Query 024476
Match_columns 267
No_of_seqs 205 out of 350
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 04:52:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024476.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024476hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1816 Ubiquitin fusion-degra 100.0 9.5E-83 2.1E-87 586.0 20.9 242 1-267 59-305 (308)
2 COG5140 UFD1 Ubiquitin fusion- 100.0 1.3E-63 2.8E-68 453.1 17.0 236 1-266 67-310 (331)
3 PF03152 UFD1: Ubiquitin fusio 100.0 3.8E-58 8.1E-63 399.9 13.1 130 1-130 47-176 (176)
4 PLN03086 PRLI-interacting fact 100.0 7.1E-51 1.5E-55 404.0 17.5 135 1-135 115-263 (567)
5 PF02933 CDC48_2: Cell divisio 96.1 0.028 6.1E-07 41.0 6.9 41 86-126 17-58 (64)
6 KOG0735 AAA+-type ATPase [Post 95.0 0.16 3.4E-06 54.0 10.0 106 24-130 58-167 (952)
7 TIGR01243 CDC48 AAA family ATP 94.5 0.23 4.9E-06 51.7 9.7 104 12-117 44-150 (733)
8 PF09262 PEX-1N: Peroxisome bi 93.1 0.095 2.1E-06 40.9 3.1 74 56-129 1-80 (80)
9 TIGR01439 lp_hng_hel_AbrB loop 87.5 2.7 5.8E-05 27.5 5.8 39 23-64 4-42 (43)
10 PF02359 CDC48_N: Cell divisio 85.7 1.1 2.3E-05 34.6 3.5 69 24-97 14-82 (87)
11 PF04014 Antitoxin-MazE: Antid 84.6 2.1 4.6E-05 29.4 4.3 39 24-65 5-43 (47)
12 PF07497 Rho_RNA_bind: Rho ter 80.1 0.88 1.9E-05 35.5 1.1 26 25-50 28-53 (78)
13 cd04459 Rho_CSD Rho_CSD: Rho p 78.7 2.2 4.8E-05 32.4 2.9 27 23-49 24-50 (68)
14 TIGR02609 doc_partner putative 77.1 4.8 0.0001 30.5 4.4 54 26-85 10-65 (74)
15 cd02786 MopB_CT_3 The MopB_CT_ 76.1 6 0.00013 31.0 4.9 30 23-52 28-57 (116)
16 PRK09521 exosome complex RNA-b 75.6 11 0.00025 32.9 6.9 95 11-108 33-141 (189)
17 PRK14132 riboflavin kinase; Pr 73.3 3.4 7.3E-05 35.1 2.9 31 12-49 94-125 (126)
18 cd02787 MopB_CT_ydeP The MopB_ 73.2 6.3 0.00014 31.0 4.3 29 24-52 29-57 (112)
19 cd02790 MopB_CT_Formate-Dh_H F 69.5 6.4 0.00014 30.6 3.6 29 23-51 32-60 (116)
20 PRK09798 antitoxin MazE; Provi 69.1 11 0.00025 29.3 4.8 49 27-85 14-62 (82)
21 cd00508 MopB_CT_Fdh-Nap-like T 68.7 8.7 0.00019 29.9 4.2 27 24-50 33-59 (120)
22 cd02776 MopB_CT_Nitrate-R-NarG 68.6 9.1 0.0002 32.1 4.5 48 3-50 2-55 (141)
23 cd02792 MopB_CT_Formate-Dh-Na- 67.4 5.8 0.00013 31.2 3.0 28 23-50 32-59 (122)
24 PRK09974 putative regulator Pr 66.8 16 0.00035 30.4 5.5 59 23-84 15-75 (111)
25 cd02789 MopB_CT_FmdC-FwdD The 65.7 7.4 0.00016 30.9 3.3 29 23-51 28-56 (106)
26 PF01982 CTP-dep_RFKase: Domai 65.3 7.9 0.00017 32.6 3.4 17 33-49 104-120 (121)
27 PRK11347 antitoxin ChpS; Provi 64.8 20 0.00043 28.0 5.4 47 27-85 13-59 (83)
28 cd02791 MopB_CT_Nitrate-R-NapA 63.0 10 0.00022 29.8 3.6 28 24-51 33-60 (122)
29 PF13550 Phage-tail_3: Putativ 62.9 9 0.0002 31.3 3.4 27 85-111 137-163 (164)
30 COG2002 AbrB Regulators of sta 62.8 14 0.0003 28.8 4.2 42 23-66 11-52 (89)
31 cd02788 MopB_CT_NDH-1_NuoG2-N7 62.1 13 0.00029 28.7 4.0 35 17-51 20-54 (96)
32 cd05705 S1_Rrp5_repeat_hs14 S1 59.1 18 0.00039 26.9 4.2 66 40-114 1-68 (74)
33 PRK15095 FKBP-type peptidyl-pr 58.9 48 0.0011 28.4 7.3 94 17-132 33-130 (156)
34 cd02778 MopB_CT_Thiosulfate-R- 57.9 24 0.00051 27.8 4.9 28 23-50 27-54 (123)
35 cd02779 MopB_CT_Arsenite-Ox Th 57.3 26 0.00056 27.7 5.0 29 23-51 30-58 (115)
36 PF02359 CDC48_N: Cell divisio 57.0 41 0.00088 25.7 5.9 41 11-51 41-84 (87)
37 PRK08577 hypothetical protein; 56.8 16 0.00035 30.2 3.9 44 23-68 10-53 (136)
38 cd02775 MopB_CT Molybdopterin- 56.6 16 0.00035 27.4 3.6 29 23-51 20-48 (101)
39 cd02785 MopB_CT_4 The MopB_CT_ 56.4 17 0.00037 29.0 3.9 28 24-51 30-57 (124)
40 cd02781 MopB_CT_Acetylene-hydr 55.9 16 0.00034 29.2 3.6 29 24-52 31-59 (130)
41 cd02793 MopB_CT_DMSOR-BSOR-TMA 55.9 28 0.00061 28.1 5.1 29 23-51 30-58 (129)
42 TIGR02851 spore_V_T stage V sp 55.7 20 0.00044 31.6 4.5 46 17-65 4-49 (180)
43 COG1153 FwdD Formylmethanofura 55.6 11 0.00024 32.1 2.7 29 22-50 27-55 (128)
44 cd02777 MopB_CT_DMSOR-like The 55.4 16 0.00035 29.3 3.6 26 25-50 33-58 (127)
45 PRK10737 FKBP-type peptidyl-pr 55.2 44 0.00095 30.1 6.7 37 88-132 90-126 (196)
46 COG1188 Ribosome-associated he 55.1 18 0.0004 29.6 3.8 26 86-111 47-72 (100)
47 PF01568 Molydop_binding: Moly 54.8 18 0.00038 27.9 3.6 27 24-50 27-54 (110)
48 PF01191 RNA_pol_Rpb5_C: RNA p 53.0 29 0.00064 26.8 4.5 35 28-62 37-71 (74)
49 COG2336 MazE Growth regulator 52.9 16 0.00034 29.0 3.0 35 27-64 13-47 (82)
50 cd02782 MopB_CT_1 The MopB_CT_ 50.7 21 0.00046 28.5 3.6 29 23-51 30-58 (129)
51 cd02794 MopB_CT_DmsA-EC The Mo 49.7 22 0.00048 28.2 3.5 28 25-52 29-56 (121)
52 PRK09570 rpoH DNA-directed RNA 48.8 26 0.00055 27.6 3.6 31 32-62 44-74 (79)
53 COG1935 Uncharacterized conser 47.9 20 0.00044 30.3 3.1 26 33-58 32-60 (122)
54 PF12148 DUF3590: Protein of u 47.8 12 0.00026 29.8 1.7 20 80-99 58-77 (85)
55 cd02783 MopB_CT_2 The MopB_CT_ 47.6 24 0.00052 29.9 3.6 29 23-51 29-57 (156)
56 smart00553 SEP Domain present 47.4 11 0.00024 30.3 1.4 15 162-176 73-87 (93)
57 PF03459 TOBE: TOBE domain; I 46.0 24 0.00052 24.8 2.9 23 28-50 35-57 (64)
58 cd06166 Sortase_D_5 Sortase D 44.2 36 0.00078 27.7 4.0 31 81-111 58-88 (126)
59 cd02780 MopB_CT_Tetrathionate_ 42.9 37 0.0008 27.9 3.9 28 23-50 27-54 (143)
60 cd05829 Sortase_E Sortase E (S 42.8 34 0.00074 28.7 3.8 27 84-110 69-96 (144)
61 cd04456 S1_IF1A_like S1_IF1A_l 42.6 14 0.00031 28.5 1.4 25 25-49 24-48 (78)
62 TIGR02227 sigpep_I_bact signal 41.9 1.3E+02 0.0028 25.5 7.3 40 86-125 50-91 (163)
63 cd05706 S1_Rrp5_repeat_sc10 S1 41.1 56 0.0012 23.4 4.3 56 40-97 1-57 (73)
64 cd05704 S1_Rrp5_repeat_hs13 S1 37.2 49 0.0011 24.3 3.4 56 40-98 1-59 (72)
65 PRK08059 general stress protei 36.7 81 0.0017 25.7 5.0 59 34-97 1-61 (123)
66 PF00717 Peptidase_S24: Peptid 36.4 1.5E+02 0.0032 20.7 7.2 33 87-119 24-57 (70)
67 PRK05807 hypothetical protein; 35.9 1.3E+02 0.0029 25.2 6.3 55 39-97 2-58 (136)
68 cd05828 Sortase_D_4 Sortase D 35.3 62 0.0014 26.3 4.1 31 81-111 55-85 (127)
69 cd05830 Sortase_D_5 Sortase D 35.2 60 0.0013 26.8 4.0 30 82-111 60-89 (137)
70 TIGR01076 sortase_fam LPXTG-si 34.8 56 0.0012 27.0 3.8 28 83-110 59-86 (136)
71 cd02784 MopB_CT_PHLH The MopB_ 33.4 63 0.0014 27.2 3.9 27 25-51 37-63 (137)
72 COG0539 RpsA Ribosomal protein 32.6 4.3E+02 0.0094 27.6 10.4 94 11-110 239-349 (541)
73 COG0243 BisC Anaerobic dehydro 31.9 71 0.0015 33.5 4.9 29 23-51 668-696 (765)
74 cd06165 Sortase_A_1 Sortase A 31.4 73 0.0016 25.7 3.9 28 84-111 60-87 (127)
75 TIGR01243 CDC48 AAA family ATP 31.4 1E+02 0.0022 32.4 5.9 71 24-98 15-85 (733)
76 cd00004 Sortase Sortases are c 31.3 77 0.0017 25.5 4.0 26 86-111 63-88 (128)
77 TIGR03711 acc_sec_asp3 accesso 31.3 1.4E+02 0.0031 25.6 5.8 20 42-61 23-42 (135)
78 PRK09376 rho transcription ter 29.7 87 0.0019 31.6 4.8 38 12-49 48-100 (416)
79 cd04453 S1_RNase_E S1_RNase_E: 29.0 90 0.0019 24.1 3.9 59 40-98 5-67 (88)
80 PF10636 hemP: Hemin uptake pr 29.0 1.1E+02 0.0024 21.0 3.8 22 88-109 9-30 (38)
81 PRK07899 rpsA 30S ribosomal pr 28.3 3.2E+02 0.0069 27.9 8.6 84 10-97 165-261 (486)
82 PF11717 Tudor-knot: RNA bindi 27.9 96 0.0021 21.9 3.6 27 88-114 1-28 (55)
83 PRK07252 hypothetical protein; 27.8 1.8E+02 0.0038 24.0 5.6 54 41-97 2-57 (120)
84 PF02362 B3: B3 DNA binding do 27.5 76 0.0016 23.9 3.2 73 25-103 13-90 (100)
85 COG0836 {ManC} Mannose-1-phosp 27.2 1.3E+02 0.0028 29.6 5.3 75 45-122 246-326 (333)
86 KOG2086 Protein tyrosine phosp 27.1 27 0.00059 34.7 0.8 16 159-174 252-267 (380)
87 PF11302 DUF3104: Protein of u 26.8 1.6E+02 0.0034 23.1 4.8 48 85-132 3-75 (75)
88 cd05696 S1_Rrp5_repeat_hs4 S1_ 26.0 2.1E+02 0.0047 20.7 5.3 42 53-97 14-56 (71)
89 TIGR00638 Mop molybdenum-pteri 25.8 1.1E+02 0.0024 21.5 3.6 22 29-50 38-59 (69)
90 PF01272 GreA_GreB: Transcript 25.4 1.2E+02 0.0026 22.6 3.9 24 88-111 53-76 (77)
91 PF11644 DUF3256: Protein of u 25.3 97 0.0021 28.1 3.9 51 72-122 41-95 (199)
92 TIGR03698 clan_AA_DTGF clan AA 25.2 2.1E+02 0.0046 22.7 5.5 40 3-45 4-46 (107)
93 PRK07217 replication factor A; 25.1 1.2E+02 0.0027 29.4 4.8 45 5-51 94-139 (311)
94 PRK13806 rpsA 30S ribosomal pr 25.1 4.4E+02 0.0096 26.6 8.9 92 11-113 341-440 (491)
95 PRK10183 hypothetical protein; 25.0 1E+02 0.0023 22.9 3.3 22 88-109 27-48 (56)
96 PRK12678 transcription termina 24.7 1.7E+02 0.0037 31.3 6.0 43 13-56 294-348 (672)
97 PRK10348 ribosome-associated h 24.4 1.2E+02 0.0025 26.0 4.0 25 87-111 48-72 (133)
98 TIGR02693 arsenite_ox_L arseni 24.4 89 0.0019 33.5 4.1 49 3-51 695-750 (806)
99 PF04203 Sortase: Sortase fami 24.3 1.3E+02 0.0028 23.8 4.1 24 88-111 61-85 (128)
100 PTZ00061 DNA-directed RNA poly 24.0 96 0.0021 28.5 3.6 31 32-62 172-202 (205)
101 PF00667 FAD_binding_1: FAD bi 24.0 91 0.002 27.6 3.5 68 4-73 18-107 (219)
102 COG0187 GyrB Type IIA topoisom 24.0 80 0.0017 33.5 3.5 46 54-99 165-210 (635)
103 PF01176 eIF-1a: Translation i 23.8 62 0.0013 23.7 2.0 24 27-50 29-52 (65)
104 TIGR01706 NAPA periplasmic nit 23.6 66 0.0014 34.4 2.9 48 3-51 716-771 (830)
105 KOG3184 60S ribosomal protein 23.3 48 0.001 30.9 1.6 47 53-99 103-159 (235)
106 cd03701 IF2_IF5B_II IF2_IF5B_I 23.3 1.1E+02 0.0023 24.1 3.4 34 85-118 24-64 (95)
107 PRK13532 nitrate reductase cat 22.7 82 0.0018 33.6 3.4 48 3-51 716-771 (830)
108 PRK08582 hypothetical protein; 22.3 3.2E+02 0.0069 23.0 6.3 56 39-97 2-59 (139)
109 TIGR03595 Obg_CgtA_exten Obg f 21.8 75 0.0016 23.8 2.1 16 36-51 50-65 (69)
110 PF12436 USP7_ICP0_bdg: ICP0-b 21.4 2.6E+02 0.0055 25.6 6.0 81 2-99 72-152 (249)
111 KOG0741 AAA+-type ATPase [Post 21.3 3.7E+02 0.008 28.8 7.5 73 39-111 73-156 (744)
112 TIGR00767 rho transcription te 21.3 1.8E+02 0.0038 29.4 5.2 36 13-48 49-99 (415)
113 PLN03111 DNA-directed RNA poly 20.6 1.2E+02 0.0027 27.7 3.7 31 32-62 173-203 (206)
114 cd05689 S1_RPS1_repeat_ec4 S1_ 20.2 1.5E+02 0.0034 21.0 3.5 56 41-97 2-58 (72)
No 1
>KOG1816 consensus Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=9.5e-83 Score=586.02 Aligned_cols=242 Identities=54% Similarity=0.915 Sum_probs=198.3
Q ss_pred CeEEEEeCCCCcEEEEEeeeeeeCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccCchHHHhh
Q 024476 1 MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILET 80 (267)
Q Consensus 1 MlF~l~N~~~~r~th~GVLEF~A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~~Fl~isnpKavLE~ 80 (267)
|||+|+|.+..|+||||||||+||||+||||+|||++|+|++||+|+|++++||+||||||||||.|||||+|||||||+
T Consensus 59 MlFkLtn~~~~r~THcGVLEF~AeEG~vyLP~WMmq~L~le~gdlv~i~~v~lpkgtyvKLqP~s~dFLDItNpKAvLE~ 138 (308)
T KOG1816|consen 59 MLFKLTNVDVDRVTHCGVLEFTAEEGRVYLPYWMMQNLLLEEGDLVRIRSVTLPKGTYVKLQPHSVDFLDITNPKAVLEN 138 (308)
T ss_pred eEEEEeccccceeeeeeEEEEEecCceEEeehHhhhhccCCCCCeEEEEEeeccccceeeeccCCCCccccCChHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccceecccCCEEEEEECCEEEEEEEEEecCCCeeEEEeCceeeeecCCCCCCCCCCcccccc-cchhhhhhhcccc--
Q 024476 81 TLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDFAPPLDYKEPEKPIASAS-SRATAKAEEASVE-- 157 (267)
Q Consensus 81 ~LRnystLT~Gd~I~I~yn~~~y~l~V~e~kP~~aVsIIeTDleVDf~pPldy~Epe~~~~~~~-~~~~~~~~~~~~~-- 157 (267)
+||||+|||+||+|+|+||++.|+|+|+|+||++|||||||||+|||+||+||+||+++.++.. .+..+...+..+.
T Consensus 139 ~LRn~acLT~gDvi~i~Yn~k~y~i~V~e~kPa~aVsIiEtD~~VDF~pP~gyke~~~~~~~~~~~k~~~~~v~~~ag~~ 218 (308)
T KOG1816|consen 139 ALRNYACLTTGDVILINYNEKTYELKVVETKPANAVSIIETDLNVDFDPPLGYKEPERQVAPAEKAKGEAEVVGSYAGYK 218 (308)
T ss_pred HHhhccccccCCEEEEecCCeEEEEEEEEecCCceeEEEEcceeecccCCcCccCcccccChhhcccccceeeccccccc
Confidence 9999999999999999999999999999999999999999999999999999999999855432 2211111110111
Q ss_pred --CCCcccceeeeccccCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCeEEEccCCCCCCCCCCC
Q 024476 158 --TEPKFSPFTGVARRLDGKPLTYQPPPVPSLGSKDKQPATSNGTGQPSAGSTSQNAARQSQGKLVFGSNASLHPKETQK 235 (267)
Q Consensus 158 --~~~~~~~F~G~G~rLdGK~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~g~L~Fg~~~~~~~~~~~~ 235 (267)
-++++.+|.|+|+|||||+...++.+.+ +.. + ......+...+++.|+|+||+|..+.++...
