheeeeEEEEEcChHHhhhhcc
Confidence 9999999999999999999876 677889999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCC
Q 030863 161 KNHQKRHS 168 (170)
Q Consensus 161 ~~~~~~~~ 168 (170)
..|..|++
T Consensus 160 ~~~~~~~~ 167 (174)
T KOG1568|consen 160 ESPGRRVP 167 (174)
T ss_pred cCCccccc
Confidence 99998875
No 4
>PRK10861 signal peptidase I; Provisional
Probab=100.00 E-value=5.2e-35 Score=245.51 Aligned_cols=139 Identities=29% Similarity=0.398 Sum_probs=124.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhceeEEEEEcCCCcccccCCCCCCCCCCCCCcEEEEEccccc------------cCCCcc
Q 030863 6 FLWSLTKNCFTFGLIGLTVSDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQ------------KYKFSH 73 (170)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~------------~~~~~r 73 (170)
.+..++..++.+++++++++.|+++++.|+|+||+|||.. ||+++++|+.|. ..+++|
T Consensus 59 ~~~~~~~~~~~~l~i~~~ir~fv~~~~~Ips~SM~PTL~~----------GD~IlVnK~~yg~~~p~~~~~~~~~~~p~R 128 (324)
T PRK10861 59 GWLETGASVFPVLAIVLIVRSFIYEPFQIPSGSMMPTLLI----------GDFILVEKFAYGIKDPITQTTLIETGHPKR 128 (324)
T ss_pred hHHHHHHHHHHHHhHHHHHHhhEEEEEEECCCcCcCcccC----------CCEEEEEEeecCccCccccccccccCCCCC
Confidence 3667788888888999999999999999999999999999 999999998874 257899
Q ss_pred ceEEEEecCCCCCCceEEEEEEeCCCeEecc---------C---------------------------------------
Q 030863 74 GDVIVFCSPSNHKEKHVKRIIGLPGDWIGTP---------M--------------------------------------- 105 (170)
Q Consensus 74 GDiV~f~~p~~~~~~~vKRVvg~~GD~v~~~---------~--------------------------------------- 105 (170)
||||+|+.|.+++..+||||+|+|||+|++. .
T Consensus 129 GDIVVF~~P~~~~~~yIKRVIGlPGD~I~~~~~~~~l~iNg~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~ 208 (324)
T PRK10861 129 GDIVVFKYPEDPKLDYIKRVVGLPGDKVTYDPVSKEVTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSG 208 (324)
T ss_pred CCEEEEecCCCCCCcEEEEeeecCCcEEEEEeCCCEEEEcCccccccccccccccccccccccccccccccccccccccc
Confidence 9999999999888899999999999999862 0
Q ss_pred ----------------C---------------------------------CCeEEccCCeEEEecCCCCCCCCCCccccc
Q 030863 106 ----------------T---------------------------------NDVVKVPNGHCWVEGDNPSSSLDSRSFGPI 136 (170)
Q Consensus 106 ----------------~---------------------------------~~~~~vp~g~~~v~gDn~~~S~DSR~~G~V 136 (170)
. ...++||+|+||++|||+++|.||||||+|
T Consensus 209 ~~~~~~~~~~~~~~~~~~~~E~l~~~~h~i~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~yf~mgdnr~~S~DSRy~G~V 288 (324)
T PRK10861 209 FFQVPLNETKENGIRLSERKETLGDVTHRILTVPGAQDQVGMYYQQPGQPLATWVVPPGQYFMMGDNRDNSADSRYWGFV 288 (324)
T ss_pred cccccccccccccccceeEEEecCCccceeeecCCcccccccccccCCCcCceEEECCCeEEEeCCCCCCCcccCccccc
Confidence 0 012389999999999999999999999999
Q ss_pred cCCCEeEEEEEEEeCCCC
Q 030863 137 PLGLVKGRVTHILWPPQR 154 (170)
Q Consensus 137 ~~~~I~Gkv~~~~~P~~~ 154 (170)
|.++|+|||..++|+++.
T Consensus 289 p~~~i~G~a~~i~~s~d~ 306 (324)
T PRK10861 289 PEANLVGKATAIWMSFEK 306 (324)
T ss_pred CHHHcEEEEEEEEEEcCC
Confidence 999999999999999873
No 5
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=99.93 E-value=9.6e-25 Score=169.89 Aligned_cols=93 Identities=23% Similarity=0.369 Sum_probs=75.5
Q ss_pred CcEEEEEccccccCCCccceEEEEecCCCC-------------------CCceEEEEEEeCCCeEeccC-----------
Q 030863 56 DDHVLMEKFCLQKYKFSHGDVIVFCSPSNH-------------------KEKHVKRIIGLPGDWIGTPM----------- 105 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~rGDiV~f~~p~~~-------------------~~~~vKRVvg~~GD~v~~~~----------- 105 (170)
.+.+.++++.+...++++||+|+|+.|.++ ...++|||+|+|||+|++..
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 456777776654568999999999988643 13599999999999998820
Q ss_pred ------C--------CCeEEccCCeEEEecCCCCCCCCCCccccccCCCEeEEEEEEE
Q 030863 106 ------T--------NDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHIL 149 (170)
Q Consensus 106 ------~--------~~~~~vp~g~~~v~gDn~~~S~DSR~~G~V~~~~I~Gkv~~~~ 149 (170)
. ....+||+|+|||+||| .+|+||||||+|++++|+|+|..++
T Consensus 116 ~~~~~~~~~g~~l~~~~~~~vp~g~~fvlgd~-~~S~DSRy~G~V~~~~I~G~a~pi~ 172 (176)
T PRK13838 116 SSVRRRDGEGRPLTPFPGGVVPPGHLFLHSSF-AGSYDSRYFGPVPASGLLGLARPVL 172 (176)
T ss_pred cccccccccCCcCCCCCccCcCCCeEEEECCC-CCCCcccccCcccHHHeEEEEEEEE
Confidence 0 11357999999999998 5899999999999999999998765
No 6
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=99.90 E-value=8.8e-23 Score=159.17 Aligned_cols=81 Identities=21% Similarity=0.409 Sum_probs=67.9
Q ss_pred CCCccceEEEEecCCCC-------------------CCceEEEEEEeCCCeEeccC------------------------
Q 030863 69 YKFSHGDVIVFCSPSNH-------------------KEKHVKRIIGLPGDWIGTPM------------------------ 105 (170)
Q Consensus 69 ~~~~rGDiV~f~~p~~~-------------------~~~~vKRVvg~~GD~v~~~~------------------------ 105 (170)
..+++||+|+|+.|... ...++|||+|+|||+|++..
T Consensus 49 ~~~~~Gd~V~f~~p~~~~~~~a~~rgyl~~g~~p~~~~~liKRVva~pGD~V~~~~~~l~VNG~~v~~~~~~~~d~~g~~ 128 (178)
T PRK13884 49 APVEKGAYVLFCPPQRGVFDDAKERGYIGAGFCPGGYGYMMKRVLAAKGDAVSVTDDGVRVNGELLPLSKPILADGAGRP 128 (178)
T ss_pred CCCCCCCEEEEeCCchHHHHHHHhCCccccCcCCCCCCceEEEEEeeCCcEEEEECCEEEECCEEccccccccccccCCc
Confidence 37999999999987631 13789999999999999810
Q ss_pred ----CCCeEEccCCeEEEecCCCCCCCCCCccccccCCCEeEEEEEEE
Q 030863 106 ----TNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHIL 149 (170)
Q Consensus 106 ----~~~~~~vp~g~~~v~gDn~~~S~DSR~~G~V~~~~I~Gkv~~~~ 149 (170)
....++||+|+||++|||+++|+||||||+|++++|+|++..++
T Consensus 129 l~~~~~~~~~lp~g~~fvlgd~~~~S~DSRYfG~V~~~~I~G~~~Pl~ 176 (178)
T PRK13884 129 LPRYQANSYTLGESELLLMSDVSATSFDGRYFGPINRSQIKTVIRPVI 176 (178)
T ss_pred ccccCCCceEECCCEEEEECCCCCCCCcccccCcccHHHEEEEEEEeE
Confidence 01135899999999999999999999999999999999998764
No 7
>TIGR02771 TraF_Ti conjugative transfer signal peptidase TraF. This protein is found in apparent operons encoding elements of conjugative transfer systems. This family is homologous to a broader family of signal (leader) peptidases such as lepB. This family is present in both Ti-type and I-type conjugative systems.
Probab=99.89 E-value=7.9e-23 Score=158.51 Aligned_cols=80 Identities=38% Similarity=0.657 Sum_probs=68.0
Q ss_pred CCCccceEEEEecCCCCC-------------------CceEEEEEEeCCCeEeccC------------------------
Q 030863 69 YKFSHGDVIVFCSPSNHK-------------------EKHVKRIIGLPGDWIGTPM------------------------ 105 (170)
Q Consensus 69 ~~~~rGDiV~f~~p~~~~-------------------~~~vKRVvg~~GD~v~~~~------------------------ 105 (170)
.+++|||+|+|+.|.++. ..++|||+|+|||+|++..
T Consensus 45 ~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRViglpGD~V~i~~~~v~INg~~~~~~~~~~~~~~g~~ 124 (171)
T TIGR02771 45 KPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVLGLPGDRVTVRADVVAINGQLLPYSKPLATDSSGRP 124 (171)
T ss_pred CCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEEEeCCCEEEEECCEEEECCEEcccccccccccCCCc
Confidence 379999999999886432 2799999999999999811
Q ss_pred --CCCeEEccCCeEEEecCCCCCCCCCCccccccCCCEeEEEEEEE
Q 030863 106 --TNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHIL 149 (170)
Q Consensus 106 --~~~~~~vp~g~~~v~gDn~~~S~DSR~~G~V~~~~I~Gkv~~~~ 149 (170)
...+.+||+| ||++|||+++|+||||||+|++++|+||+..++
T Consensus 125 l~~~~~~~vp~g-yf~lgdn~~~S~DSRy~G~V~~~~IiGk~~pl~ 169 (171)
T TIGR02771 125 LPPFPEGVIPPG-FFVVHDTSPTSFDSRYFGPISREQVIGRVKPLF 169 (171)
T ss_pred cccCCCcEECCC-EEEECCCCCCCCcccccceecHHHeEEEEEEeE
Confidence 0125789999 999999999999999999999999999998654
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=99.89 E-value=9.8e-23 Score=141.85 Aligned_cols=89 Identities=33% Similarity=0.514 Sum_probs=78.7
Q ss_pred EEcCCCcccccCCCCCCCCCCCCCcEEEEEccccccCCCccceEEEEecCCCCCCceEEEEEEeCCCeEeccCCCCeEEc
Q 030863 33 PVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKV 112 (170)
Q Consensus 33 ~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD~v~~~~~~~~~~v 112 (170)
.|+|+||+|||.+ ||+|++++.......+++||+|+|+.|.++++.++||++++++
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 9999999865433456789999999987667899999999875
Q ss_pred cCCeEEEecCCCCCCCCCCccccccCCCEeEEEEE
Q 030863 113 PNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTH 147 (170)
Q Consensus 113 p~g~~~v~gDn~~~S~DSR~~G~V~~~~I~Gkv~~ 147 (170)
+++|++|||+..|.|||++|+|+..+|+|||++
T Consensus 58 --~~~~l~~dN~~~~~d~~~~g~v~~~~I~G~v~~ 90 (90)
T TIGR02754 58 --NGLFLLGDNPKASTDSRQLGPVPRSLLLGKVLW 90 (90)
T ss_pred --CeEEEeCCCCCCCCcccccCCCcHHHEEEEEEC
Confidence 589999999999999999999999999999863
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=99.88 E-value=1.1e-23 Score=158.07 Aligned_cols=89 Identities=33% Similarity=0.636 Sum_probs=32.9
Q ss_pred cEEEEEccccccCCCccceEEEEecCCC------------CCCceEEEEEEeCCCeEecc--------------------
Q 030863 57 DHVLMEKFCLQKYKFSHGDVIVFCSPSN------------HKEKHVKRIIGLPGDWIGTP-------------------- 104 (170)
Q Consensus 57 d~vlv~k~~~~~~~~~rGDiV~f~~p~~------------~~~~~vKRVvg~~GD~v~~~-------------------- 104 (170)
-+.++.+.. .+++||+|+|+.|.. .+..++|||+|+|||+|++.
