Query 047222
Match_columns 342
No_of_seqs 219 out of 350
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 08:58:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047222.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047222hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1816 Ubiquitin fusion-degra 100.0 1.7E-98 4E-103 711.4 26.9 293 6-342 10-305 (308)
2 COG5140 UFD1 Ubiquitin fusion- 100.0 6.1E-78 1.3E-82 562.4 20.4 286 7-341 19-310 (331)
3 PF03152 UFD1: Ubiquitin fusio 100.0 1.4E-73 3E-78 513.1 18.2 173 9-181 1-176 (176)
4 PLN03086 PRLI-interacting fact 100.0 2.4E-59 5.3E-64 479.8 21.9 174 6-186 74-263 (567)
5 KOG0735 AAA+-type ATPase [Post 96.1 0.079 1.7E-06 58.0 12.8 145 33-180 17-166 (952)
6 PF02933 CDC48_2: Cell divisio 96.1 0.031 6.8E-07 42.3 7.3 48 129-177 10-58 (64)
7 TIGR01243 CDC48 AAA family ATP 95.5 0.31 6.8E-06 52.6 14.6 133 29-168 15-150 (733)
8 PF09262 PEX-1N: Peroxisome bi 91.5 0.16 3.5E-06 41.0 2.7 74 107-180 1-80 (80)
9 TIGR01439 lp_hng_hel_AbrB loop 83.4 4.8 0.0001 27.3 5.7 39 74-115 4-42 (43)
10 PF04014 Antitoxin-MazE: Antid 77.1 4.8 0.0001 28.6 4.1 39 75-116 5-43 (47)
11 PF07497 Rho_RNA_bind: Rho ter 76.3 1.5 3.2E-05 35.5 1.4 26 76-101 28-53 (78)
12 PF02359 CDC48_N: Cell divisio 75.9 36 0.00078 27.0 9.3 68 29-102 14-84 (87)
13 PF02359 CDC48_N: Cell divisio 75.8 2.1 4.5E-05 34.2 2.2 69 75-148 14-82 (87)
14 cd04459 Rho_CSD Rho_CSD: Rho p 72.4 4 8.6E-05 32.1 2.9 27 74-100 24-50 (68)
15 TIGR02609 doc_partner putative 71.7 8.2 0.00018 30.3 4.6 55 77-137 10-66 (74)
16 cd02790 MopB_CT_Formate-Dh_H F 70.3 6 0.00013 32.0 3.7 29 74-102 32-60 (116)
17 PRK09521 exosome complex RNA-b 69.8 15 0.00032 33.4 6.5 124 30-159 4-141 (189)
18 PRK14132 riboflavin kinase; Pr 68.4 4.8 0.0001 35.3 2.9 31 63-100 94-125 (126)
19 COG1935 Uncharacterized conser 67.9 9.7 0.00021 33.3 4.6 47 37-109 11-60 (122)
20 PRK09974 putative regulator Pr 61.2 27 0.00059 30.1 6.1 59 74-135 15-75 (111)
21 PF01982 CTP-dep_RFKase: Domai 60.9 10 0.00022 33.1 3.5 18 83-100 103-120 (121)
22 cd02787 MopB_CT_ydeP The MopB_ 60.8 14 0.00031 30.1 4.2 29 75-103 29-57 (112)
23 cd02786 MopB_CT_3 The MopB_CT_ 60.6 11 0.00025 30.6 3.6 30 74-103 28-57 (116)
24 PRK09798 antitoxin MazE; Provi 58.1 23 0.0005 28.7 4.9 50 78-137 14-63 (82)
25 COG2002 AbrB Regulators of sta 56.9 18 0.00039 29.2 4.1 42 74-117 11-52 (89)
26 PF13550 Phage-tail_3: Putativ 56.3 13 0.00028 31.6 3.4 27 136-162 137-163 (164)
27 PRK11347 antitoxin ChpS; Provi 55.7 32 0.0007 27.9 5.3 48 78-137 13-60 (83)
28 cd02776 MopB_CT_Nitrate-R-NarG 54.7 21 0.00045 31.1 4.4 33 70-102 24-56 (141)
29 cd02788 MopB_CT_NDH-1_NuoG2-N7 53.8 20 0.00043 28.8 3.9 34 69-102 21-54 (96)
30 cd02792 MopB_CT_Formate-Dh-Na- 53.7 13 0.00028 30.4 2.8 28 74-101 32-59 (122)
31 COG1339 Transcriptional regula 53.6 14 0.00031 35.1 3.3 19 83-101 194-212 (214)
32 PRK15095 FKBP-type peptidyl-pr 51.9 50 0.0011 29.4 6.4 92 69-182 34-129 (156)
33 PRK08577 hypothetical protein; 51.4 20 0.00044 30.7 3.8 44 74-119 10-53 (136)
34 TIGR02851 spore_V_T stage V sp 51.0 25 0.00054 32.2 4.5 46 68-116 4-49 (180)
35 cd00508 MopB_CT_Fdh-Nap-like T 50.6 22 0.00048 28.7 3.7 27 75-101 33-59 (120)
36 cd02789 MopB_CT_FmdC-FwdD The 50.5 16 0.00035 30.1 2.9 29 74-102 28-56 (106)
37 smart00553 SEP Domain present 50.5 13 0.00028 31.0 2.3 16 240-255 72-87 (93)
38 COG1188 Ribosome-associated he 48.7 26 0.00055 29.8 3.8 25 138-162 48-72 (100)
39 cd02775 MopB_CT Molybdopterin- 48.7 23 0.0005 27.6 3.5 28 75-102 21-48 (101)
40 COG1153 FwdD Formylmethanofura 48.4 15 0.00034 32.3 2.5 29 73-101 27-55 (128)
41 cd02785 MopB_CT_4 The MopB_CT_ 48.3 24 0.00053 29.3 3.7 28 75-102 30-57 (124)
42 cd02781 MopB_CT_Acetylene-hydr 47.1 24 0.00052 29.3 3.5 29 75-103 31-59 (130)
43 cd02791 MopB_CT_Nitrate-R-NapA 46.4 27 0.00058 28.5 3.6 28 75-102 33-60 (122)
44 PF01568 Molydop_binding: Moly 46.3 25 0.00054 28.1 3.4 26 76-101 28-54 (110)
45 cd04456 S1_IF1A_like S1_IF1A_l 46.2 21 0.00046 28.6 2.9 24 77-100 25-48 (78)
46 cd02777 MopB_CT_DMSOR-like The 46.2 25 0.00055 29.3 3.5 26 76-101 33-58 (127)
47 COG2336 MazE Growth regulator 46.2 22 0.00048 29.2 3.0 34 79-115 14-47 (82)
48 PF01191 RNA_pol_Rpb5_C: RNA p 45.7 42 0.00091 26.9 4.5 31 83-113 41-71 (74)
49 PF04322 DUF473: Protein of un 44.8 28 0.00061 30.4 3.6 47 36-108 10-59 (119)
50 cd02778 MopB_CT_Thiosulfate-R- 43.4 33 0.00072 28.0 3.8 29 73-101 26-54 (123)
51 cd02782 MopB_CT_1 The MopB_CT_ 43.1 30 0.00066 28.7 3.5 29 74-102 30-58 (129)
52 cd02794 MopB_CT_DmsA-EC The Mo 42.9 31 0.00067 28.5 3.5 28 76-103 29-56 (121)
53 cd05705 S1_Rrp5_repeat_hs14 S1 42.8 32 0.00069 26.6 3.3 65 91-164 1-67 (74)
54 COG0243 BisC Anaerobic dehydro 42.8 38 0.00083 36.9 5.1 31 73-103 667-697 (765)
55 PRK14165 winged helix-turn-hel 42.5 21 0.00045 33.9 2.7 39 63-101 158-215 (217)
56 TIGR03243 arg_catab_AOST argin 42.1 33 0.00071 34.8 4.1 34 67-100 300-333 (335)
57 cd02779 MopB_CT_Arsenite-Ox Th 41.6 37 0.00081 27.9 3.8 29 74-102 30-58 (115)
58 PRK09570 rpoH DNA-directed RNA 41.2 37 0.0008 27.7 3.5 30 84-113 45-74 (79)
59 PRK10737 FKBP-type peptidyl-pr 38.9 95 0.0021 29.1 6.4 94 68-183 30-126 (196)
60 cd02793 MopB_CT_DMSOR-BSOR-TMA 38.8 39 0.00085 28.4 3.6 29 74-102 30-58 (129)
61 cd02783 MopB_CT_2 The MopB_CT_ 37.6 41 0.00088 29.6 3.6 32 74-108 29-60 (156)
62 cd05829 Sortase_E Sortase E (S 37.4 45 0.00097 29.1 3.8 27 135-161 69-96 (144)
63 cd06166 Sortase_D_5 Sortase D 37.4 49 0.0011 28.0 3.9 31 132-162 58-88 (126)
64 PF03459 TOBE: TOBE domain; I 36.2 41 0.00088 24.6 2.9 23 79-101 35-57 (64)
65 TIGR02227 sigpep_I_bact signal 35.5 1.8E+02 0.004 25.6 7.4 41 136-176 49-91 (163)
66 cd02780 MopB_CT_Tetrathionate_ 35.2 50 0.0011 28.2 3.7 28 74-101 27-54 (143)
67 TIGR03244 arg_catab_AstA argin 34.3 52 0.0011 33.4 4.1 46 54-100 289-334 (336)
68 PRK10456 arginine succinyltran 34.2 52 0.0011 33.5 4.1 47 54-101 290-336 (344)
69 TIGR03245 arg_AOST_alph argini 32.9 55 0.0012 33.2 4.1 32 69-100 302-334 (336)
70 PF00717 Peptidase_S24: Peptid 32.0 2E+02 0.0043 20.9 7.1 33 138-170 24-57 (70)
71 KOG2086 Protein tyrosine phosp 30.6 27 0.00058 36.0 1.5 16 238-253 252-267 (380)
72 cd05828 Sortase_D_4 Sortase D 30.1 82 0.0018 26.6 4.2 30 133-162 56-85 (127)
73 PF12148 DUF3590: Protein of u 28.9 32 0.0007 28.4 1.4 21 131-151 58-78 (85)
74 cd05830 Sortase_D_5 Sortase D 28.7 80 0.0017 27.1 3.9 30 133-162 60-89 (137)
75 TIGR01076 sortase_fam LPXTG-si 27.9 78 0.0017 27.2 3.7 24 138-161 63-86 (136)
76 PLN03086 PRLI-interacting fact 27.8 2.9E+02 0.0063 30.1 8.6 72 29-102 149-227 (567)
77 cd05706 S1_Rrp5_repeat_sc10 S1 26.5 99 0.0021 23.0 3.6 56 91-148 1-57 (73)
78 PF04958 AstA: Arginine N-succ 26.4 81 0.0018 32.1 4.0 48 52-100 292-340 (342)
79 COG0836 {ManC} Mannose-1-phosp 26.2 1.6E+02 0.0034 30.1 5.9 76 95-173 245-326 (333)
80 PF01176 eIF-1a: Translation i 26.2 88 0.0019 23.8 3.3 24 78-101 29-52 (65)
81 PRK08059 general stress protei 25.8 1.2E+02 0.0026 25.7 4.4 59 85-148 1-61 (123)
82 cd02784 MopB_CT_PHLH The MopB_ 25.5 94 0.002 27.2 3.8 27 76-102 37-63 (137)
83 cd00004 Sortase Sortases are c 25.4 1E+02 0.0022 25.8 3.9 25 138-162 64-88 (128)
84 PF11302 DUF3104: Protein of u 25.3 1.7E+02 0.0037 23.8 4.8 48 136-183 3-75 (75)
85 PF10636 hemP: Hemin uptake pr 25.1 1.5E+02 0.0033 21.1 4.0 22 139-160 9-30 (38)
86 cd06165 Sortase_A_1 Sortase A 24.6 1E+02 0.0022 25.9 3.8 24 139-162 64-87 (127)
87 PF11717 Tudor-knot: RNA bindi 24.0 1.1E+02 0.0025 22.4 3.5 27 139-165 1-28 (55)
88 PF01272 GreA_GreB: Transcript 23.8 1.2E+02 0.0027 23.5 3.8 24 139-162 53-76 (77)
89 cd05704 S1_Rrp5_repeat_hs13 S1 23.2 87 0.0019 23.8 2.8 56 91-149 1-59 (72)
90 PRK05807 hypothetical protein; 23.1 2.5E+02 0.0053 24.5 5.9 55 90-148 2-58 (136)
91 cd05793 S1_IF1A S1_IF1A: Trans 23.0 1.1E+02 0.0024 24.4 3.5 24 77-100 25-48 (77)
92 TIGR02693 arsenite_ox_L arseni 22.7 1E+02 0.0022 34.3 4.3 30 73-102 721-750 (806)
93 PRK09376 rho transcription ter 22.4 1.4E+02 0.003 31.3 4.9 39 63-101 48-101 (416)
94 PRK13532 nitrate reductase cat 22.1 85 0.0018 34.8 3.5 51 49-102 713-771 (830)
95 PF00667 FAD_binding_1: FAD bi 21.5 1.3E+02 0.0028 27.6 4.1 87 49-137 6-121 (219)
96 TIGR01243 CDC48 AAA family ATP 20.9 1E+02 0.0022 33.7 3.7 70 76-149 16-85 (733)
97 PRK10183 hypothetical protein; 20.8 1.3E+02 0.0029 23.1 3.3 22 139-160 27-48 (56)
98 PRK10348 ribosome-associated h 20.5 1.5E+02 0.0032 26.3 4.0 25 138-162 48-72 (133)
No 1
>KOG1816 consensus Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.7e-98 Score=711.44 Aligned_cols=293 Identities=51% Similarity=0.875 Sum_probs=241.6
Q ss_pred ccccccccEEEeeeecccCC---CCCCCCeEecCHHHHHHHHhcCCCCCeEEEEEeCCCCCEEEEEEeeeeeCCCcEecc
Q 047222 6 HDAAFERKYRCYPISFIDKP---HLENGDKIVMPPSALDRLAYLHIEYPMLFELSNTSAGRVTYCGVMEFIADEGLIYLP 82 (342)
Q Consensus 6 ~~~~F~~~~rcyp~s~~~k~---~~~~GdKIiLPpSaL~~L~~l~i~~PmlF~L~n~~~~r~th~GVLEF~AeEG~i~LP 82 (342)
+|..|+++|||||++|+..+ ++++|||||||||||++|+++||.|||+|+|+|.+..|+||||||||+||||+||||
T Consensus 10 ~g~~f~~~yrcy~~~~l~~~~~s~~~~GgKIilPPSaL~~Ls~lnI~yPMlFkLtn~~~~r~THcGVLEF~AeEG~vyLP 89 (308)
T KOG1816|consen 10 RGFQFETSYRCYPVSFLPGPDRSDVNKGGKIILPPSALDRLSSLNITYPMLFKLTNVDVDRVTHCGVLEFTAEEGRVYLP 89 (308)
T ss_pred CCcceeeeeEecccccccCccccccccCCeEEeCHHHHHHHHHhcCCCceEEEEeccccceeeeeeEEEEEecCceEEee
Confidence 46779999999999999654 999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcCCCCCCEEEEEEeecCCcceEEEeeCCcCcCCcCCcHHHHHHhhccCeeccCCCEEEEeeCCEEEEEEEEeec
Q 047222 83 YWMMENMLLQEGDIVEVKNASLAKGSYVKLQPHTKDFLDISNPKAVLETTLRSYSCLTTGDTIMVPYNNKKYYINVVETK 162 (342)
Q Consensus 83 ~WMm~~L~l~~gd~V~i~~~~LPkGt~vkLqP~s~~FldisnpKavLE~~LRnystLT~Gd~I~I~yn~~~y~l~V~e~k 162 (342)
+|||++|+|+|||+|+|++++||+||||||||||.|||||+|||||||++||||+|||+||+|+|+||++.|+|+|+|+|
T Consensus 90 ~WMmq~L~le~gdlv~i~~v~lpkgtyvKLqP~s~dFLDItNpKAvLE~~LRn~acLT~gDvi~i~Yn~k~y~i~V~e~k 169 (308)
T KOG1816|consen 90 YWMMQNLLLEEGDLVRIRSVTLPKGTYVKLQPHSVDFLDITNPKAVLENALRNYACLTTGDVILINYNEKTYELKVVETK 169 (308)
T ss_pred hHhhhhccCCCCCeEEEEEeeccccceeeeccCCCCccccCChHHHHHHHHhhccccccCCEEEEecCCeEEEEEEEEec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCeeEEEecceeEeecCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccc
Q 047222 163 PSTAVSIIETDCEVDFIPPLDFKEPEKPSSSSLSNRTLPEVKEEPPLDFKGPEKPSSSSLSNRTPPEVKEEPPKKIAKFS 242 (342)
Q Consensus 163 P~~aVsIIdTDleVDf~pPldy~ep~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~ 242 (342)
|++|||||||||+|||+||+||+||+++.++....++..++ . .. +....... +.+|+
T Consensus 170 Pa~aVsIiEtD~~VDF~pP~gyke~~~~~~~~~~~k~~~~~-----------v--------~~--~ag~~~~~--e~~~~ 226 (308)
T KOG1816|consen 170 PANAVSIIETDLNVDFDPPLGYKEPERQVAPAEKAKGEAEV-----------V--------GS--YAGYKNVI--ENKVE 226 (308)
