Query 020791
Match_columns 321
No_of_seqs 214 out of 347
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 05:11:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020791.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020791hhsearch_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 2E-102 5E-107 732.6 26.7 296 1-321 2-305 (308)
2 PF03152 UFD1: Ubiquitin fusio 100.0 2.3E-74 5E-79 513.9 18.2 173 12-184 1-176 (176)
3 COG5140 UFD1 Ubiquitin fusion- 100.0 1.7E-73 3.7E-78 529.0 21.8 280 11-320 20-310 (331)
4 PLN03086 PRLI-interacting fact 100.0 3.7E-60 8.1E-65 481.8 22.0 173 10-189 75-263 (567)
5 PF02933 CDC48_2: Cell divisio 96.2 0.026 5.6E-07 42.4 7.2 48 132-180 10-58 (64)
6 KOG0735 AAA+-type ATPase [Post 96.2 0.074 1.6E-06 57.8 13.0 146 36-184 17-167 (952)
7 TIGR01243 CDC48 AAA family ATP 95.8 0.2 4.3E-06 53.6 14.6 133 32-171 15-150 (733)
8 PF09262 PEX-1N: Peroxisome bi 91.7 0.18 3.8E-06 40.4 3.1 74 110-183 1-80 (80)
9 TIGR01439 lp_hng_hel_AbrB loop 83.6 4.8 0.0001 27.1 5.8 39 77-118 4-42 (43)
10 PF02359 CDC48_N: Cell divisio 81.6 17 0.00038 28.6 9.0 68 32-105 14-84 (87)
11 PF02359 CDC48_N: Cell divisio 80.1 1.6 3.5E-05 34.5 2.7 69 78-151 14-82 (87)
12 PF04014 Antitoxin-MazE: Antid 79.9 3.7 8E-05 29.0 4.2 39 78-119 5-43 (47)
13 PRK09521 exosome complex RNA-b 77.0 7.4 0.00016 35.0 6.3 124 33-162 4-141 (189)
14 PF07497 Rho_RNA_bind: Rho ter 75.4 1.5 3.4E-05 35.1 1.3 26 79-104 28-53 (78)
15 cd02790 MopB_CT_Formate-Dh_H F 73.2 4.8 0.0001 32.2 3.7 29 77-105 32-60 (116)
16 TIGR02609 doc_partner putative 73.0 7.2 0.00016 30.4 4.5 55 80-140 10-66 (74)
17 cd04459 Rho_CSD Rho_CSD: Rho p 72.1 3.9 8.4E-05 31.9 2.8 28 77-104 24-51 (68)
18 cd00508 MopB_CT_Fdh-Nap-like T 70.8 7.5 0.00016 31.1 4.3 27 78-104 33-59 (120)
19 COG1935 Uncharacterized conser 69.4 8.6 0.00019 33.3 4.5 47 40-112 11-60 (122)
20 PRK14132 riboflavin kinase; Pr 65.2 5.9 0.00013 34.5 2.8 31 66-103 94-125 (126)
21 cd02787 MopB_CT_ydeP The MopB_ 64.4 11 0.00025 30.4 4.2 29 78-106 29-57 (112)
22 cd02786 MopB_CT_3 The MopB_CT_ 63.2 9.9 0.00021 30.6 3.6 30 77-106 28-57 (116)
23 PRK09974 putative regulator Pr 62.7 22 0.00049 30.4 5.7 59 77-138 15-75 (111)
24 PRK09798 antitoxin MazE; Provi 62.0 18 0.00039 29.0 4.9 50 81-140 14-63 (82)
25 PRK11347 antitoxin ChpS; Provi 60.3 25 0.00054 28.3 5.4 47 81-139 13-59 (83)
26 PF13550 Phage-tail_3: Putativ 60.0 11 0.00023 31.8 3.5 27 139-165 137-163 (164)
27 cd02776 MopB_CT_Nitrate-R-NarG 57.3 18 0.00039 31.2 4.4 33 73-105 24-56 (141)
28 cd02792 MopB_CT_Formate-Dh-Na- 56.7 11 0.00023 30.6 2.8 29 77-105 32-60 (122)
29 PF01982 CTP-dep_RFKase: Domai 55.9 14 0.00031 32.0 3.5 18 86-103 103-120 (121)
30 cd02788 MopB_CT_NDH-1_NuoG2-N7 55.7 18 0.00039 28.8 3.9 35 71-105 20-54 (96)
31 cd02789 MopB_CT_FmdC-FwdD The 53.7 13 0.00029 30.3 2.9 30 77-106 28-57 (106)
32 COG2002 AbrB Regulators of sta 53.6 23 0.00049 28.4 4.1 42 77-120 11-52 (89)
33 COG1339 Transcriptional regula 51.3 16 0.00035 34.4 3.3 32 66-104 180-212 (214)
34 cd02785 MopB_CT_4 The MopB_CT_ 50.7 22 0.00048 29.2 3.8 28 78-105 30-57 (124)
35 cd02781 MopB_CT_Acetylene-hydr 50.4 20 0.00044 29.4 3.5 29 78-106 31-59 (130)
36 cd02775 MopB_CT Molybdopterin- 50.3 22 0.00047 27.5 3.5 28 78-105 21-48 (101)
37 COG2336 MazE Growth regulator 49.9 18 0.00039 29.5 3.0 34 82-118 14-47 (82)
38 COG1153 FwdD Formylmethanofura 49.8 15 0.00031 32.2 2.6 29 76-104 27-55 (128)
39 PF01568 Molydop_binding: Moly 49.6 22 0.00047 28.2 3.5 26 79-104 28-54 (110)
40 cd02777 MopB_CT_DMSOR-like The 48.8 22 0.00048 29.3 3.5 27 79-105 33-59 (127)
41 cd02791 MopB_CT_Nitrate-R-NapA 48.8 24 0.00053 28.5 3.7 28 78-105 33-60 (122)
42 COG1188 Ribosome-associated he 48.3 27 0.00058 29.5 3.9 25 141-165 48-72 (100)
43 PF01191 RNA_pol_Rpb5_C: RNA p 48.2 37 0.00081 27.0 4.5 31 86-116 41-71 (74)
44 PRK08577 hypothetical protein; 48.2 25 0.00054 29.9 3.8 44 77-122 10-53 (136)
45 cd05705 S1_Rrp5_repeat_hs14 S1 47.7 31 0.00068 26.4 4.0 66 94-168 1-68 (74)
46 COG0243 BisC Anaerobic dehydro 46.2 32 0.0007 37.1 5.1 30 76-105 667-696 (765)
47 PRK15095 FKBP-type peptidyl-pr 46.1 78 0.0017 27.9 6.7 31 72-103 34-64 (156)
48 TIGR03243 arg_catab_AOST argin 45.8 27 0.00059 35.1 4.1 34 70-103 300-333 (335)
49 TIGR02851 spore_V_T stage V sp 45.6 34 0.00074 31.1 4.5 46 71-119 4-49 (180)
50 cd02778 MopB_CT_Thiosulfate-R- 45.5 30 0.00066 28.0 3.8 29 77-105 27-55 (123)
51 smart00553 SEP Domain present 45.1 13 0.00028 30.7 1.5 14 216-229 73-86 (93)
52 cd04456 S1_IF1A_like S1_IF1A_l 45.1 25 0.00054 28.0 3.1 24 80-103 25-48 (78)
53 cd02782 MopB_CT_1 The MopB_CT_ 45.1 27 0.00059 28.7 3.5 29 77-105 30-58 (129)
54 PRK10737 FKBP-type peptidyl-pr 44.7 60 0.0013 30.1 6.0 16 171-186 111-126 (196)
55 cd02794 MopB_CT_DmsA-EC The Mo 44.7 27 0.00059 28.5 3.4 28 79-106 29-56 (121)
56 cd02779 MopB_CT_Arsenite-Ox Th 44.6 32 0.0007 28.0 3.8 29 77-105 30-58 (115)
57 PRK09570 rpoH DNA-directed RNA 44.2 32 0.0007 27.8 3.6 30 87-116 45-74 (79)
58 cd06166 Sortase_D_5 Sortase D 42.8 39 0.00084 28.3 4.1 31 135-165 58-88 (126)
59 PF04322 DUF473: Protein of un 42.2 36 0.00078 29.4 3.8 47 39-111 10-59 (119)
60 cd02793 MopB_CT_DMSOR-BSOR-TMA 41.2 35 0.00077 28.4 3.6 29 77-105 30-58 (129)
61 cd02783 MopB_CT_2 The MopB_CT_ 40.8 35 0.00075 29.7 3.6 29 77-105 29-57 (156)
62 cd05829 Sortase_E Sortase E (S 40.1 40 0.00086 29.1 3.9 26 139-164 70-96 (144)
63 PRK14165 winged helix-turn-hel 39.3 24 0.00053 33.1 2.6 19 86-104 197-215 (217)
64 PF03459 TOBE: TOBE domain; I 39.0 37 0.0008 24.5 3.0 23 82-104 35-57 (64)
65 PRK10456 arginine succinyltran 37.6 44 0.00095 33.7 4.2 35 70-104 302-336 (344)
66 TIGR03244 arg_catab_AstA argin 37.6 44 0.00094 33.6 4.2 34 70-103 301-334 (336)
67 TIGR02227 sigpep_I_bact signal 37.5 1.7E+02 0.0036 25.6 7.4 40 140-179 50-91 (163)
68 cd02780 MopB_CT_Tetrathionate_ 37.2 48 0.001 28.0 3.8 28 77-104 27-54 (143)
69 TIGR03245 arg_AOST_alph argini 35.7 48 0.001 33.4 4.1 34 70-103 300-334 (336)
70 PF00717 Peptidase_S24: Peptid 35.3 1.7E+02 0.0037 21.1 7.0 33 141-173 24-57 (70)
71 cd05828 Sortase_D_4 Sortase D 33.8 68 0.0015 26.9 4.2 30 136-165 56-85 (127)
72 cd05830 Sortase_D_5 Sortase D 33.0 66 0.0014 27.3 4.1 30 136-165 60-89 (137)
73 TIGR01076 sortase_fam LPXTG-si 32.2 65 0.0014 27.4 3.9 24 141-164 63-86 (136)
74 PF12148 DUF3590: Protein of u 30.0 35 0.00075 28.0 1.7 20 134-153 58-77 (85)
75 PLN03086 PRLI-interacting fact 30.0 2.9E+02 0.0063 29.8 8.9 72 32-105 149-227 (567)
76 TIGR02620 cas_VVA1548 putative 29.7 34 0.00074 28.6 1.7 30 24-53 26-57 (93)
77 cd00004 Sortase Sortases are c 29.7 83 0.0018 26.0 4.1 25 141-165 64-88 (128)
78 cd06165 Sortase_A_1 Sortase A 29.4 81 0.0018 26.2 4.0 24 142-165 64-87 (127)
79 PF10636 hemP: Hemin uptake pr 29.4 1.2E+02 0.0025 21.5 4.0 22 142-163 9-30 (38)
80 PF04958 AstA: Arginine N-succ 29.3 67 0.0015 32.4 4.0 34 70-103 306-340 (342)
81 cd05706 S1_Rrp5_repeat_sc10 S1 28.9 1.1E+02 0.0024 22.5 4.2 56 94-151 1-57 (73)
82 KOG2086 Protein tyrosine phosp 28.3 60 0.0013 33.2 3.5 16 213-228 252-267 (380)
83 PF11717 Tudor-knot: RNA bindi 28.3 92 0.002 22.7 3.6 27 142-168 1-28 (55)
84 KOG3293 Small nuclear ribonucl 27.4 1.1E+02 0.0024 26.9 4.5 30 38-75 2-31 (134)
85 cd02784 MopB_CT_PHLH The MopB_ 27.4 85 0.0018 27.2 3.8 27 79-105 37-63 (137)
86 PF01176 eIF-1a: Translation i 27.0 87 0.0019 23.6 3.4 24 81-104 29-52 (65)
87 TIGR03711 acc_sec_asp3 accesso 26.7 1.8E+02 0.0039 25.7 5.7 20 96-115 23-42 (135)
88 PF01272 GreA_GreB: Transcript 26.4 1.1E+02 0.0024 23.5 3.9 24 142-165 53-76 (77)
89 TIGR01243 CDC48 AAA family ATP 26.0 1.3E+02 0.0028 32.5 5.7 71 78-152 15-85 (733)
90 PRK08059 general stress protei 25.4 1.3E+02 0.0028 25.2 4.5 59 88-151 1-61 (123)
91 PRK13532 nitrate reductase cat 25.2 69 0.0015 35.1 3.5 51 52-105 713-771 (830)
92 cd05704 S1_Rrp5_repeat_hs13 S1 24.9 94 0.002 23.4 3.2 56 94-152 1-59 (72)
93 TIGR02693 arsenite_ox_L arseni 24.8 90 0.0019 34.4 4.3 29 77-105 722-750 (806)
94 COG0836 {ManC} Mannose-1-phosp 24.8 1.6E+02 0.0034 29.8 5.6 76 98-176 245-326 (333)
95 PF11302 DUF3104: Protein of u 24.5 2E+02 0.0043 23.2 5.1 48 139-186 3-75 (75)
96 PF12945 YcgR_2: Flagellar pro 23.8 2.3E+02 0.0049 21.3 5.3 56 51-106 3-60 (87)
97 PRK10183 hypothetical protein; 23.4 1.2E+02 0.0025 23.3 3.4 22 142-163 27-48 (56)
98 PRK10348 ribosome-associated h 22.3 1.3E+02 0.0029 26.4 4.1 25 141-165 48-72 (133)
99 PF04203 Sortase: Sortase fami 22.3 1.4E+02 0.0031 24.3 4.2 23 143-165 62-85 (128)
100 PRK05807 hypothetical protein; 22.1 3E+02 0.0065 23.7 6.2 55 93-151 2-58 (136)
101 cd05793 S1_IF1A S1_IF1A: Trans 22.1 1.3E+02 0.0027 23.9 3.5 24 80-103 25-48 (77)
102 PRK09376 rho transcription ter 22.0 1.4E+02 0.003 31.0 4.7 39 66-104 48-101 (416)
103 cd05827 Sortase_C_3 Sortase C 22.0 1.5E+02 0.0033 24.8 4.3 24 142-165 67-90 (131)
104 PRK06944 sulfur carrier protei 21.3 2.6E+02 0.0057 20.3 5.0 22 82-103 38-59 (65)
105 COG0187 GyrB Type IIA topoisom 21.1 1E+02 0.0022 33.6 3.7 46 108-153 165-210 (635)
106 PTZ00061 DNA-directed RNA poly 21.0 1.2E+02 0.0025 28.7 3.6 31 86-116 172-202 (205)
107 PF00667 FAD_binding_1: FAD bi 20.6 1.3E+02 0.0028 27.4 3.8 87 52-140 6-121 (219)
108 cd04453 S1_RNase_E S1_RNase_E: 20.5 1.4E+02 0.0029 23.8 3.5 59 94-152 5-67 (88)
109 PRK07860 NADH dehydrogenase su 20.4 96 0.0021 34.1 3.4 41 65-105 702-743 (797)
110 TIGR01553 formate-DH-alph form 20.3 68 0.0015 36.5 2.3 56 51-106 881-939 (1009)
111 TIGR00638 Mop molybdenum-pteri 20.2 1.4E+02 0.003 21.6 3.3 23 82-104 37-59 (69)
No 1
>KOG1816 consensus Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.2e-102 Score=732.58 Aligned_cols=296 Identities=55% Similarity=0.938 Sum_probs=250.6
Q ss_pred CCcCCCCCCCCccceeeEEeecccccC---CCCCCCCeEecCHHHHHHHHhCCCCCCeeEEEEeCCCCCEEEEEEeeeEe
Q 020791 1 MFFDGYGYHGTSFEQSYRCYPASFIEK---PQIESGDKIIMPPSALDRLASLHIDYPMLFELRNNAAERVSHCGVLEFIA 77 (321)
Q Consensus 1 ~~f~~~~~~~~~F~~~yrcyp~s~~~k---~~~~~GdKIiLPpSaL~~L~~l~i~~PmlFel~n~~~~r~thcGVLEF~A 77 (321)
|+|++|++++..|+++|||||++|+.. +++++|||||||||||++|+++||.|||+|+|+|.+..|+||||||||+|
T Consensus 2 ~~f~~~~~~g~~f~~~yrcy~~~~l~~~~~s~~~~GgKIilPPSaL~~Ls~lnI~yPMlFkLtn~~~~r~THcGVLEF~A 81 (308)
T KOG1816|consen 2 MFFDGFGPRGFQFETSYRCYPVSFLPGPDRSDVNKGGKIILPPSALDRLSSLNITYPMLFKLTNVDVDRVTHCGVLEFTA 81 (308)
T ss_pred ccccccCcCCcceeeeeEecccccccCccccccccCCeEEeCHHHHHHHHHhcCCCceEEEEeccccceeeeeeEEEEEe
Confidence 689999988899999999999999954 49999999999999999999999999999999999999999999999999
Q ss_pred CCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccccHHHHHhhcccceecccCCEEEEEECCEEE
Q 020791 78 EEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKY 157 (321)
Q Consensus 78 ~EG~i~LP~WMm~~L~l~egd~V~v~~~~LPkGt~vkLqP~s~~FldIsnpKavLE~~LRnys~LT~GD~I~I~yn~k~Y 157 (321)
|||.||||+|||++|+|+|||+|+|+|++||+||||||||||.|||||+|||||||++||||+|||+||+|+|+||++.|
T Consensus 82 eEG~vyLP~WMmq~L~le~gdlv~i~~v~lpkgtyvKLqP~s~dFLDItNpKAvLE~~LRn~acLT~gDvi~i~Yn~k~y 161 (308)
T KOG1816|consen 82 EEGRVYLPYWMMQNLLLEEGDLVRIRSVTLPKGTYVKLQPHSVDFLDITNPKAVLENALRNYACLTTGDVILINYNEKTY 161 (308)
T ss_pred cCceEEeehHhhhhccCCCCCeEEEEEeeccccceeeeccCCCCccccCChHHHHHHHHhhccccccCCEEEEecCCeEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEEecCCCeeEEEeCceeeeecCCCCCCCCCCcccCcccch-hhhhhhccc----CCCCcccceeeeccccCCccCC
Q 020791 158 YIDIIETKPSNAISIIETDCEVDFAPPLDYKEPEKPIASASSRA-TAKAEEASV----ETEPKFSPFTGVARRLDGKPLT 232 (321)
Q Consensus 158 ~l~V~e~kP~~aVsIIeTDleVDF~pPldy~ep~~~~~~~~~~~-~~~~~~~~~----~~~~~~~~F~G~G~rLdGK~~~ 232 (321)
+|+|+|+||++|||||||||+|||+||+||+||+++.++..... .++..+.-+ .-+++|.+|+|+|+|||||+..
