Query 033057
Match_columns 128
No_of_seqs 117 out of 767
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 09:17:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033057.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033057hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK01310 hypothetical protein; 100.0 8.7E-30 1.9E-34 182.9 12.4 96 30-127 3-103 (104)
2 PRK01530 hypothetical protein; 100.0 9.2E-30 2E-34 183.2 11.4 89 37-125 11-103 (105)
3 COG1872 Uncharacterized conser 100.0 1.7E-29 3.8E-34 180.8 10.2 96 30-126 4-101 (102)
4 KOG3276 Uncharacterized conser 100.0 4.7E-29 1E-33 182.2 11.5 119 1-124 1-120 (125)
5 PRK05090 hypothetical protein; 100.0 9.4E-29 2E-33 175.1 10.8 83 30-113 2-84 (95)
6 PRK00647 hypothetical protein; 100.0 8.1E-29 1.8E-33 175.8 10.4 91 37-127 3-93 (96)
7 PF02594 DUF167: Uncharacteris 100.0 5.6E-29 1.2E-33 170.0 8.5 76 37-112 1-77 (77)
8 PRK04021 hypothetical protein; 100.0 4.1E-28 9E-33 170.9 11.8 88 32-123 2-91 (92)
9 TIGR00251 conserved hypothetic 99.9 6E-26 1.3E-30 158.5 10.2 73 37-112 5-79 (87)
10 PF09581 Spore_III_AF: Stage I 87.4 1.7 3.6E-05 32.9 5.4 55 42-98 125-187 (188)
11 PF01187 MIF: Macrophage migra 86.0 3.3 7.1E-05 29.3 6.0 58 41-99 36-98 (114)
12 PTZ00397 macrophage migration 82.5 8.1 0.00018 27.1 6.7 58 41-99 38-100 (116)
13 PF02738 Ald_Xan_dh_C2: Molybd 67.0 12 0.00027 32.9 5.2 46 59-104 328-373 (547)
14 COG1451 Predicted metal-depend 61.6 15 0.00032 29.4 4.3 49 37-89 7-55 (223)
15 PF08968 DUF1885: Domain of un 59.2 4.6 0.0001 30.3 0.9 38 60-101 81-123 (130)
16 TIGR02416 CO_dehy_Mo_lg carbon 56.0 21 0.00045 33.3 4.8 46 59-104 484-529 (770)
17 TIGR02965 xanthine_xdhB xanthi 53.2 25 0.00054 32.8 4.8 45 60-104 457-501 (758)
18 PF12685 SpoIIIAH: SpoIIIAH-li 52.4 33 0.00072 26.5 4.8 47 52-98 150-196 (196)
19 TIGR03311 Se_dep_Molyb_1 selen 50.1 33 0.00072 32.5 5.2 49 57-105 600-648 (848)
20 PTZ00450 macrophage migration 48.1 22 0.00048 25.5 3.0 59 40-99 37-100 (113)
21 PRK01964 4-oxalocrotonate taut 46.6 24 0.00051 22.1 2.6 24 76-99 20-43 (64)
22 PRK02220 4-oxalocrotonate taut 46.5 24 0.00051 21.6 2.6 23 77-99 21-43 (61)
23 cd00491 4Oxalocrotonate_Tautom 46.2 28 0.00061 20.8 2.9 23 77-99 20-42 (58)
24 PRK09800 putative hypoxanthine 45.8 50 0.0011 31.9 5.7 46 59-104 673-718 (956)
25 KOG1759 Macrophage migration i 45.1 38 0.00082 25.0 3.8 56 42-98 38-98 (115)
26 TIGR03313 Se_sel_red_Mo probab 44.9 44 0.00095 32.2 5.2 46 59-104 669-714 (951)
27 PF01361 Tautomerase: Tautomer 43.3 32 0.00069 21.1 2.8 22 77-98 20-41 (60)
28 TIGR03194 4hydrxCoA_A 4-hydrox 43.0 49 0.0011 30.8 5.1 46 59-104 453-498 (746)
29 TIGR00013 taut 4-oxalocrotonat 42.9 34 0.00073 21.0 2.9 23 76-98 20-42 (63)
30 TIGR03196 pucD xanthine dehydr 42.7 1E+02 0.0022 28.9 7.1 45 60-104 475-521 (768)
31 PRK00745 4-oxalocrotonate taut 42.5 29 0.00063 21.3 2.5 23 77-99 21-43 (62)
32 PRK02289 4-oxalocrotonate taut 39.7 40 0.00086 21.0 2.9 24 76-99 20-43 (60)
33 PF14552 Tautomerase_2: Tautom 39.1 33 0.00071 23.3 2.6 42 59-100 26-72 (82)
34 PF02738 Ald_Xan_dh_C2: Molybd 38.6 48 0.001 29.3 4.2 42 53-99 52-94 (547)
35 PLN02906 xanthine dehydrogenas 36.5 60 0.0013 32.4 4.8 47 59-105 1021-1067(1319)
36 PF15656 Tox-HDC: Toxin with a 36.3 47 0.001 24.6 3.2 33 72-104 9-41 (119)
37 TIGR02969 mam_aldehyde_ox alde 35.3 69 0.0015 32.1 5.0 46 59-104 1026-1071(1330)
38 PF12116 SpoIIID: Stage III sp 33.1 15 0.00032 25.7 0.1 19 77-95 18-36 (82)
39 PRK09970 xanthine dehydrogenas 29.9 1.1E+02 0.0025 28.5 5.3 45 59-103 469-514 (759)
40 COG0384 Predicted epimerase, P 29.8 1E+02 0.0022 25.8 4.6 47 65-111 217-265 (291)
41 PF07805 HipA_N: HipA-like N-t 29.4 75 0.0016 20.7 3.0 31 72-102 40-70 (81)
42 smart00213 UBQ Ubiquitin homol 29.1 62 0.0014 19.1 2.5 25 77-101 22-46 (64)
43 smart00760 Bac_DnaA_C Bacteria 27.4 30 0.00065 21.6 0.8 18 78-95 3-20 (60)
44 PRK01271 4-oxalocrotonate taut 26.7 82 0.0018 21.2 2.9 21 78-98 23-43 (76)
45 cd01769 UBL Ubiquitin-like dom 25.8 90 0.002 18.7 2.8 25 77-101 20-44 (69)
46 PF02542 YgbB: YgbB family; I 25.5 1.1E+02 0.0024 23.5 3.7 36 67-102 99-134 (157)
47 PF15609 PRTase_2: Phosphoribo 25.2 76 0.0017 25.2 2.8 37 63-101 154-190 (191)
48 PF00240 ubiquitin: Ubiquitin 24.7 1.1E+02 0.0024 18.8 3.1 24 78-101 19-42 (69)
49 PF02567 PhzC-PhzF: Phenazine 24.3 86 0.0019 24.7 3.1 42 67-108 210-252 (281)
50 KOG4079 Putative mitochondrial 23.8 59 0.0013 25.2 1.9 19 72-90 91-109 (169)
51 COG3579 PepC Aminopeptidase C 23.7 99 0.0022 27.4 3.5 46 77-123 207-252 (444)
52 COG1942 Uncharacterized protei 23.1 1.1E+02 0.0024 20.2 2.9 36 63-98 4-43 (69)
53 COG0245 IspF 2C-methyl-D-eryth 23.1 81 0.0017 24.5 2.6 33 69-101 101-133 (159)
54 PF01257 2Fe-2S_thioredx: Thio 22.9 34 0.00073 25.2 0.4 51 76-126 29-92 (145)
55 cd01796 DDI1_N DNA damage indu 22.2 91 0.002 19.9 2.4 26 77-102 22-47 (71)
56 PRK05457 heat shock protein Ht 22.0 4.5E+02 0.0097 21.5 7.1 48 79-126 81-142 (284)
57 PHA02564 V virion protein; Pro 21.8 1E+02 0.0022 23.3 2.9 30 65-95 73-102 (141)
58 TIGR03853 matur_matur probable 20.3 2.1E+02 0.0046 19.6 3.9 37 77-124 20-56 (77)
59 cd02552 PseudoU_synth_TruD_lik 20.1 83 0.0018 25.3 2.2 42 60-105 30-71 (232)
60 cd00196 UBQ Ubiquitin-like pro 20.1 1.2E+02 0.0027 16.2 2.4 27 77-103 20-46 (69)
61 cd06406 PB1_P67 A PB1 domain i 20.1 1.8E+02 0.0039 20.0 3.6 53 64-118 12-64 (80)
No 1
>PRK01310 hypothetical protein; Validated
Probab=99.97 E-value=8.7e-30 Score=182.93 Aligned_cols=96 Identities=25% Similarity=0.402 Sum_probs=88.5
Q ss_pred cceEEeCCCeEEEEEEEecCCCccccccccC-----CeEEEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEeecCCCC
Q 033057 30 SCIRLVPPSSVSITIHAKPGSKSCSITDVSD-----EAVGVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIGSGSKSR 104 (128)
Q Consensus 30 ~~i~~~~~~~v~I~I~VkP~Ak~~~I~~~~~-----~~l~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~~SR 104 (128)
.+++.. +++++|.|+|+|+|+++.|.++++ +.|+|+|++||++|+||++|++|||+.|+||+++|+|++|++||
T Consensus 3 ~~~~~~-~~~~~i~v~V~P~A~~~~i~g~~~~~~g~~~lkv~v~apPv~GkAN~ali~~LA~~l~v~ks~I~iv~G~tsR 81 (104)
T PRK01310 3 EPWRYS-ADGLRLAVRLTPRGGRDAIDGIETLADGRAVLKVRVRAVPEGGEANRALIELLAKALGVPKSSVRLLSGATSR 81 (104)
T ss_pred CceEEC-CCcEEEEEEEeeCCCcceeccccccCCCccEEEEEEecCCCCChHHHHHHHHHHHHhCCChhhEEEEecCCCC
Confidence 456666 589999999999999999998853 38999999999999999999999999999999999999999999
Q ss_pred ceEEEEccCCHHHHHHHHhhhhC
Q 033057 105 DKIVIVEEITPENVLNSLGKASS 127 (128)
Q Consensus 105 ~K~v~I~g~~~e~l~~~L~~~~~ 127 (128)
+|+|+|.+ +++++.++|...++
T Consensus 82 ~K~v~I~~-~~~~l~~~l~~~~~ 103 (104)
T PRK01310 82 LKQLRIDG-DPEDLGEALRALTA 103 (104)
T ss_pred ceEEEEeC-CHHHHHHHHHHHhc
Confidence 99999999 99999999988764
No 2
>PRK01530 hypothetical protein; Reviewed
Probab=99.96 E-value=9.2e-30 Score=183.17 Aligned_cols=89 Identities=17% Similarity=0.307 Sum_probs=84.8
Q ss_pred CCeEEEEEEEecCCCcccccccc----CCeEEEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEeecCCCCceEEEEcc
Q 033057 37 PSSVSITIHAKPGSKSCSITDVS----DEAVGVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIGSGSKSRDKIVIVEE 112 (128)
Q Consensus 37 ~~~v~I~I~VkP~Ak~~~I~~~~----~~~l~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~~SR~K~v~I~g 112 (128)
.+++.|+|+|+|+|+++.|.+++ ++.|+|+|+|||++|+||+||++|||+.||||+|+|+|++|++||+|+|+|.|
T Consensus 11 ~~gv~l~V~V~P~Akk~~i~g~~~~~~~~~Lki~v~ApPvdGkAN~ali~~LAk~l~v~ks~I~IvsG~tSR~K~i~I~g 90 (105)
T PRK01530 11 SHQALLNLKVKPNAKQNLISNFVIINNIPYLKLSIKAIPEQGKANEEIINYLAKEWKLSRSNIEIIKGHTHSLKTILIKN 90 (105)
T ss_pred CCcEEEEEEEeeCCCcccccceeccCCCCEEEEEEecCCCCChHHHHHHHHHHHHhCCChhhEEEEecCCCCceEEEEeC
Confidence 58999999999999999998874 46999999999999999999999999999999999999999999999999999
Q ss_pred CCHHHHHHHHhhh
Q 033057 113 ITPENVLNSLGKA 125 (128)
Q Consensus 113 ~~~e~l~~~L~~~ 125 (128)
++++++..+|...