T ss_pred CCceeEEEEcceeecccCCcCccCcccccChhhccccccee-----------e--------cc--cccccccc--cccee
Confidence 99999999999999999999999999985443220000000 0 00 11101111 67899
Q ss_pred cceeeceecCCCcCCCCCCCCCCCCCCCcccCcCCCCCCCCCCCCCCCCCCCeEEEccCCCCCCCCCCcccCCCCCCCCC
Q 047222 243 PFTGSGRCLNGKSSTQPTVSPSSPLIDNPQQNAANGINGSKSSSASSRQKSGKLVFGSNANQSSNGTPKVLPKSSSGEPP 322 (342)
Q Consensus 243 ~F~G~G~rLdGK~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gkl~Fg~~~~~~~~~~~~~~~~~~~~~~~ 322 (342)
+|+|+|+|||||+...+.++ .|+... ......+..++++.|+|+||+|.....+ ..+|++
T Consensus 227 ~f~gsg~rLdgK~~~~e~~~--~pv~~~---------~~~~~~~~~~d~~~G~l~F~~~~~~~~~---------~~~E~~ 286 (308)
T KOG1816|consen 227 PFTGSGRRLDGKKKVEEVSK--HPVKNG---------DLIQRGVPNHDFKLGKLVFGRNVDPLKK---------ESEEKE 286 (308)
T ss_pred eeccccceecccccccccCC--CcccCc---------ccccCCCCccccCCceEEEecCCCcccc---------ccchhh
Confidence 99999999999988766432 222111 0112344556999999999999532211 122212
Q ss_pred CCCCCCCcccccccccccCC
Q 047222 323 QVEEKPKFQAFTGKKYSLRG 342 (342)
Q Consensus 323 ~~~~~~~f~aF~G~g~sLr~ 342 (342)
....++|++|+|+|+||||
T Consensus 287 -a~k~~~~~~F~G~~~slr~ 305 (308)
T KOG1816|consen 287 -AGKDSKFEAFSGAGYSLRK 305 (308)
T ss_pred -cccccceeEecCCceeccc
Confidence 2333899999999999996
No 2
>COG5140 UFD1 Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.1e-78 Score=562.39 Aligned_cols=286 Identities=36% Similarity=0.589 Sum_probs=238.6
Q ss_pred cccccccEEEeeeecc---cCCCCCCCCeEecCHHHHHHHHhcCCCCCeEEEEEeCCCCCEEEEEEeeeeeCCCcEeccH
Q 047222 7 DAAFERKYRCYPISFI---DKPHLENGDKIVMPPSALDRLAYLHIEYPMLFELSNTSAGRVTYCGVMEFIADEGLIYLPY 83 (342)
Q Consensus 7 ~~~F~~~~rcyp~s~~---~k~~~~~GdKIiLPpSaL~~L~~l~i~~PmlF~L~n~~~~r~th~GVLEF~AeEG~i~LP~ 83 (342)
-+.|.+.|||||++|+ .++++++|+|||||||||..|+++||.|||+|+|++..+.++||||||||+||||.||||+
T Consensus 19 ~q~F~e~~rcyp~am~~d~~r~n~NfGGKvilPpSaL~kLs~lni~yPmlF~~s~~~~~~~THgGVLEFiaEEGrVylP~ 98 (331)
T COG5140 19 FQLFGEKPRCYPRAMKFDGCRQNANFGGKVILPPSALVKLSSLNIQYPMLFEISHSDGIYRTHGGVLEFIAEEGRVYLPS 98 (331)
T ss_pred hhhhccCccceeeecccCccccCCCcCceEEcCHHHHHHHHhhccCCceEEEEecccceeEecccEEEEeecCCcEeehH
Confidence 4789999999999997 3578999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHcCCCCCCEEEEEEeecCCcceEEEeeCCcCcCCcCCcHHHHHHhhccCeeccCCCEEEEeeCCEEEEEEEEeecC
Q 047222 84 WMMENMLLQEGDIVEVKNASLAKGSYVKLQPHTKDFLDISNPKAVLETTLRSYSCLTTGDTIMVPYNNKKYYINVVETKP 163 (342)
Q Consensus 84 WMm~~L~l~~gd~V~i~~~~LPkGt~vkLqP~s~~FldisnpKavLE~~LRnystLT~Gd~I~I~yn~~~y~l~V~e~kP 163 (342)
|||++|.+++||+|+|+|.++|.|+||||+|||.|||||+|||||||++||||+|||+||+|.|.||++.|.|++++++|
T Consensus 99 WMm~tLs~epgdlv~~~~td~plG~fVKL~PqSVdFLdI~dpkavLEn~LRNfstLt~~D~iei~ynd~v~~Ik~~~v~p 178 (331)
T COG5140 99 WMMQTLSMEPGDLVVLRYTDFPLGKFVKLIPQSVDFLDIEDPKAVLENCLRNFSTLTEGDEIEIQYNDEVGSIKFTVVHP 178 (331)
T ss_pred HHHHhccCCCCcEEEEEeccccccceEEecccccceEeccChHHHHHHHHhhccccccCCEEEEEECCeeeEEEEEEecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred C---CeeEEEecceeEeecCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCc
Q 047222 164 S---TAVSIIETDCEVDFIPPLDFKEPEKPSSSSLSNRTLPEVKEEPPLDFKGPEKPSSSSLSNRTPPEVKEEPPKKIAK 240 (342)
Q Consensus 164 ~---~aVsIIdTDleVDf~pPldy~ep~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 240 (342)
+ ++||||||||.|||+||+||+|+..+...... +. -.++|+..|.+..-... .+
T Consensus 179 e~S~~~i~vveTDLvvDF~pPiGy~e~~qq~ke~n~------------~g-------vqgtm~t~I~y~~~~~~----~~ 235 (331)
T COG5140 179 EPSANAIYVVETDLVVDFLPPIGYKEKAQQDKERNS------------FG-------VQGTMATYIEYIDSSHD----VK 235 (331)
T ss_pred CCCcceEEEEecceeeeccCCccccchhhhhhhhcc------------cc-------ccceeEEEEeeeccccc----cc
Confidence 6 89999999999999999999998433221110 00 12455566666432221 12
Q ss_pred cccceeeceecCCCcCCCCCCCCCCCCCCCcccCcCCCCCCCCCCCCCCCCCCCeEEEccCCCCCCCCCCcccCCCCCCC
Q 047222 241 FSPFTGSGRCLNGKSSTQPTVSPSSPLIDNPQQNAANGINGSKSSSASSRQKSGKLVFGSNANQSSNGTPKVLPKSSSGE 320 (342)
Q Consensus 241 f~~F~G~G~rLdGK~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gkl~Fg~~~~~~~~~~~~~~~~~~~~~ 320 (342)
-.--.|.|..|.||..+..+... +.+ -.-++.|+++++|.|+||||++ .++|+.+ +|
T Consensus 236 ~~lmKg~G~~l~gk~~~~~pk~~---------i~d----~~~~~~pa~l~lp~g~~ffg~p---------~~~p~~d-ee 292 (331)
T COG5140 236 PILMKGLGLYLYGKVDKAEPKQD---------IKD----MKIDGEPAKLDLPEGQLFFGFP---------MVLPKED-EE 292 (331)
T ss_pred hhhhhcccceecccccccccccc---------hhh----hhccCCcccccccCcceEeccc---------cccCccc-hh
Confidence 24456999999999887653321 111 1125789999999999999999 5566532 22
Q ss_pred CCCCCCCCCcccccccccccC
Q 047222 321 PPQVEEKPKFQAFTGKKYSLR 341 (342)
Q Consensus 321 ~~~~~~~~~f~aF~G~g~sLr 341 (342)
. ...+.-+-|+|+|-|||
T Consensus 293 -s--~~~~~~~~fqg~g~slr 310 (331)
T COG5140 293 -S--AAKSSEQNFQGQGISLR 310 (331)
T ss_pred -h--ccCchhhccccCceeee
Confidence 2 33466667999999998
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=1.4e-73 Score=513.15 Aligned_cols=173 Identities=66% Similarity=1.121 Sum_probs=150.0
Q ss_pred cccccEEEeeeecc---cCCCCCCCCeEecCHHHHHHHHhcCCCCCeEEEEEeCCCCCEEEEEEeeeeeCCCcEeccHHH
Q 047222 9 AFERKYRCYPISFI---DKPHLENGDKIVMPPSALDRLAYLHIEYPMLFELSNTSAGRVTYCGVMEFIADEGLIYLPYWM 85 (342)
Q Consensus 9 ~F~~~~rcyp~s~~---~k~~~~~GdKIiLPpSaL~~L~~l~i~~PmlF~L~n~~~~r~th~GVLEF~AeEG~i~LP~WM 85 (342)
+|+++|||||++|+ +++++++||||+||||||++|.+++++|||+|+|+|..++++||||||||+|+||+||||+||
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 59999999999999 899999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHcCCCCCCEEEEEEeecCCcceEEEeeCCcCcCCcCCcHHHHHHhhccCeeccCCCEEEEeeCCEEEEEEEEeecCCC
Q 047222 86 MENMLLQEGDIVEVKNASLAKGSYVKLQPHTKDFLDISNPKAVLETTLRSYSCLTTGDTIMVPYNNKKYYINVVETKPST 165 (342)
Q Consensus 86 m~~L~l~~gd~V~i~~~~LPkGt~vkLqP~s~~FldisnpKavLE~~LRnystLT~Gd~I~I~yn~~~y~l~V~e~kP~~ 165 (342)
|++|++++||.|+|++++||||||||||||+.+|++|+|||||||++||||+|||+||+|.|+|+++.|+|+|+|++|++
T Consensus 81 m~~L~l~~g~~V~v~~~~LPkgt~vkLqP~~~~F~~i~n~KavLE~~Lr~ystLT~Gd~I~i~~~~~~y~l~V~e~kP~~ 160 (176)
T PF03152_consen 81 MQNLGLQEGDIVRVEYVSLPKGTFVKLQPQSSDFLDISNPKAVLERALRNYSTLTKGDTISIEYNNKTYELDVVEVKPEN 160 (176)
T ss_dssp HHHHT--TTEEEEEEEEE----SEEEEEESCHHHHCSS-HHHHHHHHHCC-SEEETTSEEEEECTTEEEEEEEEEECSSS
T ss_pred HhhcCCCCCCEEEEEEeECCCCCEEEEeECCCccccccchHHHHHhhcccCceeecCCEEEEEeCCEEEEEEEEEEcCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeEEEecceeEeecCC
Q 047222 166 AVSIIETDCEVDFIPP 181 (342)
Q Consensus 166 aVsIIdTDleVDf~pP 181 (342)
|||||||||+|||+||
T Consensus 161 aV~IidTDl~vDf~~P 176 (176)
T PF03152_consen 161 AVSIIDTDLEVDFEPP 176 (176)
T ss_dssp CEE-SSS-SEEEE---
T ss_pred EEEEEeCceEEEecCC
Confidence 9999999999999997
No 4
>PLN03086 PRLI-interacting factor K; Provisional
Probab=100.00 E-value=2.4e-59 Score=479.84 Aligned_cols=174 Identities=39% Similarity=0.626 Sum_probs=161.7
Q ss_pred ccccccccEEEeeeecccCCCCCCCCeEecCHHHHHHHHhcCC--CCCeEEEEEeC-----------CCCCEEEEEEeee
Q 047222 6 HDAAFERKYRCYPISFIDKPHLENGDKIVMPPSALDRLAYLHI--EYPMLFELSNT-----------SAGRVTYCGVMEF 72 (342)
Q Consensus 6 ~~~~F~~~~rcyp~s~~~k~~~~~GdKIiLPpSaL~~L~~l~i--~~PmlF~L~n~-----------~~~r~th~GVLEF 72 (342)
.|-.|.+.++. ++|. ..||||+||||||++|+++|+ .|||+|+|+|. ..+++||||||||
T Consensus 74 ~g~~~~~~~~~--~~~~-----~~GdKI~LPpSaL~~L~~~~~~~~~Pm~F~l~~~~~~~~~~~~~~~~~~~th~GVlEF 146 (567)
T PLN03086 74 RGIVFSRIFEA--VSFQ-----GNGDKIKLPPSCFTELSDQGAFDKGPLYFRLSVVHQEGSGEMKDTDSQKTTHSGVLEF 146 (567)
T ss_pred CCeEEEEEeec--cccC-----CCCCeEEcCHHHHHHHHhcCCCCCCCeEEEEeccccccccccccccCCcEEEEEEEEE
Confidence 45567777665 5555 599999999999999999998 89999999984 3478999999999
Q ss_pred eeCCCcEeccHHHHHHcCCCC---CCEEEEEEeecCCcceEEEeeCCcCcCCcCCcHHHHHHhhccCeeccCCCEEEEee
Q 047222 73 IADEGLIYLPYWMMENMLLQE---GDIVEVKNASLAKGSYVKLQPHTKDFLDISNPKAVLETTLRSYSCLTTGDTIMVPY 149 (342)
Q Consensus 73 ~AeEG~i~LP~WMm~~L~l~~---gd~V~i~~~~LPkGt~vkLqP~s~~FldisnpKavLE~~LRnystLT~Gd~I~I~y 149 (342)
+|+||.||||+|||++|++.+ |++|+|+++.||||||||||||+.+|+||+|||||||++||||+|||+||+|.|+|
T Consensus 147 ~A~EG~v~lP~wm~~~L~~~~~~~~~~v~v~~~~Lpkgt~vklqP~~~~f~di~npKavLE~~Lr~~stLT~Gd~i~i~~ 226 (567)
T PLN03086 147 TAEEGSVGLPPHVWSNLFPSDPPDVPLVEVRYIWLPKGTYAKLQPDGVGFSDLPNHKAVLETALRQHATLSEDDVLVVNY 226 (567)
T ss_pred EcCCCeEEcCHHHHhhcCCCCCCCCCeEEEEEeecCCCCEEEEeeccCCcCCcccHHHHHHHHhhcCccccCCCEEEEec
Confidence 999999999999999999974 89999999999999999999999999999999999999999999999999999999
Q ss_pred CCEEEEEEEEeecCCCeeEEEecceeEeecCCCCCCC
Q 047222 150 NNKKYYINVVETKPSTAVSIIETDCEVDFIPPLDFKE 186 (342)
Q Consensus 150 n~~~y~l~V~e~kP~~aVsIIdTDleVDf~pPldy~e 186 (342)
|++.|+|+|+|++|++|||||||||+|||+||.++.+
T Consensus 227 ~~~~y~~~V~ev~P~~aVsiieTDi~VDf~~p~~~~~ 263 (567)
T PLN03086 227 GQLTYKLKVLELKPASSVSVLETDIEVDIVGPDSVSN 263 (567)
T ss_pred CCEEEEEEEEEEcCCCeeEEEeCceEEEeccCCcchh
Confidence 9999999999999999999999999999999999743
No 5
>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=96.11 E-value=0.079 Score=58.00 Aligned_cols=145 Identities=18% Similarity=0.175 Sum_probs=111.8
Q ss_pred EecCHHHHHHHHhcCCCCCeEEEEEeCCCCCEEEEEEeeee-eCCCcEeccHHHHHHcCCCCCCEEEEEEe-ecCCcceE
Q 047222 33 IVMPPSALDRLAYLHIEYPMLFELSNTSAGRVTYCGVMEFI-ADEGLIYLPYWMMENMLLQEGDIVEVKNA-SLAKGSYV 110 (342)
Q Consensus 33 IiLPpSaL~~L~~l~i~~PmlF~L~n~~~~r~th~GVLEF~-AeEG~i~LP~WMm~~L~l~~gd~V~i~~~-~LPkGt~v 110 (342)
|.||...+..|....-.|++.-........+.-..| -|+ ..|..|-+=.-..+.|+|.+|+.|.++-+ ..++++-|
T Consensus 17 v~lP~ql~~ai~~~~~~~av~~v~~~~~~~~s~~~g--~~s~~se~~ieIn~~~A~~l~L~e~~~V~l~~~~~v~~~~~V 94 (952)
T KOG0735|consen 17 VNLPEQLLEAISEPVQNYAVQAVVSKNPIKKSWVFG--HGSGSSENVIEINRVYAHTLGLAENQEVKLSIIDHVHEATQV 94 (952)
T ss_pred hccHHHHHHHHhccccCceeEEEEcCCChhheeecc--cCCCCccceEEeehhhHhhccCCCCCeEEEEEcCCccceeEE
Confidence 568999998887665556655433322222333444 333 33667778888899999999999999976 79999999
Q ss_pred EEeeCCcCcCCcCCcHHH-HHHhhc-cCeeccCCCEEEEeeCCE-EEEEEEEeecCCCeeEEEecceeEeecC
Q 047222 111 KLQPHTKDFLDISNPKAV-LETTLR-SYSCLTTGDTIMVPYNNK-KYYINVVETKPSTAVSIIETDCEVDFIP 180 (342)
Q Consensus 111 kLqP~s~~FldisnpKav-LE~~LR-nystLT~Gd~I~I~yn~~-~y~l~V~e~kP~~aVsIIdTDleVDf~p 180 (342)
.+.|.++|=|+|-+--|+ ||..|- .+--+|. .+..|+++.. .-.|.|..+.|.-.+.=++++-+|=++|
T Consensus 95 ~VeP~TsdDWEIiElnA~~~e~~lL~Q~RIv~~-~~f~iwl~~~t~i~fqv~rl~Ps~~~gRl~~~Tev~VaP 166 (952)
T KOG0735|consen 95 EVEPVTSDDWEIIELNAEWLEENLLVQTRIVTP-EIFIIWLPSGTVIQFQVDRLIPSMLYGRLLRGTEVLVAP 166 (952)
T ss_pred EEeeccCccHHHHHhhHHHHhhhhhhheeeccc-ceeEEEEcCccEEEEEEeeeecccceeeecCCceEEEec
Confidence 999999988898776665 677666 5888999 8888888875 4568999999999898899999999887
No 6
>PF02933 CDC48_2: Cell division protein 48 (CDC48), domain 2; InterPro: IPR004201 This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the C terminus. The VAT-N domain found in AAA ATPases (IPR003959 from INTERPRO) is a substrate 185-residue recognition domain [].; GO: 0005524 ATP binding; PDB: 1QDN_B 1QCS_A 1CR5_C 3QQ8_A 3HU2_A 3HU1_E 3HU3_A 3QWZ_A 3TIW_B 3QQ7_A ....