T Consensus 162 ~i~V~e~kPa~aVsIiEtD~~VDF~pP~gyke~~~~~~~~~~~k~~~~~v~~~ag~~~~~e~~~~~f~gsg~rLdgK~~~ 241 (308)
T KOG1816|consen 162 ELKVVETKPANAVSIIETDLNVDFDPPLGYKEPERQVAPAEKAKGEAEVVGSYAGYKNVIENKVEPFTGSGRRLDGKKKV 241 (308)
T ss_pred EEEEEEecCCceeEEEEcceeecccCCcCccCcccccChhhcccccceeeccccccccccccceeeeccccceecccccc
Confidence 99999999999999999999999999999999999865543221 111111001 1178899999999999999887
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCcCCeEEEccCCCCCCCCCCCchhhhhhcccCccccCCCCcccc
Q 020791 233 YQPPPVPSLGSKDKQPATSNGTGQPSAGSTSQNAARQSQGKLVFGSNASLHPKETQKPVAEKEIKQELPEKKEEPKFRPF 312 (321)
Q Consensus 233 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gkl~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~aF 312 (321)
.++++ .|+.. . . ...++.++. +++.|+|+||||.... ++ ..++.+. ...++|++|
T Consensus 242 ~e~~~--~pv~~---~-----~---~~~~~~~~~-d~~~G~l~F~~~~~~~----~~------~~~E~~a-~k~~~~~~F 296 (308)
T KOG1816|consen 242 EEVSK--HPVKN---G-----D---LIQRGVPNH-DFKLGKLVFGRNVDPL----KK------ESEEKEA-GKDSKFEAF 296 (308)
T ss_pred cccCC--CcccC---c-----c---cccCCCCcc-ccCCceEEEecCCCcc----cc------ccchhhc-ccccceeEe
Confidence 66533 22221 0 0 112455555 9999999999996422 11 1111111 223899999
Q ss_pred ccCccccCC
Q 020791 313 TGKKYSLKG 321 (321)
Q Consensus 313 ~G~~~sL~~ 321 (321)
+|+|||||+
T Consensus 297 ~G~~~slr~ 305 (308)
T KOG1816|consen 297 SGAGYSLRK 305 (308)
T ss_pred cCCceeccc
Confidence 999999986
No 2
>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=2.3e-74 Score=513.93 Aligned_cols=173 Identities=66% Similarity=1.166 Sum_probs=150.0
Q ss_pred ccceeeEEeecccc---cCCCCCCCCeEecCHHHHHHHHhCCCCCCeeEEEEeCCCCCEEEEEEeeeEeCCCeEeccHHH
Q 020791 12 SFEQSYRCYPASFI---EKPQIESGDKIIMPPSALDRLASLHIDYPMLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWM 88 (321)
Q Consensus 12 ~F~~~yrcyp~s~~---~k~~~~~GdKIiLPpSaL~~L~~l~i~~PmlFel~n~~~~r~thcGVLEF~A~EG~i~LP~WM 88 (321)
.|+++|||||++|+ +++++++||||+||||||++|.+++++|||+|+|+|..+++.||||||||+|+||+||||+||
T Consensus 1 ~f~~~~~~~~~~~~~~~~~~~~~~gdKiiLP~s~L~~L~~~~~~~P~~F~i~n~~~~~~th~GVlEFsA~eG~i~lP~wm 80 (176)
T PF03152_consen 1 KFDQTYRCYPVSFLPGADRPELEYGDKIILPPSALDELSRLNIPYPMLFEISNPDNGKRTHCGVLEFSAEEGTIYLPPWM 80 (176)
T ss_dssp -EEEEEEEEECCCSSTTS-CCCCCTTEEEE-HHHHHHHHHTT--SS-EEEEEETTTTEEEEEEEEEE--CTTEEEE-CHH
T ss_pred CccceEEEEeEEeecCCCCcccCCCCeEEcCHHHHHHHHhccCCCCEEEEEecCCCCcEEEEEEEEeEcCCCeEEeCccH
Confidence 48999999999999 899999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccccHHHHHhhcccceecccCCEEEEEECCEEEEEEEEEecCCC
Q 020791 89 MENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSN 168 (321)
Q Consensus 89 m~~L~l~egd~V~v~~~~LPkGt~vkLqP~s~~FldIsnpKavLE~~LRnys~LT~GD~I~I~yn~k~Y~l~V~e~kP~~ 168 (321)
|++|++++||.|+|++++||||||||||||+.+|++|+|||||||++||||+|||+||+|.|+|+++.|+|+|+|++|++
T Consensus 81 m~~L~l~~g~~V~v~~~~LPkgt~vkLqP~~~~F~~i~n~KavLE~~Lr~ystLT~Gd~I~i~~~~~~y~l~V~e~kP~~ 160 (176)
T PF03152_consen 81 MQNLGLQEGDIVRVEYVSLPKGTFVKLQPQSSDFLDISNPKAVLERALRNYSTLTKGDTISIEYNNKTYELDVVEVKPEN 160 (176)
T ss_dssp HHHHT--TTEEEEEEEEE----SEEEEEESCHHHHCSS-HHHHHHHHHCC-SEEETTSEEEEECTTEEEEEEEEEECSSS
T ss_pred HhhcCCCCCCEEEEEEeECCCCCEEEEeECCCccccccchHHHHHhhcccCceeecCCEEEEEeCCEEEEEEEEEEcCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeEEEeCceeeeecCC
Q 020791 169 AISIIETDCEVDFAPP 184 (321)
Q Consensus 169 aVsIIeTDleVDF~pP 184 (321)
|||||||||+|||++|
T Consensus 161 aV~IidTDl~vDf~~P 176 (176)
T PF03152_consen 161 AVSIIDTDLEVDFEPP 176 (176)
T ss_dssp CEE-SSS-SEEEE---
T ss_pred EEEEEeCceEEEecCC
Confidence 9999999999999997
No 3
>COG5140 UFD1 Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.7e-73 Score=528.99 Aligned_cols=280 Identities=37% Similarity=0.592 Sum_probs=229.5
Q ss_pred CccceeeEEeecccc---cCCCCCCCCeEecCHHHHHHHHhCCCCCCeeEEEEeCCCCCEEEEEEeeeEeCCCeEeccHH
Q 020791 11 TSFEQSYRCYPASFI---EKPQIESGDKIIMPPSALDRLASLHIDYPMLFELRNNAAERVSHCGVLEFIAEEGMIYMPYW 87 (321)
Q Consensus 11 ~~F~~~yrcyp~s~~---~k~~~~~GdKIiLPpSaL~~L~~l~i~~PmlFel~n~~~~r~thcGVLEF~A~EG~i~LP~W 87 (321)
+.|.+.|||||++|+ .|++.++|+|||||||||..|+++||.|||+|+|++.++.+.||||||||+|+||.||||+|
T Consensus 20 q~F~e~~rcyp~am~~d~~r~n~NfGGKvilPpSaL~kLs~lni~yPmlF~~s~~~~~~~THgGVLEFiaEEGrVylP~W 99 (331)
T COG5140 20 QLFGEKPRCYPRAMKFDGCRQNANFGGKVILPPSALVKLSSLNIQYPMLFEISHSDGIYRTHGGVLEFIAEEGRVYLPSW 99 (331)
T ss_pred hhhccCccceeeecccCccccCCCcCceEEcCHHHHHHHHhhccCCceEEEEecccceeEecccEEEEeecCCcEeehHH
Confidence 679999999999998 46789999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccccHHHHHhhcccceecccCCEEEEEECCEEEEEEEEEecCC
Q 020791 88 MMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPS 167 (321)
Q Consensus 88 Mm~~L~l~egd~V~v~~~~LPkGt~vkLqP~s~~FldIsnpKavLE~~LRnys~LT~GD~I~I~yn~k~Y~l~V~e~kP~ 167 (321)
||+.|.+++||+|+|+|.++|.|+||||+|||.|||||+|||||||++||||+|||+||+|.|.||++.|.|++++++|+
T Consensus 100 Mm~tLs~epgdlv~~~~td~plG~fVKL~PqSVdFLdI~dpkavLEn~LRNfstLt~~D~iei~ynd~v~~Ik~~~v~pe 179 (331)
T COG5140 100 MMQTLSMEPGDLVVLRYTDFPLGKFVKLIPQSVDFLDIEDPKAVLENCLRNFSTLTEGDEIEIQYNDEVGSIKFTVVHPE 179 (331)
T ss_pred HHHhccCCCCcEEEEEeccccccceEEecccccceEeccChHHHHHHHHhhccccccCCEEEEEECCeeeEEEEEEeccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999995
Q ss_pred ---CeeEEEeCceeeeecCCCCCCCCCCcccCcccchhhhhhh-----cccCCCCcccceeeeccccCCccCCCCCCCCC
Q 020791 168 ---NAISIIETDCEVDFAPPLDYKEPEKPIASASSRATAKAEE-----ASVETEPKFSPFTGVARRLDGKPLTYQPPPVP 239 (321)
Q Consensus 168 ---~aVsIIeTDleVDF~pPldy~ep~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~F~G~G~rLdGK~~~~~~~~~~ 239 (321)
++|||||||+.|||+||+||+|+..+-+....-.....+. .......+-.--.|.|..|.||..+..+...-
T Consensus 180 ~S~~~i~vveTDLvvDF~pPiGy~e~~qq~ke~n~~gvqgtm~t~I~y~~~~~~~~~~lmKg~G~~l~gk~~~~~pk~~i 259 (331)
T COG5140 180 PSANAIYVVETDLVVDFLPPIGYKEKAQQDKERNSFGVQGTMATYIEYIDSSHDVKPILMKGLGLYLYGKVDKAEPKQDI 259 (331)
T ss_pred CCcceEEEEecceeeeccCCccccchhhhhhhhccccccceeEEEEeeeccccccchhhhhcccceecccccccccccch
Confidence 8999999999999999999999843311110000000111 11222233355669999999998876554321
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCcccCcCCeEEEccCCCCCCCCCCCchhhhhhcccCccccCCCCccccccCcccc
Q 020791 240 SLGSKDKQPATSNGTGQPSAGSTSQNAARQSQGKLVFGSNASLHPKETQKPVAEKEIKQELPEKKEEPKFRPFTGKKYSL 319 (321)
Q Consensus 240 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gkl~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~aF~G~~~sL 319 (321)
-.+. -.+.|.....+-|+|+||..-..+ + .. |+.+..+.-|.|.|.|-||
T Consensus 260 ~d~~----------------~~~~pa~l~lp~g~~ffg~p~~~p----~--------~d--ees~~~~~~~~fqg~g~sl 309 (331)
T COG5140 260 KDMK----------------IDGEPAKLDLPEGQLFFGFPMVLP----K--------ED--EESAAKSSEQNFQGQGISL 309 (331)
T ss_pred hhhh----------------ccCCcccccccCcceEeccccccC----c--------cc--hhhccCchhhccccCceee
Confidence 1111 134566778999999999886532 1 11 1112234558899999999
Q ss_pred C
Q 020791 320 K 320 (321)
Q Consensus 320 ~ 320 (321)
|
T Consensus 310 r 310 (331)
T COG5140 310 R 310 (331)
T ss_pred e
Confidence 7
No 4
>PLN03086 PRLI-interacting factor K; Provisional
Probab=100.00 E-value=3.7e-60 Score=481.80 Aligned_cols=173 Identities=38% Similarity=0.648 Sum_probs=161.5
Q ss_pred CCccceeeEEeecccccCCCCCCCCeEecCHHHHHHHHhCCC--CCCeeEEEEeC-----------CCCCEEEEEEeeeE
Q 020791 10 GTSFEQSYRCYPASFIEKPQIESGDKIIMPPSALDRLASLHI--DYPMLFELRNN-----------AAERVSHCGVLEFI 76 (321)
Q Consensus 10 ~~~F~~~yrcyp~s~~~k~~~~~GdKIiLPpSaL~~L~~l~i--~~PmlFel~n~-----------~~~r~thcGVLEF~ 76 (321)
|-.|.+.+.. ++|. ..|||||||||||++|+++|| .|||+|+|+|. ..+++||||||||+
T Consensus 75 g~~~~~~~~~--~~~~-----~~GdKI~LPpSaL~~L~~~~~~~~~Pm~F~l~~~~~~~~~~~~~~~~~~~th~GVlEF~ 147 (567)
T PLN03086 75 GIVFSRIFEA--VSFQ-----GNGDKIKLPPSCFTELSDQGAFDKGPLYFRLSVVHQEGSGEMKDTDSQKTTHSGVLEFT 147 (567)
T ss_pred CeEEEEEeec--cccC-----CCCCeEEcCHHHHHHHHhcCCCCCCCeEEEEeccccccccccccccCCcEEEEEEEEEE
Confidence 4557666665 5666 599999999999999999998 89999999984 34799999999999
Q ss_pred eCCCeEeccHHHHHHcCCCC---CCeEEEEEeecCCcceEEEeeCCcCcCCccccHHHHHhhcccceecccCCEEEEEEC
Q 020791 77 AEEGMIYMPYWMMENLLLQE---GDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYN 153 (321)
Q Consensus 77 A~EG~i~LP~WMm~~L~l~e---gd~V~v~~~~LPkGt~vkLqP~s~~FldIsnpKavLE~~LRnys~LT~GD~I~I~yn 153 (321)
|+||.||||+|||++|++.+ |++|+|++++||||||||||||+.+|+||+|||||||++||||+|||+||+|.|+||
T Consensus 148 A~EG~v~lP~wm~~~L~~~~~~~~~~v~v~~~~Lpkgt~vklqP~~~~f~di~npKavLE~~Lr~~stLT~Gd~i~i~~~ 227 (567)
T PLN03086 148 AEEGSVGLPPHVWSNLFPSDPPDVPLVEVRYIWLPKGTYAKLQPDGVGFSDLPNHKAVLETALRQHATLSEDDVLVVNYG 227 (567)
T ss_pred cCCCeEEcCHHHHhhcCCCCCCCCCeEEEEEeecCCCCEEEEeeccCCcCCcccHHHHHHHHhhcCccccCCCEEEEecC
Confidence 99999999999999999975 899999999999999999999999999999999999999999999999999999999
Q ss_pred CEEEEEEEEEecCCCeeEEEeCceeeeecCCCCCCC
Q 020791 154 NKKYYIDIIETKPSNAISIIETDCEVDFAPPLDYKE 189 (321)
Q Consensus 154 ~k~Y~l~V~e~kP~~aVsIIeTDleVDF~pPldy~e 189 (321)
++.|+|+|+|++|++|||||||||+|||+||.++.+
T Consensus 228 ~~~y~~~V~ev~P~~aVsiieTDi~VDf~~p~~~~~ 263 (567)
T PLN03086 228 QLTYKLKVLELKPASSVSVLETDIEVDIVGPDSVSN 263 (567)
T ss_pred CEEEEEEEEEEcCCCeeEEEeCceEEEeccCCcchh
Confidence 999999999999999999999999999999999743
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=96.21 E-value=0.026 Score=42.36 Aligned_cols=48 Identities=23% Similarity=0.479 Sum_probs=35.9
Q ss_pred HHhhcccceecccCCEEEEEECCEEEEEEEEEecCCCeeEEE-eCceeee
Q 020791 132 LETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISII-ETDCEVD 180 (321)
Q Consensus 132 LE~~LRnys~LT~GD~I~I~yn~k~Y~l~V~e~kP~~aVsII-eTDleVD 180 (321)
|-+.|.+ --|++||+|.|.+.++.+.|.|.+++|.++|.|- +|.+++.