T Consensus 219 ~~~e~~~~~f~gsg~rLdgK~~~~e~~~~p--v~~--------~----~~~~~~~~~~d~~~G~l~F~~~~~~~~~~~~- 283 (308)
T KOG1816|consen 219 NVIENKVEPFTGSGRRLDGKKKVEEVSKHP--VKN--------G----DLIQRGVPNHDFKLGKLVFGRNVDPLKKESE- 283 (308)
T ss_pred cccccceeeeccccceecccccccccCCCc--ccC--------c----ccccCCCCccccCCceEEEecCCCccccccc-
Confidence 1678999999999999998865542221 110 1 1122344556999999999998633322111
Q ss_pred chhhhhhhccCccccCCCCcCCccccccccCC
Q 024476 236 PVAEKEIKQELPEKKEEPKFRPFTGKKYSLKG 267 (267)
Q Consensus 236 ~~~~~~~~~~~~~~~~~~~f~aF~G~g~SLr~ 267 (267)
+ ++....++|++|+|+||||||
T Consensus 284 ---------E-~~a~k~~~~~~F~G~~~slr~ 305 (308)
T KOG1816|consen 284 ---------E-KEAGKDSKFEAFSGAGYSLRK 305 (308)
T ss_pred ---------h-hhcccccceeEecCCceeccc
Confidence 1 122223899999999999996
No 2
>COG5140 UFD1 Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.3e-63 Score=453.10 Aligned_cols=236 Identities=36% Similarity=0.560 Sum_probs=191.7
Q ss_pred CeEEEEeCCCCcEEEEEeeeeeeCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccCchHHHhh
Q 024476 1 MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILET 80 (267)
Q Consensus 1 MlF~l~N~~~~r~th~GVLEF~A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~~Fl~isnpKavLE~ 80 (267)
|||+|+|.++.++||||||||+|+||.||||+|||++|.+++||+|+|+|.++|.|+||||+|||+|||||+|||||||+
T Consensus 67 mlF~~s~~~~~~~THgGVLEFiaEEGrVylP~WMm~tLs~epgdlv~~~~td~plG~fVKL~PqSVdFLdI~dpkavLEn 146 (331)
T COG5140 67 MLFEISHSDGIYRTHGGVLEFIAEEGRVYLPSWMMQTLSMEPGDLVVLRYTDFPLGKFVKLIPQSVDFLDIEDPKAVLEN 146 (331)
T ss_pred eEEEEecccceeEecccEEEEeecCCcEeehHHHHHhccCCCCcEEEEEeccccccceEEecccccceEeccChHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccceecccCCEEEEEECCEEEEEEEEEecCC---CeeEEEeCceeeeecCCCCCCCCCCccccc-c-c-chhhhh-h-
Q 024476 81 TLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPS---NAISIIETDCEVDFAPPLDYKEPEKPIASA-S-S-RATAKA-E- 152 (267)
Q Consensus 81 ~LRnystLT~Gd~I~I~yn~~~y~l~V~e~kP~---~aVsIIeTDleVDf~pPldy~Epe~~~~~~-~-~-~~~~~~-~- 152 (267)
+||||+|||+||+|.|.||++.|.|++++++|+ ++||||||||.|||+||+||+|+..+-+.. . . +.+... .
T Consensus 147 ~LRNfstLt~~D~iei~ynd~v~~Ik~~~v~pe~S~~~i~vveTDLvvDF~pPiGy~e~~qq~ke~n~~gvqgtm~t~I~ 226 (331)
T COG5140 147 CLRNFSTLTEGDEIEIQYNDEVGSIKFTVVHPEPSANAIYVVETDLVVDFLPPIGYKEKAQQDKERNSFGVQGTMATYIE 226 (331)
T ss_pred HHhhccccccCCEEEEEECCeeeEEEEEEeccCCCcceEEEEecceeeeccCCccccchhhhhhhhccccccceeEEEEe
Confidence 999999999999999999999999999999995 899999999999999999999984331111 0 0 101000 0
Q ss_pred hccccCCCcccceeeeccccCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCeEEEccCCCCCCCC
Q 024476 153 EASVETEPKFSPFTGVARRLDGKPLTYQPPPVPSLGSKDKQPATSNGTGQPSAGSTSQNAARQSQGKLVFGSNASLHPKE 232 (267)
Q Consensus 153 ~~~~~~~~~~~~F~G~G~rLdGK~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~g~L~Fg~~~~~~~~~ 232 (267)
-.......+-.--.|.|..|.||..+..+.... .+ ..-.+.|+++++|.|+||||+|.+.|+.+
T Consensus 227 y~~~~~~~~~~lmKg~G~~l~gk~~~~~pk~~i---------------~d-~~~~~~pa~l~lp~g~~ffg~p~~~p~~d 290 (331)
T COG5140 227 YIDSSHDVKPILMKGLGLYLYGKVDKAEPKQDI---------------KD-MKIDGEPAKLDLPEGQLFFGFPMVLPKED 290 (331)
T ss_pred eeccccccchhhhhcccceecccccccccccch---------------hh-hhccCCcccccccCcceEeccccccCccc
Confidence 011112233345669999999998765532211 11 11256899999999999999999999763
Q ss_pred CCCchhhhhhhccCccccCCCCcCCccccccccC
Q 024476 233 TQKPVAEKEIKQELPEKKEEPKFRPFTGKKYSLK 266 (267)
Q Consensus 233 ~~~~~~~~~~~~~~~~~~~~~~f~aF~G~g~SLr 266 (267)
+. . +..+.-+.|.|+|-|||
T Consensus 291 ee-------------s-~~~~~~~~fqg~g~slr 310 (331)
T COG5140 291 EE-------------S-AAKSSEQNFQGQGISLR 310 (331)
T ss_pred hh-------------h-ccCchhhccccCceeee
Confidence 32 1 11244466999999998
No 3
>PF03152 UFD1: Ubiquitin fusion degradation protein UFD1; InterPro: IPR004854 Post-translational ubiquitin-protein conjugates are recognised for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified []. This family includes UFD1, a 40kDa protein that is essential for vegetative cell viability []. The human UFD1 gene is expressed at high levels during embryogenesis, especially in the eyes and in the inner ear primordia and is thought to be important in the determination of ectoderm-derived structures, including neural crest cells. In addition, this gene is deleted in the CATCH-22 (cardiac defects, abnormal facies, thymic hypoplasia, cleft palate and hypocalcaemia with deletions on chromosome 22) syndrome. This clinical syndrome is associated with a variety of developmental defects, all characterised by microdeletions on 22q11.2. Two such developmental defects are the DiGeorge syndrome OMIM:188400, and the velo-cardio- facial syndrome OMIM:145410. Several of the abnormalities associated with these conditions are thought to be due to defective neural crest cell differentiation []. ; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 1ZC1_A 2YUJ_A.
Probab=100.00 E-value=3.8e-58 Score=399.95 Aligned_cols=130 Identities=68% Similarity=1.123 Sum_probs=112.5
Q ss_pred CeEEEEeCCCCcEEEEEeeeeeeCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccCchHHHhh
Q 024476 1 MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILET 80 (267)
Q Consensus 1 MlF~l~N~~~~r~th~GVLEF~A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~~Fl~isnpKavLE~ 80 (267)
|+|+|+|..++++||||||||+|+||+||||+|||++|++++||.|+|++++||||||||||||+.+|++|+|||||||+
T Consensus 47 ~~F~i~n~~~~~~th~GVlEFsA~eG~i~lP~wmm~~L~l~~g~~V~v~~~~LPkgt~vkLqP~~~~F~~i~n~KavLE~ 126 (176)
T PF03152_consen 47 MLFEISNPDNGKRTHCGVLEFSAEEGTIYLPPWMMQNLGLQEGDIVRVEYVSLPKGTFVKLQPQSSDFLDISNPKAVLER 126 (176)
T ss_dssp -EEEEEETTTTEEEEEEEEEE--CTTEEEE-CHHHHHHT--TTEEEEEEEEE----SEEEEEESCHHHHCSS-HHHHHHH
T ss_pred EEEEEecCCCCcEEEEEEEEeEcCCCeEEeCccHHhhcCCCCCCEEEEEEeECCCCCEEEEeECCCccccccchHHHHHh
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccceecccCCEEEEEECCEEEEEEEEEecCCCeeEEEeCceeeeecCC
Q 024476 81 TLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDFAPP 130 (267)
Q Consensus 81 ~LRnystLT~Gd~I~I~yn~~~y~l~V~e~kP~~aVsIIeTDleVDf~pP 130 (267)
+||||+|||+||+|.|+|+++.|+|+|+|++|++|||||||||+|||+||
T Consensus 127 ~Lr~ystLT~Gd~I~i~~~~~~y~l~V~e~kP~~aV~IidTDl~vDf~~P 176 (176)
T PF03152_consen 127 ALRNYSTLTKGDTISIEYNNKTYELDVVEVKPENAVSIIDTDLEVDFEPP 176 (176)
T ss_dssp HHCC-SEEETTSEEEEECTTEEEEEEEEEECSSSCEE-SSS-SEEEE---
T ss_pred hcccCceeecCCEEEEEeCCEEEEEEEEEEcCCCEEEEEeCceEEEecCC
Confidence 99999999999999999999999999999999999999999999999997
No 4
>PLN03086 PRLI-interacting factor K; Provisional
Probab=100.00 E-value=7.1e-51 Score=404.04 Aligned_cols=135 Identities=39% Similarity=0.656 Sum_probs=129.6
Q ss_pred CeEEEEeC-----------CCCcEEEEEeeeeeeCCCeEeccHHHHHHcCCCC---CCeEEEEEeecCCcceEEEeeCCc
Q 024476 1 MLFELRNN-----------AAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQE---GDIVRVKNVTLPKGTYVKLQPHTK 66 (267)
Q Consensus 1 MlF~l~N~-----------~~~r~th~GVLEF~A~EG~i~LP~Wmm~~L~l~~---gd~V~I~~~~LPkGt~vkLqP~s~ 66 (267)
|+|+|+|. ..+++||||||||+|+||.||||+|||++|++.+ |++|+|++++||+|||||||||+.
T Consensus 115 m~F~l~~~~~~~~~~~~~~~~~~~th~GVlEF~A~EG~v~lP~wm~~~L~~~~~~~~~~v~v~~~~Lpkgt~vklqP~~~ 194 (567)
T PLN03086 115 LYFRLSVVHQEGSGEMKDTDSQKTTHSGVLEFTAEEGSVGLPPHVWSNLFPSDPPDVPLVEVRYIWLPKGTYAKLQPDGV 194 (567)
T ss_pred eEEEEeccccccccccccccCCcEEEEEEEEEEcCCCeEEcCHHHHhhcCCCCCCCCCeEEEEEeecCCCCEEEEeeccC
Confidence 89999994 3579999999999999999999999999999874 899999999999999999999999
Q ss_pred CcCCccCchHHHhhccccceecccCCEEEEEECCEEEEEEEEEecCCCeeEEEeCceeeeecCCCCCCC
Q 024476 67 DFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDFAPPLDYKE 135 (267)
Q Consensus 67 ~Fl~isnpKavLE~~LRnystLT~Gd~I~I~yn~~~y~l~V~e~kP~~aVsIIeTDleVDf~pPldy~E 135 (267)
+|+||+|||||||++||||+|||+||+|.|+||++.|+|+|+|++|++|||||||||+|||+||.++.+
T Consensus 195 ~f~di~npKavLE~~Lr~~stLT~Gd~i~i~~~~~~y~~~V~ev~P~~aVsiieTDi~VDf~~p~~~~~ 263 (567)
T PLN03086 195 GFSDLPNHKAVLETALRQHATLSEDDVLVVNYGQLTYKLKVLELKPASSVSVLETDIEVDIVGPDSVSN 263 (567)
T ss_pred CcCCcccHHHHHHHHhhcCccccCCCEEEEecCCEEEEEEEEEEcCCCeeEEEeCceEEEeccCCcchh
Confidence 999999999999999999999999999999999999999999999999999999999999999999743
No 5
>PF02933 CDC48_2: Cell division protein 48 (CDC48), domain 2; InterPro: IPR004201 This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the C terminus. The VAT-N domain found in AAA ATPases (IPR003959 from INTERPRO) is a substrate 185-residue recognition domain [].; GO: 0005524 ATP binding; PDB: 1QDN_B 1QCS_A 1CR5_C 3QQ8_A 3HU2_A 3HU1_E 3HU3_A 3QWZ_A 3TIW_B 3QQ7_A ....
Probab=96.12 E-value=0.028 Score=41.02 Aligned_cols=41 Identities=27% Similarity=0.505 Sum_probs=33.0
Q ss_pred eecccCCEEEEEECCEEEEEEEEEecCCCeeEEEe-Cceeee
Q 024476 86 SCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE-TDCEVD 126 (267)
Q Consensus 86 stLT~Gd~I~I~yn~~~y~l~V~e~kP~~aVsIIe-TDleVD 126 (267)
--|++||+|.|.+.++.+.|.|.+++|.+++-|-+ |.+++-
T Consensus 17 ~pv~~Gd~i~~~~~~~~~~~~V~~~~P~~~v~it~~T~i~i~ 58 (64)
T PF02933_consen 17 RPVTKGDTIVFPFFGQALPFKVVSTEPSGPVIITEDTEIEIK 58 (64)
T ss_dssp EEEETT-EEEEEETTEEEEEEEEEECSSSEEEEETTSEEEES
T ss_pred CCccCCCEEEEEeCCcEEEEEEEEEEcCCCEEECCCcEEEEc
Confidence 45999999999999999999999999998665553 555554
No 6
>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=95.00 E-value=0.16 Score=54.05 Aligned_cols=106 Identities=22% Similarity=0.211 Sum_probs=90.9
Q ss_pred CCCeEeccHHHHHHcCCCCCCeEEEEEe-ecCCcceEEEeeCCcCcCCccCchHH-Hhhccc-cceecccCCEEEEEECC
Q 024476 24 EEGMIYMPYWMMENLLLQEGDIVRVKNV-TLPKGTYVKLQPHTKDFLDISNPKAI-LETTLR-NYSCLTTGDSIMVAYNN 100 (267)
Q Consensus 24 ~EG~i~LP~Wmm~~L~l~~gd~V~I~~~-~LPkGt~vkLqP~s~~Fl~isnpKav-LE~~LR-nystLT~Gd~I~I~yn~ 100 (267)
.|..|-+=.-..+.|+|.+|+.|.++-+ ..+.++-|.+.|.++|=|+|-+--|. ||..|- ++--+|. .++.|+++.
T Consensus 58 se~~ieIn~~~A~~l~L~e~~~V~l~~~~~v~~~~~V~VeP~TsdDWEIiElnA~~~e~~lL~Q~RIv~~-~~f~iwl~~ 136 (952)
T KOG0735|consen 58 SENVIEINRVYAHTLGLAENQEVKLSIIDHVHEATQVEVEPVTSDDWEIIELNAEWLEENLLVQTRIVTP-EIFIIWLPS 136 (952)
T ss_pred ccceEEeehhhHhhccCCCCCeEEEEEcCCccceeEEEEeeccCccHHHHHhhHHHHhhhhhhheeeccc-ceeEEEEcC
Confidence 4666777788899999999999999976 79999999999999998898777666 677665 6888999 888899987
Q ss_pred EEE-EEEEEEecCCCeeEEEeCceeeeecCC
Q 024476 101 KKY-YIDIIETKPSNAISIIETDCEVDFAPP 130 (267)
Q Consensus 101 ~~y-~l~V~e~kP~~aVsIIeTDleVDf~pP 130 (267)
.+| .|.|..+.|+..+.=++++-+|=++|-
T Consensus 137 ~t~i~fqv~rl~Ps~~~gRl~~~Tev~VaPK 167 (952)
T KOG0735|consen 137 GTVIQFQVDRLIPSMLYGRLLRGTEVLVAPK 167 (952)
T ss_pred ccEEEEEEeeeecccceeeecCCceEEEecC
Confidence 655 788999999999999999999999883
No 7
>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily. This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.
Probab=94.46 E-value=0.23 Score=51.74 Aligned_cols=104 Identities=17% Similarity=0.182 Sum_probs=75.5
Q ss_pred cEEEEEeee-ee--eCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccCchHHHhhccccceec
Q 024476 12 RVSHCGVLE-FI--AEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCL 88 (267)
Q Consensus 12 r~th~GVLE-F~--A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~~Fl~isnpKavLE~~LRnystL 88 (267)
+.+.|-|+. .. ...|.|.|..-+.+++++..||.|.|+.+.++.+..|.+.|.. ....-.+...++-..|.+ ..|
T Consensus 44 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~-~~~ 121 (733)
T TIGR01243 44 RSVVAIVWPLRPDDEGRGIIRMDGYLRANAGVTIGDTVTVERAEVKEAKKVVLAPTQ-PIRFGRDFVDYVKEFLLG-KPI 121 (733)
T ss_pred CceeEEEEecCccccCCCEEeecHHHHhhcCCCCCCeEEEeecCCCccceEeecccc-ccccccchHHHHHHHHcC-CCC
Confidence 445566654 22 2468999999999999999999999999999999999999953 111001222333333333 458
Q ss_pred ccCCEEEEEECCEEEEEEEEEecCCCeeE
Q 024476 89 TTGDSIMVAYNNKKYYIDIIETKPSNAIS 117 (267)
Q Consensus 89 T~Gd~I~I~yn~~~y~l~V~e~kP~~aVs 117 (267)
++||.|.+.+....+.+.|+++.|...+.
T Consensus 122 ~~g~~~~~~~~~~~~~~~v~~~~p~~~~~ 150 (733)
T TIGR01243 122 SKGETVIVPVLEGALPFVVVSTQPAGFVY 150 (733)
T ss_pred CCCCEEEecccCcceeEEEEecCCCCcEE
Confidence 99999999988878889999999965443
No 8
>PF09262 PEX-1N: Peroxisome biogenesis factor 1, N-terminal ; InterPro: IPR015342 This domain adopts a double psi beta-barrel fold, similar in structure to the Cdc48 N-terminal domain. It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation []. ; GO: 0005524 ATP binding, 0007031 peroxisome organization, 0005777 peroxisome; PDB: 1WLF_A.
Probab=93.13 E-value=0.095 Score=40.86 Aligned_cols=74 Identities=24% Similarity=0.314 Sum_probs=49.3
Q ss_pred cceEEEeeCCcCcCCc-cCchHHHhhccc-cceecccCCEEEEEE-CCEEEEEEEEEecCCCe---eEEEeCceeeeecC
Q 024476 56 GTYVKLQPHTKDFLDI-SNPKAILETTLR-NYSCLTTGDSIMVAY-NNKKYYIDIIETKPSNA---ISIIETDCEVDFAP 129 (267)
Q Consensus 56 Gt~vkLqP~s~~Fl~i-snpKavLE~~LR-nystLT~Gd~I~I~y-n~~~y~l~V~e~kP~~a---VsIIeTDleVDf~p 129 (267)
++.|.+.|.+.|=++| ...-..||..|- +-.+++.|.++.++- ++..-.|.|..+.|... ...+..|.||=++|
T Consensus 1 A~~V~veP~T~dDWEIlEl~A~~lE~~lL~QiRvv~~~~~~~v~v~~~~~i~~~V~~i~p~~~~~~~~~L~~~TEv~VaP 80 (80)
T PF09262_consen 1 AKSVEVEPLTSDDWEILELHAEFLEDQLLSQIRVVFPGQVFPVWVSQNTVIKFKVVSIEPSSSAEGCARLSPDTEVIVAP 80 (80)
T ss_dssp -SEEEEEESSHHHHHHHHHS-SSHHHHHHHH--EE-TT-EEEEESSSS-EEEEEEEEEES--S---SEE--TT-EEEE--
T ss_pred CcEEEEEcCCccHHHHHHHhHHHHHHHHHHhheeecCCCEEEEEEcCCeEEEEEEEEccCCCCceeEEEeCCCcEEEECC
Confidence 4678999999887764 555666777766 589999999999998 56777999999999866 78899999887765
No 9
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=87.53 E-value=2.7 Score=27.54 Aligned_cols=39 Identities=33% Similarity=0.461 Sum_probs=31.3
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeC
Q 024476 23 AEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPH 64 (267)
Q Consensus 23 A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~ 64 (267)
.+.|.|.||.-+.+.|++.+||.+.|... +. .-+.|.|.