T Consensus 91 ~~~~~l~~~l~~~ 103 (105)
T PRK01530 91 INEDYLNLIINSY 103 (105)
T ss_pred CCHHHHHHHHHhh
Confidence 9999999998764
No 3
>COG1872 Uncharacterized conserved protein [Function unknown]
Probab=99.96 E-value=1.7e-29 Score=180.81 Aligned_cols=96 Identities=30% Similarity=0.512 Sum_probs=89.0
Q ss_pred cceEEeCCCeEEEEEEEecCCCccccccccCCe--EEEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEeecCCCCceE
Q 033057 30 SCIRLVPPSSVSITIHAKPGSKSCSITDVSDEA--VGVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIGSGSKSRDKI 107 (128)
Q Consensus 30 ~~i~~~~~~~v~I~I~VkP~Ak~~~I~~~~~~~--l~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~~SR~K~ 107 (128)
++++.. ++++.|+|+|+|+|+++.|.+++++. |+|+|++||++||||++|++|||+.|++|+|+|+|++|++||.|+
T Consensus 4 ~~~~~~-~~~~~l~V~V~P~a~~~~i~g~~~~~~~Lkv~i~apP~~GKAN~~li~~Lak~~~v~kS~V~ivsGetsR~K~ 82 (102)
T COG1872 4 SAVKEL-DDGVLLRVRVKPKAKRDSIVGLDEWRKRLKVRITAPPVDGKANEELIKFLAKTFGVPKSSVEIVSGETSRLKT 82 (102)
T ss_pred hhHhhc-CCceEEEEEECCCCccCcccceecCcceEEEEEecCCCCcchhHHHHHHHHHHhCCCcccEEEEecCcccceE
Confidence 456666 48999999999999999999887665 999999999999999999999999999999999999999999999
Q ss_pred EEEccCCHHHHHHHHhhhh
Q 033057 108 VIVEEITPENVLNSLGKAS 126 (128)
Q Consensus 108 v~I~g~~~e~l~~~L~~~~ 126 (128)
|+|.+++++++..+|...+
T Consensus 83 v~i~~i~~d~~~~~~~~~~ 101 (102)
T COG1872 83 VLIKNIDPDQLPERLAALI 101 (102)
T ss_pred EEecCCCHHHHHHHHHhhc
Confidence 9999999999999887654
No 4
>KOG3276 consensus Uncharacterized conserved protein, contains YggU domain [Function unknown]
Probab=99.96 E-value=4.7e-29 Score=182.20 Aligned_cols=119 Identities=46% Similarity=0.769 Sum_probs=107.9
Q ss_pred CCCcccCcccccCCCCcccccCCCCCCCCcceEEeCCCeEEEEEEEecCCCccccccccCCeEEEEEeCCCCcChhHHHH
Q 033057 1 MAPAKKGKSKAKSAGSTQSKIKTNDENLPSCIRLVPPSSVSITIHAKPGSKSCSITDVSDEAVGVQIDAPAKDGEANAAL 80 (128)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~i~~~~~~~v~I~I~VkP~Ak~~~I~~~~~~~l~v~V~apP~~GkAN~eL 80 (128)
|.|+++|++..+++.+++ .+.++|+||.+..++.+.|.|+++|||++++|+++.++.+.|.|.|||.+|+||.||
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 VMPKKKGKSTKGAETSKV-----DDKPVPPCISVDTGGLVQIAIHAKPGAKQSAITDVGDEAVGVAIAAPPREGEANAEL 75 (125)
T ss_pred CccccccccccccccCCC-----ccCCCCCceEecCCCeEEEEEEecCCccccceeeccccccceEEecCCccchhhHHH
Confidence 679999999999988764 456788999999888899999999999999999999999999999999999999999
Q ss_pred HHHHHhhhCCcCccEEEeecCCCCceEEEEccC-CHHHHHHHHhh
Q 033057 81 LEYMSSVLGVKRRQVSIGSGSKSRDKIVIVEEI-TPENVLNSLGK 124 (128)
Q Consensus 81 i~~LAk~l~Vpks~I~Iv~G~~SR~K~v~I~g~-~~e~l~~~L~~ 124 (128)
++||+++||+++|++++-+|++||+|+|.|... ...+.++.|..
T Consensus 76 l~ylskvLgLRksdv~ldkG~kSrsKvv~i~~~~~~~e~i~~l~a 120 (125)
T KOG3276|consen 76 LEYLSKVLGLRKSDVTLDKGWKSRSKVVVIEDLSATQEYIELLEA 120 (125)
T ss_pred HHHHHHHhhhhhhheeecccccccceEEEEecCcccHHHHHHHhc
Confidence 999999999999999999999999999999875 45556665543
No 5
>PRK05090 hypothetical protein; Validated
Probab=99.96 E-value=9.4e-29 Score=175.13 Aligned_cols=83 Identities=27% Similarity=0.400 Sum_probs=78.8
Q ss_pred cceEEeCCCeEEEEEEEecCCCccccccccCCeEEEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEeecCCCCceEEE
Q 033057 30 SCIRLVPPSSVSITIHAKPGSKSCSITDVSDEAVGVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIGSGSKSRDKIVI 109 (128)
Q Consensus 30 ~~i~~~~~~~v~I~I~VkP~Ak~~~I~~~~~~~l~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~~SR~K~v~ 109 (128)
+|++.. +++++|+|+|+|+|+++.|.+++++.|+|+|+|||+||+||++|++|||+.|+||+|+|+|++|++||+|+|+
T Consensus 2 ~~~~~~-~~~~~l~i~V~P~A~~~~i~~~~~~~lkv~v~ApPveGkAN~ali~~LAk~l~v~ks~I~i~~G~tsr~K~v~ 80 (95)
T PRK05090 2 SAVTWD-GDGLVLRLYIQPKASRDQIVGLHGDELKVAITAPPVDGQANAHLLKFLAKQFRVAKSQVVIEKGELGRHKQVR 80 (95)
T ss_pred CceEEe-CCeEEEEEEEeeCCCcceeccccCCEEEEEEecCCCCChHHHHHHHHHHHHhCCChhhEEEEecCCCCceEEE
Confidence 567766 6899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EccC
Q 033057 110 VEEI 113 (128)
Q Consensus 110 I~g~ 113 (128)
|.+.