T Consensus 10 ~~~~l~~-~pv~~Gd~i~~~~~~~~~~~~V~~~~P~~~v~it~~T~i~i~ 58 (64)
T PF02933_consen 10 FKRQLEG-RPVTKGDTIVFPFFGQALPFKVVSTEPSGPVIITEDTEIEIK 58 (64)
T ss_dssp HHHHHTT-EEEETT-EEEEEETTEEEEEEEEEECSSSEEEEETTSEEEES
T ss_pred HHHHHcC-CCccCCCEEEEEeCCcEEEEEEEEEEcCCCEEECCCcEEEEc
Confidence 3344444 4599999999999999999999999999877555 3445554
No 6
>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=96.18 E-value=0.074 Score=57.78 Aligned_cols=146 Identities=19% Similarity=0.203 Sum_probs=112.3
Q ss_pred EecCHHHHHHHHhCCCCCCeeEEEEeCCCCCEEEEEEeeeE-eCCCeEeccHHHHHHcCCCCCCeEEEEEe-ecCCcceE
Q 020791 36 IIMPPSALDRLASLHIDYPMLFELRNNAAERVSHCGVLEFI-AEEGMIYMPYWMMENLLLQEGDIVRVKNV-TLPKGTYV 113 (321)
Q Consensus 36 IiLPpSaL~~L~~l~i~~PmlFel~n~~~~r~thcGVLEF~-A~EG~i~LP~WMm~~L~l~egd~V~v~~~-~LPkGt~v 113 (321)
|.||-+.+..|....-.|++.-........+.-..| -++ ..|..|-+=.-..+.|+|.+|+.|.++-+ ..+.++-|
T Consensus 17 v~lP~ql~~ai~~~~~~~av~~v~~~~~~~~s~~~g--~~s~~se~~ieIn~~~A~~l~L~e~~~V~l~~~~~v~~~~~V 94 (952)
T KOG0735|consen 17 VNLPEQLLEAISEPVQNYAVQAVVSKNPIKKSWVFG--HGSGSSENVIEINRVYAHTLGLAENQEVKLSIIDHVHEATQV 94 (952)
T ss_pred hccHHHHHHHHhccccCceeEEEEcCCChhheeecc--cCCCCccceEEeehhhHhhccCCCCCeEEEEEcCCccceeEE
Confidence 578999999888776556655433222222233344 333 33667778888999999999999999966 79999999
Q ss_pred EEeeCCcCcCCccccHHH-HHhhcc-cceecccCCEEEEEECCE-EEEEEEEEecCCCeeEEEeCceeeeecCC
Q 020791 114 KLQPHTKDFLDISNPKAI-LETTLR-NYSCLTTGDSIMVAYNNK-KYYIDIIETKPSNAISIIETDCEVDFAPP 184 (321)
Q Consensus 114 kLqP~s~~FldIsnpKav-LE~~LR-nys~LT~GD~I~I~yn~k-~Y~l~V~e~kP~~aVsIIeTDleVDF~pP 184 (321)
...|.++|=|+|-+--|+ ||..|- .+--+|. ....|+++.. .-.|.|..+.|+..+.=|+++-+|=++|-
T Consensus 95 ~VeP~TsdDWEIiElnA~~~e~~lL~Q~RIv~~-~~f~iwl~~~t~i~fqv~rl~Ps~~~gRl~~~Tev~VaPK 167 (952)
T KOG0735|consen 95 EVEPVTSDDWEIIELNAEWLEENLLVQTRIVTP-EIFIIWLPSGTVIQFQVDRLIPSMLYGRLLRGTEVLVAPK 167 (952)
T ss_pred EEeeccCccHHHHHhhHHHHhhhhhhheeeccc-ceeEEEEcCccEEEEEEeeeecccceeeecCCceEEEecC
Confidence 999999998898776665 677666 6888999 7888888865 55789999999999999999999988773
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=95.84 E-value=0.2 Score=53.58 Aligned_cols=133 Identities=16% Similarity=0.189 Sum_probs=94.2
Q ss_pred CCCeEecCHHHHHHHHhCCCCCCeeEEEEeCCCCCEEEEEEee-eE--eCCCeEeccHHHHHHcCCCCCCeEEEEEeecC
Q 020791 32 SGDKIIMPPSALDRLASLHIDYPMLFELRNNAAERVSHCGVLE-FI--AEEGMIYMPYWMMENLLLQEGDIVRVKNVTLP 108 (321)
Q Consensus 32 ~GdKIiLPpSaL~~L~~l~i~~PmlFel~n~~~~r~thcGVLE-F~--A~EG~i~LP~WMm~~L~l~egd~V~v~~~~LP 108 (321)
..+.+-|.++++++|. +..==.-+|.. ..|.+.|-|+. .. ...|.|.|..-+.+|+++..||.|.|+-+.++
T Consensus 15 ~~~~~~~~~~~~~~~~---~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (733)
T TIGR01243 15 GRGIVRIDRQTAARLG---VEPGDFVEIEK--GDRSVVAIVWPLRPDDEGRGIIRMDGYLRANAGVTIGDTVTVERAEVK 89 (733)
T ss_pred CCCeEeeCHHHHHhcC---CCCCCEEEEec--CCCceeEEEEecCccccCCCEEeecHHHHhhcCCCCCCeEEEeecCCC
Confidence 4577889999988763 32222445542 34456666664 22 24689999999999999999999999999999
Q ss_pred CcceEEEeeCCcCcCCccccHHHHHhhcccceecccCCEEEEEECCEEEEEEEEEecCCCeeE
Q 020791 109 KGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAIS 171 (321)
Q Consensus 109 kGt~vkLqP~s~~FldIsnpKavLE~~LRnys~LT~GD~I~I~yn~k~Y~l~V~e~kP~~aVs 171 (321)
.+..|.+.|.. ....-.+...++...|.+ ..|++||.|.+.+....+.+.|+++.|...+.
T Consensus 90 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~-~~~~~g~~~~~~~~~~~~~~~v~~~~p~~~~~ 150 (733)
T TIGR01243 90 EAKKVVLAPTQ-PIRFGRDFVDYVKEFLLG-KPISKGETVIVPVLEGALPFVVVSTQPAGFVY 150 (733)
T ss_pred ccceEeecccc-ccccccchHHHHHHHHcC-CCCCCCCEEEecccCcceeEEEEecCCCCcEE
Confidence 99999999953 111011223334444443 46899999999988888899999999965443
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=91.73 E-value=0.18 Score=40.40 Aligned_cols=74 Identities=23% Similarity=0.308 Sum_probs=49.0
Q ss_pred cceEEEeeCCcCcCC-ccccHHHHHhhcc-cceecccCCEEEEEE-CCEEEEEEEEEecCCCe---eEEEeCceeeeecC
Q 020791 110 GTYVKLQPHTKDFLD-ISNPKAILETTLR-NYSCLTTGDSIMVAY-NNKKYYIDIIETKPSNA---ISIIETDCEVDFAP 183 (321)
Q Consensus 110 Gt~vkLqP~s~~Fld-IsnpKavLE~~LR-nys~LT~GD~I~I~y-n~k~Y~l~V~e~kP~~a---VsIIeTDleVDF~p 183 (321)
++.|.+.|.+.|=++ |+..-..||..|- +-.+++.|.++.|+- ++..-.|.|..+.|... ...+..|.||=++|
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 467889999987666 4555566777766 588999999999998 56788999999999866 78999999887765
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=83.61 E-value=4.8 Score=27.05 Aligned_cols=39 Identities=33% Similarity=0.461 Sum_probs=31.1
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeC
Q 020791 77 AEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPH 118 (321)
Q Consensus 77 A~EG~i~LP~WMm~~L~l~egd~V~v~~~~LPkGt~vkLqP~ 118 (321)
.+.|.|.||.=+.+.|++.+||.+.+... +. .-+.|.|.
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 45799999999999999999999988853 33 34666664
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=81.59 E-value=17 Score=28.59 Aligned_cols=68 Identities=16% Similarity=0.130 Sum_probs=51.0
Q ss_pred CCCeEecCHHHHHHHHhCCCCCCeeEEEEeCCCCCEEEEEEeeeEe---CCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 020791 32 SGDKIIMPPSALDRLASLHIDYPMLFELRNNAAERVSHCGVLEFIA---EEGMIYMPYWMMENLLLQEGDIVRVKNV 105 (321)
Q Consensus 32 ~GdKIiLPpSaL~~L~~l~i~~PmlFel~n~~~~r~thcGVLEF~A---~EG~i~LP~WMm~~L~l~egd~V~v~~~ 105 (321)
..+-++|.|..++ .+++..--+-.|.. .+.|+|=|+---. +.|.|-|-.-+-+|+++.-||.|.|+-+
T Consensus 14 ~~n~v~v~~~~m~---~l~l~~gd~v~i~g---~~~tv~~v~~~~~~~~~~g~I~l~~~~R~n~~v~igd~V~V~~~ 84 (87)
T PF02359_consen 14 GTNCVRVSPEDME---ELGLFPGDVVLISG---KRKTVAFVFPDRPDDSPPGVIRLSGIQRKNAGVSIGDRVTVRPY 84 (87)
T ss_dssp CTTEEEEEHHHHH---CTTT-TTEEEEEET---TTEEEEEEEEECCSTTCTTEEEE-HHHHHHCT--TTSEEEEEEE
T ss_pred CCCEEEEcHHHHH---HcCCCCccEEEEeC---CceEEEEEEECCCCCCCCCEEEECHHHHhhCCcCCCCEEEEEEC
Confidence 5678999999986 45566666777874 4458888876543 3799999999999999999999999865
No 11
>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=80.09 E-value=1.6 Score=34.48 Aligned_cols=69 Identities=23% Similarity=0.235 Sum_probs=46.6
Q ss_pred CCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccccHHHHHhhcccceecccCCEEEEE
Q 020791 78 EEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVA 151 (321)
Q Consensus 78 ~EG~i~LP~WMm~~L~l~egd~V~v~~~~LPkGt~vkLqP~s~~FldIsnpKavLE~~LRnys~LT~GD~I~I~ 151 (321)
..|.++|..-.|+.|++.+||.|.|... +-|.+.+.|...+ +...=.--|-...|...-+..||.|.|.
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 4689999999999999999999999872 2267777765332 1111111145677888888999999986
No 12
>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=79.89 E-value=3.7 Score=28.98 Aligned_cols=39 Identities=26% Similarity=0.418 Sum_probs=30.3
Q ss_pred CCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCC
Q 020791 78 EEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHT 119 (321)
Q Consensus 78 ~EG~i~LP~WMm~~L~l~egd~V~v~~~~LPkGt~vkLqP~s 119 (321)
..+.|.||.-+.+.|+|++||.|.|... ..| -+.|.|..
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 4678999999999999999999999876 233 66676653
No 13
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=77.03 E-value=7.4 Score=35.04 Aligned_cols=124 Identities=15% Similarity=0.147 Sum_probs=74.5
Q ss_pred CCeEecCHHHHHHHHhCCCCCCeeEEEEeCCCCCEEEEEEeeeEeCCCeEeccHHHHHHcCCCCCCeEEEEEe-ecCCcc
Q 020791 33 GDKIIMPPSALDRLASLHIDYPMLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNV-TLPKGT 111 (321)
Q Consensus 33 GdKIiLPpSaL~~L~~l~i~~PmlFel~n~~~~r~thcGVLEF~A~EG~i~LP~WMm~~L~l~egd~V~v~~~-~LPkGt 111 (321)
..++.||-..|...... +.-+=+|+.. ..-+.+++|.++...+.-.|.|=.|.-.....+.||+|.-+-+ ..+.|=
T Consensus 4 ~~~~V~PGe~l~~~~e~-~~G~Gty~~~--~~i~as~~G~~~id~~~~~Isv~P~~~~~~~~~~GdiV~GkV~~i~~~g~ 80 (189)
T PRK09521 4 QGDLVLPGDYLAVIEEY-LPGEGTYEDN--GEVYASVVGKVFIDDINRKISVIPFKKTPPLLKKGDIVYGRVVDVKEQRA 80 (189)
T ss_pred cCCEECCCCccccccce-EcCCCEEeeC--CEEEEEeeEEEEEcCCCCEEEEecCcCCCCCCCCCCEEEEEEEEEcCCeE
Confidence 45677776655322111 2334455532 3356889999999777778888778755566789999987765 467888
Q ss_pred eEEEeeC-------C---cCcCCccccHHHHHhhccc-ceecccCCEEEEEECC--EEEEEEEE
Q 020791 112 YVKLQPH-------T---KDFLDISNPKAILETTLRN-YSCLTTGDSIMVAYNN--KKYYIDII 162 (321)
Q Consensus 112 ~vkLqP~-------s---~~FldIsnpKavLE~~LRn-ys~LT~GD~I~I~yn~--k~Y~l~V~ 162 (321)
+|.|-.. . ..|+.+++... ....+ ..++..||+|....-. ..+.|.+.
T Consensus 81 ~V~I~~~~~~~~~l~~~~~G~l~~s~i~~---~~~~~~~~~~~~GD~V~akV~~i~~~i~LS~k 141 (189)
T PRK09521 81 LVRIVSIEGSERELATSKLAYIHISQVSD---GYVESLTDAFKIGDIVRAKVISYTDPLQLSTK 141 (189)
T ss_pred EEEEEEecccccccCCCceeeEEhhHcCh---hhhhhHHhccCCCCEEEEEEEecCCcEEEEEe
Confidence 8887421 1 23443443221 12222 5668999999875321 34544443
No 14
>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=75.37 E-value=1.5 Score=35.08 Aligned_cols=26 Identities=19% Similarity=0.286 Sum_probs=19.1
Q ss_pred CCeEeccHHHHHHcCCCCCCeEEEEE
Q 020791 79 EGMIYMPYWMMENLLLQEGDIVRVKN 104 (321)
Q Consensus 79 EG~i~LP~WMm~~L~l~egd~V~v~~ 104 (321)
+.-||+|.++.+.++|+.||.|.=.-
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 45689999999999999999987543
No 15
>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=73.24 E-value=4.8 Score=32.24 Aligned_cols=29 Identities=24% Similarity=0.248 Sum_probs=25.8
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 020791 77 AEEGMIYMPYWMMENLLLQEGDIVRVKNV 105 (321)
Q Consensus 77 A~EG~i~LP~WMm~~L~l~egd~V~v~~~ 105 (321)
.++..|+|-.=-++.|+|++||.|+|.+-
T Consensus 32 ~~~~~v~in~~dA~~lgi~~Gd~V~v~~~ 60 (116)
T cd02790 32 APEEYVEINPEDAKRLGIEDGEKVRVSSR 60 (116)
T ss_pred CCCcEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 45778999999999999999999999874
No 16
>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=73.03 E-value=7.2 Score=30.37 Aligned_cols=55 Identities=22% Similarity=0.343 Sum_probs=37.3
Q ss_pred CeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCc--CcCCccccHHHHHhhcccce
Q 020791 80 GMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTK--DFLDISNPKAILETTLRNYS 140 (321)
Q Consensus 80 G~i~LP~WMm~~L~l~egd~V~v~~~~LPkGt~vkLqP~s~--~FldIsnpKavLE~~LRnys 140 (321)
-.|-||.=+++.|+|.+||.|.|... +.-+.|.|... +|- .....+++..++.|-
T Consensus 10 ~~vtIPk~i~~~lgl~~Gd~v~v~~~----~~~iii~~~~~~~~~~--~~~~~~~~~~~~~y~ 66 (74)
T TIGR02609 10 LVVTLPKEVLESLGLKEGDTLYVDEE----EGGLKLKRFDEGKELE--KKMQMAVERAMSKYD 66 (74)
T ss_pred eEEEECHHHHHHcCcCCCCEEEEEEE----CCEEEEEECCCCccHH--HHHHHHHHHHHHHHH
Confidence 45889999999999999999977543 34467778765 442 111235666666553
No 17
>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=72.10 E-value=3.9 Score=31.92 Aligned_cols=28 Identities=21% Similarity=0.211 Sum_probs=23.4
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEE
Q 020791 77 AEEGMIYMPYWMMENLLLQEGDIVRVKN 104 (321)
Q Consensus 77 A~EG~i~LP~WMm~~L~l~egd~V~v~~ 104 (321)
+.+.-||+|.++.+..+|+.||.|.=.-
T Consensus 24 ~~~~DvyVs~~~Irr~~LR~GD~V~G~v 51 (68)
T cd04459 24 PGPDDIYVSPSQIRRFNLRTGDTVVGQI 51 (68)
T ss_pred CCCCCEEECHHHHHHhCCCCCCEEEEEE
Confidence 3456689999999999999999987643
No 18
>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=70.75 E-value=7.5 Score=31.13 Aligned_cols=27 Identities=26% Similarity=0.339 Sum_probs=24.7
Q ss_pred CCCeEeccHHHHHHcCCCCCCeEEEEE
Q 020791 78 EEGMIYMPYWMMENLLLQEGDIVRVKN 104 (321)
Q Consensus 78 ~EG~i~LP~WMm~~L~l~egd~V~v~~ 104 (321)
++..|+|..--++.|+|.+||.|+|.+
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 19
>COG1935 Uncharacterized conserved protein [Function unknown]
Probab=69.41 E-value=8.6 Score=33.35 Aligned_cols=47 Identities=30% Similarity=0.444 Sum_probs=35.4
Q ss_pred HHHHHHHHhCCCCCCeeEEEEeCCCCCEEEEEEeeeEeCCCeEeccHHHHHHcCCCCCCeEEEEEe---ecCCcce
Q 020791 40 PSALDRLASLHIDYPMLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNV---TLPKGTY 112 (321)
Q Consensus 40 pSaL~~L~~l~i~~PmlFel~n~~~~r~thcGVLEF~A~EG~i~LP~WMm~~L~l~egd~V~v~~~---~LPkGt~ 112 (321)
-+++++|.+.++. +|+|.|..+ ..--++|+|||+|.++++ +|-+|+.