T Consensus 4 ~~kgri~iP~~~r~~l~~~~gd~~~i~~~--~~-~~l~l~p~ 42 (43)
T TIGR01439 4 DKKGQIVIPKEIREKLGLKEGDRLEVIRV--ED-GEIILRPA 42 (43)
T ss_pred CcCCeEEecHHHHHHcCcCCCCEEEEEEe--CC-CEEEEEEC
Confidence 46799999999999999999999988753 33 35666664
No 10
>PF02359 CDC48_N: Cell division protein 48 (CDC48), N-terminal domain; InterPro: IPR003338 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The VAT protein of the archaebacterium Thermoplasma acidophilum, like all other members of the Cdc48/p97 family of AAA ATPases, has two ATPase domains and a 185-residue amino-terminal substrate-recognition domain, VAT-N. VAT shows activity in protein folding and unfolding and thus shares the common function of these ATPases in disassembly and/or degradation of protein complexes. VAT-N is composed of two equally sized subdomains. The amino-terminal subdomain VAT-Nn forms a double-psi beta-barrel whose pseudo-twofold symmetry is mirrored by an internal sequence repeat of 42 residues. The carboxy-terminal subdomain VAT-Nc forms a novel six-stranded beta-clam fold []. Together, VAT-Nn and VAT-Nc form a kidney-shaped structure, in close agreement with results from electron microscopy. VAT-Nn is related to numerous proteins including prokaryotic transcription factors, metabolic enzymes, the protease cofactors UFD1 and PrlF, and aspartic proteinases. ; GO: 0005524 ATP binding; PDB: 1CZ4_A 1CZ5_A 3CF3_C 3CF1_A 3CF2_A 1S3S_D 1E32_A 1R7R_A 2PJH_B 1CR5_B ....
Probab=85.68 E-value=1.1 Score=34.57 Aligned_cols=69 Identities=23% Similarity=0.235 Sum_probs=46.9
Q ss_pred CCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccCchHHHhhccccceecccCCEEEEE
Q 024476 24 EEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVA 97 (267)
Q Consensus 24 ~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~~Fl~isnpKavLE~~LRnystLT~Gd~I~I~ 97 (267)
..|.++|..-.|+.|++.+||.|.|... +-|.+.+.|...+ +...=.--|-...|+..-+..||.|.|.
T Consensus 14 ~~n~v~v~~~~m~~l~l~~gd~v~i~g~---~~tv~~v~~~~~~--~~~~g~I~l~~~~R~n~~v~igd~V~V~ 82 (87)
T PF02359_consen 14 GTNCVRVSPEDMEELGLFPGDVVLISGK---RKTVAFVFPDRPD--DSPPGVIRLSGIQRKNAGVSIGDRVTVR 82 (87)
T ss_dssp CTTEEEEEHHHHHCTTT-TTEEEEEETT---TEEEEEEEEECCS--TTCTTEEEE-HHHHHHCT--TTSEEEEE
T ss_pred CCCEEEEcHHHHHHcCCCCccEEEEeCC---ceEEEEEEECCCC--CCCCCEEEECHHHHhhCCcCCCCEEEEE
Confidence 5689999999999999999999999872 2266777665322 1111111256677888889999999986
No 11
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=84.63 E-value=2.1 Score=29.39 Aligned_cols=39 Identities=26% Similarity=0.418 Sum_probs=30.4
Q ss_pred CCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCC
Q 024476 24 EEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHT 65 (267)
Q Consensus 24 ~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s 65 (267)
..+.|.||.-+++.|+|++||.|.|... ..| -+.|.|..
T Consensus 5 ~s~~v~iPk~~~~~l~l~~Gd~v~i~~~--~~g-~i~i~p~~ 43 (47)
T PF04014_consen 5 NSGQVTIPKEIREKLGLKPGDEVEIEVE--GDG-KIVIRPVK 43 (47)
T ss_dssp TCSEEEE-HHHHHHTTSSTTTEEEEEEE--TTS-EEEEEEST
T ss_pred CCceEECCHHHHHHcCCCCCCEEEEEEe--CCC-EEEEEECC
Confidence 4688999999999999999999998865 233 66666653
No 12
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=80.12 E-value=0.88 Score=35.50 Aligned_cols=26 Identities=19% Similarity=0.286 Sum_probs=19.1
Q ss_pred CCeEeccHHHHHHcCCCCCCeEEEEE
Q 024476 25 EGMIYMPYWMMENLLLQEGDIVRVKN 50 (267)
Q Consensus 25 EG~i~LP~Wmm~~L~l~~gd~V~I~~ 50 (267)
+.-||+|.++.+.++|+.||.|.=.-
T Consensus 28 ~~DvYVs~~qIrrf~LR~GD~V~G~v 53 (78)
T PF07497_consen 28 PDDVYVSPSQIRRFGLRTGDLVEGQV 53 (78)
T ss_dssp TTSEEE-CCCCCCTT--TTEEEEEEE
T ss_pred CCCEEECHHHHHHcCCCCCCEEEEEE
Confidence 45689999999999999999887543
No 13
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=78.72 E-value=2.2 Score=32.37 Aligned_cols=27 Identities=22% Similarity=0.253 Sum_probs=23.0
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEE
Q 024476 23 AEEGMIYMPYWMMENLLLQEGDIVRVK 49 (267)
Q Consensus 23 A~EG~i~LP~Wmm~~L~l~~gd~V~I~ 49 (267)
+.+.-||+|.++.+..+|+.||.|.=.
T Consensus 24 ~~~~DvyVs~~~Irr~~LR~GD~V~G~ 50 (68)
T cd04459 24 PGPDDIYVSPSQIRRFNLRTGDTVVGQ 50 (68)
T ss_pred CCCCCEEECHHHHHHhCCCCCCEEEEE
Confidence 345568999999999999999998764
No 14
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=77.11 E-value=4.8 Score=30.48 Aligned_cols=54 Identities=22% Similarity=0.346 Sum_probs=36.6
Q ss_pred CeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCc--CcCCccCchHHHhhccccc
Q 024476 26 GMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTK--DFLDISNPKAILETTLRNY 85 (267)
Q Consensus 26 G~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~--~Fl~isnpKavLE~~LRny 85 (267)
-.|-||.=+++.|+|.+||.|.|... +.-+.|.|... +|- ......++..++.|
T Consensus 10 ~~vtIPk~i~~~lgl~~Gd~v~v~~~----~~~iii~~~~~~~~~~--~~~~~~~~~~~~~y 65 (74)
T TIGR02609 10 LVVTLPKEVLESLGLKEGDTLYVDEE----EGGLKLKRFDEGKELE--KKMQMAVERAMSKY 65 (74)
T ss_pred eEEEECHHHHHHcCcCCCCEEEEEEE----CCEEEEEECCCCccHH--HHHHHHHHHHHHHH
Confidence 45889999999999999999976443 23466778765 442 11123566666655
No 15
>cd02786 MopB_CT_3 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=76.14 E-value=6 Score=31.02 Aligned_cols=30 Identities=20% Similarity=0.103 Sum_probs=26.3
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEee
Q 024476 23 AEEGMIYMPYWMMENLLLQEGDIVRVKNVT 52 (267)
Q Consensus 23 A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~ 52 (267)
.++..|+|..--++.|||++||.|+|.+..
T Consensus 28 ~~~~~v~i~p~dA~~lgi~~Gd~V~v~s~~ 57 (116)
T cd02786 28 EGEPTLLIHPADAAARGIADGDLVVVFNDR 57 (116)
T ss_pred CCCCEEEECHHHHHHcCCCCCCEEEEEcCC
Confidence 356789999999999999999999988653
No 16
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=75.57 E-value=11 Score=32.91 Aligned_cols=95 Identities=16% Similarity=0.137 Sum_probs=61.4
Q ss_pred CcEEEEEeeeeeeCCCeEeccHHHHHHcCCCCCCeEEEEEee-cCCcceEEEeeC-------C---cCcCCccCchHHHh
Q 024476 11 ERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVT-LPKGTYVKLQPH-------T---KDFLDISNPKAILE 79 (267)
Q Consensus 11 ~r~th~GVLEF~A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~-LPkGt~vkLqP~-------s---~~Fl~isnpKavLE 79 (267)
-+.+++|.++...+.-.|.|=+|.-.....+.||+|.-+-++ .+.|=+|.|-.. . ..|+.+++...
T Consensus 33 i~as~~G~~~id~~~~~Isv~P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~--- 109 (189)
T PRK09521 33 VYASVVGKVFIDDINRKISVIPFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSD--- 109 (189)
T ss_pred EEEEeeEEEEEcCCCCEEEEecCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcCh---
Confidence 357889999997777788887887555667899999877664 578888887421 1 23444443321
Q ss_pred hcccc-ceecccCCEEEEEECC--EEEEEEEE
Q 024476 80 TTLRN-YSCLTTGDSIMVAYNN--KKYYIDII 108 (267)
Q Consensus 80 ~~LRn-ystLT~Gd~I~I~yn~--~~y~l~V~ 108 (267)
...++ ..++..||+|....-. ..+.|.+.
T Consensus 110 ~~~~~~~~~~~~GD~V~akV~~i~~~i~LS~k 141 (189)
T PRK09521 110 GYVESLTDAFKIGDIVRAKVISYTDPLQLSTK 141 (189)
T ss_pred hhhhhHHhccCCCCEEEEEEEecCCcEEEEEe
Confidence 22223 5668999999875321 34444443
No 17
>PRK14132 riboflavin kinase; Provisional
Probab=73.29 E-value=3.4 Score=35.05 Aligned_cols=31 Identities=35% Similarity=0.551 Sum_probs=24.7
Q ss_pred cEEE-EEeeeeeeCCCeEeccHHHHHHcCCCCCCeEEEE
Q 024476 12 RVSH-CGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVK 49 (267)
Q Consensus 12 r~th-~GVLEF~A~EG~i~LP~Wmm~~L~l~~gd~V~I~ 49 (267)
|+.| -.|+|++|+.. +=+.|+|+.||.|.|+
T Consensus 94 rT~h~~~~lEiIAp~~-------LR~~L~LkDGD~V~I~ 125 (126)
T PRK14132 94 KTDHSKNVLEIIAPIK-------LRKFLNLKDGDVVKIV 125 (126)
T ss_pred cCCCCCCeEEEECCcc-------hHhhcCCCCCCEEEEE
Confidence 4455 45888888765 8899999999999986
No 18
>cd02787 MopB_CT_ydeP The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=73.16 E-value=6.3 Score=30.98 Aligned_cols=29 Identities=21% Similarity=0.283 Sum_probs=25.9
Q ss_pred CCCeEeccHHHHHHcCCCCCCeEEEEEee
Q 024476 24 EEGMIYMPYWMMENLLLQEGDIVRVKNVT 52 (267)
Q Consensus 24 ~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~ 52 (267)
++..|+|-.--++.|+|.+||.|+|.+..
T Consensus 29 ~~~~v~i~p~dA~~lgI~dGd~V~v~s~~ 57 (112)
T cd02787 29 RRDVVFMNPDDIARLGLKAGDRVDLESAF 57 (112)
T ss_pred CccEEEECHHHHHHhCCCCCCEEEEEecC
Confidence 46789999999999999999999998753
No 19
>cd02790 MopB_CT_Formate-Dh_H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a Mo active site region and a [4Fe-4S] center. This CD (MopB_CT_Formate-Dh_H) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=69.48 E-value=6.4 Score=30.60 Aligned_cols=29 Identities=24% Similarity=0.248 Sum_probs=25.8
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 024476 23 AEEGMIYMPYWMMENLLLQEGDIVRVKNV 51 (267)
Q Consensus 23 A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~ 51 (267)
.++..|+|..=-+..|+|++||.|+|.+-
T Consensus 32 ~~~~~v~in~~dA~~lgi~~Gd~V~v~~~ 60 (116)
T cd02790 32 APEEYVEINPEDAKRLGIEDGEKVRVSSR 60 (116)
T ss_pred CCCcEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 46778999999999999999999999873
No 20
>PRK09798 antitoxin MazE; Provisional
Probab=69.07 E-value=11 Score=29.32 Aligned_cols=49 Identities=22% Similarity=0.331 Sum_probs=36.0
Q ss_pred eEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccCchHHHhhccccc
Q 024476 27 MIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNY 85 (267)
Q Consensus 27 ~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~~Fl~isnpKavLE~~LRny 85 (267)
-|-||.=+++.|+|.+||.|.|+.. +.-+.|+|... .++.-||.-|.+|
T Consensus 14 ~vRIPk~~l~~l~l~~g~~vei~v~----~~~iiI~p~~~------~~r~~l~eLla~~ 62 (82)
T PRK09798 14 AVRIPATLMQALNLNIDDEVKIDLV----DGKLIIEPVRK------EPVFTLAELVNDI 62 (82)
T ss_pred eEEcCHHHHHHcCCCCCCEEEEEEE----CCEEEEEECCC------CCCCCHHHHHhcC
Confidence 3779999999999999999988874 35567898642 3344566666554
No 21
>cd00508 MopB_CT_Fdh-Nap-like This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. Formate dehydrogenase N (alpha subunit) is the major electron donor to the bacterial nitrate respiratory chain and nitrate reductases, Nap and Nas, catalyze the reduction of nitrate to nitrite. This CD (MopB_CT_Fdh-Nap-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=68.65 E-value=8.7 Score=29.87 Aligned_cols=27 Identities=26% Similarity=0.339 Sum_probs=24.8
Q ss_pred CCCeEeccHHHHHHcCCCCCCeEEEEE
Q 024476 24 EEGMIYMPYWMMENLLLQEGDIVRVKN 50 (267)
Q Consensus 24 ~EG~i~LP~Wmm~~L~l~~gd~V~I~~ 50 (267)
++..|+|..--++.|||.+||.|+|.+
T Consensus 33 ~~~~v~inp~dA~~lgi~~Gd~V~v~~ 59 (120)
T cd00508 33 PEPFVEIHPEDAARLGIKDGDLVRVSS 59 (120)
T ss_pred CCCEEEECHHHHHHcCCCCCCEEEEEe
Confidence 567899999999999999999999987
No 22
>cd02776 MopB_CT_Nitrate-R-NarG-like Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. Found in prokaryotes and some archaea, NarGHI usually functions as a heterotrimer. The alpha chain contains the molybdenum cofactor-containing Mo-bisMGD catalytic subunit. This CD (MopB_CT_Nitrate-R-NarG-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=68.59 E-value=9.1 Score=32.10 Aligned_cols=48 Identities=17% Similarity=0.172 Sum_probs=34.4
Q ss_pred EEEEeCCCCcEEEEE------eeeeeeCCCeEeccHHHHHHcCCCCCCeEEEEE
Q 024476 3 FELRNNAAERVSHCG------VLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKN 50 (267)
Q Consensus 3 F~l~N~~~~r~th~G------VLEF~A~EG~i~LP~Wmm~~L~l~~gd~V~I~~ 50 (267)
|.|.........|.- .++...++..|+|-.=-++.|+|++||.|+|.+
T Consensus 2 l~Lit~~~~~~~hS~~~~~~~ll~~~~~~~~v~inp~dA~~lgI~dGd~V~v~~ 55 (141)
T cd02776 2 LNYLTPHGKWSIHSTYRDNLLMLRLQRGGPVVWMNPKDAAELGIKDNDWVEVFN 55 (141)
T ss_pred eEEECCCCCCceECCCCCCHHHHhcCCCCCEEEECHHHHHHcCCCCCCEEEEEe
Confidence 444444444444431 134555678899999999999999999999877
No 23
>cd02792 MopB_CT_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. This CD (MopB_CT_Formate-Dh-Na-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=67.41 E-value=5.8 Score=31.20 Aligned_cols=28 Identities=18% Similarity=0.222 Sum_probs=25.2
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEE
Q 024476 23 AEEGMIYMPYWMMENLLLQEGDIVRVKN 50 (267)
Q Consensus 23 A~EG~i~LP~Wmm~~L~l~~gd~V~I~~ 50 (267)
.++..|+|..=-++.|+|.+||.|+|.+
T Consensus 32 ~~~~~v~i~p~dA~~lgi~~Gd~V~v~s 59 (122)
T cd02792 32 QPEMFVEISPELAAERGIKNGDMVWVSS 59 (122)
T ss_pred CCCcEEEECHHHHHHcCCCCCCEEEEEc
Confidence 4677899999999999999999999876
No 24
>PRK09974 putative regulator PrlF; Provisional
Probab=66.76 E-value=16 Score=30.40 Aligned_cols=59 Identities=17% Similarity=0.204 Sum_probs=39.2
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCC--ccCchHHHhhcccc
Q 024476 23 AEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLD--ISNPKAILETTLRN 84 (267)
Q Consensus 23 A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~~Fl~--isnpKavLE~~LRn 84 (267)
...|+|-+|.-+-+.|+|.+||.|.+. +..+-.|.|.+...+--| |-..-.+||+-+++
T Consensus 15 TsKGQvTIPk~IR~~Lgl~~GdkI~f~---i~~dG~V~i~~~~~~~~Dp~ig~FL~fLa~Di~~ 75 (111)
T PRK09974 15 TDRGQTTVPAPVRKALKLKKRDSIHYE---ILPGGQVFICRLGDEEEDPVLGAFLDFLAADIQN 75 (111)
T ss_pred ecCCCEeccHHHHHHcCCCCCCEEEEE---EeCCCEEEEEECCCCCCCchHHHHHHHHHHHHHh
Confidence 478999999999999999999988763 333445566665432222 23335566665544
No 25
>cd02789 MopB_CT_FmdC-FwdD The MopB_FmdC-FwdD CD includes the C-terminus of subunit C of molybdenum formylmethanofuran dehydrogenase (FmdC) and subunit D of tungsten formylmethanofuran dehydrogenase (FwdD), and other related proteins. Formylmethanofuran dehydrogenase catalyzes the first step in methane formation from CO2 in methanogenic archaea and some eubacteria. Members of this CD belong to the molybdopterin_binding superfamily of proteins. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=65.74 E-value=7.4 Score=30.88 Aligned_cols=29 Identities=21% Similarity=0.015 Sum_probs=25.7
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 024476 23 AEEGMIYMPYWMMENLLLQEGDIVRVKNV 51 (267)
Q Consensus 23 A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~ 51 (267)
.++..|+|-.=-++.|+|.+||.|+|.+.
T Consensus 28 ~~~~~v~i~p~dA~~lgi~~Gd~V~v~~~ 56 (106)
T cd02789 28 DACAYCEINPEDYKLLGKPEGDKVKVTSE 56 (106)
T ss_pred CCCcEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 46678999999999999999999998764
No 26
>PF01982 CTP-dep_RFKase: Domain of unknown function DUF120; InterPro: IPR023602 Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (2.7.1.26 from EC), which converts it into FMN, and FAD synthetase (2.7.7.2 from EC), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme [], the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family []. The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases []. This entry represents a CTP-dependent riboflavin kinase domain, found primarily in archaea, that catalyses the phosphorylation of riboflavin to form flavin mononucleotide in riboflavin biosynthesis. Its structure resembles a RIFT barrel, structurally similar to but topologically distinct from bacterial and eukaryotic examples []. The N-terminal is a winged helix-turn-helix DNA-binding domain, and the C-terminal half is most similar in sequence to a group of cradle-loop barrels.; GO: 0016773 phosphotransferase activity, alcohol group as acceptor; PDB: 2VBV_A 2VBU_A 2VBS_A 2VBT_A 2P3M_A 2OYN_A 3CTA_A.