Probab=96.10 E-value=0.031 Score=42.31 Aligned_cols=48 Identities=33% Similarity=0.535 Sum_probs=35.6
Q ss_pred HHHhhccCeeccCCCEEEEeeCCEEEEEEEEeecCCCeeEEE-ecceeEe
Q 047222 129 LETTLRSYSCLTTGDTIMVPYNNKKYYINVVETKPSTAVSII-ETDCEVD 177 (342)
Q Consensus 129 LE~~LRnystLT~Gd~I~I~yn~~~y~l~V~e~kP~~aVsII-dTDleVD 177 (342)
|-+.|.+ --|++||+|.|.+.++.+.|.|.+++|.+++.|- +|.+++.
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 4699999999999999999999999999866554 3445544
No 7
>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily. This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.
Probab=95.50 E-value=0.31 Score=52.65 Aligned_cols=133 Identities=20% Similarity=0.217 Sum_probs=94.0
Q ss_pred CCCeEecCHHHHHHHHhcCCCCCeEEEEEeCCCCCEEEEEEee-ee--eCCCcEeccHHHHHHcCCCCCCEEEEEEeecC
Q 047222 29 NGDKIVMPPSALDRLAYLHIEYPMLFELSNTSAGRVTYCGVME-FI--ADEGLIYLPYWMMENMLLQEGDIVEVKNASLA 105 (342)
Q Consensus 29 ~GdKIiLPpSaL~~L~~l~i~~PmlF~L~n~~~~r~th~GVLE-F~--AeEG~i~LP~WMm~~L~l~~gd~V~i~~~~LP 105 (342)
.-+.+-|.++++++|. +..==.-+|.. ..|.+.|-|.. .. ...|.|.|..-+.+++++..||.|.|+-+.++
T Consensus 15 ~~~~~~~~~~~~~~~~---~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (733)
T TIGR01243 15 GRGIVRIDRQTAARLG---VEPGDFVEIEK--GDRSVVAIVWPLRPDDEGRGIIRMDGYLRANAGVTIGDTVTVERAEVK 89 (733)
T ss_pred CCCeEeeCHHHHHhcC---CCCCCEEEEec--CCCceeEEEEecCccccCCCEEeecHHHHhhcCCCCCCeEEEeecCCC
Confidence 4577888999987773 32222444542 34456666664 22 24689999999999999999999999999999
Q ss_pred CcceEEEeeCCcCcCCcCCcHHHHHHhhccCeeccCCCEEEEeeCCEEEEEEEEeecCCCeeE
Q 047222 106 KGSYVKLQPHTKDFLDISNPKAVLETTLRSYSCLTTGDTIMVPYNNKKYYINVVETKPSTAVS 168 (342)
Q Consensus 106 kGt~vkLqP~s~~FldisnpKavLE~~LRnystLT~Gd~I~I~yn~~~y~l~V~e~kP~~aVs 168 (342)
.+..|.+.|.. ....-.+...++...|.+ ..|++||.|.+.+....+.+.|+++.|...+.
T Consensus 90 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~-~~~~~g~~~~~~~~~~~~~~~v~~~~p~~~~~ 150 (733)
T TIGR01243 90 EAKKVVLAPTQ-PIRFGRDFVDYVKEFLLG-KPISKGETVIVPVLEGALPFVVVSTQPAGFVY 150 (733)
T ss_pred ccceEeecccc-ccccccchHHHHHHHHcC-CCCCCCCEEEecccCcceeEEEEecCCCCcEE
Confidence 99999999953 111112223344444443 46899999999988878889999999965443
No 8
>PF09262 PEX-1N: Peroxisome biogenesis factor 1, N-terminal ; InterPro: IPR015342 This domain adopts a double psi beta-barrel fold, similar in structure to the Cdc48 N-terminal domain. It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation []. ; GO: 0005524 ATP binding, 0007031 peroxisome organization, 0005777 peroxisome; PDB: 1WLF_A.
Probab=91.54 E-value=0.16 Score=41.02 Aligned_cols=74 Identities=26% Similarity=0.303 Sum_probs=47.7
Q ss_pred cceEEEeeCCcCcCCc-CCcHHHHHHhhc-cCeeccCCCEEEEee-CCEEEEEEEEeecCCCe---eEEEecceeEeecC
Q 047222 107 GSYVKLQPHTKDFLDI-SNPKAVLETTLR-SYSCLTTGDTIMVPY-NNKKYYINVVETKPSTA---VSIIETDCEVDFIP 180 (342)
Q Consensus 107 Gt~vkLqP~s~~Fldi-snpKavLE~~LR-nystLT~Gd~I~I~y-n~~~y~l~V~e~kP~~a---VsIIdTDleVDf~p 180 (342)
++.|.+.|.+.|=++| +..-..||..|- .-.+++.|.++.|+- ++..-.|+|..+.|... ...+..|.||=++|
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 4678899998776564 344445676666 588999999999998 56788899999999866 78899999987765
No 9
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=83.36 E-value=4.8 Score=27.34 Aligned_cols=39 Identities=33% Similarity=0.511 Sum_probs=31.3
Q ss_pred eCCCcEeccHHHHHHcCCCCCCEEEEEEeecCCcceEEEeeC
Q 047222 74 ADEGLIYLPYWMMENMLLQEGDIVEVKNASLAKGSYVKLQPH 115 (342)
Q Consensus 74 AeEG~i~LP~WMm~~L~l~~gd~V~i~~~~LPkGt~vkLqP~ 115 (342)
.+.|.|.||.=+.+.|++.+||.+.|... +.| -+.|.|.
T Consensus 4 ~~kgri~iP~~~r~~l~~~~gd~~~i~~~--~~~-~l~l~p~ 42 (43)
T TIGR01439 4 DKKGQIVIPKEIREKLGLKEGDRLEVIRV--EDG-EIILRPA 42 (43)
T ss_pred CcCCeEEecHHHHHHcCcCCCCEEEEEEe--CCC-EEEEEEC
Confidence 45799999999999999999999988853 333 4666664
No 10
>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=77.13 E-value=4.8 Score=28.65 Aligned_cols=39 Identities=26% Similarity=0.478 Sum_probs=30.4
Q ss_pred CCCcEeccHHHHHHcCCCCCCEEEEEEeecCCcceEEEeeCC
Q 047222 75 DEGLIYLPYWMMENMLLQEGDIVEVKNASLAKGSYVKLQPHT 116 (342)
Q Consensus 75 eEG~i~LP~WMm~~L~l~~gd~V~i~~~~LPkGt~vkLqP~s 116 (342)
..+.|.||.=+++.|+|++||.|.|... ..| -+.|.|..
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 4578999999999999999999998866 333 57777753
No 11
>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=76.26 E-value=1.5 Score=35.51 Aligned_cols=26 Identities=23% Similarity=0.312 Sum_probs=19.2
Q ss_pred CCcEeccHHHHHHcCCCCCCEEEEEE
Q 047222 76 EGLIYLPYWMMENMLLQEGDIVEVKN 101 (342)
Q Consensus 76 EG~i~LP~WMm~~L~l~~gd~V~i~~ 101 (342)
+.-||+|.++.+.++|+.||.|.=.-
T Consensus 28 ~~DvYVs~~qIrrf~LR~GD~V~G~v 53 (78)
T PF07497_consen 28 PDDVYVSPSQIRRFGLRTGDLVEGQV 53 (78)
T ss_dssp TTSEEE-CCCCCCTT--TTEEEEEEE
T ss_pred CCCEEECHHHHHHcCCCCCCEEEEEE
Confidence 45689999999999999999987543
No 12
>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=75.94 E-value=36 Score=27.05 Aligned_cols=68 Identities=21% Similarity=0.148 Sum_probs=50.4
Q ss_pred CCCeEecCHHHHHHHHhcCCCCCeEEEEEeCCCCCEEEEEEeeeee---CCCcEeccHHHHHHcCCCCCCEEEEEEe
Q 047222 29 NGDKIVMPPSALDRLAYLHIEYPMLFELSNTSAGRVTYCGVMEFIA---DEGLIYLPYWMMENMLLQEGDIVEVKNA 102 (342)
Q Consensus 29 ~GdKIiLPpSaL~~L~~l~i~~PmlF~L~n~~~~r~th~GVLEF~A---eEG~i~LP~WMm~~L~l~~gd~V~i~~~ 102 (342)
..+-++|.|..+++ +.+..--+-.|.. .+.|+|=|+---. ..|.|-|-.-+.+++++.-||.|.|+-+
T Consensus 14 ~~n~v~v~~~~m~~---l~l~~gd~v~i~g---~~~tv~~v~~~~~~~~~~g~I~l~~~~R~n~~v~igd~V~V~~~ 84 (87)
T PF02359_consen 14 GTNCVRVSPEDMEE---LGLFPGDVVLISG---KRKTVAFVFPDRPDDSPPGVIRLSGIQRKNAGVSIGDRVTVRPY 84 (87)
T ss_dssp CTTEEEEEHHHHHC---TTT-TTEEEEEET---TTEEEEEEEEECCSTTCTTEEEE-HHHHHHCT--TTSEEEEEEE
T ss_pred CCCEEEEcHHHHHH---cCCCCccEEEEeC---CceEEEEEEECCCCCCCCCEEEECHHHHhhCCcCCCCEEEEEEC
Confidence 56789999998754 4566666777774 4458888876543 4799999999999999999999999865
No 13
>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=75.77 E-value=2.1 Score=34.19 Aligned_cols=69 Identities=20% Similarity=0.227 Sum_probs=46.2
Q ss_pred CCCcEeccHHHHHHcCCCCCCEEEEEEeecCCcceEEEeeCCcCcCCcCCcHHHHHHhhccCeeccCCCEEEEe
Q 047222 75 DEGLIYLPYWMMENMLLQEGDIVEVKNASLAKGSYVKLQPHTKDFLDISNPKAVLETTLRSYSCLTTGDTIMVP 148 (342)
Q Consensus 75 eEG~i~LP~WMm~~L~l~~gd~V~i~~~~LPkGt~vkLqP~s~~FldisnpKavLE~~LRnystLT~Gd~I~I~ 148 (342)
..|+++|..=.|+.|++.+||.|.|... +-|.+.+.|...+ +...=.--|-...|+..-+..||.|.|.
T Consensus 14 ~~n~v~v~~~~m~~l~l~~gd~v~i~g~---~~tv~~v~~~~~~--~~~~g~I~l~~~~R~n~~v~igd~V~V~ 82 (87)
T PF02359_consen 14 GTNCVRVSPEDMEELGLFPGDVVLISGK---RKTVAFVFPDRPD--DSPPGVIRLSGIQRKNAGVSIGDRVTVR 82 (87)
T ss_dssp CTTEEEEEHHHHHCTTT-TTEEEEEETT---TEEEEEEEEECCS--TTCTTEEEE-HHHHHHCT--TTSEEEEE
T ss_pred CCCEEEEcHHHHHHcCCCCccEEEEeCC---ceEEEEEEECCCC--CCCCCEEEECHHHHhhCCcCCCCEEEEE
Confidence 4689999999999999999999999872 2266777665332 1111111145677777888999999986
No 14
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=72.37 E-value=4 Score=32.12 Aligned_cols=27 Identities=22% Similarity=0.251 Sum_probs=23.1
Q ss_pred eCCCcEeccHHHHHHcCCCCCCEEEEE
Q 047222 74 ADEGLIYLPYWMMENMLLQEGDIVEVK 100 (342)
Q Consensus 74 AeEG~i~LP~WMm~~L~l~~gd~V~i~ 100 (342)
+.+.-||+|.++.+..+|+.||.|.=.
T Consensus 24 ~~~~DvyVs~~~Irr~~LR~GD~V~G~ 50 (68)
T cd04459 24 PGPDDIYVSPSQIRRFNLRTGDTVVGQ 50 (68)
T ss_pred CCCCCEEECHHHHHHhCCCCCCEEEEE
Confidence 345668999999999999999998764
No 15
>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=71.66 E-value=8.2 Score=30.30 Aligned_cols=55 Identities=22% Similarity=0.360 Sum_probs=37.5
Q ss_pred CcEeccHHHHHHcCCCCCCEEEEEEeecCCcceEEEeeCCc--CcCCcCCcHHHHHHhhccCe
Q 047222 77 GLIYLPYWMMENMLLQEGDIVEVKNASLAKGSYVKLQPHTK--DFLDISNPKAVLETTLRSYS 137 (342)
Q Consensus 77 G~i~LP~WMm~~L~l~~gd~V~i~~~~LPkGt~vkLqP~s~--~FldisnpKavLE~~LRnys 137 (342)
-.|-||.=+++.|+|.+||.|.|... +.-+.|.|... +|- .....+++..++.|-
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 35789999999999999999976543 33477778765 441 122235677766553
No 16
>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=70.31 E-value=6 Score=31.97 Aligned_cols=29 Identities=17% Similarity=0.204 Sum_probs=25.8
Q ss_pred eCCCcEeccHHHHHHcCCCCCCEEEEEEe
Q 047222 74 ADEGLIYLPYWMMENMLLQEGDIVEVKNA 102 (342)
Q Consensus 74 AeEG~i~LP~WMm~~L~l~~gd~V~i~~~ 102 (342)
..+..|+|-.=-++.|+|++||.|+|.+-
T Consensus 32 ~~~~~v~in~~dA~~lgi~~Gd~V~v~~~ 60 (116)
T cd02790 32 APEEYVEINPEDAKRLGIEDGEKVRVSSR 60 (116)
T ss_pred CCCcEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 45778999999999999999999999873
No 17
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=69.83 E-value=15 Score=33.43 Aligned_cols=124 Identities=15% Similarity=0.132 Sum_probs=73.7
Q ss_pred CCeEecCHHHHHHHHhcCCCCCeEEEEEeCCCCCEEEEEEeeeeeCCCcEeccHHHHHHcCCCCCCEEEEEEe-ecCCcc
Q 047222 30 GDKIVMPPSALDRLAYLHIEYPMLFELSNTSAGRVTYCGVMEFIADEGLIYLPYWMMENMLLQEGDIVEVKNA-SLAKGS 108 (342)
Q Consensus 30 GdKIiLPpSaL~~L~~l~i~~PmlF~L~n~~~~r~th~GVLEF~AeEG~i~LP~WMm~~L~l~~gd~V~i~~~-~LPkGt 108 (342)
..++.||=..|...... +..+=+|+.. ..-+.+++|.++...+...|.|=+|.-.....+.||+|.-+-+ ..++|=
T Consensus 4 ~~~~V~PGe~l~~~~e~-~~G~Gty~~~--~~i~as~~G~~~id~~~~~Isv~P~~~~~~~~~~GdiV~GkV~~i~~~g~ 80 (189)
T PRK09521 4 QGDLVLPGDYLAVIEEY-LPGEGTYEDN--GEVYASVVGKVFIDDINRKISVIPFKKTPPLLKKGDIVYGRVVDVKEQRA 80 (189)
T ss_pred cCCEECCCCccccccce-EcCCCEEeeC--CEEEEEeeEEEEEcCCCCEEEEecCcCCCCCCCCCCEEEEEEEEEcCCeE
Confidence 45677776655322111 2233345432 2346789999999777778888888755566789999987755 467888
Q ss_pred eEEEeeC-------C---cCcCCcCCcHHHHHHhhcc-CeeccCCCEEEEeeCC--EEEEEEEE
Q 047222 109 YVKLQPH-------T---KDFLDISNPKAVLETTLRS-YSCLTTGDTIMVPYNN--KKYYINVV 159 (342)
Q Consensus 109 ~vkLqP~-------s---~~FldisnpKavLE~~LRn-ystLT~Gd~I~I~yn~--~~y~l~V~ 159 (342)
+|.|-.. . ..|+.+++... ....+ ..++..||+|....-. ..+.|.+.
