Query 034235
Match_columns 100
No_of_seqs 114 out of 735
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 11:15:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034235.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034235hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3276 Uncharacterized conser 99.9 1.2E-24 2.6E-29 153.7 8.5 93 1-98 1-93 (125)
2 PRK05090 hypothetical protein; 99.9 2.4E-23 5.1E-28 142.0 8.7 68 29-97 1-68 (95)
3 PF02594 DUF167: Uncharacteris 99.9 2.5E-22 5.4E-27 132.0 6.8 60 38-97 2-62 (77)
4 PRK00647 hypothetical protein; 99.9 5.9E-22 1.3E-26 135.6 7.6 60 38-97 4-63 (96)
5 PRK01310 hypothetical protein; 99.9 9.4E-22 2E-26 135.9 8.5 67 30-97 3-74 (104)
6 PRK01530 hypothetical protein; 99.8 4E-21 8.6E-26 133.2 7.9 62 36-97 10-75 (105)
7 COG1872 Uncharacterized conser 99.8 2.2E-21 4.7E-26 134.1 6.5 68 29-97 3-72 (102)
8 TIGR00251 conserved hypothetic 99.8 4.9E-20 1.1E-24 123.9 8.0 61 33-97 2-64 (87)
9 PRK04021 hypothetical protein; 99.8 3.5E-19 7.6E-24 120.7 8.3 58 32-90 2-61 (92)
10 PF09581 Spore_III_AF: Stage I 91.1 0.64 1.4E-05 33.6 5.2 57 41-99 124-188 (188)
11 PF01187 MIF: Macrophage migra 88.0 1.9 4.2E-05 29.2 5.5 57 41-98 36-97 (114)
12 PTZ00397 macrophage migration 84.1 6.4 0.00014 26.5 6.5 58 41-99 38-100 (116)
13 KOG1759 Macrophage migration i 78.5 4.5 9.8E-05 28.7 4.2 59 41-100 37-100 (115)
14 PF08968 DUF1885: Domain of un 68.3 2.7 5.8E-05 30.5 1.0 28 61-89 82-114 (130)
15 COG1451 Predicted metal-depend 66.7 14 0.0003 28.3 4.8 47 39-89 9-55 (223)
16 PTZ00450 macrophage migration 52.8 12 0.00026 25.8 2.1 58 40-98 37-99 (113)
17 cd00491 4Oxalocrotonate_Tautom 51.5 22 0.00048 20.4 2.9 24 76-99 19-42 (58)
18 TIGR00013 taut 4-oxalocrotonat 51.2 22 0.00048 20.9 2.9 24 76-99 20-43 (63)
19 PF01361 Tautomerase: Tautomer 51.1 20 0.00044 21.0 2.7 23 77-99 20-42 (60)
20 PRK01964 4-oxalocrotonate taut 47.1 24 0.00051 21.1 2.6 24 76-99 20-43 (64)
21 PF12685 SpoIIIAH: SpoIIIAH-li 46.4 47 0.001 24.5 4.6 46 52-97 150-195 (196)
22 PRK00745 4-oxalocrotonate taut 44.4 28 0.0006 20.5 2.6 22 77-98 21-42 (62)
23 PF14552 Tautomerase_2: Tautom 43.8 25 0.00054 23.0 2.4 41 59-99 26-71 (82)
24 PRK02220 4-oxalocrotonate taut 43.4 29 0.00064 20.3 2.6 23 76-98 20-42 (61)
25 PRK02289 4-oxalocrotonate taut 42.7 34 0.00074 20.4 2.8 24 76-99 20-43 (60)
26 cd02552 PseudoU_synth_TruD_lik 40.7 21 0.00046 27.5 2.0 36 60-98 30-65 (232)
27 smart00760 Bac_DnaA_C Bacteria 40.6 13 0.00029 22.3 0.7 19 78-96 3-21 (60)
28 PF04969 CS: CS domain; Inter 39.8 79 0.0017 18.5 4.3 35 34-69 7-43 (79)
29 PF02738 Ald_Xan_dh_C2: Molybd 39.6 50 0.0011 27.8 4.2 45 54-98 322-367 (547)
30 cd02575 PseudoU_synth_EcTruD P 37.3 27 0.00058 27.5 2.1 37 59-98 23-59 (253)
31 cd06490 p23_NCB5OR p23_like do 36.5 84 0.0018 20.2 4.1 39 30-70 2-42 (87)
32 cd06463 p23_like Proteins cont 35.0 85 0.0018 18.4 3.8 31 39-69 7-37 (84)
33 PHA02564 V virion protein; Pro 34.3 45 0.00096 24.2 2.7 29 66-95 74-102 (141)
34 PRK01271 4-oxalocrotonate taut 32.2 58 0.0013 21.0 2.8 22 78-99 23-44 (76)
35 PF09098 Dehyd-heme_bind: Quin 31.8 32 0.0007 25.9 1.7 25 71-95 50-74 (167)
36 TIGR00094 tRNA_TruD_broad tRNA 31.5 40 0.00087 27.4 2.4 36 60-98 41-76 (387)
37 cd02576 PseudoU_synth_ScPUS7 P 30.5 41 0.00089 27.2 2.3 35 61-98 29-63 (371)
38 PRK06290 aspartate aminotransf 29.7 68 0.0015 25.9 3.4 28 61-88 376-403 (410)
39 PF08299 Bac_DnaA_C: Bacterial 29.3 22 0.00047 22.2 0.4 19 78-96 3-21 (70)
40 PF01257 2Fe-2S_thioredx: Thio 29.1 22 0.00048 25.1 0.4 21 76-96 29-49 (145)
41 PF00046 Homeobox: Homeobox do 27.9 28 0.00062 20.0 0.7 19 77-95 26-44 (57)
42 PF14804 Jag_N: Jag N-terminus 27.8 79 0.0017 19.0 2.7 26 74-99 4-29 (52)
43 PF12116 SpoIIID: Stage III sp 27.4 21 0.00045 24.0 0.0 19 77-95 18-36 (82)
44 TIGR01958 nuoE_fam NADH-quinon 27.1 28 0.0006 24.7 0.6 20 77-96 33-52 (148)
45 KOG4079 Putative mitochondrial 26.6 47 0.001 24.8 1.8 20 72-91 91-110 (169)
46 PF10410 DnaB_bind: DnaB-helic 26.6 65 0.0014 18.6 2.1 22 74-95 38-59 (59)
47 PF01142 TruD: tRNA pseudourid 26.1 66 0.0014 26.0 2.7 37 59-98 42-78 (378)
48 PRK00984 truD tRNA pseudouridi 26.1 51 0.0011 26.7 2.1 37 59-98 40-76 (341)
49 cd02577 PSTD1 PSTD1: Pseudouri 26.0 52 0.0011 26.5 2.1 36 60-98 24-59 (319)
50 cd00086 homeodomain Homeodomai 25.7 27 0.00059 19.8 0.3 20 77-96 26-45 (59)
51 PF00550 PP-binding: Phosphopa 25.1 56 0.0012 18.9 1.6 19 78-96 1-19 (67)
52 PRK07199 phosphoribosylpyropho 24.3 64 0.0014 25.6 2.3 28 73-100 7-34 (301)
53 COG0245 IspF 2C-methyl-D-eryth 24.3 82 0.0018 23.5 2.7 30 69-98 101-130 (159)
54 COG0462 PrsA Phosphoribosylpyr 24.3 66 0.0014 26.3 2.4 27 74-100 10-36 (314)
55 PF08381 BRX: Transcription fa 23.6 1.2E+02 0.0026 19.1 2.9 22 30-52 5-26 (59)
56 PRK07539 NADH dehydrogenase su 23.5 35 0.00077 24.3 0.6 20 77-96 39-58 (154)
57 PRK04923 ribose-phosphate pyro 23.2 68 0.0015 25.8 2.3 27 74-100 12-38 (319)
58 PRK07571 bidirectional hydroge 22.8 37 0.0008 25.1 0.6 23 74-96 50-72 (169)
59 cd00298 ACD_sHsps_p23-like Thi 22.8 1.6E+02 0.0034 16.5 3.6 35 39-73 7-41 (80)
60 PF07805 HipA_N: HipA-like N-t 21.9 1.1E+02 0.0023 19.1 2.6 26 72-97 40-65 (81)
61 COG0851 MinE Septum formation 21.9 1E+02 0.0022 20.9 2.6 23 77-99 43-65 (88)
62 COG3382 Solo B3/4 domain (OB-f 21.7 3.3E+02 0.0071 21.4 5.7 65 25-89 149-213 (229)
63 PRK00553 ribose-phosphate pyro 20.7 81 0.0018 25.5 2.2 27 74-100 15-41 (332)
64 smart00389 HOX Homeodomain. DN 20.4 40 0.00087 19.0 0.3 20 77-96 26-45 (56)
65 PF03776 MinE: Septum formatio 20.4 1.3E+02 0.0029 18.9 2.8 23 77-99 31-53 (70)
66 TIGR03311 Se_dep_Molyb_1 selen 20.3 1.7E+02 0.0038 26.6 4.4 44 55-98 598-641 (848)
67 TIGR02416 CO_dehy_Mo_lg carbon 20.2 1.4E+02 0.0031 26.7 3.8 43 56-98 480-523 (770)
No 1
>KOG3276 consensus Uncharacterized conserved protein, contains YggU domain [Function unknown]
Probab=99.91 E-value=1.2e-24 Score=153.69 Aligned_cols=93 Identities=47% Similarity=0.745 Sum_probs=86.9
Q ss_pred CCCcccCcccccCCCCccccCCCCCCCCCcceEeeCCCeEEEEEEEecCCCccccccccCCeEEEEEeCCCCcChhHHHH
Q 034235 1 MAPAKKGKSKAKSAGSTQSKIKTNDENLPSCIRLVPPSSVSITIHAKPGSKSCSITDVSDEAVGVQIDAPAKDGEANAAL 80 (100)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~i~~~~~g~v~l~v~VkP~Ak~~~I~~~~~~~l~V~V~ApP~dGkAN~aL 80 (100)
|.|+|+|++++..+.+ +.+..++|+||..+..|.+.|.||++|||++++|+++.++.+.|.|.|||.+|+||+||
T Consensus 1 i~pkk~g~s~k~~~t~-----~~~~~~~p~~i~~d~~g~V~i~IhakpgaK~s~It~v~~e~V~V~IaApp~eGeANaeL 75 (125)
T KOG3276|consen 1 VMPKKKGKSTKGAETS-----KVDDKPVPPCISVDTGGLVQIAIHAKPGAKQSAITDVGDEAVGVAIAAPPREGEANAEL 75 (125)
T ss_pred CccccccccccccccC-----CCccCCCCCceEecCCCeEEEEEEecCCccccceeeccccccceEEecCCccchhhHHH
Confidence 6899999998877655 36778899999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcCCCCCceEee
Q 034235 81 LEYMSSLIHVSVGEFVES 98 (100)
Q Consensus 81 i~~LAk~LgV~ks~I~~~ 98 (100)
++||++.||+++|++++.
T Consensus 76 l~ylskvLgLRksdv~ld 93 (125)
T KOG3276|consen 76 LEYLSKVLGLRKSDVTLD 93 (125)
T ss_pred HHHHHHHhhhhhhheeec
Confidence 999999999999999873
No 2
>PRK05090 hypothetical protein; Validated
Probab=99.90 E-value=2.4e-23 Score=141.99 Aligned_cols=68 Identities=24% Similarity=0.377 Sum_probs=64.9
Q ss_pred CcceEeeCCCeEEEEEEEecCCCccccccccCCeEEEEEeCCCCcChhHHHHHHHHHhhcCCCCCceEe
Q 034235 29 PSCIRLVPPSSVSITIHAKPGSKSCSITDVSDEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVE 97 (100)
Q Consensus 29 P~~i~~~~~g~v~l~v~VkP~Ak~~~I~~~~~~~l~V~V~ApP~dGkAN~aLi~~LAk~LgV~ks~I~~ 97 (100)
|.|+++.++ +++|+|+|+|+|++++|.++++++|+|+|+|||+||+||++|++|||+.|+|++|+|+.