Probab=65.25 E-value=7.9 Score=32.61 Aligned_cols=17 Identities=35% Similarity=0.503 Sum_probs=11.8
Q ss_pred HHHHHcCCCCCCeEEEE
Q 024476 33 WMMENLLLQEGDIVRVK 49 (267)
Q Consensus 33 Wmm~~L~l~~gd~V~I~ 49 (267)
-+=+.|+|++||.|.|+
T Consensus 104 ~LR~~L~L~DGD~V~v~ 120 (121)
T PF01982_consen 104 KLRDTLGLKDGDEVEVE 120 (121)
T ss_dssp -HHHHTT--TT-EEEEE
T ss_pred chHhhcCCCCCCEEEEE
Confidence 48899999999999986
No 27
>PRK11347 antitoxin ChpS; Provisional
Probab=64.75 E-value=20 Score=28.02 Aligned_cols=47 Identities=23% Similarity=0.321 Sum_probs=34.9
Q ss_pred eEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccCchHHHhhccccc
Q 024476 27 MIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNY 85 (267)
Q Consensus 27 ~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~~Fl~isnpKavLE~~LRny 85 (267)
-|-||.=|++.|+|++||.|.|.-.. .-+.|+|.... .-||.-|..|
T Consensus 13 ~vriPk~il~~l~l~~G~~v~i~v~~----~~iii~p~~~~--------~tL~eLla~~ 59 (83)
T PRK11347 13 GMVIPNIVMKELNLQPGQSVEAQVSN----NQLILTPISRR--------YSLDELLAQC 59 (83)
T ss_pred eEEeCHHHHHHcCCCCCCEEEEEEEC----CEEEEEECCCC--------CCHHHHHhcC
Confidence 37799999999999999999887643 34888997433 3466655443
No 28
>cd02791 MopB_CT_Nitrate-R-NapA-like Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. This CD (MopB_CT_Nitrate-R-Nap) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs
Probab=62.97 E-value=10 Score=29.80 Aligned_cols=28 Identities=32% Similarity=0.306 Sum_probs=24.9
Q ss_pred CCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 024476 24 EEGMIYMPYWMMENLLLQEGDIVRVKNV 51 (267)
Q Consensus 24 ~EG~i~LP~Wmm~~L~l~~gd~V~I~~~ 51 (267)
.+..|+|-.-.++.|+|.+||.|+|.+-
T Consensus 33 ~~~~v~in~~dA~~lgi~~Gd~V~v~~~ 60 (122)
T cd02791 33 PEPYVEIHPEDAARLGLKEGDLVRVTSR 60 (122)
T ss_pred CCCEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 4667999999999999999999998864
No 29
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=62.87 E-value=9 Score=31.30 Aligned_cols=27 Identities=22% Similarity=0.300 Sum_probs=23.5
Q ss_pred ceecccCCEEEEEECCEEEEEEEEEec
Q 024476 85 YSCLTTGDSIMVAYNNKKYYIDIIETK 111 (267)
Q Consensus 85 ystLT~Gd~I~I~yn~~~y~l~V~e~k 111 (267)
+..|..||+|.|.+.+..+.++|.+++
T Consensus 137 ~~~l~pGDvi~l~~~~~~~~~RI~~i~ 163 (164)
T PF13550_consen 137 GLALEPGDVIALSDDGRDMRFRITEIE 163 (164)
T ss_pred hccCCCCCEEEEEeCCCceEEEEEEEe
Confidence 456899999999999999999998875
No 30
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=62.78 E-value=14 Score=28.82 Aligned_cols=42 Identities=24% Similarity=0.353 Sum_probs=31.8
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCc
Q 024476 23 AEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTK 66 (267)
Q Consensus 23 A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~ 66 (267)
...|+|.+|.-+=+.||+++||.|.+.... .+..+-|+|...
T Consensus 11 ~~~GqIvIPkeiR~~lgi~~Gd~lei~~~~--~~~~ivl~k~~~ 52 (89)
T COG2002 11 DRKGQIVIPKEIREALGIKEGDVLEIIVDG--DGGRIVLKKYKP 52 (89)
T ss_pred CcCceEEecHHHHHHhCCCCCCEEEEEEeC--CCCEEEEEECCc
Confidence 467999999999999999999998886542 112266666553
No 31
>cd02788 MopB_CT_NDH-1_NuoG2-N7 MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, the largest subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the functional enzyme. The NuoG subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain, is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Unique to this group, compared to the other prokaryotic and eukaryotic groups
Probab=62.10 E-value=13 Score=28.72 Aligned_cols=35 Identities=20% Similarity=0.067 Sum_probs=28.5
Q ss_pred EeeeeeeCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 024476 17 GVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNV 51 (267)
Q Consensus 17 GVLEF~A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~ 51 (267)
..|.-.+++..|+|-.=-++.|+|.+||.|+|.+.
T Consensus 20 ~~l~~~~~~~~v~inp~dA~~lGi~~Gd~V~v~s~ 54 (96)
T cd02788 20 PVIAERAPAPYARLSPADAARLGLADGDLVEFSLG 54 (96)
T ss_pred HHHHhcCCCCEEEECHHHHHHcCCCCCCEEEEEEC
Confidence 33433457889999999999999999999998764
No 32
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=59.07 E-value=18 Score=26.94 Aligned_cols=66 Identities=14% Similarity=0.264 Sum_probs=40.8
Q ss_pred CCCCCeEEEEEe-ecCCcceEEEeeCCcCcCCccCchHHHhhccccc-eecccCCEEEEEECCEEEEEEEEEecCCC
Q 024476 40 LQEGDIVRVKNV-TLPKGTYVKLQPHTKDFLDISNPKAILETTLRNY-SCLTTGDSIMVAYNNKKYYIDIIETKPSN 114 (267)
Q Consensus 40 l~~gd~V~I~~~-~LPkGt~vkLqP~s~~Fl~isnpKavLE~~LRny-stLT~Gd~I~I~yn~~~y~l~V~e~kP~~ 114 (267)
+++||.|.-.-. -.+.|-||.|-|.-..|+.++|.-.-.-..++++ ..+..||.|. ..|+++.+++
T Consensus 1 ~k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~---------~kVl~id~~~ 68 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLT---------AKVLSVNSEK 68 (74)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEE---------EEEEEEECCC
Confidence 478998876543 2499999999998888886433211100111222 3467888776 5677776653
No 33
>PRK15095 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=58.92 E-value=48 Score=28.40 Aligned_cols=94 Identities=22% Similarity=0.228 Sum_probs=51.9
Q ss_pred EeeeeeeCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccCchHHHhhccccce---ecccCCE
Q 024476 17 GVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYS---CLTTGDS 93 (267)
Q Consensus 17 GVLEF~A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~~Fl~isnpKavLE~~LRnys---tLT~Gd~ 93 (267)
.-+.|+--.|.+ +|.|=-.=++++.|+.+.|. || |. ..|- -.|+..|.+--+.+|. -+-.|..
T Consensus 33 ~P~~f~~G~g~v-i~gle~aL~gm~~Ge~~~v~---ip--------p~-~ayG-~~d~~~v~~vp~~~f~~~~~~~~G~~ 98 (156)
T PRK15095 33 KPALFRLGDGSL-SEGLEQQLLGLKVGDKKTFS---LE--------PE-AAFG-VPSPDLIQYFSRRDFMDAGEPEIGAI 98 (156)
T ss_pred CCEEEEeCCCCc-cHHHHHHHcCCCCCCEEEEE---EC--------hH-HhcC-CCChHHEEEecHHHCCcccCCCCCCE
Confidence 456787777765 79999988999999987753 22 21 1222 2344444443333332 3556666
Q ss_pred EEEEE-CCEEEEEEEEEecCCCeeEEEeCceeeeecCCCC
Q 024476 94 IMVAY-NNKKYYIDIIETKPSNAISIIETDCEVDFAPPLD 132 (267)
Q Consensus 94 I~I~y-n~~~y~l~V~e~kP~~aVsIIeTDleVDf~pPld 132 (267)
+.+.- .+..+...|++ |-+..+.|||..||-
T Consensus 99 ~~~~~~~G~~~~~~V~~--------i~~~~v~vD~NHPLA 130 (156)
T PRK15095 99 MLFTAMDGSEMPGVIRE--------INGDSITVDFNHPLA 130 (156)
T ss_pred EEEECCCCCEEEEEEEE--------EcCCEEEEECCCcCC
Confidence 55542 12233333444 334556666666653
No 34
>cd02778 MopB_CT_Thiosulfate-R-like The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Also included in this CD is the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), which has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. The MopB_CT_Thiosulfate-R-like CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=57.94 E-value=24 Score=27.81 Aligned_cols=28 Identities=21% Similarity=0.326 Sum_probs=25.3
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEE
Q 024476 23 AEEGMIYMPYWMMENLLLQEGDIVRVKN 50 (267)
Q Consensus 23 A~EG~i~LP~Wmm~~L~l~~gd~V~I~~ 50 (267)
.++..|+|..=-+..|+|.+||.|+|.+
T Consensus 27 ~~~~~v~i~p~dA~~~gi~~Gd~V~v~s 54 (123)
T cd02778 27 TPENTLWINPETAARLGIKDGDRVEVSS 54 (123)
T ss_pred CCCCeEEECHHHHHHcCCCCCCEEEEEe
Confidence 4677899999999999999999999876
No 35
>cd02779 MopB_CT_Arsenite-Ox This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of Arsenite oxidase (Arsenite-Ox) and related proteins. Arsenite oxidase oxidizes arsenite to the less toxic arsenate; it transfers the electrons obtained from the oxidation of arsenite towards the soluble periplasmic electron carriers cytochrome c and/or amicyanin.
Probab=57.28 E-value=26 Score=27.73 Aligned_cols=29 Identities=24% Similarity=0.079 Sum_probs=25.7
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 024476 23 AEEGMIYMPYWMMENLLLQEGDIVRVKNV 51 (267)
Q Consensus 23 A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~ 51 (267)
.++..|.|-.=-++.|+|.+||.|.|.+-
T Consensus 30 ~~~~~v~in~~dA~~lgi~~Gd~V~v~s~ 58 (115)
T cd02779 30 VPLPYIEVNPEDAKREGLKNGDLVEVYND 58 (115)
T ss_pred CCCCEEEECHHHHHHcCCCCCCEEEEEeC
Confidence 46778999999999999999999998764
No 36
>PF02359 CDC48_N: Cell division protein 48 (CDC48), N-terminal domain; InterPro: IPR003338 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The VAT protein of the archaebacterium Thermoplasma acidophilum, like all other members of the Cdc48/p97 family of AAA ATPases, has two ATPase domains and a 185-residue amino-terminal substrate-recognition domain, VAT-N. VAT shows activity in protein folding and unfolding and thus shares the common function of these ATPases in disassembly and/or degradation of protein complexes. VAT-N is composed of two equally sized subdomains. The amino-terminal subdomain VAT-Nn forms a double-psi beta-barrel whose pseudo-twofold symmetry is mirrored by an internal sequence repeat of 42 residues. The carboxy-terminal subdomain VAT-Nc forms a novel six-stranded beta-clam fold []. Together, VAT-Nn and VAT-Nc form a kidney-shaped structure, in close agreement with results from electron microscopy. VAT-Nn is related to numerous proteins including prokaryotic transcription factors, metabolic enzymes, the protease cofactors UFD1 and PrlF, and aspartic proteinases. ; GO: 0005524 ATP binding; PDB: 1CZ4_A 1CZ5_A 3CF3_C 3CF1_A 3CF2_A 1S3S_D 1E32_A 1R7R_A 2PJH_B 1CR5_B ....
Probab=56.98 E-value=41 Score=25.70 Aligned_cols=41 Identities=22% Similarity=0.135 Sum_probs=31.3
Q ss_pred CcEEEEEeeeeee---CCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 024476 11 ERVSHCGVLEFIA---EEGMIYMPYWMMENLLLQEGDIVRVKNV 51 (267)
Q Consensus 11 ~r~th~GVLEF~A---~EG~i~LP~Wmm~~L~l~~gd~V~I~~~ 51 (267)
.+.|+|=|+---. +.|.|-|-.-+-+++++.-||.|.|+.+
T Consensus 41 ~~~tv~~v~~~~~~~~~~g~I~l~~~~R~n~~v~igd~V~V~~~ 84 (87)
T PF02359_consen 41 KRKTVAFVFPDRPDDSPPGVIRLSGIQRKNAGVSIGDRVTVRPY 84 (87)
T ss_dssp TTEEEEEEEEECCSTTCTTEEEE-HHHHHHCT--TTSEEEEEEE
T ss_pred CceEEEEEEECCCCCCCCCEEEECHHHHhhCCcCCCCEEEEEEC
Confidence 4458888876543 4799999999999999999999999865
No 37
>PRK08577 hypothetical protein; Provisional
Probab=56.80 E-value=16 Score=30.17 Aligned_cols=44 Identities=25% Similarity=0.250 Sum_probs=32.7
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCc
Q 024476 23 AEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDF 68 (267)
Q Consensus 23 A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~~F 68 (267)
...|+|.+|.=+-+.|++.+||.|.+..-. .+.-+.|.|....+
T Consensus 10 ~~~g~i~ip~~~r~~l~~~~g~~~~~~~~~--~~~~~~~~~~~~~~ 53 (136)
T PRK08577 10 DSKGRITIPLEIREALGIREGMYVLLIADT--DKKEIHLEPIALPG 53 (136)
T ss_pred CcCCeEEecHHHHHHcCcCCCCEEEEEEEC--CCCEEEEEEcCCCC
Confidence 478999999999999999999999875321 12256666765444
No 38
>cd02775 MopB_CT Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is
Probab=56.61 E-value=16 Score=27.36 Aligned_cols=29 Identities=28% Similarity=0.328 Sum_probs=25.0
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 024476 23 AEEGMIYMPYWMMENLLLQEGDIVRVKNV 51 (267)
Q Consensus 23 A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~ 51 (267)
..+..|+|..=-+..|+|++||.|.|.+-
T Consensus 20 ~~~~~v~~~~~da~~lgl~~Gd~v~v~~~ 48 (101)
T cd02775 20 APEPVVEINPEDAAALGIKDGDLVRVESR 48 (101)
T ss_pred CCCCEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 35578999999999999999999988753
No 39
>cd02785 MopB_CT_4 The MopB_CT_4 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=56.43 E-value=17 Score=29.01 Aligned_cols=28 Identities=21% Similarity=0.121 Sum_probs=25.3
Q ss_pred CCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 024476 24 EEGMIYMPYWMMENLLLQEGDIVRVKNV 51 (267)
Q Consensus 24 ~EG~i~LP~Wmm~~L~l~~gd~V~I~~~ 51 (267)
++..|+|-.=-++.|+|.+||.|+|.+-
T Consensus 30 ~~~~v~i~p~dA~~~gi~~Gd~V~v~s~ 57 (124)
T cd02785 30 PEPRVKINPIDAAARGIAHGDLVEVYND 57 (124)
T ss_pred CCCeEEECHHHHHHcCCCCCCEEEEEeC
Confidence 5678999999999999999999998864
No 40
>cd02781 MopB_CT_Acetylene-hydratase The MopB_CT_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=55.95 E-value=16 Score=29.19 Aligned_cols=29 Identities=17% Similarity=0.137 Sum_probs=25.5
Q ss_pred CCCeEeccHHHHHHcCCCCCCeEEEEEee
Q 024476 24 EEGMIYMPYWMMENLLLQEGDIVRVKNVT 52 (267)
Q Consensus 24 ~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~ 52 (267)
++..|+|-.=-++.|+|.+||.|+|.+..
T Consensus 31 ~~~~v~inp~dA~~~gi~~Gd~V~v~s~~ 59 (130)
T cd02781 31 PDPVAEINPETAAKLGIADGDWVWVETPR 59 (130)
T ss_pred CCCEEEECHHHHHHcCCCCCCEEEEECCC
Confidence 56789999999999999999999988643
No 41
>cd02793 MopB_CT_DMSOR-BSOR-TMAOR The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO.This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=55.93 E-value=28 Score=28.13 Aligned_cols=29 Identities=28% Similarity=0.144 Sum_probs=25.6
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 024476 23 AEEGMIYMPYWMMENLLLQEGDIVRVKNV 51 (267)
Q Consensus 23 A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~ 51 (267)
.++..|+|=.=-++.|+|++||.|+|.+.
T Consensus 30 ~~~~~v~i~p~dA~~~gi~~Gd~V~v~s~ 58 (129)
T cd02793 30 QGREPIRINPADAAARGIADGDIVRVFND 58 (129)
T ss_pred CCCCEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 45678999999999999999999998864
No 42
>TIGR02851 spore_V_T stage V sporulation protein T. Members of this protein family are the stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB (See PFAM model pfam04014).
Probab=55.66 E-value=20 Score=31.62 Aligned_cols=46 Identities=24% Similarity=0.385 Sum_probs=35.9
Q ss_pred EeeeeeeCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCC
Q 024476 17 GVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHT 65 (267)
Q Consensus 17 GVLEF~A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s 65 (267)
|+.==+.+-|+|.+|.=|-+.|+|++||.|.|.... .| .|.|++.+
T Consensus 4 g~v~~id~~Gri~iP~~iR~~l~i~~gd~~~~~~~~--~~-~iil~k~~ 49 (180)
T TIGR02851 4 GIVRRIDDLGRVVIPKEIRRTLRIREGDPLEIFTDR--EG-EVILKKYS 49 (180)
T ss_pred ceEEEECCCCcEEEeHHHHHHcCCCCCCeEEEEEeC--CC-EEEEEECC
Confidence 444456688999999999999999999999986532 23 37777765
No 43
>COG1153 FwdD Formylmethanofuran dehydrogenase subunit D [Energy production and conversion]
Probab=55.61 E-value=11 Score=32.09 Aligned_cols=29 Identities=28% Similarity=0.248 Sum_probs=24.8
Q ss_pred eeCCCeEeccHHHHHHcCCCCCCeEEEEE
Q 024476 22 IAEEGMIYMPYWMMENLLLQEGDIVRVKN 50 (267)
Q Consensus 22 ~A~EG~i~LP~Wmm~~L~l~~gd~V~I~~ 50 (267)
.-.-..|+|-.-.|..|++++||.|.|++
T Consensus 27 ~~a~a~~~inp~D~~~Lgv~EGD~VkVks 55 (128)
T COG1153 27 FNACAVCEINPEDMKQLGVSEGDKVKVKS 55 (128)
T ss_pred hhheeEEEECHHHHHHhCCCcCCeEEEEe
Confidence 34456788888999999999999999987
No 44
>cd02777 MopB_CT_DMSOR-like The MopB_CT_DMSOR-like CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Also included in this group is the pyrogallol-phloroglucinol transhydroxylase from Pelobacter acidigallici. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB hom
Probab=55.44 E-value=16 Score=29.27 Aligned_cols=26 Identities=27% Similarity=0.333 Sum_probs=24.0
Q ss_pred CCeEeccHHHHHHcCCCCCCeEEEEE
Q 024476 25 EGMIYMPYWMMENLLLQEGDIVRVKN 50 (267)
Q Consensus 25 EG~i~LP~Wmm~~L~l~~gd~V~I~~ 50 (267)
+..|+|-.=.++.|+|.+||.|+|.+
T Consensus 33 ~~~v~i~p~dA~~lgi~~Gd~V~v~s 58 (127)
T cd02777 33 REPVWINPLDAAARGIKDGDIVRVFN 58 (127)
T ss_pred CCeEEECHHHHHHcCCCCCCEEEEEc
Confidence 56799999999999999999999886
No 45
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=55.22 E-value=44 Score=30.14 Aligned_cols=37 Identities=16% Similarity=0.182 Sum_probs=20.6
Q ss_pred cccCCEEEEEECCEEEEEEEEEecCCCeeEEEeCceeeeecCCCC
Q 024476 88 LTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDFAPPLD 132 (267)
Q Consensus 88 LT~Gd~I~I~yn~~~y~l~V~e~kP~~aVsIIeTDleVDf~pPld 132 (267)
|..|+.+...-.+-.+...|++ |-+..+.|||.-||-
T Consensus 90 l~~G~~~~~~~~~G~~~~~V~e--------v~~d~V~vD~NHPLA 126 (196)
T PRK10737 90 LQVGMRFLAETDQGPVPVEITA--------VEDDHVVVDGNHMLA 126 (196)
T ss_pred CCCCCEEEEeCCCCcEEEEEEE--------EcCCEEEEECCCcCC
Confidence 5555555554333233333333 445678899988875
No 46
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=55.06 E-value=18 Score=29.60 Aligned_cols=26 Identities=15% Similarity=0.478 Sum_probs=22.9
Q ss_pred eecccCCEEEEEECCEEEEEEEEEec
Q 024476 86 SCLTTGDSIMVAYNNKKYYIDIIETK 111 (267)
Q Consensus 86 stLT~Gd~I~I~yn~~~y~l~V~e~k 111 (267)
..+-.||+|.|.|+++.+.+.|+.+.