T Consensus 81 ~V~I~~~~~~~~~l~~~~~G~l~~s~i~~---~~~~~~~~~~~~GD~V~akV~~i~~~i~LS~k 141 (189)
T PRK09521 81 LVRIVSIEGSERELATSKLAYIHISQVSD---GYVESLTDAFKIGDIVRAKVISYTDPLQLSTK 141 (189)
T ss_pred EEEEEEecccccccCCCceeeEEhhHcCh---hhhhhHHhccCCCCEEEEEEEecCCcEEEEEe
Confidence 8887421 1 23443433221 12223 5668999999876321 34444443
No 18
>PRK14132 riboflavin kinase; Provisional
Probab=68.36 E-value=4.8 Score=35.35 Aligned_cols=31 Identities=26% Similarity=0.414 Sum_probs=24.7
Q ss_pred CEEE-EEEeeeeeCCCcEeccHHHHHHcCCCCCCEEEEE
Q 047222 63 RVTY-CGVMEFIADEGLIYLPYWMMENMLLQEGDIVEVK 100 (342)
Q Consensus 63 r~th-~GVLEF~AeEG~i~LP~WMm~~L~l~~gd~V~i~ 100 (342)
|+.| --|+|++|+.. +-+.|+|++||.|.|+
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 3445 45888888764 8999999999999986
No 19
>COG1935 Uncharacterized conserved protein [Function unknown]
Probab=67.92 E-value=9.7 Score=33.29 Aligned_cols=47 Identities=23% Similarity=0.403 Sum_probs=35.2
Q ss_pred HHHHHHHHhcCCCCCeEEEEEeCCCCCEEEEEEeeeeeCCCcEeccHHHHHHcCCCCCCEEEEEEe---ecCCcce
Q 047222 37 PSALDRLAYLHIEYPMLFELSNTSAGRVTYCGVMEFIADEGLIYLPYWMMENMLLQEGDIVEVKNA---SLAKGSY 109 (342)
Q Consensus 37 pSaL~~L~~l~i~~PmlF~L~n~~~~r~th~GVLEF~AeEG~i~LP~WMm~~L~l~~gd~V~i~~~---~LPkGt~ 109 (342)
-+++++|.+.++. +|+|+|..+ +..-++|++||+|.++++ +|-+|+.
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 3577777766553 788887654 445688999999999998 6788875
No 20
>PRK09974 putative regulator PrlF; Provisional
Probab=61.23 E-value=27 Score=30.13 Aligned_cols=59 Identities=17% Similarity=0.209 Sum_probs=39.2
Q ss_pred eCCCcEeccHHHHHHcCCCCCCEEEEEEeecCCcceEEEeeCCcCcCC--cCCcHHHHHHhhcc
Q 047222 74 ADEGLIYLPYWMMENMLLQEGDIVEVKNASLAKGSYVKLQPHTKDFLD--ISNPKAVLETTLRS 135 (342)
Q Consensus 74 AeEG~i~LP~WMm~~L~l~~gd~V~i~~~~LPkGt~vkLqP~s~~Fld--isnpKavLE~~LRn 135 (342)
...|.|-+|.-+-+.|+|.+||.|.+. .++.|. |.+.+...+--| |...-.+||+-+++
T Consensus 15 TsKGQvTIPk~IR~~Lgl~~GdkI~f~--i~~dG~-V~i~~~~~~~~Dp~ig~FL~fLa~Di~~ 75 (111)
T PRK09974 15 TDRGQTTVPAPVRKALKLKKRDSIHYE--ILPGGQ-VFICRLGDEEEDPVLGAFLDFLAADIQN 75 (111)
T ss_pred ecCCCEeccHHHHHHcCCCCCCEEEEE--EeCCCE-EEEEECCCCCCCchHHHHHHHHHHHHHh
Confidence 457999999999999999999998773 334444 666666432211 12235566666554
No 21
>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=60.94 E-value=10 Score=33.11 Aligned_cols=18 Identities=33% Similarity=0.492 Sum_probs=12.3
Q ss_pred HHHHHHcCCCCCCEEEEE
Q 047222 83 YWMMENMLLQEGDIVEVK 100 (342)
Q Consensus 83 ~WMm~~L~l~~gd~V~i~ 100 (342)
.-+-+.|+|++||.|.|+
T Consensus 103 ~~LR~~L~L~DGD~V~v~ 120 (121)
T PF01982_consen 103 VKLRDTLGLKDGDEVEVE 120 (121)
T ss_dssp S-HHHHTT--TT-EEEEE
T ss_pred cchHhhcCCCCCCEEEEE
Confidence 348999999999999986
No 22
>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=60.81 E-value=14 Score=30.11 Aligned_cols=29 Identities=17% Similarity=0.300 Sum_probs=25.9
Q ss_pred CCCcEeccHHHHHHcCCCCCCEEEEEEee
Q 047222 75 DEGLIYLPYWMMENMLLQEGDIVEVKNAS 103 (342)
Q Consensus 75 eEG~i~LP~WMm~~L~l~~gd~V~i~~~~ 103 (342)
++..|+|-.=-++.|+|.+||.|+|.+..
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 46789999999999999999999999853
No 23
>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=60.60 E-value=11 Score=30.59 Aligned_cols=30 Identities=20% Similarity=0.144 Sum_probs=26.3
Q ss_pred eCCCcEeccHHHHHHcCCCCCCEEEEEEee
Q 047222 74 ADEGLIYLPYWMMENMLLQEGDIVEVKNAS 103 (342)
Q Consensus 74 AeEG~i~LP~WMm~~L~l~~gd~V~i~~~~ 103 (342)
.++..|+|..--++.|||++||.|+|.+..
T Consensus 28 ~~~~~v~i~p~dA~~lgi~~Gd~V~v~s~~ 57 (116)
T cd02786 28 EGEPTLLIHPADAAARGIADGDLVVVFNDR 57 (116)
T ss_pred CCCCEEEECHHHHHHcCCCCCCEEEEEcCC
Confidence 356789999999999999999999998753
No 24
>PRK09798 antitoxin MazE; Provisional
Probab=58.13 E-value=23 Score=28.66 Aligned_cols=50 Identities=18% Similarity=0.296 Sum_probs=36.8
Q ss_pred cEeccHHHHHHcCCCCCCEEEEEEeecCCcceEEEeeCCcCcCCcCCcHHHHHHhhccCe
Q 047222 78 LIYLPYWMMENMLLQEGDIVEVKNASLAKGSYVKLQPHTKDFLDISNPKAVLETTLRSYS 137 (342)
Q Consensus 78 ~i~LP~WMm~~L~l~~gd~V~i~~~~LPkGt~vkLqP~s~~FldisnpKavLE~~LRnys 137 (342)
-|-||.=+++.|+|.+||.|.|+.. +.-+.|+|... .++.-||.-|.+|+
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 3679999999999999999988874 34577999642 23445676665554
No 25
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=56.86 E-value=18 Score=29.23 Aligned_cols=42 Identities=24% Similarity=0.405 Sum_probs=31.6
Q ss_pred eCCCcEeccHHHHHHcCCCCCCEEEEEEeecCCcceEEEeeCCc
Q 047222 74 ADEGLIYLPYWMMENMLLQEGDIVEVKNASLAKGSYVKLQPHTK 117 (342)
Q Consensus 74 AeEG~i~LP~WMm~~L~l~~gd~V~i~~~~LPkGt~vkLqP~s~ 117 (342)
...|+|++|.-+-+.|||++||.|.+.... .+-.+-|+|...
T Consensus 11 ~~~GqIvIPkeiR~~lgi~~Gd~lei~~~~--~~~~ivl~k~~~ 52 (89)
T COG2002 11 DRKGQIVIPKEIREALGIKEGDVLEIIVDG--DGGRIVLKKYKP 52 (89)
T ss_pred CcCceEEecHHHHHHhCCCCCCEEEEEEeC--CCCEEEEEECCc
Confidence 457999999999999999999998886542 112266666553
No 26
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=56.33 E-value=13 Score=31.60 Aligned_cols=27 Identities=19% Similarity=0.308 Sum_probs=23.3
Q ss_pred CeeccCCCEEEEeeCCEEEEEEEEeec
Q 047222 136 YSCLTTGDTIMVPYNNKKYYINVVETK 162 (342)
Q Consensus 136 ystLT~Gd~I~I~yn~~~y~l~V~e~k 162 (342)
+..|..||+|.|.+.++.+.++|.+++
T Consensus 137 ~~~l~pGDvi~l~~~~~~~~~RI~~i~ 163 (164)
T PF13550_consen 137 GLALEPGDVIALSDDGRDMRFRITEIE 163 (164)
T ss_pred hccCCCCCEEEEEeCCCceEEEEEEEe
Confidence 346889999999999999999998875
No 27
>PRK11347 antitoxin ChpS; Provisional
Probab=55.73 E-value=32 Score=27.88 Aligned_cols=48 Identities=23% Similarity=0.350 Sum_probs=35.9
Q ss_pred cEeccHHHHHHcCCCCCCEEEEEEeecCCcceEEEeeCCcCcCCcCCcHHHHHHhhccCe
Q 047222 78 LIYLPYWMMENMLLQEGDIVEVKNASLAKGSYVKLQPHTKDFLDISNPKAVLETTLRSYS 137 (342)
Q Consensus 78 ~i~LP~WMm~~L~l~~gd~V~i~~~~LPkGt~vkLqP~s~~FldisnpKavLE~~LRnys 137 (342)
-|-||.=|++.|+|++||.|.|+-.. .-+.|+|.... .-||.-|..|.
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 36799999999999999999887653 34888998543 34666665443
No 28
>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=54.73 E-value=21 Score=31.10 Aligned_cols=33 Identities=15% Similarity=0.216 Sum_probs=28.0
Q ss_pred eeeeeCCCcEeccHHHHHHcCCCCCCEEEEEEe
Q 047222 70 MEFIADEGLIYLPYWMMENMLLQEGDIVEVKNA 102 (342)
Q Consensus 70 LEF~AeEG~i~LP~WMm~~L~l~~gd~V~i~~~ 102 (342)
++...++..|+|-.=-++.|+|++||.|+|.+.
T Consensus 24 l~~~~~~~~v~inp~dA~~lgI~dGd~V~v~~~ 56 (141)
T cd02776 24 LRLQRGGPVVWMNPKDAAELGIKDNDWVEVFND 56 (141)
T ss_pred HhcCCCCCEEEECHHHHHHcCCCCCCEEEEEeC
Confidence 345556788999999999999999999999873
No 29
>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=53.80 E-value=20 Score=28.82 Aligned_cols=34 Identities=24% Similarity=0.150 Sum_probs=28.1
Q ss_pred EeeeeeCCCcEeccHHHHHHcCCCCCCEEEEEEe
Q 047222 69 VMEFIADEGLIYLPYWMMENMLLQEGDIVEVKNA 102 (342)
Q Consensus 69 VLEF~AeEG~i~LP~WMm~~L~l~~gd~V~i~~~ 102 (342)
.|.-.+++..|+|-.=-++.|+|.+||.|+|.+.
T Consensus 21 ~l~~~~~~~~v~inp~dA~~lGi~~Gd~V~v~s~ 54 (96)
T cd02788 21 VIAERAPAPYARLSPADAARLGLADGDLVEFSLG 54 (96)
T ss_pred HHHhcCCCCEEEECHHHHHHcCCCCCCEEEEEEC
Confidence 3333456788999999999999999999998764
No 30
>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=53.70 E-value=13 Score=30.42 Aligned_cols=28 Identities=18% Similarity=0.202 Sum_probs=25.2
Q ss_pred eCCCcEeccHHHHHHcCCCCCCEEEEEE
Q 047222 74 ADEGLIYLPYWMMENMLLQEGDIVEVKN 101 (342)
Q Consensus 74 AeEG~i~LP~WMm~~L~l~~gd~V~i~~ 101 (342)
.++..|.|..=-++.|+|.+||.|+|.+
T Consensus 32 ~~~~~v~i~p~dA~~lgi~~Gd~V~v~s 59 (122)
T cd02792 32 QPEMFVEISPELAAERGIKNGDMVWVSS 59 (122)
T ss_pred CCCcEEEECHHHHHHcCCCCCCEEEEEc
Confidence 4577899999999999999999999886
No 31
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=53.56 E-value=14 Score=35.09 Aligned_cols=19 Identities=21% Similarity=0.389 Sum_probs=16.5
Q ss_pred HHHHHHcCCCCCCEEEEEE
Q 047222 83 YWMMENMLLQEGDIVEVKN 101 (342)
Q Consensus 83 ~WMm~~L~l~~gd~V~i~~ 101 (342)
-.+-+.|+|..||.|+|+-
T Consensus 194 v~LR~~LnLkDGD~V~ieV 212 (214)
T COG1339 194 VKLRDELNLKDGDEVTIEV 212 (214)
T ss_pred HhHHHHhCCCCCCEEEEEE
Confidence 4688999999999999874
No 32
>PRK15095 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=51.93 E-value=50 Score=29.43 Aligned_cols=92 Identities=20% Similarity=0.221 Sum_probs=54.8
Q ss_pred EeeeeeCCCcEeccHHHHHHcCCCCCCEEEEEEeecCCcceEEEeeCCcCcCCcCCcHHHHHHhhccCe---eccCCCEE
Q 047222 69 VMEFIADEGLIYLPYWMMENMLLQEGDIVEVKNASLAKGSYVKLQPHTKDFLDISNPKAVLETTLRSYS---CLTTGDTI 145 (342)
Q Consensus 69 VLEF~AeEG~i~LP~WMm~~L~l~~gd~V~i~~~~LPkGt~vkLqP~s~~FldisnpKavLE~~LRnys---tLT~Gd~I 145 (342)
-++|+--.|.+ +|.|=-.=++++.|+.+.|. || |. ..| --.|+..|.+--+.+|. -+-.|..+
T Consensus 34 P~~f~~G~g~v-i~gle~aL~gm~~Ge~~~v~---ip--------p~-~ay-G~~d~~~v~~vp~~~f~~~~~~~~G~~~ 99 (156)
T PRK15095 34 PALFRLGDGSL-SEGLEQQLLGLKVGDKKTFS---LE--------PE-AAF-GVPSPDLIQYFSRRDFMDAGEPEIGAIM 99 (156)
T ss_pred CEEEEeCCCCc-cHHHHHHHcCCCCCCEEEEE---EC--------hH-Hhc-CCCChHHEEEecHHHCCcccCCCCCCEE
Confidence 45666666655 89999999999999987653 22 21 133 23455555443333443 36677776
Q ss_pred EEeeC-CEEEEEEEEeecCCCeeEEEecceeEeecCCC
Q 047222 146 MVPYN-NKKYYINVVETKPSTAVSIIETDCEVDFIPPL 182 (342)
Q Consensus 146 ~I~yn-~~~y~l~V~e~kP~~aVsIIdTDleVDf~pPl 182 (342)
.+.-. +..+...|++ |-+..+.|||.-||
T Consensus 100 ~~~~~~G~~~~~~V~~--------i~~~~v~vD~NHPL 129 (156)
T PRK15095 100 LFTAMDGSEMPGVIRE--------INGDSITVDFNHPL 129 (156)
T ss_pred EEECCCCCEEEEEEEE--------EcCCEEEEECCCcC
Confidence 66532 2344444554 44566778888776
No 33
>PRK08577 hypothetical protein; Provisional
Probab=51.39 E-value=20 Score=30.74 Aligned_cols=44 Identities=20% Similarity=0.249 Sum_probs=32.9
Q ss_pred eCCCcEeccHHHHHHcCCCCCCEEEEEEeecCCcceEEEeeCCcCc
Q 047222 74 ADEGLIYLPYWMMENMLLQEGDIVEVKNASLAKGSYVKLQPHTKDF 119 (342)
Q Consensus 74 AeEG~i~LP~WMm~~L~l~~gd~V~i~~~~LPkGt~vkLqP~s~~F 119 (342)
...|.|.+|.=+-+.|+|.+||.|.+..-. ...-+.|.|....+
T Consensus 10 ~~~g~i~ip~~~r~~l~~~~g~~~~~~~~~--~~~~~~~~~~~~~~ 53 (136)
T PRK08577 10 DSKGRITIPLEIREALGIREGMYVLLIADT--DKKEIHLEPIALPG 53 (136)
T ss_pred CcCCeEEecHHHHHHcCcCCCCEEEEEEEC--CCCEEEEEEcCCCC
Confidence 467999999999999999999999886331 11246677765444
No 34
>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=51.04 E-value=25 Score=32.24 Aligned_cols=46 Identities=26% Similarity=0.430 Sum_probs=35.9
Q ss_pred EEeeeeeCCCcEeccHHHHHHcCCCCCCEEEEEEeecCCcceEEEeeCC
Q 047222 68 GVMEFIADEGLIYLPYWMMENMLLQEGDIVEVKNASLAKGSYVKLQPHT 116 (342)
Q Consensus 68 GVLEF~AeEG~i~LP~WMm~~L~l~~gd~V~i~~~~LPkGt~vkLqP~s 116 (342)
|+.==+.+.|.|.+|-=|-+.|+|++||.|.|.... .| .|.|++.+
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 444446678999999999999999999999886532 23 37777765
No 35
>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=50.57 E-value=22 Score=28.66 Aligned_cols=27 Identities=19% Similarity=0.277 Sum_probs=24.7
Q ss_pred CCCcEeccHHHHHHcCCCCCCEEEEEE
Q 047222 75 DEGLIYLPYWMMENMLLQEGDIVEVKN 101 (342)
Q Consensus 75 eEG~i~LP~WMm~~L~l~~gd~V~i~~ 101 (342)
++..|+|..=-++.|||.+||.|+|.+
T Consensus 33 ~~~~v~inp~dA~~lgi~~Gd~V~v~~ 59 (120)
T cd00508 33 PEPFVEIHPEDAARLGIKDGDLVRVSS 59 (120)
T ss_pred CCCEEEECHHHHHHcCCCCCCEEEEEe
Confidence 467899999999999999999999987
No 36
>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=50.53 E-value=16 Score=30.05 Aligned_cols=29 Identities=17% Similarity=0.008 Sum_probs=25.7
Q ss_pred eCCCcEeccHHHHHHcCCCCCCEEEEEEe
Q 047222 74 ADEGLIYLPYWMMENMLLQEGDIVEVKNA 102 (342)
Q Consensus 74 AeEG~i~LP~WMm~~L~l~~gd~V~i~~~ 102 (342)
.++..|+|-.=-++.|||.+||.|+|.+.