T Consensus 81 I~~~ 84 (95)
T PRK05090 81 IINP 84 (95)
T ss_pred EcCc
Confidence 9864
No 6
>PRK00647 hypothetical protein; Validated
Probab=99.96 E-value=8.1e-29 Score=175.82 Aligned_cols=91 Identities=19% Similarity=0.332 Sum_probs=80.4
Q ss_pred CCeEEEEEEEecCCCccccccccCCeEEEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEeecCCCCceEEEEccCCHH
Q 033057 37 PSSVSITIHAKPGSKSCSITDVSDEAVGVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIGSGSKSRDKIVIVEEITPE 116 (128)
Q Consensus 37 ~~~v~I~I~VkP~Ak~~~I~~~~~~~l~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~~SR~K~v~I~g~~~e 116 (128)
++.|+|.|+|+|+|+++.|.+++++.|+|+|+|||+|||||++|++|||+.|+||+++|+|++|++||+|+|+|.+-..+
T Consensus 3 ~~~~~l~V~V~P~Ak~~~I~g~~~~~Lkvrv~ApPvdGKAN~ali~~LAk~l~vpks~I~Iv~G~tSr~K~v~i~~~~~~ 82 (96)
T PRK00647 3 EGFWILEVKVTPKARENKIVGFEGGILKVRVTEVPEKGKANDAVIALLAKFLSLPKRDVTLIAGETSRKKKVLLPRSIKA 82 (96)
T ss_pred CCcEEEEEEEeeCCCcceeccccCCEEEEEEecCCCCChHHHHHHHHHHHHhCCChhhEEEEecCCCCceEEEEChhHHH
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999764444
Q ss_pred HHHHHHhhhhC
Q 033057 117 NVLNSLGKASS 127 (128)
Q Consensus 117 ~l~~~L~~~~~ 127 (128)
.+.+.+..+.|
T Consensus 83 ~l~~~~~~~~~ 93 (96)
T PRK00647 83 ILFEQFPSESS 93 (96)
T ss_pred HHHHhhcccCC
Confidence 44444444433
No 7
>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=99.96 E-value=5.6e-29 Score=170.03 Aligned_cols=76 Identities=36% Similarity=0.660 Sum_probs=66.7
Q ss_pred CCeEEEEEEEecCCCccccccccCC-eEEEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEeecCCCCceEEEEcc
Q 033057 37 PSSVSITIHAKPGSKSCSITDVSDE-AVGVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIGSGSKSRDKIVIVEE 112 (128)
Q Consensus 37 ~~~v~I~I~VkP~Ak~~~I~~~~~~-~l~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~~SR~K~v~I~g 112 (128)
+++++|.|+|+|+|++++|.+++++ .|+|+|+|||++|+||++|++|||+.|+||+|+|+|++|++||+|+|+|+|
T Consensus 1 ~~~~~l~v~V~P~ak~~~i~~~~~~~~l~i~v~app~~GkAN~ali~~La~~l~v~ks~i~i~~G~~Sr~K~v~i~~ 77 (77)
T PF02594_consen 1 GDGVILSVRVKPGAKRNAIVGVEGDGALKIRVTAPPVDGKANKALIRFLAKALGVPKSDIEIVSGHTSRNKVVRIEN 77 (77)
T ss_dssp TTEEEEEEECEBSSSS-EEEEE-TTT-EEEEBSTTCCCCCHHHHHHHHHHHHCT--TTCEEECC-CCCSEEEEEEE-
T ss_pred CCeEEEEEEEEeCCCccccccccCceEEEEEEecCCCcChhHHHHHHHHHHHhCCCcccEEEEecCCCCceEEEEeC
Confidence 3789999999999999999999885 999999999999999999999999999999999999999999999999975
No 8
>PRK04021 hypothetical protein; Reviewed
Probab=99.96 E-value=4.1e-28 Score=170.87 Aligned_cols=88 Identities=31% Similarity=0.487 Sum_probs=82.0
Q ss_pred eEEeCCCeEEEEEEEecCCCcccccccc--CCeEEEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEeecCCCCceEEE
Q 033057 32 IRLVPPSSVSITIHAKPGSKSCSITDVS--DEAVGVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIGSGSKSRDKIVI 109 (128)
Q Consensus 32 i~~~~~~~v~I~I~VkP~Ak~~~I~~~~--~~~l~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~~SR~K~v~ 109 (128)
+++. ++++.|.|+|+|+|++++|.+++ ++.|+|+|++||++|+||+||++|||+.||+ +|+|++|++||+|+|+
T Consensus 2 ~~~~-~~~v~l~v~v~P~a~~~~i~g~~~~~~~lkv~v~apP~~GkAN~ali~~LAk~l~~---~I~I~~G~~sr~K~v~ 77 (92)
T PRK04021 2 LKET-KEGVILQVYVQPKAKENEIEGVDEWRGRLKVKIKAPPVKGKANKELVKFFSKLLGA---EVEIIRGETSREKDLL 77 (92)
T ss_pred eEEe-CCcEEEEEEEeeCCCcceEccccCCCCEEEEEEecCCCCChHHHHHHHHHHHHhCC---CEEEEecCCcCceEEE
Confidence 5556 57899999999999999999875 4899999999999999999999999999997 8999999999999999
Q ss_pred EccCCHHHHHHHHh
Q 033057 110 VEEITPENVLNSLG 123 (128)
Q Consensus 110 I~g~~~e~l~~~L~ 123 (128)
|.|+++|++.++|.
T Consensus 78 i~g~~~e~l~~~L~ 91 (92)
T PRK04021 78 VKGISLEEVKKKLK 91 (92)
T ss_pred EecCCHHHHHHHhc
Confidence 99999999999874
No 9
>TIGR00251 conserved hypothetical protein TIGR00251.
Probab=99.93 E-value=6e-26 Score=158.52 Aligned_cols=73 Identities=32% Similarity=0.517 Sum_probs=71.1
Q ss_pred CCeEEEEEEEecCCCccccccccC--CeEEEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEeecCCCCceEEEEcc
Q 033057 37 PSSVSITIHAKPGSKSCSITDVSD--EAVGVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIGSGSKSRDKIVIVEE 112 (128)
Q Consensus 37 ~~~v~I~I~VkP~Ak~~~I~~~~~--~~l~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~~SR~K~v~I~g 112 (128)
+++++|.|+|+|+|+++.|.++++ +.|+|+|+|||+||+||++|++|||+.|++ +|+|++|++||+|+|+|.+
T Consensus 5 ~~g~~l~v~V~P~A~~~~i~g~~~~~~~Lki~v~ApP~~GkAN~ali~~La~~l~v---~I~i~~G~tsR~K~v~I~~ 79 (87)
T TIGR00251 5 DDGLLIRIYVQPKASKDSIVGYNEWRKRVEVKIKAPPVEGKANRELIKFFGEIFGV---DVEIVSGELSRQKTIKIIN 79 (87)
T ss_pred CCeEEEEEEEeeCCCcceeccccCCCCeEEEEEecCCCCChHHHHHHHHHHHHhCc---eEEEEecCCCCceEEEEeC
Confidence 589999999999999999999888 899999999999999999999999999999 9999999999999999998
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=87.40 E-value=1.7 Score=32.94 Aligned_cols=55 Identities=18% Similarity=0.396 Sum_probs=37.5
Q ss_pred EEEEEecCCCcc--ccccccCCeEEEEE------eCCCCcChhHHHHHHHHHhhhCCcCccEEEe
Q 033057 42 ITIHAKPGSKSC--SITDVSDEAVGVQI------DAPAKDGEANAALLEYMSSVLGVKRRQVSIG 98 (128)
Q Consensus 42 I~I~VkP~Ak~~--~I~~~~~~~l~v~V------~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv 98 (128)
|.|.++++.... ....+ +-+.|.+ ...+.+.+..++|.++||..|||++++|+|.
T Consensus 125 I~v~l~~~~~~~~~~~~~V--e~V~I~~~~~~~~~~~~~~~~~~~~i~~~la~~~~i~~~~I~V~ 187 (188)
T PF09581_consen 125 IKVTLSEEEEQKEEAVEPV--EPVEIDIEKESDSSKSPEDSEEEEEIKQYLADFYGISPEQIKVY 187 (188)
T ss_pred EEEEEcCCCccccccCCcc--cceEecccccccccccccchHHHHHHHHHHHHHhCCCHHHeEEe
Confidence 666777654322 11111 3345554 4566777888999999999999999999873
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=85.98 E-value=3.3 Score=29.26 Aligned_cols=58 Identities=24% Similarity=0.365 Sum_probs=37.8
Q ss_pred EEEEEEecCCCccccccccCCeEEEEEeCCCC-cChhH----HHHHHHHHhhhCCcCccEEEee
Q 033057 41 SITIHAKPGSKSCSITDVSDEAVGVQIDAPAK-DGEAN----AALLEYMSSVLGVKRRQVSIGS 99 (128)
Q Consensus 41 ~I~I~VkP~Ak~~~I~~~~~~~l~v~V~apP~-~GkAN----~eLi~~LAk~l~Vpks~I~Iv~ 99 (128)
+|-|.|.+++.-. ..+-.+....+.|+.--. +.+.| ++|.+||.+.||||+.+|-|..
T Consensus 36 ~i~V~v~~~~~m~-fgGs~~P~a~v~l~sig~~~~~~n~~~s~~i~~~l~~~LgIp~~Riyi~f 98 (114)
T PF01187_consen 36 YIMVTVEDGQRMS-FGGSDDPAAFVELKSIGGLDPEQNKKYSAAITEFLEEELGIPPDRIYINF 98 (114)
T ss_dssp GEEEEEEESTEEE-ETTB-SS-EEEEEEESSSSSHHHHHHHHHHHHHHHHHHHT--GGGEEEEE
T ss_pred hEEEEeeCCceEE-ECCCCCCEEEEEEEEccCCCHHHHHHHHHHHHHHHHHHhCCCcCceEEEE
Confidence 4667778877654 334345667777766553 44444 6789999999999999998763
No 12
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=82.48 E-value=8.1 Score=27.15 Aligned_cols=58 Identities=21% Similarity=0.115 Sum_probs=37.1
Q ss_pred EEEEEEecCCCccccccccCCeEEEEEeCCC-CcChhH----HHHHHHHHhhhCCcCccEEEee
Q 033057 41 SITIHAKPGSKSCSITDVSDEAVGVQIDAPA-KDGEAN----AALLEYMSSVLGVKRRQVSIGS 99 (128)
Q Consensus 41 ~I~I~VkP~Ak~~~I~~~~~~~l~v~V~apP-~~GkAN----~eLi~~LAk~l~Vpks~I~Iv~ 99 (128)
++-|.+.|+..-. +.+-++..+.|.|+.-. ...+.| ++|.++|++.||||+.+|-|..
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 4455555554332 22445677788888543 333334 5677889999999999998864
No 13
>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=66.97 E-value=12 Score=32.94 Aligned_cols=46 Identities=22% Similarity=0.274 Sum_probs=37.4
Q ss_pred cCCeEEEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEeecCCCC
Q 033057 59 SDEAVGVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIGSGSKSR 104 (128)
Q Consensus 59 ~~~~l~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~~SR 104 (128)
.++.+.|.+......-=....+....|+.||||..+|.++.|-|..