T Consensus 1 ~~~~~~~~~-~~~l~i~V~P~A~~~~i~~~~~~~lkv~v~ApPveGkAN~ali~~LAk~l~v~ks~I~i 68 (95)
T PRK05090 1 MSAVTWDGD-GLVLRLYIQPKASRDQIVGLHGDELKVAITAPPVDGQANAHLLKFLAKQFRVAKSQVVI 68 (95)
T ss_pred CCceEEeCC-eEEEEEEEeeCCCcceeccccCCEEEEEEecCCCCChHHHHHHHHHHHHhCCChhhEEE
Confidence 578888776 89999999999999999999999999999999999999999999999999999999986
No 3
>PF02594 DUF167: Uncharacterised ACR, YggU family COG1872; InterPro: IPR003746 This entry describes proteins of unknown function. Structures for two of these proteins, YggU from Escherichia coli and MTH637 from the archaea Methanobacterium thermoautotrophicum, have been determined; they have a core 2-layer alpha/beta structure consisting of beta(2)-loop-alpha-beta(2)-alpha [, ].; PDB: 1YH5_A 1N91_A 1JRM_A.
Probab=99.87 E-value=2.5e-22 Score=131.99 Aligned_cols=60 Identities=28% Similarity=0.557 Sum_probs=52.9
Q ss_pred CeEEEEEEEecCCCccccccccCC-eEEEEEeCCCCcChhHHHHHHHHHhhcCCCCCceEe
Q 034235 38 SSVSITIHAKPGSKSCSITDVSDE-AVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVE 97 (100)
Q Consensus 38 g~v~l~v~VkP~Ak~~~I~~~~~~-~l~V~V~ApP~dGkAN~aLi~~LAk~LgV~ks~I~~ 97 (100)
++++|.|+|+|+|++++|.+++++ +|+|+|+|||+||+||+||++|||++|+||+|+|+.
T Consensus 2 ~~~~l~v~V~P~ak~~~i~~~~~~~~l~i~v~app~~GkAN~ali~~La~~l~v~ks~i~i 62 (77)
T PF02594_consen 2 DGVILSVRVKPGAKRNAIVGVEGDGALKIRVTAPPVDGKANKALIRFLAKALGVPKSDIEI 62 (77)
T ss_dssp TEEEEEEECEBSSSS-EEEEE-TTT-EEEEBSTTCCCCCHHHHHHHHHHHHCT--TTCEEE
T ss_pred CeEEEEEEEEeCCCccccccccCceEEEEEEecCCCcChhHHHHHHHHHHHhCCCcccEEE
Confidence 489999999999999999999996 999999999999999999999999999999999986
No 4
>PRK00647 hypothetical protein; Validated
Probab=99.86 E-value=5.9e-22 Score=135.55 Aligned_cols=60 Identities=12% Similarity=0.275 Sum_probs=58.3
Q ss_pred CeEEEEEEEecCCCccccccccCCeEEEEEeCCCCcChhHHHHHHHHHhhcCCCCCceEe
Q 034235 38 SSVSITIHAKPGSKSCSITDVSDEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVE 97 (100)
Q Consensus 38 g~v~l~v~VkP~Ak~~~I~~~~~~~l~V~V~ApP~dGkAN~aLi~~LAk~LgV~ks~I~~ 97 (100)
+.++|.|+|+|+|++++|.++++++|+|+|+|||+|||||+||++|||+.||||+++|+.
T Consensus 4 ~~~~l~V~V~P~Ak~~~I~g~~~~~Lkvrv~ApPvdGKAN~ali~~LAk~l~vpks~I~I 63 (96)
T PRK00647 4 GFWILEVKVTPKARENKIVGFEGGILKVRVTEVPEKGKANDAVIALLAKFLSLPKRDVTL 63 (96)
T ss_pred CcEEEEEEEeeCCCcceeccccCCEEEEEEecCCCCChHHHHHHHHHHHHhCCChhhEEE
Confidence 579999999999999999999999999999999999999999999999999999999985
No 5
>PRK01310 hypothetical protein; Validated
Probab=99.86 E-value=9.4e-22 Score=135.92 Aligned_cols=67 Identities=19% Similarity=0.296 Sum_probs=61.9
Q ss_pred cceEeeCCCeEEEEEEEecCCCccccccccC-----CeEEEEEeCCCCcChhHHHHHHHHHhhcCCCCCceEe
Q 034235 30 SCIRLVPPSSVSITIHAKPGSKSCSITDVSD-----EAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVE 97 (100)
Q Consensus 30 ~~i~~~~~g~v~l~v~VkP~Ak~~~I~~~~~-----~~l~V~V~ApP~dGkAN~aLi~~LAk~LgV~ks~I~~ 97 (100)
.++++.++ +++|.|+|+|+|++++|.++++ +.|+|+|+|||+|||||++|++|||++||||+++|+.
T Consensus 3 ~~~~~~~~-~~~i~v~V~P~A~~~~i~g~~~~~~g~~~lkv~v~apPv~GkAN~ali~~LA~~l~v~ks~I~i 74 (104)
T PRK01310 3 EPWRYSAD-GLRLAVRLTPRGGRDAIDGIETLADGRAVLKVRVRAVPEGGEANRALIELLAKALGVPKSSVRL 74 (104)
T ss_pred CceEECCC-cEEEEEEEeeCCCcceeccccccCCCccEEEEEEecCCCCChHHHHHHHHHHHHhCCChhhEEE
Confidence 46788786 8999999999999999999864 3899999999999999999999999999999999986
No 6
>PRK01530 hypothetical protein; Reviewed
Probab=99.85 E-value=4e-21 Score=133.17 Aligned_cols=62 Identities=18% Similarity=0.298 Sum_probs=57.9
Q ss_pred CCCeEEEEEEEecCCCcccccccc----CCeEEEEEeCCCCcChhHHHHHHHHHhhcCCCCCceEe
Q 034235 36 PPSSVSITIHAKPGSKSCSITDVS----DEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVE 97 (100)
Q Consensus 36 ~~g~v~l~v~VkP~Ak~~~I~~~~----~~~l~V~V~ApP~dGkAN~aLi~~LAk~LgV~ks~I~~ 97 (100)
..+++.|.|+|+|+|++++|.+++ +++|+|+|+|||+|||||+||++|||+.||||+|+|+.
T Consensus 10 ~~~gv~l~V~V~P~Akk~~i~g~~~~~~~~~Lki~v~ApPvdGkAN~ali~~LAk~l~v~ks~I~I 75 (105)
T PRK01530 10 SSHQALLNLKVKPNAKQNLISNFVIINNIPYLKLSIKAIPEQGKANEEIINYLAKEWKLSRSNIEI 75 (105)
T ss_pred CCCcEEEEEEEeeCCCcccccceeccCCCCEEEEEEecCCCCChHHHHHHHHHHHHhCCChhhEEE
Confidence 345899999999999999999985 47999999999999999999999999999999999986
No 7
>COG1872 Uncharacterized conserved protein [Function unknown]
Probab=99.85 E-value=2.2e-21 Score=134.05 Aligned_cols=68 Identities=25% Similarity=0.399 Sum_probs=63.2
Q ss_pred CcceEeeCCCeEEEEEEEecCCCccccccccCCe--EEEEEeCCCCcChhHHHHHHHHHhhcCCCCCceEe
Q 034235 29 PSCIRLVPPSSVSITIHAKPGSKSCSITDVSDEA--VGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVE 97 (100)
Q Consensus 29 P~~i~~~~~g~v~l~v~VkP~Ak~~~I~~~~~~~--l~V~V~ApP~dGkAN~aLi~~LAk~LgV~ks~I~~ 97 (100)
..+++..++ +++|+|+|+|+|+++.|.++++++ |+|+|+|||++||||++|++|||+.|++|+|+|++
T Consensus 3 ~~~~~~~~~-~~~l~V~V~P~a~~~~i~g~~~~~~~Lkv~i~apP~~GKAN~~li~~Lak~~~v~kS~V~i 72 (102)
T COG1872 3 ESAVKELDD-GVLLRVRVKPKAKRDSIVGLDEWRKRLKVRITAPPVDGKANEELIKFLAKTFGVPKSSVEI 72 (102)
T ss_pred hhhHhhcCC-ceEEEEEECCCCccCcccceecCcceEEEEEecCCCCcchhHHHHHHHHHHhCCCcccEEE
Confidence 356677776 899999999999999999999876 99999999999999999999999999999999986
No 8
>TIGR00251 conserved hypothetical protein TIGR00251.
Probab=99.82 E-value=4.9e-20 Score=123.89 Aligned_cols=61 Identities=26% Similarity=0.414 Sum_probs=55.9
Q ss_pred EeeCCCeEEEEEEEecCCCccccccccC--CeEEEEEeCCCCcChhHHHHHHHHHhhcCCCCCceEe
Q 034235 33 RLVPPSSVSITIHAKPGSKSCSITDVSD--EAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVE 97 (100)
Q Consensus 33 ~~~~~g~v~l~v~VkP~Ak~~~I~~~~~--~~l~V~V~ApP~dGkAN~aLi~~LAk~LgV~ks~I~~ 97 (100)
++.++ +++|.|+|+|+|++++|.++++ ++|+|+|+|||+|||||+||++|||+.|++ +|+.
T Consensus 2 ~~~~~-g~~l~v~V~P~A~~~~i~g~~~~~~~Lki~v~ApP~~GkAN~ali~~La~~l~v---~I~i 64 (87)
T TIGR00251 2 RENDD-GLLIRIYVQPKASKDSIVGYNEWRKRVEVKIKAPPVEGKANRELIKFFGEIFGV---DVEI 64 (87)
T ss_pred eEeCC-eEEEEEEEeeCCCcceeccccCCCCeEEEEEecCCCCChHHHHHHHHHHHHhCc---eEEE
Confidence 45555 8999999999999999999999 899999999999999999999999999999 5654
No 9
>PRK04021 hypothetical protein; Reviewed
Probab=99.79 E-value=3.5e-19 Score=120.73 Aligned_cols=58 Identities=26% Similarity=0.471 Sum_probs=54.1
Q ss_pred eEeeCCCeEEEEEEEecCCCccccccccC--CeEEEEEeCCCCcChhHHHHHHHHHhhcCC
Q 034235 32 IRLVPPSSVSITIHAKPGSKSCSITDVSD--EAVGVQIDAPAKDGEANAALLEYMSSLIHV 90 (100)
Q Consensus 32 i~~~~~g~v~l~v~VkP~Ak~~~I~~~~~--~~l~V~V~ApP~dGkAN~aLi~~LAk~LgV 90 (100)
+++..+ +++|.|+|+|+|++++|.++++ +.|+|+|+|||+||+||+||++|||+.||+
T Consensus 2 ~~~~~~-~v~l~v~v~P~a~~~~i~g~~~~~~~lkv~v~apP~~GkAN~ali~~LAk~l~~ 61 (92)
T PRK04021 2 LKETKE-GVILQVYVQPKAKENEIEGVDEWRGRLKVKIKAPPVKGKANKELVKFFSKLLGA 61 (92)
T ss_pred eEEeCC-cEEEEEEEeeCCCcceEccccCCCCEEEEEEecCCCCChHHHHHHHHHHHHhCC
Confidence 566676 8999999999999999999865 899999999999999999999999999997
No 10
>PF09581 Spore_III_AF: Stage III sporulation protein AF (Spore_III_AF); InterPro: IPR014245 This family represents the stage III sporulation protein AF (SpoIIIAF) of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of these proteins is poorly conserved.