T Consensus 28 ~~~~~v~i~p~dA~~lgi~~Gd~V~v~~~ 56 (106)
T cd02789 28 DACAYCEINPEDYKLLGKPEGDKVKVTSE 56 (106)
T ss_pred CCCcEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 45678999999999999999999998864
No 37
>smart00553 SEP Domain present in Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47.
Probab=50.52 E-value=13 Score=30.98 Aligned_cols=16 Identities=44% Similarity=0.864 Sum_probs=13.6
Q ss_pred ccccceeeceecCCCc
Q 047222 240 KFSPFTGSGRCLNGKS 255 (342)
Q Consensus 240 ~f~~F~G~G~rLdGK~ 255 (342)
.+.+|.|+|+||++-.
T Consensus 72 ~~~~F~G~G~~LGs~~ 87 (93)
T smart00553 72 AFKPFSGSGQKLGSPG 87 (93)
T ss_pred CccCCccCCccCCCCC
Confidence 5899999999998743
No 38
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=48.70 E-value=26 Score=29.83 Aligned_cols=25 Identities=20% Similarity=0.502 Sum_probs=22.6
Q ss_pred eccCCCEEEEeeCCEEEEEEEEeec
Q 047222 138 CLTTGDTIMVPYNNKKYYINVVETK 162 (342)
Q Consensus 138 tLT~Gd~I~I~yn~~~y~l~V~e~k 162 (342)
.+-.||+|.|.|+++.+.+.|+.+.
T Consensus 48 ~VK~GD~l~i~~~~~~~~v~Vl~~~ 72 (100)
T COG1188 48 EVKVGDILTIRFGNKEFTVKVLALG 72 (100)
T ss_pred ccCCCCEEEEEeCCcEEEEEEEecc
Confidence 4678999999999999999999974
No 39
>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=48.67 E-value=23 Score=27.57 Aligned_cols=28 Identities=18% Similarity=0.266 Sum_probs=24.6
Q ss_pred CCCcEeccHHHHHHcCCCCCCEEEEEEe
Q 047222 75 DEGLIYLPYWMMENMLLQEGDIVEVKNA 102 (342)
Q Consensus 75 eEG~i~LP~WMm~~L~l~~gd~V~i~~~ 102 (342)
.+..|+|..=-++.|+|++||.|.|.+-
T Consensus 21 ~~~~v~~~~~da~~lgl~~Gd~v~v~~~ 48 (101)
T cd02775 21 PEPVVEINPEDAAALGIKDGDLVRVESR 48 (101)
T ss_pred CCCEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 4578999999999999999999988754
No 40
>COG1153 FwdD Formylmethanofuran dehydrogenase subunit D [Energy production and conversion]
Probab=48.36 E-value=15 Score=32.29 Aligned_cols=29 Identities=24% Similarity=0.219 Sum_probs=24.4
Q ss_pred eeCCCcEeccHHHHHHcCCCCCCEEEEEE
Q 047222 73 IADEGLIYLPYWMMENMLLQEGDIVEVKN 101 (342)
Q Consensus 73 ~AeEG~i~LP~WMm~~L~l~~gd~V~i~~ 101 (342)
.-.-..|+|-.-.|..|++.+||.|.|++
T Consensus 27 ~~a~a~~~inp~D~~~Lgv~EGD~VkVks 55 (128)
T COG1153 27 FNACAVCEINPEDMKQLGVSEGDKVKVKS 55 (128)
T ss_pred hhheeEEEECHHHHHHhCCCcCCeEEEEe
Confidence 33445788888899999999999999987
No 41
>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=48.31 E-value=24 Score=29.26 Aligned_cols=28 Identities=25% Similarity=0.191 Sum_probs=25.3
Q ss_pred CCCcEeccHHHHHHcCCCCCCEEEEEEe
Q 047222 75 DEGLIYLPYWMMENMLLQEGDIVEVKNA 102 (342)
Q Consensus 75 eEG~i~LP~WMm~~L~l~~gd~V~i~~~ 102 (342)
++..|+|-.=-++.|||.+||.|+|.+-
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 5678999999999999999999999874
No 42
>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=47.14 E-value=24 Score=29.27 Aligned_cols=29 Identities=14% Similarity=0.120 Sum_probs=25.4
Q ss_pred CCCcEeccHHHHHHcCCCCCCEEEEEEee
Q 047222 75 DEGLIYLPYWMMENMLLQEGDIVEVKNAS 103 (342)
Q Consensus 75 eEG~i~LP~WMm~~L~l~~gd~V~i~~~~ 103 (342)
++..|+|-.=-++.|+|.+||.|+|.+..
T Consensus 31 ~~~~v~inp~dA~~~gi~~Gd~V~v~s~~ 59 (130)
T cd02781 31 PDPVAEINPETAAKLGIADGDWVWVETPR 59 (130)
T ss_pred CCCEEEECHHHHHHcCCCCCCEEEEECCC
Confidence 46789999999999999999999988643
No 43
>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=46.45 E-value=27 Score=28.48 Aligned_cols=28 Identities=25% Similarity=0.261 Sum_probs=24.9
Q ss_pred CCCcEeccHHHHHHcCCCCCCEEEEEEe
Q 047222 75 DEGLIYLPYWMMENMLLQEGDIVEVKNA 102 (342)
Q Consensus 75 eEG~i~LP~WMm~~L~l~~gd~V~i~~~ 102 (342)
.+..|+|-.-.++.|||.+||.|+|.+-
T Consensus 33 ~~~~v~in~~dA~~lgi~~Gd~V~v~~~ 60 (122)
T cd02791 33 PEPYVEIHPEDAARLGLKEGDLVRVTSR 60 (122)
T ss_pred CCCEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 4567999999999999999999999874
No 44
>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=46.28 E-value=25 Score=28.14 Aligned_cols=26 Identities=19% Similarity=0.247 Sum_probs=21.7
Q ss_pred CC-cEeccHHHHHHcCCCCCCEEEEEE
Q 047222 76 EG-LIYLPYWMMENMLLQEGDIVEVKN 101 (342)
Q Consensus 76 EG-~i~LP~WMm~~L~l~~gd~V~i~~ 101 (342)
+. .|+|-.=-++.|||++||.|+|.+
T Consensus 28 ~~~~v~inp~dA~~~Gi~~Gd~V~v~s 54 (110)
T PF01568_consen 28 EPPFVEINPEDAAKLGIKDGDWVRVSS 54 (110)
T ss_dssp STEEEEEEHHHHHHCT--TTCEEEEEE
T ss_pred CCCEEEEcHHHHHHhcCcCCCEEEEEe
Confidence 44 899999999999999999999987
No 45
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=46.23 E-value=21 Score=28.58 Aligned_cols=24 Identities=25% Similarity=0.487 Sum_probs=20.8
Q ss_pred CcEeccHHHHHHcCCCCCCEEEEE
Q 047222 77 GLIYLPYWMMENMLLQEGDIVEVK 100 (342)
Q Consensus 77 G~i~LP~WMm~~L~l~~gd~V~i~ 100 (342)
-.+.||.-|..++-+.+||.|.|+
T Consensus 25 ~l~~i~gK~Rk~iwI~~GD~VlV~ 48 (78)
T cd04456 25 RLVSIPGKLRKNIWIKRGDFLIVD 48 (78)
T ss_pred EEEEEchhhccCEEEcCCCEEEEE
Confidence 358899999999999999998884
No 46
>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=46.21 E-value=25 Score=29.26 Aligned_cols=26 Identities=23% Similarity=0.290 Sum_probs=23.9
Q ss_pred CCcEeccHHHHHHcCCCCCCEEEEEE
Q 047222 76 EGLIYLPYWMMENMLLQEGDIVEVKN 101 (342)
Q Consensus 76 EG~i~LP~WMm~~L~l~~gd~V~i~~ 101 (342)
+..|+|-.=.++.|||.+||.|+|++
T Consensus 33 ~~~v~i~p~dA~~lgi~~Gd~V~v~s 58 (127)
T cd02777 33 REPVWINPLDAAARGIKDGDIVRVFN 58 (127)
T ss_pred CCeEEECHHHHHHcCCCCCCEEEEEc
Confidence 56799999999999999999999886
No 47
>COG2336 MazE Growth regulator [Signal transduction mechanisms]
Probab=46.20 E-value=22 Score=29.22 Aligned_cols=34 Identities=24% Similarity=0.424 Sum_probs=25.5
Q ss_pred EeccHHHHHHcCCCCCCEEEEEEeecCCcceEEEeeC
Q 047222 79 IYLPYWMMENMLLQEGDIVEVKNASLAKGSYVKLQPH 115 (342)
Q Consensus 79 i~LP~WMm~~L~l~~gd~V~i~~~~LPkGt~vkLqP~ 115 (342)
|.||.=||+.|+|.+||-|.|+-. .+..+.+.|.
T Consensus 14 vrIP~~l~kql~l~~g~~v~v~v~---n~~~i~~~p~ 47 (82)
T COG2336 14 VRIPAALLKQLNLTIGDEVEVEVG---NDQSILIRPV 47 (82)
T ss_pred eeccHHHHHHhCCCcCceEEEEEc---CCcEEEeccc
Confidence 679999999999999999887643 2334455554
No 48
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=45.65 E-value=42 Score=26.93 Aligned_cols=31 Identities=23% Similarity=0.318 Sum_probs=24.8
Q ss_pred HHHHHHcCCCCCCEEEEEEeecCCcceEEEe
Q 047222 83 YWMMENMLLQEGDIVEVKNASLAKGSYVKLQ 113 (342)
Q Consensus 83 ~WMm~~L~l~~gd~V~i~~~~LPkGt~vkLq 113 (342)
.-|.+.||+++||.|+|.-.+---|.++..+
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 4588999999999999999998888888654
No 49
>PF04322 DUF473: Protein of unknown function (DUF473); InterPro: IPR007417 This is a family of uncharacterised archaeal proteins.
Probab=44.83 E-value=28 Score=30.38 Aligned_cols=47 Identities=23% Similarity=0.295 Sum_probs=32.7
Q ss_pred CHHHHHHHHhcCCCCCeEEEEEeCCCCCEEEEEEeeeeeCCCcEeccHHHHHHcCCCCCCEEEEEEe---ecCCcc
Q 047222 36 PPSALDRLAYLHIEYPMLFELSNTSAGRVTYCGVMEFIADEGLIYLPYWMMENMLLQEGDIVEVKNA---SLAKGS 108 (342)
Q Consensus 36 PpSaL~~L~~l~i~~PmlF~L~n~~~~r~th~GVLEF~AeEG~i~LP~WMm~~L~l~~gd~V~i~~~---~LPkGt 108 (342)
-+.+|++|.+.++ =+|+|+|..|- ..-+.+++||.|.++++ +|-.||
T Consensus 10 s~~vi~eL~~~~~---RTiEirSa~N~-----------------------~~~~~~~~Gd~VFlT~~~~~Dl~~Gt 59 (119)
T PF04322_consen 10 SRRVIDELKKNHI---RTIEIRSAHNV-----------------------IALESLDPGDRVFLTSVSLEDLTPGT 59 (119)
T ss_pred CHHHHHHHHhCCc---eEEEEEcchhe-----------------------eeeecCCCCCEEEEecCCHHHCCCCC
Confidence 3678888876543 58999986542 12346789999999988 455555
No 50
>cd02778 MopB_CT_Thiosulfate-R-like The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Also included in this CD is the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), which has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. The MopB_CT_Thiosulfate-R-like CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=43.45 E-value=33 Score=28.04 Aligned_cols=29 Identities=21% Similarity=0.363 Sum_probs=25.6
Q ss_pred eeCCCcEeccHHHHHHcCCCCCCEEEEEE
Q 047222 73 IADEGLIYLPYWMMENMLLQEGDIVEVKN 101 (342)
Q Consensus 73 ~AeEG~i~LP~WMm~~L~l~~gd~V~i~~ 101 (342)
..++..|+|..=-++.|+|.+||.|+|.+
T Consensus 26 ~~~~~~v~i~p~dA~~~gi~~Gd~V~v~s 54 (123)
T cd02778 26 LTPENTLWINPETAARLGIKDGDRVEVSS 54 (123)
T ss_pred cCCCCeEEECHHHHHHcCCCCCCEEEEEe
Confidence 34567899999999999999999999886
No 51
>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=43.09 E-value=30 Score=28.73 Aligned_cols=29 Identities=21% Similarity=0.161 Sum_probs=25.8
Q ss_pred eCCCcEeccHHHHHHcCCCCCCEEEEEEe
Q 047222 74 ADEGLIYLPYWMMENMLLQEGDIVEVKNA 102 (342)
Q Consensus 74 AeEG~i~LP~WMm~~L~l~~gd~V~i~~~ 102 (342)
.++..|+|-.=-++.|+|.+||.|+|++.
T Consensus 30 ~~~~~v~i~p~dA~~~gi~~Gd~V~v~s~ 58 (129)
T cd02782 30 RNRCTLRIHPDDAAALGLADGDKVRVTSA 58 (129)
T ss_pred CCCceEEECHHHHHHcCCCCCCEEEEEcC
Confidence 46778999999999999999999999874
No 52
>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=42.88 E-value=31 Score=28.50 Aligned_cols=28 Identities=18% Similarity=0.131 Sum_probs=24.1
Q ss_pred CCcEeccHHHHHHcCCCCCCEEEEEEee
Q 047222 76 EGLIYLPYWMMENMLLQEGDIVEVKNAS 103 (342)
Q Consensus 76 EG~i~LP~WMm~~L~l~~gd~V~i~~~~ 103 (342)
+..|+|-.=.++.|||.+||.|+|++..
