Query psy1724
Match_columns 473
No_of_seqs 324 out of 574
Neff 4.3
Searched_HMMs 46136
Date Fri Aug 16 16:53:38 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1724.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1724hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1816|consensus 100.0 3.9E-91 8.6E-96 685.8 26.1 270 200-471 4-281 (308)
2 COG5140 UFD1 Ubiquitin fusion- 100.0 7.1E-71 1.5E-75 533.1 21.2 261 206-472 18-291 (331)
3 PF03152 UFD1: Ubiquitin fusio 100.0 3.4E-70 7.4E-75 510.8 18.3 176 209-384 1-176 (176)
4 KOG1816|consensus 100.0 1.5E-56 3.2E-61 441.3 15.9 186 6-192 11-280 (308)
5 PLN03086 PRLI-interacting fact 100.0 1.3E-55 2.9E-60 470.2 21.2 158 232-389 90-263 (567)
6 PF03152 UFD1: Ubiquitin fusio 100.0 3.7E-45 8E-50 342.3 11.1 139 8-146 1-156 (176)
7 COG5140 UFD1 Ubiquitin fusion- 100.0 3.6E-40 7.9E-45 319.8 10.6 128 5-132 18-162 (331)
8 PLN03086 PRLI-interacting fact 100.0 1.2E-32 2.7E-37 294.4 11.6 106 30-135 89-227 (567)
9 KOG0735|consensus 95.8 0.12 2.7E-06 58.8 12.9 147 235-384 16-167 (952)
10 PF02933 CDC48_2: Cell divisio 95.7 0.06 1.3E-06 42.6 7.6 48 332-380 10-58 (64)
11 TIGR01243 CDC48 AAA family ATP 95.1 0.39 8.5E-06 54.3 14.6 134 232-372 15-151 (733)
12 PF09262 PEX-1N: Peroxisome bi 88.1 0.4 8.7E-06 40.5 2.6 74 310-383 1-80 (80)
13 TIGR01439 lp_hng_hel_AbrB loop 78.9 7.5 0.00016 27.7 5.6 39 277-318 4-42 (43)
14 PF02359 CDC48_N: Cell divisio 73.8 3.2 7E-05 34.7 2.9 69 278-351 14-82 (87)
15 PF02359 CDC48_N: Cell divisio 71.6 28 0.0006 29.0 8.0 69 231-305 13-84 (87)
16 PF04014 Antitoxin-MazE: Antid 71.4 7.2 0.00016 29.1 4.0 39 278-319 5-43 (47)
17 PF07497 Rho_RNA_bind: Rho ter 68.6 3.6 7.8E-05 34.8 2.1 26 279-304 28-53 (78)
18 PRK14132 riboflavin kinase; Pr 66.9 4.8 0.00011 36.9 2.7 31 266-303 94-125 (126)
19 cd02790 MopB_CT_Formate-Dh_H F 62.9 9.4 0.0002 32.4 3.6 29 277-305 32-60 (116)
20 cd04459 Rho_CSD Rho_CSD: Rho p 62.7 7.7 0.00017 32.0 2.9 28 277-304 24-51 (68)
21 COG1935 Uncharacterized conser 61.3 14 0.0003 33.8 4.4 47 240-312 11-60 (122)
22 PRK09521 exosome complex RNA-b 59.4 29 0.00064 33.0 6.6 124 233-362 4-141 (189)
23 COG1339 Transcriptional regula 59.1 9.2 0.0002 37.9 3.2 33 265-304 179-212 (214)
24 TIGR02609 doc_partner putative 58.7 17 0.00036 30.0 4.2 55 280-340 10-66 (74)
25 PF01982 CTP-dep_RFKase: Domai 58.3 11 0.00024 34.4 3.3 27 270-303 94-120 (121)
26 cd02787 MopB_CT_ydeP The MopB_ 54.0 20 0.00043 30.7 4.1 29 278-306 29-57 (112)
27 cd02786 MopB_CT_3 The MopB_CT_ 53.4 16 0.00035 31.2 3.5 30 277-306 28-57 (116)
28 PRK09974 putative regulator Pr 51.5 38 0.00082 30.6 5.5 59 277-338 15-75 (111)
29 COG2002 AbrB Regulators of sta 50.2 24 0.00052 29.9 4.0 42 277-320 11-52 (89)
30 cd02776 MopB_CT_Nitrate-R-NarG 50.2 24 0.00051 32.3 4.2 33 273-305 24-56 (141)
31 PF04322 DUF473: Protein of un 47.8 25 0.00054 32.1 3.9 47 239-311 10-59 (119)
32 cd04459 Rho_CSD Rho_CSD: Rho p 47.4 30 0.00064 28.6 3.9 27 77-103 25-51 (68)
33 cd00508 MopB_CT_Fdh-Nap-like T 47.4 27 0.00058 29.6 3.9 27 278-304 33-59 (120)
34 PRK09798 antitoxin MazE; Provi 46.4 43 0.00094 28.4 4.9 50 281-340 14-63 (82)
35 PF04014 Antitoxin-MazE: Antid 45.1 32 0.00069 25.6 3.5 28 77-104 5-32 (47)
36 cd02788 MopB_CT_NDH-1_NuoG2-N7 44.8 30 0.00066 29.1 3.8 33 273-305 22-54 (96)
37 PRK11347 antitoxin ChpS; Provi 44.7 56 0.0012 27.8 5.3 48 281-340 13-60 (83)
38 TIGR01439 lp_hng_hel_AbrB loop 44.6 31 0.00067 24.4 3.3 28 76-103 4-31 (43)
39 PRK08577 hypothetical protein; 42.6 30 0.00066 31.1 3.7 44 277-322 10-53 (136)
40 PF13550 Phage-tail_3: Putativ 42.2 28 0.00061 31.0 3.4 27 339-365 137-163 (164)
41 TIGR02851 spore_V_T stage V sp 41.9 39 0.00084 32.5 4.4 46 271-319 4-49 (180)
42 PRK14165 winged helix-turn-hel 41.5 20 0.00043 35.6 2.5 32 266-304 183-215 (217)
43 cd02785 MopB_CT_4 The MopB_CT_ 41.3 33 0.00072 29.9 3.6 28 278-305 30-57 (124)
44 PF07497 Rho_RNA_bind: Rho ter 41.2 20 0.00043 30.4 2.1 38 67-104 2-54 (78)
45 cd02792 MopB_CT_Formate-Dh-Na- 40.6 33 0.00072 29.4 3.5 29 277-305 32-60 (122)
46 cd02789 MopB_CT_FmdC-FwdD The 40.0 27 0.00059 30.1 2.8 30 277-306 28-57 (106)
47 COG2336 MazE Growth regulator 39.4 30 0.00065 29.8 2.9 35 281-318 13-47 (82)
48 cd02775 MopB_CT Molybdopterin- 39.1 37 0.0008 27.7 3.4 28 278-305 21-48 (101)
49 PRK14132 riboflavin kinase; Pr 38.7 28 0.0006 32.1 2.8 31 65-102 94-125 (126)
50 cd02791 MopB_CT_Nitrate-R-NapA 37.9 40 0.00087 28.8 3.6 28 278-305 33-60 (122)
51 COG1153 FwdD Formylmethanofura 37.9 26 0.00057 32.3 2.4 28 277-304 28-55 (128)
52 cd02781 MopB_CT_Acetylene-hydr 37.8 38 0.00081 29.5 3.4 29 278-306 31-59 (130)
53 cd02777 MopB_CT_DMSOR-like The 37.7 38 0.00082 29.6 3.4 27 279-305 33-59 (127)
54 PF01568 Molydop_binding: Moly 36.1 39 0.00084 28.4 3.1 24 281-304 31-54 (110)
55 PF01982 CTP-dep_RFKase: Domai 35.8 40 0.00087 30.8 3.3 28 69-103 94-121 (121)
56 cd02779 MopB_CT_Arsenite-Ox Th 35.2 50 0.0011 28.5 3.7 30 277-306 30-59 (115)
57 cd02778 MopB_CT_Thiosulfate-R- 35.2 49 0.0011 28.4 3.7 29 277-305 27-55 (123)
58 cd02782 MopB_CT_1 The MopB_CT_ 35.0 45 0.00098 29.1 3.5 29 277-305 30-58 (129)
59 PF01191 RNA_pol_Rpb5_C: RNA p 34.4 76 0.0017 26.7 4.5 31 286-316 41-71 (74)
60 cd02794 MopB_CT_DmsA-EC The Mo 34.0 48 0.001 28.7 3.4 28 279-306 29-56 (121)
61 COG0243 BisC Anaerobic dehydro 33.7 60 0.0013 37.1 5.0 54 251-306 638-697 (765)
62 COG2336 MazE Growth regulator 33.6 49 0.0011 28.5 3.2 31 81-111 14-47 (82)
63 cd06166 Sortase_D_5 Sortase D 33.4 60 0.0013 28.8 4.0 31 335-365 58-88 (126)
64 COG1188 Ribosome-associated he 33.3 57 0.0012 29.0 3.8 26 340-365 47-72 (100)
65 TIGR03243 arg_catab_AOST argin 32.7 53 0.0011 34.8 4.1 46 257-303 288-333 (335)
66 smart00553 SEP Domain present 32.1 18 0.0004 31.5 0.5 16 414-429 73-88 (93)
67 cd05829 Sortase_E Sortase E (S 31.7 60 0.0013 29.7 3.8 28 337-364 68-96 (144)
68 cd02793 MopB_CT_DMSOR-BSOR-TMA 31.1 58 0.0012 28.7 3.5 29 277-305 30-58 (129)
69 cd02783 MopB_CT_2 The MopB_CT_ 30.3 58 0.0013 30.0 3.5 32 277-311 29-60 (156)
70 PRK09570 rpoH DNA-directed RNA 29.3 69 0.0015 27.3 3.5 29 288-316 46-74 (79)
71 COG2002 AbrB Regulators of sta 29.2 71 0.0015 27.0 3.6 30 76-105 11-40 (89)
72 cd02780 MopB_CT_Tetrathionate_ 27.9 73 0.0016 28.5 3.7 28 277-304 27-54 (143)
73 PRK15095 FKBP-type peptidyl-pr 26.6 1.7E+02 0.0038 27.2 6.0 93 272-386 34-130 (156)
74 TIGR02227 sigpep_I_bact signal 26.5 2.8E+02 0.0061 25.6 7.4 41 339-379 49-91 (163)
75 TIGR03244 arg_catab_AstA argin 26.0 82 0.0018 33.5 4.1 46 257-303 289-334 (336)
76 PRK10456 arginine succinyltran 26.0 82 0.0018 33.6 4.1 47 257-304 290-336 (344)
77 cd05828 Sortase_D_4 Sortase D 25.4 1E+02 0.0023 27.3 4.1 30 336-365 56-85 (127)
78 TIGR03245 arg_AOST_alph argini 24.7 88 0.0019 33.3 4.0 46 257-303 288-334 (336)
79 PRK11347 antitoxin ChpS; Provi 24.2 88 0.0019 26.6 3.2 39 81-119 14-57 (83)
80 cd05830 Sortase_D_5 Sortase D 23.9 1.1E+02 0.0023 27.6 4.0 30 336-365 60-89 (137)
81 TIGR01076 sortase_fam LPXTG-si 23.2 1.1E+02 0.0023 27.6 3.8 27 338-364 60-86 (136)
82 PF00717 Peptidase_S24: Peptid 23.2 3.4E+02 0.0074 20.7 7.2 33 341-373 24-57 (70)
83 PF03459 TOBE: TOBE domain; I 22.8 84 0.0018 24.0 2.7 23 282-304 35-57 (64)
84 PRK08577 hypothetical protein; 22.5 1E+02 0.0022 27.7 3.5 30 75-104 9-38 (136)
85 PRK09974 putative regulator Pr 22.5 1.1E+02 0.0024 27.7 3.7 46 76-121 15-76 (111)
86 COG1339 Transcriptional regula 22.5 74 0.0016 31.7 2.8 32 65-103 180-212 (214)
87 cd02790 MopB_CT_Formate-Dh_H F 21.9 99 0.0022 26.1 3.2 29 76-104 32-60 (116)
88 cd00004 Sortase Sortases are c 21.6 1.3E+02 0.0028 26.4 4.0 25 341-365 64-88 (128)
89 cd06165 Sortase_A_1 Sortase A 21.3 1.3E+02 0.0028 26.6 3.9 25 341-365 63-87 (127)
90 TIGR02851 spore_V_T stage V sp 21.1 1.4E+02 0.003 28.7 4.3 35 70-104 4-38 (180)
91 cd02784 MopB_CT_PHLH The MopB_ 20.6 1.2E+02 0.0027 27.7 3.7 27 279-305 37-63 (137)
92 PRK09798 antitoxin MazE; Provi 20.1 1.2E+02 0.0027 25.6 3.3 40 81-120 15-61 (82)
No 1
>KOG1816|consensus
Probab=100.00 E-value=3.9e-91 Score=685.83 Aligned_cols=270 Identities=56% Similarity=0.953 Sum_probs=237.3
Q ss_pred cCCCCCCCCCCccceEEeeeeccCCCCCCCCCCCCeEeeCHHHHHHHHhCCCCCceeEEEEeCCCCceEEEEEEeeeeCC
Q psy1724 200 FNMFPDIPRPFNRSYKCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLEFVADE 279 (473)
Q Consensus 200 ~~~~~~~~~~f~~~yrcyp~s~~~~~~r~~~~~GdKIiLPpSaL~~L~~~~i~~Pm~F~L~n~~~~r~th~GVLEFsA~E 279 (473)
|+.|.+....|+++|||||++|+++++++++++|||||||||||++|+++||.|||+|+|+|.+..|+||||||||+|||
T Consensus 4 f~~~~~~g~~f~~~yrcy~~~~l~~~~~s~~~~GgKIilPPSaL~~Ls~lnI~yPMlFkLtn~~~~r~THcGVLEF~AeE 83 (308)
T KOG1816|consen 4 FDGFGPRGFQFETSYRCYPVSFLPGPDRSDVNKGGKIILPPSALDRLSSLNITYPMLFKLTNVDVDRVTHCGVLEFTAEE 83 (308)
T ss_pred ccccCcCCcceeeeeEecccccccCccccccccCCeEEeCHHHHHHHHHhcCCCceEEEEeccccceeeeeeEEEEEecC
Confidence 44444334679999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcEEcCHHHHhhcCCCCCCeEEEEEeecCCceEEEEEeCccCcCCCCCcHHHHHHhcccceecccCCEEEEEECCEEEEE
Q psy1724 280 GKVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQTCDFLDITNPKAVLENCLRNFACLTSGDMIAINYNSKIYEL 359 (473)
Q Consensus 280 G~v~LP~WMm~~L~l~egd~V~I~~v~LPkGtfvkLqP~s~~FldIsnpKavLE~~LRnystLT~GD~I~I~yn~~~Y~l 359 (473)
|.||||+|||++|+|+|||+|+|++++||+||||||||||.|||||+|||||||++||||+|||+||+|+|+||++.|+|
T Consensus 84 G~vyLP~WMmq~L~le~gdlv~i~~v~lpkgtyvKLqP~s~dFLDItNpKAvLE~~LRn~acLT~gDvi~i~Yn~k~y~i 163 (308)
T KOG1816|consen 84 GRVYLPYWMMQNLLLEEGDLVRIRSVTLPKGTYVKLQPHSVDFLDITNPKAVLENALRNYACLTTGDVILINYNEKTYEL 163 (308)
T ss_pred ceEEeehHhhhhccCCCCCeEEEEEeeccccceeeeccCCCCccccCChHHHHHHHHhhccccccCCEEEEecCCeEEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEecCCCeEEEEccceEEEecCCCCCCCCCccccccccC--CCCCCC-CCCC----CCccceeeeeeeecCCccCCCC
Q psy1724 360 CVLETKPGNAVTIIECDMNVDFAPPVGYTEPEKVKEKEEDN--MIDPVD-LMPE----PSGFVAFHGTGNRLDGKRKKKD 432 (473)
Q Consensus 360 ~V~e~kP~~aVsIIdTDleVDf~pP~~y~ep~~~~~~~~~~--~~~~~~-~~~~----~~~~~~F~G~G~rLdGK~~~~~ 432 (473)
+|+|+||++|||||||||+|||+||+||+||+++.++.... +.+... .+.. +.++++|+|+|+|||||+.. .
