Query 038196
Match_columns 122
No_of_seqs 104 out of 264
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 08:33:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038196.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038196hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04525 Tub_2: Tubby C 2; In 99.9 1.5E-24 3.3E-29 163.1 8.8 99 2-103 82-187 (187)
2 COG4894 Uncharacterized conser 99.0 1.7E-09 3.6E-14 80.1 7.1 61 43-109 98-158 (159)
3 PF03803 Scramblase: Scramblas 97.7 0.00064 1.4E-08 51.9 10.9 70 41-110 140-220 (221)
4 PF04525 Tub_2: Tubby C 2; In 90.5 1.4 3E-05 32.9 6.8 59 8-71 10-71 (187)
5 PF03803 Scramblase: Scramblas 75.3 20 0.00043 27.0 7.4 21 51-71 128-148 (221)
6 PF00384 Molybdopterin: Molybd 64.1 8.2 0.00018 31.4 3.3 31 80-110 156-187 (432)
7 cd02769 MopB_DMSOR-BSOR-TMAOR 55.8 7.5 0.00016 34.1 1.8 25 82-106 226-251 (609)
8 KOG0643 Translation initiation 48.6 99 0.0022 25.7 7.0 38 41-79 63-101 (327)
9 COG5148 RPN10 26S proteasome r 48.5 10 0.00022 29.9 1.3 59 49-107 161-221 (243)
10 PF03017 Transposase_23: TNP1/ 47.8 62 0.0013 21.1 4.8 38 52-89 4-48 (73)
11 TIGR02164 torA trimethylamine- 46.7 13 0.00029 33.8 2.0 22 85-106 272-294 (822)
12 KOG1693 emp24/gp25L/p24 family 46.7 50 0.0011 25.9 4.9 44 43-86 50-96 (209)
13 TIGR00509 bisC_fam molybdopter 45.2 15 0.00032 33.2 2.0 25 82-106 222-247 (770)
14 KOG0621 Phospholipid scramblas 45.0 64 0.0014 26.5 5.5 73 41-113 198-283 (292)
15 cd02750 MopB_Nitrate-R-NarG-li 43.3 18 0.00039 30.5 2.1 23 84-106 218-241 (461)
16 TIGR03479 DMSO_red_II_alp DMSO 42.4 13 0.00028 34.5 1.2 24 84-107 272-296 (912)
17 PF04881 Adeno_GP19K: Adenovir 40.1 87 0.0019 23.0 5.0 51 32-93 2-58 (139)
18 PRK14991 tetrathionate reducta 39.6 16 0.00035 34.5 1.5 27 80-106 337-364 (1031)
19 TIGR01580 narG respiratory nit 38.1 18 0.0004 35.1 1.5 28 83-110 292-320 (1235)
20 PF13585 CHU_C: C-terminal dom 36.1 1.2E+02 0.0027 19.7 5.2 58 32-89 5-72 (87)
21 PRK14990 anaerobic dimethyl su 34.9 24 0.00052 32.0 1.8 23 84-106 284-307 (814)
22 PF13541 ChlI: Subunit ChlI of 34.0 63 0.0014 22.9 3.4 36 75-110 36-79 (121)
23 cd02756 MopB_Arsenite-Ox Arsen 33.2 35 0.00077 30.9 2.5 23 82-104 295-317 (676)
24 PF06891 P2_Phage_GpR: P2 phag 32.1 1.5E+02 0.0031 21.2 5.1 46 61-108 31-80 (135)
25 cd02760 MopB_Phenylacetyl-CoA- 31.9 30 0.00064 31.7 1.8 24 83-106 221-245 (760)
26 cd02770 MopB_DmsA-EC This CD ( 31.2 32 0.0007 30.2 1.9 22 83-104 217-238 (617)
27 COG0146 HyuB N-methylhydantoin 29.7 37 0.0008 30.4 2.0 19 52-70 39-57 (563)
28 cd02765 MopB_4 The MopB_4 CD i 28.8 41 0.0009 29.3 2.1 22 83-104 206-227 (567)
29 cd02762 MopB_1 The MopB_1 CD i 27.7 41 0.0009 28.9 1.9 22 83-104 209-230 (539)
30 TIGR02693 arsenite_ox_L arseni 27.5 46 0.001 30.6 2.3 21 83-103 291-311 (806)
31 PF01167 Tub: Tub family; Int 26.8 1.1E+02 0.0024 24.1 4.1 49 8-60 34-87 (246)
32 cd02754 MopB_Nitrate-R-NapA-li 26.1 51 0.0011 28.4 2.2 22 83-104 206-227 (565)
33 cd02758 MopB_Tetrathionate-Ra 24.6 81 0.0018 28.8 3.3 26 80-105 262-288 (735)
34 COG4385 gpI Bacteriophage P2-r 24.2 1.8E+02 0.0039 22.8 4.7 40 82-121 113-157 (206)
35 cd02766 MopB_3 The MopB_3 CD i 23.8 51 0.0011 28.2 1.8 21 84-104 205-225 (501)
36 PRK15102 trimethylamine N-oxid 23.3 55 0.0012 29.9 2.0 19 85-103 275-293 (825)
37 cd03444 Thioesterase_II_repeat 22.5 98 0.0021 20.7 2.7 20 52-71 82-101 (104)
38 TIGR02166 dmsA_ynfE anaerobic 22.1 63 0.0014 29.2 2.1 21 83-103 266-286 (797)
39 cd02759 MopB_Acetylene-hydrata 22.1 61 0.0013 27.4 1.9 22 83-104 208-229 (477)
40 TIGR01706 NAPA periplasmic nit 22.0 61 0.0013 29.7 2.0 21 84-104 256-276 (830)
41 cd02751 MopB_DMSOR-like The Mo 20.9 70 0.0015 28.0 2.1 21 83-103 225-245 (609)
42 PRK13532 nitrate reductase cat 20.9 74 0.0016 29.1 2.3 23 84-106 256-279 (830)
43 PF12863 DUF3821: Domain of un 20.7 88 0.0019 24.4 2.4 20 2-21 65-84 (209)
44 PF13860 FlgD_ig: FlgD Ig-like 20.3 2.4E+02 0.0053 17.9 5.0 18 54-71 28-45 (81)
45 COG0243 BisC Anaerobic dehydro 20.3 60 0.0013 29.3 1.6 20 85-104 251-270 (765)
46 TIGR03876 cas_csaX CRISPR-asso 20.0 2.1E+02 0.0046 23.0 4.4 44 78-121 142-198 (281)
No 1
>PF04525 Tub_2: Tubby C 2; InterPro: IPR007612 This is a family of plant and bacterial uncharacterised proteins.; PDB: 1ZXU_A 2Q4M_A.