T Consensus 11 ~~vie~l~~~~~r---TieiRsa~N-----------------------~~tv~rl~~GDlVFlT~~~~~Dl~~Gts 60 (122)
T COG1935 11 RRVIESLLRNPIR---TIEIRSARN-----------------------LLTVLRLHEGDLVFLTSTSLEDLTKGTS 60 (122)
T ss_pred HHHHHHHHhCCce---EEEEEcccc-----------------------hHHhhcCCCCCEEEEehhHhhHhhcCcc
Confidence 3577777776554 688887654 455678999999999998 6778875
No 20
>PRK14132 riboflavin kinase; Provisional
Probab=65.21 E-value=5.9 Score=34.50 Aligned_cols=31 Identities=35% Similarity=0.551 Sum_probs=24.7
Q ss_pred CEEE-EEEeeeEeCCCeEeccHHHHHHcCCCCCCeEEEE
Q 020791 66 RVSH-CGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVK 103 (321)
Q Consensus 66 r~th-cGVLEF~A~EG~i~LP~WMm~~L~l~egd~V~v~ 103 (321)
|+.| -.|+|++|+.. +=+.|+|++||.|.|+
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 7889999999999986
No 21
>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=64.39 E-value=11 Score=30.37 Aligned_cols=29 Identities=21% Similarity=0.283 Sum_probs=25.9
Q ss_pred CCCeEeccHHHHHHcCCCCCCeEEEEEee
Q 020791 78 EEGMIYMPYWMMENLLLQEGDIVRVKNVT 106 (321)
Q Consensus 78 ~EG~i~LP~WMm~~L~l~egd~V~v~~~~ 106 (321)
++..|+|-.=-++.|+|.+||.|+|.+..
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 46789999999999999999999998864
No 22
>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=63.24 E-value=9.9 Score=30.64 Aligned_cols=30 Identities=20% Similarity=0.103 Sum_probs=26.3
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEee
Q 020791 77 AEEGMIYMPYWMMENLLLQEGDIVRVKNVT 106 (321)
Q Consensus 77 A~EG~i~LP~WMm~~L~l~egd~V~v~~~~ 106 (321)
.++..|+|..--++.|+|++||.|+|++..
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 356789999999999999999999998753
No 23
>PRK09974 putative regulator PrlF; Provisional
Probab=62.67 E-value=22 Score=30.39 Aligned_cols=59 Identities=17% Similarity=0.204 Sum_probs=39.4
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCC--ccccHHHHHhhccc
Q 020791 77 AEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLD--ISNPKAILETTLRN 138 (321)
Q Consensus 77 A~EG~i~LP~WMm~~L~l~egd~V~v~~~~LPkGt~vkLqP~s~~Fld--IsnpKavLE~~LRn 138 (321)
...|.|-+|.-+-+.|+|.+||.|.+. +..+-.|.+.+...+--| |...-.+||+-+++
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 467999999999999999999998874 233445666665433222 23335566666554
No 24
>PRK09798 antitoxin MazE; Provisional
Probab=62.00 E-value=18 Score=28.99 Aligned_cols=50 Identities=22% Similarity=0.335 Sum_probs=36.7
Q ss_pred eEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccccHHHHHhhcccce
Q 020791 81 MIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYS 140 (321)
Q Consensus 81 ~i~LP~WMm~~L~l~egd~V~v~~~~LPkGt~vkLqP~s~~FldIsnpKavLE~~LRnys 140 (321)
-|-||.=+++.|+|.+||.|.|+.. +.-+.++|... .++.-||.-|-+|.
T Consensus 14 ~vRIPk~~l~~l~l~~g~~vei~v~----~~~iiI~p~~~------~~r~~l~eLla~~~ 63 (82)
T PRK09798 14 AVRIPATLMQALNLNIDDEVKIDLV----DGKLIIEPVRK------EPVFTLAELVNDIT 63 (82)
T ss_pred eEEcCHHHHHHcCCCCCCEEEEEEE----CCEEEEEECCC------CCCCCHHHHHhcCC
Confidence 3779999999999999999988874 45577999642 33445666665543
No 25
>PRK11347 antitoxin ChpS; Provisional
Probab=60.27 E-value=25 Score=28.29 Aligned_cols=47 Identities=23% Similarity=0.321 Sum_probs=35.2
Q ss_pred eEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccccHHHHHhhcccc
Q 020791 81 MIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNY 139 (321)
Q Consensus 81 ~i~LP~WMm~~L~l~egd~V~v~~~~LPkGt~vkLqP~s~~FldIsnpKavLE~~LRny 139 (321)
-|-||.=++++|+|++||.|.|+-.. .-+.|+|.... ..||.-|-.|
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 36799999999999999999887653 34888998543 3466655543
No 26
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=60.01 E-value=11 Score=31.76 Aligned_cols=27 Identities=22% Similarity=0.300 Sum_probs=23.7
Q ss_pred ceecccCCEEEEEECCEEEEEEEEEec
Q 020791 139 YSCLTTGDSIMVAYNNKKYYIDIIETK 165 (321)
Q Consensus 139 ys~LT~GD~I~I~yn~k~Y~l~V~e~k 165 (321)
+..|..||+|.|.+.++.+.++|.+++
T Consensus 137 ~~~l~pGDvi~l~~~~~~~~~RI~~i~ 163 (164)
T PF13550_consen 137 GLALEPGDVIALSDDGRDMRFRITEIE 163 (164)
T ss_pred hccCCCCCEEEEEeCCCceEEEEEEEe
Confidence 456899999999999999999998875
No 27
>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=57.27 E-value=18 Score=31.21 Aligned_cols=33 Identities=21% Similarity=0.186 Sum_probs=27.9
Q ss_pred eeeEeCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 020791 73 LEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNV 105 (321)
Q Consensus 73 LEF~A~EG~i~LP~WMm~~L~l~egd~V~v~~~ 105 (321)
++...++..|+|-.=-++.|+|++||.|+|.+.
T Consensus 24 l~~~~~~~~v~inp~dA~~lgI~dGd~V~v~~~ 56 (141)
T cd02776 24 LRLQRGGPVVWMNPKDAAELGIKDNDWVEVFND 56 (141)
T ss_pred HhcCCCCCEEEECHHHHHHcCCCCCCEEEEEeC
Confidence 344556788999999999999999999998773
No 28
>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=56.74 E-value=11 Score=30.58 Aligned_cols=29 Identities=17% Similarity=0.194 Sum_probs=25.5
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 020791 77 AEEGMIYMPYWMMENLLLQEGDIVRVKNV 105 (321)
Q Consensus 77 A~EG~i~LP~WMm~~L~l~egd~V~v~~~ 105 (321)
.++..|.|-.=-++.|+|.+||.|+|.+-
T Consensus 32 ~~~~~v~i~p~dA~~lgi~~Gd~V~v~s~ 60 (122)
T cd02792 32 QPEMFVEISPELAAERGIKNGDMVWVSSP 60 (122)
T ss_pred CCCcEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 46778999999999999999999998863
No 29
>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=55.92 E-value=14 Score=31.96 Aligned_cols=18 Identities=33% Similarity=0.455 Sum_probs=12.1
Q ss_pred HHHHHHcCCCCCCeEEEE
Q 020791 86 YWMMENLLLQEGDIVRVK 103 (321)
Q Consensus 86 ~WMm~~L~l~egd~V~v~ 103 (321)
.-+=+.|+|++||.|.|+
T Consensus 103 ~~LR~~L~L~DGD~V~v~ 120 (121)
T PF01982_consen 103 VKLRDTLGLKDGDEVEVE 120 (121)
T ss_dssp S-HHHHTT--TT-EEEEE
T ss_pred cchHhhcCCCCCCEEEEE
Confidence 347889999999999986
No 30
>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=55.69 E-value=18 Score=28.76 Aligned_cols=35 Identities=20% Similarity=0.067 Sum_probs=28.5
Q ss_pred EEeeeEeCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 020791 71 GVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNV 105 (321)
Q Consensus 71 GVLEF~A~EG~i~LP~WMm~~L~l~egd~V~v~~~ 105 (321)
..|.-.+++..|+|-.=-++.|+|.+||.|+|.+.
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 33443456789999999999999999999998764
No 31
>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=53.74 E-value=13 Score=30.27 Aligned_cols=30 Identities=20% Similarity=-0.010 Sum_probs=26.1
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEee
Q 020791 77 AEEGMIYMPYWMMENLLLQEGDIVRVKNVT 106 (321)
Q Consensus 77 A~EG~i~LP~WMm~~L~l~egd~V~v~~~~ 106 (321)
.++..|+|-.=-++.|+|.+||.|+|.+..
T Consensus 28 ~~~~~v~i~p~dA~~lgi~~Gd~V~v~~~~ 57 (106)
T cd02789 28 DACAYCEINPEDYKLLGKPEGDKVKVTSEF 57 (106)
T ss_pred CCCcEEEECHHHHHHcCCCCCCEEEEEcCC
Confidence 466789999999999999999999988653
No 32
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=53.57 E-value=23 Score=28.37 Aligned_cols=42 Identities=24% Similarity=0.353 Sum_probs=31.7
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCc
Q 020791 77 AEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTK 120 (321)
Q Consensus 77 A~EG~i~LP~WMm~~L~l~egd~V~v~~~~LPkGt~vkLqP~s~ 120 (321)
...|+|++|.-+=+.||+++||.|.+.... .+..+-|+|...
T Consensus 11 ~~~GqIvIPkeiR~~lgi~~Gd~lei~~~~--~~~~ivl~k~~~ 52 (89)
T COG2002 11 DRKGQIVIPKEIREALGIKEGDVLEIIVDG--DGGRIVLKKYKP 52 (89)
T ss_pred CcCceEEecHHHHHHhCCCCCCEEEEEEeC--CCCEEEEEECCc
Confidence 457999999999999999999998887542 112266666553
No 33
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=51.33 E-value=16 Score=34.44 Aligned_cols=32 Identities=34% Similarity=0.522 Sum_probs=23.3
Q ss_pred CEEE-EEEeeeEeCCCeEeccHHHHHHcCCCCCCeEEEEE
Q 020791 66 RVSH-CGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKN 104 (321)
Q Consensus 66 r~th-cGVLEF~A~EG~i~LP~WMm~~L~l~egd~V~v~~ 104 (321)
|+.| ..|+|++|+ -.+-+.|+|..||.|.|+-
T Consensus 180 rT~h~~dviEIIap-------v~LR~~LnLkDGD~V~ieV 212 (214)
T COG1339 180 RTHHPTDVIEIIAP-------VKLRDELNLKDGDEVTIEV 212 (214)
T ss_pred cccCCcceEEEEcc-------HhHHHHhCCCCCCEEEEEE
Confidence 4445 556665553 4578899999999999974
No 34
>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=50.69 E-value=22 Score=29.19 Aligned_cols=28 Identities=21% Similarity=0.121 Sum_probs=25.3
Q ss_pred CCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 020791 78 EEGMIYMPYWMMENLLLQEGDIVRVKNV 105 (321)
Q Consensus 78 ~EG~i~LP~WMm~~L~l~egd~V~v~~~ 105 (321)
++..|+|-.=-++.|+|.+||.|+|.+-
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 5678999999999999999999999875
No 35
>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=50.44 E-value=20 Score=29.38 Aligned_cols=29 Identities=17% Similarity=0.137 Sum_probs=25.4
Q ss_pred CCCeEeccHHHHHHcCCCCCCeEEEEEee
Q 020791 78 EEGMIYMPYWMMENLLLQEGDIVRVKNVT 106 (321)
Q Consensus 78 ~EG~i~LP~WMm~~L~l~egd~V~v~~~~ 106 (321)
++..|+|-.=-++.|+|.+||.|+|.+..
T Consensus 31 ~~~~v~inp~dA~~~gi~~Gd~V~v~s~~ 59 (130)
T cd02781 31 PDPVAEINPETAAKLGIADGDWVWVETPR 59 (130)
T ss_pred CCCEEEECHHHHHHcCCCCCCEEEEECCC
Confidence 56789999999999999999999988653
No 36
>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=50.30 E-value=22 Score=27.46 Aligned_cols=28 Identities=25% Similarity=0.311 Sum_probs=24.6
Q ss_pred CCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 020791 78 EEGMIYMPYWMMENLLLQEGDIVRVKNV 105 (321)
Q Consensus 78 ~EG~i~LP~WMm~~L~l~egd~V~v~~~ 105 (321)
.+..|+|..=-+..|+|++||.|.|.+-
T Consensus 21 ~~~~v~~~~~da~~lgl~~Gd~v~v~~~ 48 (101)
T cd02775 21 PEPVVEINPEDAAALGIKDGDLVRVESR 48 (101)
T ss_pred CCCEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 4578999999999999999999988754
No 37
>COG2336 MazE Growth regulator [Signal transduction mechanisms]
Probab=49.91 E-value=18 Score=29.50 Aligned_cols=34 Identities=24% Similarity=0.362 Sum_probs=25.3
Q ss_pred EeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeC
Q 020791 82 IYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPH 118 (321)
Q Consensus 82 i~LP~WMm~~L~l~egd~V~v~~~~LPkGt~vkLqP~ 118 (321)
+-||.=||+.|+|.+||-|.|+.. .+..+-+.|.