T Consensus 164 ~V~e~kPa~aVsIiEtD~~VDF~pP~gyke~~~~~~~~~~~k~~~~~v~~~ag~~~~~e~~~~~f~gsg~rLdgK~~~-~ 242 (308)
T KOG1816|consen 164 KVVETKPANAVSIIETDLNVDFDPPLGYKEPERQVAPAEKAKGEAEVVGSYAGYKNVIENKVEPFTGSGRRLDGKKKV-E 242 (308)
T ss_pred EEEEecCCceeEEEEcceeecccCCcCccCcccccChhhcccccceeeccccccccccccceeeeccccceecccccc-c
Confidence 99999999999999999999999999999999885443221 111111 2211 67899999999999999876 3
Q ss_pred CcccCCCCccc-cccCCCCCCCCCCCeEEEeecccCCCcC
Q psy1724 433 TVETGGTPTKR-EYQRGIPHYDYEPNTLVFLRNIKPASAH 471 (473)
Q Consensus 433 ~~~~~~~~~~~-~~~~~~p~~~~~~g~l~f~~~~~p~~~~ 471 (473)
++.. .++... ...+++|++|++.|+|+|+||..|.++.
T Consensus 243 e~~~-~pv~~~~~~~~~~~~~d~~~G~l~F~~~~~~~~~~ 281 (308)
T KOG1816|consen 243 EVSK-HPVKNGDLIQRGVPNHDFKLGKLVFGRNVDPLKKE 281 (308)
T ss_pred ccCC-CcccCcccccCCCCccccCCceEEEecCCCccccc
Confidence 3222 344333 4789999999999999999996665443
No 2
>COG5140 UFD1 Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7.1e-71 Score=533.15 Aligned_cols=261 Identities=38% Similarity=0.653 Sum_probs=224.5
Q ss_pred CCCCCccceEEeeeeccCCCCCCCCCCCCeEeeCHHHHHHHHhCCCCCceeEEEEeCCCCceEEEEEEeeeeCCCcEEcC
Q psy1724 206 IPRPFNRSYKCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLEFVADEGKVYLP 285 (473)
Q Consensus 206 ~~~~f~~~yrcyp~s~~~~~~r~~~~~GdKIiLPpSaL~~L~~~~i~~Pm~F~L~n~~~~r~th~GVLEFsA~EG~v~LP 285 (473)
..+.|.+.|||||++|+++..|.++|+|+|||||||||.+|+++||.|||+|+|++.++.++||||||||+||||.||||
T Consensus 18 ~~q~F~e~~rcyp~am~~d~~r~n~NfGGKvilPpSaL~kLs~lni~yPmlF~~s~~~~~~~THgGVLEFiaEEGrVylP 97 (331)
T COG5140 18 LFQLFGEKPRCYPRAMKFDGCRQNANFGGKVILPPSALVKLSSLNIQYPMLFEISHSDGIYRTHGGVLEFIAEEGRVYLP 97 (331)
T ss_pred hhhhhccCccceeeecccCccccCCCcCceEEcCHHHHHHHHhhccCCceEEEEecccceeEecccEEEEeecCCcEeeh
Confidence 35789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhcCCCCCCeEEEEEeecCCceEEEEEeCccCcCCCCCcHHHHHHhcccceecccCCEEEEEECCEEEEEEEEEec
Q psy1724 286 YWMMRNLLLDEGELVNIESVSLPVATFSKFQPQTCDFLDITNPKAVLENCLRNFACLTSGDMIAINYNSKIYELCVLETK 365 (473)
Q Consensus 286 ~WMm~~L~l~egd~V~I~~v~LPkGtfvkLqP~s~~FldIsnpKavLE~~LRnystLT~GD~I~I~yn~~~Y~l~V~e~k 365 (473)
+|||+.|++++||+|+|+++++|.|+||||+|||.+||||+|||||||++||||+|||+||+|.|.||+++|.|+|.+++
T Consensus 98 ~WMm~tLs~epgdlv~~~~td~plG~fVKL~PqSVdFLdI~dpkavLEn~LRNfstLt~~D~iei~ynd~v~~Ik~~~v~ 177 (331)
T COG5140 98 SWMMQTLSMEPGDLVVLRYTDFPLGKFVKLIPQSVDFLDIEDPKAVLENCLRNFSTLTEGDEIEIQYNDEVGSIKFTVVH 177 (331)
T ss_pred HHHHHhccCCCCcEEEEEeccccccceEEecccccceEeccChHHHHHHHHhhccccccCCEEEEEECCeeeEEEEEEec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CC---CeEEEEccceEEEecCCCCCCCCCccccccc------cC--CCCCCCCCCCCCccceeeeeeeecCCccCCCCCc
Q psy1724 366 PG---NAVTIIECDMNVDFAPPVGYTEPEKVKEKEE------DN--MIDPVDLMPEPSGFVAFHGTGNRLDGKRKKKDTV 434 (473)
Q Consensus 366 P~---~aVsIIdTDleVDf~pP~~y~ep~~~~~~~~------~~--~~~~~~~~~~~~~~~~F~G~G~rLdGK~~~~~~~ 434 (473)
|+ +||||||||+.|||+||+||+|+..+.++.. .| -++....+- ..+...-.|.|..|.||..+.. +
T Consensus 178 pe~S~~~i~vveTDLvvDF~pPiGy~e~~qq~ke~n~~gvqgtm~t~I~y~~~~~-~~~~~lmKg~G~~l~gk~~~~~-p 255 (331)
T COG5140 178 PEPSANAIYVVETDLVVDFLPPIGYKEKAQQDKERNSFGVQGTMATYIEYIDSSH-DVKPILMKGLGLYLYGKVDKAE-P 255 (331)
T ss_pred cCCCcceEEEEecceeeeccCCccccchhhhhhhhccccccceeEEEEeeecccc-ccchhhhhcccceecccccccc-c
Confidence 94 7999999999999999999999954433220 01 122222221 2233456699999999987722 1
Q ss_pred ccCCCCc-cccccCCCC-CCCCCCCeEEEeecccCCCcCC
Q psy1724 435 ETGGTPT-KREYQRGIP-HYDYEPNTLVFLRNIKPASAHK 472 (473)
Q Consensus 435 ~~~~~~~-~~~~~~~~p-~~~~~~g~l~f~~~~~p~~~~~ 472 (473)
..+ +.....|-| .+++|-|+||||+..+-.+..+
T Consensus 256 ----k~~i~d~~~~~~pa~l~lp~g~~ffg~p~~~p~~de 291 (331)
T COG5140 256 ----KQDIKDMKIDGEPAKLDLPEGQLFFGFPMVLPKEDE 291 (331)
T ss_pred ----ccchhhhhccCCcccccccCcceEeccccccCccch
Confidence 111 223335666 9999999999999876555443
No 3
>PF03152 UFD1: Ubiquitin fusion degradation protein UFD1; InterPro: IPR004854 Post-translational ubiquitin-protein conjugates are recognised for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified []. This family includes UFD1, a 40kDa protein that is essential for vegetative cell viability []. The human UFD1 gene is expressed at high levels during embryogenesis, especially in the eyes and in the inner ear primordia and is thought to be important in the determination of ectoderm-derived structures, including neural crest cells. In addition, this gene is deleted in the CATCH-22 (cardiac defects, abnormal facies, thymic hypoplasia, cleft palate and hypocalcaemia with deletions on chromosome 22) syndrome. This clinical syndrome is associated with a variety of developmental defects, all characterised by microdeletions on 22q11.2. Two such developmental defects are the DiGeorge syndrome OMIM:188400, and the velo-cardio- facial syndrome OMIM:145410. Several of the abnormalities associated with these conditions are thought to be due to defective neural crest cell differentiation []. ; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 1ZC1_A 2YUJ_A.
Probab=100.00 E-value=3.4e-70 Score=510.77 Aligned_cols=176 Identities=60% Similarity=1.064 Sum_probs=152.7
Q ss_pred CCccceEEeeeeccCCCCCCCCCCCCeEeeCHHHHHHHHhCCCCCceeEEEEeCCCCceEEEEEEeeeeCCCcEEcCHHH
Q psy1724 209 PFNRSYKCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLEFVADEGKVYLPYWM 288 (473)
Q Consensus 209 ~f~~~yrcyp~s~~~~~~r~~~~~GdKIiLPpSaL~~L~~~~i~~Pm~F~L~n~~~~r~th~GVLEFsA~EG~v~LP~WM 288 (473)
.|+++|||||++|+++++++++++||||+||||||++|.+++++|||+|+|+|..++++||||||||+|+||+|+||+||
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 48999999999999998999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcCCCCCCeEEEEEeecCCceEEEEEeCccCcCCCCCcHHHHHHhcccceecccCCEEEEEECCEEEEEEEEEecCCC
Q psy1724 289 MRNLLLDEGELVNIESVSLPVATFSKFQPQTCDFLDITNPKAVLENCLRNFACLTSGDMIAINYNSKIYELCVLETKPGN 368 (473)
Q Consensus 289 m~~L~l~egd~V~I~~v~LPkGtfvkLqP~s~~FldIsnpKavLE~~LRnystLT~GD~I~I~yn~~~Y~l~V~e~kP~~ 368 (473)
|++|++++||.|+|++++||||||||||||+.+|++|+|||||||++||||+|||+||+|.|+|+++.|+|+|+|++|++
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 eEEEEccceEEEecCC
Q psy1724 369 AVTIIECDMNVDFAPP 384 (473)
Q Consensus 369 aVsIIdTDleVDf~pP 384 (473)
|||||||||+|||++|
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 9999999999999998
No 4
>KOG1816|consensus
Probab=100.00 E-value=1.5e-56 Score=441.32 Aligned_cols=186 Identities=40% Similarity=0.700 Sum_probs=158.3
Q ss_pred CcccccceeeeeeeccCCCCCCCCCCCCeeecCHHHHHHHHhCCCCCceeEEEEeCCCCCeEEEEEeeeEecCCcEeccH
Q psy1724 6 PRPFNRSYKCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLEFVADEGKVYLPY 85 (473)
Q Consensus 6 ~~~f~~~y~cy~~s~~~~~~~~~~~~GdKIiLP~SaL~~L~~~~i~~PmlF~l~n~~~~~~th~GVLEF~AeEG~v~LP~ 85 (473)
...|++.|||||++|+++++|+++++|||||||||||++|+++||+|||+|+|+|.+..|+|||||||||||||.||||+
T Consensus 11 g~~f~~~yrcy~~~~l~~~~~s~~~~GgKIilPPSaL~~Ls~lnI~yPMlFkLtn~~~~r~THcGVLEF~AeEG~vyLP~ 90 (308)
T KOG1816|consen 11 GFQFETSYRCYPVSFLPGPDRSDVNKGGKIILPPSALDRLSSLNITYPMLFKLTNVDVDRVTHCGVLEFTAEEGRVYLPY 90 (308)
T ss_pred CcceeeeeEecccccccCccccccccCCeEEeCHHHHHHHHHhcCCCceEEEEeccccceeeeeeEEEEEecCceEEeeh
Confidence 45699999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHhhcCCCCCCcEEEEEeee-----------------ccCCHHHHHhhcccccccccceee------------------
Q psy1724 86 WCFSVSMFPGNEREDVERGGK-----------------IIMPPSALEQLTRLNICYPMLFKL------------------ 130 (473)
Q Consensus 86 wmm~nL~l~~~~~v~ie~~~l-----------------I~n~KavLE~~Lr~~~cLt~g~~~------------------ 130 (473)
||||||+|++||+|+|+++++ |+||||||||+||||||||+|+.|
T Consensus 91 WMmq~L~le~gdlv~i~~v~lpkgtyvKLqP~s~dFLDItNpKAvLE~~LRn~acLT~gDvi~i~Yn~k~y~i~V~e~kP 170 (308)
T KOG1816|consen 91 WMMQNLLLEEGDLVRIRSVTLPKGTYVKLQPHSVDFLDITNPKAVLENALRNYACLTTGDVILINYNEKTYELKVVETKP 170 (308)
T ss_pred HhhhhccCCCCCeEEEEEeeccccceeeeccCCCCccccCChHHHHHHHHhhccccccCCEEEEecCCeEEEEEEEEecC
Confidence 999999999999999999987 999999999999999999655544
Q ss_pred -----------------------ccccc----------cccc-CC--------------C-ccccCccccccccccCCCC
Q psy1724 131 -----------------------TNQKM----------GRIT-HS--------------G-VLELDGKRKKKDTVETGGT 161 (473)
Q Consensus 131 -----------------------~~~~~----------~~~~-~~--------------~-~~~ldgk~kk~~~~~~~~~ 161 (473)
|.+.. ...+ .. + ..+|||||++...+..+..
T Consensus 171 a~aVsIiEtD~~VDF~pP~gyke~~~~~~~~~~~k~~~~~v~~~ag~~~~~e~~~~~f~gsg~rLdgK~~~~e~~~~pv~ 250 (308)
T KOG1816|consen 171 ANAVSIIETDLNVDFDPPLGYKEPERQVAPAEKAKGEAEVVGSYAGYKNVIENKVEPFTGSGRRLDGKKKVEEVSKHPVK 250 (308)
T ss_pred CceeEEEEcceeecccCCcCccCcccccChhhcccccceeeccccccccccccceeeeccccceecccccccccCCCccc
Confidence 43310 0011 11 1 2449999776665555555
Q ss_pred CCccccccCCCCCCCCCCeEEEeeccCCCCc
Q psy1724 162 PTKREYQRGIPHYDYEPNTLVFLRNIKPASA 192 (473)
Q Consensus 162 ~~~~~~~rgip~ydy~~g~~~Fir~~~~~~~ 192 (473)
. ....+||+|++||+.|+|.|+||..|...