Probab=99.91 E-value=1.5e-24 Score=163.12 Aligned_cols=99 Identities=29% Similarity=0.490 Sum_probs=59.1
Q ss_pred CcCCcCCCCeeEEEEEcCCCcccccccceEEEEEcCC-------CCcceEEEEeecCCceeEEEcCCCCeEEEEeeeccc
Q 038196 2 YAFDYERSKKLVFTLKEPPNSSCLVRNSSIRISTETT-------ARSNNFEVKGYFPDKYCIIVDPSGNIVAQIGVKKEI 74 (122)
Q Consensus 2 y~~d~~~~~~~lFtvkrs~~~~i~~~k~~~~V~~~~~-------~~~~~~~i~G~~~~rsc~I~~~~g~vVAev~rK~~~ 74 (122)
|++++.+.++|+|++|+++ .++.+++..+|+... +..++|+|+|+|.+++|+|++..|++||||+||+..
T Consensus 82 ~~~~~~~~~~~i~tvkk~~---~~~~~~~~~~f~~~~~~~~~~~~~~~~~~i~G~~~~~~~~I~~~~g~~VA~i~rk~~~ 158 (187)
T PF04525_consen 82 YRGGGSEGKKPIFTVKKKS---MLQNKDSFDVFLPPKSNISIDDSEGPDFEIKGNFWDRSFTIYDSGGRVVAEISRKYSS 158 (187)
T ss_dssp EETT---GGGEEEEEE-------------EEEEET--T----------SEEEES-TTTT--EEEECC--EEEEEEE----
T ss_pred EECCCCccCceEEEEEEec---ccCCCcceeEEEecccceeecCCCCceEEEEEEecCcEEEEEEcCCCEEEEEecccce
Confidence 5666666789999999886 588899999999743 367899999999999999998779999999999888
Q ss_pred ceeeeeeeeEEEEEeCCCcHHHHHHHHHh
Q 038196 75 EDLMESKDLYHIVVKPGIDQAFIAVVIAT 103 (122)
Q Consensus 75 ~~v~~G~dvf~v~V~PgvD~AfimaLvvi 103 (122)
++++.|+|+|+|+|+||+|+|||||||+|
T Consensus 159 k~~~~~~dty~l~V~pg~D~~lv~alvvi 187 (187)
T PF04525_consen 159 KKWFSGRDTYTLTVAPGVDQALVVALVVI 187 (187)
T ss_dssp ------B-SEEEEE-TTSBHHHHHHHHHH
T ss_pred eeEEecCcEEEEEEcCCCCHHHheeEEeC
Confidence 99999999999999999999999999986
No 2
>COG4894 Uncharacterized conserved protein [Function unknown]
Probab=98.98 E-value=1.7e-09 Score=80.07 Aligned_cols=61 Identities=28% Similarity=0.443 Sum_probs=56.1
Q ss_pred eEEEEeecCCceeEEEcCCCCeEEEEeeecccceeeeeeeeEEEEEeCCCcHHHHHHHHHhhchhcC
Q 038196 43 NFEVKGYFPDKYCIIVDPSGNIVAQIGVKKEIEDLMESKDLYHIVVKPGIDQAFIAVVIATLDYIYG 109 (122)
Q Consensus 43 ~~~i~G~~~~rsc~I~~~~g~vVAev~rK~~~~~v~~G~dvf~v~V~PgvD~AfimaLvvilD~i~~ 109 (122)
+++|.|++.+-.++..++ ++++|||++| ++.++|+|+|+|.|+-|.++|.|++|+||++..