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 4568999999999999999999988643
No 53
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=42.80 E-value=32 Score=26.62 Aligned_cols=65 Identities=14% Similarity=0.248 Sum_probs=39.2
Q ss_pred CCCCCEEEEEEe-ecCCcceEEEeeCCcCcCCcCCcHHHHHHhhccC-eeccCCCEEEEeeCCEEEEEEEEeecCC
Q 047222 91 LQEGDIVEVKNA-SLAKGSYVKLQPHTKDFLDISNPKAVLETTLRSY-SCLTTGDTIMVPYNNKKYYINVVETKPS 164 (342)
Q Consensus 91 l~~gd~V~i~~~-~LPkGt~vkLqP~s~~FldisnpKavLE~~LRny-stLT~Gd~I~I~yn~~~y~l~V~e~kP~ 164 (342)
+++||.|.-.-. ..+.|-||.|-|.-..|+.++|.-.-.-..++++ ..+..||.|. .+|++++++
T Consensus 1 ~k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~---------~kVl~id~~ 67 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLT---------AKVLSVNSE 67 (74)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEE---------EEEEEEECC
Confidence 468888875533 3599999999998888885432111000011111 3467788776 557777665
No 54
>COG0243 BisC Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]
Probab=42.80 E-value=38 Score=36.91 Aligned_cols=31 Identities=23% Similarity=0.390 Sum_probs=27.5
Q ss_pred eeCCCcEeccHHHHHHcCCCCCCEEEEEEee
Q 047222 73 IADEGLIYLPYWMMENMLLQEGDIVEVKNAS 103 (342)
Q Consensus 73 ~AeEG~i~LP~WMm~~L~l~~gd~V~i~~~~ 103 (342)
..+++.|+|-.--++.|||++||+|+|.+.+
T Consensus 667 ~~~~~~v~inp~DA~~~GI~~GD~V~V~~~r 697 (765)
T COG0243 667 IAPRPFVWINPEDAAKLGIKDGDLVRVENRR 697 (765)
T ss_pred CCCCceEEECHHHHHHcCCCcCCEEEEEcCC
Confidence 4577899999999999999999999998753
No 55
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=42.46 E-value=21 Score=33.86 Aligned_cols=39 Identities=28% Similarity=0.463 Sum_probs=27.2
Q ss_pred CEEEEEEeeeeeC----CCcEecc---------------HHHHHHcCCCCCCEEEEEE
Q 047222 63 RVTYCGVMEFIAD----EGLIYLP---------------YWMMENMLLQEGDIVEVKN 101 (342)
Q Consensus 63 r~th~GVLEF~Ae----EG~i~LP---------------~WMm~~L~l~~gd~V~i~~ 101 (342)
..|+|+|.=|-+- +|.|++| .-+-+.|+|.+||.|.|+-
T Consensus 158 ~r~~g~~~~~~~~i~~i~~aiv~P~rt~h~~~~~EiIap~~LR~~l~l~dgd~v~i~i 215 (217)
T PRK14165 158 ERTFGGVKCYPVKVEGIECAVIVPERTHYPSDLIEIISPVYLRKELNLKDGDRVEVLV 215 (217)
T ss_pred CceeEEEEEEEEEECceeEEEEeecCCCCCCCeEEEECChhhHHhcCCCCCCEEEEEE
Confidence 4467777666433 4445544 3588999999999999873
No 56
>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=42.13 E-value=33 Score=34.79 Aligned_cols=34 Identities=26% Similarity=0.303 Sum_probs=28.7
Q ss_pred EEEeeeeeCCCcEeccHHHHHHcCCCCCCEEEEE
Q 047222 67 CGVMEFIADEGLIYLPYWMMENMLLQEGDIVEVK 100 (342)
Q Consensus 67 ~GVLEF~AeEG~i~LP~WMm~~L~l~~gd~V~i~ 100 (342)
|.+.....+.+.+.|+.-+++.|++++||.|++-
T Consensus 300 a~~~~~~~~~~~~~l~~~~a~aL~v~~Gd~Vr~~ 333 (335)
T TIGR03243 300 AVLAPLSADAGTLILSADAADALGVSEGDTVRVV 333 (335)
T ss_pred EEEecccCCCCeeecCHHHHHhcCCCCCCeEEEe
Confidence 4446666678889999999999999999999874
No 57
>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=41.61 E-value=37 Score=27.86 Aligned_cols=29 Identities=28% Similarity=0.157 Sum_probs=25.7
Q ss_pred eCCCcEeccHHHHHHcCCCCCCEEEEEEe
Q 047222 74 ADEGLIYLPYWMMENMLLQEGDIVEVKNA 102 (342)
Q Consensus 74 AeEG~i~LP~WMm~~L~l~~gd~V~i~~~ 102 (342)
.++..|.|-.=-++.|+|.+||.|+|.+.
T Consensus 30 ~~~~~v~in~~dA~~lgi~~Gd~V~v~s~ 58 (115)
T cd02779 30 VPLPYIEVNPEDAKREGLKNGDLVEVYND 58 (115)
T ss_pred CCCCEEEECHHHHHHcCCCCCCEEEEEeC
Confidence 45778999999999999999999998874
No 58
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=41.21 E-value=37 Score=27.66 Aligned_cols=30 Identities=17% Similarity=0.274 Sum_probs=25.3
Q ss_pred HHHHHcCCCCCCEEEEEEeecCCcceEEEe
Q 047222 84 WMMENMLLQEGDIVEVKNASLAKGSYVKLQ 113 (342)
Q Consensus 84 WMm~~L~l~~gd~V~i~~~~LPkGt~vkLq 113 (342)
-+.+.+|+++||.|+|..-+---|.||..+
T Consensus 45 Pv~r~~g~k~GdVvkI~R~S~taG~~v~YR 74 (79)
T PRK09570 45 PVVKAIGAKPGDVIKIVRKSPTAGEAVYYR 74 (79)
T ss_pred hhhhhcCCCCCCEEEEEECCCCCCccEEEE
Confidence 377889999999999998887788887654
No 59
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=38.91 E-value=95 Score=29.08 Aligned_cols=94 Identities=11% Similarity=0.126 Sum_probs=56.1
Q ss_pred EEeeeeeCCCcEeccHHHHHHcCCCCCCEEEEEEeecCCcceEEEeeCCcCcCCcCCcHHHHHHhhccCe---eccCCCE
Q 047222 68 GVMEFIADEGLIYLPYWMMENMLLQEGDIVEVKNASLAKGSYVKLQPHTKDFLDISNPKAVLETTLRSYS---CLTTGDT 144 (342)
Q Consensus 68 GVLEF~AeEG~i~LP~WMm~~L~l~~gd~V~i~~~~LPkGt~vkLqP~s~~FldisnpKavLE~~LRnys---tLT~Gd~ 144 (342)
.-++|+--.|. ++|..--.=+++++|+...|+ |.|.. .| =.-|+..|.+--...|. -|..|+.
T Consensus 30 ~Pl~~~~G~g~-lipglE~aL~G~~~Gd~~~v~-----------l~pee-Ay-Ge~d~~lV~~vpr~~F~~~~~l~~G~~ 95 (196)
T PRK10737 30 APLDYLHGHGS-LISGLETALEGHEVGDKFDVA-----------VGAND-AY-GQYDENLVQRVPKDVFMGVDELQVGMR 95 (196)
T ss_pred CCeEEEeCCCc-chHHHHHHHcCCCCCCEEEEE-----------EChHH-hc-CCCChHHEEEecHHHCCCccCCCCCCE
Confidence 35556555443 567766667789999988754 22321 23 22444444443333442 3788988
Q ss_pred EEEeeCCEEEEEEEEeecCCCeeEEEecceeEeecCCCC
Q 047222 145 IMVPYNNKKYYINVVETKPSTAVSIIETDCEVDFIPPLD 183 (342)
Q Consensus 145 I~I~yn~~~y~l~V~e~kP~~aVsIIdTDleVDf~pPld 183 (342)
+...-.+..+...|++ |-+..+.|||.-||-
T Consensus 96 ~~~~~~~G~~~~~V~e--------v~~d~V~vD~NHPLA 126 (196)
T PRK10737 96 FLAETDQGPVPVEITA--------VEDDHVVVDGNHMLA 126 (196)
T ss_pred EEEeCCCCcEEEEEEE--------EcCCEEEEECCCcCC
Confidence 8876555455555555 446678888888873
No 60
>cd02793 MopB_CT_DMSOR-BSOR-TMAOR The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO.This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=38.81 E-value=39 Score=28.37 Aligned_cols=29 Identities=24% Similarity=0.146 Sum_probs=25.6
Q ss_pred eCCCcEeccHHHHHHcCCCCCCEEEEEEe
Q 047222 74 ADEGLIYLPYWMMENMLLQEGDIVEVKNA 102 (342)
Q Consensus 74 AeEG~i~LP~WMm~~L~l~~gd~V~i~~~ 102 (342)
.++..|+|=.=-++.|+|++||.|+|.+.
T Consensus 30 ~~~~~v~i~p~dA~~~gi~~Gd~V~v~s~ 58 (129)
T cd02793 30 QGREPIRINPADAAARGIADGDIVRVFND 58 (129)
T ss_pred CCCCEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 45678999999999999999999999874
No 61
>cd02783 MopB_CT_2 The MopB_CT_2 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=37.60 E-value=41 Score=29.58 Aligned_cols=32 Identities=19% Similarity=0.348 Sum_probs=27.7
Q ss_pred eCCCcEeccHHHHHHcCCCCCCEEEEEEeecCCcc
Q 047222 74 ADEGLIYLPYWMMENMLLQEGDIVEVKNASLAKGS 108 (342)
Q Consensus 74 AeEG~i~LP~WMm~~L~l~~gd~V~i~~~~LPkGt 108 (342)
.++..|+|-.=-++.|||++||.|+|.+ +.|+
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 62
>cd05829 Sortase_E Sortase E (SrtE) is a membrane transpeptidase found in gram-positive bacteria that cleaves surface proteins at a cell sorting motif and catalyzes a transpeptidation reaction in which the surface protein substrate is covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The function of Sortase E is unknown. In two different sortase families, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one sortase and it is thought that the different sortases anchor different surface protein classes. The sortase domain is a modified beta-barrel flanked by two (SrtA) or three (SrtB) short alpha-helices.
Probab=37.43 E-value=45 Score=29.08 Aligned_cols=27 Identities=19% Similarity=0.217 Sum_probs=21.0
Q ss_pred cCeeccCCCEEEEee-CCEEEEEEEEee
Q 047222 135 SYSCLTTGDTIMVPY-NNKKYYINVVET 161 (342)
Q Consensus 135 nystLT~Gd~I~I~y-n~~~y~l~V~e~ 161 (342)
+...|.+||.|.|.. +++.|...|.++
T Consensus 69 ~L~~l~~GD~I~v~~~~g~~~~Y~V~~~ 96 (144)
T cd05829 69 RLGDLRKGDKVEVTRADGQTATFRVDRV 96 (144)
T ss_pred chhcCCCCCEEEEEECCCCEEEEEEeEE
Confidence 334677999999999 677777777764
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=37.37 E-value=49 Score=28.00 Aligned_cols=31 Identities=19% Similarity=0.270 Sum_probs=24.9
Q ss_pred hhccCeeccCCCEEEEeeCCEEEEEEEEeec
Q 047222 132 TLRSYSCLTTGDTIMVPYNNKKYYINVVETK 162 (342)
Q Consensus 132 ~LRnystLT~Gd~I~I~yn~~~y~l~V~e~k 162 (342)
.+++...|.+||.|.|...++.|...|.+++
T Consensus 58 ~F~~L~~l~~Gd~v~v~~~~~~~~Y~V~~~~ 88 (126)
T cd06166 58 IFNRLDEVEKGDEIKVTTKNGTYKYKITSIF 88 (126)
T ss_pred ccCChHHCCCCCEEEEEECCEEEEEEEEEEE
Confidence 3455566789999999999999988888754
No 64
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=36.20 E-value=41 Score=24.55 Aligned_cols=23 Identities=22% Similarity=0.081 Sum_probs=18.4
Q ss_pred EeccHHHHHHcCCCCCCEEEEEE
Q 047222 79 IYLPYWMMENMLLQEGDIVEVKN 101 (342)
Q Consensus 79 i~LP~WMm~~L~l~~gd~V~i~~ 101 (342)
+.++.|-++.|+|++||.|.+..
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 67999999999999999998753
No 65
>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=35.50 E-value=1.8e+02 Score=25.60 Aligned_cols=41 Identities=22% Similarity=0.254 Sum_probs=28.4
Q ss_pred CeeccCCCEEEEeeC--CEEEEEEEEeecCCCeeEEEecceeE
Q 047222 136 YSCLTTGDTIMVPYN--NKKYYINVVETKPSTAVSIIETDCEV 176 (342)
Q Consensus 136 ystLT~Gd~I~I~yn--~~~y~l~V~e~kP~~aVsIIdTDleV 176 (342)
+..+..||+|.+... ...+.++-+--.|.+.|+|.+--+-|
T Consensus 49 ~~~~~rGDiVvf~~~~~~~~~~iKRVig~pGd~v~i~~~~l~v 91 (163)
T TIGR02227 49 TSDPKRGDIVVFKDPDDNKNIYVKRVIGLPGDKVEFRDGKLYI 91 (163)
T ss_pred CCCCCCCcEEEEecCCCCCceeEEEEEecCCCEEEEECCEEEE
Confidence 356778998888864 34566666666689999887755544
No 66
>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=35.24 E-value=50 Score=28.16 Aligned_cols=28 Identities=18% Similarity=0.203 Sum_probs=25.2
Q ss_pred eCCCcEeccHHHHHHcCCCCCCEEEEEE
Q 047222 74 ADEGLIYLPYWMMENMLLQEGDIVEVKN 101 (342)
Q Consensus 74 AeEG~i~LP~WMm~~L~l~~gd~V~i~~ 101 (342)
.++..|+|-.=-++.|+|++||.|.|++
T Consensus 27 ~~~~~v~inp~dA~~lgI~~Gd~V~v~s 54 (143)
T cd02780 27 KPENPVWINPEDAAKLGIKTGDRVRVVT 54 (143)
T ss_pred CCCCEEEECHHHHHHcCCCCCCEEEEEe
Confidence 4567899999999999999999999987
No 67
>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=34.34 E-value=52 Score=33.40 Aligned_cols=46 Identities=20% Similarity=0.234 Sum_probs=32.9
Q ss_pred EEEEeCCCCCEEEEEEeeeeeCCCcEeccHHHHHHcCCCCCCEEEEE
Q 047222 54 FELSNTSAGRVTYCGVMEFIADEGLIYLPYWMMENMLLQEGDIVEVK 100 (342)
Q Consensus 54 F~L~n~~~~r~th~GVLEF~AeEG~i~LP~WMm~~L~l~~gd~V~i~ 100 (342)
+-|.|..-.. --|-+.....+.+.+.|+.-+++.|++++||.|++-
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 4466643221 123345666677889999999999999999999874
No 68
>PRK10456 arginine succinyltransferase; Provisional
Probab=34.19 E-value=52 Score=33.48 Aligned_cols=47 Identities=11% Similarity=0.051 Sum_probs=33.3
Q ss_pred EEEEeCCCCCEEEEEEeeeeeCCCcEeccHHHHHHcCCCCCCEEEEEE
Q 047222 54 FELSNTSAGRVTYCGVMEFIADEGLIYLPYWMMENMLLQEGDIVEVKN 101 (342)
Q Consensus 54 F~L~n~~~~r~th~GVLEF~AeEG~i~LP~WMm~~L~l~~gd~V~i~~ 101 (342)
+-|.|..-.. --|-+.....+.+.+.|+.-+++.|++++||.|++-.
T Consensus 290 ~Lv~n~~~~~-FRa~~~~~~~~~~~~~l~~~~a~aL~v~~Gd~Vr~~~ 336 (344)
T PRK10456 290 CLVANENYHH-FRAVLVRTDPATERLILTAAQLDALKCHAGDRVRLVR 336 (344)
T ss_pred EEEECCCCCC-eEEEEecccCCCCeEecCHHHHHhcCCCCCCeEEEEe
Confidence 4456543211 1233456666778899999999999999999998754
No 69
>TIGR03245 arg_AOST_alph arginine/ornithine succinyltransferase, alpha subunit. In some bacteria, including Pseudomonas aeruginosa, the astB gene (arginine N-succinyltransferase) is replaced by tandem paralogs that form a heterodimer. This heterodimer from P. aeruginosa is characterized as arginine and ornithine N-2 succinyltransferase (AOST). Members of this protein family represent the less widespread paralog, designated AruI, or arginine/ornithine succinyltransferase, alpha subunit.
Probab=32.85 E-value=55 Score=33.20 Aligned_cols=32 Identities=25% Similarity=0.280 Sum_probs=26.8
Q ss_pred Eeeee-eCCCcEeccHHHHHHcCCCCCCEEEEE
Q 047222 69 VMEFI-ADEGLIYLPYWMMENMLLQEGDIVEVK 100 (342)
Q Consensus 69 VLEF~-AeEG~i~LP~WMm~~L~l~~gd~V~i~ 100 (342)
++... .+.+.+.|+.-+++.|++++||.|++-
T Consensus 302 ~~~~~~~~~~~~~l~~~~a~aL~v~~Gd~Vr~~ 334 (336)
T TIGR03245 302 LADVTDVDGDLLRLKRDAAEALGVSEGDNVRFA 334 (336)
T ss_pred EeccccCCCCeeecCHHHHHhcCCCCCCeEEEe
Confidence 35555 567788999999999999999999874
No 70
>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification. ; InterPro: IPR019759 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ].; PDB: 1KCA_H 3BDN_A 1F39_A 1JHH_A 1JHE_B 3JSP_A 1JHF_B 1JHC_A 3JSO_B 1B12_D ....
Probab=32.01 E-value=2e+02 Score=20.89 Aligned_cols=33 Identities=24% Similarity=0.386 Sum_probs=22.7
Q ss_pred eccCCCEEEEeeCCEE-EEEEEEeecCCCeeEEE
Q 047222 138 CLTTGDTIMVPYNNKK-YYINVVETKPSTAVSII 170 (342)
Q Consensus 138 tLT~Gd~I~I~yn~~~-y~l~V~e~kP~~aVsII 170 (342)
.+..||++.+.+++.. +.++-+...+.+.+-+.