Probab=91.07 E-value=0.64 Score=33.63 Aligned_cols=57 Identities=18% Similarity=0.318 Sum_probs=38.5
Q ss_pred EEEEEEecCCCcc--ccccccCCeEEEEE------eCCCCcChhHHHHHHHHHhhcCCCCCceEeee
Q 034235 41 SITIHAKPGSKSC--SITDVSDEAVGVQI------DAPAKDGEANAALLEYMSSLIHVSVGEFVESV 99 (100)
Q Consensus 41 ~l~v~VkP~Ak~~--~I~~~~~~~l~V~V------~ApP~dGkAN~aLi~~LAk~LgV~ks~I~~~~ 99 (100)
.|.|.+++..... ....+ +-+.|.+ ...+.+.+..++|.++||+.|||++++|..+|
T Consensus 124 ~I~v~l~~~~~~~~~~~~~V--e~V~I~~~~~~~~~~~~~~~~~~~~i~~~la~~~~i~~~~I~V~~ 188 (188)
T PF09581_consen 124 EIKVTLSEEEEQKEEAVEPV--EPVEIDIEKESDSSKSPEDSEEEEEIKQYLADFYGISPEQIKVYV 188 (188)
T ss_pred EEEEEEcCCCccccccCCcc--cceEecccccccccccccchHHHHHHHHHHHHHhCCCHHHeEEeC
Confidence 4666666654322 11122 3344444 45667778899999999999999999998765
No 11
>PF01187 MIF: Macrophage migration inhibitory factor (MIF); InterPro: IPR001398 Macrophage migration inhibitory factor (MIF) is a key regulatory cytokine within innate and adaptive immune responses, capable of promoting and modulating the magnitude of the response []. MIF is released from T-cells and macrophages, and acts within the neuroendocrine system. MIF is capable of tautomerase activity, although its biological function has not been fully characterised. It is induced by glucocorticoid and is capable of overriding the anti-inflammatory actions of glucocorticoid []. MIF regulates cytokine secretion and the expression of receptors involved in the immune response. It can be taken up into target cells in order to interact with intracellular signalling molecules, inhibiting p53 function, and/or activating components of the mitogen-activated protein kinase and Jun-activation domain-binding protein-1 (Jab-1) []. MIF has been linked to various inflammatory diseases, such as rheumatoid arthritis and atherosclerosis []. The MIF homologue D-dopachrome tautomerase (4.1.1.84 from EC) is involved in detoxification through the conversion of dopaminechrome (and possibly norepinephrinechrome), the toxic quinine product of the neurotransmitter dopamine (and norepinephrine), to an indole derivative that can serve as a precursor to neuromelanin [, ].; PDB: 1UIZ_C 3FWT_A 1HFO_F 2WKB_D 3RF4_B 2OS5_A 3RF5_A 2XCZ_A 3FWU_A 3B64_A ....
Probab=88.03 E-value=1.9 Score=29.16 Aligned_cols=57 Identities=19% Similarity=0.281 Sum_probs=37.5
Q ss_pred EEEEEEecCCCccccccccCCeEEEEEeCCCC-cChhH----HHHHHHHHhhcCCCCCceEee
Q 034235 41 SITIHAKPGSKSCSITDVSDEAVGVQIDAPAK-DGEAN----AALLEYMSSLIHVSVGEFVES 98 (100)
Q Consensus 41 ~l~v~VkP~Ak~~~I~~~~~~~l~V~V~ApP~-dGkAN----~aLi~~LAk~LgV~ks~I~~~ 98 (100)
+|-|.|+++..=. ..|-++.+..+.|++.-. +.+.| ++|.+||.+.||||+.+|-..
T Consensus 36 ~i~V~v~~~~~m~-fgGs~~P~a~v~l~sig~~~~~~n~~~s~~i~~~l~~~LgIp~~Riyi~ 97 (114)
T PF01187_consen 36 YIMVTVEDGQRMS-FGGSDDPAAFVELKSIGGLDPEQNKKYSAAITEFLEEELGIPPDRIYIN 97 (114)
T ss_dssp GEEEEEEESTEEE-ETTB-SS-EEEEEEESSSSSHHHHHHHHHHHHHHHHHHHT--GGGEEEE
T ss_pred hEEEEeeCCceEE-ECCCCCCEEEEEEEEccCCCHHHHHHHHHHHHHHHHHHhCCCcCceEEE
Confidence 5667777877653 444456677777766553 44444 678999999999999998765
No 12
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=84.14 E-value=6.4 Score=26.49 Aligned_cols=58 Identities=12% Similarity=0.035 Sum_probs=36.1
Q ss_pred EEEEEEecCCCccccccccCCeEEEEEeCCCC-cChh----HHHHHHHHHhhcCCCCCceEeee
Q 034235 41 SITIHAKPGSKSCSITDVSDEAVGVQIDAPAK-DGEA----NAALLEYMSSLIHVSVGEFVESV 99 (100)
Q Consensus 41 ~l~v~VkP~Ak~~~I~~~~~~~l~V~V~ApP~-dGkA----N~aLi~~LAk~LgV~ks~I~~~~ 99 (100)
++-|.+.|...-. +.|-++..+.|+|+.-.. ..+. -++|.++|++.|||++.+|-..+
T Consensus 38 ~~~v~~~~~~~m~-f~g~~~p~a~v~i~~~g~~~~e~k~~l~~~i~~~l~~~lgi~~~rv~I~f 100 (116)
T PTZ00397 38 YIMSGYDYQKHMR-FGGSHDGCCFVRVTSIGGISRSNNSSIAAAITKILASHLKVKSERVYIEF 100 (116)
T ss_pred HEEEEEeCCceEE-ECCCCCceEEEEEEEecCCCHHHHHHHHHHHHHHHHHHhCcCcccEEEEE
Confidence 3444444443321 224456788888885433 2333 45678888999999999997653
No 13
>KOG1759 consensus Macrophage migration inhibitory factor [Defense mechanisms]
Probab=78.52 E-value=4.5 Score=28.72 Aligned_cols=59 Identities=10% Similarity=0.117 Sum_probs=38.7
Q ss_pred EEEEEEecCCCccccccccC-----CeEEEEEeCCCCcChhHHHHHHHHHhhcCCCCCceEeeeC
Q 034235 41 SITIHAKPGSKSCSITDVSD-----EAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVESVF 100 (100)
Q Consensus 41 ~l~v~VkP~Ak~~~I~~~~~-----~~l~V~V~ApP~dGkAN~aLi~~LAk~LgV~ks~I~~~~~ 100 (100)
+|.|++.++..- ...+-++ +-..+..-.+-++.+=-++|.++|.+.|++++++|-++.|
T Consensus 37 ~i~V~l~~~~~i-~fggt~eP~A~~~l~Sig~v~~~~N~~~sa~l~~il~~~L~l~~~rv~I~f~ 100 (115)
T KOG1759|consen 37 YIMVELAGGVRI-AFGGTTEPAAYASLKSIGGVGAIVNRSYSAALTEILEKELSLDPDRVYIKFY 100 (115)
T ss_pred hEEEEecCCceE-eccCCCCccEEEEEEeccccChhHhHHHHHHHHHHHHHHhCCCCCeEEEEEe
Confidence 466777776654 2333333 2333444444555555677899999999999999988764
No 14
>PF08968 DUF1885: Domain of unknown function (DUF1885); InterPro: IPR015062 This family consists of hypothetical proteins produced by bacteria of the Bacillus genus. ; PDB: 1T6A_A.
Probab=68.30 E-value=2.7 Score=30.47 Aligned_cols=28 Identities=21% Similarity=0.430 Sum_probs=18.2
Q ss_pred CeEEEEEeCCCC-----cChhHHHHHHHHHhhcC
Q 034235 61 EAVGVQIDAPAK-----DGEANAALLEYMSSLIH 89 (100)
Q Consensus 61 ~~l~V~V~ApP~-----dGkAN~aLi~~LAk~Lg 89 (100)
+.--|.|.=|+. .|||| |+++|||+.|.
T Consensus 82 e~~~IQv~LP~~AThGDK~KAN-EfckfLAk~l~ 114 (130)
T PF08968_consen 82 EQSYIQVVLPDGATHGDKGKAN-EFCKFLAKKLK 114 (130)
T ss_dssp TEEEEEEE--TT--HHHHHHHH-HHHHHHHHHH-
T ss_pred cceEEEEECCCCCccCcchhHH-HHHHHHHHHhh
Confidence 444566655553 58998 58999999875
No 15
>COG1451 Predicted metal-dependent hydrolase [General function prediction only]
Probab=66.70 E-value=14 Score=28.34 Aligned_cols=47 Identities=11% Similarity=0.258 Sum_probs=37.6
Q ss_pred eEEEEEEEecCCCccccccccCCeEEEEEeCCCCcChhHHHHHHHHHhhcC
Q 034235 39 SVSITIHAKPGSKSCSITDVSDEAVGVQIDAPAKDGEANAALLEYMSSLIH 89 (100)
Q Consensus 39 ~v~l~v~VkP~Ak~~~I~~~~~~~l~V~V~ApP~dGkAN~aLi~~LAk~Lg 89 (100)
+..+.|.+++++++..|.-..++ .|+|.+|+- ..++++..||.+..+
T Consensus 9 ~~~~~v~~~r~~r~~~i~i~~~~--~v~v~~P~~--~~~~~~~~fl~k~~~ 55 (223)
T COG1451 9 GLPLEVQVKRRAKRLTIRIPPGG--TVRVSVPPG--LSDEEVENFLAKKLG 55 (223)
T ss_pred CccEEEEEeecccceeEEecCCC--eEEEEeCCC--CCHHHHHHHHHHHHH
Confidence 78999999999999888744445 999999975 467788888887654
No 16
>PTZ00450 macrophage migration inhibitory factor-like protein; Provisional
Probab=52.79 E-value=12 Score=25.79 Aligned_cols=58 Identities=7% Similarity=0.008 Sum_probs=35.8
Q ss_pred EEEEEEEecCCCccccccccCCeEEEEEeC--C---CCcChhHHHHHHHHHhhcCCCCCceEee
Q 034235 40 VSITIHAKPGSKSCSITDVSDEAVGVQIDA--P---AKDGEANAALLEYMSSLIHVSVGEFVES 98 (100)
Q Consensus 40 v~l~v~VkP~Ak~~~I~~~~~~~l~V~V~A--p---P~dGkAN~aLi~~LAk~LgV~ks~I~~~ 98 (100)
-+|-|.+.|+..-. +.|-++.+--+.|+. . ....+-.++|+++|.+.||||+.+|-..