T Consensus 98 ~~eihGNi~d~efkl~dg-~~~~aeVsKk-----wf~~rdTY~l~vapde~a~lii~i~VaLD~v~~ 158 (159)
T COG4894 98 NWEIHGNIWDDEFKLTDG-ENVRAEVSKK-----WFSWRDTYHLQVAPDEDALLIIAIAVALDMVLY 158 (159)
T ss_pred CeEEecceeceEEEEecC-Cceehhheee-----eEeccceEEEEEcCchhhHHHHHHHHHHHHHhc
Confidence 489999999999999988 5699999998 467899999999999999999999999999854
No 3
>PF03803 Scramblase: Scramblase ; InterPro: IPR005552 Scramblase is palmitoylated and contains a potential protein kinase C phosphorylation site. Scramblase exhibits Ca2+-activated phospholipid scrambling activity in vitro. There are also possible SH3 and WW binding motifs. Scramblase is involved in the redistribution of phospholipids after cell activation or injury [].
Probab=97.73 E-value=0.00064 Score=51.88 Aligned_cols=70 Identities=30% Similarity=0.368 Sum_probs=56.3
Q ss_pred cceEEEEeec------CCceeEEEcCCCCeEEEEeeeccc--ceeeeeeeeEEEEEeCCCcH---HHHHHHHHhhchhcC
Q 038196 41 SNNFEVKGYF------PDKYCIIVDPSGNIVAQIGVKKEI--EDLMESKDLYHIVVKPGIDQ---AFIAVVIATLDYIYG 109 (122)
Q Consensus 41 ~~~~~i~G~~------~~rsc~I~~~~g~vVAev~rK~~~--~~v~~G~dvf~v~V~PgvD~---AfimaLvvilD~i~~ 109 (122)
...|+|+|.. .+..+.|++.+|+.||+|+||+.. .+.+...|.|.|+..|..|. |+++|.++.+|-++-
T Consensus 140 ~~~~~I~gp~~~~~~~~~~~F~I~~~~~~~vg~I~k~w~G~~~e~~t~~d~f~i~Fp~~l~~~~Kalll~a~~liD~~~F 219 (221)
T PF03803_consen 140 NPIFTIKGPCCCCSCCCDWEFEIKDPNGQEVGSITKKWSGFCRELFTDADNFVIEFPPDLDVEQKALLLGAAFLIDYMYF 219 (221)
T ss_pred ceEEEEeCCcceeccccceeeeeecccCcEEEEEEEecCCcchhhccccceEEEEcCCCCCHHHHHHHHHHHHHhhhhhh
Confidence 4568888873 456789999778999999999543 24667899999999888765 789999999999875
Q ss_pred C
Q 038196 110 E 110 (122)
Q Consensus 110 ~ 110 (122)
|
T Consensus 220 e 220 (221)
T PF03803_consen 220 E 220 (221)
T ss_pred c
Confidence 5
No 4
>PF04525 Tub_2: Tubby C 2; InterPro: IPR007612 This is a family of plant and bacterial uncharacterised proteins.; PDB: 1ZXU_A 2Q4M_A.
Probab=90.51 E-value=1.4 Score=32.89 Aligned_cols=59 Identities=24% Similarity=0.300 Sum_probs=30.0
Q ss_pred CCCeeEEEEEcCCCcccccccceEEEEEcCCCCcceEEEEe-ec--CCceeEEEcCCCCeEEEEeee
Q 038196 8 RSKKLVFTLKEPPNSSCLVRNSSIRISTETTARSNNFEVKG-YF--PDKYCIIVDPSGNIVAQIGVK 71 (122)
Q Consensus 8 ~~~~~lFtvkrs~~~~i~~~k~~~~V~~~~~~~~~~~~i~G-~~--~~rsc~I~~~~g~vVAev~rK 71 (122)
.++.-.|+|++.++ +.......|+=.. ....|+|+| .+ ..+.-.|+|.+|+.++.|++|
T Consensus 10 ~~~~~~l~v~~k~~---~~~~~~f~V~D~~--G~~vf~V~g~~~~s~~~~~~l~D~~G~~L~~i~~k 71 (187)
T PF04525_consen 10 SPQPVTLTVKKKSL---SFSGDDFTVYDEN--GNVVFRVDGGKFFSIGKKRTLMDASGNPLFTIRRK 71 (187)
T ss_dssp -SS-EEEEEE-------------EEEEETT--S-EEEEEE--SCTTBTTEEEEE-TTS-EEEEEE--
T ss_pred CCCceEEEEEEEEe---eecCCCEEEEcCC--CCEEEEEEEecccCCCCEEEEECCCCCEEEEEEee
Confidence 34455678865442 2234457777554 367899999 43 446678888889999999887
No 5
>PF03803 Scramblase: Scramblase ; InterPro: IPR005552 Scramblase is palmitoylated and contains a potential protein kinase C phosphorylation site. Scramblase exhibits Ca2+-activated phospholipid scrambling activity in vitro. There are also possible SH3 and WW binding motifs. Scramblase is involved in the redistribution of phospholipids after cell activation or injury [].
Probab=75.30 E-value=20 Score=27.04 Aligned_cols=21 Identities=24% Similarity=0.123 Sum_probs=12.6
Q ss_pred CCceeEEEcCCCCeEEEEeee
Q 038196 51 PDKYCIIVDPSGNIVAQIGVK 71 (122)
Q Consensus 51 ~~rsc~I~~~~g~vVAev~rK 71 (122)
..+.+.|+|+.|+.++.|+..