T Consensus 251 ~-~~~~~~~~~~~d~~~G~l~F~~~~~~~~~ 280 (308)
T KOG1816|consen 251 N-GDLIQRGVPNHDFKLGKLVFGRNVDPLKK 280 (308)
T ss_pred C-cccccCCCCccccCCceEEEecCCCcccc
Confidence 3 33589999999999999999999655543
No 5
>PLN03086 PRLI-interacting factor K; Provisional
Probab=100.00 E-value=1.3e-55 Score=470.15 Aligned_cols=158 Identities=39% Similarity=0.644 Sum_probs=152.2
Q ss_pred CCCeEeeCHHHHHHHHhCCC--CCceeEEEEeC-----------CCCceEEEEEEeeeeCCCcEEcCHHHHhhcCCCC--
Q psy1724 232 RGGKIIMPPSALEQLTRLNI--CYPMLFKLTNQ-----------KMGRITHSGVLEFVADEGKVYLPYWMMRNLLLDE-- 296 (473)
Q Consensus 232 ~GdKIiLPpSaL~~L~~~~i--~~Pm~F~L~n~-----------~~~r~th~GVLEFsA~EG~v~LP~WMm~~L~l~e-- 296 (473)
.||||+||||||++|+++|| +|||+|+|+|. .++++||||||||+|+||.||||+|||++|++.+
T Consensus 90 ~GdKI~LPpSaL~~L~~~~~~~~~Pm~F~l~~~~~~~~~~~~~~~~~~~th~GVlEF~A~EG~v~lP~wm~~~L~~~~~~ 169 (567)
T PLN03086 90 NGDKIKLPPSCFTELSDQGAFDKGPLYFRLSVVHQEGSGEMKDTDSQKTTHSGVLEFTAEEGSVGLPPHVWSNLFPSDPP 169 (567)
T ss_pred CCCeEEcCHHHHHHHHhcCCCCCCCeEEEEeccccccccccccccCCcEEEEEEEEEEcCCCeEEcCHHHHhhcCCCCCC
Confidence 89999999999999999998 89999999994 3479999999999999999999999999999875
Q ss_pred -CCeEEEEEeecCCceEEEEEeCccCcCCCCCcHHHHHHhcccceecccCCEEEEEECCEEEEEEEEEecCCCeEEEEcc
Q psy1724 297 -GELVNIESVSLPVATFSKFQPQTCDFLDITNPKAVLENCLRNFACLTSGDMIAINYNSKIYELCVLETKPGNAVTIIEC 375 (473)
Q Consensus 297 -gd~V~I~~v~LPkGtfvkLqP~s~~FldIsnpKavLE~~LRnystLT~GD~I~I~yn~~~Y~l~V~e~kP~~aVsIIdT 375 (473)
|++|+|++++||||||||||||+++|+||+|||||||++||||+|||+||+|.|+|+++.|+|+|+|++|++|||||||
T Consensus 170 ~~~~v~v~~~~Lpkgt~vklqP~~~~f~di~npKavLE~~Lr~~stLT~Gd~i~i~~~~~~y~~~V~ev~P~~aVsiieT 249 (567)
T PLN03086 170 DVPLVEVRYIWLPKGTYAKLQPDGVGFSDLPNHKAVLETALRQHATLSEDDVLVVNYGQLTYKLKVLELKPASSVSVLET 249 (567)
T ss_pred CCCeEEEEEeecCCCCEEEEeeccCCcCCcccHHHHHHHHhhcCccccCCCEEEEecCCEEEEEEEEEEcCCCeeEEEeC
Confidence 8899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceEEEecCCCCCCC
Q psy1724 376 DMNVDFAPPVGYTE 389 (473)
Q Consensus 376 DleVDf~pP~~y~e 389 (473)
||+|||+||.++.+
T Consensus 250 Di~VDf~~p~~~~~ 263 (567)
T PLN03086 250 DIEVDIVGPDSVSN 263 (567)
T ss_pred ceEEEeccCCcchh
Confidence 99999999999743
No 6
>PF03152 UFD1: Ubiquitin fusion degradation protein UFD1; InterPro: IPR004854 Post-translational ubiquitin-protein conjugates are recognised for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified []. This family includes UFD1, a 40kDa protein that is essential for vegetative cell viability []. The human UFD1 gene is expressed at high levels during embryogenesis, especially in the eyes and in the inner ear primordia and is thought to be important in the determination of ectoderm-derived structures, including neural crest cells. In addition, this gene is deleted in the CATCH-22 (cardiac defects, abnormal facies, thymic hypoplasia, cleft palate and hypocalcaemia with deletions on chromosome 22) syndrome. This clinical syndrome is associated with a variety of developmental defects, all characterised by microdeletions on 22q11.2. Two such developmental defects are the DiGeorge syndrome OMIM:188400, and the velo-cardio- facial syndrome OMIM:145410. Several of the abnormalities associated with these conditions are thought to be due to defective neural crest cell differentiation []. ; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 1ZC1_A 2YUJ_A.
Probab=100.00 E-value=3.7e-45 Score=342.32 Aligned_cols=139 Identities=38% Similarity=0.656 Sum_probs=117.7
Q ss_pred ccccceeeeeeeccCCCCCCCCCCCCeeecCHHHHHHHHhCCCCCceeEEEEeCCCCCeEEEEEeeeEecCCcEeccHhh
Q psy1724 8 PFNRSYKCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLEFVADEGKVYLPYWC 87 (473)
Q Consensus 8 ~f~~~y~cy~~s~~~~~~~~~~~~GdKIiLP~SaL~~L~~~~i~~PmlF~l~n~~~~~~th~GVLEF~AeEG~v~LP~wm 87 (473)
.|+++|||||++|+++++++++++||||+||||||++|++++++|||+|+|+|..+++.||||||||+|+||+|+||+||
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 49999999999999888899999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcCCCCCCcEEEEEeee-----------------ccCCHHHHHhhcccccccccceeecccccccccCCCcccc
Q psy1724 88 FSVSMFPGNEREDVERGGK-----------------IIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLEL 146 (473)
Q Consensus 88 m~nL~l~~~~~v~ie~~~l-----------------I~n~KavLE~~Lr~~~cLt~g~~~~~~~~~~~~~~~~~~l 146 (473)
|++|++++|+.|+|+++++ |+|||||||++||+|+|||+|+++...++.......++++
T Consensus 81 m~~L~l~~g~~V~v~~~~LPkgt~vkLqP~~~~F~~i~n~KavLE~~Lr~ystLT~Gd~I~i~~~~~~y~l~V~e~ 156 (176)
T PF03152_consen 81 MQNLGLQEGDIVRVEYVSLPKGTFVKLQPQSSDFLDISNPKAVLERALRNYSTLTKGDTISIEYNNKTYELDVVEV 156 (176)
T ss_dssp HHHHT--TTEEEEEEEEE----SEEEEEESCHHHHCSS-HHHHHHHHHCC-SEEETTSEEEEECTTEEEEEEEEEE
T ss_pred HhhcCCCCCCEEEEEEeECCCCCEEEEeECCCccccccchHHHHHhhcccCceeecCCEEEEEeCCEEEEEEEEEE
Confidence 9999999999999999976 9999999999999999999999999987766555555554
No 7
>COG5140 UFD1 Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.6e-40 Score=319.81 Aligned_cols=128 Identities=33% Similarity=0.497 Sum_probs=123.0
Q ss_pred CCcccccceeeeeeeccCCCCCCCCCCCCeeecCHHHHHHHHhCCCCCceeEEEEeCCCCCeEEEEEeeeEecCCcEecc
Q psy1724 5 IPRPFNRSYKCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLEFVADEGKVYLP 84 (473)
Q Consensus 5 ~~~~f~~~y~cy~~s~~~~~~~~~~~~GdKIiLP~SaL~~L~~~~i~~PmlF~l~n~~~~~~th~GVLEF~AeEG~v~LP 84 (473)
.++.|.+.|||||++|+.+..|.++++|+|||||||||..|+++||.|||+|+|++.+..++||||||||+||||.||||
T Consensus 18 ~~q~F~e~~rcyp~am~~d~~r~n~NfGGKvilPpSaL~kLs~lni~yPmlF~~s~~~~~~~THgGVLEFiaEEGrVylP 97 (331)
T COG5140 18 LFQLFGEKPRCYPRAMKFDGCRQNANFGGKVILPPSALVKLSSLNIQYPMLFEISHSDGIYRTHGGVLEFIAEEGRVYLP 97 (331)
T ss_pred hhhhhccCccceeeecccCccccCCCcCceEEcCHHHHHHHHhhccCCceEEEEecccceeEecccEEEEeecCCcEeeh
Confidence 56889999999999999998999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhHhhcCCCCCCcEEEEEeee-----------------ccCCHHHHHhhcccccccccceeecc
Q psy1724 85 YWCFSVSMFPGNEREDVERGGK-----------------IIMPPSALEQLTRLNICYPMLFKLTN 132 (473)
Q Consensus 85 ~wmm~nL~l~~~~~v~ie~~~l-----------------I~n~KavLE~~Lr~~~cLt~g~~~~~ 132 (473)
+|||+.|.+++||+|+|.+... |+||||+|||+||||++||+|..+-.
T Consensus 98 ~WMm~tLs~epgdlv~~~~td~plG~fVKL~PqSVdFLdI~dpkavLEn~LRNfstLt~~D~iei 162 (331)
T COG5140 98 SWMMQTLSMEPGDLVVLRYTDFPLGKFVKLIPQSVDFLDIEDPKAVLENCLRNFSTLTEGDEIEI 162 (331)
T ss_pred HHHHHhccCCCCcEEEEEeccccccceEEecccccceEeccChHHHHHHHHhhccccccCCEEEE
Confidence 9999999999999999998743 99999999999999999999998855
No 8
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.98 E-value=1.2e-32 Score=294.45 Aligned_cols=106 Identities=28% Similarity=0.284 Sum_probs=98.6
Q ss_pred CCCCeeecCHHHHHHHHhCCC--CCceeEEEEeC-----------CCCCeEEEEEeeeEecCCcEeccHhhHhhcCCCC-
Q psy1724 30 ERGGKIIMPPSALEQLTRLNI--CYPMLFKLTNQ-----------KMGRITHSGVLEFVADEGKVYLPYWCFSVSMFPG- 95 (473)
Q Consensus 30 ~~GdKIiLP~SaL~~L~~~~i--~~PmlF~l~n~-----------~~~~~th~GVLEF~AeEG~v~LP~wmm~nL~l~~- 95 (473)
..||||+||||||++|+++|| +|||+|+|+|. +.++.||||||||+|+||.||||+|||+||++.+
T Consensus 89 ~~GdKI~LPpSaL~~L~~~~~~~~~Pm~F~l~~~~~~~~~~~~~~~~~~~th~GVlEF~A~EG~v~lP~wm~~~L~~~~~ 168 (567)
T PLN03086 89 GNGDKIKLPPSCFTELSDQGAFDKGPLYFRLSVVHQEGSGEMKDTDSQKTTHSGVLEFTAEEGSVGLPPHVWSNLFPSDP 168 (567)
T ss_pred CCCCeEEcCHHHHHHHHhcCCCCCCCeEEEEeccccccccccccccCCcEEEEEEEEEEcCCCeEEcCHHHHhhcCCCCC
Confidence 589999999999999999999 89999999994 2469999999999999999999999999999865
Q ss_pred --CCcEEEEEeee-----------------ccCCHHHHHhhcccccccccceeeccccc
Q psy1724 96 --NEREDVERGGK-----------------IIMPPSALEQLTRLNICYPMLFKLTNQKM 135 (473)
Q Consensus 96 --~~~v~ie~~~l-----------------I~n~KavLE~~Lr~~~cLt~g~~~~~~~~ 135 (473)
|++|+|++++| |+|||||||+.||+|+|||+|++|....+
T Consensus 169 ~~~~~v~v~~~~Lpkgt~vklqP~~~~f~di~npKavLE~~Lr~~stLT~Gd~i~i~~~ 227 (567)
T PLN03086 169 PDVPLVEVRYIWLPKGTYAKLQPDGVGFSDLPNHKAVLETALRQHATLSEDDVLVVNYG 227 (567)
T ss_pred CCCCeEEEEEeecCCCCEEEEeeccCCcCCcccHHHHHHHHhhcCccccCCCEEEEecC
Confidence 78999999977 99999999999999999999999988643
No 9
>KOG0735|consensus
Probab=95.76 E-value=0.12 Score=58.79 Aligned_cols=147 Identities=19% Similarity=0.161 Sum_probs=113.7
Q ss_pred eEeeCHHHHHHHHhCCCCCceeEEEEeCCCCceEEEEEEeee-eCCCcEEcCHHHHhhcCCCCCCeEEEEEe-ecCCceE
Q psy1724 235 KIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLEFV-ADEGKVYLPYWMMRNLLLDEGELVNIESV-SLPVATF 312 (473)
Q Consensus 235 KIiLPpSaL~~L~~~~i~~Pm~F~L~n~~~~r~th~GVLEFs-A~EG~v~LP~WMm~~L~l~egd~V~I~~v-~LPkGtf 312 (473)
-|.||.+.+..|....-.+++.=........+.-..| -++ ..|..|-+=.-..+.|+|.+|+.|.++-. ..++++-
T Consensus 16 fv~lP~ql~~ai~~~~~~~av~~v~~~~~~~~s~~~g--~~s~~se~~ieIn~~~A~~l~L~e~~~V~l~~~~~v~~~~~ 93 (952)
T KOG0735|consen 16 FVNLPEQLLEAISEPVQNYAVQAVVSKNPIKKSWVFG--HGSGSSENVIEINRVYAHTLGLAENQEVKLSIIDHVHEATQ 93 (952)
T ss_pred hhccHHHHHHHHhccccCceeEEEEcCCChhheeecc--cCCCCccceEEeehhhHhhccCCCCCeEEEEEcCCccceeE
Confidence 4679999999998765555655433332223344444 343 33667777788899999999999999976 7999999
Q ss_pred EEEEeCccCcCCCCCcHHH-HHHhcc-cceecccCCEEEEEECCE-EEEEEEEEecCCCeEEEEccceEEEecCC
Q psy1724 313 SKFQPQTCDFLDITNPKAV-LENCLR-NFACLTSGDMIAINYNSK-IYELCVLETKPGNAVTIIECDMNVDFAPP 384 (473)
Q Consensus 313 vkLqP~s~~FldIsnpKav-LE~~LR-nystLT~GD~I~I~yn~~-~Y~l~V~e~kP~~aVsIIdTDleVDf~pP 384 (473)
|.+.|.+++=|+|-+--|+ ||..|- ++--+|. .+..|+++.. .-.|.|+.+.|...+.=++++-+|=++|-
T Consensus 94 V~VeP~TsdDWEIiElnA~~~e~~lL~Q~RIv~~-~~f~iwl~~~t~i~fqv~rl~Ps~~~gRl~~~Tev~VaPK 167 (952)
T KOG0735|consen 94 VEVEPVTSDDWEIIELNAEWLEENLLVQTRIVTP-EIFIIWLPSGTVIQFQVDRLIPSMLYGRLLRGTEVLVAPK 167 (952)
T ss_pred EEEeeccCccHHHHHhhHHHHhhhhhhheeeccc-ceeEEEEcCccEEEEEEeeeecccceeeecCCceEEEecC
Confidence 9999999998898776666 677665 5888999 8888888864 56899999999999888999989988764
No 10
>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=95.71 E-value=0.06 Score=42.62 Aligned_cols=48 Identities=21% Similarity=0.412 Sum_probs=36.6
Q ss_pred HHHhcccceecccCCEEEEEECCEEEEEEEEEecCCCeEEEE-ccceEEE
Q psy1724 332 LENCLRNFACLTSGDMIAINYNSKIYELCVLETKPGNAVTII-ECDMNVD 380 (473)
Q Consensus 332 LE~~LRnystLT~GD~I~I~yn~~~Y~l~V~e~kP~~aVsII-dTDleVD 380 (473)
+-+.|.+ --+++||+|.|.+.++.+.|.|.+++|.++|.|- +|.+++.