T Consensus 328 ~DG~v~v~~~~~e~GqG~~T~~~qiaAe~Lgi~~~~V~v~~~dT~~ 373 (547)
T PF02738_consen 328 PDGSVTVYTGGVEMGQGSRTALAQIAAEELGIPPEDVRVVSGDTDT 373 (547)
T ss_dssp TTS-EEEEES--BSSSSHHHHHHHHHHHHHTS-GGGEEEEECBTTT
T ss_pred eCCCEEEEEecccCCcchhhhHHHHHHHHhCCChhhEEEEeCCCcC
Confidence 3688999998888877789999999999999999999999998764
No 14
>COG1451 Predicted metal-dependent hydrolase [General function prediction only]
Probab=61.63 E-value=15 Score=29.41 Aligned_cols=49 Identities=14% Similarity=0.305 Sum_probs=39.4
Q ss_pred CCeEEEEEEEecCCCccccccccCCeEEEEEeCCCCcChhHHHHHHHHHhhhC
Q 033057 37 PSSVSITIHAKPGSKSCSITDVSDEAVGVQIDAPAKDGEANAALLEYMSSVLG 89 (128)
Q Consensus 37 ~~~v~I~I~VkP~Ak~~~I~~~~~~~l~v~V~apP~~GkAN~eLi~~LAk~l~ 89 (128)
..+..+.|.+++++++..|.-..++ .|.|.+||- ..++++..||.+..+
T Consensus 7 ~~~~~~~v~~~r~~r~~~i~i~~~~--~v~v~~P~~--~~~~~~~~fl~k~~~ 55 (223)
T COG1451 7 GDGLPLEVQVKRRAKRLTIRIPPGG--TVRVSVPPG--LSDEEVENFLAKKLG 55 (223)
T ss_pred ccCccEEEEEeecccceeEEecCCC--eEEEEeCCC--CCHHHHHHHHHHHHH
Confidence 3678899999999999988654445 889999976 777888888887665
No 15
>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=59.15 E-value=4.6 Score=30.33 Aligned_cols=38 Identities=21% Similarity=0.399 Sum_probs=23.4
Q ss_pred CCeEEEEEeCCCC-----cChhHHHHHHHHHhhhCCcCccEEEeecC
Q 033057 60 DEAVGVQIDAPAK-----DGEANAALLEYMSSVLGVKRRQVSIGSGS 101 (128)
Q Consensus 60 ~~~l~v~V~apP~-----~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~ 101 (128)
.+.=.|.|.=|+- .||||+ +++|||+.|. ..+.+-.|.
T Consensus 81 ~e~~~IQv~LP~~AThGDK~KANE-fckfLAk~l~---~EL~LFNGR 123 (130)
T PF08968_consen 81 NEQSYIQVVLPDGATHGDKGKANE-FCKFLAKKLK---GELHLFNGR 123 (130)
T ss_dssp TTEEEEEEE--TT--HHHHHHHHH-HHHHHHHHH----EEEE-TTS-
T ss_pred CcceEEEEECCCCCccCcchhHHH-HHHHHHHHhh---heeEEecCe
Confidence 3445566666664 589995 8999999997 555555553
No 16
>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=55.95 E-value=21 Score=33.32 Aligned_cols=46 Identities=7% Similarity=0.228 Sum_probs=41.8
Q ss_pred cCCeEEEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEeecCCCC
Q 033057 59 SDEAVGVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIGSGSKSR 104 (128)
Q Consensus 59 ~~~~l~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~~SR 104 (128)
.++.+.|.+......-=.+..+.+..|+.||||..+|+++.|-|.+
T Consensus 484 ~dG~v~v~~g~~e~GQG~~T~~aQiaAe~LGip~e~V~v~~~DT~~ 529 (770)
T TIGR02416 484 PTGSAIARMGTKSQGQGHETTYAQIIATELGIPAEDIMVEEGDTDT 529 (770)
T ss_pred CCceEEEEECCCCCCCCchHHHHHHHHHHHCCCHHHEEEEecCCCC
Confidence 3688999999998887889999999999999999999999998854
No 17
>TIGR02965 xanthine_xdhB xanthine dehydrogenase, molybdopterin binding subunit. Members of the protein family are the molybdopterin-containing large subunit (or, in, eukaryotes, the molybdopterin-binding domain) of xanthine dehydrogenase, and enzyme that reduces the purine pool by catabolizing xanthine to urate. This model is based primarily on bacterial sequences; it does not manage to include all eukaryotic xanthine dehydrogenases and thereby discriminate them from the closely related enzyme aldehyde dehydrogenase.
Probab=53.16 E-value=25 Score=32.75 Aligned_cols=45 Identities=11% Similarity=0.176 Sum_probs=40.5
Q ss_pred CCeEEEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEeecCCCC
Q 033057 60 DEAVGVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIGSGSKSR 104 (128)
Q Consensus 60 ~~~l~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~~SR 104 (128)
++.+.|.+-.....-=.+..+....|+.|||+..+|+++.|-|+.
T Consensus 457 dG~v~v~~g~~e~GQG~~T~laQIaAe~LGi~~d~V~v~~~DT~~ 501 (758)
T TIGR02965 457 DGSIHLNHGGTEMGQGLNTKVAQVVAEEFQVDIDRVKITATDTDK 501 (758)
T ss_pred CCcEEEEECCCCCCCCHHHHHHHHHHHHhCCCHHHEEEEecCccC
Confidence 678888888888877789999999999999999999999998874
No 18
>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=52.39 E-value=33 Score=26.51 Aligned_cols=47 Identities=17% Similarity=0.291 Sum_probs=34.6
Q ss_pred ccccccccCCeEEEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEe
Q 033057 52 SCSITDVSDEAVGVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIG 98 (128)
Q Consensus 52 ~~~I~~~~~~~l~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv 98 (128)
.++|..+.++.+.|-|.++=..-+-=..+++...+.+||+..+|+|.
T Consensus 150 ~davv~~~~~~v~VvV~~~~L~~~~~~~I~diV~~~~~v~~~~I~V~ 196 (196)
T PF12685_consen 150 EDAVVFIEDDSVDVVVKADKLSDAEAAQIIDIVMRETGVPAENISVT 196 (196)
T ss_dssp SEEEEE-SSSEEEEEEE-S---HHHHHHHHHHHHHHHC-STSEEEEE
T ss_pred CceEEEeeCCEEEEEEeCCCCCHHHHHHHHHHHHHHhCCCcCeEEeC
Confidence 45666677888999999887777777789999999999999999873
No 19
>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=50.12 E-value=33 Score=32.54 Aligned_cols=49 Identities=12% Similarity=0.129 Sum_probs=43.0
Q ss_pred cccCCeEEEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEeecCCCCc
Q 033057 57 DVSDEAVGVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIGSGSKSRD 105 (128)
Q Consensus 57 ~~~~~~l~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~~SR~ 105 (128)
...++.+.|.+......-=.+..+....|+.||||.++|+++.|-|++.
T Consensus 600 ~~~DGsv~v~~g~~e~GQG~~T~~aQiaAe~LGip~e~V~v~~~DT~~~ 648 (848)
T TIGR03311 600 AVEDGKVHIRTSAACIGQGLGTVLTQIVCETTGLPPEVIVCELPDTALT 648 (848)
T ss_pred EEcCCEEEEEECCCCcCcCHHHHHHHHHHHHHCCCHHHEEEEcCCCCCC
Confidence 3458899999998888777889999999999999999999999988764
No 20
>PTZ00450 macrophage migration inhibitory factor-like protein; Provisional
Probab=48.13 E-value=22 Score=25.53 Aligned_cols=59 Identities=8% Similarity=0.070 Sum_probs=36.4
Q ss_pred EEEEEEEecCCCccccccccCCeEEEEEeC--C---CCcChhHHHHHHHHHhhhCCcCccEEEee
Q 033057 40 VSITIHAKPGSKSCSITDVSDEAVGVQIDA--P---AKDGEANAALLEYMSSVLGVKRRQVSIGS 99 (128)
Q Consensus 40 v~I~I~VkP~Ak~~~I~~~~~~~l~v~V~a--p---P~~GkAN~eLi~~LAk~l~Vpks~I~Iv~ 99 (128)
-+|.|.+.|+..-. +.+-.+..-.+.|+. - ....+-.++|.++|.+.||||+.+|=|..