T Consensus 37 ~yvmV~~~~~~~m~-fgGs~~P~A~~~l~siG~~~~~~n~~~s~~i~~~l~~~LgIp~dRiYI~ 99 (113)
T PTZ00450 37 DFVMTAFSDSTPMS-FQGSTAPAAYVRVEAWGEYAPSKPKMMTPRITAAITKECGIPAERIYVF 99 (113)
T ss_pred HHEEEEEeCCceEE-EcCCCCCEEEEEEEEecCcCHHHHHHHHHHHHHHHHHHcCCCcccEEEE
Confidence 35677777775442 333344444444433 2 2233445678999999999999998654
No 17
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=51.48 E-value=22 Score=20.42 Aligned_cols=24 Identities=13% Similarity=0.117 Sum_probs=19.4
Q ss_pred hHHHHHHHHHhhcCCCCCceEeee
Q 034235 76 ANAALLEYMSSLIHVSVGEFVESV 99 (100)
Q Consensus 76 AN~aLi~~LAk~LgV~ks~I~~~~ 99 (100)
--++|.+.|++.||++...+...+
T Consensus 19 l~~~i~~~l~~~~g~~~~~v~V~i 42 (58)
T cd00491 19 LIERVTEAVSEILGAPEATIVVII 42 (58)
T ss_pred HHHHHHHHHHHHhCcCcccEEEEE
Confidence 346788999999999999887654
No 18
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=51.18 E-value=22 Score=20.89 Aligned_cols=24 Identities=13% Similarity=0.142 Sum_probs=19.9
Q ss_pred hHHHHHHHHHhhcCCCCCceEeee
Q 034235 76 ANAALLEYMSSLIHVSVGEFVESV 99 (100)
Q Consensus 76 AN~aLi~~LAk~LgV~ks~I~~~~ 99 (100)
--++|.+.|++.||++...+...+
T Consensus 20 l~~~it~~l~~~lg~~~~~v~V~i 43 (63)
T TIGR00013 20 LIEGVTEAMAETLGANLESIVVII 43 (63)
T ss_pred HHHHHHHHHHHHhCCCcccEEEEE
Confidence 457888999999999999988654
No 19
>PF01361 Tautomerase: Tautomerase enzyme; InterPro: IPR004370 4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerisation of beta,gamma-unsaturated enones to their alpha,beta-isomers. The enzyme is part of a plasmid-encoded pathway, which enables bacteria harbouring the plasmid to use various aromatic hydrocarbons as their sole sources of carbon and energy. The enzyme is a barrel-shaped hexamer, which can be viewed as a trimer of dimers. The hexamer contains a hydrophobic core formed by three beta-sheets and surrounded by three pairs of alpha-helices. Each 4-OT monomer of 62 amino acids has a relatively simple beta-alpha-beta fold as described by the structure of the enzyme from Pseudomonas putida []. The monomer begins with a conserved proline at the start of a beta-strand, followed by an alpha-helix and a 310 helix preceding a second parallel beta-strand, and ends with a beta-hairpin near the C terminus. The dimer results from antiparallel interactions between the beta-sheets and alpha-helices of the two monomers, forming a four-stranded beta-sheet with antiparallel alpha-helices on one side, creating two active sites, one at each end of the beta-sheet. Three dimers further associate to form a hexamer by the interactions of the strands of the C-terminal beta-hairpin loops with the edges of the four-stranded beta-sheets of neighbouring dimers, creating a series of cross-links that stabilise the hexamer Pro-1 of the mature protein functions as the general base while Arg-39 and an ordered water molecule each provide a hydrogen bond to the C-2 oxygen of substrate. Arg-39 plays an additional role in the binding of the C-1 carboxylate group. Arg-11 participates both in substrate binding and in catalysis. It interacts with the C-6 carboxylate group, thereby holding the substrate in place and drawing electron density to the C-5 position. The hydrophobic nature of the active site, which lowers the pKa of Pro-1 and provides a favourable environment for catalysis, is largely maintained by Phe-50. Because several Arg residues located near the active site are not conserved among all members of this family and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.; GO: 0016853 isomerase activity, 0006725 cellular aromatic compound metabolic process; PDB: 4OTA_H 4OTC_G 4OTB_J 2FM7_A 1BJP_B 1S0Y_K 3EJ9_E 3EJ7_K 3EJ3_I 3MB2_A ....
Probab=51.09 E-value=20 Score=21.04 Aligned_cols=23 Identities=4% Similarity=0.141 Sum_probs=17.8
Q ss_pred HHHHHHHHHhhcCCCCCceEeee
Q 034235 77 NAALLEYMSSLIHVSVGEFVESV 99 (100)
Q Consensus 77 N~aLi~~LAk~LgV~ks~I~~~~ 99 (100)
-++|.+.+++.||++...|+..+
T Consensus 20 ~~~it~~~~~~lg~~~~~i~V~i 42 (60)
T PF01361_consen 20 AEAITDAVVEVLGIPPERISVVI 42 (60)
T ss_dssp HHHHHHHHHHHHTS-GGGEEEEE
T ss_pred HHHHHHHHHHHhCcCCCeEEEEE
Confidence 35778889999999999987654
No 20
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=47.07 E-value=24 Score=21.13 Aligned_cols=24 Identities=17% Similarity=0.065 Sum_probs=19.3
Q ss_pred hHHHHHHHHHhhcCCCCCceEeee
Q 034235 76 ANAALLEYMSSLIHVSVGEFVESV 99 (100)
Q Consensus 76 AN~aLi~~LAk~LgV~ks~I~~~~ 99 (100)
--++|.+.|++.||+|..++...+
T Consensus 20 l~~~it~~l~~~lg~p~~~v~V~i 43 (64)
T PRK01964 20 LIREVTEAISATLDVPKERVRVIV 43 (64)
T ss_pred HHHHHHHHHHHHhCcChhhEEEEE
Confidence 456788889999999999987643
No 21
>PF12685 SpoIIIAH: SpoIIIAH-like protein; InterPro: IPR024232 Stage III sporulation protein AH (SpoIIIAH) is a protein that is involved in forespore engulfment. It forms a channel with SpoIIIAH that is open on the forespore end and closed (or gated) on the mother cell end. This allows sigma-E-directed gene expression in the mother-cell compartment of the sporangium to trigger the activation of sigma-G forespore-specific gene expression by a pathway of intercellular signaling. This family of proteins is found in bacteria, archaea and eukaryotes and so must have a wider function than in sporulation. Proteins in this family are typically between 174 and 223 amino acids in length.; PDB: 3UZ0_A 3TUF_A.
Probab=46.37 E-value=47 Score=24.52 Aligned_cols=46 Identities=13% Similarity=0.177 Sum_probs=34.3
Q ss_pred ccccccccCCeEEEEEeCCCCcChhHHHHHHHHHhhcCCCCCceEe
Q 034235 52 SCSITDVSDEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVE 97 (100)
Q Consensus 52 ~~~I~~~~~~~l~V~V~ApP~dGkAN~aLi~~LAk~LgV~ks~I~~ 97 (100)
.+.++-++++.+.|-|.+.=..-+-=..|.+.+.+.+||+..+|+.
T Consensus 150 ~davv~~~~~~v~VvV~~~~L~~~~~~~I~diV~~~~~v~~~~I~V 195 (196)
T PF12685_consen 150 EDAVVFIEDDSVDVVVKADKLSDAEAAQIIDIVMRETGVPAENISV 195 (196)
T ss_dssp SEEEEE-SSSEEEEEEE-S---HHHHHHHHHHHHHHHC-STSEEEE
T ss_pred CceEEEeeCCEEEEEEeCCCCCHHHHHHHHHHHHHHhCCCcCeEEe
Confidence 4567778889999999998877777778999999999999999975
No 22
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=44.42 E-value=28 Score=20.47 Aligned_cols=22 Identities=0% Similarity=-0.179 Sum_probs=17.8
Q ss_pred HHHHHHHHHhhcCCCCCceEee
Q 034235 77 NAALLEYMSSLIHVSVGEFVES 98 (100)
Q Consensus 77 N~aLi~~LAk~LgV~ks~I~~~ 98 (100)
-++|.+.|.+.||+|..+|...
T Consensus 21 ~~~it~~l~~~~~~p~~~v~V~ 42 (62)
T PRK00745 21 VEEITRVTVETLGCPPESVDII 42 (62)
T ss_pred HHHHHHHHHHHcCCChhHEEEE
Confidence 3677888999999999988654
No 23
>PF14552 Tautomerase_2: Tautomerase enzyme; PDB: 2AAG_C 2AAL_A 2AAJ_A 1MWW_C.
Probab=43.82 E-value=25 Score=22.97 Aligned_cols=41 Identities=22% Similarity=0.287 Sum_probs=23.3
Q ss_pred cCCeEEEEEeCC-CCcChhHHH----HHHHHHhhcCCCCCceEeee
Q 034235 59 SDEAVGVQIDAP-AKDGEANAA----LLEYMSSLIHVSVGEFVESV 99 (100)
Q Consensus 59 ~~~~l~V~V~Ap-P~dGkAN~a----Li~~LAk~LgV~ks~I~~~~ 99 (100)
+++.+.|.|+.- ++.-++=++ |.+.|+..+||++.+|..++
T Consensus 26 s~~~v~I~It~~~gRs~e~K~~ly~~l~~~L~~~~gi~p~Dv~I~l 71 (82)
T PF14552_consen 26 SDDFVIIQITSGAGRSTEQKKALYRALAERLAEKLGIRPEDVMIVL 71 (82)
T ss_dssp -TT-EEEEEEECS---HHHHHHHHHHHHHHHHHHH---GGGEEEEE
T ss_pred CCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHcCCCHHHEEEEE
Confidence 457788888887 444444444 45556667799999998775
No 24
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=43.36 E-value=29 Score=20.28 Aligned_cols=23 Identities=4% Similarity=-0.162 Sum_probs=18.4
Q ss_pred hHHHHHHHHHhhcCCCCCceEee
Q 034235 76 ANAALLEYMSSLIHVSVGEFVES 98 (100)
Q Consensus 76 AN~aLi~~LAk~LgV~ks~I~~~ 98 (100)
--++|.+.|++.||+|..+|...
T Consensus 20 l~~~it~~l~~~~~~p~~~v~V~ 42 (61)
T PRK02220 20 LVKDVTAAVSKNTGAPAEHIHVI 42 (61)
T ss_pred HHHHHHHHHHHHhCcChhhEEEE
Confidence 34677888999999999988754
No 25
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=42.71 E-value=34 Score=20.41 Aligned_cols=24 Identities=8% Similarity=0.037 Sum_probs=19.7
Q ss_pred hHHHHHHHHHhhcCCCCCceEeee
Q 034235 76 ANAALLEYMSSLIHVSVGEFVESV 99 (100)
Q Consensus 76 AN~aLi~~LAk~LgV~ks~I~~~~ 99 (100)
=-++|.+.+++.||+|...|+..+
T Consensus 20 L~~~it~a~~~~~~~p~~~v~V~i 43 (60)
T PRK02289 20 LAREVTEVVSRIAKAPKEAIHVFI 43 (60)
T ss_pred HHHHHHHHHHHHhCcCcceEEEEE
Confidence 356788899999999999888654
No 26
>cd02552 PseudoU_synth_TruD_like PseudoU_synth_TruD_like: Pseudouridine synthase, TruD family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruD and Saccharomyces cerevisiae Pus7. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruD and S. cerevisiae Pus7 make psi13 in cytoplasmic tRNAs. In addition S. cerevisiae Pus7 makes psi35 in U2 small nuclear RNA (U2 snRNA) and psi35 in pre-tRNATyr. Psi35 in U2 snRNA and psi13 in tRNAs are highly phylogenetically conserved. Psi34 is the mammalian U2 snRNA counterpart of yeast U2 snRNA psi35.
Probab=40.68 E-value=21 Score=27.50 Aligned_cols=36 Identities=8% Similarity=0.091 Sum_probs=29.1
Q ss_pred CCeEEEEEeCCCCcChhHHHHHHHHHhhcCCCCCceEee
Q 034235 60 DEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVES 98 (100)
Q Consensus 60 ~~~l~V~V~ApP~dGkAN~aLi~~LAk~LgV~ks~I~~~ 98 (100)
+..+.+.+.- .|.-..+++..||+.|||+.++|.+.
T Consensus 30 G~~~~~~l~K---~~~~T~~a~~~la~~l~i~~~~i~yA 65 (232)
T cd02552 30 GEYLHFTLYK---ENKDTMEALREIAKALGVPPRDIGYA 65 (232)
T ss_pred CCEEEEEEEE---CCCCHHHHHHHHHHHcCCCHHHEeEc
Confidence 4566666653 56789999999999999999999874
No 27
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=40.58 E-value=13 Score=22.27 Aligned_cols=19 Identities=11% Similarity=0.237 Sum_probs=15.8
Q ss_pred HHHHHHHHhhcCCCCCceE
Q 034235 78 AALLEYMSSLIHVSVGEFV 96 (100)
Q Consensus 78 ~aLi~~LAk~LgV~ks~I~ 96 (100)
++|++.+|+.|||+..+|.
T Consensus 3 ~~I~~~Va~~~~i~~~~i~ 21 (60)
T smart00760 3 EEIIEAVAEYFGVKPEDLK 21 (60)
T ss_pred HHHHHHHHHHhCCCHHHHh
Confidence 5789999999999887763
No 28
>PF04969 CS: CS domain; InterPro: IPR017447 The function of the CS domain is unknown. The CS domain is sometimes found C-terminal to the CHORD domain (IPR007051 from INTERPRO) in metazoan proteins, but occurs separately from the CHORD domain in plants. This association is thought to be indicative of an functional interaction between CS and CHORD domains [].; PDB: 1WGV_A 2KMW_A 2O30_B 1WH0_A 1EJF_A 2RH0_B 1RL1_A 2CR0_A 1WFI_A 2XCM_D ....