T Consensus 128 ~~~~f~I~d~~~~~~~~I~gp 148 (221)
T PF03803_consen 128 CRPNFDIFDANGNPIFTIKGP 148 (221)
T ss_pred cceEEEEEECCCceEEEEeCC
Confidence 355666666656666666554
No 6
>PF00384 Molybdopterin: Molybdopterin oxidoreductase; InterPro: IPR006656 This domain is found in a number of molybdopterin-containing oxidoreductases, tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where a single domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a molybdopterin dinucleotide cofactor []. ; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1TI2_G 1VLE_M 1VLD_U 1VLF_O 1TI4_I 1TI6_E 3DMR_A 4DMR_A 1H5N_C 1E5V_A ....
Probab=64.10 E-value=8.2 Score=31.45 Aligned_cols=31 Identities=23% Similarity=0.264 Sum_probs=24.5
Q ss_pred eeeeEEEEEeCCCcHHHHHHHH-HhhchhcCC
Q 038196 80 SKDLYHIVVKPGIDQAFIAVVI-ATLDYIYGE 110 (122)
Q Consensus 80 G~dvf~v~V~PgvD~AfimaLv-vilD~i~~~ 110 (122)
..-...|-|.||-|.||++||+ +++++...+
T Consensus 156 ~~ad~~i~i~PGtD~al~~a~~~~ii~~~~~d 187 (432)
T PF00384_consen 156 AKADEWIPIRPGTDAALALAMAHVIIDEGLYD 187 (432)
T ss_dssp GGTSEEEEE-TTTHHHHHHHHHHHHHHTTTST
T ss_pred hhccccccccccccHHhhcccccceeeccccc
Confidence 4677899999999999999998 777766544
No 7
>cd02769 MopB_DMSOR-BSOR-TMAOR The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Members of this CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=55.76 E-value=7.5 Score=34.14 Aligned_cols=25 Identities=20% Similarity=0.365 Sum_probs=20.4
Q ss_pred eeEEEEEeCCCcHHHHHHHH-Hhhch
Q 038196 82 DLYHIVVKPGIDQAFIAVVI-ATLDY 106 (122)
Q Consensus 82 dvf~v~V~PgvD~AfimaLv-vilD~ 106 (122)
|...|-|.||-|.||++||+ +++++
T Consensus 226 dd~~l~irPGTD~ALalam~~~ii~e 251 (609)
T cd02769 226 GAEWIAIRPGTDVALMLALAHTLVTE 251 (609)
T ss_pred cCcEeccCCCcHHHHHHHHHHHHHHc
Confidence 55788999999999999999 44443
No 8
>KOG0643 consensus Translation initiation factor 3, subunit i (eIF-3i)/TGF-beta receptor-interacting protein (TRIP-1) [Translation, ribosomal structure and biogenesis; Signal transduction mechanisms]
Probab=48.57 E-value=99 Score=25.69 Aligned_cols=38 Identities=13% Similarity=0.174 Sum_probs=27.7
Q ss_pred cceEEEEeecCCceeEEEc-CCCCeEEEEeeecccceeee
Q 038196 41 SNNFEVKGYFPDKYCIIVD-PSGNIVAQIGVKKEIEDLME 79 (122)
Q Consensus 41 ~~~~~i~G~~~~rsc~I~~-~~g~vVAev~rK~~~~~v~~ 79 (122)
..++.|.|+. +.+|++-| ++|+.+|+.+-+-.++.+-+
T Consensus 63 ~s~~liTGSA-D~t~kLWDv~tGk~la~~k~~~~Vk~~~F 101 (327)
T KOG0643|consen 63 DSKHLITGSA-DQTAKLWDVETGKQLATWKTNSPVKRVDF 101 (327)
T ss_pred Ccceeeeccc-cceeEEEEcCCCcEEEEeecCCeeEEEee
Confidence 4456778864 67889988 78999999987755554433
No 9
>COG5148 RPN10 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=48.52 E-value=10 Score=29.85 Aligned_cols=59 Identities=14% Similarity=0.207 Sum_probs=35.2
Q ss_pred ecCCceeEEEc-CCCCeEEEEeeecccc-eeeeeeeeEEEEEeCCCcHHHHHHHHHhhchh
Q 038196 49 YFPDKYCIIVD-PSGNIVAQIGVKKEIE-DLMESKDLYHIVVKPGIDQAFIAVVIATLDYI 107 (122)
Q Consensus 49 ~~~~rsc~I~~-~~g~vVAev~rK~~~~-~v~~G~dvf~v~V~PgvD~AfimaLvvilD~i 107 (122)
++.++||-.+- ++-+++-++-.-...+ |++.++--|---|-|++|.-|++||=+-+.|-
T Consensus 161 N~~dsshl~~~~P~p~ll~~~~~~spig~g~~g~~~~~e~gvDp~lDpELA~AlrLSmeEe 221 (243)
T COG5148 161 NFSDSSHLEVKPPNPELLDRVLPFSPIGQGVVGDDLQLEYGVDPNLDPELAEALRLSMEEE 221 (243)
T ss_pred ccccceeeEecCCCHHHHHhhccCCccccccccCccceecCCCCCCCHHHHHHHHhhHHHH
Confidence 45666776665 3333333222222233 55544443555599999999999998877653
No 10
>PF03017 Transposase_23: TNP1/EN/SPM transposase; InterPro: IPR004264 Proteins in this group are TNP1/EN/SPM-like transposon proteins with no known function mostly from Arabidopsis thaliana []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=47.81 E-value=62 Score=21.12 Aligned_cols=38 Identities=18% Similarity=0.354 Sum_probs=26.4
Q ss_pred CceeEEEc--CCCCeEEEEeee-----cccceeeeeeeeEEEEEe
Q 038196 52 DKYCIIVD--PSGNIVAQIGVK-----KEIEDLMESKDLYHIVVK 89 (122)
Q Consensus 52 ~rsc~I~~--~~g~vVAev~rK-----~~~~~v~~G~dvf~v~V~ 89 (122)
+..|.++| .++++|||-+-- +...++-+|.+-..|.|.