T Consensus 37 ~yvmV~~~~~~~m~-fgGs~~P~A~~~l~siG~~~~~~n~~~s~~i~~~l~~~LgIp~dRiYI~f 100 (113)
T PTZ00450 37 DFVMTAFSDSTPMS-FQGSTAPAAYVRVEAWGEYAPSKPKMMTPRITAAITKECGIPAERIYVFY 100 (113)
T ss_pred HHEEEEEeCCceEE-EcCCCCCEEEEEEEEecCcCHHHHHHHHHHHHHHHHHHcCCCcccEEEEE
Confidence 45677777776543 223233443344432 2 22334456789999999999999998764
No 21
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=46.65 E-value=24 Score=22.07 Aligned_cols=24 Identities=21% Similarity=0.216 Sum_probs=19.6
Q ss_pred hHHHHHHHHHhhhCCcCccEEEee
Q 033057 76 ANAALLEYMSSVLGVKRRQVSIGS 99 (128)
Q Consensus 76 AN~eLi~~LAk~l~Vpks~I~Iv~ 99 (128)
--++|-+.|++.||+|..++.++-
T Consensus 20 l~~~it~~l~~~lg~p~~~v~V~i 43 (64)
T PRK01964 20 LIREVTEAISATLDVPKERVRVIV 43 (64)
T ss_pred HHHHHHHHHHHHhCcChhhEEEEE
Confidence 356778889999999999998763
No 22
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=46.55 E-value=24 Score=21.61 Aligned_cols=23 Identities=9% Similarity=0.040 Sum_probs=19.2
Q ss_pred HHHHHHHHHhhhCCcCccEEEee
Q 033057 77 NAALLEYMSSVLGVKRRQVSIGS 99 (128)
Q Consensus 77 N~eLi~~LAk~l~Vpks~I~Iv~ 99 (128)
-++|.+.|++.||+|..+|.++-
T Consensus 21 ~~~it~~l~~~~~~p~~~v~V~i 43 (61)
T PRK02220 21 VKDVTAAVSKNTGAPAEHIHVII 43 (61)
T ss_pred HHHHHHHHHHHhCcChhhEEEEE
Confidence 46778889999999999998764
No 23
>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=46.25 E-value=28 Score=20.85 Aligned_cols=23 Identities=17% Similarity=0.211 Sum_probs=19.3
Q ss_pred HHHHHHHHHhhhCCcCccEEEee
Q 033057 77 NAALLEYMSSVLGVKRRQVSIGS 99 (128)
Q Consensus 77 N~eLi~~LAk~l~Vpks~I~Iv~ 99 (128)
-++|.+.|++.||+|...+.++-
T Consensus 20 ~~~i~~~l~~~~g~~~~~v~V~i 42 (58)
T cd00491 20 IERVTEAVSEILGAPEATIVVII 42 (58)
T ss_pred HHHHHHHHHHHhCcCcccEEEEE
Confidence 46788899999999999887763
No 24
>PRK09800 putative hypoxanthine oxidase; Provisional
Probab=45.83 E-value=50 Score=31.90 Aligned_cols=46 Identities=17% Similarity=0.183 Sum_probs=41.0
Q ss_pred cCCeEEEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEeecCCCC
Q 033057 59 SDEAVGVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIGSGSKSR 104 (128)
Q Consensus 59 ~~~~l~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~~SR 104 (128)
.++.+.|.+......-=.+..+.+..|+.||+|.++|+++.|-|.+
T Consensus 673 ~dGsv~v~~g~~e~GqG~~T~~~QiaAe~LGip~d~V~v~~~DT~~ 718 (956)
T PRK09800 673 SDGTFIVHSGGADIGTGLDTVVTKLAAEVLHCPPQDVHVISGDTDH 718 (956)
T ss_pred CCceEEEEECCCCCCccHHHHHHHHHHHHHCCCceeEEEEeCCCCC
Confidence 4688999888888877788999999999999999999999998865
No 25
>KOG1759 consensus Macrophage migration inhibitory factor [Defense mechanisms]
Probab=45.09 E-value=38 Score=24.99 Aligned_cols=56 Identities=16% Similarity=0.169 Sum_probs=34.4
Q ss_pred EEEEEecCCCccccccccCC-----eEEEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEe
Q 033057 42 ITIHAKPGSKSCSITDVSDE-----AVGVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIG 98 (128)
Q Consensus 42 I~I~VkP~Ak~~~I~~~~~~-----~l~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv 98 (128)
|.|++.++..-. ..+-++. ...+..-.+-++.+=-++|.+||.+.|++++++|=|-
T Consensus 38 i~V~l~~~~~i~-fggt~eP~A~~~l~Sig~v~~~~N~~~sa~l~~il~~~L~l~~~rv~I~ 98 (115)
T KOG1759|consen 38 IMVELAGGVRIA-FGGTTEPAAYASLKSIGGVGAIVNRSYSAALTEILEKELSLDPDRVYIK 98 (115)
T ss_pred EEEEecCCceEe-ccCCCCccEEEEEEeccccChhHhHHHHHHHHHHHHHHhCCCCCeEEEE
Confidence 677777776543 2222332 2223333444444444678899999999999998764
No 26
>TIGR03313 Se_sel_red_Mo probable selenate reductase, molybdenum-binding subunit. Our comparative genomics suggests this protein family to be a subunit of a selenium-dependent molybdenum hydroxylase, although the substrate is not specified. This protein is suggested by Bebien, et al., to be the molybdenum-binding subunit of a molydbopterin-containing selenate reductase. Xi, et al, however, show that mutation of this gene in E. coli conferred sensitivity to adenine, suggesting a defect in purine interconversion. This finding, plus homology of nearby genes in a 23-gene purine catabolism region in E. coli to xanthine dehydrogase subunits suggests xanthine dehydrogenase activity.
Probab=44.91 E-value=44 Score=32.23 Aligned_cols=46 Identities=17% Similarity=0.159 Sum_probs=41.2
Q ss_pred cCCeEEEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEeecCCCC
Q 033057 59 SDEAVGVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIGSGSKSR 104 (128)
Q Consensus 59 ~~~~l~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~~SR 104 (128)
.++.+.|.+......-=.+..+.+..|+.||+|..+|+++.|-|..
T Consensus 669 ~dG~v~v~~g~~e~GqG~~T~~~QiaAe~LGvp~d~V~v~~~DT~~ 714 (951)
T TIGR03313 669 SDGTFIVHSGGADIGTGLDTVVSKLTAEVLHCPMDDVHVISGDTDH 714 (951)
T ss_pred CCceEEEEECCCCCCccHHHHHHHHHHHHHCCCHHhEEEEeCCCCC
Confidence 4678999998888888889999999999999999999999998764
No 27
>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=43.34 E-value=32 Score=21.06 Aligned_cols=22 Identities=23% Similarity=0.418 Sum_probs=17.5
Q ss_pred HHHHHHHHHhhhCCcCccEEEe
Q 033057 77 NAALLEYMSSVLGVKRRQVSIG 98 (128)
Q Consensus 77 N~eLi~~LAk~l~Vpks~I~Iv 98 (128)
-+++-+.+++.||.|...|.++
T Consensus 20 ~~~it~~~~~~lg~~~~~i~V~ 41 (60)
T PF01361_consen 20 AEAITDAVVEVLGIPPERISVV 41 (60)
T ss_dssp HHHHHHHHHHHHTS-GGGEEEE
T ss_pred HHHHHHHHHHHhCcCCCeEEEE
Confidence 3567788999999999998876
No 28
>TIGR03194 4hydrxCoA_A 4-hydroxybenzoyl-CoA reductase, alpha subunit. This model represents the largest chain, alpha, of the enzyme 4-hydroxybenzoyl-CoA reductase. In species capable of degrading various aromatic compounds by way of benzoyl-CoA, this enzyme can convert 4-hydroxybenzoyl-CoA to benzoyl-CoA.
Probab=42.97 E-value=49 Score=30.83 Aligned_cols=46 Identities=15% Similarity=0.180 Sum_probs=40.7
Q ss_pred cCCeEEEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEeecCCCC
Q 033057 59 SDEAVGVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIGSGSKSR 104 (128)
Q Consensus 59 ~~~~l~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~~SR 104 (128)
.++.+.|.+......-=.+..+.+..|+.||+|..+|+++.|-|+.
T Consensus 453 ~dG~v~v~~g~~e~GqG~~T~~~qiaAe~LGip~d~V~v~~~DT~~ 498 (746)
T TIGR03194 453 FDGGITLLTGAADIGQGSSTIASQVAAEVLGVRLSRIRVISADSAL 498 (746)
T ss_pred CCccEEEEEcCCCCCCCHHHHHHHHHHHHhCCCHHhEEEEccCCCC
Confidence 3678888888888877788899999999999999999999998865
No 29
>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=42.86 E-value=34 Score=20.99 Aligned_cols=23 Identities=17% Similarity=0.213 Sum_probs=19.2
Q ss_pred hHHHHHHHHHhhhCCcCccEEEe
Q 033057 76 ANAALLEYMSSVLGVKRRQVSIG 98 (128)
Q Consensus 76 AN~eLi~~LAk~l~Vpks~I~Iv 98 (128)
--++|.+.|++.||+|...+.++
T Consensus 20 l~~~it~~l~~~lg~~~~~v~V~ 42 (63)
T TIGR00013 20 LIEGVTEAMAETLGANLESIVVI 42 (63)
T ss_pred HHHHHHHHHHHHhCCCcccEEEE
Confidence 35678889999999999988765
No 30
>TIGR03196 pucD xanthine dehydrogenase D subunit. This gene has been characterized in B. subtilis as the molybdopterin binding-subunit of xanthine dehydrogenase (pucD), acting in conjunction with pucC, the FAD-binding subunit and pucE, the FeS-binding subunit. The more common XDH complex (GenProp0640) includes the xdhB gene which is related to pucD. It appears that most of the relatives of pucD outside of this narrow clade are involved in other processes as they are found in unrelated genomic contexts, contain the more common XDH complex and/or do not appear to process purines to allantoin.
Probab=42.71 E-value=1e+02 Score=28.92 Aligned_cols=45 Identities=16% Similarity=0.153 Sum_probs=38.5
Q ss_pred CC--eEEEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEeecCCCC
Q 033057 60 DE--AVGVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIGSGSKSR 104 (128)
Q Consensus 60 ~~--~l~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~~SR 104 (128)
++ .+.|.+......-=.+..+....|+.||||.++|+++.|-|.+
T Consensus 475 dGsv~v~v~~g~~d~GQG~~T~~aQiaAe~LGip~e~V~v~~~DT~~ 521 (768)
T TIGR03196 475 DGTVKIRAHFACAECGQGFLAAAEQIAMEELGCAAEDISIAIADTAK 521 (768)
T ss_pred CCCeEEEEEECCCCcCCCHHHHHHHHHHHHhCCCHHHEEEecCCCCC
Confidence 55 3777787877776789999999999999999999999998865
No 31
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=42.48 E-value=29 Score=21.28 Aligned_cols=23 Identities=17% Similarity=0.125 Sum_probs=18.8
Q ss_pred HHHHHHHHHhhhCCcCccEEEee
Q 033057 77 NAALLEYMSSVLGVKRRQVSIGS 99 (128)
Q Consensus 77 N~eLi~~LAk~l~Vpks~I~Iv~ 99 (128)
-++|.+.|.+.||+|..+|.++-
T Consensus 21 ~~~it~~l~~~~~~p~~~v~V~i 43 (62)
T PRK00745 21 VEEITRVTVETLGCPPESVDIII 43 (62)
T ss_pred HHHHHHHHHHHcCCChhHEEEEE
Confidence 35678889999999999987764
No 32
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=39.72 E-value=40 Score=20.98 Aligned_cols=24 Identities=8% Similarity=0.095 Sum_probs=19.9
Q ss_pred hHHHHHHHHHhhhCCcCccEEEee
Q 033057 76 ANAALLEYMSSVLGVKRRQVSIGS 99 (128)
Q Consensus 76 AN~eLi~~LAk~l~Vpks~I~Iv~ 99 (128)
--++|-+.+++.|++|...|+++-
T Consensus 20 L~~~it~a~~~~~~~p~~~v~V~i 43 (60)
T PRK02289 20 LAREVTEVVSRIAKAPKEAIHVFI 43 (60)
T ss_pred HHHHHHHHHHHHhCcCcceEEEEE
Confidence 346788899999999999998764
No 33
>PF14552 Tautomerase_2: Tautomerase enzyme; PDB: 2AAG_C 2AAL_A 2AAJ_A 1MWW_C.