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 4699999999999999999999999999877655 4556654
No 11
>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=95.15 E-value=0.39 Score=54.30 Aligned_cols=134 Identities=13% Similarity=0.116 Sum_probs=94.7
Q ss_pred CCCeEeeCHHHHHHHHhCCCCCceeEEEEeCCCCceEEEEEEe-ee--eCCCcEEcCHHHHhhcCCCCCCeEEEEEeecC
Q psy1724 232 RGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLE-FV--ADEGKVYLPYWMMRNLLLDEGELVNIESVSLP 308 (473)
Q Consensus 232 ~GdKIiLPpSaL~~L~~~~i~~Pm~F~L~n~~~~r~th~GVLE-Fs--A~EG~v~LP~WMm~~L~l~egd~V~I~~v~LP 308 (473)
.-+.+-|.++++++|. +..==.-+|.. ..+.+.|-|+. .. ...|.|.+..-+.+++++..||.|.|+.+.++
T Consensus 15 ~~~~~~~~~~~~~~~~---~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (733)
T TIGR01243 15 GRGIVRIDRQTAARLG---VEPGDFVEIEK--GDRSVVAIVWPLRPDDEGRGIIRMDGYLRANAGVTIGDTVTVERAEVK 89 (733)
T ss_pred CCCeEeeCHHHHHhcC---CCCCCEEEEec--CCCceeEEEEecCccccCCCEEeecHHHHhhcCCCCCCeEEEeecCCC
Confidence 4567888999888873 22222334432 34556676664 22 24689999999999999999999999999999
Q ss_pred CceEEEEEeCccCcCCCCCcHHHHHHhcccceecccCCEEEEEECCEEEEEEEEEecCCCeEEE
Q psy1724 309 VATFSKFQPQTCDFLDITNPKAVLENCLRNFACLTSGDMIAINYNSKIYELCVLETKPGNAVTI 372 (473)
Q Consensus 309 kGtfvkLqP~s~~FldIsnpKavLE~~LRnystLT~GD~I~I~yn~~~Y~l~V~e~kP~~aVsI 372 (473)
.++.|.+.|... ...-.+...++...|.+ ..+++||.|.+.+....+.+.|+++.|...+.+
T Consensus 90 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~-~~~~~g~~~~~~~~~~~~~~~v~~~~p~~~~~~ 151 (733)
T TIGR01243 90 EAKKVVLAPTQP-IRFGRDFVDYVKEFLLG-KPISKGETVIVPVLEGALPFVVVSTQPAGFVYV 151 (733)
T ss_pred ccceEeeccccc-cccccchHHHHHHHHcC-CCCCCCCEEEecccCcceeEEEEecCCCCcEEE
Confidence 999999999531 11012223344444444 468999999999888788999999999655543
No 12
>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=88.11 E-value=0.4 Score=40.47 Aligned_cols=74 Identities=20% Similarity=0.292 Sum_probs=48.1
Q ss_pred ceEEEEEeCccCcCCC-CCcHHHHHHhcc-cceecccCCEEEEEE-CCEEEEEEEEEecCCCe---EEEEccceEEEecC
Q psy1724 310 ATFSKFQPQTCDFLDI-TNPKAVLENCLR-NFACLTSGDMIAINY-NSKIYELCVLETKPGNA---VTIIECDMNVDFAP 383 (473)
Q Consensus 310 GtfvkLqP~s~~FldI-snpKavLE~~LR-nystLT~GD~I~I~y-n~~~Y~l~V~e~kP~~a---VsIIdTDleVDf~p 383 (473)
|+.|.+.|.+.|=++| +..-..||..|- +--+++.|.++.++- ++..-.|.|..+.|.+. ...+..|-||=++|
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 4678899998776664 444555776665 588999999999998 56778999999999766 78888888887664
No 13
>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=78.91 E-value=7.5 Score=27.66 Aligned_cols=39 Identities=21% Similarity=0.319 Sum_probs=31.4
Q ss_pred eCCCcEEcCHHHHhhcCCCCCCeEEEEEeecCCceEEEEEeC
Q psy1724 277 ADEGKVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQ 318 (473)
Q Consensus 277 A~EG~v~LP~WMm~~L~l~egd~V~I~~v~LPkGtfvkLqP~ 318 (473)
.+.|.+.||.=+.+.|++++||.+.+... +. .-+.|.|.
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 45799999999999999999999998853 33 35666664
No 14
>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=73.84 E-value=3.2 Score=34.65 Aligned_cols=69 Identities=23% Similarity=0.166 Sum_probs=47.2
Q ss_pred CCCcEEcCHHHHhhcCCCCCCeEEEEEeecCCceEEEEEeCccCcCCCCCcHHHHHHhcccceecccCCEEEEE
Q psy1724 278 DEGKVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQTCDFLDITNPKAVLENCLRNFACLTSGDMIAIN 351 (473)
Q Consensus 278 ~EG~v~LP~WMm~~L~l~egd~V~I~~v~LPkGtfvkLqP~s~~FldIsnpKavLE~~LRnystLT~GD~I~I~ 351 (473)
..|.++|..-.|+.|++.+||.|.|... +-|.+.+.|...+ +...=.--|-...|+-.-+..||.|.|.
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 4689999999999999999999999972 2277777775332 1111112255677888889999999986
No 15
>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=71.58 E-value=28 Score=29.04 Aligned_cols=69 Identities=16% Similarity=0.141 Sum_probs=50.8
Q ss_pred CCCCeEeeCHHHHHHHHhCCCCCceeEEEEeCCCCceEEEEEEeeee---CCCcEEcCHHHHhhcCCCCCCeEEEEEe
Q psy1724 231 ERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLEFVA---DEGKVYLPYWMMRNLLLDEGELVNIESV 305 (473)
Q Consensus 231 ~~GdKIiLPpSaL~~L~~~~i~~Pm~F~L~n~~~~r~th~GVLEFsA---~EG~v~LP~WMm~~L~l~egd~V~I~~v 305 (473)
-..+-++|.|..+++| ++..--+-.|.. .+.|+|=|+.-.. +.|.|-|..-+.+++++.-||.|.|+-+
T Consensus 13 ~~~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 13 AGTNCVRVSPEDMEEL---GLFPGDVVLISG---KRKTVAFVFPDRPDDSPPGVIRLSGIQRKNAGVSIGDRVTVRPY 84 (87)
T ss_dssp HCTTEEEEEHHHHHCT---TT-TTEEEEEET---TTEEEEEEEEECCSTTCTTEEEE-HHHHHHCT--TTSEEEEEEE
T ss_pred CCCCEEEEcHHHHHHc---CCCCccEEEEeC---CceEEEEEEECCCCCCCCCEEEECHHHHhhCCcCCCCEEEEEEC
Confidence 3567899999988865 555556666665 3458988886543 3799999999999999999999999865
No 16
>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=71.42 E-value=7.2 Score=29.07 Aligned_cols=39 Identities=26% Similarity=0.301 Sum_probs=30.5
Q ss_pred CCCcEEcCHHHHhhcCCCCCCeEEEEEeecCCceEEEEEeCc
Q psy1724 278 DEGKVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQT 319 (473)
Q Consensus 278 ~EG~v~LP~WMm~~L~l~egd~V~I~~v~LPkGtfvkLqP~s 319 (473)
..+.|.||.-+.+.|++++||.|.+... ..| -+.+.|..
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 4678999999999999999999998876 233 66777753
No 17
>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=68.64 E-value=3.6 Score=34.81 Aligned_cols=26 Identities=27% Similarity=0.368 Sum_probs=19.5
Q ss_pred CCcEEcCHHHHhhcCCCCCCeEEEEE
Q psy1724 279 EGKVYLPYWMMRNLLLDEGELVNIES 304 (473)
Q Consensus 279 EG~v~LP~WMm~~L~l~egd~V~I~~ 304 (473)
+.-||+|.++.+..+|+.||.|.=.-
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 56799999999999999999987543
No 18
>PRK14132 riboflavin kinase; Provisional
Probab=66.93 E-value=4.8 Score=36.93 Aligned_cols=31 Identities=32% Similarity=0.516 Sum_probs=26.4
Q ss_pred ceEE-EEEEeeeeCCCcEEcCHHHHhhcCCCCCCeEEEE
Q psy1724 266 RITH-SGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIE 303 (473)
Q Consensus 266 r~th-~GVLEFsA~EG~v~LP~WMm~~L~l~egd~V~I~ 303 (473)
|+.| -.|+|++|+.. +-+.|+|++||.|.|+
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 4556 46999999865 9999999999999986
No 19
>cd02790 MopB_CT_Formate-Dh_H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a Mo active site region and a [4Fe-4S] center. This CD (MopB_CT_Formate-Dh_H) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=62.89 E-value=9.4 Score=32.37 Aligned_cols=29 Identities=28% Similarity=0.232 Sum_probs=25.8
Q ss_pred eCCCcEEcCHHHHhhcCCCCCCeEEEEEe
Q psy1724 277 ADEGKVYLPYWMMRNLLLDEGELVNIESV 305 (473)
Q Consensus 277 A~EG~v~LP~WMm~~L~l~egd~V~I~~v 305 (473)
.++..|+|..=-++.|||++||.|+|++-
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 20
>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=62.68 E-value=7.7 Score=31.96 Aligned_cols=28 Identities=18% Similarity=0.250 Sum_probs=23.7
Q ss_pred eCCCcEEcCHHHHhhcCCCCCCeEEEEE
Q psy1724 277 ADEGKVYLPYWMMRNLLLDEGELVNIES 304 (473)
Q Consensus 277 A~EG~v~LP~WMm~~L~l~egd~V~I~~ 304 (473)
+.+.-||+|.++.+..+|+.||.|.=.-
T Consensus 24 ~~~~DvyVs~~~Irr~~LR~GD~V~G~v 51 (68)
T cd04459 24 PGPDDIYVSPSQIRRFNLRTGDTVVGQI 51 (68)
T ss_pred CCCCCEEECHHHHHHhCCCCCCEEEEEE
Confidence 4566799999999999999999987643
No 21
>COG1935 Uncharacterized conserved protein [Function unknown]
Probab=61.25 E-value=14 Score=33.81 Aligned_cols=47 Identities=28% Similarity=0.357 Sum_probs=36.9
Q ss_pred HHHHHHHHhCCCCCceeEEEEeCCCCceEEEEEEeeeeCCCcEEcCHHHHhhcCCCCCCeEEEEEe---ecCCceE
Q psy1724 240 PSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIESV---SLPVATF 312 (473)
Q Consensus 240 pSaL~~L~~~~i~~Pm~F~L~n~~~~r~th~GVLEFsA~EG~v~LP~WMm~~L~l~egd~V~I~~v---~LPkGtf 312 (473)
-+++++|.+.++. +|+|.|..+ ...-++|+|||.|.++++ +|-+|+.
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 3678888776553 688888765 677789999999999998 6778875
No 22
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=59.41 E-value=29 Score=33.02 Aligned_cols=124 Identities=12% Similarity=0.139 Sum_probs=73.0
Q ss_pred CCeEeeCHHHHHHHHhCCCCCceeEEEEeCCCCceEEEEEEeeeeCCCcEEcCHHHHhhcCCCCCCeEEEEEee-cCCce
Q psy1724 233 GGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIESVS-LPVAT 311 (473)
Q Consensus 233 GdKIiLPpSaL~~L~~~~i~~Pm~F~L~n~~~~r~th~GVLEFsA~EG~v~LP~WMm~~L~l~egd~V~I~~v~-LPkGt 311 (473)
..++.||-..|...... ...+=+|... ..-+++++|.++...+.-.|.|=.|.-.....+.||+|.-+-++ .++|=
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 34566665544332211 2334444432 33468899999998777788887787555667889999877663 56888
Q ss_pred EEEEEeC-------c---cCcCCCCCcHHHHHHhccc-ceecccCCEEEEEECC--EEEEEEEE
Q psy1724 312 FSKFQPQ-------T---CDFLDITNPKAVLENCLRN-FACLTSGDMIAINYNS--KIYELCVL 362 (473)
Q Consensus 312 fvkLqP~-------s---~~FldIsnpKavLE~~LRn-ystLT~GD~I~I~yn~--~~Y~l~V~ 362 (473)
+|.|-.. . ..|+.+++... ....+ ..++..||+|....-. ..+.|.+.