T Consensus 12 g~Y~~~~~~----~~~rGd~V~f~~p~~~~~~~~~~gy~~~~~~~iKrV~a~pGD~V~v~~~~v~iNG~~~~~~~~~d~~ 87 (138)
T PF10502_consen 12 GIYLIDPSD----KIERGDLVVFCPPAEVAFFAAERGYLPEGQPLIKRVAAVPGDTVEVTDGGVYINGRPVGEPLATDSD 87 (138)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred ccccccccc----ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence 455555544 589999999999862 24589999999999999981
Q ss_pred -----CCCCeEEccCCeEEEecCCCCCCCCCCccccccCCCEeEEEEEEE
Q 030863 105 -----MTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHIL 149 (170)
Q Consensus 105 -----~~~~~~~vp~g~~~v~gDn~~~S~DSR~~G~V~~~~I~Gkv~~~~ 149 (170)
....+.+||+|+||++|||+.+|+||||||+|++++|+|||..++
T Consensus 88 g~~l~~~~~~~~vp~g~~~v~gd~~~~S~DSRy~G~V~~~~I~g~~~pl~ 137 (138)
T PF10502_consen 88 GRPLPQFSGSGTVPEGEYFVLGDNRPNSFDSRYFGPVPRSQIIGKARPLW 137 (138)
T ss_dssp -S-T----TEEE--TTEEEEE-SBTTS--SHHHH--EEGGGEEEEEEEEE
T ss_pred cccccccCCceEeCCCEEEEecCCCCCccccCEecccCHHHEEEEEEEEE
Confidence 112478999999999999999999999999999999999998876
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=99.85 E-value=5.2e-21 Score=131.49 Aligned_cols=84 Identities=44% Similarity=0.698 Sum_probs=75.9
Q ss_pred EEEEcCCCcccccCCCCCCCCCCCCCcEEEEEccccccCCCccceEEEEecCCCCCCceEEEEEEeCCCeEeccCCCCeE
Q 030863 31 IVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVV 110 (170)
Q Consensus 31 ~~~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD~v~~~~~~~~~ 110 (170)
.+.|.|+||+|++.. ||++++++.......+++||+|+|+.|.+++..++|||++
T Consensus 2 ~~~v~g~SM~P~i~~----------gd~v~v~~~~~~~~~~~~GDiv~~~~~~~~~~~~vkRv~~--------------- 56 (85)
T cd06530 2 PVVVPGGSMEPTLQP----------GDLVLVNKLSYGFREPKRGDVVVFKSPGDPGKPIIKRVIG--------------- 56 (85)
T ss_pred eeEEcCCCCcCcccC----------CCEEEEEEeecccCCCCCCCEEEEeCCCCCCCEEEEEEEE---------------
Confidence 578999999999999 9999999877433469999999999987656889999997
Q ss_pred EccCCeEEEecCCCCCCCCCCccccccCCCEeEEE
Q 030863 111 KVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRV 145 (170)
Q Consensus 111 ~vp~g~~~v~gDn~~~S~DSR~~G~V~~~~I~Gkv 145 (170)
||++|||+.+|.|||+||+++.++|+|++
T Consensus 57 ------~~~~gDn~~ns~d~~~~g~~~~~~i~G~~ 85 (85)
T cd06530 57 ------YFVLGDNRNNSLDSRYWGPVPEDDIVGKV 85 (85)
T ss_pred ------EEEeeCCCCCCCccCCcCCCcHHHeEEeC
Confidence 99999999999999999999999999985
No 11
>TIGR02228 sigpep_I_arch signal peptidase I, archaeal type. This model represents signal peptidase I from most archaea, a subunit of the eukaryotic endoplasmic reticulum signal peptidase I complex, and an apparent signal peptidase I from a small number of bacteria. It is related to but does not overlap in hits with TIGR02227, the bacterial and mitochondrial signal peptidase I.
Probab=99.80 E-value=7.3e-19 Score=134.72 Aligned_cols=85 Identities=29% Similarity=0.358 Sum_probs=69.8
Q ss_pred EcCCCcccccCCCCCCCCCCCCCcEEEEEccccccCCCccceEEEEecCCCCCCceEEEEEEeCCCeEeccCCCCeEEcc
Q 030863 34 VRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVP 113 (170)
Q Consensus 34 v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD~v~~~~~~~~~~vp 113 (170)
|.|+||+||+++ ||++++++... .++++||+|+|+.|.++ +.++|||+++.++. .
T Consensus 36 V~g~SM~Ptl~~----------GD~vlv~~~~~--~~~~~GDIVvf~~~~~~-~~iihRVi~v~~~~------------g 90 (158)
T TIGR02228 36 VLSGSMEPTFNT----------GDLILVTGADP--NDIQVGDVITYKSPGFN-TPVTHRVIEINNSG------------G 90 (158)
T ss_pred EcCCCCcCCccC----------CCEEEEEeccc--CCCCCCCEEEEEECCCC-ccEEEEEEEEECCC------------C
Confidence 999999999999 99999998543 48999999999998643 78999999987641 0
Q ss_pred CCeEEEecCCCCCCCCCCccccccCCCEeEEEEE
Q 030863 114 NGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTH 147 (170)
Q Consensus 114 ~g~~~v~gDn~~~S~DSR~~G~V~~~~I~Gkv~~ 147 (170)
+-.+++.|||+ ...| .++|+.++|+||+..
T Consensus 91 ~~~~~tkGDnN-~~~D---~~~v~~~~IiG~v~~ 120 (158)
T TIGR02228 91 ELGFITKGDNN-PAPD---GEPVPSENVIGKYLG 120 (158)
T ss_pred cEEEEEEecCC-CCCC---cccCCHHHEEEEEEE
Confidence 11377889996 4556 689999999999983
No 12
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=99.65 E-value=1.8e-15 Score=115.07 Aligned_cols=130 Identities=29% Similarity=0.284 Sum_probs=104.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHH--HhceeEEEEEcCCCcccccCCCCCCCCCCCCCcEEEEEccccccCCCccceEEEEec
Q 030863 4 HNFLWSLTKNCFTFGLIGLTV--SDRYASIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCS 81 (170)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~i--~~~~~~~~~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~rGDiV~f~~ 81 (170)
...+..++..++.++++++++ +.++++++.|+|+||+||++. ||+++++|..+....+..+|++ ..
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~V~s~SM~Ptl~~----------GD~v~v~k~~~~~~~~~~~~~~--~~ 71 (166)
T COG0681 4 LLKFLELISSLLIAIILALIIGVRTFVFEPVVVPSGSMEPTLNV----------GDRVLVKKFSYGFGKLKVPDII--VL 71 (166)
T ss_pred HHHHHHHHHHHHHHHHHhheeeeEEEEEEEEEECCCcccccccc----------CCEEEEEeccccccCCccceee--ec
Confidence 333557888888888888888 899999999999999999999 9999999999887889999988 45
Q ss_pred CCCCCCceEEEEEEeCCCeEeccCCCC--eEEccCCeEEEecCC-------CCCCCCCCccccccCCCEeEEE
Q 030863 82 PSNHKEKHVKRIIGLPGDWIGTPMTND--VVKVPNGHCWVEGDN-------PSSSLDSRSFGPIPLGLVKGRV 145 (170)
Q Consensus 82 p~~~~~~~vKRVvg~~GD~v~~~~~~~--~~~vp~g~~~v~gDn-------~~~S~DSR~~G~V~~~~I~Gkv 145 (170)
|......++||+++++||.+.+..... ...+|+++.++.++| ...+.+++.++.......+.++
T Consensus 72 ~~~~~~~~~kr~~~~~GD~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 144 (166)
T COG0681 72 PAVVEGDLIKRVIGLRGDIVVFKDDRLYVVPIIPRVYGLVEKDNGKHLVDVIVNANSSRVFGIITKKDYIKRV 144 (166)
T ss_pred CCCCCcceEEEeccCCCCEEEEECCEEEeecccCcchhhhhcccccccccccccccCccccccccccccccce
Confidence 556678899999999999999854332 356677777766544 3467777777777777777777
No 13
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.58 E-value=3.8e-15 Score=112.17 Aligned_cols=89 Identities=28% Similarity=0.466 Sum_probs=73.3
Q ss_pred EEEEEccccccCCCccceEEEEecCCC------------CCCceEEEEEEeCCCeEec----------------------
Q 030863 58 HVLMEKFCLQKYKFSHGDVIVFCSPSN------------HKEKHVKRIIGLPGDWIGT---------------------- 103 (170)
Q Consensus 58 ~vlv~k~~~~~~~~~rGDiV~f~~p~~------------~~~~~vKRVvg~~GD~v~~---------------------- 103 (170)
...++|.. ..+++||+|+++.|.. +.-.++|||.|+|||+|++
T Consensus 44 lyrv~k~~---~Pvt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq~Vci~~~~I~I~G~~v~~sl~~D~~G 120 (173)
T COG4959 44 LYRVSKLS---APVTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQHVCITSQGIAIDGKPVAASLPVDRVG 120 (173)
T ss_pred EEEecccC---CCcccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCCCcEEEecceEEECCEEeeeeccccccC
Confidence 45566655 3469999999999974 2457899999999999998
Q ss_pred ---cCCCCeEEccCCeEEEecCCCCCCCCCCccccccCCCEeEEEEEEE
Q 030863 104 ---PMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHIL 149 (170)
Q Consensus 104 ---~~~~~~~~vp~g~~~v~gDn~~~S~DSR~~G~V~~~~I~Gkv~~~~ 149 (170)
+....+..+-++++|+++|..+.|+|||||||||.++|+|.+..+|
T Consensus 121 R~lp~~~gcR~l~~~el~lL~~~~~~SfDsRYfGpipas~vig~aRPvw 169 (173)
T COG4959 121 RALPRWQGCRYLAPSELLLLTDRSSTSFDSRYFGPIPASQVIGVARPVW 169 (173)
T ss_pred CcCCcccCCceecCCeEEEEeccCCcccccceecccCHHHcceeeeeee
Confidence 1223455688899999999999999999999999999999998765
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=99.26 E-value=5e-11 Score=80.48 Aligned_cols=83 Identities=48% Similarity=0.753 Sum_probs=65.1
Q ss_pred EEEEcCCCcccccCCCCCCCCCCCCCcEEEEEccccccCCCccceEEEEecCCCCCCceEEEEEEeCCCeEeccCCCCeE
Q 030863 31 IVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVV 110 (170)
Q Consensus 31 ~~~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD~v~~~~~~~~~ 110 (170)
.+.+.|+||+|++.. ||++++++.. ..++.||+|++..+. +..++||+...++
T Consensus 2 ~~~v~g~SM~P~i~~----------gd~v~i~~~~---~~~~~G~iv~~~~~~--~~~~ikrl~~~~~------------ 54 (84)
T cd06462 2 ALRVEGDSMEPTIPD----------GDLVLVDKSS---YEPKRGDIVVFRLPG--GELTVKRVIGLPG------------ 54 (84)
T ss_pred eeEEcCCCccCcccC----------CCEEEEEecC---CCCcCCEEEEEEcCC--CcEEEEEEEEECC------------
Confidence 468999999999999 9999999876 248999999999864 4789999999875
Q ss_pred EccCCeEEEecCCCCCCCCCCccccccCCCEeEEE
Q 030863 111 KVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRV 145 (170)
Q Consensus 111 ~vp~g~~~v~gDn~~~S~DSR~~G~V~~~~I~Gkv 145 (170)
++++++.+||+ +..+.+..+. ....++|++
T Consensus 55 ---~~~~~l~~~N~-~~~~~~~~~~-~~~~i~g~v 84 (84)
T cd06462 55 ---EGHYFLLGDNP-NSPDSRIDGP-PELDIVGVV 84 (84)
T ss_pred ---CCEEEEECCCC-CCCcccccCC-CHHHEEEeC
Confidence 25899999994 5555554332 455666653
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=99.24 E-value=1.8e-11 Score=80.64 Aligned_cols=56 Identities=34% Similarity=0.520 Sum_probs=45.5
Q ss_pred EEcCCCcccccCCCCCCCCCCCCCcEEEEEccccccCCCccceEEEEecCCCCCCceEEEEEEeCCCeEec
Q 030863 33 PVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGT 103 (170)
Q Consensus 33 ~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD~v~~ 103 (170)
+|.|+||+|++.. ||+|++++.. +++.||+|+|..+.+. ..++||+++.+|+.+.+
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 9999999877 8999999999987532 38999999999875443
No 16
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.05 E-value=1.5e-09 Score=81.92 Aligned_cols=89 Identities=28% Similarity=0.392 Sum_probs=65.9
Q ss_pred EEEEcCCCcccccCCCCCCCCCCCCCcEEEEEccccccCCCccceEEEEecCCCCCCceEEEEEEeCCCeEeccCCCCeE
Q 030863 31 IVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVV 110 (170)
Q Consensus 31 ~~~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD~v~~~~~~~~~ 110 (170)
+..|-++||||.++. ||.++...... ...+.||||+|+-+. ..-.++|||+-+-+..