Probab=39.08 E-value=33 Score=23.31 Aligned_cols=42 Identities=31% Similarity=0.362 Sum_probs=24.3
Q ss_pred cCCeEEEEEeCC-CCcChhHHH----HHHHHHhhhCCcCccEEEeec
Q 033057 59 SDEAVGVQIDAP-AKDGEANAA----LLEYMSSVLGVKRRQVSIGSG 100 (128)
Q Consensus 59 ~~~~l~v~V~ap-P~~GkAN~e----Li~~LAk~l~Vpks~I~Iv~G 100 (128)
+++.+.|.|+.- +..-++=++ |.+.|+..+||++.+|.|+=-
T Consensus 26 s~~~v~I~It~~~gRs~e~K~~ly~~l~~~L~~~~gi~p~Dv~I~l~ 72 (82)
T PF14552_consen 26 SDDFVIIQITSGAGRSTEQKKALYRALAERLAEKLGIRPEDVMIVLV 72 (82)
T ss_dssp -TT-EEEEEEECS---HHHHHHHHHHHHHHHHHHH---GGGEEEEEE
T ss_pred CCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHcCCCHHHEEEEEE
Confidence 467788888887 444444444 556667778999999988643
No 34
>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=38.55 E-value=48 Score=29.28 Aligned_cols=42 Identities=14% Similarity=0.079 Sum_probs=31.8
Q ss_pred ccccccc-CCeEEEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEee
Q 033057 53 CSITDVS-DEAVGVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIGS 99 (128)
Q Consensus 53 ~~I~~~~-~~~l~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~ 99 (128)
.++..+. ++.|.|....+-. ..+...||+.||+|.++|+|+.
T Consensus 52 ~~~A~~~~~g~l~v~~~tQ~p-----~~~r~~va~~lglp~~~V~V~~ 94 (547)
T PF02738_consen 52 GAVAWWDEDGRLTVWSSTQWP-----FHVRRAVAEALGLPPEKVRVIS 94 (547)
T ss_dssp EEEEEEETTTEEEEEES-SSH-----HHHHHHHHHHHTS-GGGEEEEE
T ss_pred eEEEEEccCCCEEEEECCcCH-----hHHHHHHhhhhcCChhHEEEee
Confidence 3455556 7999999887654 4567889999999999999986
No 35
>PLN02906 xanthine dehydrogenase
Probab=36.52 E-value=60 Score=32.44 Aligned_cols=47 Identities=15% Similarity=0.111 Sum_probs=41.5
Q ss_pred cCCeEEEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEeecCCCCc
Q 033057 59 SDEAVGVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIGSGSKSRD 105 (128)
Q Consensus 59 ~~~~l~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~~SR~ 105 (128)
.++.+.|.+-.....-=.+..+....|+.||||..+|+|+.|-|.+.
T Consensus 1021 ~DGsV~V~~G~~e~GQG~~T~~aQiaAe~LGip~d~V~v~~~DT~~~ 1067 (1319)
T PLN02906 1021 TDGTVLVTHGGVEMGQGLHTKVAQVAASAFNIPLSSVFISETSTDKV 1067 (1319)
T ss_pred CCceEEEEECCccCCCChHHHHHHHHHHHHCCCHHHEEEEccCCCCC
Confidence 46889999888888777899999999999999999999999988653
No 36
>PF15656 Tox-HDC: Toxin with a H, D/N and C signature
Probab=36.35 E-value=47 Score=24.56 Aligned_cols=33 Identities=21% Similarity=0.157 Sum_probs=27.8
Q ss_pred CcChhHHHHHHHHHhhhCCcCccEEEeecCCCC
Q 033057 72 KDGEANAALLEYMSSVLGVKRRQVSIGSGSKSR 104 (128)
Q Consensus 72 ~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~~SR 104 (128)
..|--.++-+++||+-+..+.+.|.|++|.+..
T Consensus 9 ~~~~~i~~pl~~Iar~~s~~~~~I~IlSGtHG~ 41 (119)
T PF15656_consen 9 INGYDINAPLETIARRPSGDNGDIHILSGTHGY 41 (119)
T ss_pred ecchhhHHHHHHHHhCcCCCCCCEEEEeCCCCC
Confidence 344447788999999999999999999998754
No 37
>TIGR02969 mam_aldehyde_ox aldehyde oxidase. Members of this family are mammalian aldehyde oxidase (EC 1.2.3.1) isozymes, closely related to xanthine dehydrogenase/oxidase.
Probab=35.30 E-value=69 Score=32.07 Aligned_cols=46 Identities=15% Similarity=0.123 Sum_probs=41.7
Q ss_pred cCCeEEEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEeecCCCC
Q 033057 59 SDEAVGVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIGSGSKSR 104 (128)
Q Consensus 59 ~~~~l~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~~SR 104 (128)
.++.+.|.+-.....-=.+..+....|+.||||..+|+|+.|-|..
T Consensus 1026 ~DGsV~V~~G~~e~GQG~~T~~aQiaAe~LGip~e~V~v~~~DT~~ 1071 (1330)
T TIGR02969 1026 LDGSVLVTHGGIEMGQGVHTKMIQVVSRELKMPMSNVHLRGTSTET 1071 (1330)
T ss_pred CCceEEEEECCcCcCCChHHHHHHHHHHHhCCCHHHEEEEcCCCCC
Confidence 3788999999988887889999999999999999999999998865
No 38
>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=33.08 E-value=15 Score=25.66 Aligned_cols=19 Identities=26% Similarity=0.415 Sum_probs=13.1
Q ss_pred HHHHHHHHHhhhCCcCccE
Q 033057 77 NAALLEYMSSVLGVKRRQV 95 (128)
Q Consensus 77 N~eLi~~LAk~l~Vpks~I 95 (128)
|.+-++-.|+.|||++|-|
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 5667889999999999875
No 39
>PRK09970 xanthine dehydrogenase subunit XdhA; Provisional
Probab=29.86 E-value=1.1e+02 Score=28.46 Aligned_cols=45 Identities=18% Similarity=0.240 Sum_probs=39.1
Q ss_pred cCCeEEEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEeec-CCC
Q 033057 59 SDEAVGVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIGSG-SKS 103 (128)
Q Consensus 59 ~~~~l~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G-~~S 103 (128)
.++.+.|.+......-=....+.+..|+.||+|.++|+++.+ -|.
T Consensus 469 ~dGsv~v~~g~~e~GQG~~T~~aQiaAe~LGi~~~~V~v~~~~dT~ 514 (759)
T PRK09970 469 QDGTVQVQSGATEIGQGSDTVFSQMVAETVGIPVSDVRVISTQDTD 514 (759)
T ss_pred cCceEEEEECCCCcCCCHHHHHHHHHHHHhCCCHHhEEEEccCCCC
Confidence 367888888888888888999999999999999999999987 443
No 40
>COG0384 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]
Probab=29.85 E-value=1e+02 Score=25.78 Aligned_cols=47 Identities=21% Similarity=0.356 Sum_probs=38.7
Q ss_pred EEEeCCCCcChhHHHHHHHHHhhhCCc-CccEEEeecCC-CCceEEEEc
Q 033057 65 VQIDAPAKDGEANAALLEYMSSVLGVK-RRQVSIGSGSK-SRDKIVIVE 111 (128)
Q Consensus 65 v~V~apP~~GkAN~eLi~~LAk~l~Vp-ks~I~Iv~G~~-SR~K~v~I~ 111 (128)
+-|.+-|+-|-||..|-.||.+....+ ..++.|..|.. .|.=.|+++
T Consensus 217 ~Gi~EDPaTGSA~~~La~yl~~~~~~~~~~~~~~~QG~~~gR~s~i~~~ 265 (291)
T COG0384 217 IGVVEDPATGSAAGALAAYLAKHGGLPDKLRLLIEQGTELGRPSRIEVR 265 (291)
T ss_pred cCCCCCCCcchhhhHHHHHHHHhCCCCCcccEEEEeccccCCCcEEEEE
Confidence 447788999999999999999999999 59999999776 555555544
No 41
>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=29.38 E-value=75 Score=20.67 Aligned_cols=31 Identities=10% Similarity=-0.030 Sum_probs=21.0
Q ss_pred CcChhHHHHHHHHHhhhCCcCccEEEeecCC
Q 033057 72 KDGEANAALLEYMSSVLGVKRRQVSIGSGSK 102 (128)
Q Consensus 72 ~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~~ 102 (128)
.+--.|+.+.-.||+.+|++....+++.-..
T Consensus 40 ~~~~~nE~~~~~lA~~~Gi~v~~~~l~~~~~ 70 (81)
T PF07805_consen 40 PDLVENEYACMRLARAAGIPVPETRLIRFGD 70 (81)
T ss_dssp TTHHHHHHHHHHHHHHTT-----EEEEEETT
T ss_pred cchHHHHHHHHHHHHHcCCCcCceEEEEECC
Confidence 3447899999999999999999999865444
No 42
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=29.11 E-value=62 Score=19.15 Aligned_cols=25 Identities=16% Similarity=0.146 Sum_probs=21.7
Q ss_pred HHHHHHHHHhhhCCcCccEEEeecC
Q 033057 77 NAALLEYMSSVLGVKRRQVSIGSGS 101 (128)
Q Consensus 77 N~eLi~~LAk~l~Vpks~I~Iv~G~ 101 (128)
=.+|-..|+..+|+|..++.|+.+.
T Consensus 22 v~~lk~~i~~~~~~~~~~~~L~~~g 46 (64)
T smart00213 22 VSELKEKIAELTGIPVEQQRLIYKG 46 (64)
T ss_pred HHHHHHHHHHHHCCCHHHEEEEECC
Confidence 3678889999999999999998774
No 43
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=27.39 E-value=30 Score=21.59 Aligned_cols=18 Identities=22% Similarity=0.486 Sum_probs=16.2
Q ss_pred HHHHHHHHhhhCCcCccE
Q 033057 78 AALLEYMSSVLGVKRRQV 95 (128)
Q Consensus 78 ~eLi~~LAk~l~Vpks~I 95 (128)
+++++..|+.|||+..+|
T Consensus 3 ~~I~~~Va~~~~i~~~~i 20 (60)
T smart00760 3 EEIIEAVAEYFGVKPEDL 20 (60)
T ss_pred HHHHHHHHHHhCCCHHHH
Confidence 578999999999999885
No 44
>PRK01271 4-oxalocrotonate tautomerase; Provisional
Probab=26.72 E-value=82 Score=21.18 Aligned_cols=21 Identities=24% Similarity=0.316 Sum_probs=18.2
Q ss_pred HHHHHHHHhhhCCcCccEEEe
Q 033057 78 AALLEYMSSVLGVKRRQVSIG 98 (128)
Q Consensus 78 ~eLi~~LAk~l~Vpks~I~Iv 98 (128)
+++-+.+++.||.+...|.|+
T Consensus 23 ~~iT~a~~~~lg~~~e~v~V~ 43 (76)
T PRK01271 23 ADITDVIIRHLNSKDSSISIA 43 (76)
T ss_pred HHHHHHHHHHhCcCcceEEEE
Confidence 578889999999999998764
No 45
>cd01769 UBL Ubiquitin-like domain of UBL. UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.