T Consensus 47 ~~VK~GD~l~i~~~~~~~~v~Vl~~~ 72 (100)
T COG1188 47 KEVKVGDILTIRFGNKEFTVKVLALG 72 (100)
T ss_pred cccCCCCEEEEEeCCcEEEEEEEecc
Confidence 34678999999999999999999874
No 47
>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=54.75 E-value=18 Score=27.90 Aligned_cols=27 Identities=26% Similarity=0.291 Sum_probs=22.2
Q ss_pred CCC-eEeccHHHHHHcCCCCCCeEEEEE
Q 024476 24 EEG-MIYMPYWMMENLLLQEGDIVRVKN 50 (267)
Q Consensus 24 ~EG-~i~LP~Wmm~~L~l~~gd~V~I~~ 50 (267)
.+. .|+|-.--++.|||++||.|+|.+
T Consensus 27 ~~~~~v~inp~dA~~~Gi~~Gd~V~v~s 54 (110)
T PF01568_consen 27 PEPPFVEINPEDAAKLGIKDGDWVRVSS 54 (110)
T ss_dssp HSTEEEEEEHHHHHHCT--TTCEEEEEE
T ss_pred CCCCEEEEcHHHHHHhcCcCCCEEEEEe
Confidence 344 899999999999999999999987
No 48
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=53.03 E-value=29 Score=26.82 Aligned_cols=35 Identities=23% Similarity=0.309 Sum_probs=26.3
Q ss_pred EeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEe
Q 024476 28 IYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQ 62 (267)
Q Consensus 28 i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLq 62 (267)
|..-.-|.+.||+++||.|.|.-.+---|.++..+
T Consensus 37 I~~~DPv~r~~g~k~GdVvkI~R~S~taG~~v~YR 71 (74)
T PF01191_consen 37 ILSSDPVARYLGAKPGDVVKIIRKSETAGEYVTYR 71 (74)
T ss_dssp EETTSHHHHHTT--TTSEEEEEEEETTTSEEEEEE
T ss_pred ccccChhhhhcCCCCCCEEEEEecCCCCCCcEEEE
Confidence 33345588999999999999999998888887643
No 49
>COG2336 MazE Growth regulator [Signal transduction mechanisms]
Probab=52.91 E-value=16 Score=29.04 Aligned_cols=35 Identities=23% Similarity=0.345 Sum_probs=25.5
Q ss_pred eEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeC
Q 024476 27 MIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPH 64 (267)
Q Consensus 27 ~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~ 64 (267)
-+-+|.=||+.|+|.+||-|.|... .+..+.+.|.
T Consensus 13 avrIP~~l~kql~l~~g~~v~v~v~---n~~~i~~~p~ 47 (82)
T COG2336 13 AVRIPAALLKQLNLTIGDEVEVEVG---NDQSILIRPV 47 (82)
T ss_pred eeeccHHHHHHhCCCcCceEEEEEc---CCcEEEeccc
Confidence 3779999999999999999887643 2334444444
No 50
>cd02782 MopB_CT_1 The MopB_CT_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=50.68 E-value=21 Score=28.51 Aligned_cols=29 Identities=24% Similarity=0.187 Sum_probs=25.8
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 024476 23 AEEGMIYMPYWMMENLLLQEGDIVRVKNV 51 (267)
Q Consensus 23 A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~ 51 (267)
.++..|+|-.--+..|+|.+||.|.|++.
T Consensus 30 ~~~~~v~i~p~dA~~~gi~~Gd~V~v~s~ 58 (129)
T cd02782 30 RNRCTLRIHPDDAAALGLADGDKVRVTSA 58 (129)
T ss_pred CCCceEEECHHHHHHcCCCCCCEEEEEcC
Confidence 46778999999999999999999998874
No 51
>cd02794 MopB_CT_DmsA-EC The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-terminal iron-sulfur [4Fe-4S] cluster binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=49.70 E-value=22 Score=28.25 Aligned_cols=28 Identities=18% Similarity=0.107 Sum_probs=24.1
Q ss_pred CCeEeccHHHHHHcCCCCCCeEEEEEee
Q 024476 25 EGMIYMPYWMMENLLLQEGDIVRVKNVT 52 (267)
Q Consensus 25 EG~i~LP~Wmm~~L~l~~gd~V~I~~~~ 52 (267)
+..|+|-.=.++.|||.+||.|+|.+..
T Consensus 29 ~~~v~i~p~~A~~~gi~~Gd~V~v~s~~ 56 (121)
T cd02794 29 PQEVWINPLDAAARGIKDGDRVLVFNDR 56 (121)
T ss_pred CCCEEECHHHHHHcCCCCCCEEEEEcCC
Confidence 4569999999999999999999987643
No 52
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=48.84 E-value=26 Score=27.55 Aligned_cols=31 Identities=13% Similarity=0.224 Sum_probs=25.6
Q ss_pred HHHHHHcCCCCCCeEEEEEeecCCcceEEEe
Q 024476 32 YWMMENLLLQEGDIVRVKNVTLPKGTYVKLQ 62 (267)
Q Consensus 32 ~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLq 62 (267)
.-+...+|+++||.|.|..-+--.|.||..+
T Consensus 44 DPv~r~~g~k~GdVvkI~R~S~taG~~v~YR 74 (79)
T PRK09570 44 DPVVKAIGAKPGDVIKIVRKSPTAGEAVYYR 74 (79)
T ss_pred ChhhhhcCCCCCCEEEEEECCCCCCccEEEE
Confidence 3477889999999999998888888887654
No 53
>COG1935 Uncharacterized conserved protein [Function unknown]
Probab=47.94 E-value=20 Score=30.28 Aligned_cols=26 Identities=38% Similarity=0.538 Sum_probs=21.5
Q ss_pred HHHHHcCCCCCCeEEEEEe---ecCCcce
Q 024476 33 WMMENLLLQEGDIVRVKNV---TLPKGTY 58 (267)
Q Consensus 33 Wmm~~L~l~~gd~V~I~~~---~LPkGt~ 58 (267)
-+..-++|+|||+|.++++ +|-+|+.
T Consensus 32 N~~tv~rl~~GDlVFlT~~~~~Dl~~Gts 60 (122)
T COG1935 32 NLLTVLRLHEGDLVFLTSTSLEDLTKGTS 60 (122)
T ss_pred chHHhhcCCCCCEEEEehhHhhHhhcCcc
Confidence 3667789999999999988 6778875
No 54
>PF12148 DUF3590: Protein of unknown function (DUF3590); InterPro: IPR021991 This domain is found in eukaryotes, and is typically between 83 and 97 amino acids in length. It is found in association with PF00097 from PFAM, PF02182 from PFAM, PF00628 from PFAM, PF00240 from PFAM. There are two conserved sequence motifs: RAR and NYN. The domain is part of the protein NIRF which has zinc finger and ubiquitinating domains. The function of this domain is likely to be mainly structural, however this has not been confirmed. ; PDB: 3DB4_A 3ASK_A 3DB3_A 2L3R_A.
Probab=47.75 E-value=12 Score=29.78 Aligned_cols=20 Identities=35% Similarity=0.634 Sum_probs=12.3
Q ss_pred hccccceecccCCEEEEEEC
Q 024476 80 TTLRNYSCLTTGDSIMVAYN 99 (267)
Q Consensus 80 ~~LRnystLT~Gd~I~I~yn 99 (267)
+++-.|.-|.+|++++|+||
T Consensus 58 Rt~l~w~~L~VG~~VMvNYN 77 (85)
T PF12148_consen 58 RTILKWDELKVGQVVMVNYN 77 (85)
T ss_dssp -SBE-GGG--TT-EEEEEE-
T ss_pred eEeccHHhCCcccEEEEecC
Confidence 45557889999999999998
No 55
>cd02783 MopB_CT_2 The MopB_CT_2 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=47.60 E-value=24 Score=29.87 Aligned_cols=29 Identities=28% Similarity=0.398 Sum_probs=26.1
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 024476 23 AEEGMIYMPYWMMENLLLQEGDIVRVKNV 51 (267)
Q Consensus 23 A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~ 51 (267)
.++..|+|-.--++.|||.+||.|+|.+.
T Consensus 29 ~~~~~v~inp~dA~~~GI~dGd~V~v~s~ 57 (156)
T cd02783 29 HTRNYLYMHPKTAKELGIKDGDWVWVESV 57 (156)
T ss_pred CCCCEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 46678999999999999999999999983
No 56
>smart00553 SEP Domain present in Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47.
Probab=47.42 E-value=11 Score=30.25 Aligned_cols=15 Identities=33% Similarity=0.795 Sum_probs=12.6
Q ss_pred ccceeeeccccCCcc
Q 024476 162 FSPFTGVARRLDGKP 176 (267)
Q Consensus 162 ~~~F~G~G~rLdGK~ 176 (267)
+.+|.|+|+||++-.
T Consensus 73 ~~~F~G~G~~LGs~~ 87 (93)
T smart00553 73 FKPFSGSGQKLGSPG 87 (93)
T ss_pred ccCCccCCccCCCCC
Confidence 678999999998743
No 57
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=46.04 E-value=24 Score=24.78 Aligned_cols=23 Identities=26% Similarity=0.107 Sum_probs=18.3
Q ss_pred EeccHHHHHHcCCCCCCeEEEEE
Q 024476 28 IYMPYWMMENLLLQEGDIVRVKN 50 (267)
Q Consensus 28 i~LP~Wmm~~L~l~~gd~V~I~~ 50 (267)
+.++.|-+..|+|++||.|.+..
T Consensus 35 a~it~~~~~~L~L~~G~~V~~~i 57 (64)
T PF03459_consen 35 ARITPESAEELGLKPGDEVYASI 57 (64)
T ss_dssp EEEEHHHHHHCT-STT-EEEEEE
T ss_pred EEEcHHHHHHcCCCCCCEEEEEE
Confidence 56999999999999999998753
No 58
>cd06166 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5, represented by Clostridium perfringens CPE2315. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=44.15 E-value=36 Score=27.68 Aligned_cols=31 Identities=23% Similarity=0.284 Sum_probs=25.4
Q ss_pred ccccceecccCCEEEEEECCEEEEEEEEEec
Q 024476 81 TLRNYSCLTTGDSIMVAYNNKKYYIDIIETK 111 (267)
Q Consensus 81 ~LRnystLT~Gd~I~I~yn~~~y~l~V~e~k 111 (267)
.+++...|.+||.|.|...+..|...|.+++
T Consensus 58 ~F~~L~~l~~Gd~v~v~~~~~~~~Y~V~~~~ 88 (126)
T cd06166 58 IFNRLDEVEKGDEIKVTTKNGTYKYKITSIF 88 (126)
T ss_pred ccCChHHCCCCCEEEEEECCEEEEEEEEEEE
Confidence 4566677889999999999999988887753
No 59
>cd02780 MopB_CT_Tetrathionate_Arsenate-R This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins.
Probab=42.95 E-value=37 Score=27.89 Aligned_cols=28 Identities=25% Similarity=0.266 Sum_probs=25.2
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEE
Q 024476 23 AEEGMIYMPYWMMENLLLQEGDIVRVKN 50 (267)
Q Consensus 23 A~EG~i~LP~Wmm~~L~l~~gd~V~I~~ 50 (267)
.++..|+|-.=-++.|+|.+||.|.|.+
T Consensus 27 ~~~~~v~inp~dA~~lgI~~Gd~V~v~s 54 (143)
T cd02780 27 KPENPVWINPEDAAKLGIKTGDRVRVVT 54 (143)
T ss_pred CCCCEEEECHHHHHHcCCCCCCEEEEEe
Confidence 4567899999999999999999999887
No 60
>cd05829 Sortase_E Sortase E (SrtE) is a membrane transpeptidase found in gram-positive bacteria that cleaves surface proteins at a cell sorting motif and catalyzes a transpeptidation reaction in which the surface protein substrate is covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The function of Sortase E is unknown. In two different sortase families, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one sortase and it is thought that the different sortases anchor different surface protein classes. The sortase domain is a modified beta-barrel flanked by two (SrtA) or three (SrtB) short alpha-helices.
Probab=42.84 E-value=34 Score=28.69 Aligned_cols=27 Identities=15% Similarity=0.207 Sum_probs=20.6
Q ss_pred cceecccCCEEEEEE-CCEEEEEEEEEe
Q 024476 84 NYSCLTTGDSIMVAY-NNKKYYIDIIET 110 (267)
Q Consensus 84 nystLT~Gd~I~I~y-n~~~y~l~V~e~ 110 (267)
+...|..||.|.|.. +++.|...|.++
T Consensus 69 ~L~~l~~GD~I~v~~~~g~~~~Y~V~~~ 96 (144)
T cd05829 69 RLGDLRKGDKVEVTRADGQTATFRVDRV 96 (144)
T ss_pred chhcCCCCCEEEEEECCCCEEEEEEeEE
Confidence 344677999999999 677777777664
No 61
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=42.55 E-value=14 Score=28.48 Aligned_cols=25 Identities=20% Similarity=0.461 Sum_probs=21.1
Q ss_pred CCeEeccHHHHHHcCCCCCCeEEEE
Q 024476 25 EGMIYMPYWMMENLLLQEGDIVRVK 49 (267)
Q Consensus 25 EG~i~LP~Wmm~~L~l~~gd~V~I~ 49 (267)
+-.+.||.-|-.++.+.+||.|.|+
T Consensus 24 ~~l~~i~gK~Rk~iwI~~GD~VlV~ 48 (78)
T cd04456 24 RRLVSIPGKLRKNIWIKRGDFLIVD 48 (78)
T ss_pred EEEEEEchhhccCEEEcCCCEEEEE
Confidence 3457899999999999999999884
No 62
>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=41.85 E-value=1.3e+02 Score=25.50 Aligned_cols=40 Identities=18% Similarity=0.275 Sum_probs=27.9
Q ss_pred eecccCCEEEEEEC--CEEEEEEEEEecCCCeeEEEeCceee
Q 024476 86 SCLTTGDSIMVAYN--NKKYYIDIIETKPSNAISIIETDCEV 125 (267)
Q Consensus 86 stLT~Gd~I~I~yn--~~~y~l~V~e~kP~~aVsIIeTDleV 125 (267)
..+..||+|.+... ...+.++-+--.|.+.|+|.+--+-|
T Consensus 50 ~~~~rGDiVvf~~~~~~~~~~iKRVig~pGd~v~i~~~~l~v 91 (163)
T TIGR02227 50 SDPKRGDIVVFKDPDDNKNIYVKRVIGLPGDKVEFRDGKLYI 91 (163)
T ss_pred CCCCCCcEEEEecCCCCCceeEEEEEecCCCEEEEECCEEEE
Confidence 55778998888864 34566666666689999887755444
No 63
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=41.12 E-value=56 Score=23.38 Aligned_cols=56 Identities=14% Similarity=0.066 Sum_probs=35.5
Q ss_pred CCCCCeEEEEEee-cCCcceEEEeeCCcCcCCccCchHHHhhccccceecccCCEEEEE
Q 024476 40 LQEGDIVRVKNVT-LPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVA 97 (267)
Q Consensus 40 l~~gd~V~I~~~~-LPkGt~vkLqP~s~~Fl~isnpKavLE~~LRnystLT~Gd~I~I~ 97 (267)
|..|+.|.-+-.. .+.|-||.|.+.-..|+.+++... ....+.-..+..||+|.+.
T Consensus 1 ~~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~--~~~~~~~~~~~~Gd~v~~~ 57 (73)
T cd05706 1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALD--DYSEALPYKFKKNDIVRAC 57 (73)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccC--ccccccccccCCCCEEEEE
Confidence 4678888766553 578999999887777876654321 0001113457889988864
No 64
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=37.16 E-value=49 Score=24.26 Aligned_cols=56 Identities=18% Similarity=0.240 Sum_probs=36.9
Q ss_pred CCCCCeEEEEEeec-C-CcceEEEeeCCcCcCCccCchHHHhhcccc-ceecccCCEEEEEE
Q 024476 40 LQEGDIVRVKNVTL-P-KGTYVKLQPHTKDFLDISNPKAILETTLRN-YSCLTTGDSIMVAY 98 (267)
Q Consensus 40 l~~gd~V~I~~~~L-P-kGt~vkLqP~s~~Fl~isnpKavLE~~LRn-ystLT~Gd~I~I~y 98 (267)
|++|+.|.=+-+.+ + .|-|+.|-|.-..|+-|++... ...++ ...+..||.|.+..
T Consensus 1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~---~~~~~~~~~~~~Gd~v~~kV 59 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSD---SYTENPLEGFKPGKIVRCCI 59 (72)
T ss_pred CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcC---cccCCHHHhCCCCCEEEEEE
Confidence 46788887555554 3 6999999998888886653311 22333 24467899998754
No 65
>PRK08059 general stress protein 13; Validated
Probab=36.66 E-value=81 Score=25.74 Aligned_cols=59 Identities=27% Similarity=0.445 Sum_probs=37.3
Q ss_pred HHHHcCCCCCCeEEEEEe-ecCCcceEEEeeCCcCcCCccCchHHHhhcccc-ceecccCCEEEEE
Q 024476 34 MMENLLLQEGDIVRVKNV-TLPKGTYVKLQPHTKDFLDISNPKAILETTLRN-YSCLTTGDSIMVA 97 (267)
Q Consensus 34 mm~~L~l~~gd~V~I~~~-~LPkGt~vkLqP~s~~Fl~isnpKavLE~~LRn-ystLT~Gd~I~I~ 97 (267)
||.. ++.|+.|.-.-+ .-+.|-||.|.+.-..|+-+++-.. ...++ ...+..||+|.+.
T Consensus 1 ~~~~--~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~---~~~~~~~~~~~vGD~I~vk 61 (123)
T PRK08059 1 MMSQ--YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITH---GFVKDIHDFLSVGDEVKVK 61 (123)
T ss_pred Cccc--CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCc---ccccCHHHcCCCCCEEEEE
Confidence 4555 567888876655 4478999999876666664332110 01122 3568899999875
No 66
>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=36.45 E-value=1.5e+02 Score=20.73 Aligned_cols=33 Identities=24% Similarity=0.390 Sum_probs=22.6
Q ss_pred ecccCCEEEEEECCEE-EEEEEEEecCCCeeEEE
Q 024476 87 CLTTGDSIMVAYNNKK-YYIDIIETKPSNAISII 119 (267)
Q Consensus 87 tLT~Gd~I~I~yn~~~-y~l~V~e~kP~~aVsII 119 (267)
.+..||++.+.+++.. +.++-+...+...+-+.
T Consensus 24 ~~~~gdivv~~~~~~~~~~iKrv~~~~~~~~~~~ 57 (70)
T PF00717_consen 24 EPKDGDIVVVKIDGDEELYIKRVVGEPGGIILIS 57 (70)
T ss_dssp ---TTSEEEEEETTEESEEEEEEEEETTEEEEE-
T ss_pred CCccCeEEEEEECCceeeEEEEEEEeCCCEEEEe
Confidence 5568999999999887 77777666776666554
No 67
>PRK05807 hypothetical protein; Provisional
Probab=35.94 E-value=1.3e+02 Score=25.16 Aligned_cols=55 Identities=22% Similarity=0.318 Sum_probs=35.5
Q ss_pred CCCCCCeEEEEEe-ecCCcceEEEeeCCcCcCCccCchHHHhhcccc-ceecccCCEEEEE
Q 024476 39 LLQEGDIVRVKNV-TLPKGTYVKLQPHTKDFLDISNPKAILETTLRN-YSCLTTGDSIMVA 97 (267)
Q Consensus 39 ~l~~gd~V~I~~~-~LPkGt~vkLqP~s~~Fl~isnpKavLE~~LRn-ystLT~Gd~I~I~ 97 (267)
.++.|+.|.-.-. ..+-|-||.| .....|+-+++... ...++ +..|..||.|.+.
T Consensus 2 ~~~vG~vv~G~Vt~i~~~GafV~L-~~~~Glvhiseis~---~~v~~~~~~~kvGd~V~Vk 58 (136)
T PRK05807 2 TLKAGSILEGTVVNITNFGAFVEV-EGKTGLVHISEVAD---TYVKDIREHLKEQDKVKVK 58 (136)
T ss_pred CccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEhhhccc---ccccCccccCCCCCEEEEE
Confidence 4677888876654 4699999999 44456665543321 11222 3558999998864
No 68
>cd05828 Sortase_D_4 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-4. These sortases recognize a unique sorting signal (LPXTA) and they constitute a specialized sorting pathway found in bacilli. Their substrates are predicted to be predominantly enzymes such as 5'-nucleotidases, glycosyl hydrolase, and subtilase.