T Consensus 50 iVVVLSgSMePaF~R----------GDlLfL~N~~~--~p~~vGdivVf~veg-R~IPiVHRviK~he~~---------- 106 (180)
T KOG3342|consen 50 IVVVLSGSMEPAFHR----------GDLLFLTNRNE--DPIRVGDIVVFKVEG-REIPIVHRVIKQHEKS---------- 106 (180)
T ss_pred EEEEEcCCcCccccc----------ccEEEEecCCC--CcceeccEEEEEECC-ccCchhHHHHHHhccc----------
Confidence 578999999999999 99999875442 357999999999874 2567999998754421
Q ss_pred EccCC--eEEEecCCCCCCCCCCc-c----ccccCCCEeEEEEE
Q 030863 111 KVPNG--HCWVEGDNPSSSLDSRS-F----GPIPLGLVKGRVTH 147 (170)
Q Consensus 111 ~vp~g--~~~v~gDn~~~S~DSR~-~----G~V~~~~I~Gkv~~ 147 (170)
+| ++...|||+ ..|-|. | -...+++|+|+|.-
T Consensus 107 ---~~~~~~LTKGDNN--~~dD~~Ly~~gq~~L~r~~Ivg~~~G 145 (180)
T KOG3342|consen 107 ---NGHIKFLTKGDNN--AVDDRGLYAQGQNWLERKDIVGRVRG 145 (180)
T ss_pred ---CCcEEEEecCCCC--cccchhcccccccceeccceeeEEee
Confidence 23 467789995 445553 2 23788999999863
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=98.92 E-value=9.7e-09 Score=69.06 Aligned_cols=61 Identities=34% Similarity=0.446 Sum_probs=53.2
Q ss_pred EEEEcCCCcccccCCCCCCCCCCCCCcEEEEEccccccCCCccceEEEEecCCCCCCceEEEEEEeCCCeEeccCCCCeE
Q 030863 31 IVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVV 110 (170)
Q Consensus 31 ~~~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD~v~~~~~~~~~ 110 (170)
...+.|+||+|++.. ||++++++.. .++.||++++..+ +..++||+...++
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 9999999865 6999999999986 3789999998775
Q ss_pred EccCCeEEEecCCC
Q 030863 111 KVPNGHCWVEGDNP 124 (170)
Q Consensus 111 ~vp~g~~~v~gDn~ 124 (170)
+.+++.++|+
T Consensus 53 ----~~~~L~s~N~ 62 (81)
T cd06529 53 ----GRLRLISDNP 62 (81)
T ss_pred ----CcEEEEeCCC
Confidence 3788899986
No 18
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=98.89 E-value=1.5e-08 Score=80.83 Aligned_cols=89 Identities=25% Similarity=0.244 Sum_probs=65.9
Q ss_pred EEEEEcCCCcccccCCCCCCCCCCCCCcEEEEEccccccCCCccceEEEEecCCCCCCceEEEEEEeCCCeEeccCCCCe
Q 030863 30 SIVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDV 109 (170)
Q Consensus 30 ~~~~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD~v~~~~~~~~ 109 (170)
....|.|+||+|++.+ ||.++|+.-. ...+||.|++..- .++.++||+...+|
T Consensus 124 ~~i~V~GDSMeP~~~~----------Gd~ilVd~~~----~~~~gd~v~v~~~--g~~~~VK~l~~~~~----------- 176 (214)
T COG2932 124 FALRVTGDSMEPTYED----------GDTLLVDPGV----NTRRGDRVYVETD--GGELYVKKLQREPG----------- 176 (214)
T ss_pred EEEEEeCCcccccccC----------CCEEEECCCC----ceeeCCEEEEEEe--CCeEEEEEEEEecC-----------
Confidence 5679999999999999 9999999876 6789996666543 36899999998886
Q ss_pred EEccCCeEEEecCCCCCCCCCCccccccCCCEeEEEEEEEeC
Q 030863 110 VKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWP 151 (170)
Q Consensus 110 ~~vp~g~~~v~gDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~P 151 (170)
|.+.+..+|+....|--..-.-. =.|+|||++..-+
T Consensus 177 -----~~~~l~S~N~~~~~~~~~~~~~~-v~iIgrVv~~~~~ 212 (214)
T COG2932 177 -----GLLRLVSLNPDYYPDEIFSEDDD-VEIIGRVVWVSRL 212 (214)
T ss_pred -----CeEEEEeCCCCCCcccccCccce-EEEEEEEEEEeee
Confidence 56779999985433333211111 3489999987654
No 19
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=98.59 E-value=6.7e-07 Score=66.95 Aligned_cols=85 Identities=22% Similarity=0.196 Sum_probs=60.5
Q ss_pred eEEEEEcCCCcc-cccCCCCCCCCCCCCCcEEEEEccccccCCCccceEEEEecCCCCCCceEEEEEEeCCCeEeccCCC
Q 030863 29 ASIVPVRGSSMS-PTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTN 107 (170)
Q Consensus 29 ~~~~~v~~~SM~-Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD~v~~~~~~ 107 (170)
....+|.|+||. |++.. ||++++++-. +++.||+|++... ++..+||+.-.
T Consensus 51 ~f~l~V~GdSM~~~~I~~----------GD~liVd~~~----~~~~Gdivv~~~~---g~~~vKrl~~~----------- 102 (139)
T PRK10276 51 TYFVKASGDSMIDAGISD----------GDLLIVDSAI----TASHGDIVIAAVD---GEFTVKKLQLR----------- 102 (139)
T ss_pred EEEEEEecCCCCCCCCCC----------CCEEEEECCC----CCCCCCEEEEEEC---CEEEEEEEEEC-----------
Confidence 456899999998 68999 9999999765 6789999998762 46789998742
Q ss_pred CeEEccCCeEEEecCCCCCCCCCCccccccCCCEeEEEEEEEe
Q 030863 108 DVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILW 150 (170)
Q Consensus 108 ~~~~vp~g~~~v~gDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~ 150 (170)
+++++..+|+.. ....+-.-..=.|+|+|++++-
T Consensus 103 -------~~~~L~s~N~~y--~~i~i~~~~~~~IiG~V~~~~~ 136 (139)
T PRK10276 103 -------PTVQLIPMNSAY--SPITISSEDTLDVFGVVTHIVK 136 (139)
T ss_pred -------CcEEEEcCCCCC--CCEEcCCCCcEEEEEEEEEEEE
Confidence 257788888632 1211111112279999988764
No 20
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=98.50 E-value=1.8e-06 Score=67.95 Aligned_cols=88 Identities=17% Similarity=0.192 Sum_probs=65.5
Q ss_pred eeEEEEEcCCCcc-cccCCCCCCCCCCCCCcEEEEEccccccCCCccceEEEEecCCCCCCceEEEEEEeCCCeEeccCC
Q 030863 28 YASIVPVRGSSMS-PTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMT 106 (170)
Q Consensus 28 ~~~~~~v~~~SM~-Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD~v~~~~~ 106 (170)
-...+.+.|+||. |++.. ||++++++.. .++.||+|++.. .++..+||+.-. +
T Consensus 110 ~~f~~~V~GdSM~~~~i~~----------Gd~v~v~~~~----~~~~G~ivvv~~---~~~~~vKrl~~~-~-------- 163 (199)
T TIGR00498 110 AVFLLKVMGDSMVDAGICD----------GDLLIVRSQK----DARNGEIVAAMI---DGEVTVKRFYKD-G-------- 163 (199)
T ss_pred CEEEEEecCCCCCCCCCCC----------CCEEEEecCC----CCCCCCEEEEEE---CCEEEEEEEEEE-C--------
Confidence 4567899999996 57999 9999999754 789999999997 357899998754 2
Q ss_pred CCeEEccCCeEEEecCCCCCCCCCCccccccCCCEeEEEEEEEeCC
Q 030863 107 NDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPP 152 (170)
Q Consensus 107 ~~~~~vp~g~~~v~gDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~P~ 152 (170)
+++++..+|+... ...... ..=.|+|+|+..+..+
T Consensus 164 --------~~i~L~s~N~~y~--~i~~~~-~~~~IiG~Vv~~~r~~ 198 (199)
T TIGR00498 164 --------TKVELKPENPEFD--PIVLNA-EDVTILGKVVGVIRNF 198 (199)
T ss_pred --------CEEEEEcCCCCCc--CCcCCC-CcEEEEEEEEEEEEec
Confidence 4788899987421 111110 1348999999888654
No 21
>PRK00215 LexA repressor; Validated
Probab=98.47 E-value=2.2e-06 Score=67.79 Aligned_cols=86 Identities=26% Similarity=0.326 Sum_probs=63.8
Q ss_pred eeEEEEEcCCCcc-cccCCCCCCCCCCCCCcEEEEEccccccCCCccceEEEEecCCCCCCceEEEEEEeCCCeEeccCC
Q 030863 28 YASIVPVRGSSMS-PTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMT 106 (170)
Q Consensus 28 ~~~~~~v~~~SM~-Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD~v~~~~~ 106 (170)
-.....|.|+||. |++.+ ||++++++.. .++.||+|++... +...+||+.-..
T Consensus 117 ~~~~~~V~GdSM~~~~i~~----------Gd~v~v~~~~----~~~~G~ivv~~~~---~~~~vKrl~~~~--------- 170 (205)
T PRK00215 117 EDFLLRVRGDSMIDAGILD----------GDLVIVRKQQ----TARNGQIVVALID---DEATVKRFRREG--------- 170 (205)
T ss_pred CeEEEEEccCCCCCCCcCC----------CCEEEEeCCC----CCCCCCEEEEEEC---CEEEEEEEEEeC---------
Confidence 3556889999995 79999 9999999754 6789999999875 378999998542
Q ss_pred CCeEEccCCeEEEecCCCCCCCCCCccccccCCCEeEEEEEEEe
Q 030863 107 NDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILW 150 (170)
Q Consensus 107 ~~~~~vp~g~~~v~gDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~ 150 (170)
|.+++..||+.. +.....+= .-.|+|+|+..+-
T Consensus 171 --------~~~~L~s~Np~y--~~~~~~~~-~~~IiG~Vv~~~r 203 (205)
T PRK00215 171 --------GHIRLEPENPAY--EPIIVDPD-RVTIEGKVVGLIR 203 (205)
T ss_pred --------CEEEEEcCCCCC--CCEEeCCC-cEEEEEEEEEEEE
Confidence 478888998742 22221110 3589999988764
No 22
>PRK12423 LexA repressor; Provisional
Probab=98.43 E-value=2.6e-06 Score=67.57 Aligned_cols=85 Identities=18% Similarity=0.160 Sum_probs=62.8
Q ss_pred EEEEEcCCCcc-cccCCCCCCCCCCCCCcEEEEEccccccCCCccceEEEEecCCCCCCceEEEEEEeCCCeEeccCCCC
Q 030863 30 SIVPVRGSSMS-PTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTND 108 (170)
Q Consensus 30 ~~~~v~~~SM~-Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD~v~~~~~~~ 108 (170)
....|.|+||. |++.. ||++++++-. .++.||+|++... ++..+||+.-..
T Consensus 115 f~l~V~GdSM~~~~i~~----------Gd~viv~~~~----~~~~Gdivv~~~~---~~~~vKrl~~~~----------- 166 (202)
T PRK12423 115 YLLQVQGDSMIDDGILD----------GDLVGVHRSP----EARDGQIVVARLD---GEVTIKRLERSG----------- 166 (202)
T ss_pred EEEEEecCcCCCCCcCC----------CCEEEEeCCC----cCCCCCEEEEEEC---CEEEEEEEEEeC-----------
Confidence 46799999997 79999 9999999754 7889999999863 468899997543
Q ss_pred eEEccCCeEEEecCCCCCCCCCCccccccCCCEeEEEEEEEe
Q 030863 109 VVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILW 150 (170)
Q Consensus 109 ~~~vp~g~~~v~gDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~ 150 (170)
+.+++..+|+. ++...+-+-..=.|+|+++..+-
T Consensus 167 ------~~~~L~s~N~~--y~~i~~~~~~~~~I~Gvv~g~~r 200 (202)
T PRK12423 167 ------DRIRLLPRNPA--YAPIVVAPDQDFAIEGVFCGLIR 200 (202)
T ss_pred ------CEEEEEcCCCC--CCCEEcCCCCcEEEEEEEEEEEE
Confidence 37888889863 22222211123479999988764
No 23
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=97.84 E-value=0.00035 Score=55.61 Aligned_cols=89 Identities=19% Similarity=0.217 Sum_probs=66.7
Q ss_pred eeEEEEEcCCCccc-ccCCCCCCCCCCCCCcEEEEEccccccCCCccceEEEEecCCCCCCceEEEEEEeCCCeEeccCC
Q 030863 28 YASIVPVRGSSMSP-TFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMT 106 (170)
Q Consensus 28 ~~~~~~v~~~SM~P-tl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD~v~~~~~ 106 (170)
-.+..+|.|+||.. .+.. ||.|+|++-. +++.||+|+...+. ++..+||..--.
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 35578999999974 4555 9999999765 89999999999864 568899988643
Q ss_pred CCeEEccCCeEEEecCCCCCCCCCCccccccCCCEeEEEEEEEeCC
Q 030863 107 NDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPP 152 (170)
Q Consensus 107 ~~~~~vp~g~~~v~gDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~P~ 152 (170)
++++++.-|+ .+.+..+..- .-.|.|+++.++|+.
T Consensus 166 --------~~i~L~p~Np--~~~~i~~~~~-~~~I~G~vvgv~r~~ 200 (201)
T COG1974 166 --------NQILLKPENP--AYPPIPVDAD-SVTILGKVVGVIRDI 200 (201)
T ss_pred --------CEEEEEeCCC--CCCCcccCcc-ceEEEEEEEEEEecC
Confidence 3788888886 2333332222 457999999999975
No 24
>TIGR02594 conserved hypothetical protein TIGR02594. Members of this protein family known so far are restricted to the bacteria, and for the most to the proteobacteria. The function is unknown.
Probab=86.60 E-value=3.8 Score=30.21 Aligned_cols=54 Identities=19% Similarity=0.131 Sum_probs=35.0
Q ss_pred CCccceEEEEecCCCCCCceEEEEEEeCCCeEeccCCCCeEEccCCeEEEecCCCCCCCCCCccccccCCCEeE
Q 030863 70 KFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKG 143 (170)
Q Consensus 70 ~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD~v~~~~~~~~~~vp~g~~~v~gDn~~~S~DSR~~G~V~~~~I~G 143 (170)
++++||+|+|+.. +.-.+.-+++...+ .|+++++|-|..+..- .-..+++.|+|
T Consensus 73 ~p~~GDiv~f~~~---~~~HVGi~~g~~~~--------------~g~i~~lgGNq~~~V~---~~~~~~~~~~~ 126 (129)
T TIGR02594 73 KPAYGCIAVKRRG---GGGHVGFVVGKDKQ--------------TGTIIVLGGNQGDRVR---EALYSRSRIVA 126 (129)
T ss_pred CCCccEEEEEECC---CCCEEEEEEeEcCC--------------CCEEEEeeCCCCCeEE---EEEEecccEEE
Confidence 6899999999854 23467777766543 3688999988654332 22345555554
No 25
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=80.68 E-value=2 Score=31.99 Aligned_cols=13 Identities=31% Similarity=0.414 Sum_probs=10.9
Q ss_pred CCccceEEEEecC
Q 030863 70 KFSHGDVIVFCSP 82 (170)
Q Consensus 70 ~~~rGDiV~f~~p 82 (170)
...+||+|+|+.+
T Consensus 84 ~~~~GD~i~~~~~ 96 (166)
T COG0681 84 IGLRGDIVVFKDD 96 (166)
T ss_pred ccCCCCEEEEECC
Confidence 4689999999984
No 26
>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism [, ]. The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands [, ]. Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigenes putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2LRJ_A 2VPM_B 2VOB_B 2VPS_A 2K3A_A 2IO9_A 2IO8_A 2IOB_A 2IOA_B 2IO7_B ....