Probab=25.80 E-value=90 Score=18.66 Aligned_cols=25 Identities=20% Similarity=0.101 Sum_probs=21.2
Q ss_pred HHHHHHHHHhhhCCcCccEEEeecC
Q 033057 77 NAALLEYMSSVLGVKRRQVSIGSGS 101 (128)
Q Consensus 77 N~eLi~~LAk~l~Vpks~I~Iv~G~ 101 (128)
=.+|-+.|++.+|++.+++.|..+.
T Consensus 20 i~~lK~~i~~~~~~~~~~~~l~~~g 44 (69)
T cd01769 20 VAELKAKIAAKEGVPPEQQRLIYAG 44 (69)
T ss_pred HHHHHHHHHHHHCcChHHEEEEECC
Confidence 4567788999999999999997765
No 46
>PF02542 YgbB: YgbB family; InterPro: IPR003526 MECDP (2-C-methyl-D-erythritol 2,4-cyclodiphosphate) synthetase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis, isoprenoids being essential in all organisms. Isoprenoids can also be synthesized through the mevalonate pathway. The non-mevolante route is used by many bacteria and human pathogens, including Mycobacterium tuberculosis and Plasmodium falciparum. This route appears to involve seven enzymes. MECDP synthetase catalyses the intramolecular attack by a phosphate group on a diphosphate, with cytidine monophosphate (CMP) acting as the leaving group to give the cyclic diphosphate product MEDCP. The enzyme is a trimer with three active sites shared between adjacent copies of the protein. The enzyme also has two metal binding sites, the metals playing key roles in catalysis[]. A number of proteins from eukaryotes and prokaryotes share this common N-terminal signature and appear to be involved in terpenoid biosynthesis. The YgbB protein is a putative enzyme of this type [].; GO: 0008685 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity, 0016114 terpenoid biosynthetic process; PDB: 3T80_B 3GHZ_A 2PMP_A 3F6M_A 3FPI_A 3RE3_A 1T0A_C 1W57_A 1W55_A 3B6N_A ....
Probab=25.49 E-value=1.1e+02 Score=23.55 Aligned_cols=36 Identities=22% Similarity=0.316 Sum_probs=28.3
Q ss_pred EeCCCCcChhHHHHHHHHHhhhCCcCccEEEeecCC
Q 033057 67 IDAPAKDGEANAALLEYMSSVLGVKRRQVSIGSGSK 102 (128)
Q Consensus 67 V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~~ 102 (128)
+.+.|.=+.-=.++.+.||+.|+++.++|.|..=.+
T Consensus 99 i~e~PKi~p~~~~m~~~la~~L~~~~~~V~iKatT~ 134 (157)
T PF02542_consen 99 IAERPKISPYRPAMRENLAKLLGIPPDRVNIKATTT 134 (157)
T ss_dssp ESSSSTTGGGHHHHHHHHHHHHTS-GGGEEEEEE-T
T ss_pred EcCCCccHHHHHHHHHHHHHHhCCCcceEEEEEecC
Confidence 456677777788999999999999999999875443
No 47
>PF15609 PRTase_2: Phosphoribosyl transferase
Probab=25.17 E-value=76 Score=25.24 Aligned_cols=37 Identities=27% Similarity=0.258 Sum_probs=29.0
Q ss_pred EEEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEeecC
Q 033057 63 VGVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIGSGS 101 (128)
Q Consensus 63 l~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~ 101 (128)
+.+.+.- -.+.+|.+-.+-+++.||+|-+-|++++|.
T Consensus 154 vvasL~d--~~~~~~~~~~~~~~~~lgi~i~~vsL~~G~ 190 (191)
T PF15609_consen 154 VVASLLD--WRSEEDRARFEALAEELGIPIDVVSLLSGE 190 (191)
T ss_pred EEEEEee--CCCHHHHHHHHHHHHHcCCcEEEEEeeccc
Confidence 3344443 234788888999999999999999999985
No 48
>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....
Probab=24.74 E-value=1.1e+02 Score=18.78 Aligned_cols=24 Identities=17% Similarity=0.155 Sum_probs=21.3
Q ss_pred HHHHHHHHhhhCCcCccEEEeecC
Q 033057 78 AALLEYMSSVLGVKRRQVSIGSGS 101 (128)
Q Consensus 78 ~eLi~~LAk~l~Vpks~I~Iv~G~ 101 (128)
.+|-+.|+..+++|..++.|+.+.
T Consensus 19 ~~lK~~i~~~~~~~~~~~~L~~~G 42 (69)
T PF00240_consen 19 ADLKQKIAEETGIPPEQQRLIYNG 42 (69)
T ss_dssp HHHHHHHHHHHTSTGGGEEEEETT
T ss_pred HHhhhhcccccccccccceeeeee
Confidence 578889999999999999998864
No 49
>PF02567 PhzC-PhzF: Phenazine biosynthesis-like protein; InterPro: IPR003719 Five genes, phzF, phzA, phzB, phzC and phzD, encode enzymes for phenazine biosynthesis in the biological control bacterium Pseudomonas chlororaphis (also known as Pseudomonas aureofaciens). Protein PhzF is similar to 3-deoxy-D-arabino-heptulosonate-7-phosphate synthases of solanaceous plants. PhzC is responsible for the conversion of phenazine-I-carboxylic acid to 2-hydroxy-phenazine-I-carboxylic acid [].; GO: 0003824 catalytic activity, 0009058 biosynthetic process; PDB: 1U0K_A 1QYA_B 1QY9_D 1SDJ_A 1U1X_A 1U1W_B 1T6K_A 1XUA_A 1XUB_A 1U1V_A ....
Probab=24.25 E-value=86 Score=24.72 Aligned_cols=42 Identities=21% Similarity=0.254 Sum_probs=33.7
Q ss_pred EeCCCCcChhHHHHHHHHHhhhCC-cCccEEEeecCCCCceEE
Q 033057 67 IDAPAKDGEANAALLEYMSSVLGV-KRRQVSIGSGSKSRDKIV 108 (128)
Q Consensus 67 V~apP~~GkAN~eLi~~LAk~l~V-pks~I~Iv~G~~SR~K~v 108 (128)
|.+-|.-|-||-.|..||++..++ ....+.|..|+.+.+.-.
T Consensus 210 i~EDpaTGSA~~~La~yl~~~~~~~~~~~~~i~QG~~~gR~g~ 252 (281)
T PF02567_consen 210 IPEDPATGSAAGALAAYLAEKGGKPGSHRFTIEQGQEMGRPGR 252 (281)
T ss_dssp EEEESS-HHHHHHHHHHHHHHTTSSSCEEEEEEEEGGGTS-EE
T ss_pred CCCCCCchhhHHHHHHHHHHhCCCCCCceEEEEcccEeCCCEE
Confidence 567788999999999999999998 677889999987665543
No 50
>KOG4079 consensus Putative mitochondrial ribosomal protein mRpS25 [Translation, ribosomal structure and biogenesis]
Probab=23.76 E-value=59 Score=25.15 Aligned_cols=19 Identities=21% Similarity=0.335 Sum_probs=17.2
Q ss_pred CcChhHHHHHHHHHhhhCC
Q 033057 72 KDGEANAALLEYMSSVLGV 90 (128)
Q Consensus 72 ~~GkAN~eLi~~LAk~l~V 90 (128)
.||+-|+++++.|++.||-
T Consensus 91 ld~~~r~eI~~hl~K~lGK 109 (169)
T KOG4079|consen 91 LDGMKREEIEKHLAKTLGK 109 (169)
T ss_pred cccccHHHHHHHHHHHhCc
Confidence 4899999999999999993
No 51
>COG3579 PepC Aminopeptidase C [Amino acid transport and metabolism]
Probab=23.71 E-value=99 Score=27.36 Aligned_cols=46 Identities=13% Similarity=0.268 Sum_probs=34.8
Q ss_pred HHHHHHHHHhhhCCcCccEEEeecCCCCceEEEEccCCHHHHHHHHh
Q 033057 77 NAALLEYMSSVLGVKRRQVSIGSGSKSRDKIVIVEEITPENVLNSLG 123 (128)
Q Consensus 77 N~eLi~~LAk~l~Vpks~I~Iv~G~~SR~K~v~I~g~~~e~l~~~L~ 123 (128)
=.|+..||+..||+|+.+.+..+--+.. |.=.+.+++|.+++.++-
T Consensus 207 l~eif~~l~~~lg~PP~~Fdf~YrdKd~-~~h~~k~lTP~eFy~kyv 252 (444)
T COG3579 207 LQEIFNFLAMTLGLPPEKFDFAYRDKDN-KYHKEKGLTPQEFYKKYV 252 (444)
T ss_pred HHHHHHHHHHHcCCCchhcceEEecccc-chhhhcCCCHHHHHHHhc
Confidence 4678899999999999999988744331 222456899999887653
No 52
>COG1942 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]
Probab=23.10 E-value=1.1e+02 Score=20.24 Aligned_cols=36 Identities=17% Similarity=0.228 Sum_probs=23.8
Q ss_pred EEEEEeCC-CCcC-hhH--HHHHHHHHhhhCCcCccEEEe
Q 033057 63 VGVQIDAP-AKDG-EAN--AALLEYMSSVLGVKRRQVSIG 98 (128)
Q Consensus 63 l~v~V~ap-P~~G-kAN--~eLi~~LAk~l~Vpks~I~Iv 98 (128)
+.|++... +.+. |+. ++|-+.+++.||-+++.|.++
T Consensus 4 v~Ik~~~g~~~~~~K~~la~~vT~~~~~~lg~~~~~i~Vi 43 (69)
T COG1942 4 VNIKLFEGRLDEEQKAELAAEVTEVTVETLGKDPSAIHVI 43 (69)
T ss_pred EEEEecCCCCCHHHHHHHHHHHHHHHHHHhCCCcccEEEE
Confidence 45666642 2322 332 456788999999999998765
No 53
>COG0245 IspF 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase [Lipid metabolism]
Probab=23.08 E-value=81 Score=24.51 Aligned_cols=33 Identities=15% Similarity=0.301 Sum_probs=25.9
Q ss_pred CCCCcChhHHHHHHHHHhhhCCcCccEEEeecC
Q 033057 69 APAKDGEANAALLEYMSSVLGVKRRQVSIGSGS 101 (128)
Q Consensus 69 apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~ 101 (128)
+.|-=+=-=+++.++||+.|+++.++|.|..=.