T Consensus 14 vrIP~~l~kql~l~~g~~v~v~v~---n~~~i~~~p~ 47 (82)
T COG2336 14 VRIPAALLKQLNLTIGDEVEVEVG---NDQSILIRPV 47 (82)
T ss_pred eeccHHHHHHhCCCcCceEEEEEc---CCcEEEeccc
Confidence 679999999999999999887643 2224444444
No 38
>COG1153 FwdD Formylmethanofuran dehydrogenase subunit D [Energy production and conversion]
Probab=49.83 E-value=15 Score=32.21 Aligned_cols=29 Identities=28% Similarity=0.248 Sum_probs=24.4
Q ss_pred EeCCCeEeccHHHHHHcCCCCCCeEEEEE
Q 020791 76 IAEEGMIYMPYWMMENLLLQEGDIVRVKN 104 (321)
Q Consensus 76 ~A~EG~i~LP~WMm~~L~l~egd~V~v~~ 104 (321)
.-.-..|+|-.-.|..|++.+||.|.|++
T Consensus 27 ~~a~a~~~inp~D~~~Lgv~EGD~VkVks 55 (128)
T COG1153 27 FNACAVCEINPEDMKQLGVSEGDKVKVKS 55 (128)
T ss_pred hhheeEEEECHHHHHHhCCCcCCeEEEEe
Confidence 33445788888899999999999999987
No 39
>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=49.61 E-value=22 Score=28.19 Aligned_cols=26 Identities=27% Similarity=0.308 Sum_probs=21.6
Q ss_pred CC-eEeccHHHHHHcCCCCCCeEEEEE
Q 020791 79 EG-MIYMPYWMMENLLLQEGDIVRVKN 104 (321)
Q Consensus 79 EG-~i~LP~WMm~~L~l~egd~V~v~~ 104 (321)
+. .|+|-.=-++.|+|++||.|+|.+
T Consensus 28 ~~~~v~inp~dA~~~Gi~~Gd~V~v~s 54 (110)
T PF01568_consen 28 EPPFVEINPEDAAKLGIKDGDWVRVSS 54 (110)
T ss_dssp STEEEEEEHHHHHHCT--TTCEEEEEE
T ss_pred CCCEEEEcHHHHHHhcCcCCCEEEEEe
Confidence 44 899999999999999999999987
No 40
>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=48.85 E-value=22 Score=29.30 Aligned_cols=27 Identities=26% Similarity=0.285 Sum_probs=24.3
Q ss_pred CCeEeccHHHHHHcCCCCCCeEEEEEe
Q 020791 79 EGMIYMPYWMMENLLLQEGDIVRVKNV 105 (321)
Q Consensus 79 EG~i~LP~WMm~~L~l~egd~V~v~~~ 105 (321)
+..|+|-.=.++.|+|.+||.|+|++-
T Consensus 33 ~~~v~i~p~dA~~lgi~~Gd~V~v~s~ 59 (127)
T cd02777 33 REPVWINPLDAAARGIKDGDIVRVFND 59 (127)
T ss_pred CCeEEECHHHHHHcCCCCCCEEEEEcC
Confidence 567999999999999999999999863
No 41
>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=48.79 E-value=24 Score=28.46 Aligned_cols=28 Identities=32% Similarity=0.306 Sum_probs=24.9
Q ss_pred CCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 020791 78 EEGMIYMPYWMMENLLLQEGDIVRVKNV 105 (321)
Q Consensus 78 ~EG~i~LP~WMm~~L~l~egd~V~v~~~ 105 (321)
.+..|+|-.-.++.|+|.+||.|+|.+-
T Consensus 33 ~~~~v~in~~dA~~lgi~~Gd~V~v~~~ 60 (122)
T cd02791 33 PEPYVEIHPEDAARLGLKEGDLVRVTSR 60 (122)
T ss_pred CCCEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 4567999999999999999999999865
No 42
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=48.28 E-value=27 Score=29.45 Aligned_cols=25 Identities=16% Similarity=0.496 Sum_probs=22.6
Q ss_pred ecccCCEEEEEECCEEEEEEEEEec
Q 020791 141 CLTTGDSIMVAYNNKKYYIDIIETK 165 (321)
Q Consensus 141 ~LT~GD~I~I~yn~k~Y~l~V~e~k 165 (321)
.+-.||+|.|.|+++.+.+.|+.+.
T Consensus 48 ~VK~GD~l~i~~~~~~~~v~Vl~~~ 72 (100)
T COG1188 48 EVKVGDILTIRFGNKEFTVKVLALG 72 (100)
T ss_pred ccCCCCEEEEEeCCcEEEEEEEecc
Confidence 4678999999999999999999874
No 43
>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=48.24 E-value=37 Score=27.00 Aligned_cols=31 Identities=23% Similarity=0.316 Sum_probs=24.9
Q ss_pred HHHHHHcCCCCCCeEEEEEeecCCcceEEEe
Q 020791 86 YWMMENLLLQEGDIVRVKNVTLPKGTYVKLQ 116 (321)
Q Consensus 86 ~WMm~~L~l~egd~V~v~~~~LPkGt~vkLq 116 (321)
.-|.+.||+++||.|.|.-.+--.|.++..+
T Consensus 41 DPv~r~~g~k~GdVvkI~R~S~taG~~v~YR 71 (74)
T PF01191_consen 41 DPVARYLGAKPGDVVKIIRKSETAGEYVTYR 71 (74)
T ss_dssp SHHHHHTT--TTSEEEEEEEETTTSEEEEEE
T ss_pred ChhhhhcCCCCCCEEEEEecCCCCCCcEEEE
Confidence 4588999999999999999998889888654
No 44
>PRK08577 hypothetical protein; Provisional
Probab=48.22 E-value=25 Score=29.87 Aligned_cols=44 Identities=25% Similarity=0.250 Sum_probs=33.0
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCc
Q 020791 77 AEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDF 122 (321)
Q Consensus 77 A~EG~i~LP~WMm~~L~l~egd~V~v~~~~LPkGt~vkLqP~s~~F 122 (321)
...|.|.+|.=+-+.|+|.+||.|.+..-. ...-+.+.|...++
T Consensus 10 ~~~g~i~ip~~~r~~l~~~~g~~~~~~~~~--~~~~~~~~~~~~~~ 53 (136)
T PRK08577 10 DSKGRITIPLEIREALGIREGMYVLLIADT--DKKEIHLEPIALPG 53 (136)
T ss_pred CcCCeEEecHHHHHHcCcCCCCEEEEEEEC--CCCEEEEEEcCCCC
Confidence 467999999999999999999999886431 12356667765444
No 45
>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=47.73 E-value=31 Score=26.40 Aligned_cols=66 Identities=14% Similarity=0.264 Sum_probs=39.9
Q ss_pred CCCCCeEEEEEe-ecCCcceEEEeeCCcCcCCccccHHHHHhhcccc-eecccCCEEEEEECCEEEEEEEEEecCCC
Q 020791 94 LQEGDIVRVKNV-TLPKGTYVKLQPHTKDFLDISNPKAILETTLRNY-SCLTTGDSIMVAYNNKKYYIDIIETKPSN 168 (321)
Q Consensus 94 l~egd~V~v~~~-~LPkGt~vkLqP~s~~FldIsnpKavLE~~LRny-s~LT~GD~I~I~yn~k~Y~l~V~e~kP~~ 168 (321)
+++||.|.-.-. -.+.|-||.|-|.-..|+.++|.-.-.-..++++ ..+..||.|. ..|+++++++
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 478898875533 3599999999998888876433211000011111 3467788776 4577776653
No 46
>COG0243 BisC Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]
Probab=46.24 E-value=32 Score=37.08 Aligned_cols=30 Identities=30% Similarity=0.446 Sum_probs=27.1
Q ss_pred EeCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 020791 76 IAEEGMIYMPYWMMENLLLQEGDIVRVKNV 105 (321)
Q Consensus 76 ~A~EG~i~LP~WMm~~L~l~egd~V~v~~~ 105 (321)
..+++.|+|-.--++.|||++||+|+|.+.
T Consensus 667 ~~~~~~v~inp~DA~~~GI~~GD~V~V~~~ 696 (765)
T COG0243 667 IAPRPFVWINPEDAAKLGIKDGDLVRVENR 696 (765)
T ss_pred CCCCceEEECHHHHHHcCCCcCCEEEEEcC
Confidence 356789999999999999999999999875
No 47
>PRK15095 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=46.15 E-value=78 Score=27.93 Aligned_cols=31 Identities=19% Similarity=0.081 Sum_probs=23.4
Q ss_pred EeeeEeCCCeEeccHHHHHHcCCCCCCeEEEE
Q 020791 72 VLEFIAEEGMIYMPYWMMENLLLQEGDIVRVK 103 (321)
Q Consensus 72 VLEF~A~EG~i~LP~WMm~~L~l~egd~V~v~ 103 (321)
-+.|+--.|.+ +|.|=-.=++++.|+.+.|.
T Consensus 34 P~~f~~G~g~v-i~gle~aL~gm~~Ge~~~v~ 64 (156)
T PRK15095 34 PALFRLGDGSL-SEGLEQQLLGLKVGDKKTFS 64 (156)
T ss_pred CEEEEeCCCCc-cHHHHHHHcCCCCCCEEEEE
Confidence 45666556654 89999999999999987664
No 48
>TIGR03243 arg_catab_AOST arginine and ornithine succinyltransferase subunits. In many bacteria, the sole member of this protein family is arginine N-succinyltransferase (EC 2.3.1.109), the AstA protein of the arginine succinyltransferase (ast) pathway. However, in Pseudomonas aeruginosa and several other species, a tandem gene pair encodes alpha and beta subunits of a heterodimer that is designated arginine and ornithine succinyltransferase (AOST).
Probab=45.79 E-value=27 Score=35.06 Aligned_cols=34 Identities=26% Similarity=0.327 Sum_probs=28.8
Q ss_pred EEEeeeEeCCCeEeccHHHHHHcCCCCCCeEEEE
Q 020791 70 CGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVK 103 (321)
Q Consensus 70 cGVLEF~A~EG~i~LP~WMm~~L~l~egd~V~v~ 103 (321)
|.+.....+.+.+.|+.-+++.|++++||.|++-
T Consensus 300 a~~~~~~~~~~~~~l~~~~a~aL~v~~Gd~Vr~~ 333 (335)
T TIGR03243 300 AVLAPLSADAGTLILSADAADALGVSEGDTVRVV 333 (335)
T ss_pred EEEecccCCCCeeecCHHHHHhcCCCCCCeEEEe
Confidence 4456666678889999999999999999999874
No 49
>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=45.59 E-value=34 Score=31.06 Aligned_cols=46 Identities=24% Similarity=0.385 Sum_probs=35.7
Q ss_pred EEeeeEeCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCC
Q 020791 71 GVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHT 119 (321)
Q Consensus 71 GVLEF~A~EG~i~LP~WMm~~L~l~egd~V~v~~~~LPkGt~vkLqP~s 119 (321)
|+.==+.+.|.|.+|.=|-+.|+|++||.|.|.... .| .+.|++.+
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 444445678999999999999999999999887542 23 37777765
No 50
>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=45.50 E-value=30 Score=28.00 Aligned_cols=29 Identities=21% Similarity=0.316 Sum_probs=25.5
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 020791 77 AEEGMIYMPYWMMENLLLQEGDIVRVKNV 105 (321)
Q Consensus 77 A~EG~i~LP~WMm~~L~l~egd~V~v~~~ 105 (321)
.++..|+|..=-++.|+|.+||.|+|.+-
T Consensus 27 ~~~~~v~i~p~dA~~~gi~~Gd~V~v~s~ 55 (123)
T cd02778 27 TPENTLWINPETAARLGIKDGDRVEVSSA 55 (123)
T ss_pred CCCCeEEECHHHHHHcCCCCCCEEEEEeC
Confidence 45678999999999999999999998763
No 51
>smart00553 SEP Domain present in Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47.
Probab=45.14 E-value=13 Score=30.73 Aligned_cols=14 Identities=36% Similarity=0.890 Sum_probs=12.2
Q ss_pred ccceeeeccccCCc
Q 020791 216 FSPFTGVARRLDGK 229 (321)
Q Consensus 216 ~~~F~G~G~rLdGK 229 (321)
+.+|+|.|+||++-
T Consensus 73 ~~~F~G~G~~LGs~ 86 (93)
T smart00553 73 FKPFSGSGQKLGSP 86 (93)
T ss_pred ccCCccCCccCCCC
Confidence 57899999999874
No 52
>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=45.11 E-value=25 Score=27.96 Aligned_cols=24 Identities=21% Similarity=0.475 Sum_probs=20.9
Q ss_pred CeEeccHHHHHHcCCCCCCeEEEE
Q 020791 80 GMIYMPYWMMENLLLQEGDIVRVK 103 (321)
Q Consensus 80 G~i~LP~WMm~~L~l~egd~V~v~ 103 (321)
-.|.||.-|-.++-+.+||.|.|+
T Consensus 25 ~l~~i~gK~Rk~iwI~~GD~VlV~ 48 (78)
T cd04456 25 RLVSIPGKLRKNIWIKRGDFLIVD 48 (78)
T ss_pred EEEEEchhhccCEEEcCCCEEEEE
Confidence 358899999999999999999884
No 53
>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=45.11 E-value=27 Score=28.72 Aligned_cols=29 Identities=24% Similarity=0.187 Sum_probs=25.8
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 020791 77 AEEGMIYMPYWMMENLLLQEGDIVRVKNV 105 (321)
Q Consensus 77 A~EG~i~LP~WMm~~L~l~egd~V~v~~~ 105 (321)
.++..|+|-.=-++.|+|.+||.|.|++.
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 46778999999999999999999999874
No 54
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=44.75 E-value=60 Score=30.10 Aligned_cols=16 Identities=19% Similarity=0.117 Sum_probs=11.7
Q ss_pred EEEeCceeeeecCCCC
Q 020791 171 SIIETDCEVDFAPPLD 186 (321)
Q Consensus 171 sIIeTDleVDF~pPld 186 (321)
.|-+..+.|||.-||-
T Consensus 111 ev~~d~V~vD~NHPLA 126 (196)
T PRK10737 111 AVEDDHVVVDGNHMLA 126 (196)
T ss_pred EEcCCEEEEECCCcCC
Confidence 3456678899988875
No 55
>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=44.68 E-value=27 Score=28.52 Aligned_cols=28 Identities=18% Similarity=0.107 Sum_probs=24.0
Q ss_pred CCeEeccHHHHHHcCCCCCCeEEEEEee
Q 020791 79 EGMIYMPYWMMENLLLQEGDIVRVKNVT 106 (321)
Q Consensus 79 EG~i~LP~WMm~~L~l~egd~V~v~~~~ 106 (321)
+..|+|-.=.++.|+|.+||.|+|++..
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 4468999999999999999999988653
No 56
>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=44.58 E-value=32 Score=27.96 Aligned_cols=29 Identities=24% Similarity=0.079 Sum_probs=25.7
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 020791 77 AEEGMIYMPYWMMENLLLQEGDIVRVKNV 105 (321)
Q Consensus 77 A~EG~i~LP~WMm~~L~l~egd~V~v~~~ 105 (321)
.++..|.|-.=-++.|+|.+||.|.|.+.
T Consensus 30 ~~~~~v~in~~dA~~lgi~~Gd~V~v~s~ 58 (115)
T cd02779 30 VPLPYIEVNPEDAKREGLKNGDLVEVYND 58 (115)
T ss_pred CCCCEEEECHHHHHHcCCCCCCEEEEEeC
Confidence 46778999999999999999999998874
No 57
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=44.19 E-value=32 Score=27.75 Aligned_cols=30 Identities=13% Similarity=0.263 Sum_probs=25.5
Q ss_pred HHHHHcCCCCCCeEEEEEeecCCcceEEEe
Q 020791 87 WMMENLLLQEGDIVRVKNVTLPKGTYVKLQ 116 (321)
Q Consensus 87 WMm~~L~l~egd~V~v~~~~LPkGt~vkLq 116 (321)
-+.+.+|+++||.|.|..-+--.|.||..+
T Consensus 45 Pv~r~~g~k~GdVvkI~R~S~taG~~v~YR 74 (79)
T PRK09570 45 PVVKAIGAKPGDVIKIVRKSPTAGEAVYYR 74 (79)
T ss_pred hhhhhcCCCCCCEEEEEECCCCCCccEEEE
Confidence 377889999999999998888888887654
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=42.80 E-value=39 Score=28.33 Aligned_cols=31 Identities=23% Similarity=0.284 Sum_probs=25.0
Q ss_pred hcccceecccCCEEEEEECCEEEEEEEEEec
Q 020791 135 TLRNYSCLTTGDSIMVAYNNKKYYIDIIETK 165 (321)
Q Consensus 135 ~LRnys~LT~GD~I~I~yn~k~Y~l~V~e~k 165 (321)
.+++...|.+||.|.|...++.|...|.+++
T Consensus 58 ~F~~L~~l~~Gd~v~v~~~~~~~~Y~V~~~~ 88 (126)
T cd06166 58 IFNRLDEVEKGDEIKVTTKNGTYKYKITSIF 88 (126)
T ss_pred ccCChHHCCCCCEEEEEECCEEEEEEEEEEE
Confidence 3455566779999999999999999887754
No 59
>PF04322 DUF473: Protein of unknown function (DUF473); InterPro: IPR007417 This is a family of uncharacterised archaeal proteins.