Probab=69.73 E-value=12 Score=26.63 Aligned_cols=35 Identities=26% Similarity=0.252 Sum_probs=21.0
Q ss_pred CCCccceEEEEecCCCCCCceEEEEEEe-CCCeEec
Q 030863 69 YKFSHGDVIVFCSPSNHKEKHVKRIIGL-PGDWIGT 103 (170)
Q Consensus 69 ~~~~rGDiV~f~~p~~~~~~~vKRVvg~-~GD~v~~ 103 (170)
..|+.|||++|.......--.+--|.++ .+++|.+
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 5799999999953222334478888888 6665544
No 27
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=69.50 E-value=37 Score=24.88 Aligned_cols=26 Identities=19% Similarity=0.397 Sum_probs=17.0
Q ss_pred CCeEEEecCCCCCCCCCCccccccCCC
Q 030863 114 NGHCWVEGDNPSSSLDSRSFGPIPLGL 140 (170)
Q Consensus 114 ~g~~~v~gDn~~~S~DSR~~G~V~~~~ 140 (170)
++.+-++.++ ....-+|-||||.++.
T Consensus 81 dNA~Viin~~-g~P~GtrI~GPVaREl 106 (122)
T COG0093 81 DNAAVIINPD-GEPRGTRIFGPVAREL 106 (122)
T ss_pred CceEEEECCC-CCcccceEecchhHHH
Confidence 3444444333 4778899999998763
No 28
>COG0234 GroS Co-chaperonin GroES (HSP10) [Posttranslational modification, protein turnover, chaperones]
Probab=67.39 E-value=35 Score=24.01 Aligned_cols=68 Identities=16% Similarity=0.164 Sum_probs=38.6
Q ss_pred CCcEEEEEccccc-------------cCCCccceEEEEecC-CCCCCceEEEEEEeCCCeEec-cCCCCeEEccCCeEEE
Q 030863 55 SDDHVLMEKFCLQ-------------KYKFSHGDVIVFCSP-SNHKEKHVKRIIGLPGDWIGT-PMTNDVVKVPNGHCWV 119 (170)
Q Consensus 55 ~gd~vlv~k~~~~-------------~~~~~rGDiV~f~~p-~~~~~~~vKRVvg~~GD~v~~-~~~~~~~~vp~g~~~v 119 (170)
.||+|++.+.... ..++++|.+|+.-.- .+.+... ...-=..||+|.+ .|...+.++-..+|.+
T Consensus 6 L~DRVlVk~~e~EekT~gGIvlpdsakeK~~~g~VvAVG~G~~~~~g~~-~~~~VkvGD~Vlf~ky~G~evk~dgeeyli 84 (96)
T COG0234 6 LGDRVLVKRVEEEEKTAGGIVLPDSAKEKPQEGEVVAVGPGRRDENGEL-VPLDVKVGDRVLFGKYAGTEVKIDGEEYLI 84 (96)
T ss_pred cCCEEEEEEchhhccccCcEEecCccccCCcceEEEEEccceecCCCCE-eccccccCCEEEECccCCcEEEECCEEEEE
Confidence 3789998876432 245677777777541 1111111 2222345777776 4555667776667777
Q ss_pred ecCC
Q 030863 120 EGDN 123 (170)
Q Consensus 120 ~gDn 123 (170)
+.+.
T Consensus 85 l~e~ 88 (96)
T COG0234 85 LSES 88 (96)
T ss_pred echH
Confidence 6553
No 29
>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=60.53 E-value=65 Score=23.64 Aligned_cols=78 Identities=10% Similarity=-0.039 Sum_probs=41.1
Q ss_pred CCCccceEEEEecCCCCC----------CceEEEEEEeCCC-----eEec-----cCC-CCeEEccCCeEEEecCCC-CC
Q 030863 69 YKFSHGDVIVFCSPSNHK----------EKHVKRIIGLPGD-----WIGT-----PMT-NDVVKVPNGHCWVEGDNP-SS 126 (170)
Q Consensus 69 ~~~~rGDiV~f~~p~~~~----------~~~vKRVvg~~GD-----~v~~-----~~~-~~~~~vp~g~~~v~gDn~-~~ 126 (170)
..++.||+|+++.+..+. ..+|-||..+.-+ .+.. +.. .-...-.+.++|+. |+- ..
T Consensus 4 ~~i~vGD~V~v~~d~~~~~~~~~~~~~~~~~i~~V~~~~e~~~g~~~~h~~W~yrp~eTv~g~~~~~~ElFLS-d~c~~~ 82 (130)
T cd04712 4 LTIRVGDVVSVERDDADSTTKWNDDHRWLPLVQFVEYMKKGSDGSKMFHGRWLYRGCDTVLGNYANERELFLT-NECTCL 82 (130)
T ss_pred CEEeCCCEEEEcCCCCCccccccccccccceEEEEEEeeecCCCceEEEEEEEEcchhccccccCCCceEEEe-cccccc
Confidence 357788888888765431 4567777765443 1111 100 01113344555554 332 11
Q ss_pred CCCCCccccccCCCEeEEEEEEEeCCC
Q 030863 127 SLDSRSFGPIPLGLVKGRVTHILWPPQ 153 (170)
Q Consensus 127 S~DSR~~G~V~~~~I~Gkv~~~~~P~~ 153 (170)
+.++ + .+.|.||+..-+.+..
T Consensus 83 ~~~~-----~-~~~I~~k~~V~~~~~~ 103 (130)
T cd04712 83 ELDL-----L-STEIKGVHKVDWSGTP 103 (130)
T ss_pred cccc-----c-cceeEEEEEEEEecCc
Confidence 1111 1 5599999998887654
No 30
>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=57.81 E-value=27 Score=25.67 Aligned_cols=35 Identities=17% Similarity=0.242 Sum_probs=22.9
Q ss_pred CCceEEEEEEeCCCeEeccCCCCeEEccCCeEEEe
Q 030863 86 KEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVE 120 (170)
Q Consensus 86 ~~~~vKRVvg~~GD~v~~~~~~~~~~vp~g~~~v~ 120 (170)
..+++.||+.++--.+......+++.+|.|..|..
T Consensus 89 ~~w~vgrI~~~e~~~v~~~~~~Npy~Lp~Gt~~y~ 123 (129)
T PF10377_consen 89 REWIVGRIVSIEECQVKDDKDSNPYNLPVGTKFYR 123 (129)
T ss_pred CCEEEEEEEEEEEEEeccCCCCCCCcCCCCCEEEE
Confidence 45778888877654443335667778888876643
No 31
>PRK00364 groES co-chaperonin GroES; Reviewed
Probab=54.89 E-value=69 Score=22.19 Aligned_cols=86 Identities=12% Similarity=0.103 Sum_probs=39.1
Q ss_pred CcEEEEEccccccCCCccceEEEEecCCCCCCceEEEEEEeCCCeEeccCCCCeEEccCCeEEEecCCCC--CCCCCCcc
Q 030863 56 DDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPS--SSLDSRSF 133 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD~v~~~~~~~~~~vp~g~~~v~gDn~~--~S~DSR~~ 133 (170)
||+||+.+.... +-..|-|++=.. ...+.....|+|+.-....-.-...+..|..|..-+..+... --.|...|
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 899999876532 334555554221 224455666776653221110011122233333333332211 11233444
Q ss_pred ccccCCCEeEEE
Q 030863 134 GPIPLGLVKGRV 145 (170)
Q Consensus 134 G~V~~~~I~Gkv 145 (170)
=.++.++|+|++
T Consensus 83 ~iv~~~DIlavi 94 (95)
T PRK00364 83 LILRESDILAIV 94 (95)
T ss_pred EEEEHHHEEEEe
Confidence 456666777654
No 32
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=54.36 E-value=14 Score=24.91 Aligned_cols=19 Identities=26% Similarity=0.431 Sum_probs=11.3
Q ss_pred CcEEEEEccccccCCCccceEE
Q 030863 56 DDHVLMEKFCLQKYKFSHGDVI 77 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~rGDiV 77 (170)
||.|++....+ ++++|||+
T Consensus 50 GD~V~Ve~~~~---d~~kg~I~ 68 (75)
T COG0361 50 GDVVLVELSPY---DLTKGRIV 68 (75)
T ss_pred CCEEEEEeccc---ccccccEE
Confidence 66666665553 35666654
No 33
>PF00238 Ribosomal_L14: Ribosomal protein L14p/L23e; InterPro: IPR000218 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L14 is one of the proteins from the large ribosomal subunit. In eubacteria, L14 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins, which have been grouped on the basis of sequence similarities []. Based on amino-acid sequence homology, it is predicted that ribosomal protein L14 is a member of a recently identified family of structurally related RNA-binding proteins []. L14 is a protein of 119 to 137 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZR_M 4A1C_J 4A1E_J 4A1A_J 4A17_J 1VSP_I 3D5D_O 1VSA_I 3MRZ_K 3F1F_O ....
Probab=52.85 E-value=52 Score=24.00 Aligned_cols=28 Identities=25% Similarity=0.496 Sum_probs=21.6
Q ss_pred EccCCeEEEecCCCCCCCCCCccccccCC
Q 030863 111 KVPNGHCWVEGDNPSSSLDSRSFGPIPLG 139 (170)
Q Consensus 111 ~vp~g~~~v~gDn~~~S~DSR~~G~V~~~ 139 (170)
.-.++.+-++.++ .+...+|-+|||+.+
T Consensus 78 ~F~~Na~VLln~~-~~p~GtrI~Gpv~~e 105 (122)
T PF00238_consen 78 KFDDNAVVLLNKK-GNPLGTRIFGPVPRE 105 (122)
T ss_dssp EESSEEEEEEETT-SSBSSSSBCSEEEHH
T ss_pred EeCCccEEEEcCC-CCEeeeEEEeeehHH
Confidence 3446677777777 488999999999864
No 34
>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=50.51 E-value=24 Score=25.41 Aligned_cols=29 Identities=31% Similarity=0.330 Sum_probs=22.2
Q ss_pred CCccceEEEEecCCCCCCceEEEEEEeCC
Q 030863 70 KFSHGDVIVFCSPSNHKEKHVKRIIGLPG 98 (170)
Q Consensus 70 ~~~rGDiV~f~~p~~~~~~~vKRVvg~~G 98 (170)
.++.||-|.++++..++..+|.||..+-.
T Consensus 3 ~~~vGD~V~v~~~~~~~~pyIgrI~~i~e 31 (121)
T cd04714 3 IIRVGDCVLFKSPGRPSLPYVARIESLWE 31 (121)
T ss_pred EEEcCCEEEEeCCCCCCCCEEEEEEEEEE
Confidence 46789999999876556778888877543
No 35
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=49.24 E-value=19 Score=23.67 Aligned_cols=19 Identities=21% Similarity=0.305 Sum_probs=9.4
Q ss_pred CcEEEEEccccccCCCccceEE
Q 030863 56 DDHVLMEKFCLQKYKFSHGDVI 77 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~rGDiV 77 (170)
||.|.+....| ++.+||||
T Consensus 48 GD~V~Ve~spy---d~tkgrIi 66 (68)
T TIGR00008 48 GDKVKVELSPY---DLTRGRIT 66 (68)
T ss_pred CCEEEEEECcc---cCCcEeEE
Confidence 55555554442 34555554
No 36
>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=49.15 E-value=73 Score=24.71 Aligned_cols=79 Identities=10% Similarity=0.090 Sum_probs=44.9
Q ss_pred CcEEEEEccccccCCCccceEEEEecCCCCCCceEEEEEEeCC----CeEecc----CC-----C-Ce--E-------Ec
Q 030863 56 DDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPG----DWIGTP----MT-----N-DV--V-------KV 112 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~rGDiV~f~~p~~~~~~~vKRVvg~~G----D~v~~~----~~-----~-~~--~-------~v 112 (170)
++.+...|..- ...++.||.|+++.+.. +...+..|..+-- +.+.+. +. . .. . .+
T Consensus 39 ~~~i~l~R~~d-~~~~~vGD~Vlik~~~~-~~~~V~iI~ei~~~~~~~~v~i~v~Wy~r~~Ei~~~~~~~~~~~~~~~~~ 116 (179)
T cd04720 39 KRKIFLARDSD-GLELSVGDTILVKDDVA-NSPSVYLIHEIRLNTLNNEVELWVMWFLRWFEINPARYYKQFDPEFRSES 116 (179)
T ss_pred CCcEEEEEccC-CeEEeCCCEEEEeCCCC-CCCEEEEEEEEEeCCCCCEEEEEEEEcCCHHHcccccccccccchhcccC
Confidence 34444444421 14689999999998854 5555666655422 334440 00 0 00 0 23
Q ss_pred cCCeEEEecCCCCCCCCCCccccccCCCEeEEEE
Q 030863 113 PNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVT 146 (170)
Q Consensus 113 p~g~~~v~gDn~~~S~DSR~~G~V~~~~I~Gkv~ 146 (170)
.++++|+..+-. .++...|+|++.