Probab=39.80 E-value=79 Score=18.53 Aligned_cols=35 Identities=29% Similarity=0.375 Sum_probs=23.6
Q ss_pred eeCCCeEEEEEEEecCC--CccccccccCCeEEEEEeC
Q 034235 34 LVPPSSVSITIHAKPGS--KSCSITDVSDEAVGVQIDA 69 (100)
Q Consensus 34 ~~~~g~v~l~v~VkP~A--k~~~I~~~~~~~l~V~V~A 69 (100)
+..+ .+.|.|.++|.- +.+--..+.++.|.|.+..
T Consensus 7 Qt~~-~V~v~i~~~~~~~~~~dv~v~~~~~~l~v~~~~ 43 (79)
T PF04969_consen 7 QTDD-EVTVTIPVKPVDISKEDVKVDFTDTSLSVSIKS 43 (79)
T ss_dssp EESS-EEEEEEE-TTTTSSGGGEEEEEETTEEEEEEEE
T ss_pred ECCC-EEEEEEEEcCCCCChHHeEEEEEeeEEEEEEEc
Confidence 3343 799999998874 4444445778888888763
No 29
>PF02738 Ald_Xan_dh_C2: Molybdopterin-binding domain of aldehyde dehydrogenase; InterPro: IPR008274 Aldehyde oxidase (1.2.3.1 from EC) catalyses the conversion of an aldehyde in the presence of oxygen and water to an acid and hydrogen peroxide. The enzyme is a homodimer, and requires FAD, molybdenum and two 2FE-2S clusters as cofactors. Xanthine dehydrogenase (1.1.1.204 from EC) catalyses the hydrogenation of xanthine to urate, and also requires FAD, molybdenum and two 2FE-2S clusters as cofactors. This activity is often found in a bifunctional enzyme with xanthine oxidase (1.1.3.22 from EC) activity too. The enzyme can be converted from the dehydrogenase form to the oxidase form irreversibly by proteolysis or reversibly through oxidation of sulphydryl groups.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3NVZ_C 3NVY_C 1FO4_B 3NRZ_L 3AM9_A 3B9J_C 3AX7_B 3NVW_L 3BDJ_A 3ETR_N ....
Probab=39.59 E-value=50 Score=27.84 Aligned_cols=45 Identities=11% Similarity=0.083 Sum_probs=33.0
Q ss_pred ccccc-cCCeEEEEEeCCCCcChhHHHHHHHHHhhcCCCCCceEee
Q 034235 54 SITDV-SDEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVES 98 (100)
Q Consensus 54 ~I~~~-~~~~l~V~V~ApP~dGkAN~aLi~~LAk~LgV~ks~I~~~ 98 (100)
..+.+ .++.+.|.+.....---....+...+|+.|||+..+|.+.
T Consensus 322 a~v~l~~DG~v~v~~~~~e~GqG~~T~~~qiaAe~Lgi~~~~V~v~ 367 (547)
T PF02738_consen 322 ARVRLNPDGSVTVYTGGVEMGQGSRTALAQIAAEELGIPPEDVRVV 367 (547)
T ss_dssp EEEEE-TTS-EEEEES--BSSSSHHHHHHHHHHHHHTS-GGGEEEE
T ss_pred EEEEEEeCCCEEEEEecccCCcchhhhHHHHHHHHhCCChhhEEEE
Confidence 33344 3588899988887766688899999999999999999874
No 30
>cd02575 PseudoU_synth_EcTruD PseudoU_synth_EcTruD: Pseudouridine synthase, TruD family. This group consists of bacterial pseudouridine synthases similar to Escherichia coli TruD. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruD makes the highly phylogenetically conserved psi13 in tRNAs.
Probab=37.34 E-value=27 Score=27.48 Aligned_cols=37 Identities=11% Similarity=0.110 Sum_probs=29.6
Q ss_pred cCCeEEEEEeCCCCcChhHHHHHHHHHhhcCCCCCceEee
Q 034235 59 SDEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVES 98 (100)
Q Consensus 59 ~~~~l~V~V~ApP~dGkAN~aLi~~LAk~LgV~ks~I~~~ 98 (100)
.++.+.+.|.- .|.-..++++.||+.|||+.++|.+.
T Consensus 23 ~Ge~l~~~l~K---~~~~T~~ai~~LAr~lgi~~~~igyA 59 (253)
T cd02575 23 EGEHLLLHIRK---TGLNTREVAKELAKALGVKERDVGYA 59 (253)
T ss_pred CCCEEEEEEEE---CCCCHHHHHHHHHHHhCCChhheeec
Confidence 34667777663 56678999999999999999999764
No 31
>cd06490 p23_NCB5OR p23_like domain found in NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR) and similar proteins. NCB5OR is widely expressed in human organs and tissues and is localized in the ER (endoplasmic reticulum). It appears to play a critical role in maintaining viable pancreatic beta cells. Mice homozygous for a targeted knockout (KO) of the gene encoding NCB5OR develop an early-onset nonautoimmune diabetes phenotype with a non-inflammatory beta-cell deficiency. The role of NCB5OR in beta cells may be in maintaining or regulating their redox status. Proteins in this group in addition contain an N-terminal cytochrome b5 domain and a C-terminal cytochrome b5 oxidoreductase domain. The gene encoding NCB5OR has been considered as a positional candidate for type II diabetes and other diabetes subtypes related to B-cell dysfunction, however variation in its coding region does not appear not to be a major contributor to the pathogenesis of these diseases.
Probab=36.52 E-value=84 Score=20.16 Aligned_cols=39 Identities=18% Similarity=0.171 Sum_probs=24.4
Q ss_pred cceEeeCCCeEEEEEEEe--cCCCccccccccCCeEEEEEeCC
Q 034235 30 SCIRLVPPSSVSITIHAK--PGSKSCSITDVSDEAVGVQIDAP 70 (100)
Q Consensus 30 ~~i~~~~~g~v~l~v~Vk--P~Ak~~~I~~~~~~~l~V~V~Ap 70 (100)
+|++..+ .+.|.|..+ +....+-+....++.|.|++.-+
T Consensus 2 DWyQt~~--~Vtitiy~K~~~~~~~~v~v~~~~~~l~v~~~~~ 42 (87)
T cd06490 2 DWFQTDS--EVTIVVYTKSKGNPADIVIVDDQQRELRVEIILG 42 (87)
T ss_pred CceECCC--EEEEEEEEcccCCCCccEEEECCCCEEEEEEECC
Confidence 4565544 689999877 44444434445556788887643
No 32
>cd06463 p23_like Proteins containing this p23_like domain include p23 and its Saccharomyces cerevisiae (Sc) homolog Sba1. Both are co-chaperones for the heat shock protein (Hsp) 90. p23 binds Hsp90 and participates in the folding of a number of Hsp90 clients, including the progesterone receptor. p23 also has a passive chaperoning activity and in addition may participate in prostaglandin synthesis. Both p23 and Sba1p can regulate telomerase activity. This group includes domains similar to the C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1). Sgt1 interacts with multiple protein complexes and has the features of a co-chaperone. Human (h) Sgt1 interacts with both Hsp70 and Hsp90, and has been shown to bind Hsp90 through its CS domain. Saccharomyces cerevisiae (Sc) Sgt1 is a subunit of both core kinetochore and SCF (Skp1-Cul1-F-box) ubiquitin ligase complexes. Sgt1 is required for pathogen resistance in plants. This group also includes the p23_like domains of
Probab=34.99 E-value=85 Score=18.43 Aligned_cols=31 Identities=23% Similarity=0.274 Sum_probs=21.4
Q ss_pred eEEEEEEEecCCCccccccccCCeEEEEEeC
Q 034235 39 SVSITIHAKPGSKSCSITDVSDEAVGVQIDA 69 (100)
Q Consensus 39 ~v~l~v~VkP~Ak~~~I~~~~~~~l~V~V~A 69 (100)
.+.|.|.+....+.+--+.+.++.|.|++..
T Consensus 7 ~v~i~v~~~~~~~~~~~v~~~~~~l~i~~~~ 37 (84)
T cd06463 7 EVTITIPLKDVTKKDVKVEFTPKSLTVSVKG 37 (84)
T ss_pred EEEEEEEcCCCCccceEEEEecCEEEEEeeC
Confidence 6788888776665554555677778877764
No 33
>PHA02564 V virion protein; Provisional
Probab=34.26 E-value=45 Score=24.24 Aligned_cols=29 Identities=14% Similarity=0.060 Sum_probs=23.3
Q ss_pred EEeCCCCcChhHHHHHHHHHhhcCCCCCce
Q 034235 66 QIDAPAKDGEANAALLEYMSSLIHVSVGEF 95 (100)
Q Consensus 66 ~V~ApP~dGkAN~aLi~~LAk~LgV~ks~I 95 (100)
.-=|||.|+ -.++-+.++|+.+||++.+.
T Consensus 74 ~rwAP~~EN-nT~aYi~~Vs~~~GV~~~~~ 102 (141)
T PHA02564 74 ARWAPSNEN-DTRAYATAVANAMGVPPQAG 102 (141)
T ss_pred HhcCCCCCC-CHHHHHHHHHHHHCCCCCCc
Confidence 345888875 37889999999999998764
No 34
>PRK01271 4-oxalocrotonate tautomerase; Provisional
Probab=32.25 E-value=58 Score=21.04 Aligned_cols=22 Identities=5% Similarity=0.075 Sum_probs=18.8
Q ss_pred HHHHHHHHhhcCCCCCceEeee
Q 034235 78 AALLEYMSSLIHVSVGEFVESV 99 (100)
Q Consensus 78 ~aLi~~LAk~LgV~ks~I~~~~ 99 (100)
++|.+.+++.||.+...|...+
T Consensus 23 ~~iT~a~~~~lg~~~e~v~V~I 44 (76)
T PRK01271 23 ADITDVIIRHLNSKDSSISIAL 44 (76)
T ss_pred HHHHHHHHHHhCcCcceEEEEE
Confidence 6788999999999999887654
No 35
>PF09098 Dehyd-heme_bind: Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding; InterPro: IPR015182 Quinohemoprotein amine dehydrogenases (QHNDH) 1.4.99 from EC) are enzymes produced in the periplasmic space of certain Gram-negative bacteria, such as Paracoccus denitrificans and Pseudomonas putida, in response to primary amines, including n-butylamine and benzylamine. QHNDH catalyses the oxidative deamination of a wide range of aliphatic and aromatic amines through formation of a Schiff-base intermediate involving one of the quinone O atoms []. Catalysis requires the presence of a novel redox cofactor, cysteine tryptophylquinone (CTQ). CTQ is derived from the post-translational modification of specific residues, which involves the oxidation of the indole ring of a tryptophan residue to form tryptophylquinone, followed by covalent cross-linking with a cysteine residue []. There is one CTQ per subunit in QHNDH. In addition to CTQ, two haem c cofactors are present in QHNDH that mediate the transfer of the substrate-derived electrons from CTQ to an external electron acceptor, cytochrome c-550 [, ]. QHNDH is a heterotrimer of alpha, beta and gamma subunits. The alpha and beta subunits contain signal peptides necessary for the translocation of QHNDH to the periplasm. The alpha subunit is composed of four domains - domain 1 forming a dihaem cytochrome, and domains 2-4 forming antiparallel beta-barrel structures; the beta subunit is a 7-bladed beta-propeller that provides part of the active site; and the small, catalytic gamma subunit contains the novel cross-linked CTQ cofactor, in addition to additional thioester cross-links between Cys and Asp/Glu residues that encage CTQ. The gamma subunit assumes a globular secondary structure with two short alpha-helices having many turns and bends []. This entry represents the dihaem cytochrome c domain of the QHNDH alpha subunit. The domain contain two cysteine residues that are involved in thioether linkages to haem []. ; PDB: 1PBY_A 1JJU_A 1JMZ_A 1JMX_A.