Probab=35.31 E-value=62 Score=26.32 Aligned_cols=31 Identities=23% Similarity=0.286 Sum_probs=25.1
Q ss_pred ccccceecccCCEEEEEECCEEEEEEEEEec
Q 024476 81 TLRNYSCLTTGDSIMVAYNNKKYYIDIIETK 111 (267)
Q Consensus 81 ~LRnystLT~Gd~I~I~yn~~~y~l~V~e~k 111 (267)
.+++...|..||.|.|...+..|...|.+++
T Consensus 55 ~F~~L~~l~~Gd~i~v~~~~~~~~Y~V~~~~ 85 (127)
T cd05828 55 HFRFLGELEPGDIITLQTLGGTYTYRVTSTR 85 (127)
T ss_pred hhhChhcCCCCCEEEEEECCEEEEEEEeeEE
Confidence 3555566779999999999999998887753
No 69
>cd05830 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5 represented by Streptomyces avermitilis SAV4337. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=35.15 E-value=60 Score=26.85 Aligned_cols=30 Identities=20% Similarity=0.310 Sum_probs=24.4
Q ss_pred cccceecccCCEEEEEECCEEEEEEEEEec
Q 024476 82 LRNYSCLTTGDSIMVAYNNKKYYIDIIETK 111 (267)
Q Consensus 82 LRnystLT~Gd~I~I~yn~~~y~l~V~e~k 111 (267)
+++...|..||.|.|...+..|...|.+++
T Consensus 60 F~~L~~l~~Gd~i~v~~~~~~~~Y~V~~~~ 89 (137)
T cd05830 60 FNDLDKLRPGDKIVVETADGWYTYVVRSSE 89 (137)
T ss_pred cccHhhCCCCCEEEEEECCeEEEEEEeEEE
Confidence 455566889999999999988988887754
No 70
>TIGR01076 sortase_fam LPXTG-site transpeptidase (sortase) family protein. of an LPXTG motif to the cell wall. It also includes a protein required for correct assembly of an LPXTG-containing fimbrial protein, a set of homologous proteins from Streptococcus pneumoniae, in which LPXTG proteins are common. However, related proteins are found in Bacillus subtilis and Methanobacterium thermoautotrophicum, in which LPXTG-mediated cell wall attachment is not known.
Probab=34.76 E-value=56 Score=26.97 Aligned_cols=28 Identities=21% Similarity=0.300 Sum_probs=22.0
Q ss_pred ccceecccCCEEEEEECCEEEEEEEEEe
Q 024476 83 RNYSCLTTGDSIMVAYNNKKYYIDIIET 110 (267)
Q Consensus 83 RnystLT~Gd~I~I~yn~~~y~l~V~e~ 110 (267)
++...|.+||.|.|...+..|...|.++
T Consensus 59 ~~L~~l~~GD~i~v~~~~~~~~Y~V~~~ 86 (136)
T TIGR01076 59 TNLDKLKKGDMLYLHVGNEVLTYQVTST 86 (136)
T ss_pred CCHHHCCCCCEEEEEECCcEEEEEEEEE
Confidence 3344477999999999988888888764
No 71
>cd02784 MopB_CT_PHLH The MopB_CT_PHLH CD includes a group of related uncharacterized putative hydrogenase-like homologs (PHLH) of molybdopterin binding proteins. This CD is of the PHLH region homologous to the conserved molybdopterin-binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=33.44 E-value=63 Score=27.22 Aligned_cols=27 Identities=26% Similarity=0.371 Sum_probs=24.4
Q ss_pred CCeEeccHHHHHHcCCCCCCeEEEEEe
Q 024476 25 EGMIYMPYWMMENLLLQEGDIVRVKNV 51 (267)
Q Consensus 25 EG~i~LP~Wmm~~L~l~~gd~V~I~~~ 51 (267)
+..|+|-.--.+.|+|.+||.|+|.+-
T Consensus 37 ~~~v~InP~dA~~lGI~dGD~V~V~s~ 63 (137)
T cd02784 37 DNAALVSPRTAEALGLLQGDVVRIRRG 63 (137)
T ss_pred CceEEECHHHHHHcCCCCCCEEEEEeC
Confidence 678999999999999999999999864
No 72
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=32.63 E-value=4.3e+02 Score=27.62 Aligned_cols=94 Identities=14% Similarity=0.234 Sum_probs=67.2
Q ss_pred CcEEEEEeeeeeeCCCeEecc-------HHHHHHcCCCCCCeEEEEEee-cCCcceEEEeeCCcCcCCccCchHHHhhcc
Q 024476 11 ERVSHCGVLEFIAEEGMIYMP-------YWMMENLLLQEGDIVRVKNVT-LPKGTYVKLQPHTKDFLDISNPKAILETTL 82 (267)
Q Consensus 11 ~r~th~GVLEF~A~EG~i~LP-------~Wmm~~L~l~~gd~V~I~~~~-LPkGt~vkLqP~s~~Fl~isnpKavLE~~L 82 (267)
+....|=|+++-.+.++|-|- +|-+-.=...+|+.+.-+-+. .|.|-||.|.|-=..|.-+|.. .+
T Consensus 239 Gd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEi------sw 312 (541)
T COG0539 239 GDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEI------SW 312 (541)
T ss_pred CCEEEEEEEEEccCCCeEEEEehhcccCcHHHHhhhcCCCCEEEEEEEEeecCcEEEEecCCccceeechhh------cc
Confidence 346779999999999999864 676666678899999888765 5999999999988888876621 22
Q ss_pred ccce----ecccCCEEEEE-----ECCEEEEEEEEEe
Q 024476 83 RNYS----CLTTGDSIMVA-----YNNKKYYIDIIET 110 (267)
Q Consensus 83 Rnys----tLT~Gd~I~I~-----yn~~~y~l~V~e~ 110 (267)
.+.. .|..||++.+. ..++.-.|-+-.+
T Consensus 313 ~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~ 349 (541)
T COG0539 313 TKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQL 349 (541)
T ss_pred cccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhh
Confidence 2222 26789988764 3345555555444
No 73
>COG0243 BisC Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]
Probab=31.92 E-value=71 Score=33.53 Aligned_cols=29 Identities=28% Similarity=0.415 Sum_probs=26.6
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 024476 23 AEEGMIYMPYWMMENLLLQEGDIVRVKNV 51 (267)
Q Consensus 23 A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~ 51 (267)
.+++.|+|-+--++.|||++||+|+|.+.
T Consensus 668 ~~~~~v~inp~DA~~~GI~~GD~V~V~~~ 696 (765)
T COG0243 668 APRPFVWINPEDAAKLGIKDGDLVRVENR 696 (765)
T ss_pred CCCceEEECHHHHHHcCCCcCCEEEEEcC
Confidence 57789999999999999999999999875
No 74
>cd06165 Sortase_A_1 Sortase A (SrtA) or subfamily-1 sortases are cysteine transpeptidases found in gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal (usually a pentapeptide motif), and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. This group contains a subset of Class A (subfamily-1) sortases, excluding SrtA from Staphylococcus aureus. Sortase A cleaves between threonine and glycine of the LPXTG motif in a wide range of protein substrates. It affects the ability of a pathogen to establish successful infection. Sortase A contains an N-terminal region that functions as both a signal peptide for secretion and a stop-tra
Probab=31.42 E-value=73 Score=25.75 Aligned_cols=28 Identities=18% Similarity=0.288 Sum_probs=22.0
Q ss_pred cceecccCCEEEEEECCEEEEEEEEEec
Q 024476 84 NYSCLTTGDSIMVAYNNKKYYIDIIETK 111 (267)
Q Consensus 84 nystLT~Gd~I~I~yn~~~y~l~V~e~k 111 (267)
+...|.+||.|.|...+..|...|.+.+
T Consensus 60 ~L~~l~~Gd~I~l~~~~~~~~Y~V~~~~ 87 (127)
T cd06165 60 PLYKVKVGDKIYLTDKDNVYEYKVTSKK 87 (127)
T ss_pred CHHHCcCCCEEEEEECCEEEEEEEeeEE
Confidence 3344558999999999999998887653
No 75
>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily. This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.
Probab=31.40 E-value=1e+02 Score=32.42 Aligned_cols=71 Identities=20% Similarity=0.282 Sum_probs=46.9
Q ss_pred CCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccCchHHHhhccccceecccCCEEEEEE
Q 024476 24 EEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAY 98 (267)
Q Consensus 24 ~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~~Fl~isnpKavLE~~LRnystLT~Gd~I~I~y 98 (267)
.-|.+.|..-.|..|++.+||.|.|..- -+.+..+.-|...+ +...----|...+|....+..||.+.|+-
T Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (733)
T TIGR01243 15 GRGIVRIDRQTAARLGVEPGDFVEIEKG--DRSVVAIVWPLRPD--DEGRGIIRMDGYLRANAGVTIGDTVTVER 85 (733)
T ss_pred CCCeEeeCHHHHHhcCCCCCCEEEEecC--CCceeEEEEecCcc--ccCCCEEeecHHHHhhcCCCCCCeEEEee
Confidence 3478999999999999999999999831 11234455543222 12211222456677777799999999864
No 76
>cd00004 Sortase Sortases are cysteine transpeptidases, found in gram-positive bacteria, that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The different classes are called Sortase A or SrtA (subfamily 1), B or SrtB (subfamily 2), C or SrtC (subfamily3), D or SrtD (subfamilies 4 and 5), and E or SrtE. In two different sortase subfamilies, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one s
Probab=31.28 E-value=77 Score=25.48 Aligned_cols=26 Identities=23% Similarity=0.364 Sum_probs=21.7
Q ss_pred eecccCCEEEEEECCEEEEEEEEEec
Q 024476 86 SCLTTGDSIMVAYNNKKYYIDIIETK 111 (267)
Q Consensus 86 stLT~Gd~I~I~yn~~~y~l~V~e~k 111 (267)
..|..||.|.|...+..|...|.+++
T Consensus 63 ~~l~~Gd~v~v~~~~~~~~Y~V~~~~ 88 (128)
T cd00004 63 DNLKKGDKIYLTDGGKTYVYKVTSIL 88 (128)
T ss_pred HHCCCCCEEEEEECCEEEEEEEEEEE
Confidence 34667999999999999999988754
No 77
>TIGR03711 acc_sec_asp3 accessory Sec system protein Asp3. This protein is designated Asp3 because, along with SecY2, SecA2, and other proteins it is part of the accessory Sec system. The system is involved in the export of serine-rich glycoproteins important for virulence in a number of Gram-positive species, including Streptococcus gordonii and Staphylococcus aureus. This protein family is assigned to transport rather than glycosylation function, but the specific molecular role is unknown.
Probab=31.27 E-value=1.4e+02 Score=25.59 Aligned_cols=20 Identities=20% Similarity=0.350 Sum_probs=14.9
Q ss_pred CCCeEEEEEeecCCcceEEE
Q 024476 42 EGDIVRVKNVTLPKGTYVKL 61 (267)
Q Consensus 42 ~gd~V~I~~~~LPkGt~vkL 61 (267)
+.+.|..++--+|.|+-+.-
T Consensus 23 ~~~~V~feN~lMpsG~~I~~ 42 (135)
T TIGR03711 23 SDNEVYFENPLMPSGETIHT 42 (135)
T ss_pred cCCcEEEeccCCCCCCEEEE
Confidence 34568888888899987763
No 78
>PRK09376 rho transcription termination factor Rho; Provisional
Probab=29.71 E-value=87 Score=31.57 Aligned_cols=38 Identities=29% Similarity=0.365 Sum_probs=30.0
Q ss_pred cEEEEEeeeee---------------eCCCeEeccHHHHHHcCCCCCCeEEEE
Q 024476 12 RVSHCGVLEFI---------------AEEGMIYMPYWMMENLLLQEGDIVRVK 49 (267)
Q Consensus 12 r~th~GVLEF~---------------A~EG~i~LP~Wmm~~L~l~~gd~V~I~ 49 (267)
.....||||.. +.+.-||+|..+.+..+|+.||.|.=.
T Consensus 48 ~~~~~g~le~~~~g~gflr~~~~~y~~~~~d~yvs~~~ir~~~lr~gd~v~g~ 100 (416)
T PRK09376 48 DIFGEGVLEILPDGFGFLRSPDANYLPGPDDIYVSPSQIRRFNLRTGDTVEGK 100 (416)
T ss_pred ceEEEEEEEEcCCCCeEEeCCCcCCCCCCCCeeeCHHHHHhcCCCCCCEEEEE
Confidence 35679999933 233559999999999999999988754
No 79
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=29.04 E-value=90 Score=24.10 Aligned_cols=59 Identities=17% Similarity=0.210 Sum_probs=38.9
Q ss_pred CCCCCeEEEEEeecCC---cceEEEeeCCcCcCCccCchHHHhhcccc-ceecccCCEEEEEE
Q 024476 40 LQEGDIVRVKNVTLPK---GTYVKLQPHTKDFLDISNPKAILETTLRN-YSCLTTGDSIMVAY 98 (267)
Q Consensus 40 l~~gd~V~I~~~~LPk---Gt~vkLqP~s~~Fl~isnpKavLE~~LRn-ystLT~Gd~I~I~y 98 (267)
.+.|+++.-+-+++-+ |-||.|-+.-..|+-+++.-...=...++ -..|.+||.|.+..
T Consensus 5 ~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV 67 (88)
T cd04453 5 PIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQV 67 (88)
T ss_pred CCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEE
Confidence 4578888877666544 99999998777888776431111012223 34588999998764
No 80
>PF10636 hemP: Hemin uptake protein hemP; InterPro: IPR019600 This entry represents bacterial proteins that are involved in the uptake of the iron source hemin []. ; PDB: 2JRA_B 2LOJ_A.
Probab=29.02 E-value=1.1e+02 Score=20.99 Aligned_cols=22 Identities=14% Similarity=0.321 Sum_probs=18.4
Q ss_pred cccCCEEEEEECCEEEEEEEEE
Q 024476 88 LTTGDSIMVAYNNKKYYIDIIE 109 (267)
Q Consensus 88 LT~Gd~I~I~yn~~~y~l~V~e 109 (267)
+--+..|.|.|++..|.|++..
T Consensus 9 ~~~~~ev~I~H~g~~Y~LR~Tr 30 (38)
T PF10636_consen 9 FGGGREVRIEHGGQIYRLRITR 30 (38)
T ss_dssp TTTTSEEEEEETTEEEEEEEET
T ss_pred hCCCCEEEEEeCCeEEEeeEcc
Confidence 3456889999999999999864
No 81
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=28.25 E-value=3.2e+02 Score=27.94 Aligned_cols=84 Identities=12% Similarity=0.194 Sum_probs=54.3
Q ss_pred CCcEEEEEeeeeeeCCCeEeccHH--HHH---------HcCCCCCCeEEEEEee-cCCcceEEEeeCCcCcCCccCchHH
Q 024476 10 AERVSHCGVLEFIAEEGMIYMPYW--MME---------NLLLQEGDIVRVKNVT-LPKGTYVKLQPHTKDFLDISNPKAI 77 (267)
Q Consensus 10 ~~r~th~GVLEF~A~EG~i~LP~W--mm~---------~L~l~~gd~V~I~~~~-LPkGt~vkLqP~s~~Fl~isnpKav 77 (267)
-+....|=|+++-.+.+.+.|-.- +.+ --.+.+|++|...-+. .+.|-||.|. .-..|+-+++.-.
T Consensus 165 vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdlg-gv~Glv~~Sels~- 242 (486)
T PRK07899 165 IGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLG-GVDGLVHVSELSW- 242 (486)
T ss_pred CCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHCCC-
Confidence 356789999999999999998843 221 1257899998877654 5789999994 2334654332211
Q ss_pred Hhhccccc-eecccCCEEEEE
Q 024476 78 LETTLRNY-SCLTTGDSIMVA 97 (267)
Q Consensus 78 LE~~LRny-stLT~Gd~I~I~ 97 (267)
....+. ..+..||.|.+.
T Consensus 243 --~~v~~~~~~~kvGd~V~vk 261 (486)
T PRK07899 243 --KHIDHPSEVVEVGQEVTVE 261 (486)
T ss_pred --cccCCHHHhcCCCCEEEEE
Confidence 111221 246789988765
No 82
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=27.91 E-value=96 Score=21.92 Aligned_cols=27 Identities=19% Similarity=0.556 Sum_probs=22.5
Q ss_pred cccCCEEEEEE-CCEEEEEEEEEecCCC
Q 024476 88 LTTGDSIMVAY-NNKKYYIDIIETKPSN 114 (267)
Q Consensus 88 LT~Gd~I~I~y-n~~~y~l~V~e~kP~~ 114 (267)
|.+|+.+.+.+ ++..|.=.|+++++.+
T Consensus 1 ~~vG~~v~~~~~~~~~y~A~I~~~r~~~ 28 (55)
T PF11717_consen 1 FEVGEKVLCKYKDGQWYEAKILDIREKN 28 (55)
T ss_dssp --TTEEEEEEETTTEEEEEEEEEEEECT
T ss_pred CCcCCEEEEEECCCcEEEEEEEEEEecC
Confidence 46899999999 9999999999988754
No 83
>PRK07252 hypothetical protein; Provisional
Probab=27.81 E-value=1.8e+02 Score=23.99 Aligned_cols=54 Identities=26% Similarity=0.411 Sum_probs=33.0
Q ss_pred CCCCeEEEEEe-ecCCcceEEEeeCCcCcCCccCchHHHhhcccc-ceecccCCEEEEE
Q 024476 41 QEGDIVRVKNV-TLPKGTYVKLQPHTKDFLDISNPKAILETTLRN-YSCLTTGDSIMVA 97 (267)
Q Consensus 41 ~~gd~V~I~~~-~LPkGt~vkLqP~s~~Fl~isnpKavLE~~LRn-ystLT~Gd~I~I~ 97 (267)
+.|+.+.-.-+ -.+.|-||.|.+.-..|+-+++... ....+ ...+..||+|.+.
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~---~~~~~~~~~~~vGD~V~Vk 57 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKT---GFIDNIHQLLKVGEEVLVQ 57 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCC---ccccChhhccCCCCEEEEE
Confidence 45776665544 3478999999877667775543321 11111 2447889998864
No 84
>PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A.