T Consensus 117 ~~nElflT~~~d----------~i~l~~Ii~k~~ 140 (179)
T cd04720 117 NKNELYLTAELS----------EIKLKDIIDKAN 140 (179)
T ss_pred CCceEEEecccc----------eEEhhheeeeEE
Confidence 356777664432 589999999983
No 37
>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=47.56 E-value=20 Score=23.03 Aligned_cols=12 Identities=17% Similarity=0.335 Sum_probs=6.8
Q ss_pred CCccceEEEEec
Q 030863 70 KFSHGDVIVFCS 81 (170)
Q Consensus 70 ~~~rGDiV~f~~ 81 (170)
-+++||.|+...
T Consensus 41 wI~~GD~V~V~~ 52 (65)
T PF01176_consen 41 WIKRGDFVLVEP 52 (65)
T ss_dssp ---TTEEEEEEE
T ss_pred ecCCCCEEEEEe
Confidence 367888887764
No 38
>TIGR01067 rplN_bact ribosomal protein L14, bacterial/organelle. This model distinguishes bacterial and most organellar examples of ribosomal protein L14 from all archaeal and eukaryotic forms.
Probab=47.07 E-value=1.1e+02 Score=22.33 Aligned_cols=39 Identities=18% Similarity=0.281 Sum_probs=24.4
Q ss_pred ccCCeEEEecCCCCCCCCCCccccccCCCEeEEEEEEEeCC
Q 030863 112 VPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPP 152 (170)
Q Consensus 112 vp~g~~~v~gDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~P~ 152 (170)
-.++.+-++.++ .+-.-+|-+|||+.+.= .+-+.++.++
T Consensus 79 F~~Na~VLin~~-~~p~GTrI~Gpv~~elr-~~~~~Ki~sl 117 (122)
T TIGR01067 79 FDDNACVLINKN-KEPRGTRIFGPVARELR-DKGFMKIVSL 117 (122)
T ss_pred CCCceEEEECCC-CCEeeeEEEccchHHHh-hcCCceeeec
Confidence 345666666655 36788999999997652 2334444444
No 39
>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=46.49 E-value=22 Score=23.89 Aligned_cols=10 Identities=20% Similarity=0.531 Sum_probs=5.3
Q ss_pred CccceEEEEe
Q 030863 71 FSHGDVIVFC 80 (170)
Q Consensus 71 ~~rGDiV~f~ 80 (170)
+++||+|+..
T Consensus 39 I~~GD~VlV~ 48 (78)
T cd04456 39 IKRGDFLIVD 48 (78)
T ss_pred EcCCCEEEEE
Confidence 4555555554
No 40
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=46.49 E-value=27 Score=25.45 Aligned_cols=52 Identities=13% Similarity=0.044 Sum_probs=27.0
Q ss_pred CCCccceEEEEecCCCCCCceEEEEEEe------CCCeEec-cCCCCeEEccCCeEEEe
Q 030863 69 YKFSHGDVIVFCSPSNHKEKHVKRIIGL------PGDWIGT-PMTNDVVKVPNGHCWVE 120 (170)
Q Consensus 69 ~~~~rGDiV~f~~p~~~~~~~vKRVvg~------~GD~v~~-~~~~~~~~vp~g~~~v~ 120 (170)
..++.||-|+...+.....+.=..|++. .+..+.+ .++.....+|.++++-+
T Consensus 54 ~~L~~GD~VLA~~~~~~~~Y~Pg~V~~~~~~~~~~~~~~~V~f~ng~~~~vp~~~~~~I 112 (124)
T PF15057_consen 54 HSLQVGDKVLAPWEPDDCRYGPGTVIAGPERRASEDKEYTVRFYNGKTAKVPRGEVIWI 112 (124)
T ss_pred CcCCCCCEEEEecCcCCCEEeCEEEEECccccccCCceEEEEEECCCCCccchhhEEEC
Confidence 3566677776665544444444666643 3333333 23344555666655544
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=45.14 E-value=23 Score=23.71 Aligned_cols=10 Identities=20% Similarity=0.740 Sum_probs=5.4
Q ss_pred CccceEEEEe
Q 030863 71 FSHGDVIVFC 80 (170)
Q Consensus 71 ~~rGDiV~f~ 80 (170)
+++||+|+..
T Consensus 39 I~~GD~V~Ve 48 (77)
T cd05793 39 INEGDIVLVA 48 (77)
T ss_pred EcCCCEEEEE
Confidence 4555555554
No 42
>PF10000 ACT_3: ACT domain; InterPro: IPR018717 This domain has no known function.; PDB: 1ZVP_C.
Probab=44.05 E-value=13 Score=24.60 Aligned_cols=18 Identities=39% Similarity=0.560 Sum_probs=12.2
Q ss_pred CCcccccCCCCCCCCCCCCCcEEEEEcc
Q 030863 37 SSMSPTFNPTTDSFMGSLSDDHVLMEKF 64 (170)
Q Consensus 37 ~SM~Ptl~~~~~~~~~~~~gd~vlv~k~ 64 (170)
.||+|.+++ |++|++.--
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 589999999 999999754
No 43
>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=43.89 E-value=26 Score=24.29 Aligned_cols=28 Identities=18% Similarity=0.194 Sum_probs=20.2
Q ss_pred CCccceEEEEecCCCCCCceEEEEEEeC
Q 030863 70 KFSHGDVIVFCSPSNHKEKHVKRIIGLP 97 (170)
Q Consensus 70 ~~~rGDiV~f~~p~~~~~~~vKRVvg~~ 97 (170)
.++.||.|.+..+..+....|.||..+-
T Consensus 2 ~~~vGD~V~v~~~~~~~~~~v~~I~~i~ 29 (119)
T PF01426_consen 2 TYKVGDFVYVKPDDPPEPPYVARIEEIW 29 (119)
T ss_dssp EEETTSEEEEECTSTTSEEEEEEEEEEE
T ss_pred EEeCCCEEEEeCCCCCCCCEEEEEEEEE
Confidence 3577888888877655677888877653
No 44
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=43.89 E-value=65 Score=26.43 Aligned_cols=74 Identities=24% Similarity=0.403 Sum_probs=45.8
Q ss_pred cCCCcccccCCCCCCCCCCCCCcEEEEEcccc-------------ccCCCccceEEEEecCCCCCCceEEEEEEeCCCeE
Q 030863 35 RGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCL-------------QKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWI 101 (170)
Q Consensus 35 ~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~-------------~~~~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD~v 101 (170)
....|.|.|+. ||+|...=... ...+++.|-+|-..+ ..+-|+++--|--+
T Consensus 105 ~~~~~r~~l~v----------GD~v~AkV~~vd~~~~~~L~~k~~~~GkL~~G~iv~i~p------~kVpRvig~~~sm~ 168 (239)
T COG1097 105 AEKDLRPFLNV----------GDLVYAKVVDVDRDGEVELTLKDEGLGKLKNGQIVKIPP------SKVPRVIGKKGSML 168 (239)
T ss_pred ccccccccccc----------CCEEEEEEEEccCCCceEEEeecCCCccccCCEEEEEch------hhcceEecCCCcHH
Confidence 46789999999 99988642211 145677887777653 24566776666544
Q ss_pred ec--cCCCCeE-EccCCeEEEecCCC
Q 030863 102 GT--PMTNDVV-KVPNGHCWVEGDNP 124 (170)
Q Consensus 102 ~~--~~~~~~~-~vp~g~~~v~gDn~ 124 (170)
.. ......+ .=-+|.+|+-|.|.
T Consensus 169 ~~l~~~~~~~I~VG~NG~IWV~~~~~ 194 (239)
T COG1097 169 NMLKEKTGCEIIVGQNGRIWVDGENE 194 (239)
T ss_pred HHhhhhcCeEEEEecCCEEEecCCCc
Confidence 22 1112222 23457899999986
No 45
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=43.22 E-value=26 Score=23.85 Aligned_cols=10 Identities=20% Similarity=0.587 Sum_probs=5.7
Q ss_pred CccceEEEEe
Q 030863 71 FSHGDVIVFC 80 (170)
Q Consensus 71 ~~rGDiV~f~ 80 (170)
+++||+|++.
T Consensus 44 I~~GD~VlVe 53 (83)
T smart00652 44 IRRGDIVLVD 53 (83)
T ss_pred EcCCCEEEEE
Confidence 4566666554
No 46
>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=43.20 E-value=31 Score=23.93 Aligned_cols=25 Identities=20% Similarity=0.248 Sum_probs=16.2
Q ss_pred CcEEEEEccccccCCCccceEEEEecC
Q 030863 56 DDHVLMEKFCLQKYKFSHGDVIVFCSP 82 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~rGDiV~f~~p 82 (170)
+|++.-+.... .+++.||+++|..-
T Consensus 70 ~D~i~~~~~lP--~~l~~GD~l~f~~~ 94 (116)
T PF00278_consen 70 GDVIARDVMLP--KELEVGDWLVFENM 94 (116)
T ss_dssp TSEEEEEEEEE--STTTTT-EEEESS-
T ss_pred CceEeeeccCC--CCCCCCCEEEEecC
Confidence 78886543331 27999999999763
No 47
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=42.15 E-value=29 Score=24.00 Aligned_cols=10 Identities=20% Similarity=0.318 Sum_probs=4.6
Q ss_pred CccceEEEEe
Q 030863 71 FSHGDVIVFC 80 (170)
Q Consensus 71 ~~rGDiV~f~ 80 (170)
+..||.|.+.
T Consensus 47 Il~GD~V~VE 56 (87)
T PRK12442 47 ILAGDRVTLE 56 (87)
T ss_pred ecCCCEEEEE
Confidence 3445554443
No 48
>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=41.62 E-value=39 Score=24.11 Aligned_cols=28 Identities=21% Similarity=0.363 Sum_probs=20.5
Q ss_pred CCccceEEEEecCCCCCCceEEEEEEeC
Q 030863 70 KFSHGDVIVFCSPSNHKEKHVKRIIGLP 97 (170)
Q Consensus 70 ~~~rGDiV~f~~p~~~~~~~vKRVvg~~ 97 (170)
.++.||-|.+.++.++....|-||..+-
T Consensus 3 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~ 30 (121)
T cd04717 3 QYRVGDCVYVANPEDPSKPIIFRIERLW 30 (121)
T ss_pred EEECCCEEEEeCCCCCCCCEEEEEeEEE
Confidence 4678999999887665667777776643
No 49
>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=40.76 E-value=73 Score=21.80 Aligned_cols=86 Identities=10% Similarity=0.073 Sum_probs=42.7
Q ss_pred CcEEEEEccccccCCCccceEEEEecCCCCCCceEEEEEEeCCCeEeccCCCCeEEccCCeEEEecCCCC--CCCCCCcc
Q 030863 56 DDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPS--SSLDSRSF 133 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD~v~~~~~~~~~~vp~g~~~v~gDn~~--~S~DSR~~ 133 (170)
||+|++.+... .+-..|-+++=.. ........+|+++......-.....+..+..|..-+..+... -..|...|
T Consensus 6 ~drVLV~~~~~--e~~T~~GiiLp~~--~~~~~~~G~VvaVG~G~~~~~g~~~~~~vk~GD~Vl~~~~~g~~v~~~~~~~ 81 (93)
T PF00166_consen 6 GDRVLVKKIEA--EEKTASGIILPES--AKEKPNQGKVVAVGPGRYNENGEEVPMDVKVGDKVLFPKYAGTEVKFDGEKY 81 (93)
T ss_dssp TTEEEEEECSC--TCTCTTSCCE-CC--SSSSEEEEEEEEE-SEEETTTSSEEETSS-TTSEEEEETTTSEEEEETTEEE
T ss_pred CCEEEEEEccc--cceecceEEeccc--cccccceeEEEEcCCccccCCCcEeeeeeeeccEEeccccCceEEEECCEEE
Confidence 89999998632 2444555555422 223566777777765333211111122344444444433321 22355556
Q ss_pred ccccCCCEeEEE
Q 030863 134 GPIPLGLVKGRV 145 (170)
Q Consensus 134 G~V~~~~I~Gkv 145 (170)
=.++.++|.|++
T Consensus 82 ~~~~~~dIlavi 93 (93)
T PF00166_consen 82 LIVREDDILAVI 93 (93)
T ss_dssp EEEEGGGEEEEE
T ss_pred EEEEHHHeEEEC
Confidence 667777777763
No 50
>smart00002 PLP Myelin proteolipid protein (PLP or lipophilin).
Probab=40.64 E-value=7.1 Score=25.12 Aligned_cols=20 Identities=30% Similarity=0.679 Sum_probs=17.0
Q ss_pred CCCCCCccccccCCCEeEEE
Q 030863 126 SSLDSRSFGPIPLGLVKGRV 145 (170)
Q Consensus 126 ~S~DSR~~G~V~~~~I~Gkv 145 (170)
-+.|-|.||.+|-++.-||+
T Consensus 22 lC~D~RQyGilpwna~pgK~ 41 (60)
T smart00002 22 LCVDARQYGILPWNAFPGKV 41 (60)
T ss_pred EEeechhcceeecCCCCCch
Confidence 47899999999988877775
No 51
>cd04709 BAH_MTA BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=39.19 E-value=41 Score=25.85 Aligned_cols=23 Identities=22% Similarity=0.407 Sum_probs=17.8
Q ss_pred CCCCccccccCCCEeEEEEEEEe
Q 030863 128 LDSRSFGPIPLGLVKGRVTHILW 150 (170)
Q Consensus 128 ~DSR~~G~V~~~~I~Gkv~~~~~ 150 (170)
+-|++.-.+|.+.|.||..-...