Probab=31.84 E-value=32 Score=25.87 Aligned_cols=25 Identities=16% Similarity=0.243 Sum_probs=15.7
Q ss_pred CCcChhHHHHHHHHHhhcCCCCCce
Q 034235 71 AKDGEANAALLEYMSSLIHVSVGEF 95 (100)
Q Consensus 71 P~dGkAN~aLi~~LAk~LgV~ks~I 95 (100)
+..-..=++|++|||+..|+.++..
T Consensus 50 ~Is~eer~avVkYLAd~~GLap~Et 74 (167)
T PF09098_consen 50 PISPEERRAVVKYLADTQGLAPSET 74 (167)
T ss_dssp ---HHHHHHHHHHHHHHT---CGGC
T ss_pred CCCHHHHHHHHHHHHHccCCCchhh
Confidence 3344556899999999999998764
No 36
>TIGR00094 tRNA_TruD_broad tRNA pseudouridine synthase, TruD family. MJ11364 is a strong partial match from 50 to 230 aa.
Probab=31.55 E-value=40 Score=27.39 Aligned_cols=36 Identities=14% Similarity=0.250 Sum_probs=30.3
Q ss_pred CCeEEEEEeCCCCcChhHHHHHHHHHhhcCCCCCceEee
Q 034235 60 DEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVES 98 (100)
Q Consensus 60 ~~~l~V~V~ApP~dGkAN~aLi~~LAk~LgV~ks~I~~~ 98 (100)
++.+.+.|.- .|.-..+++..||+.|||+.++|.+.
T Consensus 41 g~~~~~~l~K---~~~~T~~a~~~iar~l~i~~~~i~yA 76 (387)
T TIGR00094 41 GEFIHIRVEK---EGCNTLEVARVLAKFLGVSRREIGFA 76 (387)
T ss_pred CCEEEEEEEE---CCcCHHHHHHHHHHHhCCChhheeec
Confidence 5677777764 67889999999999999999999764
No 37
>cd02576 PseudoU_synth_ScPUS7 PseudoU_synth_ScPUS7: Pseudouridine synthase, TruD family. This group consists of eukaryotic pseudouridine synthases similar to Saccharomyces cerevisiae Pus7. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Saccharomyces cerevisiae Pus7 makes psi35 in U2 small nuclear RNA (U2 snRNA), psi13 in cytoplasmic tRNAs and psi35 in pre-tRNATyr. Psi35 in yeast U2 snRNA and psi13 in tRNAs are highly phylogenetically conserved. Psi34 is the mammalian U2 snRNA counterpart of yeast U2 snRNA psi35.
Probab=30.55 E-value=41 Score=27.22 Aligned_cols=35 Identities=9% Similarity=0.241 Sum_probs=27.5
Q ss_pred CeEEEEEeCCCCcChhHHHHHHHHHhhcCCCCCceEee
Q 034235 61 EAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVES 98 (100)
Q Consensus 61 ~~l~V~V~ApP~dGkAN~aLi~~LAk~LgV~ks~I~~~ 98 (100)
+.+.+.+.- .|.-..+++..||+.|||+.++|.+.
T Consensus 29 ~y~~~~L~K---~~~~T~~ai~~lar~l~i~~~~i~~A 63 (371)
T cd02576 29 DYLHFTLYK---ENKDTMEAINKIAKLLRVKPSDFSYA 63 (371)
T ss_pred CEEEEEEEE---CCCCHHHHHHHHHHHhCCChhheeec
Confidence 445555553 56678999999999999999999774
No 38
>PRK06290 aspartate aminotransferase; Provisional
Probab=29.66 E-value=68 Score=25.90 Aligned_cols=28 Identities=21% Similarity=0.279 Sum_probs=26.2
Q ss_pred CeEEEEEeCCCCcChhHHHHHHHHHhhc
Q 034235 61 EAVGVQIDAPAKDGEANAALLEYMSSLI 88 (100)
Q Consensus 61 ~~l~V~V~ApP~dGkAN~aLi~~LAk~L 88 (100)
+.++|.+..++.+-+-|+.+++-|++.|
T Consensus 376 ~~lRi~~~~~~~~~~~~~~~~~~l~~~~ 403 (410)
T PRK06290 376 HFLRFSVTFEAKDEEEEDRILEEIKRRL 403 (410)
T ss_pred CeEEEEEEcccccccchhHHHHHHHHHH
Confidence 6899999999999999999999999887
No 39
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=29.32 E-value=22 Score=22.24 Aligned_cols=19 Identities=21% Similarity=0.337 Sum_probs=13.6
Q ss_pred HHHHHHHHhhcCCCCCceE
Q 034235 78 AALLEYMSSLIHVSVGEFV 96 (100)
Q Consensus 78 ~aLi~~LAk~LgV~ks~I~ 96 (100)
++|++.+|+.|||+..+|.
T Consensus 3 ~~Ii~~Va~~~~v~~~~i~ 21 (70)
T PF08299_consen 3 EDIIEAVAEYFGVSVEDIR 21 (70)
T ss_dssp HHHHHHHHHHTT--HHHHH
T ss_pred HHHHHHHHHHHCCCHHHHh
Confidence 5788999999999887653
No 40
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=29.11 E-value=22 Score=25.12 Aligned_cols=21 Identities=14% Similarity=0.173 Sum_probs=15.7
Q ss_pred hHHHHHHHHHhhcCCCCCceE
Q 034235 76 ANAALLEYMSSLIHVSVGEFV 96 (100)
Q Consensus 76 AN~aLi~~LAk~LgV~ks~I~ 96 (100)
=-++.++++|+.|+|+.++|.
T Consensus 29 i~~~~~~~iA~~l~i~~~~v~ 49 (145)
T PF01257_consen 29 IPEEALEEIAEALGIPPAEVY 49 (145)
T ss_dssp --HHHHHHHHHHHTS-HHHHH
T ss_pred CCHHHHHHHHHHHCCCHHHHH
Confidence 346889999999999998763
No 41
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=27.94 E-value=28 Score=19.99 Aligned_cols=19 Identities=5% Similarity=0.024 Sum_probs=16.0
Q ss_pred HHHHHHHHHhhcCCCCCce
Q 034235 77 NAALLEYMSSLIHVSVGEF 95 (100)
Q Consensus 77 N~aLi~~LAk~LgV~ks~I 95 (100)
+.+-++.||..|||+..+|
T Consensus 26 ~~~~~~~la~~l~l~~~~V 44 (57)
T PF00046_consen 26 SKEEREELAKELGLTERQV 44 (57)
T ss_dssp HHHHHHHHHHHHTSSHHHH
T ss_pred ccccccccccccccccccc
Confidence 5667889999999998876
No 42
>PF14804 Jag_N: Jag N-terminus; PDB: 3GKU_B.
Probab=27.77 E-value=79 Score=19.01 Aligned_cols=26 Identities=19% Similarity=0.141 Sum_probs=18.2
Q ss_pred ChhHHHHHHHHHhhcCCCCCceEeee
Q 034235 74 GEANAALLEYMSSLIHVSVGEFVESV 99 (100)
Q Consensus 74 GkAN~aLi~~LAk~LgV~ks~I~~~~ 99 (100)
|+-=++.++--++.|++++.+|++.|
T Consensus 4 gkt~eeAi~~A~~~l~~~~~~~~~eV 29 (52)
T PF14804_consen 4 GKTVEEAIEKALKELGVPREELEYEV 29 (52)
T ss_dssp ESSHHHHHHHHHHHTT--GGGEEEEE
T ss_pred ECCHHHHHHHHHHHhCCChHHEEEEE
Confidence 33446677777889999999998876
No 43
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=27.41 E-value=21 Score=24.03 Aligned_cols=19 Identities=16% Similarity=0.141 Sum_probs=12.7
Q ss_pred HHHHHHHHHhhcCCCCCce
Q 034235 77 NAALLEYMSSLIHVSVGEF 95 (100)
Q Consensus 77 N~aLi~~LAk~LgV~ks~I 95 (100)
|.+-++-.|+.|||++|-|
T Consensus 18 ~~aTVR~~Ak~FGvSKSTV 36 (82)
T PF12116_consen 18 TKATVRQAAKVFGVSKSTV 36 (82)
T ss_dssp H---HHHHHHHHTS-HHHH
T ss_pred cccHHHHHHHHHCCcHHHH
Confidence 5667888999999999854
No 44
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=27.07 E-value=28 Score=24.68 Aligned_cols=20 Identities=0% Similarity=0.009 Sum_probs=16.9
Q ss_pred HHHHHHHHHhhcCCCCCceE
Q 034235 77 NAALLEYMSSLIHVSVGEFV 96 (100)
Q Consensus 77 N~aLi~~LAk~LgV~ks~I~ 96 (100)
-++.++++|+.||||.++|.
T Consensus 33 ~~~~~~~iA~~l~~~~~~v~ 52 (148)
T TIGR01958 33 TPEAIAAVAEMLGIPPVWVY 52 (148)
T ss_pred CHHHHHHHHHHhCcCHHHHH
Confidence 46789999999999998763
No 45
>KOG4079 consensus Putative mitochondrial ribosomal protein mRpS25 [Translation, ribosomal structure and biogenesis]
Probab=26.59 E-value=47 Score=24.81 Aligned_cols=20 Identities=10% Similarity=0.169 Sum_probs=17.8
Q ss_pred CcChhHHHHHHHHHhhcCCC
Q 034235 72 KDGEANAALLEYMSSLIHVS 91 (100)
Q Consensus 72 ~dGkAN~aLi~~LAk~LgV~ 91 (100)
.||+-|++|++.|++.||-.
T Consensus 91 ld~~~r~eI~~hl~K~lGKt 110 (169)
T KOG4079|consen 91 LDGMKREEIEKHLAKTLGKT 110 (169)
T ss_pred cccccHHHHHHHHHHHhCcc
Confidence 58999999999999999854
No 46
>PF10410 DnaB_bind: DnaB-helicase binding domain of primase; InterPro: IPR019475 This entry represents the C-terminal region three-helical domain of DNA primase []. Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases - this domain binds DnaB-helicase []. It is associated with the Toprim domain IPR006171 from INTERPRO, which is the central catalytic core. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=26.56 E-value=65 Score=18.55 Aligned_cols=22 Identities=5% Similarity=0.064 Sum_probs=15.3
Q ss_pred ChhHHHHHHHHHhhcCCCCCce
Q 034235 74 GEANAALLEYMSSLIHVSVGEF 95 (100)
Q Consensus 74 GkAN~aLi~~LAk~LgV~ks~I 95 (100)
+-.=+..++.||+.+|++...+
T Consensus 38 ~i~r~~y~~~la~~~~i~~~~L 59 (59)
T PF10410_consen 38 PIERELYIRELAERLGISEDAL 59 (59)
T ss_dssp HHHHHHHHHHHHHHCT-SSTT-
T ss_pred HHHHHHHHHHHHHHhCcCcccC
Confidence 3445678889999999988754
No 47
>PF01142 TruD: tRNA pseudouridine synthase D (TruD); InterPro: IPR001656 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. Pseudouridine synthase TruD modifies uracil-13 in tRNA []. TruD belongs to a recently identified and large family of pseudouridine synthases present in all kingdoms of life []. TruD folds into a V-shaped molecule with an RNA-binding cleft formed between its two domains: a catalytic domain and an insertion domain. The catalytic domain differs in sequence but is structurally very similar to the catalytic domain of other pseudouridine synthases. The insertion (or TRUD) domain displays a novel alpha/beta structure that forms a compact fold titled away from the catalytic domain to form a deep cleft in TruD which is lined with basic residues from each domain. The insertion domain is characterised by two conserved sequence motifs that form a part of the hydrophobic core, as well as by large insertions at several specific sites that are seen in many archaeal and eukaryotic homologues. The insertion domain is likely to be involved in substrate recognition and may represent a RNA binding module []. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 1SB7_B 1SI7_A 1SZW_B 1Z2Z_B.