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 8887432 1 23443333221 12223 5668999999876421 34444444
No 23
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=59.09 E-value=9.2 Score=37.87 Aligned_cols=33 Identities=33% Similarity=0.491 Sum_probs=28.6
Q ss_pred CceEE-EEEEeeeeCCCcEEcCHHHHhhcCCCCCCeEEEEE
Q psy1724 265 GRITH-SGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIES 304 (473)
Q Consensus 265 ~r~th-~GVLEFsA~EG~v~LP~WMm~~L~l~egd~V~I~~ 304 (473)
.|+.| ..|+|++|+ -.+-+.|+|++||.|+|+-
T Consensus 179 ~rT~h~~dviEIIap-------v~LR~~LnLkDGD~V~ieV 212 (214)
T COG1339 179 ERTHHPTDVIEIIAP-------VKLRDELNLKDGDEVTIEV 212 (214)
T ss_pred ccccCCcceEEEEcc-------HhHHHHhCCCCCCEEEEEE
Confidence 35778 899999987 5699999999999999874
No 24
>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=58.71 E-value=17 Score=29.95 Aligned_cols=55 Identities=16% Similarity=0.208 Sum_probs=37.4
Q ss_pred CcEEcCHHHHhhcCCCCCCeEEEEEeecCCceEEEEEeCcc--CcCCCCCcHHHHHHhcccce
Q psy1724 280 GKVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQTC--DFLDITNPKAVLENCLRNFA 340 (473)
Q Consensus 280 G~v~LP~WMm~~L~l~egd~V~I~~v~LPkGtfvkLqP~s~--~FldIsnpKavLE~~LRnys 340 (473)
-.|-||.=+++.|+|.+||.|.|... +.-+.+.|... +|- ......++..++.|-
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 45889999999999999999976543 24477778765 441 111235666666553
No 25
>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=58.28 E-value=11 Score=34.42 Aligned_cols=27 Identities=30% Similarity=0.490 Sum_probs=19.3
Q ss_pred EEEEeeeeCCCcEEcCHHHHhhcCCCCCCeEEEE
Q psy1724 270 SGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIE 303 (473)
Q Consensus 270 ~GVLEFsA~EG~v~LP~WMm~~L~l~egd~V~I~ 303 (473)
-.++|++|+.. +-+.|+|++||.|.|+
T Consensus 94 ~~~lEiIAp~~-------LR~~L~L~DGD~V~v~ 120 (121)
T PF01982_consen 94 PDILEIIAPVK-------LRDTLGLKDGDEVEVE 120 (121)
T ss_dssp TTEEEEE-SS--------HHHHTT--TT-EEEEE
T ss_pred CceEEEEcCcc-------hHhhcCCCCCCEEEEE
Confidence 46899999865 9999999999999986
No 26
>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=54.01 E-value=20 Score=30.70 Aligned_cols=29 Identities=24% Similarity=0.260 Sum_probs=26.0
Q ss_pred CCCcEEcCHHHHhhcCCCCCCeEEEEEee
Q psy1724 278 DEGKVYLPYWMMRNLLLDEGELVNIESVS 306 (473)
Q Consensus 278 ~EG~v~LP~WMm~~L~l~egd~V~I~~v~ 306 (473)
++..|+|-.=-++.|||.+||.|+|.+..
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 46789999999999999999999999764
No 27
>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=53.44 E-value=16 Score=31.15 Aligned_cols=30 Identities=13% Similarity=0.052 Sum_probs=26.3
Q ss_pred eCCCcEEcCHHHHhhcCCCCCCeEEEEEee
Q psy1724 277 ADEGKVYLPYWMMRNLLLDEGELVNIESVS 306 (473)
Q Consensus 277 A~EG~v~LP~WMm~~L~l~egd~V~I~~v~ 306 (473)
.++..|+|..--++.|||++||.|+|++..
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 356789999999999999999999988654
No 28
>PRK09974 putative regulator PrlF; Provisional
Probab=51.48 E-value=38 Score=30.64 Aligned_cols=59 Identities=15% Similarity=0.106 Sum_probs=38.4
Q ss_pred eCCCcEEcCHHHHhhcCCCCCCeEEEEEeecCCceEEEEEeCccCcCC--CCCcHHHHHHhccc
Q psy1724 277 ADEGKVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQTCDFLD--ITNPKAVLENCLRN 338 (473)
Q Consensus 277 A~EG~v~LP~WMm~~L~l~egd~V~I~~v~LPkGtfvkLqP~s~~Fld--IsnpKavLE~~LRn 338 (473)
...|+|-+|.-+-+.|||++||.|.+. +..+..|.+.+...+--| |...-.+||+-+++
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 456999999999999999999998874 333455666665432211 12224556665554
No 29
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=50.18 E-value=24 Score=29.89 Aligned_cols=42 Identities=14% Similarity=0.174 Sum_probs=32.0
Q ss_pred eCCCcEEcCHHHHhhcCCCCCCeEEEEEeecCCceEEEEEeCcc
Q psy1724 277 ADEGKVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQTC 320 (473)
Q Consensus 277 A~EG~v~LP~WMm~~L~l~egd~V~I~~v~LPkGtfvkLqP~s~ 320 (473)
...|+|++|.-+-+.||+++||.|.+.... .+..+-|+|...
T Consensus 11 ~~~GqIvIPkeiR~~lgi~~Gd~lei~~~~--~~~~ivl~k~~~ 52 (89)
T COG2002 11 DRKGQIVIPKEIREALGIKEGDVLEIIVDG--DGGRIVLKKYKP 52 (89)
T ss_pred CcCceEEecHHHHHHhCCCCCCEEEEEEeC--CCCEEEEEECCc
Confidence 457999999999999999999998887552 112266777654
No 30
>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=50.17 E-value=24 Score=32.26 Aligned_cols=33 Identities=12% Similarity=0.095 Sum_probs=27.9
Q ss_pred EeeeeCCCcEEcCHHHHhhcCCCCCCeEEEEEe
Q psy1724 273 LEFVADEGKVYLPYWMMRNLLLDEGELVNIESV 305 (473)
Q Consensus 273 LEFsA~EG~v~LP~WMm~~L~l~egd~V~I~~v 305 (473)
++...++..|+|-.=-++.|+|++||.|+|.+.
T Consensus 24 l~~~~~~~~v~inp~dA~~lgI~dGd~V~v~~~ 56 (141)
T cd02776 24 LRLQRGGPVVWMNPKDAAELGIKDNDWVEVFND 56 (141)
T ss_pred HhcCCCCCEEEECHHHHHHcCCCCCCEEEEEeC
Confidence 344556788999999999999999999998863
No 31
>PF04322 DUF473: Protein of unknown function (DUF473); InterPro: IPR007417 This is a family of uncharacterised archaeal proteins.
Probab=47.75 E-value=25 Score=32.08 Aligned_cols=47 Identities=19% Similarity=0.236 Sum_probs=35.7
Q ss_pred CHHHHHHHHhCCCCCceeEEEEeCCCCceEEEEEEeeeeCCCcEEcCHHHHhhcCCCCCCeEEEEEe---ecCCce
Q psy1724 239 PPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIESV---SLPVAT 311 (473)
Q Consensus 239 PpSaL~~L~~~~i~~Pm~F~L~n~~~~r~th~GVLEFsA~EG~v~LP~WMm~~L~l~egd~V~I~~v---~LPkGt 311 (473)
-+.+|++|.+ .++=+|+|.|..| +..-+.+++||.|.++++ +|-+||
T Consensus 10 s~~vi~eL~~---~~~RTiEirSa~N-----------------------~~~~~~~~~Gd~VFlT~~~~~Dl~~Gt 59 (119)
T PF04322_consen 10 SRRVIDELKK---NHIRTIEIRSAHN-----------------------VIALESLDPGDRVFLTSVSLEDLTPGT 59 (119)
T ss_pred CHHHHHHHHh---CCceEEEEEcchh-----------------------eeeeecCCCCCEEEEecCCHHHCCCCC
Confidence 4678999988 5667899999866 444566899999999988 455555
No 32
>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=47.42 E-value=30 Score=28.55 Aligned_cols=27 Identities=4% Similarity=-0.091 Sum_probs=22.4
Q ss_pred cCCcEeccHhhHhhcCCCCCCcEEEEE
Q psy1724 77 DEGKVYLPYWCFSVSMFPGNEREDVER 103 (473)
Q Consensus 77 eEG~v~LP~wmm~nL~l~~~~~v~ie~ 103 (473)
.+.=||+|.++.+...|..||.|.=..
T Consensus 25 ~~~DvyVs~~~Irr~~LR~GD~V~G~v 51 (68)
T cd04459 25 GPDDIYVSPSQIRRFNLRTGDTVVGQI 51 (68)
T ss_pred CCCCEEECHHHHHHhCCCCCCEEEEEE
Confidence 344579999999999999999887654
No 33
>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=47.39 E-value=27 Score=29.59 Aligned_cols=27 Identities=26% Similarity=0.213 Sum_probs=24.7
Q ss_pred CCCcEEcCHHHHhhcCCCCCCeEEEEE
Q psy1724 278 DEGKVYLPYWMMRNLLLDEGELVNIES 304 (473)
Q Consensus 278 ~EG~v~LP~WMm~~L~l~egd~V~I~~ 304 (473)
++..|+|..=-++.|||++||.|+|.+
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 34
>PRK09798 antitoxin MazE; Provisional
Probab=46.38 E-value=43 Score=28.39 Aligned_cols=50 Identities=22% Similarity=0.279 Sum_probs=37.0
Q ss_pred cEEcCHHHHhhcCCCCCCeEEEEEeecCCceEEEEEeCccCcCCCCCcHHHHHHhcccce
Q psy1724 281 KVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQTCDFLDITNPKAVLENCLRNFA 340 (473)
Q Consensus 281 ~v~LP~WMm~~L~l~egd~V~I~~v~LPkGtfvkLqP~s~~FldIsnpKavLE~~LRnys 340 (473)
-|-||.=+++.|+|.+||.|.|+.. +.-+.++|... .++.-||.-|-+|+
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 35577999642 33455666665554
No 35
>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=45.08 E-value=32 Score=25.60 Aligned_cols=28 Identities=14% Similarity=0.152 Sum_probs=24.3
Q ss_pred cCCcEeccHhhHhhcCCCCCCcEEEEEe
Q psy1724 77 DEGKVYLPYWCFSVSMFPGNEREDVERG 104 (473)
Q Consensus 77 eEG~v~LP~wmm~nL~l~~~~~v~ie~~ 104 (473)
..+.|.||.-+.+.|++++||.|.+...
T Consensus 5 ~s~~v~iPk~~~~~l~l~~Gd~v~i~~~ 32 (47)
T PF04014_consen 5 NSGQVTIPKEIREKLGLKPGDEVEIEVE 32 (47)
T ss_dssp TCSEEEE-HHHHHHTTSSTTTEEEEEEE
T ss_pred CCceEECCHHHHHHcCCCCCCEEEEEEe
Confidence 4578999999999999999999999876
No 36
>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=44.85 E-value=30 Score=29.10 Aligned_cols=33 Identities=21% Similarity=0.066 Sum_probs=27.4
Q ss_pred EeeeeCCCcEEcCHHHHhhcCCCCCCeEEEEEe
Q psy1724 273 LEFVADEGKVYLPYWMMRNLLLDEGELVNIESV 305 (473)
Q Consensus 273 LEFsA~EG~v~LP~WMm~~L~l~egd~V~I~~v 305 (473)
|.-.+++..|.|-.=-++.|||.+||.|+|.+.
T Consensus 22 l~~~~~~~~v~inp~dA~~lGi~~Gd~V~v~s~ 54 (96)
T cd02788 22 IAERAPAPYARLSPADAARLGLADGDLVEFSLG 54 (96)
T ss_pred HHhcCCCCEEEECHHHHHHcCCCCCCEEEEEEC
Confidence 333456788999999999999999999998864
No 37
>PRK11347 antitoxin ChpS; Provisional
Probab=44.74 E-value=56 Score=27.78 Aligned_cols=48 Identities=19% Similarity=0.266 Sum_probs=35.9
Q ss_pred cEEcCHHHHhhcCCCCCCeEEEEEeecCCceEEEEEeCccCcCCCCCcHHHHHHhcccce
Q psy1724 281 KVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQTCDFLDITNPKAVLENCLRNFA 340 (473)
Q Consensus 281 ~v~LP~WMm~~L~l~egd~V~I~~v~LPkGtfvkLqP~s~~FldIsnpKavLE~~LRnys 340 (473)
-|-||.=++++|++++||.|.|+-.. .-+.++|.... ..||.-|..+.
T Consensus 13 ~vriPk~il~~l~l~~G~~v~i~v~~----~~iii~p~~~~--------~tL~eLla~~~ 60 (83)
T PRK11347 13 GMVIPNIVMKELNLQPGQSVEAQVSN----NQLILTPISRR--------YSLDELLAQCD 60 (83)
T ss_pred eEEeCHHHHHHcCCCCCCEEEEEEEC----CEEEEEECCCC--------CCHHHHHhcCC
Confidence 37899999999999999999887654 34888997433 34666665443
No 38
>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=44.64 E-value=31 Score=24.43 Aligned_cols=28 Identities=18% Similarity=0.214 Sum_probs=25.4
Q ss_pred ecCCcEeccHhhHhhcCCCCCCcEEEEE
Q psy1724 76 ADEGKVYLPYWCFSVSMFPGNEREDVER 103 (473)
Q Consensus 76 AeEG~v~LP~wmm~nL~l~~~~~v~ie~ 103 (473)
.+.|.+.||.=+.+.|.++.|+.+.+..
T Consensus 4 ~~kgri~iP~~~r~~l~~~~gd~~~i~~ 31 (43)
T TIGR01439 4 DKKGQIVIPKEIREKLGLKEGDRLEVIR 31 (43)
T ss_pred CcCCeEEecHHHHHHcCcCCCCEEEEEE
Confidence 4679999999999999999999988884
No 39
>PRK08577 hypothetical protein; Provisional
Probab=42.62 E-value=30 Score=31.07 Aligned_cols=44 Identities=16% Similarity=0.181 Sum_probs=33.2
Q ss_pred eCCCcEEcCHHHHhhcCCCCCCeEEEEEeecCCceEEEEEeCccCc
Q psy1724 277 ADEGKVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQTCDF 322 (473)
Q Consensus 277 A~EG~v~LP~WMm~~L~l~egd~V~I~~v~LPkGtfvkLqP~s~~F 322 (473)
...|+|.+|.=+-+.||+++||.|.+..-. .+.-+.+.|....+
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 40
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=42.23 E-value=28 Score=31.01 Aligned_cols=27 Identities=22% Similarity=0.324 Sum_probs=23.7
Q ss_pred ceecccCCEEEEEECCEEEEEEEEEec
Q psy1724 339 FACLTSGDMIAINYNSKIYELCVLETK 365 (473)
Q Consensus 339 ystLT~GD~I~I~yn~~~Y~l~V~e~k 365 (473)
+..|..||+|.|.+.+..+.++|.+++
T Consensus 137 ~~~l~pGDvi~l~~~~~~~~~RI~~i~ 163 (164)
T PF13550_consen 137 GLALEPGDVIALSDDGRDMRFRITEIE 163 (164)
T ss_pred hccCCCCCEEEEEeCCCceEEEEEEEe
Confidence 456899999999999999999998875
No 41
>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=41.87 E-value=39 Score=32.45 Aligned_cols=46 Identities=22% Similarity=0.330 Sum_probs=35.9
Q ss_pred EEEeeeeCCCcEEcCHHHHhhcCCCCCCeEEEEEeecCCceEEEEEeCc
Q psy1724 271 GVLEFVADEGKVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQT 319 (473)
Q Consensus 271 GVLEFsA~EG~v~LP~WMm~~L~l~egd~V~I~~v~LPkGtfvkLqP~s 319 (473)
|+.==+.+-|+|.+|.=|-+.|++++||.|.|.... .| -+.|++.+
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 444446678999999999999999999999987542 23 37788765
No 42
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=41.52 E-value=20 Score=35.56 Aligned_cols=32 Identities=22% Similarity=0.359 Sum_probs=26.5
Q ss_pred ceEE-EEEEeeeeCCCcEEcCHHHHhhcCCCCCCeEEEEE
Q psy1724 266 RITH-SGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIES 304 (473)
Q Consensus 266 r~th-~GVLEFsA~EG~v~LP~WMm~~L~l~egd~V~I~~ 304 (473)
|+.| --|+|++|+.. +-+.|+|++||.|.|+-
T Consensus 183 rt~h~~~~~EiIap~~-------LR~~l~l~dgd~v~i~i 215 (217)
T PRK14165 183 RTHYPSDLIEIISPVY-------LRKELNLKDGDRVEVLV 215 (217)
T ss_pred CCCCCCCeEEEECChh-------hHHhcCCCCCCEEEEEE
Confidence 4556 45999999865 99999999999999873
No 43
>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=41.34 E-value=33 Score=29.85 Aligned_cols=28 Identities=18% Similarity=0.121 Sum_probs=25.2
Q ss_pred CCCcEEcCHHHHhhcCCCCCCeEEEEEe
Q psy1724 278 DEGKVYLPYWMMRNLLLDEGELVNIESV 305 (473)
Q Consensus 278 ~EG~v~LP~WMm~~L~l~egd~V~I~~v 305 (473)
++..|+|-.=-++.|||++||.|+|.+-
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 5678999999999999999999998875
No 44
>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=41.21 E-value=20 Score=30.42 Aligned_cols=38 Identities=18% Similarity=0.142 Sum_probs=25.2
Q ss_pred EEEEEeeeEec---------------CCcEeccHhhHhhcCCCCCCcEEEEEe
Q psy1724 67 THSGVLEFVAD---------------EGKVYLPYWCFSVSMFPGNEREDVERG 104 (473)
Q Consensus 67 th~GVLEF~Ae---------------EG~v~LP~wmm~nL~l~~~~~v~ie~~ 104 (473)
.-.||||...+ +.=||+|.++.+..+|..||.|.-...