Probab=27.45 E-value=76 Score=23.87 Aligned_cols=73 Identities=11% Similarity=0.106 Sum_probs=34.9
Q ss_pred CCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEee----CCcCcCCccCchHHHhhccccceecccCCEEEEEECC
Q 024476 25 EGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQP----HTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNN 100 (267)
Q Consensus 25 EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP----~s~~Fl~isnpKavLE~~LRnystLT~Gd~I~I~yn~ 100 (267)
.+.++||...++..++.+.....|...+ +.|..-.++= .+..++=-..|+.+... -.|-.||.+.+.+.+
T Consensus 13 ~~~l~iP~~f~~~~~~~~~~~~~v~l~~-~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv~~-----n~L~~GD~~~F~~~~ 86 (100)
T PF02362_consen 13 SCRLIIPKEFAKKHGGNKRKSREVTLKD-PDGRSWPVKLKYRKNSGRYYLTGGWKKFVRD-----NGLKEGDVCVFELIG 86 (100)
T ss_dssp TT-EEE-HHHHTTTS--SS--CEEEEEE-TTTEEEEEEEEEECCTTEEEEETTHHHHHHH-----CT--TT-EEEEEE-S
T ss_pred CCEEEeCHHHHHHhCCCcCCCeEEEEEe-CCCCEEEEEEEEEccCCeEEECCCHHHHHHH-----cCCCCCCEEEEEEec
Confidence 4679999999998876643333333333 7775543333 11121111355544322 247799999999864
Q ss_pred -EEE
Q 024476 101 -KKY 103 (267)
Q Consensus 101 -~~y 103 (267)
..+
T Consensus 87 ~~~~ 90 (100)
T PF02362_consen 87 NSNF 90 (100)
T ss_dssp SSCE
T ss_pred CCCc
Confidence 444
No 85
>COG0836 {ManC} Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane]
Probab=27.19 E-value=1.3e+02 Score=29.62 Aligned_cols=75 Identities=12% Similarity=0.241 Sum_probs=54.8
Q ss_pred eEEEEEeecCCcceEEEeeCCcCcCCccCchHHHhhcccc-ceecccCCEEEEEEC-CEEEE----EEEEEecCCCeeEE
Q 024476 45 IVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRN-YSCLTTGDSIMVAYN-NKKYY----IDIIETKPSNAISI 118 (267)
Q Consensus 45 ~V~I~~~~LPkGt~vkLqP~s~~Fl~isnpKavLE~~LRn-ystLT~Gd~I~I~yn-~~~y~----l~V~e~kP~~aVsI 118 (267)
-+.|.|.-+.|..-+..-|.+-.+-||-+|.|+.|-.-+. --....||++.+.-. +..|. +.++.++ =+-|
T Consensus 246 ~iSIDYAiMEkt~~~aVVp~~f~WsDlGsW~Al~~~~~~d~~gNv~~gd~~~~dt~n~~v~s~~~lia~vGl~---DlvV 322 (333)
T COG0836 246 AISIDYAIMEKTSKAAVVPADFGWSDLGSWHALWEVLDKDENGNVCEGDVVTIDTENSLISSNNKLISVVGLE---DLVV 322 (333)
T ss_pred ccchhHHHHhhhcceEEEecCCCcccccCHHHHHHHhhcCCCCCEEecceEEeccCCcEEEeCCceEEEeccc---eEEE
Confidence 4667788888999999999998899999999999877664 355778999888643 34443 3444433 3555
Q ss_pred EeCc
Q 024476 119 IETD 122 (267)
Q Consensus 119 IeTD 122 (267)
|+|+
T Consensus 323 V~t~ 326 (333)
T COG0836 323 VDTK 326 (333)
T ss_pred EecC
Confidence 5554
No 86
>KOG2086 consensus Protein tyrosine phosphatase SHP1/Cofactor for p97 ATPase-mediated vesicle membrane fusion [Nuclear structure]
Probab=27.07 E-value=27 Score=34.70 Aligned_cols=16 Identities=44% Similarity=0.962 Sum_probs=14.2
Q ss_pred CCcccceeeeccccCC
Q 024476 159 EPKFSPFTGVARRLDG 174 (267)
Q Consensus 159 ~~~~~~F~G~G~rLdG 174 (267)
.+.|.+|+|.|+||.+
T Consensus 252 ~~~~~pF~G~Gq~LGs 267 (380)
T KOG2086|consen 252 KPVFKPFSGEGQRLGS 267 (380)
T ss_pred CcccCCCCCcCeecCC
Confidence 4569999999999997
No 87
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=26.80 E-value=1.6e+02 Score=23.07 Aligned_cols=48 Identities=23% Similarity=0.578 Sum_probs=31.4
Q ss_pred ceecccCCEEEEEECC-------EEEEE-EEEEec-----C------------CCeeEEEeCceeeeecCCCC
Q 024476 85 YSCLTTGDSIMVAYNN-------KKYYI-DIIETK-----P------------SNAISIIETDCEVDFAPPLD 132 (267)
Q Consensus 85 ystLT~Gd~I~I~yn~-------~~y~l-~V~e~k-----P------------~~aVsIIeTDleVDf~pPld 132 (267)
|-.+..||++.|..++ +.|++ .|+.+. | ..-|+.|++|....+.+++|
T Consensus 3 FL~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~ggaR~P~~~tlFQVadVDtG~I~wVnaD~Vt~Iv~~~~ 75 (75)
T PF11302_consen 3 FLSVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGGARDPKVPTLFQVADVDTGVIRWVNADEVTHIVPSLD 75 (75)
T ss_pred ccccCCCCEEEEecCccccccCCCCcEEEEEEEEeccccCCCCCceEEEEEccCCeEEEEEchheeeeeeccC
Confidence 4456678888887665 34443 244432 2 14689999999998888764
No 88
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=25.98 E-value=2.1e+02 Score=20.71 Aligned_cols=42 Identities=14% Similarity=0.165 Sum_probs=27.0
Q ss_pred cCCcceEEEeeCCcCcCCccCchHHHhhcccc-ceecccCCEEEEE
Q 024476 53 LPKGTYVKLQPHTKDFLDISNPKAILETTLRN-YSCLTTGDSIMVA 97 (267)
Q Consensus 53 LPkGt~vkLqP~s~~Fl~isnpKavLE~~LRn-ystLT~Gd~I~I~ 97 (267)
.+.|-||+|.|.-..|+-+++... ....+ ...+..||.|.+.
T Consensus 14 ~~~G~~V~l~~gv~G~i~~s~l~~---~~~~~~~~~~~vG~~v~~k 56 (71)
T cd05696 14 PDLGAVFELKDGLLGFVHISHLSD---DKVPSDTGPFKAGTTHKAR 56 (71)
T ss_pred cCceEEEEeCCCCEEEEEHHHCCc---chhcCcccccCCCCEEEEE
Confidence 489999999886667775543211 11222 4558899988754
No 89
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=25.84 E-value=1.1e+02 Score=21.51 Aligned_cols=22 Identities=18% Similarity=0.071 Sum_probs=19.5
Q ss_pred eccHHHHHHcCCCCCCeEEEEE
Q 024476 29 YMPYWMMENLLLQEGDIVRVKN 50 (267)
Q Consensus 29 ~LP~Wmm~~L~l~~gd~V~I~~ 50 (267)
.+|.+-.+.|+|.+|+.|.+..
T Consensus 38 ~i~~~~~~~l~l~~G~~v~~~i 59 (69)
T TIGR00638 38 VITLESVAELGLKPGKEVYAVI 59 (69)
T ss_pred EecHHHHhhCCCCCCCEEEEEE
Confidence 6999999999999999887654
No 90
>PF01272 GreA_GreB: Transcription elongation factor, GreA/GreB, C-term; InterPro: IPR001437 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 2P4V_E 2ETN_B 3BMB_B 2PN0_D 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A.
Probab=25.35 E-value=1.2e+02 Score=22.60 Aligned_cols=24 Identities=21% Similarity=0.317 Sum_probs=18.9
Q ss_pred cccCCEEEEEECCEEEEEEEEEec
Q 024476 88 LTTGDSIMVAYNNKKYYIDIIETK 111 (267)
Q Consensus 88 LT~Gd~I~I~yn~~~y~l~V~e~k 111 (267)
...||++.+...+..+.+.|++++
T Consensus 53 ~~~Gd~v~~~~~~g~~~~~I~~I~ 76 (77)
T PF01272_consen 53 KKVGDEVEVELPGGERKYEILEIE 76 (77)
T ss_dssp -BTT-EEEEEETTBEEEEEEEEEE
T ss_pred CCCCCEEEEEeCCceEEEEEEEEE
Confidence 468999999999888888888763
No 91
>PF11644 DUF3256: Protein of unknown function (DUF3256); InterPro: IPR021670 This family of proteins with unknown function appears to be restricted to Bacteroidales. ; PDB: 2P3P_B.
Probab=25.34 E-value=97 Score=28.11 Aligned_cols=51 Identities=18% Similarity=0.258 Sum_probs=37.5
Q ss_pred cCchHHHhhccccceecc--cCCEEEEEECC-EEEEEEEEEecCC-CeeEEEeCc
Q 024476 72 SNPKAILETTLRNYSCLT--TGDSIMVAYNN-KKYYIDIIETKPS-NAISIIETD 122 (267)
Q Consensus 72 snpKavLE~~LRnystLT--~Gd~I~I~yn~-~~y~l~V~e~kP~-~aVsIIeTD 122 (267)
...||-..|.|-..+.++ ..|.|.|.-++ -..+++++-+... +.||+|.|=
T Consensus 41 ~k~ka~V~N~~gg~s~m~~lT~dYl~vqls~~st~emKlLp~~~~~~vicvV~T~ 95 (199)
T PF11644_consen 41 MKMKAEVKNRFGGTSEMEKLTDDYLSVQLSESSTWEMKLLPLNDSTSVICVVKTV 95 (199)
T ss_dssp S-EEEEEE-TTSSEEEEE-EETTEEEEEETTTEEEEEEEEESSSS-EEEEEEEEE
T ss_pred cCcceeeecccCCEEEEEEeccceEEEEecCCceEEEEEeccCCCCeEEEEEEEe
Confidence 456777888888765543 34999999976 5799999988775 689999864
No 92
>TIGR03698 clan_AA_DTGF clan AA aspartic protease, AF_0612 family. Members of this protein family are clan AA aspartic proteases, related to family TIGR02281. These proteins resemble retropepsins, pepsin-like proteases of retroviruses such as HIV. Members of this family are found in archaea and bacteria.
Probab=25.18 E-value=2.1e+02 Score=22.72 Aligned_cols=40 Identities=23% Similarity=0.267 Sum_probs=30.1
Q ss_pred EEEEeCCCCcEEEEEeeeeeeCCCe---EeccHHHHHHcCCCCCCe
Q 024476 3 FELRNNAAERVSHCGVLEFIAEEGM---IYMPYWMMENLLLQEGDI 45 (267)
Q Consensus 3 F~l~N~~~~r~th~GVLEF~A~EG~---i~LP~Wmm~~L~l~~gd~ 45 (267)
++|+|+.+.. +.-.+|.-|.|. +.||.-+.+.|+|.+...
T Consensus 4 v~~~~p~~~~---~~~v~~LVDTGat~~~~l~~~~a~~lgl~~~~~ 46 (107)
T TIGR03698 4 VELSNPKNPE---FMEVRALVDTGFSGFLLVPPDIVNKLGLPELDQ 46 (107)
T ss_pred EEEeCCCCCC---ceEEEEEEECCCCeEEecCHHHHHHcCCCcccC
Confidence 5788886544 555788777665 359999999999987653
No 93
>PRK07217 replication factor A; Reviewed
Probab=25.14 E-value=1.2e+02 Score=29.41 Aligned_cols=45 Identities=27% Similarity=0.422 Sum_probs=33.8
Q ss_pred EEeCCCCcEEEEEeeeeeeCCCeEeccHHHHH-HcCCCCCCeEEEEEe
Q 024476 5 LRNNAAERVSHCGVLEFIAEEGMIYMPYWMME-NLLLQEGDIVRVKNV 51 (267)
Q Consensus 5 l~N~~~~r~th~GVLEF~A~EG~i~LP~Wmm~-~L~l~~gd~V~I~~~ 51 (267)
|..++.......|+ .-.+.|+|-+=-|=-. ...|++|+.|+|.++
T Consensus 94 l~e~~~~si~qvGl--lgDETG~IkfT~W~~s~~~~leeGd~~rI~na 139 (311)
T PRK07217 94 LWEPSSDSIAQVGL--LGDETGTIKFTKWAKSDLPELEEGKSYLLKNV 139 (311)
T ss_pred ecCCCCCceEEEEE--EEcCCceEEEEEccCCCCCcccCCCEEEEEeE
Confidence 44455566777886 3457899999999873 444999999999976
No 94
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=25.10 E-value=4.4e+02 Score=26.55 Aligned_cols=92 Identities=17% Similarity=0.190 Sum_probs=59.9
Q ss_pred CcEEEEEeeeeeeCCCeEecc-------HHHHHHcCCCCCCeEEEEEe-ecCCcceEEEeeCCcCcCCccCchHHHhhcc
Q 024476 11 ERVSHCGVLEFIAEEGMIYMP-------YWMMENLLLQEGDIVRVKNV-TLPKGTYVKLQPHTKDFLDISNPKAILETTL 82 (267)
Q Consensus 11 ~r~th~GVLEF~A~EG~i~LP-------~Wmm~~L~l~~gd~V~I~~~-~LPkGt~vkLqP~s~~Fl~isnpKavLE~~L 82 (267)
+....|=|+++-.+.+.|.|. +|.--.-.+..|+.|.-+-+ ..+.|-||.|.|-=..|.-+++.-. +..-
T Consensus 341 Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~~~~vG~~v~G~V~~i~~~G~FV~l~~gv~Gli~~se~s~--~~~~ 418 (491)
T PRK13806 341 GDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISR--AGKP 418 (491)
T ss_pred CCEEEEEEEEEEccCCEEEEEEeecccChhHHhhhhCCCCCEEEEEEEEEecCceEEEcCCCcEEEEEHHHcCc--cccc
Confidence 345678899998888998874 56544446778999887765 4599999999875445654332111 1110
Q ss_pred ccceecccCCEEEEEECCEEEEEEEEEecCC
Q 024476 83 RNYSCLTTGDSIMVAYNNKKYYIDIIETKPS 113 (267)
Q Consensus 83 RnystLT~Gd~I~I~yn~~~y~l~V~e~kP~ 113 (267)
.....|..||.|.+ .|+++.++
T Consensus 419 ~~~~~~~~Gd~v~~---------~V~~id~e 440 (491)
T PRK13806 419 ATYEKLKPGDSVTL---------VVEEIDTA 440 (491)
T ss_pred chhhcCCCCCEEEE---------EEEEEeCC
Confidence 11344688998764 56777765
No 95
>PRK10183 hypothetical protein; Provisional
Probab=25.03 E-value=1e+02 Score=22.86 Aligned_cols=22 Identities=9% Similarity=0.366 Sum_probs=19.3
Q ss_pred cccCCEEEEEECCEEEEEEEEE
Q 024476 88 LTTGDSIMVAYNNKKYYIDIIE 109 (267)
Q Consensus 88 LT~Gd~I~I~yn~~~y~l~V~e 109 (267)
|.-+..|.|.+++..|.|++..
T Consensus 27 l~g~~~v~I~H~G~~Y~LR~Tr 48 (56)
T PRK10183 27 LGPDGKVIIDHDGQEYLLRKTQ 48 (56)
T ss_pred hCCCCEEEEEECCcEEEeEEcc
Confidence 6677899999999999999864
No 96
>PRK12678 transcription termination factor Rho; Provisional
Probab=24.70 E-value=1.7e+02 Score=31.31 Aligned_cols=43 Identities=23% Similarity=0.404 Sum_probs=32.6
Q ss_pred EEEEEeeeee------------eCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCc
Q 024476 13 VSHCGVLEFI------------AEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKG 56 (267)
Q Consensus 13 ~th~GVLEF~------------A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkG 56 (267)
...+||||.. +..+-|||+.++....+|..||.|. -.++.|+.
T Consensus 294 ~~~~GiLdi~dg~gFlR~~~y~~~~~Dvyvs~~qirr~~Lr~Gd~v~-G~vr~p~~ 348 (672)
T PRK12678 294 VPVAGILDVLDNYAFVRTSGYLPGPNDVYVSMNQVRKNGLRKGDAVT-GAVRAPRE 348 (672)
T ss_pred eEeeEEEEecCCeeEeeCCCCCCCCCCeeeCHHHHHHcCCCCCCEEE-EeecCCCC
Confidence 4578999933 3445689999999999999999887 33455653
No 97
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=24.43 E-value=1.2e+02 Score=25.99 Aligned_cols=25 Identities=4% Similarity=0.064 Sum_probs=22.0
Q ss_pred ecccCCEEEEEECCEEEEEEEEEec
Q 024476 87 CLTTGDSIMVAYNNKKYYIDIIETK 111 (267)
Q Consensus 87 tLT~Gd~I~I~yn~~~y~l~V~e~k 111 (267)
.+..||+|.|.++...|.|.|+.+.
T Consensus 48 ~V~~gd~l~v~~~~~~~~v~Vl~l~ 72 (133)
T PRK10348 48 IVELNATLTLRQGNDERTVIVKAIT 72 (133)
T ss_pred ccCCCCEEEEEECCEEEEEEEeECc
Confidence 3568999999999999999999864
No 98
>TIGR02693 arsenite_ox_L arsenite oxidase, large subunit. This model represents the large subunit of an arsenite oxidase complex. The small subunit is a Rieske protein. Homologs to both large and small subunits that score in the gray zone between the set trusted and noise bit score cutoffs for the respective models are found in Aeropyrum pernix K1 and in Sulfolobus tokodaii str. 7. This enzyme acts in energy metabolim by arsenite oxidation, rather than detoxification by reduction of arsenate to arsenite prior to export.
Probab=24.42 E-value=89 Score=33.50 Aligned_cols=49 Identities=24% Similarity=0.148 Sum_probs=35.3
Q ss_pred EEEEeCCCCcEEEEEee-------eeeeCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 024476 3 FELRNNAAERVSHCGVL-------EFIAEEGMIYMPYWMMENLLLQEGDIVRVKNV 51 (267)
Q Consensus 3 F~l~N~~~~r~th~GVL-------EF~A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~ 51 (267)
|.|.+.......|.+.. .-..++..|+|-.--++.|||.+||.|+|.+-
T Consensus 695 l~L~tgr~~~~~~s~~~~~~~~~l~~~~p~p~v~InP~DA~~lGI~dGD~V~V~n~ 750 (806)
T TIGR02693 695 FWVNNGRANTVWQSAYHDQHNDFVALRLPLPYIEVNPEDAKRLGLKSGDLVEVYND 750 (806)
T ss_pred EEEEecCccceecCCcccCCcHHHHhcCCCCEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 55666554434444432 22347788999999999999999999999764
No 99
>PF04203 Sortase: Sortase family; InterPro: IPR005754 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C60 (clan C-) and include the members of both subfamilies of sortases. The Staphylococcus aureus sortase is a transpeptidase that attaches surface proteins to the cell wall; it cleaves between the Gly and Thr of the LPXTG motif and catalyses the formation of an amide bond between the carboxyl-group of threonine and the amino-group of the cell-wall peptidoglycan []. Sortase homologues are found in almost all Gram-positives, a single Gram-negative (Shewanella putrefaciens) and an archaean (Methanobacterium thermoautotrophicum), where cell wall LPXTG-mediated decoration has not been reported [, ]. Surface proteins not only promote interaction between the invading pathogen and animal tissues, but also provide ingenious strategies for bacterial escape from the host's immune response. In the case of S. aureus protein A, immunoglobulins are captured on the microbial surface and camouflage bacteria during the invasion of host tissues. S. aureus mutants lacking the srtA gene fail to anchor and display some surface proteins and are impaired in the ability to cause animal infections. Sortase acts on surface proteins that are initiated into the secretion (Sec) pathway and have their signal peptide removed by signal peptidase. The S. aureus genome encodes two sets of sortase and secretion genes. It is conceivable that S. aureus has evolved more than one pathway for the transport of 20 surface proteins to the cell wall envelope. ; PDB: 2W1K_A 2OQZ_A 1RZ2_A 2OQW_A 1T2W_A 1IJA_A 1T2P_A 1T2O_C 2KID_A 3RCC_N ....