Probab=26.07 E-value=66 Score=26.00 Aligned_cols=37 Identities=5% Similarity=0.091 Sum_probs=27.4
Q ss_pred cCCeEEEEEeCCCCcChhHHHHHHHHHhhcCCCCCceEee
Q 034235 59 SDEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVES 98 (100)
Q Consensus 59 ~~~~l~V~V~ApP~dGkAN~aLi~~LAk~LgV~ks~I~~~ 98 (100)
.++.+.+.+.- .|.-..+++..||+.|||+.++|.+.
T Consensus 42 ~g~~~~~~l~K---~~~~T~~a~~~ia~~l~i~~~~i~~a 78 (378)
T PF01142_consen 42 EGEYLVFTLEK---RNIDTMEAIRIIARKLGISPKDISYA 78 (378)
T ss_dssp -SSEEEEEEEE---ESS-HHHHHHHHHHHCTS-CCCEEES
T ss_pred CCCEEEEEEEE---cCCCHHHHHHHHHHHhCCChhhceec
Confidence 45666666663 56788999999999999999999763
No 48
>PRK00984 truD tRNA pseudouridine synthase D; Reviewed
Probab=26.06 E-value=51 Score=26.73 Aligned_cols=37 Identities=14% Similarity=0.161 Sum_probs=29.2
Q ss_pred cCCeEEEEEeCCCCcChhHHHHHHHHHhhcCCCCCceEee
Q 034235 59 SDEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVES 98 (100)
Q Consensus 59 ~~~~l~V~V~ApP~dGkAN~aLi~~LAk~LgV~ks~I~~~ 98 (100)
.++.+.+.|.- .|.-..+++..||+.|||+.++|.+.
T Consensus 40 ~G~~~~~~l~K---~~~~T~~~~~~lar~l~i~~~~i~yA 76 (341)
T PRK00984 40 EGEHLLVRIRK---RGWNTLFVARALAKFLGISLRDVGYA 76 (341)
T ss_pred CcCEEEEEEEE---CCCCHHHHHHHHHHHhCCChhheeec
Confidence 34566666663 56678999999999999999999764
No 49
>cd02577 PSTD1 PSTD1: Pseudouridine synthase, a subgroup of the TruD family. This group consists of several hypothetical archeal pseudouridine synthases assigned to the TruD family of psuedouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). The TruD family is comprised of proteins related to Escherichia coli TruD.
Probab=25.95 E-value=52 Score=26.55 Aligned_cols=36 Identities=3% Similarity=-0.035 Sum_probs=27.7
Q ss_pred CCeEEEEEeCCCCcChhHHHHHHHHHhhcCCCCCceEee
Q 034235 60 DEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVES 98 (100)
Q Consensus 60 ~~~l~V~V~ApP~dGkAN~aLi~~LAk~LgV~ks~I~~~ 98 (100)
++.+.+.+.- .|.-.-+++..||+.|||+.++|.|.
T Consensus 24 g~y~~f~l~K---~n~dT~~ai~~lar~l~i~~~~i~~A 59 (319)
T cd02577 24 GKYLIYLLEK---KNWDTLDAVRRIAKALGISRKRIGYA 59 (319)
T ss_pred CCEEEEEEEE---CCCCHHHHHHHHHHHhCCChhheeec
Confidence 4555555553 56678899999999999999998763
No 50
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=25.69 E-value=27 Score=19.79 Aligned_cols=20 Identities=5% Similarity=-0.009 Sum_probs=16.4
Q ss_pred HHHHHHHHHhhcCCCCCceE
Q 034235 77 NAALLEYMSSLIHVSVGEFV 96 (100)
Q Consensus 77 N~aLi~~LAk~LgV~ks~I~ 96 (100)
+.+-++.||+.+|++.++|.
T Consensus 26 ~~~~~~~la~~~~l~~~qV~ 45 (59)
T cd00086 26 SREEREELAKELGLTERQVK 45 (59)
T ss_pred CHHHHHHHHHHHCcCHHHHH
Confidence 56778899999999988763
No 51
>PF00550 PP-binding: Phosphopantetheine attachment site; InterPro: IPR006163 Phosphopantetheine (or pantetheine 4' phosphate) is the prosthetic group of acyl carrier proteins (ACP) in some multienzyme complexes where it serves as a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups []. The amino-terminal region of the ACP proteins is well defined and consists of alpha four helices arranged in a right-handed bundle held together by interhelical hydrophobic interactions. The Asp-Ser-Leu (DSL)motif is conserved in all of the ACP sequences, and the 4'-PP prosthetic group is covalently linked via a phosphodiester bond to the serine residue. The DSL sequence is present at the amino terminus of helix II, a domain of the protein referred to as the recognition helix and which is responsible for the interaction of ACPs with the enzymes of type II fatty acid synthesis [].; GO: 0048037 cofactor binding; PDB: 3EJB_E 3EJE_G 1L0I_A 2FHS_C 3EJD_E 2FAE_B 2FAD_B 2FAC_B 2K94_A 1ACP_A ....
Probab=25.07 E-value=56 Score=18.94 Aligned_cols=19 Identities=21% Similarity=0.256 Sum_probs=14.7
Q ss_pred HHHHHHHHhhcCCCCCceE
Q 034235 78 AALLEYMSSLIHVSVGEFV 96 (100)
Q Consensus 78 ~aLi~~LAk~LgV~ks~I~ 96 (100)
+.|++.+++.|+++..+|.
T Consensus 1 e~l~~~~~~~l~~~~~~i~ 19 (67)
T PF00550_consen 1 EQLREIIAEVLGVDPEEID 19 (67)
T ss_dssp HHHHHHHHHHHTSSGGCTS
T ss_pred CHHHHHHHHHHCcCHhhCC
Confidence 4688889999998776654
No 52
>PRK07199 phosphoribosylpyrophosphate synthetase; Provisional
Probab=24.27 E-value=64 Score=25.60 Aligned_cols=28 Identities=21% Similarity=0.202 Sum_probs=25.0
Q ss_pred cChhHHHHHHHHHhhcCCCCCceEeeeC
Q 034235 73 DGEANAALLEYMSSLIHVSVGEFVESVF 100 (100)
Q Consensus 73 dGkAN~aLi~~LAk~LgV~ks~I~~~~~ 100 (100)
-|.+|..|-+-+|+.||++...++...|
T Consensus 7 ~~~~~~~la~~ia~~lg~~~~~~~~~~F 34 (301)
T PRK07199 7 ALPGNEAAAGRLAAALGVEVGRIELHRF 34 (301)
T ss_pred ECCCCHHHHHHHHHHhCCceeeeEEEEC
Confidence 3678999999999999999999998876
No 53
>COG0245 IspF 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase [Lipid metabolism]
Probab=24.27 E-value=82 Score=23.54 Aligned_cols=30 Identities=17% Similarity=0.200 Sum_probs=23.5
Q ss_pred CCCCcChhHHHHHHHHHhhcCCCCCceEee
Q 034235 69 APAKDGEANAALLEYMSSLIHVSVGEFVES 98 (100)
Q Consensus 69 ApP~dGkAN~aLi~~LAk~LgV~ks~I~~~ 98 (100)
..|-=+===+++.+.||+.|+++.++|...
T Consensus 101 ~~PK~~P~~~amr~~ia~~L~i~~~~invK 130 (159)
T COG0245 101 QRPKLGPYREAMRANIAELLGIPVDRINVK 130 (159)
T ss_pred ecCcccchHHHHHHHHHHHhCCCchheEEE
Confidence 344444456889999999999999998765
No 54
>COG0462 PrsA Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]
Probab=24.26 E-value=66 Score=26.33 Aligned_cols=27 Identities=22% Similarity=0.417 Sum_probs=24.4
Q ss_pred ChhHHHHHHHHHhhcCCCCCceEeeeC
Q 034235 74 GEANAALLEYMSSLIHVSVGEFVESVF 100 (100)
Q Consensus 74 GkAN~aLi~~LAk~LgV~ks~I~~~~~ 100 (100)
|-+|.+|-+-+|+.||++..++++.-|
T Consensus 10 g~s~~~La~~ia~~l~~~l~~~~~~rF 36 (314)
T COG0462 10 GSSNPELAEKIAKRLGIPLGKVEVKRF 36 (314)
T ss_pred CCCCHHHHHHHHHHhCCCcccceeEEc
Confidence 468999999999999999999988766
No 55
>PF08381 BRX: Transcription factor regulating root and shoot growth via Pin3; InterPro: IPR013591 This is a short domain, approximately 35 residues in length that is found near the C terminus in a number of plant proteins, being repeated in some members. It is found in Brevis radix-like proteins. These may act as a regulator of cell proliferation and elongation in the root []. It is also found in proteins annotated as involved in disease resistance and in the regulation of chromosome condensation, which also contain other domains with varied functions, such as TIR (IPR000157 from INTERPRO) and FYVE (IPR000306 from INTERPRO) respectively.
Probab=23.59 E-value=1.2e+02 Score=19.14 Aligned_cols=22 Identities=23% Similarity=0.326 Sum_probs=18.2
Q ss_pred cceEeeCCCeEEEEEEEecCCCc
Q 034235 30 SCIRLVPPSSVSITIHAKPGSKS 52 (100)
Q Consensus 30 ~~i~~~~~g~v~l~v~VkP~Ak~ 52 (100)
.|+.+..+ ||+|++.+.|+-.+
T Consensus 5 Ewveq~Ep-GVyiTl~~~p~G~~ 26 (59)
T PF08381_consen 5 EWVEQDEP-GVYITLVSLPDGGN 26 (59)
T ss_pred cEEEeeCC-eeEEEEEECCCCCe
Confidence 68888887 89999999997543
No 56
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=23.48 E-value=35 Score=24.34 Aligned_cols=20 Identities=5% Similarity=0.084 Sum_probs=16.8
Q ss_pred HHHHHHHHHhhcCCCCCceE
Q 034235 77 NAALLEYMSSLIHVSVGEFV 96 (100)
Q Consensus 77 N~aLi~~LAk~LgV~ks~I~ 96 (100)
-++.++++|+.|||+.++|.
T Consensus 39 p~~~~~~iA~~l~v~~~~v~ 58 (154)
T PRK07539 39 PDEAIEAVADYLGMPAIDVE 58 (154)
T ss_pred CHHHHHHHHHHhCcCHHHHH
Confidence 35789999999999998863
No 57
>PRK04923 ribose-phosphate pyrophosphokinase; Provisional
Probab=23.17 E-value=68 Score=25.78 Aligned_cols=27 Identities=26% Similarity=0.423 Sum_probs=24.5
Q ss_pred ChhHHHHHHHHHhhcCCCCCceEeeeC
Q 034235 74 GEANAALLEYMSSLIHVSVGEFVESVF 100 (100)
Q Consensus 74 GkAN~aLi~~LAk~LgV~ks~I~~~~~ 100 (100)
|-+|.+|-+-+|+.||++..+++...|
T Consensus 12 g~~~~~La~~ia~~lg~~l~~~~~~~F 38 (319)
T PRK04923 12 GNANKPLAQSICKELGVRMGKALVTRF 38 (319)
T ss_pred CCCCHHHHHHHHHHhCCceeeeEEEEC
Confidence 568899999999999999999998877
No 58
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=22.81 E-value=37 Score=25.11 Aligned_cols=23 Identities=17% Similarity=0.346 Sum_probs=18.1
Q ss_pred ChhHHHHHHHHHhhcCCCCCceE
Q 034235 74 GEANAALLEYMSSLIHVSVGEFV 96 (100)
Q Consensus 74 GkAN~aLi~~LAk~LgV~ks~I~ 96 (100)
|---.+.++++|+.|||+.++|.