T Consensus 24 ~~~~gdivv~~~~~~~~~~iKrv~~~~~~~~~~~ 57 (70)
T PF00717_consen 24 EPKDGDIVVVKIDGDEELYIKRVVGEPGGIILIS 57 (70)
T ss_dssp ---TTSEEEEEETTEESEEEEEEEEETTEEEEE-
T ss_pred CCccCeEEEEEECCceeeEEEEEEEeCCCEEEEe
Confidence 5668999999999987 77776666777666554
No 71
>KOG2086 consensus Protein tyrosine phosphatase SHP1/Cofactor for p97 ATPase-mediated vesicle membrane fusion [Nuclear structure]
Probab=30.63 E-value=27 Score=35.96 Aligned_cols=16 Identities=38% Similarity=0.775 Sum_probs=14.4
Q ss_pred CCccccceeeceecCC
Q 047222 238 IAKFSPFTGSGRCLNG 253 (342)
Q Consensus 238 ~~~f~~F~G~G~rLdG 253 (342)
...|.+|.|.||||.+
T Consensus 252 ~~~~~pF~G~Gq~LGs 267 (380)
T KOG2086|consen 252 KPVFKPFSGEGQRLGS 267 (380)
T ss_pred CcccCCCCCcCeecCC
Confidence 4579999999999997
No 72
>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=30.09 E-value=82 Score=26.63 Aligned_cols=30 Identities=27% Similarity=0.332 Sum_probs=24.5
Q ss_pred hccCeeccCCCEEEEeeCCEEEEEEEEeec
Q 047222 133 LRSYSCLTTGDTIMVPYNNKKYYINVVETK 162 (342)
Q Consensus 133 LRnystLT~Gd~I~I~yn~~~y~l~V~e~k 162 (342)
+++...|.+||.|.|...++.|..+|.+++
T Consensus 56 F~~L~~l~~Gd~i~v~~~~~~~~Y~V~~~~ 85 (127)
T cd05828 56 FRFLGELEPGDIITLQTLGGTYTYRVTSTR 85 (127)
T ss_pred hhChhcCCCCCEEEEEECCEEEEEEEeeEE
Confidence 445556779999999999999999888864
No 73
>PF12148 DUF3590: Protein of unknown function (DUF3590); InterPro: IPR021991 This domain is found in eukaryotes, and is typically between 83 and 97 amino acids in length. It is found in association with PF00097 from PFAM, PF02182 from PFAM, PF00628 from PFAM, PF00240 from PFAM. There are two conserved sequence motifs: RAR and NYN. The domain is part of the protein NIRF which has zinc finger and ubiquitinating domains. The function of this domain is likely to be mainly structural, however this has not been confirmed. ; PDB: 3DB4_A 3ASK_A 3DB3_A 2L3R_A.
Probab=28.88 E-value=32 Score=28.40 Aligned_cols=21 Identities=33% Similarity=0.564 Sum_probs=12.7
Q ss_pred HhhccCeeccCCCEEEEeeCC
Q 047222 131 TTLRSYSCLTTGDTIMVPYNN 151 (342)
Q Consensus 131 ~~LRnystLT~Gd~I~I~yn~ 151 (342)
+++-.|.-|.+|++++|+||-
T Consensus 58 Rt~l~w~~L~VG~~VMvNYN~ 78 (85)
T PF12148_consen 58 RTILKWDELKVGQVVMVNYNV 78 (85)
T ss_dssp -SBE-GGG--TT-EEEEEE-T
T ss_pred eEeccHHhCCcccEEEEecCC
Confidence 455578899999999999983
No 74
>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=28.74 E-value=80 Score=27.12 Aligned_cols=30 Identities=23% Similarity=0.302 Sum_probs=24.1
Q ss_pred hccCeeccCCCEEEEeeCCEEEEEEEEeec
Q 047222 133 LRSYSCLTTGDTIMVPYNNKKYYINVVETK 162 (342)
Q Consensus 133 LRnystLT~Gd~I~I~yn~~~y~l~V~e~k 162 (342)
+++...|..||.|.|...+..|..+|.+++
T Consensus 60 F~~L~~l~~Gd~i~v~~~~~~~~Y~V~~~~ 89 (137)
T cd05830 60 FNDLDKLRPGDKIVVETADGWYTYVVRSSE 89 (137)
T ss_pred cccHhhCCCCCEEEEEECCeEEEEEEeEEE
Confidence 344455889999999999988998888764
No 75
>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=27.92 E-value=78 Score=27.16 Aligned_cols=24 Identities=25% Similarity=0.310 Sum_probs=20.4
Q ss_pred eccCCCEEEEeeCCEEEEEEEEee
Q 047222 138 CLTTGDTIMVPYNNKKYYINVVET 161 (342)
Q Consensus 138 tLT~Gd~I~I~yn~~~y~l~V~e~ 161 (342)
.|.+||.|.|...+..|..+|.++
T Consensus 63 ~l~~GD~i~v~~~~~~~~Y~V~~~ 86 (136)
T TIGR01076 63 KLKKGDMLYLHVGNEVLTYQVTST 86 (136)
T ss_pred HCCCCCEEEEEECCcEEEEEEEEE
Confidence 377999999999988888888765
No 76
>PLN03086 PRLI-interacting factor K; Provisional
Probab=27.84 E-value=2.9e+02 Score=30.09 Aligned_cols=72 Identities=21% Similarity=0.206 Sum_probs=42.7
Q ss_pred CCCeEecCHHHHHHHHhcCCCCCeEEEEEeCCCCCEEEEEEeeeeeCCCcEeccHH--HHHHcC-----CCCCCEEEEEE
Q 047222 29 NGDKIVMPPSALDRLAYLHIEYPMLFELSNTSAGRVTYCGVMEFIADEGLIYLPYW--MMENML-----LQEGDIVEVKN 101 (342)
Q Consensus 29 ~GdKIiLPpSaL~~L~~l~i~~PmlF~L~n~~~~r~th~GVLEF~AeEG~i~LP~W--Mm~~L~-----l~~gd~V~i~~ 101 (342)
.-|.|.||+-+++.|...+....-+.+|++..-.+-|++-..--+++ +.=++.| ++++-. |..||+|.|.+
T Consensus 149 ~EG~v~lP~wm~~~L~~~~~~~~~~v~v~~~~Lpkgt~vklqP~~~~--f~di~npKavLE~~Lr~~stLT~Gd~i~i~~ 226 (567)
T PLN03086 149 EEGSVGLPPHVWSNLFPSDPPDVPLVEVRYIWLPKGTYAKLQPDGVG--FSDLPNHKAVLETALRQHATLSEDDVLVVNY 226 (567)
T ss_pred CCCeEEcCHHHHhhcCCCCCCCCCeEEEEEeecCCCCEEEEeeccCC--cCCcccHHHHHHHHhhcCccccCCCEEEEec
Confidence 34789999999988843222222366777655555566655532222 2234444 444332 77899999987
Q ss_pred e
Q 047222 102 A 102 (342)
Q Consensus 102 ~ 102 (342)
-
T Consensus 227 ~ 227 (567)
T PLN03086 227 G 227 (567)
T ss_pred C
Confidence 4
No 77
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=26.48 E-value=99 Score=22.96 Aligned_cols=56 Identities=14% Similarity=0.053 Sum_probs=34.6
Q ss_pred CCCCCEEEEEEe-ecCCcceEEEeeCCcCcCCcCCcHHHHHHhhccCeeccCCCEEEEe
Q 047222 91 LQEGDIVEVKNA-SLAKGSYVKLQPHTKDFLDISNPKAVLETTLRSYSCLTTGDTIMVP 148 (342)
Q Consensus 91 l~~gd~V~i~~~-~LPkGt~vkLqP~s~~FldisnpKavLE~~LRnystLT~Gd~I~I~ 148 (342)
|..|+.|.-+-. -.+.|-||.|.+.-..|+.+++... +...+.-..+..||+|.+.
T Consensus 1 ~~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~--~~~~~~~~~~~~Gd~v~~~ 57 (73)
T cd05706 1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALD--DYSEALPYKFKKNDIVRAC 57 (73)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccC--ccccccccccCCCCEEEEE
Confidence 467888765544 3678899999887777776654321 0001113457889988864
No 78
>PF04958 AstA: Arginine N-succinyltransferase beta subunit; InterPro: IPR007041 Arginine N-succinyltransferase catalyses the transfer of succinyl-CoA to arginine to produce succinylarginine. This is the first step in arginine catabolism via the arginine succinyltransferase pathway. Six major L-arginine-degrading pathways have been described for prokaryotes []. Many bacteria arginine succinyltransferase 2.3.1.109 from EC, which is the AstA protein of the succinyltransferase (ast) pathway operon consists of five genes. In a few species, such as Pseudomonas aeruginosa, a tandem gene pair encodes alpha and beta subunits of a heterodimer that is designated arginine and ornithine succinyltransferase (AOST). This entry represents the family of proteins that make up the beta subunit of the heterodimer of Ast and AOST.; GO: 0008791 arginine N-succinyltransferase activity, 0006527 arginine catabolic process; PDB: 1YLE_A.
Probab=26.38 E-value=81 Score=32.08 Aligned_cols=48 Identities=19% Similarity=0.151 Sum_probs=25.0
Q ss_pred eEEEEEeCCCCCEEEEEEeeeeeC-CCcEeccHHHHHHcCCCCCCEEEEE
Q 047222 52 MLFELSNTSAGRVTYCGVMEFIAD-EGLIYLPYWMMENMLLQEGDIVEVK 100 (342)
Q Consensus 52 mlF~L~n~~~~r~th~GVLEF~Ae-EG~i~LP~WMm~~L~l~~gd~V~i~ 100 (342)
..+-|.|..... --|-+-+.... .+.+.|+.-+++.|++++||.|++-
T Consensus 292 ~~~Lvan~~~~~-FRa~~~~~~~~~~~~~~l~~~~a~~L~v~~Gd~Vr~~ 340 (342)
T PF04958_consen 292 PPYLVANTRLED-FRATLAPAALDDGDQLVLSPEVADALQVSEGDPVRVV 340 (342)
T ss_dssp EEEEEE---STT---EEEEEE---TTS-EEE-HHHHHHHT--TT-EEEEE
T ss_pred CeEEEECCCccC-eEEEEEecccCCCCeEEcCHHHHhhcCCCCCCEEEEe
Confidence 455566643221 11333344434 8999999999999999999999874
No 79
>COG0836 {ManC} Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane]
Probab=26.16 E-value=1.6e+02 Score=30.09 Aligned_cols=76 Identities=18% Similarity=0.250 Sum_probs=55.3
Q ss_pred CEEEEEEeecCCcceEEEeeCCcCcCCcCCcHHHHHHhhcc-CeeccCCCEEEEeeCC-EEEE----EEEEeecCCCeeE
Q 047222 95 DIVEVKNASLAKGSYVKLQPHTKDFLDISNPKAVLETTLRS-YSCLTTGDTIMVPYNN-KKYY----INVVETKPSTAVS 168 (342)
Q Consensus 95 d~V~i~~~~LPkGt~vkLqP~s~~FldisnpKavLE~~LRn-ystLT~Gd~I~I~yn~-~~y~----l~V~e~kP~~aVs 168 (342)
+-+.|.|.-+.|..-+..-|.+-.+-||-+|.|+.|-.-+. =-....||++.+.-+| -.|- +-++.++ =+-
T Consensus 245 p~iSIDYAiMEkt~~~aVVp~~f~WsDlGsW~Al~~~~~~d~~gNv~~gd~~~~dt~n~~v~s~~~lia~vGl~---Dlv 321 (333)
T COG0836 245 PAISIDYAIMEKTSKAAVVPADFGWSDLGSWHALWEVLDKDENGNVCEGDVVTIDTENSLISSNNKLISVVGLE---DLV 321 (333)
T ss_pred cccchhHHHHhhhcceEEEecCCCcccccCHHHHHHHhhcCCCCCEEecceEEeccCCcEEEeCCceEEEeccc---eEE
Confidence 45777888899999999999999999999999998877664 3457789998886543 3332 3344333 455
Q ss_pred EEecc
Q 047222 169 IIETD 173 (342)
Q Consensus 169 IIdTD 173 (342)
||+|+
T Consensus 322 VV~t~ 326 (333)
T COG0836 322 VVDTK 326 (333)
T ss_pred EEecC
Confidence 56654
No 80
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=26.16 E-value=88 Score=23.83 Aligned_cols=24 Identities=25% Similarity=0.401 Sum_probs=16.9
Q ss_pred cEeccHHHHHHcCCCCCCEEEEEE
Q 047222 78 LIYLPYWMMENMLLQEGDIVEVKN 101 (342)
Q Consensus 78 ~i~LP~WMm~~L~l~~gd~V~i~~ 101 (342)
.|+||.-+...+.+.+||.|.|+-
T Consensus 29 l~~i~gK~r~~iwI~~GD~V~V~~ 52 (65)
T PF01176_consen 29 LARIPGKFRKRIWIKRGDFVLVEP 52 (65)
T ss_dssp EEEE-HHHHTCC---TTEEEEEEE
T ss_pred EEEeccceeeeEecCCCCEEEEEe
Confidence 588999998999999999888764
No 81
>PRK08059 general stress protein 13; Validated
Probab=25.76 E-value=1.2e+02 Score=25.66 Aligned_cols=59 Identities=25% Similarity=0.391 Sum_probs=36.1
Q ss_pred HHHHcCCCCCCEEEEEEe-ecCCcceEEEeeCCcCcCCcCCcHHHHHHhhcc-CeeccCCCEEEEe
Q 047222 85 MMENMLLQEGDIVEVKNA-SLAKGSYVKLQPHTKDFLDISNPKAVLETTLRS-YSCLTTGDTIMVP 148 (342)
Q Consensus 85 Mm~~L~l~~gd~V~i~~~-~LPkGt~vkLqP~s~~FldisnpKavLE~~LRn-ystLT~Gd~I~I~ 148 (342)
||+. ++.|+.|.-+-+ ..+.|-||.|.+.-..|+-+++-.. ...++ ...+..||+|.+.
T Consensus 1 ~~~~--~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~---~~~~~~~~~~~vGD~I~vk 61 (123)
T PRK08059 1 MMSQ--YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITH---GFVKDIHDFLSVGDEVKVK 61 (123)
T ss_pred Cccc--CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCc---ccccCHHHcCCCCCEEEEE
Confidence 4555 556887776644 4578999999876566664332110 00122 3467899999875
No 82
>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=25.54 E-value=94 Score=27.17 Aligned_cols=27 Identities=19% Similarity=0.346 Sum_probs=24.3
Q ss_pred CCcEeccHHHHHHcCCCCCCEEEEEEe
Q 047222 76 EGLIYLPYWMMENMLLQEGDIVEVKNA 102 (342)
Q Consensus 76 EG~i~LP~WMm~~L~l~~gd~V~i~~~ 102 (342)
+..|+|-.=-.+.|+|.+||.|+|.+-
T Consensus 37 ~~~v~InP~dA~~lGI~dGD~V~V~s~ 63 (137)
T cd02784 37 DNAALVSPRTAEALGLLQGDVVRIRRG 63 (137)
T ss_pred CceEEECHHHHHHcCCCCCCEEEEEeC
Confidence 567999999999999999999999874
No 83
>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=25.44 E-value=1e+02 Score=25.79 Aligned_cols=25 Identities=28% Similarity=0.381 Sum_probs=21.2
Q ss_pred eccCCCEEEEeeCCEEEEEEEEeec
Q 047222 138 CLTTGDTIMVPYNNKKYYINVVETK 162 (342)
Q Consensus 138 tLT~Gd~I~I~yn~~~y~l~V~e~k 162 (342)
.|.+||.|.|...++.|...|.+++
T Consensus 64 ~l~~Gd~v~v~~~~~~~~Y~V~~~~ 88 (128)
T cd00004 64 NLKKGDKIYLTDGGKTYVYKVTSIL 88 (128)
T ss_pred HCCCCCEEEEEECCEEEEEEEEEEE
Confidence 3556999999999999999988864
No 84
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=25.27 E-value=1.7e+02 Score=23.77 Aligned_cols=48 Identities=23% Similarity=0.584 Sum_probs=31.0
Q ss_pred CeeccCCCEEEEeeCC-------EEEEE-EEEeec-----C------------CCeeEEEecceeEeecCCCC
Q 047222 136 YSCLTTGDTIMVPYNN-------KKYYI-NVVETK-----P------------STAVSIIETDCEVDFIPPLD 183 (342)
Q Consensus 136 ystLT~Gd~I~I~yn~-------~~y~l-~V~e~k-----P------------~~aVsIIdTDleVDf~pPld 183 (342)
|-.+..||++.|..++ +.|++ .|+.+. | ..-|+.|++|....+.+++|
T Consensus 3 FL~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~ggaR~P~~~tlFQVadVDtG~I~wVnaD~Vt~Iv~~~~ 75 (75)
T PF11302_consen 3 FLSVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGGARDPKVPTLFQVADVDTGVIRWVNADEVTHIVPSLD 75 (75)
T ss_pred ccccCCCCEEEEecCccccccCCCCcEEEEEEEEeccccCCCCCceEEEEEccCCeEEEEEchheeeeeeccC
Confidence 4456677777777655 33433 344432 2 24789999999998887764
No 85
>PF10636 hemP: Hemin uptake protein hemP; InterPro: IPR019600 This entry represents bacterial proteins that are involved in the uptake of the iron source hemin []. ; PDB: 2JRA_B 2LOJ_A.