T Consensus 2 ~~~GvLei~~dGyGFLR~~~~~y~~~~~DvYVs~~qIrrf~LR~GD~V~G~vr 54 (78)
T PF07497_consen 2 YVEGVLEILPDGYGFLRSPDNNYLPSPDDVYVSPSQIRRFGLRTGDLVEGQVR 54 (78)
T ss_dssp EEEEEEEE-TTS-EEEE-GGGTTS-STTSEEE-CCCCCCTT--TTEEEEEEEE
T ss_pred EEEEEEEECCCCcEEeECCCcCCCCCCCCEEECHHHHHHcCCCCCCEEEEEEe
Confidence 34688885543 345899999999999999998875543
No 45
>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=40.62 E-value=33 Score=29.35 Aligned_cols=29 Identities=17% Similarity=0.094 Sum_probs=25.3
Q ss_pred eCCCcEEcCHHHHhhcCCCCCCeEEEEEe
Q psy1724 277 ADEGKVYLPYWMMRNLLLDEGELVNIESV 305 (473)
Q Consensus 277 A~EG~v~LP~WMm~~L~l~egd~V~I~~v 305 (473)
+++..|.|..=-++.|||++||.|+|.+-
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 45678999999999999999999998863
No 46
>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=40.04 E-value=27 Score=30.13 Aligned_cols=30 Identities=17% Similarity=-0.048 Sum_probs=26.1
Q ss_pred eCCCcEEcCHHHHhhcCCCCCCeEEEEEee
Q psy1724 277 ADEGKVYLPYWMMRNLLLDEGELVNIESVS 306 (473)
Q Consensus 277 A~EG~v~LP~WMm~~L~l~egd~V~I~~v~ 306 (473)
.++..|+|-.=-++.|||++||.|+|++..
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 47
>COG2336 MazE Growth regulator [Signal transduction mechanisms]
Probab=39.40 E-value=30 Score=29.78 Aligned_cols=35 Identities=23% Similarity=0.284 Sum_probs=26.1
Q ss_pred cEEcCHHHHhhcCCCCCCeEEEEEeecCCceEEEEEeC
Q psy1724 281 KVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQ 318 (473)
Q Consensus 281 ~v~LP~WMm~~L~l~egd~V~I~~v~LPkGtfvkLqP~ 318 (473)
-|-+|.=||+.|++.+||-|.++-. .+..+-+.|.
T Consensus 13 avrIP~~l~kql~l~~g~~v~v~v~---n~~~i~~~p~ 47 (82)
T COG2336 13 AVRIPAALLKQLNLTIGDEVEVEVG---NDQSILIRPV 47 (82)
T ss_pred eeeccHHHHHHhCCCcCceEEEEEc---CCcEEEeccc
Confidence 3789999999999999999987643 2334455554
No 48
>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=39.11 E-value=37 Score=27.74 Aligned_cols=28 Identities=29% Similarity=0.236 Sum_probs=24.5
Q ss_pred CCCcEEcCHHHHhhcCCCCCCeEEEEEe
Q psy1724 278 DEGKVYLPYWMMRNLLLDEGELVNIESV 305 (473)
Q Consensus 278 ~EG~v~LP~WMm~~L~l~egd~V~I~~v 305 (473)
.+..|+|..=-++.|+|++||.|.|++-
T Consensus 21 ~~~~v~~~~~da~~lgl~~Gd~v~v~~~ 48 (101)
T cd02775 21 PEPVVEINPEDAAALGIKDGDLVRVESR 48 (101)
T ss_pred CCCEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 4578999999999999999999988754
No 49
>PRK14132 riboflavin kinase; Provisional
Probab=38.66 E-value=28 Score=32.07 Aligned_cols=31 Identities=16% Similarity=0.165 Sum_probs=25.8
Q ss_pred CeEE-EEEeeeEecCCcEeccHhhHhhcCCCCCCcEEEE
Q psy1724 65 RITH-SGVLEFVADEGKVYLPYWCFSVSMFPGNEREDVE 102 (473)
Q Consensus 65 ~~th-~GVLEF~AeEG~v~LP~wmm~nL~l~~~~~v~ie 102 (473)
|+.| --|+|++|++. +-+.|.|++||.|.|+
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 45999999886 7889999999999987
No 50
>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=37.94 E-value=40 Score=28.82 Aligned_cols=28 Identities=32% Similarity=0.217 Sum_probs=24.8
Q ss_pred CCCcEEcCHHHHhhcCCCCCCeEEEEEe
Q psy1724 278 DEGKVYLPYWMMRNLLLDEGELVNIESV 305 (473)
Q Consensus 278 ~EG~v~LP~WMm~~L~l~egd~V~I~~v 305 (473)
.+..|+|..-.++.||+++||.|+|.+-
T Consensus 33 ~~~~v~in~~dA~~lgi~~Gd~V~v~~~ 60 (122)
T cd02791 33 PEPYVEIHPEDAARLGLKEGDLVRVTSR 60 (122)
T ss_pred CCCEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 4567999999999999999999998865
No 51
>COG1153 FwdD Formylmethanofuran dehydrogenase subunit D [Energy production and conversion]
Probab=37.92 E-value=26 Score=32.29 Aligned_cols=28 Identities=21% Similarity=0.182 Sum_probs=23.4
Q ss_pred eCCCcEEcCHHHHhhcCCCCCCeEEEEE
Q psy1724 277 ADEGKVYLPYWMMRNLLLDEGELVNIES 304 (473)
Q Consensus 277 A~EG~v~LP~WMm~~L~l~egd~V~I~~ 304 (473)
-.-..|++-.-.|+.|++++||.|.|++
T Consensus 28 ~a~a~~~inp~D~~~Lgv~EGD~VkVks 55 (128)
T COG1153 28 NACAVCEINPEDMKQLGVSEGDKVKVKS 55 (128)
T ss_pred hheeEEEECHHHHHHhCCCcCCeEEEEe
Confidence 3345677778899999999999999987
No 52
>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=37.82 E-value=38 Score=29.49 Aligned_cols=29 Identities=14% Similarity=0.105 Sum_probs=25.3
Q ss_pred CCCcEEcCHHHHhhcCCCCCCeEEEEEee
Q psy1724 278 DEGKVYLPYWMMRNLLLDEGELVNIESVS 306 (473)
Q Consensus 278 ~EG~v~LP~WMm~~L~l~egd~V~I~~v~ 306 (473)
++..|+|-.=-++.|||++||.|+|.+..
T Consensus 31 ~~~~v~inp~dA~~~gi~~Gd~V~v~s~~ 59 (130)
T cd02781 31 PDPVAEINPETAAKLGIADGDWVWVETPR 59 (130)
T ss_pred CCCEEEECHHHHHHcCCCCCCEEEEECCC
Confidence 46779999999999999999999988654
No 53
>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=37.68 E-value=38 Score=29.60 Aligned_cols=27 Identities=11% Similarity=0.155 Sum_probs=24.2
Q ss_pred CCcEEcCHHHHhhcCCCCCCeEEEEEe
Q psy1724 279 EGKVYLPYWMMRNLLLDEGELVNIESV 305 (473)
Q Consensus 279 EG~v~LP~WMm~~L~l~egd~V~I~~v 305 (473)
+..|+|-.=.++.|||.+||.|+|++-
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 567999999999999999999998863
No 54
>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=36.12 E-value=39 Score=28.37 Aligned_cols=24 Identities=21% Similarity=0.166 Sum_probs=20.5
Q ss_pred cEEcCHHHHhhcCCCCCCeEEEEE
Q psy1724 281 KVYLPYWMMRNLLLDEGELVNIES 304 (473)
Q Consensus 281 ~v~LP~WMm~~L~l~egd~V~I~~ 304 (473)
.|+|-.=-++.|||++||.|+|++
T Consensus 31 ~v~inp~dA~~~Gi~~Gd~V~v~s 54 (110)
T PF01568_consen 31 FVEINPEDAAKLGIKDGDWVRVSS 54 (110)
T ss_dssp EEEEEHHHHHHCT--TTCEEEEEE
T ss_pred EEEEcHHHHHHhcCcCCCEEEEEe
Confidence 788889999999999999999987
No 55
>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=35.83 E-value=40 Score=30.83 Aligned_cols=28 Identities=18% Similarity=0.181 Sum_probs=18.4
Q ss_pred EEEeeeEecCCcEeccHhhHhhcCCCCCCcEEEEE
Q psy1724 69 SGVLEFVADEGKVYLPYWCFSVSMFPGNEREDVER 103 (473)
Q Consensus 69 ~GVLEF~AeEG~v~LP~wmm~nL~l~~~~~v~ie~ 103 (473)
--++|++|+.. +-+.|.|++||.|.|+.
T Consensus 94 ~~~lEiIAp~~-------LR~~L~L~DGD~V~v~V 121 (121)
T PF01982_consen 94 PDILEIIAPVK-------LRDTLGLKDGDEVEVEV 121 (121)
T ss_dssp TTEEEEE-SS--------HHHHTT--TT-EEEEEE
T ss_pred CceEEEEcCcc-------hHhhcCCCCCCEEEEEC
Confidence 34777777765 78899999999999873
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=35.24 E-value=50 Score=28.48 Aligned_cols=30 Identities=13% Similarity=-0.015 Sum_probs=25.9
Q ss_pred eCCCcEEcCHHHHhhcCCCCCCeEEEEEee
Q psy1724 277 ADEGKVYLPYWMMRNLLLDEGELVNIESVS 306 (473)
Q Consensus 277 A~EG~v~LP~WMm~~L~l~egd~V~I~~v~ 306 (473)
.++..|.|-.=-++.|||++||.|+|.+..
T Consensus 30 ~~~~~v~in~~dA~~lgi~~Gd~V~v~s~~ 59 (115)
T cd02779 30 VPLPYIEVNPEDAKREGLKNGDLVEVYNDY 59 (115)
T ss_pred CCCCEEEECHHHHHHcCCCCCCEEEEEeCC
Confidence 457789999999999999999999988653
No 57
>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=35.23 E-value=49 Score=28.40 Aligned_cols=29 Identities=17% Similarity=0.294 Sum_probs=25.4
Q ss_pred eCCCcEEcCHHHHhhcCCCCCCeEEEEEe
Q psy1724 277 ADEGKVYLPYWMMRNLLLDEGELVNIESV 305 (473)
Q Consensus 277 A~EG~v~LP~WMm~~L~l~egd~V~I~~v 305 (473)
.++..|+|..=-++.|||++||.|+|.+-
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 45678999999999999999999998863
No 58
>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=34.96 E-value=45 Score=29.08 Aligned_cols=29 Identities=17% Similarity=0.130 Sum_probs=25.8
Q ss_pred eCCCcEEcCHHHHhhcCCCCCCeEEEEEe
Q psy1724 277 ADEGKVYLPYWMMRNLLLDEGELVNIESV 305 (473)
Q Consensus 277 A~EG~v~LP~WMm~~L~l~egd~V~I~~v 305 (473)
+++..|.|-.=-++.|+|++||.|.|++.
T Consensus 30 ~~~~~v~i~p~dA~~~gi~~Gd~V~v~s~ 58 (129)
T cd02782 30 RNRCTLRIHPDDAAALGLADGDKVRVTSA 58 (129)
T ss_pred CCCceEEECHHHHHHcCCCCCCEEEEEcC
Confidence 46778999999999999999999998874
No 59
>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=34.44 E-value=76 Score=26.70 Aligned_cols=31 Identities=19% Similarity=0.220 Sum_probs=24.8
Q ss_pred HHHHhhcCCCCCCeEEEEEeecCCceEEEEE
Q psy1724 286 YWMMRNLLLDEGELVNIESVSLPVATFSKFQ 316 (473)
Q Consensus 286 ~WMm~~L~l~egd~V~I~~v~LPkGtfvkLq 316 (473)
.-|.+.+|+++||.|.|.-.+--.|.++..+
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 3489999999999999999998889888643
No 60
>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=34.02 E-value=48 Score=28.73 Aligned_cols=28 Identities=11% Similarity=0.057 Sum_probs=24.0
Q ss_pred CCcEEcCHHHHhhcCCCCCCeEEEEEee
Q psy1724 279 EGKVYLPYWMMRNLLLDEGELVNIESVS 306 (473)
Q Consensus 279 EG~v~LP~WMm~~L~l~egd~V~I~~v~ 306 (473)
+..|+|-.=-++.|||++||.|+|++..