T Consensus 4 ~~kc~Lld~~~~~~~VAeg~~~S~dp~~~V~g~pLG~~~~~V~V~ 48 (73)
T PF03017_consen 4 GVKCILLDWSGPDDVVAEGRICSTDPDTKVGGIPLGPNACKVVVD 48 (73)
T ss_pred CceEEEEEccCCCCceEEEEEEecCCccEECCEEcCCccEEEEEE
Confidence 45777777 345688876543 456688888888888765
No 11
>TIGR02164 torA trimethylamine-N-oxide reductase TorA. This very narrowly defined family represents TorA, part of a family of related molybdoenzymes that include biotin sulfoxide reductases, dimethyl sulfoxide reductases, and at least two different subfamilies of trimethylamine-N-oxide reductases. A single enzyme from the larger family may have more than one activity. TorA typically is located in the periplasm, has a Tat (twin-arginine translocation)-dependent signal sequence, and is encoded in a torCAD operon.
Probab=46.71 E-value=13 Score=33.85 Aligned_cols=22 Identities=23% Similarity=0.380 Sum_probs=18.8
Q ss_pred EEEEeCCCcHHHHHHHH-Hhhch
Q 038196 85 HIVVKPGIDQAFIAVVI-ATLDY 106 (122)
Q Consensus 85 ~v~V~PgvD~AfimaLv-vilD~ 106 (122)
.|-|.||-|.||++||+ +++++
T Consensus 272 ~l~irPGTD~AL~lam~~vii~e 294 (822)
T TIGR02164 272 HLYVNPQTDVALMLALAHTLYSE 294 (822)
T ss_pred EeccCCCcHHHHHHHHHHHHHHC
Confidence 78999999999999999 45544
No 12
>KOG1693 consensus emp24/gp25L/p24 family of membrane trafficking proteins [Intracellular trafficking, secretion, and vesicular transport]
Probab=46.70 E-value=50 Score=25.95 Aligned_cols=44 Identities=25% Similarity=0.257 Sum_probs=30.5
Q ss_pred eEEE-EeecCCceeEEEcCCCCeEEEEeeec--ccceeeeeeeeEEE
Q 038196 43 NFEV-KGYFPDKYCIIVDPSGNIVAQIGVKK--EIEDLMESKDLYHI 86 (122)
Q Consensus 43 ~~~i-~G~~~~rsc~I~~~~g~vVAev~rK~--~~~~v~~G~dvf~v 86 (122)
.|+| .|.-++=.|.|.+++|.+|++=++|+ ++.=...++.+|+.
T Consensus 50 ~fqV~tGG~fDVD~~I~aPdgkvI~~~~kk~~~~~~f~ae~~G~Y~f 96 (209)
T KOG1693|consen 50 EFQVQTGGHFDVDYDIEAPDGKVIYSEKKKRYDSFLFKAEGKGEYTF 96 (209)
T ss_pred EEEEEeCCceeeEEEEECCCCCEEeeccccccccEEEEEecceEEEE
Confidence 4654 78888999999999999998877772 22223344555554
No 13
>TIGR00509 bisC_fam molybdopterin guanine dinucleotide-containing S/N-oxide reductases. This enzyme family shares sequence similarity and a requirement for a molydenum cofactor as the only prosthetic group. The form of the cofactor is a single molybdenum atom coordinated by two molybdopterin guanine dinucleotide molecules. Members of the family include biotin sulfoxide reductase, dimethylsulfoxide reductase, and trimethylamine-N-oxide reductase, although a single member may show all those activities and related activities; it may not be possible to resolve the primary function for members of this family by sequence comparison alone. A number of similar molybdoproteins in which the N-terminal region contains a CXXXC motif and may bind an iron-sulfur cluster are excluded from this set, including formate dehydrogenases and nitrate reductases. Also excluded is the A chain of a heteromeric, anaerobic DMSO reductase, which also contains the CXXXC motif.