Probab=25.12 E-value=1.5e+02 Score=21.09 Aligned_cols=22 Identities=9% Similarity=0.314 Sum_probs=18.5
Q ss_pred ccCCCEEEEeeCCEEEEEEEEe
Q 047222 139 LTTGDTIMVPYNNKKYYINVVE 160 (342)
Q Consensus 139 LT~Gd~I~I~yn~~~y~l~V~e 160 (342)
+--+..|.|.+++..|.|++..
T Consensus 9 ~~~~~ev~I~H~g~~Y~LR~Tr 30 (38)
T PF10636_consen 9 FGGGREVRIEHGGQIYRLRITR 30 (38)
T ss_dssp TTTTSEEEEEETTEEEEEEEET
T ss_pred hCCCCEEEEEeCCeEEEeeEcc
Confidence 3456789999999999999864
No 86
>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=24.60 E-value=1e+02 Score=25.88 Aligned_cols=24 Identities=25% Similarity=0.423 Sum_probs=20.4
Q ss_pred ccCCCEEEEeeCCEEEEEEEEeec
Q 047222 139 LTTGDTIMVPYNNKKYYINVVETK 162 (342)
Q Consensus 139 LT~Gd~I~I~yn~~~y~l~V~e~k 162 (342)
|.+||.|.|...++.|...|.+++
T Consensus 64 l~~Gd~I~l~~~~~~~~Y~V~~~~ 87 (127)
T cd06165 64 VKVGDKIYLTDKDNVYEYKVTSKK 87 (127)
T ss_pred CcCCCEEEEEECCEEEEEEEeeEE
Confidence 448999999999999998888754
No 87
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=24.01 E-value=1.1e+02 Score=22.36 Aligned_cols=27 Identities=11% Similarity=0.494 Sum_probs=22.5
Q ss_pred ccCCCEEEEee-CCEEEEEEEEeecCCC
Q 047222 139 LTTGDTIMVPY-NNKKYYINVVETKPST 165 (342)
Q Consensus 139 LT~Gd~I~I~y-n~~~y~l~V~e~kP~~ 165 (342)
|.+|+.+.+.+ ++..|.=+|+++++.+
T Consensus 1 ~~vG~~v~~~~~~~~~y~A~I~~~r~~~ 28 (55)
T PF11717_consen 1 FEVGEKVLCKYKDGQWYEAKILDIREKN 28 (55)
T ss_dssp --TTEEEEEEETTTEEEEEEEEEEEECT
T ss_pred CCcCCEEEEEECCCcEEEEEEEEEEecC
Confidence 46899999999 8999999999998754
No 88
>PF01272 GreA_GreB: Transcription elongation factor, GreA/GreB, C-term; InterPro: IPR001437 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 2P4V_E 2ETN_B 3BMB_B 2PN0_D 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A.
Probab=23.79 E-value=1.2e+02 Score=23.45 Aligned_cols=24 Identities=17% Similarity=0.254 Sum_probs=19.1
Q ss_pred ccCCCEEEEeeCCEEEEEEEEeec
Q 047222 139 LTTGDTIMVPYNNKKYYINVVETK 162 (342)
Q Consensus 139 LT~Gd~I~I~yn~~~y~l~V~e~k 162 (342)
...||++.+...+..+.+.|++++
T Consensus 53 ~~~Gd~v~~~~~~g~~~~~I~~I~ 76 (77)
T PF01272_consen 53 KKVGDEVEVELPGGERKYEILEIE 76 (77)
T ss_dssp -BTT-EEEEEETTBEEEEEEEEEE
T ss_pred CCCCCEEEEEeCCceEEEEEEEEE
Confidence 468999999999888888888863
No 89
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=23.21 E-value=87 Score=23.82 Aligned_cols=56 Identities=14% Similarity=0.160 Sum_probs=36.1
Q ss_pred CCCCCEEEEEEeec-C-CcceEEEeeCCcCcCCcCCcHHHHHHhhcc-CeeccCCCEEEEee
Q 047222 91 LQEGDIVEVKNASL-A-KGSYVKLQPHTKDFLDISNPKAVLETTLRS-YSCLTTGDTIMVPY 149 (342)
Q Consensus 91 l~~gd~V~i~~~~L-P-kGt~vkLqP~s~~FldisnpKavLE~~LRn-ystLT~Gd~I~I~y 149 (342)
|++|+.|.=+-+.+ + .|-||.|-|.-..|+-|++... ...++ ...+..||+|.+..
T Consensus 1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~---~~~~~~~~~~~~Gd~v~~kV 59 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSD---SYTENPLEGFKPGKIVRCCI 59 (72)
T ss_pred CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcC---cccCCHHHhCCCCCEEEEEE
Confidence 46788876555553 3 6999999988888886653211 12223 23467899998764
No 90
>PRK05807 hypothetical protein; Provisional
Probab=23.11 E-value=2.5e+02 Score=24.49 Aligned_cols=55 Identities=22% Similarity=0.305 Sum_probs=34.3
Q ss_pred CCCCCCEEEEEEe-ecCCcceEEEeeCCcCcCCcCCcHHHHHHhhcc-CeeccCCCEEEEe
Q 047222 90 LLQEGDIVEVKNA-SLAKGSYVKLQPHTKDFLDISNPKAVLETTLRS-YSCLTTGDTIMVP 148 (342)
Q Consensus 90 ~l~~gd~V~i~~~-~LPkGt~vkLqP~s~~FldisnpKavLE~~LRn-ystLT~Gd~I~I~ 148 (342)
.++.|+.|.-.-+ ..+-|-||.| .....|+-+++... ...++ ...|..||.|.+.
T Consensus 2 ~~~vG~vv~G~Vt~i~~~GafV~L-~~~~Glvhiseis~---~~v~~~~~~~kvGd~V~Vk 58 (136)
T PRK05807 2 TLKAGSILEGTVVNITNFGAFVEV-EGKTGLVHISEVAD---TYVKDIREHLKEQDKVKVK 58 (136)
T ss_pred CccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEhhhccc---ccccCccccCCCCCEEEEE
Confidence 3567888776644 5789999999 44456665543221 11222 3458899998864
No 91
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=23.00 E-value=1.1e+02 Score=24.36 Aligned_cols=24 Identities=33% Similarity=0.356 Sum_probs=20.8
Q ss_pred CcEeccHHHHHHcCCCCCCEEEEE
Q 047222 77 GLIYLPYWMMENMLLQEGDIVEVK 100 (342)
Q Consensus 77 G~i~LP~WMm~~L~l~~gd~V~i~ 100 (342)
-.+.+|.-|-.++.+.+||.|.|+
T Consensus 25 ~la~i~gK~rk~iwI~~GD~V~Ve 48 (77)
T cd05793 25 RLCRIRGKMRKRVWINEGDIVLVA 48 (77)
T ss_pred EEEEEchhhcccEEEcCCCEEEEE
Confidence 357899999999999999998886
No 92
>TIGR02693 arsenite_ox_L arsenite oxidase, large subunit. This model represents the large subunit of an arsenite oxidase complex. The small subunit is a Rieske protein. Homologs to both large and small subunits that score in the gray zone between the set trusted and noise bit score cutoffs for the respective models are found in Aeropyrum pernix K1 and in Sulfolobus tokodaii str. 7. This enzyme acts in energy metabolim by arsenite oxidation, rather than detoxification by reduction of arsenate to arsenite prior to export.
Probab=22.67 E-value=1e+02 Score=34.32 Aligned_cols=30 Identities=27% Similarity=0.157 Sum_probs=26.7
Q ss_pred eeCCCcEeccHHHHHHcCCCCCCEEEEEEe
Q 047222 73 IADEGLIYLPYWMMENMLLQEGDIVEVKNA 102 (342)
Q Consensus 73 ~AeEG~i~LP~WMm~~L~l~~gd~V~i~~~ 102 (342)
..++..|.|-.=-++.|||.+||.|+|.+-
T Consensus 721 ~~p~p~v~InP~DA~~lGI~dGD~V~V~n~ 750 (806)
T TIGR02693 721 RLPLPYIEVNPEDAKRLGLKSGDLVEVYND 750 (806)
T ss_pred cCCCCEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 346788999999999999999999999874
No 93
>PRK09376 rho transcription termination factor Rho; Provisional
Probab=22.44 E-value=1.4e+02 Score=31.28 Aligned_cols=39 Identities=28% Similarity=0.330 Sum_probs=30.6
Q ss_pred CEEEEEEeeee---------------eCCCcEeccHHHHHHcCCCCCCEEEEEE
Q 047222 63 RVTYCGVMEFI---------------ADEGLIYLPYWMMENMLLQEGDIVEVKN 101 (342)
Q Consensus 63 r~th~GVLEF~---------------AeEG~i~LP~WMm~~L~l~~gd~V~i~~ 101 (342)
.....||||.. +.+.-||+|..+.+..+|+.||.|.=.-
T Consensus 48 ~~~~~g~le~~~~g~gflr~~~~~y~~~~~d~yvs~~~ir~~~lr~gd~v~g~~ 101 (416)
T PRK09376 48 DIFGEGVLEILPDGFGFLRSPDANYLPGPDDIYVSPSQIRRFNLRTGDTVEGKI 101 (416)
T ss_pred ceEEEEEEEEcCCCCeEEeCCCcCCCCCCCCeeeCHHHHHhcCCCCCCEEEEEe
Confidence 35789999932 2345699999999999999999887543
No 94
>PRK13532 nitrate reductase catalytic subunit; Provisional
Probab=22.07 E-value=85 Score=34.75 Aligned_cols=51 Identities=22% Similarity=0.124 Sum_probs=36.1
Q ss_pred CCCeEEEEEeCCCCCEEEEEE--------eeeeeCCCcEeccHHHHHHcCCCCCCEEEEEEe
Q 047222 49 EYPMLFELSNTSAGRVTYCGV--------MEFIADEGLIYLPYWMMENMLLQEGDIVEVKNA 102 (342)
Q Consensus 49 ~~PmlF~L~n~~~~r~th~GV--------LEF~AeEG~i~LP~WMm~~L~l~~gd~V~i~~~ 102 (342)
.|| |.|.+......+|.+. ++. .+|..|+|=.=-++.|||.+||.|+|.+-
T Consensus 713 ~yp--l~Lit~r~~~~~hs~~~~~~~~~l~~~-~~~~~v~inp~DA~~~GI~dGD~V~V~n~ 771 (830)
T PRK13532 713 EYD--LWLSTGRVLEHWHTGSMTRRVPELYRA-FPEAVCFMHPEDAKARGLRRGDEVKVVSR 771 (830)
T ss_pred CCC--eEEecccchhhccccCccCchHHHHhh-CCCCEEEECHHHHHHcCCCCCCEEEEEeC
Confidence 477 4444444444456542 222 36788999999999999999999999875
No 95
>PF00667 FAD_binding_1: FAD binding domain; InterPro: IPR003097 This domain is found in sulphite reductase, NADPH cytochrome P450 reductase, nitric oxide synthase and methionine synthase reductase. Flavoprotein pyridine nucleotide cytochrome reductases [] (FPNCR) catalyse the interchange of reducing equivalents between one-electron carriers and the two-electron-carrying nicotinamide dinucleotides. The enzymes include ferredoxin:NADP+reductases (FNR) [], plant and fungal NAD(P)H:nitrate reductases [, ], NADH:cytochrome b5 reductases [], NADPH:P450 reductases [], NADPH:sulphite reductases [], nitric oxide synthases [], phthalate dioxygenase reductase [], and various other flavoproteins.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3QFR_B 3FJO_A 3QFC_B 3QE2_B 3QFS_A 3QFT_A 2B5O_B 2QTZ_A 2QTL_A 2BPO_B ....
Probab=21.52 E-value=1.3e+02 Score=27.60 Aligned_cols=87 Identities=22% Similarity=0.342 Sum_probs=48.9
Q ss_pred CCCeEEEEEe------CCCCCEEEEEEeeee-eCCCcEecc---------------HHHHHHcCCCCCCEEEEEEee---
Q 047222 49 EYPMLFELSN------TSAGRVTYCGVMEFI-ADEGLIYLP---------------YWMMENMLLQEGDIVEVKNAS--- 103 (342)
Q Consensus 49 ~~PmlF~L~n------~~~~r~th~GVLEF~-AeEG~i~LP---------------~WMm~~L~l~~gd~V~i~~~~--- 103 (342)
..|+..+|.. ....|.|+. +||. .+.|.-|-| .++++.|++.....|.|....
T Consensus 6 ~~p~~a~V~~~~~Lt~~~~~r~~~h--ieldl~~~~l~Y~pGD~l~V~P~N~~~~V~~~l~~lgl~~d~~v~~~~~~~~~ 83 (219)
T PF00667_consen 6 KNPFPATVLENRRLTSPGSDRSTRH--IELDLSDSGLSYQPGDHLGVYPPNDPEEVERLLKRLGLDPDEPVTLKPKEQNN 83 (219)
T ss_dssp TB-EEEEEEEEEE-SSTTSSSEEEE--EEEE-TTSTG---TT-EEEEE-SSEHHHHHHHHHHHTSGTTSEEEEEESSTTS
T ss_pred CCCEEEEEEeEEEcCCCCCCceEEE--EEEEeCCCCCcccCCCEEEEEccCCHHHHHHHHHHhCCCcceEEEEEeccccc
Confidence 3466665543 334555444 6663 344666655 579999999998899998765
Q ss_pred ---cCCcceEEEeeCCcCcCCcCC-cHHHHHHhhccCe
Q 047222 104 ---LAKGSYVKLQPHTKDFLDISN-PKAVLETTLRSYS 137 (342)
Q Consensus 104 ---LPkGt~vkLqP~s~~Fldisn-pKavLE~~LRnys 137 (342)
+|-..-+.|.=.=+.++||.. |+.-+=..|-.|+
T Consensus 84 ~~~~~~~~~~tl~~~l~~~~Di~~~p~~~~l~~la~~~ 121 (219)
T PF00667_consen 84 SVKPPFPSPITLRDLLTHYLDITSPPSRSFLRALAEFA 121 (219)
T ss_dssp SCCSSSSSSEEHHHHHHHTB-TSSB--HHHHHHHHCTB
T ss_pred ccccccccceeeeeeeeeeeecccccccceeeeeeecC
Confidence 555555665554456667776 4433334444443
No 96
>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=20.92 E-value=1e+02 Score=33.73 Aligned_cols=70 Identities=21% Similarity=0.329 Sum_probs=46.5
Q ss_pred CCcEeccHHHHHHcCCCCCCEEEEEEeecCCcceEEEeeCCcCcCCcCCcHHHHHHhhccCeeccCCCEEEEee
Q 047222 76 EGLIYLPYWMMENMLLQEGDIVEVKNASLAKGSYVKLQPHTKDFLDISNPKAVLETTLRSYSCLTTGDTIMVPY 149 (342)
Q Consensus 76 EG~i~LP~WMm~~L~l~~gd~V~i~~~~LPkGt~vkLqP~s~~FldisnpKavLE~~LRnystLT~Gd~I~I~y 149 (342)
-|.+.|..-.|+.|++.+||.|.|..- -+.+-.+.-|...+ +...----|...+|....+..||.+.|.-
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (733)
T TIGR01243 16 RGIVRIDRQTAARLGVEPGDFVEIEKG--DRSVVAIVWPLRPD--DEGRGIIRMDGYLRANAGVTIGDTVTVER 85 (733)
T ss_pred CCeEeeCHHHHHhcCCCCCCEEEEecC--CCceeEEEEecCcc--ccCCCEEeecHHHHhhcCCCCCCeEEEee
Confidence 478899999999999999999999831 11234444443222 12211222556677777799999999864
No 97
>PRK10183 hypothetical protein; Provisional
Probab=20.77 E-value=1.3e+02 Score=23.11 Aligned_cols=22 Identities=9% Similarity=0.385 Sum_probs=19.3
Q ss_pred ccCCCEEEEeeCCEEEEEEEEe
Q 047222 139 LTTGDTIMVPYNNKKYYINVVE 160 (342)
Q Consensus 139 LT~Gd~I~I~yn~~~y~l~V~e 160 (342)
|.-+..|.|.+++..|.|++..
T Consensus 27 l~g~~~v~I~H~G~~Y~LR~Tr 48 (56)
T PRK10183 27 LGPDGKVIIDHDGQEYLLRKTQ 48 (56)
T ss_pred hCCCCEEEEEECCcEEEeEEcc
Confidence 5667899999999999999865
No 98
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=20.46 E-value=1.5e+02 Score=26.30 Aligned_cols=25 Identities=12% Similarity=0.096 Sum_probs=22.1
Q ss_pred eccCCCEEEEeeCCEEEEEEEEeec
Q 047222 138 CLTTGDTIMVPYNNKKYYINVVETK 162 (342)
Q Consensus 138 tLT~Gd~I~I~yn~~~y~l~V~e~k 162 (342)
.+..||+|.|.++...+.|.|+.+.
T Consensus 48 ~V~~gd~l~v~~~~~~~~v~Vl~l~ 72 (133)
T PRK10348 48 IVELNATLTLRQGNDERTVIVKAIT 72 (133)
T ss_pred ccCCCCEEEEEECCEEEEEEEeECc
Confidence 3568999999999999999999874
Done!