T Consensus 50 GyIp~e~~~~iA~~l~v~~a~V~ 72 (169)
T PRK07571 50 GYLERDLLLYVARQLKLPLSRVY 72 (169)
T ss_pred CCCCHHHHHHHHHHhCcCHHHHH
Confidence 33446789999999999998763
No 59
>cd00298 ACD_sHsps_p23-like This domain family includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this family is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind
Probab=22.80 E-value=1.6e+02 Score=16.55 Aligned_cols=35 Identities=14% Similarity=0.156 Sum_probs=23.8
Q ss_pred eEEEEEEEecCCCccccccccCCeEEEEEeCCCCc
Q 034235 39 SVSITIHAKPGSKSCSITDVSDEAVGVQIDAPAKD 73 (100)
Q Consensus 39 ~v~l~v~VkP~Ak~~~I~~~~~~~l~V~V~ApP~d 73 (100)
.+.|.|.+..-...+--+.+.++.|.|.....+.+
T Consensus 7 ~v~i~i~~~~~~~~~i~v~~~~~~l~v~~~~~~~~ 41 (80)
T cd00298 7 EVVVTVDLPGVKKEDIKVEVEDNVLTISGKREEEE 41 (80)
T ss_pred EEEEEEECCCCCHHHeEEEEECCEEEEEEEEcCCC
Confidence 68888887766555444456677888887766543
No 60
>PF07805 HipA_N: HipA-like N-terminal domain; InterPro: IPR012894 The members of this entry contain a region that is found towards the N terminus of the HipA protein expressed by various bacterial species (for example P23874 from SWISSPROT). This protein is known to be involved in high-frequency persistence to the lethal effects of inhibition of either DNA or peptidoglycan synthesis []. When expressed alone, it is toxic to bacterial cells [], but it is usually tightly associated with HipB [], and the HipA-HipB complex may be involved in autoregulation of the hip operon. The hip proteins may be involved in cell division control and may interact with cell division genes or their products []. ; PDB: 2WIU_C 3HZI_A 3DNT_B 3FBR_A 3DNU_A 3DNV_A.
Probab=21.88 E-value=1.1e+02 Score=19.06 Aligned_cols=26 Identities=15% Similarity=-0.060 Sum_probs=17.0
Q ss_pred CcChhHHHHHHHHHhhcCCCCCceEe
Q 034235 72 KDGEANAALLEYMSSLIHVSVGEFVE 97 (100)
Q Consensus 72 ~dGkAN~aLi~~LAk~LgV~ks~I~~ 97 (100)
.+--.||.+.-.||+.+|++..+...
T Consensus 40 ~~~~~nE~~~~~lA~~~Gi~v~~~~l 65 (81)
T PF07805_consen 40 PDLVENEYACMRLARAAGIPVPETRL 65 (81)
T ss_dssp TTHHHHHHHHHHHHHHTT-----EEE
T ss_pred cchHHHHHHHHHHHHHcCCCcCceEE
Confidence 34468999999999999987765543
No 61
>COG0851 MinE Septum formation topological specificity factor [Cell division and chromosome partitioning]
Probab=21.86 E-value=1e+02 Score=20.93 Aligned_cols=23 Identities=17% Similarity=0.316 Sum_probs=20.6
Q ss_pred HHHHHHHHHhhcCCCCCceEeee
Q 034235 77 NAALLEYMSSLIHVSVGEFVESV 99 (100)
Q Consensus 77 N~aLi~~LAk~LgV~ks~I~~~~ 99 (100)
-++|++.++++..+.++.|.++.
T Consensus 43 r~eIl~VI~KYV~id~d~v~v~~ 65 (88)
T COG0851 43 RKEILEVISKYVQIDPDKVEVSL 65 (88)
T ss_pred HHHHHHHHHHHheeCcccEEEEE
Confidence 47899999999999999999874
No 62
>COG3382 Solo B3/4 domain (OB-fold DNA/RNA-binding) of Phe-aaRS-beta [General function prediction only]
Probab=21.75 E-value=3.3e+02 Score=21.42 Aligned_cols=65 Identities=15% Similarity=0.140 Sum_probs=50.2
Q ss_pred CCCCCcceEeeCCCeEEEEEEEecCCCccccccccCCeEEEEEeCCCCcChhHHHHHHHHHhhcC
Q 034235 25 DENLPSCIRLVPPSSVSITIHAKPGSKSCSITDVSDEAVGVQIDAPAKDGEANAALLEYMSSLIH 89 (100)
Q Consensus 25 ~~~~P~~i~~~~~g~v~l~v~VkP~Ak~~~I~~~~~~~l~V~V~ApP~dGkAN~aLi~~LAk~Lg 89 (100)
..++|.-+.+.++.+...+++.-=.+.++.|+.-+...|.|-=.=|.++...=.+++++|++.|.
T Consensus 149 ~~~~~geiv~~Dd~G~~~r~~~~Rds~rT~vt~~Tk~~l~I~e~vp~~~~~~l~~a~~~l~~~l~ 213 (229)
T COG3382 149 EPPLEGEIVLVDDEGAFCRRWNWRDSVRTMVTESTKNVLLIAEGVPGVEVEDLVEALDSLADLLE 213 (229)
T ss_pred CCCCCCcEEEEcCCCCeeeecccccceeeehhhccceEEEEEecCCCccHHHHHHHHHHHHHHHH
Confidence 35567778888877888888888888899888777777777666677777777888888887763
No 63
>PRK00553 ribose-phosphate pyrophosphokinase; Provisional
Probab=20.72 E-value=81 Score=25.49 Aligned_cols=27 Identities=19% Similarity=0.262 Sum_probs=24.6
Q ss_pred ChhHHHHHHHHHhhcCCCCCceEeeeC
Q 034235 74 GEANAALLEYMSSLIHVSVGEFVESVF 100 (100)
Q Consensus 74 GkAN~aLi~~LAk~LgV~ks~I~~~~~ 100 (100)
|-+|.+|-+-+|+.||++...+++.-|
T Consensus 15 ~~~~~~La~~ia~~lg~~l~~~~~~~F 41 (332)
T PRK00553 15 LSKAKKLVDSICRKLSMKPGEIVIQKF 41 (332)
T ss_pred CCCCHHHHHHHHHHhCCceeeeEEEEC
Confidence 568899999999999999999998877
No 64
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=20.44 E-value=40 Score=19.03 Aligned_cols=20 Identities=10% Similarity=0.031 Sum_probs=16.1
Q ss_pred HHHHHHHHHhhcCCCCCceE
Q 034235 77 NAALLEYMSSLIHVSVGEFV 96 (100)
Q Consensus 77 N~aLi~~LAk~LgV~ks~I~ 96 (100)
+.+-+.-||+.+|++..+|.
T Consensus 26 ~~~~~~~la~~~~l~~~qV~ 45 (56)
T smart00389 26 SREEREELAAKLGLSERQVK 45 (56)
T ss_pred CHHHHHHHHHHHCcCHHHHH
Confidence 56778899999999887763
No 65
>PF03776 MinE: Septum formation topological specificity factor MinE; InterPro: IPR005527 Cytokinesis needs to be regulated spatially in order to ensure that it occurs between the daughter genomes. In prokaryotes such as Escherichia coli, cytokinesis is initiated by FtsZ, a tubulin-like protein that assembles into a ring structure at the cell centre called the Z ring. A fundamental problem in prokaryotic cell biology is to understand how the midcell division site is identified. Two major negative regulatory systems are known to be involved in preventing Z-ring assembly at all sites except the midcell. One of these systems, called nucleoid occlusion, blocks Z-ring assembly in the area occupied by an unsegregated nucleoid until a critical stage in chromosome replication or segregation is reached. The other system consists of three proteins, MinC, MinD and MinE, which prevent assembly of Z rings in regions of the cell not covered by the nucleoid, such as the cell poles. MinC is an inhibitor of FtsZ polymerisation, resulting in the inhibition of Z ring assembly in the cell; MinD greatly enhances the inhibitory effects of MinC in vivo; and MinE antagonizes the effects of MinC and MinD []. MinE is a small bifunctional protein. The amino terminus of MinE is required to interact with MinD, while the carboxyl terminus is required for `topological specificity' - that is, the ability of MinE to antagonise MinCD inhibition of Z rings at the midcell position but not at the poles.; GO: 0032955 regulation of barrier septum formation, 0051301 cell division; PDB: 2KXO_A 3MCD_B 3KU7_A 3R9J_C 3R9I_E 1EV0_B.
Probab=20.43 E-value=1.3e+02 Score=18.88 Aligned_cols=23 Identities=13% Similarity=0.290 Sum_probs=16.9
Q ss_pred HHHHHHHHHhhcCCCCCceEeee
Q 034235 77 NAALLEYMSSLIHVSVGEFVESV 99 (100)
Q Consensus 77 N~aLi~~LAk~LgV~ks~I~~~~ 99 (100)
=++|++.+++.+.+...+|.+++
T Consensus 31 k~eil~viskYv~i~~~~v~v~l 53 (70)
T PF03776_consen 31 KKEILEVISKYVEIDEEDVEVQL 53 (70)
T ss_dssp HHHHHHHHHHHS---CCCEEEEE
T ss_pred HHHHHHHHHhheecCcccEEEEE
Confidence 36899999999999989988764
No 66
>TIGR03311 Se_dep_Molyb_1 selenium-dependent molybdenum hydroxylase 1. Members of this protein family show full length homology to the molybdenum-containing aldehyde oxido-reductase of Desulfovibrio gigas. Members, however, are found only within species that have, and near those genes that encode, a set of predicted accessory proteins for selenium-dependent molybdenum hydroxylases. The best known examples of such enzymes are forms of xanthine dehydrogenase and purine hydroxylase; this family appears to be another such enzyme.
Probab=20.33 E-value=1.7e+02 Score=26.58 Aligned_cols=44 Identities=14% Similarity=0.079 Sum_probs=36.7
Q ss_pred cccccCCeEEEEEeCCCCcChhHHHHHHHHHhhcCCCCCceEee
Q 034235 55 ITDVSDEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVES 98 (100)
Q Consensus 55 I~~~~~~~l~V~V~ApP~dGkAN~aLi~~LAk~LgV~ks~I~~~ 98 (100)
+..+.++.+.|++-....---.+..+....|+.||||.++|...
T Consensus 598 ~~~~~DGsv~v~~g~~e~GQG~~T~~aQiaAe~LGip~e~V~v~ 641 (848)
T TIGR03311 598 NLAVEDGKVHIRTSAACIGQGLGTVLTQIVCETTGLPPEVIVCE 641 (848)
T ss_pred EEEEcCCEEEEEECCCCcCcCHHHHHHHHHHHHHCCCHHHEEEE
Confidence 34456889999998888766678899999999999999999864
No 67
>TIGR02416 CO_dehy_Mo_lg carbon-monoxide dehydrogenase, large subunit. This model represents the large subunits of group of carbon-monoxide dehydrogenases that include molybdenum as part of the enzymatic cofactor. There are various forms of carbon-monoxide dehydrogenase; Salicibacter pomeroyi DSS-3, for example, has two forms. Note that, at least in some species, the active site Cys is modified with a selenium attached to (rather than replacing) the sulfur atom. This is termed selanylcysteine, and created post-translationally, in contrast to selenocysteine incorporation during translation as for many other selenoproteins.
Probab=20.18 E-value=1.4e+02 Score=26.66 Aligned_cols=43 Identities=0% Similarity=0.112 Sum_probs=36.7
Q ss_pred cccc-CCeEEEEEeCCCCcChhHHHHHHHHHhhcCCCCCceEee
Q 034235 56 TDVS-DEAVGVQIDAPAKDGEANAALLEYMSSLIHVSVGEFVES 98 (100)
Q Consensus 56 ~~~~-~~~l~V~V~ApP~dGkAN~aLi~~LAk~LgV~ks~I~~~ 98 (100)
..++ ++.+.|.+.....---.+..+....|+.||++..+|.+.
T Consensus 480 v~l~~dG~v~v~~g~~e~GQG~~T~~aQiaAe~LGip~e~V~v~ 523 (770)
T TIGR02416 480 IRIHPTGSAIARMGTKSQGQGHETTYAQIIATELGIPAEDIMVE 523 (770)
T ss_pred EEECCCceEEEEECCCCCCCCchHHHHHHHHHHHCCCHHHEEEE
Confidence 3444 688999999988877789999999999999999999874
Done!