Probab=45.18 E-value=15 Score=33.16 Aligned_cols=25 Identities=16% Similarity=0.104 Sum_probs=20.6
Q ss_pred eeEEEEEeCCCcHHHHHHHH-Hhhch
Q 038196 82 DLYHIVVKPGIDQAFIAVVI-ATLDY 106 (122)
Q Consensus 82 dvf~v~V~PgvD~AfimaLv-vilD~ 106 (122)
+...|-|.||-|.||++||+ +++++
T Consensus 222 aD~~l~irPGTD~AL~lam~~~ii~e 247 (770)
T TIGR00509 222 GAEWIPPNPQTDVALMLGLAHTLVTE 247 (770)
T ss_pred cCeEeCcCCCcHHHHHHHHHHHHHHc
Confidence 35788999999999999998 45554
No 14
>KOG0621 consensus Phospholipid scramblase [Cell wall/membrane/envelope biogenesis]
Probab=45.04 E-value=64 Score=26.47 Aligned_cols=73 Identities=19% Similarity=0.158 Sum_probs=49.5
Q ss_pred cceEEEEeecCCce--------eEEEcCCCCeEEEEeeeccc--ceeeeeeeeEEEEEeCCCcH---HHHHHHHHhhchh
Q 038196 41 SNNFEVKGYFPDKY--------CIIVDPSGNIVAQIGVKKEI--EDLMESKDLYHIVVKPGIDQ---AFIAVVIATLDYI 107 (122)
Q Consensus 41 ~~~~~i~G~~~~rs--------c~I~~~~g~vVAev~rK~~~--~~v~~G~dvf~v~V~PgvD~---AfimaLvvilD~i 107 (122)
...|.|+|.-..-. +.+..+.|++|++|.||+.. ++.+...|+|.|.=-.-.|. |+++|-+..+|.+
T Consensus 198 ~~v~~v~gp~~~~~~~~~d~~f~~~~~d~~~~vg~I~k~w~g~~rE~fTDad~f~v~FPldLdvk~kavllga~flID~~ 277 (292)
T KOG0621|consen 198 NLVFLVEGPRCCTFACCDDTVFFPKTTDNGRIVGSISRKWAGLVREAFTDADTFVVHFPLDLDVKLKALLLGSTFLIDYM 277 (292)
T ss_pred eeEEEEEcCceeEEEeecCcceeEEEcCCCeEEEEEeecccchhhhheeccceeeEecCCcCCHHHHhhhhhheeeEEEE
Confidence 33577777621112 23334568999999999543 47888888888865544553 6788888889988
Q ss_pred cCCCce
Q 038196 108 YGEYTR 113 (122)
Q Consensus 108 ~~~~~~ 113 (122)
.-|.+.
T Consensus 278 ~Fe~~~ 283 (292)
T KOG0621|consen 278 SFESRG 283 (292)
T ss_pred EEecCC
Confidence 877653
No 15
>cd02750 MopB_Nitrate-R-NarG-like Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. Found in prokaryotes and some archaea, NarGHI usually functions as a heterotrimer. The alpha chain contains the molybdenum cofactor-containing Mo-bisMGD catalytic subunit. Members of the MopB_Nitrate-R-NarG-like CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=43.27 E-value=18 Score=30.54 Aligned_cols=23 Identities=22% Similarity=0.411 Sum_probs=18.6
Q ss_pred EEEEEeCCCcHHHHHHHH-Hhhch
Q 038196 84 YHIVVKPGIDQAFIAVVI-ATLDY 106 (122)
Q Consensus 84 f~v~V~PgvD~AfimaLv-vilD~ 106 (122)
..|.|.||-|.||++||+ +++++
T Consensus 218 ~~l~i~PGtD~al~lal~~~i~~~ 241 (461)
T cd02750 218 LWVPIKPGTDAALALAMAHVIIKE 241 (461)
T ss_pred EEeccCCCcHHHHHHHHHHHHHHc
Confidence 457899999999999999 44443
No 16
>TIGR03479 DMSO_red_II_alp DMSO reductase family type II enzyme, molybdopterin subunit. This model represents the molybdopterin subunit, typically called the alpha subunit, of various proteins that also contain an iron-sulfur subunit and a heme b subunit. The group includes two distinct but very closely related periplasmic proteins of anaerobic respiration, selenate reductase and chlorate reductase. Other members of this family include dimethyl sulphide dehydrogenase, ethylbenzene dehydrogenase, and an archaeal respiratory nitrate reductase. This alpha subunit has a twin-arginine translocation (TAT) signal for Sec-independent translocation across the plasma membrane.