Probab=42.20 E-value=36 Score=29.45 Aligned_cols=47 Identities=26% Similarity=0.263 Sum_probs=33.2
Q ss_pred CHHHHHHHHhCCCCCCeeEEEEeCCCCCEEEEEEeeeEeCCCeEeccHHHHHHcCCCCCCeEEEEEe---ecCCcc
Q 020791 39 PPSALDRLASLHIDYPMLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNV---TLPKGT 111 (321)
Q Consensus 39 PpSaL~~L~~l~i~~PmlFel~n~~~~r~thcGVLEF~A~EG~i~LP~WMm~~L~l~egd~V~v~~~---~LPkGt 111 (321)
-+.+|++|.+. ++=+|+|+|..+- .--+.+++||.|.++++ +|-.||
T Consensus 10 s~~vi~eL~~~---~~RTiEirSa~N~-----------------------~~~~~~~~Gd~VFlT~~~~~Dl~~Gt 59 (119)
T PF04322_consen 10 SRRVIDELKKN---HIRTIEIRSAHNV-----------------------IALESLDPGDRVFLTSVSLEDLTPGT 59 (119)
T ss_pred CHHHHHHHHhC---CceEEEEEcchhe-----------------------eeeecCCCCCEEEEecCCHHHCCCCC
Confidence 46788888875 4458999986652 12246789999999988 455555
No 60
>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=41.16 E-value=35 Score=28.38 Aligned_cols=29 Identities=28% Similarity=0.144 Sum_probs=25.5
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 020791 77 AEEGMIYMPYWMMENLLLQEGDIVRVKNV 105 (321)
Q Consensus 77 A~EG~i~LP~WMm~~L~l~egd~V~v~~~ 105 (321)
.++..|+|=.=-++.|+|++||.|+|.+.
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 45678999999999999999999999874
No 61
>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=40.82 E-value=35 Score=29.72 Aligned_cols=29 Identities=28% Similarity=0.398 Sum_probs=26.0
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 020791 77 AEEGMIYMPYWMMENLLLQEGDIVRVKNV 105 (321)
Q Consensus 77 A~EG~i~LP~WMm~~L~l~egd~V~v~~~ 105 (321)
.++..|+|-.=-++.|||.+||.|.|.+.
T Consensus 29 ~~~~~v~inp~dA~~~GI~dGd~V~v~s~ 57 (156)
T cd02783 29 HTRNYLYMHPKTAKELGIKDGDWVWVESV 57 (156)
T ss_pred CCCCEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 45678999999999999999999999983
No 62
>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=40.15 E-value=40 Score=29.12 Aligned_cols=26 Identities=15% Similarity=0.211 Sum_probs=20.6
Q ss_pred ceecccCCEEEEEE-CCEEEEEEEEEe
Q 020791 139 YSCLTTGDSIMVAY-NNKKYYIDIIET 164 (321)
Q Consensus 139 ys~LT~GD~I~I~y-n~k~Y~l~V~e~ 164 (321)
...|.+||.|.|.. +++.|...|.++
T Consensus 70 L~~l~~GD~I~v~~~~g~~~~Y~V~~~ 96 (144)
T cd05829 70 LGDLRKGDKVEVTRADGQTATFRVDRV 96 (144)
T ss_pred hhcCCCCCEEEEEECCCCEEEEEEeEE
Confidence 34577999999999 677787777765
No 63
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=39.26 E-value=24 Score=33.09 Aligned_cols=19 Identities=32% Similarity=0.478 Sum_probs=15.9
Q ss_pred HHHHHHcCCCCCCeEEEEE
Q 020791 86 YWMMENLLLQEGDIVRVKN 104 (321)
Q Consensus 86 ~WMm~~L~l~egd~V~v~~ 104 (321)
.-+=+.|+|.+||.|.|+-
T Consensus 197 ~~LR~~l~l~dgd~v~i~i 215 (217)
T PRK14165 197 VYLRKELNLKDGDRVEVLV 215 (217)
T ss_pred hhhHHhcCCCCCCEEEEEE
Confidence 3478899999999999873
No 64
>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=38.95 E-value=37 Score=24.55 Aligned_cols=23 Identities=26% Similarity=0.107 Sum_probs=18.4
Q ss_pred EeccHHHHHHcCCCCCCeEEEEE
Q 020791 82 IYMPYWMMENLLLQEGDIVRVKN 104 (321)
Q Consensus 82 i~LP~WMm~~L~l~egd~V~v~~ 104 (321)
+.++.|-...|+|++||.|.+..
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 67999999999999999988753
No 65
>PRK10456 arginine succinyltransferase; Provisional
Probab=37.59 E-value=44 Score=33.74 Aligned_cols=35 Identities=14% Similarity=0.148 Sum_probs=29.0
Q ss_pred EEEeeeEeCCCeEeccHHHHHHcCCCCCCeEEEEE
Q 020791 70 CGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKN 104 (321)
Q Consensus 70 cGVLEF~A~EG~i~LP~WMm~~L~l~egd~V~v~~ 104 (321)
|-+.....+.+.+.|+.-+++.|++++||.|++-.
T Consensus 302 a~~~~~~~~~~~~~l~~~~a~aL~v~~Gd~Vr~~~ 336 (344)
T PRK10456 302 AVLVRTDPATERLILTAAQLDALKCHAGDRVRLVR 336 (344)
T ss_pred EEEecccCCCCeEecCHHHHHhcCCCCCCeEEEEe
Confidence 34456666788899999999999999999998753
No 66
>TIGR03244 arg_catab_AstA arginine N-succinyltransferase. In many bacteria, the arginine succinyltransferase (ast) pathway operon consists of five genes, including this protein, arginine N-succinyltransferase (EC 2.3.1.109). In a few species, such as Pseudomonas aeruginosa, the member of this family is encoded adjacent to a paralog, and the two polypeptides form a heterodimeric enzyme, active on both arginine and ornithine. In such species, this polypeptide may be treated as the beta subunit of an enzyme that may be named either arginine N-succinyltransferase (AST) or arginine and orthithine N-succinyltransferase (AOST).
Probab=37.58 E-value=44 Score=33.62 Aligned_cols=34 Identities=18% Similarity=0.256 Sum_probs=28.4
Q ss_pred EEEeeeEeCCCeEeccHHHHHHcCCCCCCeEEEE
Q 020791 70 CGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVK 103 (321)
Q Consensus 70 cGVLEF~A~EG~i~LP~WMm~~L~l~egd~V~v~ 103 (321)
|.+.....+.+.+.|+.-+++.|++++||.|++-
T Consensus 301 a~~~~~~~~~~~~~l~~~~a~aL~v~~Gd~Vr~~ 334 (336)
T TIGR03244 301 ATLAPSDLDAGELVLTAAQADALRVSAGDLVRIV 334 (336)
T ss_pred EEEecccCCCCeEecCHHHHHhcCCCCCCeEEEe
Confidence 3445666678889999999999999999999874
No 67
>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=37.50 E-value=1.7e+02 Score=25.59 Aligned_cols=40 Identities=18% Similarity=0.275 Sum_probs=27.0
Q ss_pred eecccCCEEEEEEC--CEEEEEEEEEecCCCeeEEEeCceee
Q 020791 140 SCLTTGDSIMVAYN--NKKYYIDIIETKPSNAISIIETDCEV 179 (321)
Q Consensus 140 s~LT~GD~I~I~yn--~k~Y~l~V~e~kP~~aVsIIeTDleV 179 (321)
..+..||+|.+... ...+.++-+--.|++.|+|.+--+-|
T Consensus 50 ~~~~rGDiVvf~~~~~~~~~~iKRVig~pGd~v~i~~~~l~v 91 (163)
T TIGR02227 50 SDPKRGDIVVFKDPDDNKNIYVKRVIGLPGDKVEFRDGKLYI 91 (163)
T ss_pred CCCCCCcEEEEecCCCCCceeEEEEEecCCCEEEEECCEEEE
Confidence 45678888888764 34455665555688888887755444
No 68
>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=37.18 E-value=48 Score=28.04 Aligned_cols=28 Identities=25% Similarity=0.266 Sum_probs=25.1
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEE
Q 020791 77 AEEGMIYMPYWMMENLLLQEGDIVRVKN 104 (321)
Q Consensus 77 A~EG~i~LP~WMm~~L~l~egd~V~v~~ 104 (321)
.++..|+|-.=-++.|+|.+||.|.|++
T Consensus 27 ~~~~~v~inp~dA~~lgI~~Gd~V~v~s 54 (143)
T cd02780 27 KPENPVWINPEDAAKLGIKTGDRVRVVT 54 (143)
T ss_pred CCCCEEEECHHHHHHcCCCCCCEEEEEe
Confidence 4567899999999999999999999987
No 69
>TIGR03245 arg_AOST_alph arginine/ornithine succinyltransferase, alpha subunit. In some bacteria, including Pseudomonas aeruginosa, the astB gene (arginine N-succinyltransferase) is replaced by tandem paralogs that form a heterodimer. This heterodimer from P. aeruginosa is characterized as arginine and ornithine N-2 succinyltransferase (AOST). Members of this protein family represent the less widespread paralog, designated AruI, or arginine/ornithine succinyltransferase, alpha subunit.
Probab=35.70 E-value=48 Score=33.36 Aligned_cols=34 Identities=21% Similarity=0.263 Sum_probs=27.6
Q ss_pred EEEeeeE-eCCCeEeccHHHHHHcCCCCCCeEEEE
Q 020791 70 CGVLEFI-AEEGMIYMPYWMMENLLLQEGDIVRVK 103 (321)
Q Consensus 70 cGVLEF~-A~EG~i~LP~WMm~~L~l~egd~V~v~ 103 (321)
|-++... .+.+.+.|+.-+++.|++++||.|++-
T Consensus 300 a~~~~~~~~~~~~~~l~~~~a~aL~v~~Gd~Vr~~ 334 (336)
T TIGR03245 300 ATLADVTDVDGDLLRLKRDAAEALGVSEGDNVRFA 334 (336)
T ss_pred EEEeccccCCCCeeecCHHHHHhcCCCCCCeEEEe
Confidence 3345555 567888999999999999999999874
No 70
>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=35.28 E-value=1.7e+02 Score=21.06 Aligned_cols=33 Identities=24% Similarity=0.390 Sum_probs=22.8
Q ss_pred ecccCCEEEEEECCEE-EEEEEEEecCCCeeEEE
Q 020791 141 CLTTGDSIMVAYNNKK-YYIDIIETKPSNAISII 173 (321)
Q Consensus 141 ~LT~GD~I~I~yn~k~-Y~l~V~e~kP~~aVsII 173 (321)
.+..||.+.+.+++.. +.++-+...+...+-+.
T Consensus 24 ~~~~gdivv~~~~~~~~~~iKrv~~~~~~~~~~~ 57 (70)
T PF00717_consen 24 EPKDGDIVVVKIDGDEELYIKRVVGEPGGIILIS 57 (70)
T ss_dssp ---TTSEEEEEETTEESEEEEEEEEETTEEEEE-
T ss_pred CCccCeEEEEEECCceeeEEEEEEEeCCCEEEEe
Confidence 5668999999999887 77776666777666554
No 71
>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=33.78 E-value=68 Score=26.86 Aligned_cols=30 Identities=23% Similarity=0.299 Sum_probs=24.4
Q ss_pred cccceecccCCEEEEEECCEEEEEEEEEec
Q 020791 136 LRNYSCLTTGDSIMVAYNNKKYYIDIIETK 165 (321)
Q Consensus 136 LRnys~LT~GD~I~I~yn~k~Y~l~V~e~k 165 (321)
+++...|.+||.|.|...++.|...|.+++
T Consensus 56 F~~L~~l~~Gd~i~v~~~~~~~~Y~V~~~~ 85 (127)
T cd05828 56 FRFLGELEPGDIITLQTLGGTYTYRVTSTR 85 (127)
T ss_pred hhChhcCCCCCEEEEEECCEEEEEEEeeEE
Confidence 444555779999999999999999988764
No 72
>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=33.03 E-value=66 Score=27.35 Aligned_cols=30 Identities=20% Similarity=0.310 Sum_probs=24.3
Q ss_pred cccceecccCCEEEEEECCEEEEEEEEEec
Q 020791 136 LRNYSCLTTGDSIMVAYNNKKYYIDIIETK 165 (321)
Q Consensus 136 LRnys~LT~GD~I~I~yn~k~Y~l~V~e~k 165 (321)
+++...|..||.|.|...++.|...|.+++
T Consensus 60 F~~L~~l~~Gd~i~v~~~~~~~~Y~V~~~~ 89 (137)
T cd05830 60 FNDLDKLRPGDKIVVETADGWYTYVVRSSE 89 (137)
T ss_pred cccHhhCCCCCEEEEEECCeEEEEEEeEEE
Confidence 444455889999999999999999988764
No 73
>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=32.18 E-value=65 Score=27.39 Aligned_cols=24 Identities=21% Similarity=0.293 Sum_probs=20.6
Q ss_pred ecccCCEEEEEECCEEEEEEEEEe
Q 020791 141 CLTTGDSIMVAYNNKKYYIDIIET 164 (321)
Q Consensus 141 ~LT~GD~I~I~yn~k~Y~l~V~e~ 164 (321)
-|.+||.|.|...+..|...|.++
T Consensus 63 ~l~~GD~i~v~~~~~~~~Y~V~~~ 86 (136)
T TIGR01076 63 KLKKGDMLYLHVGNEVLTYQVTST 86 (136)
T ss_pred HCCCCCEEEEEECCcEEEEEEEEE
Confidence 377999999999998888888765
No 74
>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=30.04 E-value=35 Score=28.00 Aligned_cols=20 Identities=35% Similarity=0.634 Sum_probs=12.4
Q ss_pred hhcccceecccCCEEEEEEC
Q 020791 134 TTLRNYSCLTTGDSIMVAYN 153 (321)
Q Consensus 134 ~~LRnys~LT~GD~I~I~yn 153 (321)
+++-.|.-|..|++++|+||
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 45567889999999999998
No 75
>PLN03086 PRLI-interacting factor K; Provisional
Probab=29.96 E-value=2.9e+02 Score=29.83 Aligned_cols=72 Identities=19% Similarity=0.178 Sum_probs=42.0
Q ss_pred CCCeEecCHHHHHHHHhCCCCCCeeEEEEeCCCCCEEEEEEeeeEeCCCeEeccHH--HHHHcC-----CCCCCeEEEEE
Q 020791 32 SGDKIIMPPSALDRLASLHIDYPMLFELRNNAAERVSHCGVLEFIAEEGMIYMPYW--MMENLL-----LQEGDIVRVKN 104 (321)
Q Consensus 32 ~GdKIiLPpSaL~~L~~l~i~~PmlFel~n~~~~r~thcGVLEF~A~EG~i~LP~W--Mm~~L~-----l~egd~V~v~~ 104 (321)
.-|.|.||+-+++.|........-+.+|++..-.+-|++-..--++ |+.=++.| ++++-+ |..||+|.|.|
T Consensus 149 ~EG~v~lP~wm~~~L~~~~~~~~~~v~v~~~~Lpkgt~vklqP~~~--~f~di~npKavLE~~Lr~~stLT~Gd~i~i~~ 226 (567)
T PLN03086 149 EEGSVGLPPHVWSNLFPSDPPDVPLVEVRYIWLPKGTYAKLQPDGV--GFSDLPNHKAVLETALRQHATLSEDDVLVVNY 226 (567)
T ss_pred CCCeEEcCHHHHhhcCCCCCCCCCeEEEEEeecCCCCEEEEeeccC--CcCCcccHHHHHHHHhhcCccccCCCEEEEec
Confidence 3478999999998774322222235666665544445555442222 22234444 454433 77899999987
Q ss_pred e
Q 020791 105 V 105 (321)
Q Consensus 105 ~ 105 (321)
-
T Consensus 227 ~ 227 (567)
T PLN03086 227 G 227 (567)
T ss_pred C
Confidence 4
No 76
>TIGR02620 cas_VVA1548 putative CRISPR-associated protein, VVA1548 family. This model represents a conserved domain of about 95 amino acids exclusively in species with CRISPR (Clustered Regularly Interspaced Short Palidromic Repeats). In all bacterial species with members so far (Vibrio vulnificus YJ016, Mannheimia succiniciproducens MBEL55E, and Nitrosomonas europaea ATCC 19718) and but not in the archaeon Methanothermobacter thermautotrophicus str. Delta H, the gene for this protein is in the midst of a cluster of Cas protein gene near CRISPR repeats.