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 3468899999999999999999988653
No 61
>COG0243 BisC Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]
Probab=33.71 E-value=60 Score=37.11 Aligned_cols=54 Identities=24% Similarity=0.332 Sum_probs=38.3
Q ss_pred CCCceeEEEEeCCCCceEEEEEEe------eeeCCCcEEcCHHHHhhcCCCCCCeEEEEEee
Q psy1724 251 ICYPMLFKLTNQKMGRITHSGVLE------FVADEGKVYLPYWMMRNLLLDEGELVNIESVS 306 (473)
Q Consensus 251 i~~Pm~F~L~n~~~~r~th~GVLE------FsA~EG~v~LP~WMm~~L~l~egd~V~I~~v~ 306 (473)
-.|| |.|+.......+|.+.-. -.++++.|+|-.--++.|||++||.|+|.+.+
T Consensus 638 ~~yP--l~L~t~r~~~~~hs~~~~~~~~~~~~~~~~~v~inp~DA~~~GI~~GD~V~V~~~r 697 (765)
T COG0243 638 KEYP--LQLTTGRLKNHLHSTTYNLRVPLRAIAPRPFVWINPEDAAKLGIKDGDLVRVENRR 697 (765)
T ss_pred CCCC--EEEecCCcCceecccccccchhHhhCCCCceEEECHHHHHHcCCCcCCEEEEEcCC
Confidence 3677 555554433344444333 33578899999999999999999999998753
No 62
>COG2336 MazE Growth regulator [Signal transduction mechanisms]
Probab=33.64 E-value=49 Score=28.54 Aligned_cols=31 Identities=23% Similarity=0.256 Sum_probs=26.5
Q ss_pred EeccHhhHhhcCCCCCCcEEEEEee---eccCCH
Q psy1724 81 VYLPYWCFSVSMFPGNEREDVERGG---KIIMPP 111 (473)
Q Consensus 81 v~LP~wmm~nL~l~~~~~v~ie~~~---lI~n~K 111 (473)
+-||.-||+.|++.+|+.|.++..+ ++.-|+
T Consensus 14 vrIP~~l~kql~l~~g~~v~v~v~n~~~i~~~p~ 47 (82)
T COG2336 14 VRIPAALLKQLNLTIGDEVEVEVGNDQSILIRPV 47 (82)
T ss_pred eeccHHHHHHhCCCcCceEEEEEcCCcEEEeccc
Confidence 6899999999999999999999984 455555
No 63
>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=33.36 E-value=60 Score=28.79 Aligned_cols=31 Identities=13% Similarity=0.227 Sum_probs=25.7
Q ss_pred hcccceecccCCEEEEEECCEEEEEEEEEec
Q psy1724 335 CLRNFACLTSGDMIAINYNSKIYELCVLETK 365 (473)
Q Consensus 335 ~LRnystLT~GD~I~I~yn~~~Y~l~V~e~k 365 (473)
.+++...|.+||.|.|...++.|...|.+++
T Consensus 58 ~F~~L~~l~~Gd~v~v~~~~~~~~Y~V~~~~ 88 (126)
T cd06166 58 IFNRLDEVEKGDEIKVTTKNGTYKYKITSIF 88 (126)
T ss_pred ccCChHHCCCCCEEEEEECCEEEEEEEEEEE
Confidence 4566667789999999999999999998653
No 64
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=33.29 E-value=57 Score=29.04 Aligned_cols=26 Identities=23% Similarity=0.448 Sum_probs=23.0
Q ss_pred eecccCCEEEEEECCEEEEEEEEEec
Q psy1724 340 ACLTSGDMIAINYNSKIYELCVLETK 365 (473)
Q Consensus 340 stLT~GD~I~I~yn~~~Y~l~V~e~k 365 (473)
..+-.||+|.|.++++.+.+.|+.+.
T Consensus 47 ~~VK~GD~l~i~~~~~~~~v~Vl~~~ 72 (100)
T COG1188 47 KEVKVGDILTIRFGNKEFTVKVLALG 72 (100)
T ss_pred cccCCCCEEEEEeCCcEEEEEEEecc
Confidence 35778999999999999999999874
No 65
>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=32.69 E-value=53 Score=34.84 Aligned_cols=46 Identities=20% Similarity=0.255 Sum_probs=33.7
Q ss_pred EEEEeCCCCceEEEEEEeeeeCCCcEEcCHHHHhhcCCCCCCeEEEE
Q psy1724 257 FKLTNQKMGRITHSGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIE 303 (473)
Q Consensus 257 F~L~n~~~~r~th~GVLEFsA~EG~v~LP~WMm~~L~l~egd~V~I~ 303 (473)
+-|.|..-. ---|.+.....+.+.+.|+.-+++.|++++||.|++-
T Consensus 288 ~Lv~n~~~~-~FRa~~~~~~~~~~~~~l~~~~a~aL~v~~Gd~Vr~~ 333 (335)
T TIGR03243 288 YLVCNGRLA-DFRAVLAPLSADAGTLILSADAADALGVSEGDTVRVV 333 (335)
T ss_pred EEEECCCCC-CeEEEEecccCCCCeeecCHHHHHhcCCCCCCeEEEe
Confidence 446665321 1223446666778899999999999999999999874
No 66
>smart00553 SEP Domain present in Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47.
Probab=32.13 E-value=18 Score=31.48 Aligned_cols=16 Identities=31% Similarity=0.684 Sum_probs=13.3
Q ss_pred cceeeeeeeecCCccC
Q psy1724 414 FVAFHGTGNRLDGKRK 429 (473)
Q Consensus 414 ~~~F~G~G~rLdGK~~ 429 (473)
+.+|+|.|+||++-..
T Consensus 73 ~~~F~G~G~~LGs~~p 88 (93)
T smart00553 73 FKPFSGSGQKLGSPGP 88 (93)
T ss_pred ccCCccCCccCCCCCC
Confidence 5789999999987543
No 67
>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=31.74 E-value=60 Score=29.70 Aligned_cols=28 Identities=14% Similarity=0.191 Sum_probs=22.2
Q ss_pred ccceecccCCEEEEEE-CCEEEEEEEEEe
Q psy1724 337 RNFACLTSGDMIAINY-NSKIYELCVLET 364 (473)
Q Consensus 337 RnystLT~GD~I~I~y-n~~~Y~l~V~e~ 364 (473)
++...|.+||.|.|.. +++.|...|.++
T Consensus 68 ~~L~~l~~GD~I~v~~~~g~~~~Y~V~~~ 96 (144)
T cd05829 68 FRLGDLRKGDKVEVTRADGQTATFRVDRV 96 (144)
T ss_pred cchhcCCCCCEEEEEECCCCEEEEEEeEE
Confidence 3444678999999999 778888888765
No 68
>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=31.14 E-value=58 Score=28.74 Aligned_cols=29 Identities=7% Similarity=0.030 Sum_probs=25.5
Q ss_pred eCCCcEEcCHHHHhhcCCCCCCeEEEEEe
Q psy1724 277 ADEGKVYLPYWMMRNLLLDEGELVNIESV 305 (473)
Q Consensus 277 A~EG~v~LP~WMm~~L~l~egd~V~I~~v 305 (473)
.++..|+|=.=-++.|||++||.|+|.+.
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 45678999999999999999999998874
No 69
>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=30.33 E-value=58 Score=30.00 Aligned_cols=32 Identities=19% Similarity=0.253 Sum_probs=27.4
Q ss_pred eCCCcEEcCHHHHhhcCCCCCCeEEEEEeecCCce
Q psy1724 277 ADEGKVYLPYWMMRNLLLDEGELVNIESVSLPVAT 311 (473)
Q Consensus 277 A~EG~v~LP~WMm~~L~l~egd~V~I~~v~LPkGt 311 (473)
.++..|+|-.=-++.|||++||.|.|++ +.|+
T Consensus 29 ~~~~~v~inp~dA~~~GI~dGd~V~v~s---~~G~ 60 (156)
T cd02783 29 HTRNYLYMHPKTAKELGIKDGDWVWVES---VNGR 60 (156)
T ss_pred CCCCEEEECHHHHHHcCCCCCCEEEEEc---CCee
Confidence 4567899999999999999999999998 4465
No 70
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=29.29 E-value=69 Score=27.34 Aligned_cols=29 Identities=10% Similarity=0.228 Sum_probs=25.2
Q ss_pred HHhhcCCCCCCeEEEEEeecCCceEEEEE
Q psy1724 288 MMRNLLLDEGELVNIESVSLPVATFSKFQ 316 (473)
Q Consensus 288 Mm~~L~l~egd~V~I~~v~LPkGtfvkLq 316 (473)
+.+.+|+++||.|.|..-+--.|.+|..+
T Consensus 46 v~r~~g~k~GdVvkI~R~S~taG~~v~YR 74 (79)
T PRK09570 46 VVKAIGAKPGDVIKIVRKSPTAGEAVYYR 74 (79)
T ss_pred hhhhcCCCCCCEEEEEECCCCCCccEEEE
Confidence 88899999999999998887788887654
No 71
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=29.16 E-value=71 Score=27.01 Aligned_cols=30 Identities=10% Similarity=0.122 Sum_probs=27.0
Q ss_pred ecCCcEeccHhhHhhcCCCCCCcEEEEEee
Q psy1724 76 ADEGKVYLPYWCFSVSMFPGNEREDVERGG 105 (473)
Q Consensus 76 AeEG~v~LP~wmm~nL~l~~~~~v~ie~~~ 105 (473)
...|+|.+|.-+-+.|++.+||.|.+....
T Consensus 11 ~~~GqIvIPkeiR~~lgi~~Gd~lei~~~~ 40 (89)
T COG2002 11 DRKGQIVIPKEIREALGIKEGDVLEIIVDG 40 (89)
T ss_pred CcCceEEecHHHHHHhCCCCCCEEEEEEeC
Confidence 468999999999999999999999888764
No 72
>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=27.93 E-value=73 Score=28.52 Aligned_cols=28 Identities=18% Similarity=0.205 Sum_probs=25.0
Q ss_pred eCCCcEEcCHHHHhhcCCCCCCeEEEEE
Q psy1724 277 ADEGKVYLPYWMMRNLLLDEGELVNIES 304 (473)
Q Consensus 277 A~EG~v~LP~WMm~~L~l~egd~V~I~~ 304 (473)
+++..|.|-.=-++.|+|++||.|.|++
T Consensus 27 ~~~~~v~inp~dA~~lgI~~Gd~V~v~s 54 (143)
T cd02780 27 KPENPVWINPEDAAKLGIKTGDRVRVVT 54 (143)
T ss_pred CCCCEEEECHHHHHHcCCCCCCEEEEEe
Confidence 3567899999999999999999999987
No 73
>PRK15095 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=26.57 E-value=1.7e+02 Score=27.25 Aligned_cols=93 Identities=19% Similarity=0.217 Sum_probs=49.3
Q ss_pred EEeeeeCCCcEEcCHHHHhhcCCCCCCeEEEEEeecCCceEEEEEeCccCcCCCCCcHHHHHHhcccce---ecccCCEE
Q psy1724 272 VLEFVADEGKVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQTCDFLDITNPKAVLENCLRNFA---CLTSGDMI 348 (473)
Q Consensus 272 VLEFsA~EG~v~LP~WMm~~L~l~egd~V~I~~v~LPkGtfvkLqP~s~~FldIsnpKavLE~~LRnys---tLT~GD~I 348 (473)
-++|+--.|.+ +|.|=-.=++++.|+.+.|. || | +.+|- -.|+..|.+-.+.+|. -+-.|..+
T Consensus 34 P~~f~~G~g~v-i~gle~aL~gm~~Ge~~~v~---ip--------p-~~ayG-~~d~~~v~~vp~~~f~~~~~~~~G~~~ 99 (156)
T PRK15095 34 PALFRLGDGSL-SEGLEQQLLGLKVGDKKTFS---LE--------P-EAAFG-VPSPDLIQYFSRRDFMDAGEPEIGAIM 99 (156)
T ss_pred CEEEEeCCCCc-cHHHHHHHcCCCCCCEEEEE---EC--------h-HHhcC-CCChHHEEEecHHHCCcccCCCCCCEE
Confidence 44555555655 79998888899999987654 22 1 11221 2344444333333332 35666665
Q ss_pred EEEEC-CEEEEEEEEEecCCCeEEEEccceEEEecCCCC
Q psy1724 349 AINYN-SKIYELCVLETKPGNAVTIIECDMNVDFAPPVG 386 (473)
Q Consensus 349 ~I~yn-~~~Y~l~V~e~kP~~aVsIIdTDleVDf~pP~~ 386 (473)
.+.-. +......|++ |-+..+.|||.-|+-
T Consensus 100 ~~~~~~G~~~~~~V~~--------i~~~~v~vD~NHPLA 130 (156)
T PRK15095 100 LFTAMDGSEMPGVIRE--------INGDSITVDFNHPLA 130 (156)
T ss_pred EEECCCCCEEEEEEEE--------EcCCEEEEECCCcCC
Confidence 55432 2233333443 334566677766653
No 74
>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=26.48 E-value=2.8e+02 Score=25.63 Aligned_cols=41 Identities=15% Similarity=0.187 Sum_probs=27.0
Q ss_pred ceecccCCEEEEEEC--CEEEEEEEEEecCCCeEEEEccceEE
Q psy1724 339 FACLTSGDMIAINYN--SKIYELCVLETKPGNAVTIIECDMNV 379 (473)
Q Consensus 339 ystLT~GD~I~I~yn--~~~Y~l~V~e~kP~~aVsIIdTDleV 379 (473)
+..+..||++.+... ...+.++-+--.|++.|++.+.-+-|
T Consensus 49 ~~~~~rGDiVvf~~~~~~~~~~iKRVig~pGd~v~i~~~~l~v 91 (163)
T TIGR02227 49 TSDPKRGDIVVFKDPDDNKNIYVKRVIGLPGDKVEFRDGKLYI 91 (163)
T ss_pred CCCCCCCcEEEEecCCCCCceeEEEEEecCCCEEEEECCEEEE
Confidence 356778888888764 23445555555689999887755444
No 75
>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=26.04 E-value=82 Score=33.48 Aligned_cols=46 Identities=20% Similarity=0.264 Sum_probs=33.7
Q ss_pred EEEEeCCCCceEEEEEEeeeeCCCcEEcCHHHHhhcCCCCCCeEEEE
Q psy1724 257 FKLTNQKMGRITHSGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIE 303 (473)
Q Consensus 257 F~L~n~~~~r~th~GVLEFsA~EG~v~LP~WMm~~L~l~egd~V~I~ 303 (473)
+-|.|..... --|.+.....+.+.+.|+.-+++.|++++||.|++-
T Consensus 289 ~Lv~n~~~~~-FRa~~~~~~~~~~~~~l~~~~a~aL~v~~Gd~Vr~~ 334 (336)
T TIGR03244 289 YIVANTSLSD-FRATLAPSDLDAGELVLTAAQADALRVSAGDLVRIV 334 (336)
T ss_pred EEEECCCCCC-eEEEEecccCCCCeEecCHHHHHhcCCCCCCeEEEe
Confidence 4577754321 123345666678889999999999999999999874
No 76
>PRK10456 arginine succinyltransferase; Provisional
Probab=26.02 E-value=82 Score=33.58 Aligned_cols=47 Identities=11% Similarity=0.086 Sum_probs=34.0
Q ss_pred EEEEeCCCCceEEEEEEeeeeCCCcEEcCHHHHhhcCCCCCCeEEEEE
Q psy1724 257 FKLTNQKMGRITHSGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIES 304 (473)
Q Consensus 257 F~L~n~~~~r~th~GVLEFsA~EG~v~LP~WMm~~L~l~egd~V~I~~ 304 (473)
+-|.|.... ---|-+.....+.+.+.|+.-+++.|++++||.|++-.