Probab=42.39 E-value=13 Score=34.46 Aligned_cols=24 Identities=21% Similarity=0.293 Sum_probs=19.6
Q ss_pred EEEEEeCCCcHHHHHHHH-Hhhchh
Q 038196 84 YHIVVKPGIDQAFIAVVI-ATLDYI 107 (122)
Q Consensus 84 f~v~V~PgvD~AfimaLv-vilD~i 107 (122)
..|-|.||-|.||++||+ ++++|-
T Consensus 272 ~wlpirPGTD~ALalam~~vIi~e~ 296 (912)
T TIGR03479 272 LWLPVRVGTDAALALGMVQVIIDEK 296 (912)
T ss_pred eecCCCCCcHHHHHHHHHHHHHHcC
Confidence 357899999999999999 566653
No 17
>PF04881 Adeno_GP19K: Adenovirus GP19K; InterPro: IPR006965 This 19 kDa glycoprotein binds the major histocompatibility (MHC) class I antigens in the endoplasmic reticulum (ER). The ER retention signal at the C terminus of Gp19K causes retention of the complex in the ER, preventing lysis of the cell by cytotoxic T-lymphocytes [].; GO: 0005537 mannose binding, 0050690 regulation of defense response to virus by virus
Probab=40.09 E-value=87 Score=23.03 Aligned_cols=51 Identities=16% Similarity=0.186 Sum_probs=29.9
Q ss_pred EEEEcCCCCcceEEEEeecCCceeEEEcCCCCeEEEEeeecccceeeee------eeeEEEEEeCCCc
Q 038196 32 RISTETTARSNNFEVKGYFPDKYCIIVDPSGNIVAQIGVKKEIEDLMES------KDLYHIVVKPGID 93 (122)
Q Consensus 32 ~V~~~~~~~~~~~~i~G~~~~rsc~I~~~~g~vVAev~rK~~~~~v~~G------~dvf~v~V~PgvD 93 (122)
++..+++...|.-.||..|.-++-.|...+ .+....+.+ .+-|+|+| ||-|
T Consensus 2 ~~tf~~e~~~C~vlIKC~~ec~~v~i~~kN----------Kt~~~~~~~~WqPGd~~~ytVtV-~G~d 58 (139)
T PF04881_consen 2 NLTFAPEASRCTVLIKCGWECESVNITHKN----------KTWNNTVYPTWQPGDPEWYTVTV-QGPD 58 (139)
T ss_pred ceecCCCCceeEEEEEeccccceEEEEecc----------cccCceeeeeccCCCCcceEEEE-ECCC
Confidence 455555544477778888866665554321 222222223 78899999 7766
No 18
>PRK14991 tetrathionate reductase subunit A; Provisional
Probab=39.64 E-value=16 Score=34.53 Aligned_cols=27 Identities=22% Similarity=0.370 Sum_probs=21.4
Q ss_pred eeeeEEEEEeCCCcHHHHHHHH-Hhhch
Q 038196 80 SKDLYHIVVKPGIDQAFIAVVI-ATLDY 106 (122)
Q Consensus 80 G~dvf~v~V~PgvD~AfimaLv-vilD~ 106 (122)
.+....|-|.||-|.||+|||+ +|+++
T Consensus 337 ~~Ad~wlpIrPGTD~ALalgmi~~Iie~ 364 (1031)
T PRK14991 337 GDNNRWLPIRPGTDSALAMGMIRWIIDN 364 (1031)
T ss_pred hcCCEEeCCCCCcHHHHHHHHHHHHHHc
Confidence 3445678999999999999998 45554
No 19
>TIGR01580 narG respiratory nitrate reductase, alpha subunit. The Nitrate reductase enzyme complex allows bacteria to use nitrate as an electron acceptor during anaerobic growth. The enzyme complex consists of a tetramer that has an alpha, beta and 2 gamma subunits. The alpha and beta subunits have catalytic activity and the gamma subunits attach the enzyme to the membrane and is a b-type cytochrome that receives electrons from the quinone pool and transfers them to the beta subunit. This model is specific for the alpha subunit for nitrate reductase I (narG) and nitrate reductase II (narZ) for gram positive and gram negative bacteria.A few thermophiles and archaea also match the model The seed members used to make the model include Nitrate reductases from Pseudomonas fluorescens, E.coli and B.subtilis. All seed members are experimentally characterized. Some unpublished nitrate reductases, that are shorter sequences, and probably fragments fall in between the noise and trusted cutoffs. P
Probab=38.05 E-value=18 Score=35.10 Aligned_cols=28 Identities=18% Similarity=0.086 Sum_probs=23.0
Q ss_pred eEEEEEeCCCcHHHHHHHH-HhhchhcCC
Q 038196 83 LYHIVVKPGIDQAFIAVVI-ATLDYIYGE 110 (122)
Q Consensus 83 vf~v~V~PgvD~AfimaLv-vilD~i~~~ 110 (122)
-.-|-|.||-|.||+|||+ +|+++-..+
T Consensus 292 D~WLpIrPGTD~ALaLAm~hvII~E~l~D 320 (1235)
T TIGR01580 292 DLWLAPKQGTDAALALAMGHVILREFHLD 320 (1235)
T ss_pred CEEeCCCCChHHHHHHHHHHHHHHCCCcc
Confidence 4578899999999999999 777775544
No 20
>PF13585 CHU_C: C-terminal domain of CHU protein family; PDB: 3EIF_A 1XF1_B.