T Consensus 101 ~~PK~~P~~~amr~~ia~~L~i~~~~invKatT 133 (159)
T COG0245 101 QRPKLGPYREAMRANIAELLGIPVDRINVKATT 133 (159)
T ss_pred ecCcccchHHHHHHHHHHHhCCCchheEEEEec
Confidence 445545556789999999999999999987533
No 54
>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=22.87 E-value=34 Score=25.25 Aligned_cols=51 Identities=18% Similarity=0.186 Sum_probs=29.8
Q ss_pred hHHHHHHHHHhhhCCcCccEEEeec------CCCCc-eEEEE-cc-----CCHHHHHHHHhhhh
Q 033057 76 ANAALLEYMSSVLGVKRRQVSIGSG------SKSRD-KIVIV-EE-----ITPENVLNSLGKAS 126 (128)
Q Consensus 76 AN~eLi~~LAk~l~Vpks~I~Iv~G------~~SR~-K~v~I-~g-----~~~e~l~~~L~~~~ 126 (128)
=.++.++++|+.|+||.++|.=+-. .+-+- ..|.| .| ...+++++.|++.+
T Consensus 29 i~~~~~~~iA~~l~i~~~~v~~v~tFY~~f~~~p~gk~~I~VC~g~~C~~~Ga~~l~~~l~~~l 92 (145)
T PF01257_consen 29 IPEEALEEIAEALGIPPAEVYGVATFYSMFRLEPKGKHHIRVCTGTSCHLRGAEELLEALEEEL 92 (145)
T ss_dssp --HHHHHHHHHHHTS-HHHHHHHHHHSSSS-SSS--SEEEEEE-SHHHHTTTHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHCCCHHHHHHHHHHHHHcccCCCCCcEEEeCCCchHHhCCCHHHHHHHHHHh
Confidence 3568899999999999888643321 11121 24444 43 24678888887765
No 55
>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain. DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.
Probab=22.21 E-value=91 Score=19.92 Aligned_cols=26 Identities=8% Similarity=0.036 Sum_probs=22.4
Q ss_pred HHHHHHHHHhhhCCcCccEEEeecCC
Q 033057 77 NAALLEYMSSVLGVKRRQVSIGSGSK 102 (128)
Q Consensus 77 N~eLi~~LAk~l~Vpks~I~Iv~G~~ 102 (128)
=.+|-.+++...|+|..+..|+.+-+
T Consensus 22 V~~lK~~I~~~~gip~~~q~Li~~Gk 47 (71)
T cd01796 22 LENFKALCEAESGIPASQQQLIYNGR 47 (71)
T ss_pred HHHHHHHHHHHhCCCHHHeEEEECCe
Confidence 35788999999999999999998754
No 56
>PRK05457 heat shock protein HtpX; Provisional
Probab=22.00 E-value=4.5e+02 Score=21.54 Aligned_cols=48 Identities=17% Similarity=0.256 Sum_probs=36.3
Q ss_pred HHHHHHHhhhCCcCccEEEee---------cCCCCceEEEEcc-----CCHHHHHHHHhhhh
Q 033057 79 ALLEYMSSVLGVKRRQVSIGS---------GSKSRDKIVIVEE-----ITPENVLNSLGKAS 126 (128)
Q Consensus 79 eLi~~LAk~l~Vpks~I~Iv~---------G~~SR~K~v~I~g-----~~~e~l~~~L~~~~ 126 (128)
+.++-||+..|+|..+|-++- |...++..|.+.. ++.||+...|..++
T Consensus 81 ~~v~~la~~~g~p~p~v~v~~~~~~NAfa~G~~~~~~~V~vt~gLl~~L~~~El~aVlAHEl 142 (284)
T PRK05457 81 ETVARQARQAGIGMPEVAIYHSPEINAFATGASKNNSLVAVSTGLLQNMSRDEVEAVLAHEI 142 (284)
T ss_pred HHHHHHHHhCCCCCCCEEEEeCCCceEEEecCCCCCeEEEeehHHhhhCCHHHHHHHHHHHH
Confidence 678999999999999998884 4444556676643 68999888776543
No 57
>PHA02564 V virion protein; Provisional
Probab=21.82 E-value=1e+02 Score=23.30 Aligned_cols=30 Identities=17% Similarity=0.277 Sum_probs=23.7
Q ss_pred EEEeCCCCcChhHHHHHHHHHhhhCCcCccE
Q 033057 65 VQIDAPAKDGEANAALLEYMSSVLGVKRRQV 95 (128)
Q Consensus 65 v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I 95 (128)
|.-=|||.|+. -.+-+.++|+.+||++.+.
T Consensus 73 I~rwAP~~ENn-T~aYi~~Vs~~~GV~~~~~ 102 (141)
T PHA02564 73 IARWAPSNEND-TRAYATAVANAMGVPPQAG 102 (141)
T ss_pred HHhcCCCCCCC-HHHHHHHHHHHHCCCCCCc
Confidence 44568888753 6789999999999998764
No 58
>TIGR03853 matur_matur probable metal-binding protein. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulfatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulfur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulfatase/maturase systems.
Probab=20.30 E-value=2.1e+02 Score=19.62 Aligned_cols=37 Identities=22% Similarity=0.267 Sum_probs=30.2
Q ss_pred HHHHHHHHHhhhCCcCccEEEeecCCCCceEEEEccCCHHHHHHHHhh
Q 033057 77 NAALLEYMSSVLGVKRRQVSIGSGSKSRDKIVIVEEITPENVLNSLGK 124 (128)
Q Consensus 77 N~eLi~~LAk~l~Vpks~I~Iv~G~~SR~K~v~I~g~~~e~l~~~L~~ 124 (128)
.++|...+...|| ...|.-+=...|+|.++|++.|.+
T Consensus 20 ~~~L~~~i~~~FG-----------~~arFhTCSa~~m~a~~Li~FL~~ 56 (77)
T TIGR03853 20 RESLKAAIEQKFG-----------EDARFHTCSAEGMTADELLQFLLK 56 (77)
T ss_pred HHHHHHHHHHHhC-----------CCceEeecccccCCHHHHHHHHHH
Confidence 5678888888887 677888888889999999988764
No 59
>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=20.12 E-value=83 Score=25.29 Aligned_cols=42 Identities=21% Similarity=0.394 Sum_probs=32.7
Q ss_pred CCeEEEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEeecCCCCc
Q 033057 60 DEAVGVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIGSGSKSRD 105 (128)
Q Consensus 60 ~~~l~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~~SR~ 105 (128)
++.+.+.|. -.|.-..+++..||+.|||+.++|.. .|.+.|+
T Consensus 30 G~~~~~~l~---K~~~~T~~a~~~la~~l~i~~~~i~y-AG~KDk~ 71 (232)
T cd02552 30 GEYLHFTLY---KENKDTMEALREIAKALGVPPRDIGY-AGTKDKR 71 (232)
T ss_pred CCEEEEEEE---ECCCCHHHHHHHHHHHcCCCHHHEeE-cccccCc
Confidence 456666665 36778899999999999999998864 5666665
No 60
>cd00196 UBQ Ubiquitin-like proteins. Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate.
Probab=20.11 E-value=1.2e+02 Score=16.15 Aligned_cols=27 Identities=26% Similarity=0.218 Sum_probs=22.0
Q ss_pred HHHHHHHHHhhhCCcCccEEEeecCCC
Q 033057 77 NAALLEYMSSVLGVKRRQVSIGSGSKS 103 (128)
Q Consensus 77 N~eLi~~LAk~l~Vpks~I~Iv~G~~S 103 (128)
=.+|+..++..++++.....|......
T Consensus 20 v~~l~~~i~~~~~~~~~~~~l~~~~~~ 46 (69)
T cd00196 20 VADLKEKLAKKLGLPPEQQRLLVNGKI 46 (69)
T ss_pred HHHHHHHHHHHHCcChHHeEEEECCeE
Confidence 467899999999999998888776543
No 61
>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis. PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain
Probab=20.06 E-value=1.8e+02 Score=20.01 Aligned_cols=53 Identities=25% Similarity=0.311 Sum_probs=37.6
Q ss_pred EEEEeCCCCcChhHHHHHHHHHhhhCCcCccEEEeecCCCCceEEEEccCCHHHH
Q 033057 64 GVQIDAPAKDGEANAALLEYMSSVLGVKRRQVSIGSGSKSRDKIVIVEEITPENV 118 (128)
Q Consensus 64 ~v~V~apP~~GkAN~eLi~~LAk~l~Vpks~I~Iv~G~~SR~K~v~I~g~~~e~l 118 (128)
.|.|+.|+. -.=.+|.+.|++-|++|...+.+-+-...-.+.+-+.+-+-|++
T Consensus 12 tIaIrvp~~--~~y~~L~~ki~~kLkl~~e~i~LsYkde~s~~~v~l~d~dle~a 64 (80)
T cd06406 12 TVAIQVARG--LSYATLLQKISSKLELPAEHITLSYKSEASGEDVILSDTNMEDV 64 (80)
T ss_pred EEEEEcCCC--CCHHHHHHHHHHHhCCCchhcEEEeccCCCCCccCcChHHHHHH
Confidence 355555543 55678999999999999999999887777766666644333333
Done!