T Consensus 85 F~S~~~d~~p~~~IrGKC~V~~~ 107 (164)
T cd04709 85 FLSRQVETLPATHIRGKCSVTLL 107 (164)
T ss_pred EEecccccccHHHeeeeEEEEEe
Confidence 44556788999999999876654
No 52
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.32 E-value=21 Score=26.14 Aligned_cols=17 Identities=29% Similarity=0.397 Sum_probs=14.7
Q ss_pred CCcccccCCCCCCCCCCCCCcEEEEEc
Q 030863 37 SSMSPTFNPTTDSFMGSLSDDHVLMEK 63 (170)
Q Consensus 37 ~SM~Ptl~~~~~~~~~~~~gd~vlv~k 63 (170)
.||+|.+.+ ||+|++.-
T Consensus 12 ~smtPeL~~----------G~yVfcT~ 28 (134)
T COG3602 12 ASMTPELLD----------GDYVFCTV 28 (134)
T ss_pred HhcCccccC----------CceEEEEe
Confidence 489999999 99999853
No 53
>PF06890 Phage_Mu_Gp45: Bacteriophage Mu Gp45 protein; InterPro: IPR014462 This entry is represented by the Bacteriophage Mu, Gp45. The characteristics of the protein distribution suggest prophage matches.
Probab=37.12 E-value=1.7e+02 Score=22.40 Aligned_cols=39 Identities=18% Similarity=0.250 Sum_probs=27.9
Q ss_pred cccccCCCccceEEEEecCCCCCCceEEE---EEEeCCCeEecc
Q 030863 64 FCLQKYKFSHGDVIVFCSPSNHKEKHVKR---IIGLPGDWIGTP 104 (170)
Q Consensus 64 ~~~~~~~~~rGDiV~f~~p~~~~~~~vKR---Vvg~~GD~v~~~ 104 (170)
..|+.+.++.|++.+|... .....+|| ++.+.++++.+.
T Consensus 68 ~~yR~~~L~~GEvalY~~~--G~~I~L~~~G~ii~~~~~~~~v~ 109 (162)
T PF06890_consen 68 RRYRPKGLKPGEVALYDDE--GQKIHLKRDGRIIEVTCKTVTVN 109 (162)
T ss_pred ccccccCCCCCcEEEEcCC--CCEEEEEecceEEeccCceEEEe
Confidence 3344567899999999863 24555665 777888888874
No 54
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=37.07 E-value=35 Score=24.08 Aligned_cols=10 Identities=30% Similarity=0.757 Sum_probs=5.4
Q ss_pred CccceEEEEe
Q 030863 71 FSHGDVIVFC 80 (170)
Q Consensus 71 ~~rGDiV~f~ 80 (170)
+.+||+|++.
T Consensus 60 I~~GD~VlVe 69 (100)
T PRK04012 60 IREGDVVIVA 69 (100)
T ss_pred ecCCCEEEEE
Confidence 4555555554
No 55
>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=36.44 E-value=1.4e+02 Score=20.48 Aligned_cols=40 Identities=15% Similarity=0.306 Sum_probs=23.1
Q ss_pred CcEEEEEccccccCCCccceEEEEecCCCCCCceEEEEEEeCCC
Q 030863 56 DDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGD 99 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD 99 (170)
||+|++.+.... +-..|-|++=... ..+.....|+|+.-+
T Consensus 6 ~DrVLV~~~~~e--~~T~~GI~Lp~~~--~~k~~~g~VvAVG~g 45 (93)
T cd00320 6 GDRVLVKRIEAE--EKTKGGIILPDSA--KEKPQEGKVVAVGPG 45 (93)
T ss_pred CCEEEEEEcccc--ceecceEEeCCCc--CCCceEEEEEEECCC
Confidence 899999877522 3345555543221 245566777776544
No 56
>smart00439 BAH Bromo adjacent homology domain.
Probab=36.39 E-value=66 Score=22.16 Aligned_cols=17 Identities=18% Similarity=0.347 Sum_probs=13.4
Q ss_pred cccCCCEeEEEEEEEeC
Q 030863 135 PIPLGLVKGRVTHILWP 151 (170)
Q Consensus 135 ~V~~~~I~Gkv~~~~~P 151 (170)
-++.+.|+||+.-...+
T Consensus 70 ~i~~~~I~~kc~V~~~~ 86 (120)
T smart00439 70 TVPLSDIIGKCNVLSKS 86 (120)
T ss_pred cCChHHeeeEEEEEEcc
Confidence 58999999999766543
No 57
>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=36.29 E-value=79 Score=23.05 Aligned_cols=13 Identities=38% Similarity=0.411 Sum_probs=11.0
Q ss_pred CCCccceEEEEec
Q 030863 69 YKFSHGDVIVFCS 81 (170)
Q Consensus 69 ~~~~rGDiV~f~~ 81 (170)
.++++||+|.|..
T Consensus 75 ~~~qpGDlvff~~ 87 (134)
T TIGR02219 75 DAAQPGDVLVFRW 87 (134)
T ss_pred hcCCCCCEEEEee
Confidence 3789999999974
No 58
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=36.01 E-value=1.5e+02 Score=20.51 Aligned_cols=81 Identities=9% Similarity=0.142 Sum_probs=37.9
Q ss_pred CcEEEEEccccccCCCccceEEEEecCCCCCCceEEEEEEeCCCeEeccCCCCeEEccCCeEEEecCCCC--CCCCCCcc
Q 030863 56 DDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPS--SSLDSRSF 133 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD~v~~~~~~~~~~vp~g~~~v~gDn~~--~S~DSR~~ 133 (170)
||+||+.+.... +-..|-|++=... ..+.....|+|+.... ...+..|..|..-+.++... --.|...|
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 899999876532 2344555553221 2344455566554211 01123344444333333321 11233344
Q ss_pred ccccCCCEeEEE
Q 030863 134 GPIPLGLVKGRV 145 (170)
Q Consensus 134 G~V~~~~I~Gkv 145 (170)
=.++.++|+|++
T Consensus 78 ~iv~e~DILa~i 89 (91)
T PRK14533 78 IIIDVNDILAKI 89 (91)
T ss_pred EEEEhHhEEEEe
Confidence 456666777764
No 59
>PF01568 Molydop_binding: Molydopterin dinucleotide binding domain; InterPro: IPR006657 A domain in this entry corresponds to the C-terminal domain IV in dimethyl sulphoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [].; GO: 0016491 oxidoreductase activity, 0030151 molybdenum ion binding, 0055114 oxidation-reduction process; PDB: 2IVF_A 1OGY_G 3ML1_A 3O5A_A 1TI2_G 1VLE_M 1VLD_U 1VLF_O 1TI4_I 1TI6_E ....
Probab=35.42 E-value=98 Score=21.03 Aligned_cols=48 Identities=23% Similarity=0.270 Sum_probs=31.5
Q ss_pred cEEEEEccccccCCCccceEEEEecCCCCCCceEEEEEEeCCCeEeccCCCCeEEccCCeEEEe
Q 030863 57 DHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVE 120 (170)
Q Consensus 57 d~vlv~k~~~~~~~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD~v~~~~~~~~~~vp~g~~~v~ 120 (170)
..+.++.-......++.||.|.+.++.. .+.-+|.-.++ |++|.+|+-
T Consensus 30 ~~v~inp~dA~~~Gi~~Gd~V~v~s~~G---~v~~~v~~~~~-------------v~~g~v~~~ 77 (110)
T PF01568_consen 30 PFVEINPEDAAKLGIKDGDWVRVSSPRG---SVEVRVKVTDG-------------VPPGVVFMP 77 (110)
T ss_dssp EEEEEEHHHHHHCT--TTCEEEEEETTE---EEEEEEEEETT-------------S-TTEEEEE
T ss_pred CEEEEcHHHHHHhcCcCCCEEEEEeccc---eEeeeeEEecC-------------CcCCEEEEe
Confidence 4889988776667899999999998752 44455554443 667777765
No 60
>PRK05483 rplN 50S ribosomal protein L14; Validated
Probab=34.72 E-value=1.8e+02 Score=21.22 Aligned_cols=28 Identities=18% Similarity=0.380 Sum_probs=19.8
Q ss_pred ccCCeEEEecCCCCCCCCCCccccccCCC
Q 030863 112 VPNGHCWVEGDNPSSSLDSRSFGPIPLGL 140 (170)
Q Consensus 112 vp~g~~~v~gDn~~~S~DSR~~G~V~~~~ 140 (170)
--++.+-++.++ .+..-+|-+|||+.+.
T Consensus 79 F~dNavVLin~~-~~p~GTrI~Gpv~~el 106 (122)
T PRK05483 79 FDDNAAVLLNND-GEPRGTRIFGPVAREL 106 (122)
T ss_pred cCCCEEEEECCC-CCEeEeEEeccchHHH
Confidence 345566666555 3778899999999765
No 61
>PRK11578 macrolide transporter subunit MacA; Provisional
Probab=34.69 E-value=1.1e+02 Score=25.89 Aligned_cols=15 Identities=20% Similarity=0.220 Sum_probs=9.8
Q ss_pred eEEEEEEeCCCeEec
Q 030863 89 HVKRIIGLPGDWIGT 103 (170)
Q Consensus 89 ~vKRVvg~~GD~v~~ 103 (170)
.++++.-.+||.|.-
T Consensus 71 ~V~~v~v~~G~~V~k 85 (370)
T PRK11578 71 QLKTLSVAIGDKVKK 85 (370)
T ss_pred EEEEEEcCCCCEEcC
Confidence 566666677776653
No 62
>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=33.13 E-value=1.1e+02 Score=22.43 Aligned_cols=51 Identities=12% Similarity=0.089 Sum_probs=35.3
Q ss_pred ccceEEEEecC--CCCCCceEEEEEEeCCCe--Eec----cC-CCCeEEccCCeEEEecC
Q 030863 72 SHGDVIVFCSP--SNHKEKHVKRIIGLPGDW--IGT----PM-TNDVVKVPNGHCWVEGD 122 (170)
Q Consensus 72 ~rGDiV~f~~p--~~~~~~~vKRVvg~~GD~--v~~----~~-~~~~~~vp~g~~~v~gD 122 (170)
+.||-|+|+.+ ...+.+++-+|+...++. .++ +. ....++++..++.-+=.
T Consensus 1 q~G~~VAak~~~~~~~~~WIla~Vv~~~~~~~rYeV~D~d~~~~~~~~~~~~~~iIPLP~ 60 (130)
T PF07039_consen 1 QPGDQVAAKVKQGNEEEEWILAEVVKYNSDGNRYEVEDPDPEEEKKRYKLSRKQIIPLPK 60 (130)
T ss_dssp -TT-EEEEEECTTTTTCEEEEEEEEEEETTTTEEEEEETTTCTTTEEEEEEGGGEEEE-S
T ss_pred CCCCEEEEEcCCCCCCCCEEEEEEEEEeCCCCEEEEecCCCCCCCceEEeCHHHEEECCC
Confidence 57999999876 345789999999988885 554 11 23467777778777755
No 63
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=32.40 E-value=1.4e+02 Score=21.33 Aligned_cols=42 Identities=19% Similarity=0.351 Sum_probs=26.9
Q ss_pred CcEEEEEccccccCCCccceEEEEecCCCCCCceEEEEEEeCCC
Q 030863 56 DDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGD 99 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD 99 (170)
+|...+.........+..||+|.++... +...+.+++.-.|.
T Consensus 11 ~~~y~l~n~Pf~a~glA~gDvV~~~~~~--g~~~~~~~v~~sGn 52 (117)
T PF14085_consen 11 DDTYRLDNIPFFAYGLALGDVVRAEPDD--GELWFQKVVESSGN 52 (117)
T ss_pred CCEEEEEecccccCCCCCCCEEEEEeCC--CeEEEEEEEecCCC
Confidence 4555555544334689999999999764 55555555544443
No 64
>PF11337 DUF3139: Protein of unknown function (DUF3139); InterPro: IPR021486 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=31.96 E-value=78 Score=21.24 Aligned_cols=16 Identities=6% Similarity=0.038 Sum_probs=7.1
Q ss_pred CchhHHHHHHHHHHHH
Q 030863 1 MAAHNFLWSLTKNCFT 16 (170)
Q Consensus 1 ~~~~~~~~~~~~~~~~ 16 (170)
|..++.++.++..+++
T Consensus 1 MKK~kii~iii~li~i 16 (85)
T PF11337_consen 1 MKKKKIILIIIILIVI 16 (85)
T ss_pred CCchHHHHHHHHHHHH
Confidence 5544555444433333
No 65
>cd04721 BAH_plant_1 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=31.49 E-value=1.2e+02 Score=22.26 Aligned_cols=28 Identities=25% Similarity=0.228 Sum_probs=19.1
Q ss_pred CCccceEEEEecCCCCCCceEEEEEEeCCC
Q 030863 70 KFSHGDVIVFCSPSNHKEKHVKRIIGLPGD 99 (170)
Q Consensus 70 ~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD 99 (170)
.++.||.|.+..+. ++..+.+|-.+-.|
T Consensus 7 ~i~vGD~V~v~~~~--~~~~va~Ie~i~ed 34 (130)
T cd04721 7 TISVHDFVYVLSEE--EDRYVAYIEDLYED 34 (130)
T ss_pred EEECCCEEEEeCCC--CCcEEEEEEEEEEc
Confidence 47899999998654 44566666665444
No 66
>PTZ00414 10 kDa heat shock protein; Provisional
Probab=28.15 E-value=2.2e+02 Score=20.10 Aligned_cols=10 Identities=20% Similarity=0.361 Sum_probs=8.5
Q ss_pred CcEEEEEccc
Q 030863 56 DDHVLMEKFC 65 (170)
Q Consensus 56 gd~vlv~k~~ 65 (170)
||+|++.+..