T Consensus 290 ~Lv~n~~~~-~FRa~~~~~~~~~~~~~l~~~~a~aL~v~~Gd~Vr~~~ 336 (344)
T PRK10456 290 CLVANENYH-HFRAVLVRTDPATERLILTAAQLDALKCHAGDRVRLVR 336 (344)
T ss_pred EEEECCCCC-CeEEEEecccCCCCeEecCHHHHHhcCCCCCCeEEEEe
Confidence 456665321 11233466666788899999999999999999998764
No 77
>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=25.41 E-value=1e+02 Score=27.30 Aligned_cols=30 Identities=27% Similarity=0.402 Sum_probs=24.9
Q ss_pred cccceecccCCEEEEEECCEEEEEEEEEec
Q psy1724 336 LRNFACLTSGDMIAINYNSKIYELCVLETK 365 (473)
Q Consensus 336 LRnystLT~GD~I~I~yn~~~Y~l~V~e~k 365 (473)
+++...|.+||.|.|...++.|...|.+++
T Consensus 56 F~~L~~l~~Gd~i~v~~~~~~~~Y~V~~~~ 85 (127)
T cd05828 56 FRFLGELEPGDIITLQTLGGTYTYRVTSTR 85 (127)
T ss_pred hhChhcCCCCCEEEEEECCEEEEEEEeeEE
Confidence 455566779999999999999999998763
No 78
>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=24.67 E-value=88 Score=33.25 Aligned_cols=46 Identities=15% Similarity=0.162 Sum_probs=32.6
Q ss_pred EEEEeCCCCceEEEEEEeee-eCCCcEEcCHHHHhhcCCCCCCeEEEE
Q psy1724 257 FKLTNQKMGRITHSGVLEFV-ADEGKVYLPYWMMRNLLLDEGELVNIE 303 (473)
Q Consensus 257 F~L~n~~~~r~th~GVLEFs-A~EG~v~LP~WMm~~L~l~egd~V~I~ 303 (473)
+-|.|..... --|.++... .+.+.+.|+.-+++.|++++||.|++-
T Consensus 288 ~Lvsn~~~~~-FRa~~~~~~~~~~~~~~l~~~~a~aL~v~~Gd~Vr~~ 334 (336)
T TIGR03245 288 YLVCNGLLED-FRATLADVTDVDGDLLRLKRDAAEALGVSEGDNVRFA 334 (336)
T ss_pred EEEECCCCCC-eEEEEeccccCCCCeeecCHHHHHhcCCCCCCeEEEe
Confidence 4466653211 123335555 567888999999999999999999874
No 79
>PRK11347 antitoxin ChpS; Provisional
Probab=24.20 E-value=88 Score=26.61 Aligned_cols=39 Identities=10% Similarity=0.180 Sum_probs=28.8
Q ss_pred EeccHhhHhhcCCCCCCcEEEEEeee--cc---CCHHHHHhhcc
Q psy1724 81 VYLPYWCFSVSMFPGNEREDVERGGK--II---MPPSALEQLTR 119 (473)
Q Consensus 81 v~LP~wmm~nL~l~~~~~v~ie~~~l--I~---n~KavLE~~Lr 119 (473)
+-||.=+++.|.++.|+.|.|+...- |- .+++.||..|.
T Consensus 14 vriPk~il~~l~l~~G~~v~i~v~~~~iii~p~~~~~tL~eLla 57 (83)
T PRK11347 14 MVIPNIVMKELNLQPGQSVEAQVSNNQLILTPISRRYSLDELLA 57 (83)
T ss_pred EEeCHHHHHHcCCCCCCEEEEEEECCEEEEEECCCCCCHHHHHh
Confidence 68999999999999999998887632 21 23355666553
No 80
>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=23.93 E-value=1.1e+02 Score=27.63 Aligned_cols=30 Identities=20% Similarity=0.366 Sum_probs=24.8
Q ss_pred cccceecccCCEEEEEECCEEEEEEEEEec
Q psy1724 336 LRNFACLTSGDMIAINYNSKIYELCVLETK 365 (473)
Q Consensus 336 LRnystLT~GD~I~I~yn~~~Y~l~V~e~k 365 (473)
+++...|.+||.|.|...+..|...|.+++
T Consensus 60 F~~L~~l~~Gd~i~v~~~~~~~~Y~V~~~~ 89 (137)
T cd05830 60 FNDLDKLRPGDKIVVETADGWYTYVVRSSE 89 (137)
T ss_pred cccHhhCCCCCEEEEEECCeEEEEEEeEEE
Confidence 455566889999999999999999998764
No 81
>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=23.17 E-value=1.1e+02 Score=27.65 Aligned_cols=27 Identities=26% Similarity=0.420 Sum_probs=21.9
Q ss_pred cceecccCCEEEEEECCEEEEEEEEEe
Q psy1724 338 NFACLTSGDMIAINYNSKIYELCVLET 364 (473)
Q Consensus 338 nystLT~GD~I~I~yn~~~Y~l~V~e~ 364 (473)
+...|.+||.|.|...+..|..+|.++
T Consensus 60 ~L~~l~~GD~i~v~~~~~~~~Y~V~~~ 86 (136)
T TIGR01076 60 NLDKLKKGDMLYLHVGNEVLTYQVTST 86 (136)
T ss_pred CHHHCCCCCEEEEEECCcEEEEEEEEE
Confidence 333477999999999999999888765
No 82
>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=23.16 E-value=3.4e+02 Score=20.66 Aligned_cols=33 Identities=15% Similarity=0.294 Sum_probs=22.3
Q ss_pred ecccCCEEEEEECCEE-EEEEEEEecCCCeEEEE
Q psy1724 341 CLTSGDMIAINYNSKI-YELCVLETKPGNAVTII 373 (473)
Q Consensus 341 tLT~GD~I~I~yn~~~-Y~l~V~e~kP~~aVsII 373 (473)
.+..||++.+.+++.. ..++-+.-.+++.+-+.
T Consensus 24 ~~~~gdivv~~~~~~~~~~iKrv~~~~~~~~~~~ 57 (70)
T PF00717_consen 24 EPKDGDIVVVKIDGDEELYIKRVVGEPGGIILIS 57 (70)
T ss_dssp ---TTSEEEEEETTEESEEEEEEEEETTEEEEE-
T ss_pred CCccCeEEEEEECCceeeEEEEEEEeCCCEEEEe
Confidence 6778999999999886 66666666777666554
No 83
>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=22.78 E-value=84 Score=24.04 Aligned_cols=23 Identities=17% Similarity=0.042 Sum_probs=18.5
Q ss_pred EEcCHHHHhhcCCCCCCeEEEEE
Q psy1724 282 VYLPYWMMRNLLLDEGELVNIES 304 (473)
Q Consensus 282 v~LP~WMm~~L~l~egd~V~I~~ 304 (473)
+.++.|-.+.|+|++||.|.+..
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 67899999999999999988753
No 84
>PRK08577 hypothetical protein; Provisional
Probab=22.49 E-value=1e+02 Score=27.72 Aligned_cols=30 Identities=10% Similarity=0.007 Sum_probs=26.4
Q ss_pred EecCCcEeccHhhHhhcCCCCCCcEEEEEe
Q psy1724 75 VADEGKVYLPYWCFSVSMFPGNEREDVERG 104 (473)
Q Consensus 75 ~AeEG~v~LP~wmm~nL~l~~~~~v~ie~~ 104 (473)
+...|++.+|.-+-+.|++.+|+.|.+...
T Consensus 9 ~~~~g~i~ip~~~r~~l~~~~g~~~~~~~~ 38 (136)
T PRK08577 9 VDSKGRITIPLEIREALGIREGMYVLLIAD 38 (136)
T ss_pred ECcCCeEEecHHHHHHcCcCCCCEEEEEEE
Confidence 357899999999999999999999888744
No 85
>PRK09974 putative regulator PrlF; Provisional
Probab=22.49 E-value=1.1e+02 Score=27.70 Aligned_cols=46 Identities=13% Similarity=-0.055 Sum_probs=34.7
Q ss_pred ecCCcEeccHhhHhhcCCCCCCcEEEEEee---e-------------ccCCHHHHHhhcccc
Q psy1724 76 ADEGKVYLPYWCFSVSMFPGNEREDVERGG---K-------------IIMPPSALEQLTRLN 121 (473)
Q Consensus 76 AeEG~v~LP~wmm~nL~l~~~~~v~ie~~~---l-------------I~n~KavLE~~Lr~~ 121 (473)
...|++-+|.-+-+.|++..|+.|..+... . |-.+-.+||+-.+++
T Consensus 15 TsKGQvTIPk~IR~~Lgl~~GdkI~f~i~~dG~V~i~~~~~~~~Dp~ig~FL~fLa~Di~~~ 76 (111)
T PRK09974 15 TDRGQTTVPAPVRKALKLKKRDSIHYEILPGGQVFICRLGDEEEDPVLGAFLDFLAADIQNN 76 (111)
T ss_pred ecCCCEeccHHHHHHcCCCCCCEEEEEEeCCCEEEEEECCCCCCCchHHHHHHHHHHHHHhC
Confidence 468999999999999999999988876431 1 445566666666554
No 86
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=22.45 E-value=74 Score=31.74 Aligned_cols=32 Identities=19% Similarity=0.208 Sum_probs=23.5
Q ss_pred CeEE-EEEeeeEecCCcEeccHhhHhhcCCCCCCcEEEEE
Q psy1724 65 RITH-SGVLEFVADEGKVYLPYWCFSVSMFPGNEREDVER 103 (473)
Q Consensus 65 ~~th-~GVLEF~AeEG~v~LP~wmm~nL~l~~~~~v~ie~ 103 (473)
+..| ..|+|++|+ -.+-+.|.|.+||.|.|+.
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 3444 566666554 4578899999999999986
No 87
>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=21.90 E-value=99 Score=26.07 Aligned_cols=29 Identities=17% Similarity=-0.088 Sum_probs=25.1
Q ss_pred ecCCcEeccHhhHhhcCCCCCCcEEEEEe
Q psy1724 76 ADEGKVYLPYWCFSVSMFPGNEREDVERG 104 (473)
Q Consensus 76 AeEG~v~LP~wmm~nL~l~~~~~v~ie~~ 104 (473)
..+..|+|.+=-++.|++++||.|.|+..
T Consensus 32 ~~~~~v~in~~dA~~lgi~~Gd~V~v~~~ 60 (116)
T cd02790 32 APEEYVEINPEDAKRLGIEDGEKVRVSSR 60 (116)
T ss_pred CCCcEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 45677999999999999999999998874
No 88
>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=21.55 E-value=1.3e+02 Score=26.37 Aligned_cols=25 Identities=28% Similarity=0.278 Sum_probs=21.5
Q ss_pred ecccCCEEEEEECCEEEEEEEEEec
Q psy1724 341 CLTSGDMIAINYNSKIYELCVLETK 365 (473)
Q Consensus 341 tLT~GD~I~I~yn~~~Y~l~V~e~k 365 (473)
.|.+||.|.|...++.|...|.+++
T Consensus 64 ~l~~Gd~v~v~~~~~~~~Y~V~~~~ 88 (128)
T cd00004 64 NLKKGDKIYLTDGGKTYVYKVTSIL 88 (128)
T ss_pred HCCCCCEEEEEECCEEEEEEEEEEE
Confidence 4566999999999999999998764
No 89
>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=21.34 E-value=1.3e+02 Score=26.56 Aligned_cols=25 Identities=28% Similarity=0.397 Sum_probs=21.0
Q ss_pred ecccCCEEEEEECCEEEEEEEEEec
Q psy1724 341 CLTSGDMIAINYNSKIYELCVLETK 365 (473)
Q Consensus 341 tLT~GD~I~I~yn~~~Y~l~V~e~k 365 (473)
.|.+||.|.|...++.|...|.+.+
T Consensus 63 ~l~~Gd~I~l~~~~~~~~Y~V~~~~ 87 (127)
T cd06165 63 KVKVGDKIYLTDKDNVYEYKVTSKK 87 (127)
T ss_pred HCcCCCEEEEEECCEEEEEEEeeEE
Confidence 3458999999999999999998654
No 90
>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=21.14 E-value=1.4e+02 Score=28.75 Aligned_cols=35 Identities=14% Similarity=0.204 Sum_probs=30.0
Q ss_pred EEeeeEecCCcEeccHhhHhhcCCCCCCcEEEEEe
Q psy1724 70 GVLEFVADEGKVYLPYWCFSVSMFPGNEREDVERG 104 (473)
Q Consensus 70 GVLEF~AeEG~v~LP~wmm~nL~l~~~~~v~ie~~ 104 (473)
|+.==+.+.|+|.+|--|-+.|++.+||.|++...
T Consensus 4 g~v~~id~~Gri~iP~~iR~~l~i~~gd~~~~~~~ 38 (180)
T TIGR02851 4 GIVRRIDDLGRVVIPKEIRRTLRIREGDPLEIFTD 38 (180)
T ss_pred ceEEEECCCCcEEEeHHHHHHcCCCCCCeEEEEEe
Confidence 45555678999999999999999999999988654
No 91
>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=20.62 E-value=1.2e+02 Score=27.73 Aligned_cols=27 Identities=19% Similarity=0.201 Sum_probs=24.2
Q ss_pred CCcEEcCHHHHhhcCCCCCCeEEEEEe
Q psy1724 279 EGKVYLPYWMMRNLLLDEGELVNIESV 305 (473)
Q Consensus 279 EG~v~LP~WMm~~L~l~egd~V~I~~v 305 (473)
+..|+|-.=-.+.|||++||.|+|.+-
T Consensus 37 ~~~v~InP~dA~~lGI~dGD~V~V~s~ 63 (137)
T cd02784 37 DNAALVSPRTAEALGLLQGDVVRIRRG 63 (137)
T ss_pred CceEEECHHHHHHcCCCCCCEEEEEeC
Confidence 567999999999999999999999864
No 92
>PRK09798 antitoxin MazE; Provisional
Probab=20.11 E-value=1.2e+02 Score=25.63 Aligned_cols=40 Identities=13% Similarity=0.084 Sum_probs=30.5
Q ss_pred EeccHhhHhhcCCCCCCcEEEEEee--e----c-cCCHHHHHhhccc
Q psy1724 81 VYLPYWCFSVSMFPGNEREDVERGG--K----I-IMPPSALEQLTRL 120 (473)
Q Consensus 81 v~LP~wmm~nL~l~~~~~v~ie~~~--l----I-~n~KavLE~~Lr~ 120 (473)
+-||.=+++.|++..|+.|.|+... + + ..+++-||..|..
T Consensus 15 vRIPk~~l~~l~l~~g~~vei~v~~~~iiI~p~~~~~r~~l~eLla~ 61 (82)
T PRK09798 15 VRIPATLMQALNLNIDDEVKIDLVDGKLIIEPVRKEPVFTLAELVND 61 (82)
T ss_pred EEcCHHHHHHcCCCCCCEEEEEEECCEEEEEECCCCCCCCHHHHHhc
Confidence 6899999999999999998888763 3 2 2345667777754
Done!