Probab=29.75 E-value=34 Score=28.55 Aligned_cols=30 Identities=27% Similarity=0.484 Sum_probs=25.5
Q ss_pred cccCCCCCCCCeEe--cCHHHHHHHHhCCCCC
Q 020791 24 FIEKPQIESGDKII--MPPSALDRLASLHIDY 53 (321)
Q Consensus 24 ~~~k~~~~~GdKIi--LPpSaL~~L~~l~i~~ 53 (321)
.++-.++..||+|| ||.+.+.++++.+..|
T Consensus 26 HLd~~~i~~GD~ViGtLPv~Laa~vc~kGa~y 57 (93)
T TIGR02620 26 HLDPIDISQGDKVIGTLPVSLAADICKKGARY 57 (93)
T ss_pred ccCHHHhcCCCEEEEeCCHHHHHHHHhCCcEE
Confidence 56667889999997 9999999999977655
No 77
>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=29.71 E-value=83 Score=26.03 Aligned_cols=25 Identities=24% Similarity=0.372 Sum_probs=21.3
Q ss_pred ecccCCEEEEEECCEEEEEEEEEec
Q 020791 141 CLTTGDSIMVAYNNKKYYIDIIETK 165 (321)
Q Consensus 141 ~LT~GD~I~I~yn~k~Y~l~V~e~k 165 (321)
.|.+||.|.|...++.|...|.+++
T Consensus 64 ~l~~Gd~v~v~~~~~~~~Y~V~~~~ 88 (128)
T cd00004 64 NLKKGDKIYLTDGGKTYVYKVTSIL 88 (128)
T ss_pred HCCCCCEEEEEECCEEEEEEEEEEE
Confidence 3556999999999999999998764
No 78
>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=29.42 E-value=81 Score=26.23 Aligned_cols=24 Identities=21% Similarity=0.414 Sum_probs=20.6
Q ss_pred cccCCEEEEEECCEEEEEEEEEec
Q 020791 142 LTTGDSIMVAYNNKKYYIDIIETK 165 (321)
Q Consensus 142 LT~GD~I~I~yn~k~Y~l~V~e~k 165 (321)
|.+||.|.|...++.|...|.+.+
T Consensus 64 l~~Gd~I~l~~~~~~~~Y~V~~~~ 87 (127)
T cd06165 64 VKVGDKIYLTDKDNVYEYKVTSKK 87 (127)
T ss_pred CcCCCEEEEEECCEEEEEEEeeEE
Confidence 448999999999999999988754
No 79
>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=29.37 E-value=1.2e+02 Score=21.46 Aligned_cols=22 Identities=14% Similarity=0.321 Sum_probs=18.5
Q ss_pred cccCCEEEEEECCEEEEEEEEE
Q 020791 142 LTTGDSIMVAYNNKKYYIDIIE 163 (321)
Q Consensus 142 LT~GD~I~I~yn~k~Y~l~V~e 163 (321)
+--+..|.|.|++..|.|++..
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 80
>PF04958 AstA: Arginine N-succinyltransferase beta subunit; InterPro: IPR007041 Arginine N-succinyltransferase catalyses the transfer of succinyl-CoA to arginine to produce succinylarginine. This is the first step in arginine catabolism via the arginine succinyltransferase pathway. Six major L-arginine-degrading pathways have been described for prokaryotes []. Many bacteria arginine succinyltransferase 2.3.1.109 from EC, which is the AstA protein of the succinyltransferase (ast) pathway operon consists of five genes. In a few species, such as Pseudomonas aeruginosa, a tandem gene pair encodes alpha and beta subunits of a heterodimer that is designated arginine and ornithine succinyltransferase (AOST). This entry represents the family of proteins that make up the beta subunit of the heterodimer of Ast and AOST.; GO: 0008791 arginine N-succinyltransferase activity, 0006527 arginine catabolic process; PDB: 1YLE_A.
Probab=29.31 E-value=67 Score=32.36 Aligned_cols=34 Identities=21% Similarity=0.232 Sum_probs=21.2
Q ss_pred EEEeeeEeC-CCeEeccHHHHHHcCCCCCCeEEEE
Q 020791 70 CGVLEFIAE-EGMIYMPYWMMENLLLQEGDIVRVK 103 (321)
Q Consensus 70 cGVLEF~A~-EG~i~LP~WMm~~L~l~egd~V~v~ 103 (321)
|-+-+-... .+.+.|+.-+++.|++++||.|++-
T Consensus 306 a~~~~~~~~~~~~~~l~~~~a~~L~v~~Gd~Vr~~ 340 (342)
T PF04958_consen 306 ATLAPAALDDGDQLVLSPEVADALQVSEGDPVRVV 340 (342)
T ss_dssp EEEEEE---TTS-EEE-HHHHHHHT--TT-EEEEE
T ss_pred EEEEecccCCCCeEEcCHHHHhhcCCCCCCEEEEe
Confidence 344444444 8999999999999999999999873
No 81
>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=28.92 E-value=1.1e+02 Score=22.47 Aligned_cols=56 Identities=14% Similarity=0.065 Sum_probs=34.8
Q ss_pred CCCCCeEEEEEe-ecCCcceEEEeeCCcCcCCccccHHHHHhhcccceecccCCEEEEE
Q 020791 94 LQEGDIVRVKNV-TLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVA 151 (321)
Q Consensus 94 l~egd~V~v~~~-~LPkGt~vkLqP~s~~FldIsnpKavLE~~LRnys~LT~GD~I~I~ 151 (321)
|..|+.|.-+-. -.+.|-||.|.+.-..|+.+++... +...+.-..+..||+|.+.
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 467888866544 3677899999887777776554221 0001113457889988864
No 82
>KOG2086 consensus Protein tyrosine phosphatase SHP1/Cofactor for p97 ATPase-mediated vesicle membrane fusion [Nuclear structure]
Probab=28.31 E-value=60 Score=33.21 Aligned_cols=16 Identities=44% Similarity=0.962 Sum_probs=14.2
Q ss_pred CCcccceeeeccccCC
Q 020791 213 EPKFSPFTGVARRLDG 228 (321)
Q Consensus 213 ~~~~~~F~G~G~rLdG 228 (321)
++.|.+|+|.|+||.+
T Consensus 252 ~~~~~pF~G~Gq~LGs 267 (380)
T KOG2086|consen 252 KPVFKPFSGEGQRLGS 267 (380)
T ss_pred CcccCCCCCcCeecCC
Confidence 4569999999999998
No 83
>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=28.25 E-value=92 Score=22.66 Aligned_cols=27 Identities=19% Similarity=0.556 Sum_probs=22.6
Q ss_pred cccCCEEEEEE-CCEEEEEEEEEecCCC
Q 020791 142 LTTGDSIMVAY-NNKKYYIDIIETKPSN 168 (321)
Q Consensus 142 LT~GD~I~I~y-n~k~Y~l~V~e~kP~~ 168 (321)
|.+|+.+.+.+ ++..|.=.|+++++.+
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 8999999999998754
No 84
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=27.42 E-value=1.1e+02 Score=26.87 Aligned_cols=30 Identities=37% Similarity=0.459 Sum_probs=20.0
Q ss_pred cCHHHHHHHHhCCCCCCeeEEEEeCCCCCEEEEEEeee
Q 020791 38 MPPSALDRLASLHIDYPMLFELRNNAAERVSHCGVLEF 75 (321)
Q Consensus 38 LPpSaL~~L~~l~i~~PmlFel~n~~~~r~thcGVLEF 75 (321)
||-|.|. ---.+||+-||.|.. |+-|.|.=
T Consensus 2 lPLsLL~----~aq~~pmlvELKNge----t~nGhL~~ 31 (134)
T KOG3293|consen 2 LPLSLLK----TAQNHPMLVELKNGE----TYNGHLVN 31 (134)
T ss_pred cchhHHH----hcCCCeEEEEecCCC----Eecceeec
Confidence 6666553 234689999999875 45566543
No 85
>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=27.35 E-value=85 Score=27.18 Aligned_cols=27 Identities=26% Similarity=0.371 Sum_probs=24.2
Q ss_pred CCeEeccHHHHHHcCCCCCCeEEEEEe
Q 020791 79 EGMIYMPYWMMENLLLQEGDIVRVKNV 105 (321)
Q Consensus 79 EG~i~LP~WMm~~L~l~egd~V~v~~~ 105 (321)
+..|+|-.=-.+.|+|.+||.|+|.+-
T Consensus 37 ~~~v~InP~dA~~lGI~dGD~V~V~s~ 63 (137)
T cd02784 37 DNAALVSPRTAEALGLLQGDVVRIRRG 63 (137)
T ss_pred CceEEECHHHHHHcCCCCCCEEEEEeC
Confidence 567999999999999999999999874
No 86
>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=27.02 E-value=87 Score=23.64 Aligned_cols=24 Identities=21% Similarity=0.393 Sum_probs=17.0
Q ss_pred eEeccHHHHHHcCCCCCCeEEEEE
Q 020791 81 MIYMPYWMMENLLLQEGDIVRVKN 104 (321)
Q Consensus 81 ~i~LP~WMm~~L~l~egd~V~v~~ 104 (321)
.|.||.-+...+.+.+||.|.|+-
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 588999988899999999888874
No 87
>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=26.72 E-value=1.8e+02 Score=25.72 Aligned_cols=20 Identities=20% Similarity=0.350 Sum_probs=15.3
Q ss_pred CCCeEEEEEeecCCcceEEE
Q 020791 96 EGDIVRVKNVTLPKGTYVKL 115 (321)
Q Consensus 96 egd~V~v~~~~LPkGt~vkL 115 (321)
+.+.|..++--+|.|+-++-
T Consensus 23 ~~~~V~feN~lMpsG~~I~~ 42 (135)
T TIGR03711 23 SDNEVYFENPLMPSGETIHT 42 (135)
T ss_pred cCCcEEEeccCCCCCCEEEE
Confidence 34568888889999988763
No 88
>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=26.35 E-value=1.1e+02 Score=23.48 Aligned_cols=24 Identities=21% Similarity=0.317 Sum_probs=19.3
Q ss_pred cccCCEEEEEECCEEEEEEEEEec
Q 020791 142 LTTGDSIMVAYNNKKYYIDIIETK 165 (321)
Q Consensus 142 LT~GD~I~I~yn~k~Y~l~V~e~k 165 (321)
...||++.+...+..+.+.|++++
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 468999999999988889988864
No 89
>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=25.96 E-value=1.3e+02 Score=32.52 Aligned_cols=71 Identities=20% Similarity=0.282 Sum_probs=47.2
Q ss_pred CCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccccHHHHHhhcccceecccCCEEEEEE
Q 020791 78 EEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAY 152 (321)
Q Consensus 78 ~EG~i~LP~WMm~~L~l~egd~V~v~~~~LPkGt~vkLqP~s~~FldIsnpKavLE~~LRnys~LT~GD~I~I~y 152 (321)
.-|.+.|..-.|+.|++.+||.|.|..- -+.+-.+.-|...+ +...----|...+|....+..||.+.|.-
T Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (733)
T TIGR01243 15 GRGIVRIDRQTAARLGVEPGDFVEIEKG--DRSVVAIVWPLRPD--DEGRGIIRMDGYLRANAGVTIGDTVTVER 85 (733)
T ss_pred CCCeEeeCHHHHHhcCCCCCCEEEEecC--CCceeEEEEecCcc--ccCCCEEeecHHHHhhcCCCCCCeEEEee
Confidence 3478899999999999999999999831 11234455553222 12211222556677777799999999864
No 90
>PRK08059 general stress protein 13; Validated
Probab=25.40 E-value=1.3e+02 Score=25.23 Aligned_cols=59 Identities=27% Similarity=0.445 Sum_probs=36.4
Q ss_pred HHHHcCCCCCCeEEEEEe-ecCCcceEEEeeCCcCcCCccccHHHHHhhccc-ceecccCCEEEEE
Q 020791 88 MMENLLLQEGDIVRVKNV-TLPKGTYVKLQPHTKDFLDISNPKAILETTLRN-YSCLTTGDSIMVA 151 (321)
Q Consensus 88 Mm~~L~l~egd~V~v~~~-~LPkGt~vkLqP~s~~FldIsnpKavLE~~LRn-ys~LT~GD~I~I~ 151 (321)
||.+ ++.|+.|.-+-+ .-+.|-||.|.+.-..|+-+++-.. ...++ ...+..||+|.+.
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 566888776654 4578999999876666654332110 00122 3467899999874
No 91
>PRK13532 nitrate reductase catalytic subunit; Provisional
Probab=25.19 E-value=69 Score=35.11 Aligned_cols=51 Identities=22% Similarity=0.183 Sum_probs=36.5
Q ss_pred CCCeeEEEEeCCCCCEEEEEE--------eeeEeCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 020791 52 DYPMLFELRNNAAERVSHCGV--------LEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNV 105 (321)
Q Consensus 52 ~~PmlFel~n~~~~r~thcGV--------LEF~A~EG~i~LP~WMm~~L~l~egd~V~v~~~ 105 (321)
.|| |.|.+......+|.+. .+. .++..|+|=.=-++.|+|.+||.|+|.+-
T Consensus 713 ~yp--l~Lit~r~~~~~hs~~~~~~~~~l~~~-~~~~~v~inp~DA~~~GI~dGD~V~V~n~ 771 (830)
T PRK13532 713 EYD--LWLSTGRVLEHWHTGSMTRRVPELYRA-FPEAVCFMHPEDAKARGLRRGDEVKVVSR 771 (830)
T ss_pred CCC--eEEecccchhhccccCccCchHHHHhh-CCCCEEEECHHHHHHcCCCCCCEEEEEeC
Confidence 477 4444444444566652 222 36788999999999999999999999875
No 92
>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=24.87 E-value=94 Score=23.40 Aligned_cols=56 Identities=18% Similarity=0.240 Sum_probs=36.3
Q ss_pred CCCCCeEEEEEeec-C-CcceEEEeeCCcCcCCccccHHHHHhhccc-ceecccCCEEEEEE
Q 020791 94 LQEGDIVRVKNVTL-P-KGTYVKLQPHTKDFLDISNPKAILETTLRN-YSCLTTGDSIMVAY 152 (321)
Q Consensus 94 l~egd~V~v~~~~L-P-kGt~vkLqP~s~~FldIsnpKavLE~~LRn-ys~LT~GD~I~I~y 152 (321)
|++|+.|.=+-+.+ + .|-|+.|-|.-..++-|++... ....+ ...+..||.|.+..
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 46788886555553 3 6999999988888876653211 12222 23467899998754
No 93
>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=24.83 E-value=90 Score=34.45 Aligned_cols=29 Identities=28% Similarity=0.134 Sum_probs=26.3
Q ss_pred eCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 020791 77 AEEGMIYMPYWMMENLLLQEGDIVRVKNV 105 (321)
Q Consensus 77 A~EG~i~LP~WMm~~L~l~egd~V~v~~~ 105 (321)
.++..|.|-.=-++.|||.+||.|+|.+-
T Consensus 722 ~p~p~v~InP~DA~~lGI~dGD~V~V~n~ 750 (806)
T TIGR02693 722 LPLPYIEVNPEDAKRLGLKSGDLVEVYND 750 (806)
T ss_pred CCCCEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 46788999999999999999999999875
No 94
>COG0836 {ManC} Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane]
Probab=24.79 E-value=1.6e+02 Score=29.79 Aligned_cols=76 Identities=13% Similarity=0.248 Sum_probs=55.3
Q ss_pred CeEEEEEeecCCcceEEEeeCCcCcCCccccHHHHHhhccc-ceecccCCEEEEEECC-EEEE----EEEEEecCCCeeE
Q 020791 98 DIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRN-YSCLTTGDSIMVAYNN-KKYY----IDIIETKPSNAIS 171 (321)
Q Consensus 98 d~V~v~~~~LPkGt~vkLqP~s~~FldIsnpKavLE~~LRn-ys~LT~GD~I~I~yn~-k~Y~----l~V~e~kP~~aVs 171 (321)
+-+.|.|.-+.|..-+..-|.+-.+-||-+|.|+.|-.-+. --....||++.+.-+| -+|. +.++.++ =+-
T Consensus 245 p~iSIDYAiMEkt~~~aVVp~~f~WsDlGsW~Al~~~~~~d~~gNv~~gd~~~~dt~n~~v~s~~~lia~vGl~---Dlv 321 (333)
T COG0836 245 PAISIDYAIMEKTSKAAVVPADFGWSDLGSWHALWEVLDKDENGNVCEGDVVTIDTENSLISSNNKLISVVGLE---DLV 321 (333)
T ss_pred cccchhHHHHhhhcceEEEecCCCcccccCHHHHHHHhhcCCCCCEEecceEEeccCCcEEEeCCceEEEeccc---eEE
Confidence 35778888999999999999999999999999999877764 3456789998886543 3333 3334333 455
Q ss_pred EEeCc
Q 020791 172 IIETD 176 (321)
Q Consensus 172 IIeTD 176 (321)
||+|+
T Consensus 322 VV~t~ 326 (333)
T COG0836 322 VVDTK 326 (333)
T ss_pred EEecC
Confidence 55554
No 95
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=24.53 E-value=2e+02 Score=23.18 Aligned_cols=48 Identities=23% Similarity=0.578 Sum_probs=32.8
Q ss_pred ceecccCCEEEEEECC-------EEEEE-EEEEec-----C------------CCeeEEEeCceeeeecCCCC
Q 020791 139 YSCLTTGDSIMVAYNN-------KKYYI-DIIETK-----P------------SNAISIIETDCEVDFAPPLD 186 (321)
Q Consensus 139 ys~LT~GD~I~I~yn~-------k~Y~l-~V~e~k-----P------------~~aVsIIeTDleVDF~pPld 186 (321)
|-.+..||++.|..++ +.|++ .|+.+. | ..-|+.|++|....+.+++|
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 4456788888887765 44544 355442 3 14689999999988887764
No 96
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=23.85 E-value=2.3e+02 Score=21.32 Aligned_cols=56 Identities=23% Similarity=0.265 Sum_probs=34.2
Q ss_pred CCCCeeEEEEeCCCC-CEEEEEEeeeEeCCCe-EeccHHHHHHcCCCCCCeEEEEEee
Q 020791 51 IDYPMLFELRNNAAE-RVSHCGVLEFIAEEGM-IYMPYWMMENLLLQEGDIVRVKNVT 106 (321)
Q Consensus 51 i~~PmlFel~n~~~~-r~thcGVLEF~A~EG~-i~LP~WMm~~L~l~egd~V~v~~~~ 106 (321)
+--++..++.++... ....+=|.++..+.-. |-+|.|=-+.+.|.+|+.|.|++..