T Consensus 16 ~dRVLVk~~~ 25 (100)
T PTZ00414 16 GQRVLVKRTL 25 (100)
T ss_pred CCEEEEEEcc
Confidence 8999998765
No 67
>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=28.12 E-value=73 Score=25.70 Aligned_cols=27 Identities=19% Similarity=0.411 Sum_probs=11.8
Q ss_pred EccCCe--EEEecCCCCCCCCCCccccccCCC
Q 030863 111 KVPNGH--CWVEGDNPSSSLDSRSFGPIPLGL 140 (170)
Q Consensus 111 ~vp~g~--~~v~gDn~~~S~DSR~~G~V~~~~ 140 (170)
-||++. +|.+|-|- +. ...+|-|....
T Consensus 164 gi~~~~mi~w~ign~G--~~-~~a~gtVs~k~ 192 (217)
T PF07423_consen 164 GISEDNMIVWFIGNNG--SP-QKAIGTVSDKD 192 (217)
T ss_pred CCChhheEEEhhhcCC--cc-cceeEEeccCC
Confidence 355544 44455442 11 33455555443
No 68
>PF10222 DUF2152: Uncharacterized conserved protein (DUF2152); InterPro: IPR018795 This entry includes mainly uncharacterised proteins, though some are described as belonging to the glycoside hydrolase family 65.
Probab=27.92 E-value=80 Score=29.43 Aligned_cols=67 Identities=12% Similarity=0.179 Sum_probs=39.2
Q ss_pred cEEEEEccccccCCCccceEEEEecCCCCCCceEEEEEEeCCCeEeccCCCCeEEccCCeEEEecCCCCCCCCCCcc
Q 030863 57 DHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPSSSLDSRSF 133 (170)
Q Consensus 57 d~vlv~k~~~~~~~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD~v~~~~~~~~~~vp~g~~~v~gDn~~~S~DSR~~ 133 (170)
+.++-+++........+||.++...|.......+ -.+.+ ......|..++.|+.|.++..+.+.++.
T Consensus 52 ~~Cl~~~l~~w~~~~~e~da~i~~~~~p~e~~~~---P~VGN-------G~iGl~V~~d~L~I~~~~R~l~~~~~f~ 118 (604)
T PF10222_consen 52 GKCLQDRLAPWYSQAEEGDAVILHPPKPQEKNYL---PFVGN-------GYIGLDVDSDNLYIKGSGRALSLPVPFH 118 (604)
T ss_pred chhHHHHHHHHHHHHhcCCEEEccCCCCCcccCC---ceecC-------CEEEEEEcCCeEEEEecCcccccccCCC
Confidence 4566666665545678999999985531111111 11111 1223456677899988777677777764
No 69
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=25.75 E-value=1.3e+02 Score=21.98 Aligned_cols=57 Identities=18% Similarity=0.200 Sum_probs=31.3
Q ss_pred CCccceEEEEecCCCCCCceEEEEEEeCCCeEeccCCCCeEEccCCeEEEecCCCCCCCCCCccccccCCCEe
Q 030863 70 KFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVK 142 (170)
Q Consensus 70 ~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD~v~~~~~~~~~~vp~g~~~v~gDn~~~S~DSR~~G~V~~~~I~ 142 (170)
.+++||.|.+..-.+.++ ..+|..+--+ ++.+.|.|=|...........||+.+++.
T Consensus 45 ~IkkGD~V~VisG~~KGk--~GkV~~V~~~--------------~~~V~VeGvn~~k~~G~~~e~pIh~SNV~ 101 (120)
T PRK01191 45 PVRKGDTVKVMRGDFKGE--EGKVVEVDLK--------------RGRIYVEGVTVKKADGTEVPRPIHPSNVM 101 (120)
T ss_pred eEeCCCEEEEeecCCCCc--eEEEEEEEcC--------------CCEEEEeCcEEECCCCeEEEcccchhHeE
Confidence 578999998887654442 2555554211 35677777665332111223456665553
No 70
>KOG4146 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=24.68 E-value=96 Score=21.82 Aligned_cols=27 Identities=33% Similarity=0.495 Sum_probs=18.5
Q ss_pred CcEEEEEcccc-----ccCCCccceEEEEecC
Q 030863 56 DDHVLMEKFCL-----QKYKFSHGDVIVFCSP 82 (170)
Q Consensus 56 gd~vlv~k~~~-----~~~~~~rGDiV~f~~p 82 (170)
|-++++++..- ....++.||.|+|.+.
T Consensus 66 Gii~lINd~DWEllekedy~ledgD~ivfiST 97 (101)
T KOG4146|consen 66 GIIVLINDMDWELLEKEDYPLEDGDHIVFIST 97 (101)
T ss_pred cEEEEEeccchhhhcccccCcccCCEEEEEEe
Confidence 66777776441 1246899999999763
No 71
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=24.46 E-value=1.6e+02 Score=22.23 Aligned_cols=56 Identities=7% Similarity=-0.037 Sum_probs=28.4
Q ss_pred CCccceEEEEecCCCCCCceEEEEEEeCCCeEeccCCCCeEEccCCeEEEecCCCCCCCCCCccccccCCCE
Q 030863 70 KFSHGDVIVFCSPSNHKEKHVKRIIGLPGDWIGTPMTNDVVKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLV 141 (170)
Q Consensus 70 ~~~rGDiV~f~~p~~~~~~~vKRVvg~~GD~v~~~~~~~~~~vp~g~~~v~gDn~~~S~DSR~~G~V~~~~I 141 (170)
.+++||.|.+..-.+.+.. ..|+.+-- ..+.++|.|=|......--...||+.+++
T Consensus 46 ~IkkGD~V~Vi~Gk~KGk~--GkV~~V~~--------------k~~~ViVEgvn~~Kk~gk~~e~PIh~SNV 101 (143)
T PTZ00194 46 PVRKDDEVMVVRGHHKGRE--GKVTAVYR--------------KKWVIHIEKITREKANGEPVQIGIHPSNV 101 (143)
T ss_pred eeecCCEEEEecCCCCCCc--eEEEEEEc--------------CCCEEEEeCeEEEecCCCEeecCcCchhe
Confidence 5788888887765443321 33333211 13456666666532222223456666654
No 72
>PF10030 DUF2272: Uncharacterized protein conserved in bacteria (DUF2272); InterPro: IPR019262 This is a domain of unknown function found in proteins of unknown function.
Probab=23.87 E-value=2.1e+02 Score=22.40 Aligned_cols=15 Identities=33% Similarity=0.510 Sum_probs=9.7
Q ss_pred CCCccceEEEEecCC
Q 030863 69 YKFSHGDVIVFCSPS 83 (170)
Q Consensus 69 ~~~~rGDiV~f~~p~ 83 (170)
..|+.||+|.+....
T Consensus 92 y~P~~GDlIc~~R~~ 106 (183)
T PF10030_consen 92 YKPRPGDLICYDRGR 106 (183)
T ss_pred CCCCCCCEEEecCCC
Confidence 356777777776543
No 73
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=23.86 E-value=1.2e+02 Score=21.65 Aligned_cols=27 Identities=15% Similarity=0.381 Sum_probs=18.5
Q ss_pred CCCccceEEEEecCCCCCCceEEEEEEe
Q 030863 69 YKFSHGDVIVFCSPSNHKEKHVKRIIGL 96 (170)
Q Consensus 69 ~~~~rGDiV~f~~p~~~~~~~vKRVvg~ 96 (170)
+.++.||.++|..=.+ ++.+.-+|+.+
T Consensus 30 ~~ikvGD~I~f~~~~~-~~~l~v~V~~i 56 (109)
T cd06555 30 QQIKVGDKILFNDLDT-GQQLLVKVVDI 56 (109)
T ss_pred hcCCCCCEEEEEEcCC-CcEEEEEEEEE
Confidence 4799999999976433 44555566554
No 74
>cd06836 PLPDE_III_ODC_DapDC_like_1 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Uncharacterized Proteins with similarity to Ornithine and Diaminopimelate Decarboxylases. This subfamily contains uncharacterized proteins with similarity to ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Proteins in this subfamily may function as PLP-dependent decarbo
Probab=23.70 E-value=84 Score=26.99 Aligned_cols=24 Identities=21% Similarity=0.321 Sum_probs=15.3
Q ss_pred CcEEEEEccccccCCCccceEEEEecC
Q 030863 56 DDHVLMEKFCLQKYKFSHGDVIVFCSP 82 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~rGDiV~f~~p 82 (170)
+|.+.-+. .. .+++.||+++|..-
T Consensus 332 ~D~l~~~~-~l--p~l~~GD~l~~~~~ 355 (379)
T cd06836 332 GDVLAKER-AL--PPLEPGDYVAVHDT 355 (379)
T ss_pred CCEEeecc-cC--CCCCCCCEEEEeCC
Confidence 67655442 22 36888888888753
No 75
>cd04370 BAH BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.
Probab=23.64 E-value=1.1e+02 Score=20.89 Aligned_cols=72 Identities=13% Similarity=0.134 Sum_probs=39.8
Q ss_pred CCccceEEEEecCCC--CCCceEEEEEEeCCC-----eEecc-----CC---CCeEEccCCeEEEecCCCCCCCCCCccc
Q 030863 70 KFSHGDVIVFCSPSN--HKEKHVKRIIGLPGD-----WIGTP-----MT---NDVVKVPNGHCWVEGDNPSSSLDSRSFG 134 (170)
Q Consensus 70 ~~~rGDiV~f~~p~~--~~~~~vKRVvg~~GD-----~v~~~-----~~---~~~~~vp~g~~~v~gDn~~~S~DSR~~G 134 (170)
.++.||.|.+..+.. +....+.||..+-.+ .+.+. .. .......++++|...+. -
T Consensus 3 ~y~vgd~V~v~~~~~~~~~~~~i~~I~~i~~~~~~~~~~~v~wf~rp~e~~~~~~~~~~~~Elf~s~~~----------~ 72 (123)
T cd04370 3 TYEVGDSVYVEPDDSIKSDPPYIARIEELWEDTNGSKQVKVRWFYRPEETPKGLSPFALRRELFLSDHL----------D 72 (123)
T ss_pred EEecCCEEEEecCCcCCCCCCEEEEEeeeeECCCCCEEEEEEEEEchhHhccccccccccceeEEecCc----------c
Confidence 456788888876543 355677777765443 22221 00 00012334555554322 2
Q ss_pred cccCCCEeEEEEEEEeC
Q 030863 135 PIPLGLVKGRVTHILWP 151 (170)
Q Consensus 135 ~V~~~~I~Gkv~~~~~P 151 (170)
-++.+.|.||+.-...+
T Consensus 73 ~i~v~~I~gkc~V~~~~ 89 (123)
T cd04370 73 EIPVESIIGKCKVLFVS 89 (123)
T ss_pred ccCHHHhccccEEEech
Confidence 58889999999766654
No 76
>PF05382 Amidase_5: Bacteriophage peptidoglycan hydrolase ; InterPro: IPR008044 This entry is represented by Bacteriophage SFi21, lysin (Cell wall hydrolase; 3.5.1.28 from EC). At least one of proteins in this entry, the Pal protein from the pneumococcal bacteriophage Dp-1 (O03979 from SWISSPROT) has been shown to be an N-acetylmuramoyl-L-alanine amidase []. According to the known modular structure of this and other peptidoglycan hydrolases from the pneumococcal system, the active site should reside within this domain while a C-terminal domain binds to the choline residues of the cell wall teichoic acids [, ].
Probab=22.82 E-value=1.2e+02 Score=22.86 Aligned_cols=39 Identities=5% Similarity=0.204 Sum_probs=25.7
Q ss_pred EEcCCCcccccCCCCCCCCCCCCCcEEEEEccccccCCCccceEEEEecCC
Q 030863 33 PVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPS 83 (170)
Q Consensus 33 ~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~rGDiV~f~~p~ 83 (170)
...+++|...|... | +..+..-. ..++++|||++.....
T Consensus 50 ~~nT~tl~~~L~~~---------G-~~~I~~~~--~~~~q~GDI~I~g~~g 88 (145)
T PF05382_consen 50 AGNTETLHDWLKKN---------G-FKKISENV--DWNLQRGDIFIWGRRG 88 (145)
T ss_pred ccCHHHHHHHHhhC---------C-cEEeccCC--cccccCCCEEEEcCCC
Confidence 45677888877772 3 55554331 1378999999986653
No 77
>cd06840 PLPDE_III_Bif_AspK_DapDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bifunctional Aspartate Kinase/Diaminopimelate Decarboxylase. Bifunctional aspartate kinase/diaminopimelate decarboxylase (AspK/DapDC, EC 4.1.1.20/EC 2.7.2.4) typically exists in bacteria. These proteins contain an N-terminal AspK region and a C-terminal DapDC region, which contains a PLP-binding TIM-barrel domain followed by beta-sandwich domain, characteristic of fold type III PLP-dependent enzymes. Members of this subfamily have not been fully characterized. Based on their sequence, these proteins may catalyze both reactions catalyzed by AspK and DapDC. AspK catalyzes the phosphorylation of L-aspartate to produce 4-phospho-L-aspartate while DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine.