Probab=24.31 E-value=1.3e+02 Score=23.84 Aligned_cols=24 Identities=29% Similarity=0.499 Sum_probs=18.6
Q ss_pred cccCCEEEEEE-CCEEEEEEEEEec
Q 024476 88 LTTGDSIMVAY-NNKKYYIDIIETK 111 (267)
Q Consensus 88 LT~Gd~I~I~y-n~~~y~l~V~e~k 111 (267)
|..||.|.|.. +++.|...|.+++
T Consensus 61 ~~~gd~i~~~~~~g~~~~Y~V~~~~ 85 (128)
T PF04203_consen 61 LKKGDEIYLTTPDGKTYEYRVTSVK 85 (128)
T ss_dssp GHTT-EEEEEETSSEEEEEEEEEEE
T ss_pred cCCCCEEEEEEecCEEEEEEEEEEE
Confidence 38999999999 7888788877654
No 100
>PTZ00061 DNA-directed RNA polymerase; Provisional
Probab=24.05 E-value=96 Score=28.46 Aligned_cols=31 Identities=19% Similarity=0.312 Sum_probs=25.8
Q ss_pred HHHHHHcCCCCCCeEEEEEeecCCcceEEEe
Q 024476 32 YWMMENLLLQEGDIVRVKNVTLPKGTYVKLQ 62 (267)
Q Consensus 32 ~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLq 62 (267)
.-|...+|++.||+|.|..-+--.|.||..+
T Consensus 172 DPvary~g~k~G~vvkI~R~S~taG~~v~YR 202 (205)
T PTZ00061 172 DPVARYFGLSKGQVVKIIRPSETAGRYVTYR 202 (205)
T ss_pred ChhhHhcCCCCCCEEEEEECCCCCCcceEEE
Confidence 3477889999999999998888888888654
No 101
>PF00667 FAD_binding_1: FAD binding domain; InterPro: IPR003097 This domain is found in sulphite reductase, NADPH cytochrome P450 reductase, nitric oxide synthase and methionine synthase reductase. Flavoprotein pyridine nucleotide cytochrome reductases [] (FPNCR) catalyse the interchange of reducing equivalents between one-electron carriers and the two-electron-carrying nicotinamide dinucleotides. The enzymes include ferredoxin:NADP+reductases (FNR) [], plant and fungal NAD(P)H:nitrate reductases [, ], NADH:cytochrome b5 reductases [], NADPH:P450 reductases [], NADPH:sulphite reductases [], nitric oxide synthases [], phthalate dioxygenase reductase [], and various other flavoproteins.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3QFR_B 3FJO_A 3QFC_B 3QE2_B 3QFS_A 3QFT_A 2B5O_B 2QTZ_A 2QTL_A 2BPO_B ....
Probab=23.99 E-value=91 Score=27.55 Aligned_cols=68 Identities=22% Similarity=0.395 Sum_probs=40.4
Q ss_pred EEEeCCCCcEEEEEeeeee-eCCCeEecc---------------HHHHHHcCCCCCCeEEEEEee------cCCcceEEE
Q 024476 4 ELRNNAAERVSHCGVLEFI-AEEGMIYMP---------------YWMMENLLLQEGDIVRVKNVT------LPKGTYVKL 61 (267)
Q Consensus 4 ~l~N~~~~r~th~GVLEF~-A~EG~i~LP---------------~Wmm~~L~l~~gd~V~I~~~~------LPkGt~vkL 61 (267)
+|+++...|.|+. +||. .+.|.-|-| .++++.|++.....|.|.... +|-..-+.|
T Consensus 18 ~Lt~~~~~r~~~h--ieldl~~~~l~Y~pGD~l~V~P~N~~~~V~~~l~~lgl~~d~~v~~~~~~~~~~~~~~~~~~~tl 95 (219)
T PF00667_consen 18 RLTSPGSDRSTRH--IELDLSDSGLSYQPGDHLGVYPPNDPEEVERLLKRLGLDPDEPVTLKPKEQNNSVKPPFPSPITL 95 (219)
T ss_dssp E-SSTTSSSEEEE--EEEE-TTSTG---TT-EEEEE-SSEHHHHHHHHHHHTSGTTSEEEEEESSTTSSCCSSSSSSEEH
T ss_pred EcCCCCCCceEEE--EEEEeCCCCCcccCCCEEEEEccCCHHHHHHHHHHhCCCcceEEEEEecccccccccccccceee
Confidence 3444455555544 6773 344666654 579999999998889888764 455555555
Q ss_pred eeCCcCcCCccC
Q 024476 62 QPHTKDFLDISN 73 (267)
Q Consensus 62 qP~s~~Fl~isn 73 (267)
.=.=+.++||..
T Consensus 96 ~~~l~~~~Di~~ 107 (219)
T PF00667_consen 96 RDLLTHYLDITS 107 (219)
T ss_dssp HHHHHHTB-TSS
T ss_pred eeeeeeeeeccc
Confidence 544445566655
No 102
>COG0187 GyrB Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit [DNA replication, recombination, and repair]
Probab=23.96 E-value=80 Score=33.49 Aligned_cols=46 Identities=26% Similarity=0.375 Sum_probs=41.7
Q ss_pred CCcceEEEeeCCcCcCCccCchHHHhhccccceecccCCEEEEEEC
Q 024476 54 PKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYN 99 (267)
Q Consensus 54 PkGt~vkLqP~s~~Fl~isnpKavLE~~LRnystLT~Gd~I~I~yn 99 (267)
..||.|.|.|-..-|-....--.+|.++||.++.|-.|=.|.++..
T Consensus 165 ~~GT~V~F~PD~~iF~~~~f~~~~l~~RlrelA~L~~gl~I~l~d~ 210 (635)
T COG0187 165 KTGTKVRFKPDPEIFGETEFDYEILKRRLRELAFLNKGVKITLTDE 210 (635)
T ss_pred CCccEEEEEcChHhcCCcccCHHHHHHHHHHHhccCCCCEEEEEec
Confidence 4599999999999998888889999999999999999999988754
No 103
>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=23.77 E-value=62 Score=23.73 Aligned_cols=24 Identities=21% Similarity=0.393 Sum_probs=16.7
Q ss_pred eEeccHHHHHHcCCCCCCeEEEEE
Q 024476 27 MIYMPYWMMENLLLQEGDIVRVKN 50 (267)
Q Consensus 27 ~i~LP~Wmm~~L~l~~gd~V~I~~ 50 (267)
.|+||.-+...+.+.+||.|.|+.
T Consensus 29 l~~i~gK~r~~iwI~~GD~V~V~~ 52 (65)
T PF01176_consen 29 LARIPGKFRKRIWIKRGDFVLVEP 52 (65)
T ss_dssp EEEE-HHHHTCC---TTEEEEEEE
T ss_pred EEEeccceeeeEecCCCCEEEEEe
Confidence 478999988889999999888774
No 104
>TIGR01706 NAPA periplasmic nitrate reductase, large subunit. The enzymes from Alicagenes eutrophus and Paracoccus pantotrophus have been characterized. In E. coli (as well as other organisms) this gene is part of a large nitrate reduction operon (napFDAGHBC).
Probab=23.60 E-value=66 Score=34.37 Aligned_cols=48 Identities=23% Similarity=0.159 Sum_probs=35.3
Q ss_pred EEEEeCCCCcEEEEEee--------eeeeCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 024476 3 FELRNNAAERVSHCGVL--------EFIAEEGMIYMPYWMMENLLLQEGDIVRVKNV 51 (267)
Q Consensus 3 F~l~N~~~~r~th~GVL--------EF~A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~ 51 (267)
|.|.+.......|.+.. +. .+|..|+|-.--++.|||++||.|+|.+.
T Consensus 716 l~L~t~r~~~~~hs~~~~~~~~~l~~~-~~~~~v~I~p~DA~~~GI~dGD~V~V~s~ 771 (830)
T TIGR01706 716 LWLVTGRVLEHWHSGSMTRRVPELYRA-FPEALCFMHPEDAKALGLRRGDEVWVVSR 771 (830)
T ss_pred EEEEcccchHhhcCcCcccchHHHHhh-CCCCEEEECHHHHHHcCCcCCCEEEEEeC
Confidence 44555555445565431 22 36789999999999999999999999875
No 105
>KOG3184 consensus 60S ribosomal protein L7 [Translation, ribosomal structure and biogenesis]
Probab=23.34 E-value=48 Score=30.87 Aligned_cols=47 Identities=30% Similarity=0.391 Sum_probs=38.5
Q ss_pred cCCcceEEEeeCCcCcCCc---------cCchHHHhhcccc-ceecccCCEEEEEEC
Q 024476 53 LPKGTYVKLQPHTKDFLDI---------SNPKAILETTLRN-YSCLTTGDSIMVAYN 99 (267)
Q Consensus 53 LPkGt~vkLqP~s~~Fl~i---------snpKavLE~~LRn-ystLT~Gd~I~I~yn 99 (267)
+=.|+||||-+.+..+|.| .|.|.|-|-.++. |.|++.+-.|.+..|
T Consensus 103 If~g~fVKlnk~~~~mLriVepYVa~G~pnlksv~elI~krG~~k~~~~k~i~ltdn 159 (235)
T KOG3184|consen 103 IFNGTFVKLNKATVNMLRIVEPYIAWGYPNLKSVSELIYKRGYGKKIEKKRIPLTDN 159 (235)
T ss_pred cccceeEEechhhhhhHhhcccceeeccCcHHHHHHHHhhcccccccCCceeccccc
Confidence 4478999999988777765 7999999988886 887899998888833
No 106
>cd03701 IF2_IF5B_II IF2_IF5B_II: This family represents the domain II of prokaryotic Initiation Factor 2 (IF2) and its archeal and eukaryotic homologue aeIF5B. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of the 60S ribosomal subunit. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains in EF1A, eEF1A and aeIF2gamma.
Probab=23.31 E-value=1.1e+02 Score=24.10 Aligned_cols=34 Identities=29% Similarity=0.600 Sum_probs=23.1
Q ss_pred ceecccCCEEEEE--ECCEEEEEE-----EEEecCCCeeEE
Q 024476 85 YSCLTTGDSIMVA--YNNKKYYID-----IIETKPSNAISI 118 (267)
Q Consensus 85 ystLT~Gd~I~I~--yn~~~y~l~-----V~e~kP~~aVsI 118 (267)
--||.+||+|.+- |....-.++ |.+..|..+|.|
T Consensus 24 ~GtL~~Gd~iv~G~~~GkVr~~~d~~g~~v~~a~Ps~~v~i 64 (95)
T cd03701 24 NGTLKKGDVIVAGGTYGKIRTMVDENGKALLEAGPSTPVEI 64 (95)
T ss_pred cCeEecCCEEEECCccceEEEEECCCCCCccccCCCCCEEE
Confidence 3578999999984 444455554 667778777744
No 107
>PRK13532 nitrate reductase catalytic subunit; Provisional
Probab=22.72 E-value=82 Score=33.57 Aligned_cols=48 Identities=21% Similarity=0.126 Sum_probs=36.3
Q ss_pred EEEEeCCCCcEEEEEe--------eeeeeCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 024476 3 FELRNNAAERVSHCGV--------LEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNV 51 (267)
Q Consensus 3 F~l~N~~~~r~th~GV--------LEF~A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~ 51 (267)
|.|.+......+|.+- ++. .++..|+|=.=-++.|||.+||.|+|.+-
T Consensus 716 l~Lit~r~~~~~hs~~~~~~~~~l~~~-~~~~~v~inp~DA~~~GI~dGD~V~V~n~ 771 (830)
T PRK13532 716 LWLSTGRVLEHWHTGSMTRRVPELYRA-FPEAVCFMHPEDAKARGLRRGDEVKVVSR 771 (830)
T ss_pred eEEecccchhhccccCccCchHHHHhh-CCCCEEEECHHHHHHcCCCCCCEEEEEeC
Confidence 5566665555667652 222 36788999999999999999999999875
No 108
>PRK08582 hypothetical protein; Provisional
Probab=22.30 E-value=3.2e+02 Score=23.02 Aligned_cols=56 Identities=20% Similarity=0.303 Sum_probs=36.4
Q ss_pred CCCCCCeEEEEEee-cCCcceEEEeeCCcCcCCccCchHHHhhcccc-ceecccCCEEEEE
Q 024476 39 LLQEGDIVRVKNVT-LPKGTYVKLQPHTKDFLDISNPKAILETTLRN-YSCLTTGDSIMVA 97 (267)
Q Consensus 39 ~l~~gd~V~I~~~~-LPkGt~vkLqP~s~~Fl~isnpKavLE~~LRn-ystLT~Gd~I~I~ 97 (267)
.++.|++|.-.-+. -+-|-||.|-+.-..|+-+++... ....+ ...|+.||.|.+.
T Consensus 2 ~~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~---~~v~~~~~~l~vGD~Vkvk 59 (139)
T PRK08582 2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVAD---NYVKDINDHLKVGDEVEVK 59 (139)
T ss_pred CCcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCc---ccccccccccCCCCEEEEE
Confidence 46788888766554 477999999887677765544321 01111 2568899998864
No 109
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=21.76 E-value=75 Score=23.78 Aligned_cols=16 Identities=25% Similarity=0.453 Sum_probs=12.3
Q ss_pred HHcCCCCCCeEEEEEe
Q 024476 36 ENLLLQEGDIVRVKNV 51 (267)
Q Consensus 36 ~~L~l~~gd~V~I~~~ 51 (267)
..+|+++||+|+|-..
T Consensus 50 ~~~G~~~GD~V~Ig~~ 65 (69)
T TIGR03595 50 RKAGAKDGDTVRIGDF 65 (69)
T ss_pred HHcCCCCCCEEEEccE
Confidence 4567789999999644
No 110
>PF12436 USP7_ICP0_bdg: ICP0-binding domain of Ubiquitin-specific protease 7; InterPro: IPR024729 This domain is found in eukaryotes, and is approximately 40 amino acids in length. It is found in proteins of the peptidase C19 family, which contains contains ubiquitinyl hydrolases like ubiquitin-specific protease 7 (USP7). USP7 regulates the turnover of p53 [].; PDB: 2KVR_A 2YLM_A.
Probab=21.45 E-value=2.6e+02 Score=25.65 Aligned_cols=81 Identities=14% Similarity=0.159 Sum_probs=47.2
Q ss_pred eEEEEeCCCCcEEEEEeeeeeeCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccCchHHHhhc
Q 024476 2 LFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETT 81 (267)
Q Consensus 2 lF~l~N~~~~r~th~GVLEF~A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~~Fl~isnpKavLE~~ 81 (267)
.||.-++.+++..+||-.-.....-..-|=..+.+.||+.++..+.+=--.=| .++.|. |++.-|+.
T Consensus 72 FlK~fDp~~q~L~~iGh~~v~~~~~v~~l~~~i~~~~g~p~~t~l~lyEEi~~----~~ie~i--------~~~~t~~~- 138 (249)
T PF12436_consen 72 FLKYFDPETQTLRYIGHVYVPKNDKVSELVPLINERAGLPPDTPLLLYEEIKP----NMIEPI--------DPNQTFEK- 138 (249)
T ss_dssp EEEEEETTTTEEEEEEEEEEETT-BGGGTHHHHHHHHT--TT--EEEEEEEET----TEEEE----------SSSBHHH-
T ss_pred EEEeeCCCCCEEEEEeEEEECCCCCHHHHHHHHHHHcCCCCCCceEEEEEecc----ceeeEc--------CCCCchhh-
Confidence 46778899999999998877766555556778999999988865554211111 122222 33333333
Q ss_pred cccceecccCCEEEEEEC
Q 024476 82 LRNYSCLTTGDSIMVAYN 99 (267)
Q Consensus 82 LRnystLT~Gd~I~I~yn 99 (267)
+.|.-||+|.+.-.
T Consensus 139 ----~el~~GdIi~fQ~~ 152 (249)
T PF12436_consen 139 ----AELQDGDIICFQRA 152 (249)
T ss_dssp ----TT--TTEEEEEEE-
T ss_pred ----cccCCCCEEEEEec
Confidence 67899999998753
No 111
>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=21.34 E-value=3.7e+02 Score=28.85 Aligned_cols=73 Identities=19% Similarity=0.333 Sum_probs=49.6
Q ss_pred CCCCCCeEEEEEeecCCc-ceEEEeeCCcCcCCcc-------CchHHHhhccccce--ecccCCEEEEEECC-EEEEEEE
Q 024476 39 LLQEGDIVRVKNVTLPKG-TYVKLQPHTKDFLDIS-------NPKAILETTLRNYS--CLTTGDSIMVAYNN-KKYYIDI 107 (267)
Q Consensus 39 ~l~~gd~V~I~~~~LPkG-t~vkLqP~s~~Fl~is-------npKavLE~~LRnys--tLT~Gd~I~I~yn~-~~y~l~V 107 (267)
++.-|+.|.|+.-..+.. .|+-.--.+.||++-. |-..+-+.--|.|. .+|+|..+.+.|++ +.+.+.|
T Consensus 73 ~~Sl~qev~V~~~~~~~~~~~l~~m~le~dF~~k~~~~sep~Dad~ma~qF~~~y~~q~fsvgQ~~~f~f~~~~~l~l~v 152 (744)
T KOG0741|consen 73 GWSLGQEVEVKPFTFDGSCDYLGSMTLEIDFLNKKNTTSEPFDADEMAKQFKRQYNSQAFSVGQQLVFEFNGNKLLGLKV 152 (744)
T ss_pred hcccCceeEEEecccCcccccceeEEEEehhhhcCCCCCCCCCHHHHHHHHHHHhcCcccCCccEEEEEecCceEeeeEE
Confidence 344457899984433333 6777777788888643 33444555555674 49999999999996 7777777
Q ss_pred EEec
Q 024476 108 IETK 111 (267)
Q Consensus 108 ~e~k 111 (267)
..++
T Consensus 153 ~~ie 156 (744)
T KOG0741|consen 153 KDIE 156 (744)
T ss_pred EEEe
Confidence 6654
No 112
>TIGR00767 rho transcription termination factor Rho. Members of this family differ in the specificity of RNA binding.
Probab=21.27 E-value=1.8e+02 Score=29.41 Aligned_cols=36 Identities=25% Similarity=0.356 Sum_probs=29.2
Q ss_pred EEEEEeeeee---------------eCCCeEeccHHHHHHcCCCCCCeEEE
Q 024476 13 VSHCGVLEFI---------------AEEGMIYMPYWMMENLLLQEGDIVRV 48 (267)
Q Consensus 13 ~th~GVLEF~---------------A~EG~i~LP~Wmm~~L~l~~gd~V~I 48 (267)
....||||.. ..+.-||+|..+.+..+|+.||.|.=
T Consensus 49 ~~~~g~le~~~~g~gflr~~~~~~~~~~~d~yvs~~~i~~~~lr~gd~v~g 99 (415)
T TIGR00767 49 IFGEGVLEILPDGFGFLRSPDSSYLPGPDDIYVSPSQIRRFNLRTGDTIEG 99 (415)
T ss_pred eEEEEEEEEcCCCCeEEeCCCcCCCCCCCCeeeCHHHHHhcCCCCCCEEEE
Confidence 5678999932 34556899999999999999998874
No 113
>PLN03111 DNA-directed RNA polymerase II subunit family protein; Provisional
Probab=20.56 E-value=1.2e+02 Score=27.74 Aligned_cols=31 Identities=19% Similarity=0.306 Sum_probs=25.4
Q ss_pred HHHHHHcCCCCCCeEEEEEeecCCcceEEEe
Q 024476 32 YWMMENLLLQEGDIVRVKNVTLPKGTYVKLQ 62 (267)
Q Consensus 32 ~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLq 62 (267)
.-+.+.+|+++||+|.|..-+=-.|.||..+
T Consensus 173 DPvary~g~k~G~vvkI~R~S~taG~~v~YR 203 (206)
T PLN03111 173 DPIARYYGLKRGQVVKIIRPSETAGRYVTYR 203 (206)
T ss_pred ChhhHhcCCCCCCEEEEEECCCCCCCceEEE
Confidence 3477889999999999998887888887654
No 114
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=20.19 E-value=1.5e+02 Score=20.95 Aligned_cols=56 Identities=18% Similarity=0.259 Sum_probs=32.3
Q ss_pred CCCCeEEEEEe-ecCCcceEEEeeCCcCcCCccCchHHHhhccccceecccCCEEEEE
Q 024476 41 QEGDIVRVKNV-TLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVA 97 (267)
Q Consensus 41 ~~gd~V~I~~~-~LPkGt~vkLqP~s~~Fl~isnpKavLE~~LRnystLT~Gd~I~I~ 97 (267)
.+|+.+.-.-. ..+-|-||.|.+.-..|+-+++...- +..++.-..+..||.+.+.
T Consensus 2 ~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~-~~~~~~~~~~~~Gd~v~v~ 58 (72)
T cd05689 2 PEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWT-NKNIHPSKVVSLGDEVEVM 58 (72)
T ss_pred cCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCc-ccccCcccEeCCCCEEEEE
Confidence 34555554433 35779999998765566644433210 1222334568888888764
Done!