T Consensus 3 iG~~i~i~i~~~~~~~~~y~S~v~g~~~~~~l~i~~P~~~g~~~~l~~g~~v~v~~~~ 60 (87)
T PF12945_consen 3 IGQKIEIEITNPTGEKGRYKSRVIGIDDDRYLIISMPMEKGRPIPLREGEEVIVRFIS 60 (87)
T ss_dssp TT-EEEEEEE-TTS-EEEEEEEEEEEETTTEEEEE---CCHHHCCS-TT-EEEEEEEE
T ss_pred CCCEEEEEEECCCCceEEEEEEEEEECCCCEEEEEcCccCCcEEeecCCCEEEEEEEE
Confidence 344566777766533 3567778888888443 6689777778899999999998763
No 97
>PRK10183 hypothetical protein; Provisional
Probab=23.37 E-value=1.2e+02 Score=23.28 Aligned_cols=22 Identities=9% Similarity=0.366 Sum_probs=19.3
Q ss_pred cccCCEEEEEECCEEEEEEEEE
Q 020791 142 LTTGDSIMVAYNNKKYYIDIIE 163 (321)
Q Consensus 142 LT~GD~I~I~yn~k~Y~l~V~e 163 (321)
|.-+..|.|.+++..|.|++..
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 5677899999999999999864
No 98
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=22.32 E-value=1.3e+02 Score=26.38 Aligned_cols=25 Identities=4% Similarity=0.064 Sum_probs=22.0
Q ss_pred ecccCCEEEEEECCEEEEEEEEEec
Q 020791 141 CLTTGDSIMVAYNNKKYYIDIIETK 165 (321)
Q Consensus 141 ~LT~GD~I~I~yn~k~Y~l~V~e~k 165 (321)
.+..||+|.|.+++..+.|.|+.+-
T Consensus 48 ~V~~gd~l~v~~~~~~~~v~Vl~l~ 72 (133)
T PRK10348 48 IVELNATLTLRQGNDERTVIVKAIT 72 (133)
T ss_pred ccCCCCEEEEEECCEEEEEEEeECc
Confidence 3568999999999999999999875
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=22.29 E-value=1.4e+02 Score=24.28 Aligned_cols=23 Identities=26% Similarity=0.463 Sum_probs=18.6
Q ss_pred ccCCEEEEEE-CCEEEEEEEEEec
Q 020791 143 TTGDSIMVAY-NNKKYYIDIIETK 165 (321)
Q Consensus 143 T~GD~I~I~y-n~k~Y~l~V~e~k 165 (321)
..||.|.|.. +++.|...|.+++
T Consensus 62 ~~gd~i~~~~~~g~~~~Y~V~~~~ 85 (128)
T PF04203_consen 62 KKGDEIYLTTPDGKTYEYRVTSVK 85 (128)
T ss_dssp HTT-EEEEEETSSEEEEEEEEEEE
T ss_pred CCCCEEEEEEecCEEEEEEEEEEE
Confidence 8999999999 7888888887755
No 100
>PRK05807 hypothetical protein; Provisional
Probab=22.14 E-value=3e+02 Score=23.72 Aligned_cols=55 Identities=22% Similarity=0.318 Sum_probs=34.3
Q ss_pred CCCCCCeEEEEEe-ecCCcceEEEeeCCcCcCCccccHHHHHhhccc-ceecccCCEEEEE
Q 020791 93 LLQEGDIVRVKNV-TLPKGTYVKLQPHTKDFLDISNPKAILETTLRN-YSCLTTGDSIMVA 151 (321)
Q Consensus 93 ~l~egd~V~v~~~-~LPkGt~vkLqP~s~~FldIsnpKavLE~~LRn-ys~LT~GD~I~I~ 151 (321)
.++.|+.|.-.-. ..+-|-||.| .....|+-+++... ...++ ...|..||.|.+.
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 3567888776644 5789999999 44455665443211 11222 3458899998864
No 101
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=22.08 E-value=1.3e+02 Score=23.87 Aligned_cols=24 Identities=29% Similarity=0.346 Sum_probs=21.0
Q ss_pred CeEeccHHHHHHcCCCCCCeEEEE
Q 020791 80 GMIYMPYWMMENLLLQEGDIVRVK 103 (321)
Q Consensus 80 G~i~LP~WMm~~L~l~egd~V~v~ 103 (321)
-.+.+|.-|-.++.+.+||.|.|+
T Consensus 25 ~la~i~gK~rk~iwI~~GD~V~Ve 48 (77)
T cd05793 25 RLCRIRGKMRKRVWINEGDIVLVA 48 (77)
T ss_pred EEEEEchhhcccEEEcCCCEEEEE
Confidence 357899999999999999999887
No 102
>PRK09376 rho transcription termination factor Rho; Provisional
Probab=21.98 E-value=1.4e+02 Score=30.99 Aligned_cols=39 Identities=28% Similarity=0.332 Sum_probs=30.3
Q ss_pred CEEEEEEeeeE---------------eCCCeEeccHHHHHHcCCCCCCeEEEEE
Q 020791 66 RVSHCGVLEFI---------------AEEGMIYMPYWMMENLLLQEGDIVRVKN 104 (321)
Q Consensus 66 r~thcGVLEF~---------------A~EG~i~LP~WMm~~L~l~egd~V~v~~ 104 (321)
.....||||.. +.+.-||+|..+.+..+|+.||.|.=.-
T Consensus 48 ~~~~~g~le~~~~g~gflr~~~~~y~~~~~d~yvs~~~ir~~~lr~gd~v~g~~ 101 (416)
T PRK09376 48 DIFGEGVLEILPDGFGFLRSPDANYLPGPDDIYVSPSQIRRFNLRTGDTVEGKI 101 (416)
T ss_pred ceEEEEEEEEcCCCCeEEeCCCcCCCCCCCCeeeCHHHHHhcCCCCCCEEEEEe
Confidence 35778999933 2235599999999999999999887543
No 103
>cd05827 Sortase_C_3 Sortase C (SrtC) or subfamily-3 sortases are membrane cysteine transpeptidases found in Gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves 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. Sortase C cleaves surface proteins at the LPXTG motif between Thr and Gly and catalyzes the formation of an amide bond between the carboxyl group of Thr and the amino group of cell-wall cross bridges. It is a narrow-range enzyme required for anchoring a few substrates. It plays a role in Streptococcus pneumoniae pathogenesis and is required in the assembly of pili on the surface of Corynebacterium diphtheriae. Sortase C is
Probab=21.97 E-value=1.5e+02 Score=24.78 Aligned_cols=24 Identities=13% Similarity=0.223 Sum_probs=20.8
Q ss_pred cccCCEEEEEECCEEEEEEEEEec
Q 020791 142 LTTGDSIMVAYNNKKYYIDIIETK 165 (321)
Q Consensus 142 LT~GD~I~I~yn~k~Y~l~V~e~k 165 (321)
|.+||.|.|...+..|...|.+++
T Consensus 67 l~~gd~i~l~t~~~~~~Y~V~~~~ 90 (131)
T cd05827 67 LKKGDKFYIHVLGETLAYQVDQIE 90 (131)
T ss_pred CCCCCEEEEEECCeEEEEEEEEEE
Confidence 559999999999999999888765
No 104
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=21.26 E-value=2.6e+02 Score=20.28 Aligned_cols=22 Identities=14% Similarity=0.096 Sum_probs=17.1
Q ss_pred EeccHHHHHHcCCCCCCeEEEE
Q 020791 82 IYMPYWMMENLLLQEGDIVRVK 103 (321)
Q Consensus 82 i~LP~WMm~~L~l~egd~V~v~ 103 (321)
.++|.+-++.--|++||.|.|-
T Consensus 38 ~~v~~~~~~~~~L~~gD~vei~ 59 (65)
T PRK06944 38 DFVARTQHAARALAAGDRLDLV 59 (65)
T ss_pred EEcCchhcccccCCCCCEEEEE
Confidence 3578777777789999998763
No 105
>COG0187 GyrB Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit [DNA replication, recombination, and repair]
Probab=21.14 E-value=1e+02 Score=33.60 Aligned_cols=46 Identities=26% Similarity=0.375 Sum_probs=41.4
Q ss_pred CCcceEEEeeCCcCcCCccccHHHHHhhcccceecccCCEEEEEEC
Q 020791 108 PKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYN 153 (321)
Q Consensus 108 PkGt~vkLqP~s~~FldIsnpKavLE~~LRnys~LT~GD~I~I~yn 153 (321)
..||.|.|.|-..-|-....--.+|.++||..+.|..|=.|.+...
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 4599999999999998888889999999999999999988888754
No 106
>PTZ00061 DNA-directed RNA polymerase; Provisional
Probab=21.00 E-value=1.2e+02 Score=28.70 Aligned_cols=31 Identities=19% Similarity=0.312 Sum_probs=26.2
Q ss_pred HHHHHHcCCCCCCeEEEEEeecCCcceEEEe
Q 020791 86 YWMMENLLLQEGDIVRVKNVTLPKGTYVKLQ 116 (321)
Q Consensus 86 ~WMm~~L~l~egd~V~v~~~~LPkGt~vkLq 116 (321)
.-+.+.+|++.||+|.|...+--.|.||..+
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 3478899999999999999888889888654
No 107
>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=20.56 E-value=1.3e+02 Score=27.39 Aligned_cols=87 Identities=20% Similarity=0.365 Sum_probs=47.7
Q ss_pred CCCeeEEEEe------CCCCCEEEEEEeeeE-eCCCeEecc---------------HHHHHHcCCCCCCeEEEEEee---
Q 020791 52 DYPMLFELRN------NAAERVSHCGVLEFI-AEEGMIYMP---------------YWMMENLLLQEGDIVRVKNVT--- 106 (321)
Q Consensus 52 ~~PmlFel~n------~~~~r~thcGVLEF~-A~EG~i~LP---------------~WMm~~L~l~egd~V~v~~~~--- 106 (321)
..|+..+|.. ....|.|+. +||. .+.|.-|-| .++++.|++.....|.|....
T Consensus 6 ~~p~~a~V~~~~~Lt~~~~~r~~~h--ieldl~~~~l~Y~pGD~l~V~P~N~~~~V~~~l~~lgl~~d~~v~~~~~~~~~ 83 (219)
T PF00667_consen 6 KNPFPATVLENRRLTSPGSDRSTRH--IELDLSDSGLSYQPGDHLGVYPPNDPEEVERLLKRLGLDPDEPVTLKPKEQNN 83 (219)
T ss_dssp TB-EEEEEEEEEE-SSTTSSSEEEE--EEEE-TTSTG---TT-EEEEE-SSEHHHHHHHHHHHTSGTTSEEEEEESSTTS
T ss_pred CCCEEEEEEeEEEcCCCCCCceEEE--EEEEeCCCCCcccCCCEEEEEccCCHHHHHHHHHHhCCCcceEEEEEeccccc
Confidence 3456665543 344555544 6663 344666655 579999999998899988764
Q ss_pred ---cCCcceEEEeeCCcCcCCccc-cHHHHHhhcccce
Q 020791 107 ---LPKGTYVKLQPHTKDFLDISN-PKAILETTLRNYS 140 (321)
Q Consensus 107 ---LPkGt~vkLqP~s~~FldIsn-pKavLE~~LRnys 140 (321)
+|-..-+.|.=.=+.++||.. |+.-+=..|-.|+
T Consensus 84 ~~~~~~~~~~tl~~~l~~~~Di~~~p~~~~l~~la~~~ 121 (219)
T PF00667_consen 84 SVKPPFPSPITLRDLLTHYLDITSPPSRSFLRALAEFA 121 (219)
T ss_dssp SCCSSSSSSEEHHHHHHHTB-TSSB--HHHHHHHHCTB
T ss_pred ccccccccceeeeeeeeeeeecccccccceeeeeeecC
Confidence 555555555544455667766 4333333344443
No 108
>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=20.47 E-value=1.4e+02 Score=23.78 Aligned_cols=59 Identities=17% Similarity=0.210 Sum_probs=38.4
Q ss_pred CCCCCeEEEEEeecCC---cceEEEeeCCcCcCCccccHHHHHhhccc-ceecccCCEEEEEE
Q 020791 94 LQEGDIVRVKNVTLPK---GTYVKLQPHTKDFLDISNPKAILETTLRN-YSCLTTGDSIMVAY 152 (321)
Q Consensus 94 l~egd~V~v~~~~LPk---Gt~vkLqP~s~~FldIsnpKavLE~~LRn-ys~LT~GD~I~I~y 152 (321)
.+.|+++.-+-+++-+ |-||.|-+.-..|+-+++.-...=...++ -..|.+||.|.+..
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 3578888877665544 99999998777888766431111012223 23588999998864
No 109
>PRK07860 NADH dehydrogenase subunit G; Validated
Probab=20.42 E-value=96 Score=34.09 Aligned_cols=41 Identities=17% Similarity=0.109 Sum_probs=33.3
Q ss_pred CCEEE-EEEeeeEeCCCeEeccHHHHHHcCCCCCCeEEEEEe
Q 020791 65 ERVSH-CGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNV 105 (321)
Q Consensus 65 ~r~th-cGVLEF~A~EG~i~LP~WMm~~L~l~egd~V~v~~~ 105 (321)
++.+| +..|.=.+++..+.|-.--++.|+|++||.|+|++.
T Consensus 702 g~~~~~~~~L~~~~~~~~v~i~p~dA~~lgi~~Gd~V~v~s~ 743 (797)
T PRK07860 702 GRLQDGEPHLAGTARPPVARLSAATAAEIGVADGDAVTVSTE 743 (797)
T ss_pred CchhccChhhhhcCCCCEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 34444 566666678899999999999999999999999865
No 110
>TIGR01553 formate-DH-alph formate dehydrogenase, alpha subunit, proteobacterial-type. This model is well-defined, with a large, unpopulated trusted/noise gap.
Probab=20.28 E-value=68 Score=36.47 Aligned_cols=56 Identities=16% Similarity=0.113 Sum_probs=41.1
Q ss_pred CCCCeeE---EEEeCCCCCEEEEEEeeeEeCCCeEeccHHHHHHcCCCCCCeEEEEEee
Q 020791 51 IDYPMLF---ELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVT 106 (321)
Q Consensus 51 i~~PmlF---el~n~~~~r~thcGVLEF~A~EG~i~LP~WMm~~L~l~egd~V~v~~~~ 106 (321)
-+||++. ++...-...+-+|-.|.=..+|.+|-|..-..+.|||++||.|+|++.+
T Consensus 881 ~~yP~~ltTgR~~eh~~t~Tr~~~~l~~~~p~~fveI~p~~A~~~GI~~Gd~V~v~s~r 939 (1009)
T TIGR01553 881 KRYPFVATTYRLTEHWHTWTRNTPWLLEAEPQMFCEISEELATEKGIQNGDKVILESVR 939 (1009)
T ss_pred cCCCEEEEccccceecCcccccCHHHHHhCcccEEEECHHHHHHcCCcCCCEEEEEcCC
Confidence 4689865 3332111133345566667788999999999999999999999999876
No 111
>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=20.25 E-value=1.4e+02 Score=21.59 Aligned_cols=23 Identities=17% Similarity=0.056 Sum_probs=19.9
Q ss_pred EeccHHHHHHcCCCCCCeEEEEE
Q 020791 82 IYMPYWMMENLLLQEGDIVRVKN 104 (321)
Q Consensus 82 i~LP~WMm~~L~l~egd~V~v~~ 104 (321)
+.+|.+-.+.|+|.+|+.|.+..
T Consensus 37 a~i~~~~~~~l~l~~G~~v~~~i 59 (69)
T TIGR00638 37 AVITLESVAELGLKPGKEVYAVI 59 (69)
T ss_pred EEecHHHHhhCCCCCCCEEEEEE
Confidence 36999999999999999887654
Done!