Probab=22.17 E-value=93 Score=26.62 Aligned_cols=23 Identities=22% Similarity=0.346 Sum_probs=14.1
Q ss_pred CcEEEEEccccccCCCccceEEEEec
Q 030863 56 DDHVLMEKFCLQKYKFSHGDVIVFCS 81 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~rGDiV~f~~ 81 (170)
+|++--+... .++++||+++|..
T Consensus 323 ~D~l~~~~~l---p~l~~GD~l~~~~ 345 (368)
T cd06840 323 GDVLGRDRLL---PETEEGDVILIAN 345 (368)
T ss_pred CCEEeecccC---CCCCCCCEEEEec
Confidence 6655443321 3578888888875
No 78
>PTZ00054 60S ribosomal protein L23; Provisional
Probab=22.17 E-value=2.2e+02 Score=21.32 Aligned_cols=40 Identities=8% Similarity=0.028 Sum_probs=24.9
Q ss_pred EEccCCeEEEecCCCCCCCCCCccccccCCCEeEEEEEEEeCC
Q 030863 110 VKVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPP 152 (170)
Q Consensus 110 ~~vp~g~~~v~gDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~P~ 152 (170)
+.--+|.+-++.++ .+-.-+|-||||+.+. .+-+.++-.+
T Consensus 95 i~F~dNA~VLin~~-~~p~GTRI~GpV~rEl--~~~~~KI~SL 134 (139)
T PTZ00054 95 IYFEDNAGVIVNPK-GEMKGSAITGPVAKEC--ADLWPKISSA 134 (139)
T ss_pred EEeCCcEEEEECCC-CCEeeeEEeCchhHHH--HhCccHhhcc
Confidence 34445555555554 3677889999999887 3334444433
No 79
>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=21.90 E-value=89 Score=21.03 Aligned_cols=10 Identities=20% Similarity=0.504 Sum_probs=7.1
Q ss_pred CccceEEEEe
Q 030863 71 FSHGDVIVFC 80 (170)
Q Consensus 71 ~~rGDiV~f~ 80 (170)
+++||+|+..
T Consensus 39 IkrGd~VlV~ 48 (78)
T cd05792 39 IKRGDFVLVE 48 (78)
T ss_pred EEeCCEEEEE
Confidence 5777777775
No 80
>CHL00057 rpl14 ribosomal protein L14
Probab=21.72 E-value=3.3e+02 Score=19.89 Aligned_cols=41 Identities=17% Similarity=0.259 Sum_probs=26.0
Q ss_pred EccCCeEEEecCCCCCCCCCCccccccCCCEeEEEEEEEeCCC
Q 030863 111 KVPNGHCWVEGDNPSSSLDSRSFGPIPLGLVKGRVTHILWPPQ 153 (170)
Q Consensus 111 ~vp~g~~~v~gDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~P~~ 153 (170)
.--++.+-++.++ .+-.-+|-+|||+.+. ..+-+.++.++.
T Consensus 78 ~F~~Na~VLin~~-~~p~GTrI~Gpv~~el-r~k~~~Ki~sla 118 (122)
T CHL00057 78 RFDDNAAVVIDQE-GNPKGTRVFGPIAREL-REKNFTKIVSLA 118 (122)
T ss_pred EcCCceEEEECCC-CCEeEeEEEccchHHH-hhcCCeEEEecc
Confidence 3445666666665 3778899999999765 224445555443
No 81
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=21.35 E-value=1.1e+02 Score=21.28 Aligned_cols=26 Identities=31% Similarity=0.562 Sum_probs=18.6
Q ss_pred CcEEEEEccccc-----cCCCccceEEEEec
Q 030863 56 DDHVLMEKFCLQ-----KYKFSHGDVIVFCS 81 (170)
Q Consensus 56 gd~vlv~k~~~~-----~~~~~rGDiV~f~~ 81 (170)
|-.++++...-. ...++.||+|+|.+
T Consensus 61 GiI~LINd~DWeLleke~y~ledgDiIvfis 91 (96)
T COG5131 61 GIICLINDMDWELLEKERYPLEDGDIIVFIS 91 (96)
T ss_pred cEEEEEcCccHhhhhcccccCCCCCEEEEEe
Confidence 778888765411 24678999999975
No 82
>PRK05467 Fe(II)-dependent oxygenase superfamily protein; Provisional
Probab=21.16 E-value=1.4e+02 Score=24.18 Aligned_cols=42 Identities=17% Similarity=0.405 Sum_probs=26.1
Q ss_pred CcEEEEEccccccCCCccceEEEEecCCCCCCceEEEEEE-eCCCeEec
Q 030863 56 DDHVLMEKFCLQKYKFSHGDVIVFCSPSNHKEKHVKRIIG-LPGDWIGT 103 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~rGDiV~f~~p~~~~~~~vKRVvg-~~GD~v~~ 103 (170)
|+.++-+......-+++.||+|+|.+. .+|+|.- ..|.++.+
T Consensus 130 GEl~~~~~~g~~~Vkp~aG~~vlfps~------~lH~v~pVt~G~R~~~ 172 (226)
T PRK05467 130 GELVIEDTYGEHRVKLPAGDLVLYPST------SLHRVTPVTRGVRVAS 172 (226)
T ss_pred CceEEecCCCcEEEecCCCeEEEECCC------CceeeeeccCccEEEE
Confidence 676665432222236789999999752 5677776 55665544
No 83
>TIGR03099 dCO2ase_PEP1 pyridoxal-dependent decarboxylase, exosortase system type 1 associated. The sequences in this family contain the pyridoxal binding domain (pfam02784) and C-terminal sheet domain (pfam00278) of a family of Pyridoxal-dependent decarboxylases. Characterized enzymes in this family decarboxylate substrates such as ornithine, diaminopimelate and arginine. The genes of the family modeled here, with the exception of those observed in certain Burkholderia species, are all found in the context of exopolysaccharide biosynthesis loci containing the exosortase/PEP-CTERM protein sorting system. More specifically, these are characteristic of the type 1 exosortase system represented by the Genome Property GenProp0652. The substrate of these enzymes may be a precursor of the carrier or linker which is hypothesized to release the PEP-CTERM protein from the exosortase enzyme. These enzymes are apparently most closely related to the diaminopimelate decarboxylase modeled by TIGR01048
Probab=21.06 E-value=99 Score=26.54 Aligned_cols=24 Identities=21% Similarity=0.131 Sum_probs=15.2
Q ss_pred CcEEEEEccccccCCCccceEEEEecC
Q 030863 56 DDHVLMEKFCLQKYKFSHGDVIVFCSP 82 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~rGDiV~f~~p 82 (170)
+|++.-+ ... .+++.||+++|..-
T Consensus 352 ~D~~~~~-~~l--p~~~~GD~l~~~~~ 375 (398)
T TIGR03099 352 LDLLAEK-GTL--PVAEPGDLVVIFQS 375 (398)
T ss_pred CCEEeec-CcC--CCCCCCCEEEEcCC
Confidence 7765443 222 36888888888763
No 84
>cd06839 PLPDE_III_Btrk_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Btrk Decarboxylase. This subfamily is composed of Bacillus circulans BtrK decarboxylase and similar proteins. These proteins are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases, eukaryotic ornithine decarboxylases and diaminopimelate decarboxylases. BtrK is presumed to function as a PLP-dependent decarboxylase involved in the biosynthesis of the aminoglycoside antibiotic butirosin. Homodimer formation and the presence of the PLP cofactor may be required for catalytic activity.
Probab=20.67 E-value=1.1e+02 Score=26.01 Aligned_cols=24 Identities=13% Similarity=0.019 Sum_probs=15.8
Q ss_pred CcEEEEEccccccCCCccceEEEEecC
Q 030863 56 DDHVLMEKFCLQKYKFSHGDVIVFCSP 82 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~rGDiV~f~~p 82 (170)
+|++.-+... .+++.||+++|.+-
T Consensus 336 ~D~~~~~~~l---p~l~~GD~l~~~~~ 359 (382)
T cd06839 336 LDLLGRNVEL---PPLEPGDLVAVLQS 359 (382)
T ss_pred CCEEeecccC---CCCCCCCEEEEecC
Confidence 7777644322 36788888888753
No 85
>COG4929 Uncharacterized membrane-anchored protein [Function unknown]
Probab=20.67 E-value=1.4e+02 Score=23.67 Aligned_cols=26 Identities=8% Similarity=0.231 Sum_probs=13.1
Q ss_pred CcEEEEEccccccCCCccceEEEEec
Q 030863 56 DDHVLMEKFCLQKYKFSHGDVIVFCS 81 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~rGDiV~f~~ 81 (170)
|+.++.....-.-+++=+||.+....
T Consensus 35 G~~IiLqtaPVDPRslmrGDYmtLnY 60 (190)
T COG4929 35 GREIILQTAPVDPRSLMRGDYMTLNY 60 (190)
T ss_pred CCEEEEEeCCCChHHhhccceEEeee
Confidence 55555543322223556677666553
No 86
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=20.58 E-value=1.3e+02 Score=21.78 Aligned_cols=25 Identities=24% Similarity=0.331 Sum_probs=18.8
Q ss_pred CCCccceEEEEecCCCCCCceEEEEEEe
Q 030863 69 YKFSHGDVIVFCSPSNHKEKHVKRIIGL 96 (170)
Q Consensus 69 ~~~~rGDiV~f~~p~~~~~~~vKRVvg~ 96 (170)
..+++||+|.+.++ .....-||.++
T Consensus 138 ~~l~pGDvi~l~~~---~~~~~~RI~~i 162 (164)
T PF13550_consen 138 LALEPGDVIALSDD---GRDMRFRITEI 162 (164)
T ss_pred ccCCCCCEEEEEeC---CCceEEEEEEE
Confidence 46899999999887 44567777765
No 87
>cd03695 CysN_NodQ_II CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which sho
Probab=20.55 E-value=1.9e+02 Score=18.98 Aligned_cols=33 Identities=27% Similarity=0.274 Sum_probs=22.3
Q ss_pred CCCccceEEEEecCCCCCCceEEEEE--------EeCCCeEec
Q 030863 69 YKFSHGDVIVFCSPSNHKEKHVKRII--------GLPGDWIGT 103 (170)
Q Consensus 69 ~~~~rGDiV~f~~p~~~~~~~vKRVv--------g~~GD~v~~ 103 (170)
..++.||-|.+.+ .+ ...-+|.+. |.+||.|.+
T Consensus 25 G~v~~Gd~v~~~P-~~-~~~~V~si~~~~~~~~~a~aGd~v~l 65 (81)
T cd03695 25 GSIRVGDEVVVLP-SG-KTSRVKSIETFDGELDEAGAGESVTL 65 (81)
T ss_pred ceEECCCEEEEcC-CC-CeEEEEEEEECCcEeCEEcCCCEEEE
Confidence 4788999888864 32 345667766 677777655
No 88
>KOG0557 consensus Dihydrolipoamide acetyltransferase [Energy production and conversion]
Probab=20.32 E-value=1.1e+02 Score=27.59 Aligned_cols=55 Identities=22% Similarity=0.151 Sum_probs=37.1
Q ss_pred EEEEcCCCcccccCCCCCCCCCCCCCcEEEEEccccccCCCccceEEEEecCC--------CCCCceEEEEEEeC
Q 030863 31 IVPVRGSSMSPTFNPTTDSFMGSLSDDHVLMEKFCLQKYKFSHGDVIVFCSPS--------NHKEKHVKRIIGLP 97 (170)
Q Consensus 31 ~~~v~~~SM~Ptl~~~~~~~~~~~~gd~vlv~k~~~~~~~~~rGDiV~f~~p~--------~~~~~~vKRVvg~~ 97 (170)
...+.=++|+||+.. |.++-..+..- .++..||++.--.-. ..+.++-|-++...
T Consensus 38 h~~i~MPALSPTMee----------GnIvsW~kKeG--dkls~GDvl~EVETDKAtmd~E~~ddGyLAKILi~EG 100 (470)
T KOG0557|consen 38 HKTFSMPALSPTMEE----------GNIVSWKKKEG--DKLSAGDVLLEVETDKATMDVEAQDDGYLAKILIEEG 100 (470)
T ss_pred ceEeecCCCCccccC----------CceeeEeeccC--CccCCCceEEEEecccceeeeeeccCCeeeeeeeccC
Confidence 445667899999999 88877665442 479999998653221 12456667666544
No 89
>cd06843 PLPDE_III_PvsE_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme PvsE. This subfamily is composed of PvsE from Vibrio parahaemolyticus and similar proteins. PvsE is a vibrioferrin biosynthesis protein which is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. It has been suggested that PvsE may be involved in the biosynthesis of the polycarboxylate siderophore vibrioferrin. It may catalyze the decarboxylation of serine to yield ethanolamine. PvsE may require homodimer formation and the presence of the PLP cofactor for activity.
Probab=20.29 E-value=1.1e+02 Score=26.12 Aligned_cols=24 Identities=21% Similarity=0.306 Sum_probs=16.1
Q ss_pred CcEEEEEccccccCCCccceEEEEecC
Q 030863 56 DDHVLMEKFCLQKYKFSHGDVIVFCSP 82 (170)
Q Consensus 56 gd~vlv~k~~~~~~~~~rGDiV~f~~p 82 (170)
+|++--+... .+++.||+++|..-
T Consensus 331 ~D~l~~~~~l---p~~~~GD~l~i~~~ 354 (377)
T cd06843 331 KDVLARDVPV---DRLRAGDLVVFPLA 354 (377)
T ss_pred CCEEeecccc---CCCCCCCEEEEcCC
Confidence 7866543322 36899999998763
Done!