Probab=36.08 E-value=1.2e+02 Score=19.69 Aligned_cols=58 Identities=17% Similarity=0.242 Sum_probs=28.2
Q ss_pred EEEEcCCCCcc-eEEEEe--ecCCceeEEEcCCCCeEEEEeee-cccceeeee------eeeEEEEEe
Q 038196 32 RISTETTARSN-NFEVKG--YFPDKYCIIVDPSGNIVAQIGVK-KEIEDLMES------KDLYHIVVK 89 (122)
Q Consensus 32 ~V~~~~~~~~~-~~~i~G--~~~~rsc~I~~~~g~vVAev~rK-~~~~~v~~G------~dvf~v~V~ 89 (122)
++|.++++... .|++.+ .+..-+..|++.-|++|-|.... ..+.+...| ..+|.-+++
T Consensus 5 n~fTPNgDg~ND~~~i~~~~~~~~~~~~IynrwG~~Vf~~~~~~~~WdG~~~g~g~~~p~G~Y~Y~i~ 72 (87)
T PF13585_consen 5 NAFTPNGDGINDTFKIPGIENIPNYSLTIYNRWGELVFESNDYNNGWDGTYNGSGNPLPSGTYFYVIE 72 (87)
T ss_dssp EEE--SSSSSS--BEEEESS-EEEEEEEEE-SSS-EEEE---EEG-B-SB-T-TS-B--SEEEEEEEE
T ss_pred CEEeCCCCCcCCEEEEecccccceeEEEEEeCCCcEEEEECCCCCCCCCEecCCcccCCCceEEEEEE
Confidence 34545443333 478887 35566889999889999988876 344444333 455555544
No 21
>PRK14990 anaerobic dimethyl sulfoxide reductase subunit A; Provisional
Probab=34.93 E-value=24 Score=32.01 Aligned_cols=23 Identities=22% Similarity=0.394 Sum_probs=18.7
Q ss_pred EEEEEeCCCcHHHHHHHH-Hhhch
Q 038196 84 YHIVVKPGIDQAFIAVVI-ATLDY 106 (122)
Q Consensus 84 f~v~V~PgvD~AfimaLv-vilD~ 106 (122)
-.|.|.||-|.||++||+ +++++
T Consensus 284 ~~l~irPGTD~al~lam~~~ii~e 307 (814)
T PRK14990 284 EWIPIRPGTDAALVNGLAYVMITE 307 (814)
T ss_pred eEECCCCCcHHHHHHHHHHHHHHc
Confidence 457899999999999998 44444
No 22
>PF13541 ChlI: Subunit ChlI of Mg-chelatase
Probab=33.97 E-value=63 Score=22.86 Aligned_cols=36 Identities=11% Similarity=0.126 Sum_probs=27.3
Q ss_pred ceeeeeeeeEEEEEeCC--------CcHHHHHHHHHhhchhcCC
Q 038196 75 EDLMESKDLYHIVVKPG--------IDQAFIAVVIATLDYIYGE 110 (122)
Q Consensus 75 ~~v~~G~dvf~v~V~Pg--------vD~AfimaLvvilD~i~~~ 110 (122)
.++-+......|.+.|+ +|.|.++||+..+.++...
T Consensus 36 ~g~~~p~~~i~VNlap~~l~k~g~~~DLaIA~ailsa~~~~~~~ 79 (121)
T PF13541_consen 36 SGFPFPNQDITVNLAPADLKKEGPAFDLAIAIAILSAFGQIPIP 79 (121)
T ss_pred cCCCCCcceeeeEEEeCCEEEeeeeehHHHHHHHHHhCCCcccC
Confidence 45555666677777765 8999999999988876555
No 23
>cd02756 MopB_Arsenite-Ox Arsenite oxidase (Arsenite-Ox) oxidizes arsenite to the less toxic arsenate; it transfers the electrons obtained from the oxidation of arsenite towards the soluble periplasmic electron carriers cytochrome c and/or amicyanin. Arsenite oxidase is a heterodimeric enzyme containing a large and a small subunit. The large catalytic subunit harbors the molybdopterin cofactor and the [3Fe-4S] cluster; and the small subunit belongs to the structural class of the Rieske proteins. The small subunit is not included in this alignment. Members of MopB_Arsenite-Ox CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=33.21 E-value=35 Score=30.90 Aligned_cols=23 Identities=26% Similarity=0.541 Sum_probs=19.7
Q ss_pred eeEEEEEeCCCcHHHHHHHHHhh
Q 038196 82 DLYHIVVKPGIDQAFIAVVIATL 104 (122)
Q Consensus 82 dvf~v~V~PgvD~AfimaLvvil 104 (122)
.+..|-|.||-|.||+.||+-++
T Consensus 295 ~~lhL~I~PGTD~AL~~al~~~I 317 (676)
T cd02756 295 RVLHLQVNPGTDTALANAIARYI 317 (676)
T ss_pred cceEEeecCChHHHHHHHHHHHH
Confidence 35789999999999999998554
No 24
>PF06891 P2_Phage_GpR: P2 phage tail completion protein R (GpR); InterPro: IPR009678 This family consists of P2 phage tail completion protein R (GpR) and similar sequences from related phage. GpR is thought to be a tail completion protein which is essential for stable head joining []. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=32.09 E-value=1.5e+02 Score=21.21 Aligned_cols=46 Identities=20% Similarity=0.163 Sum_probs=28.2
Q ss_pred CCCeEEEEeeecccceeeeeeeeEEEEE----eCCCcHHHHHHHHHhhchhc
Q 038196 61 SGNIVAQIGVKKEIEDLMESKDLYHIVV----KPGIDQAFIAVVIATLDYIY 108 (122)
Q Consensus 61 ~g~vVAev~rK~~~~~v~~G~dvf~v~V----~PgvD~AfimaLvvilD~i~ 108 (122)
.|+++|.=+. .+.+.+-.+.-.|+++| +|| |.+.+|++++.+=..|
T Consensus 31 ~G~i~~t~~~-~~~s~~~~~~~~Y~~~i~i~df~~-~~d~l~~~v~~WL~~n 80 (135)
T PF06891_consen 31 NGEIVATGKD-PGLSFYRLAEYRYTAVISIEDFPG-DPDLLMAPVLAWLREN 80 (135)
T ss_pred CcEEEECccc-CCCCccEEEEEEEEEEEEEEECCC-CHHHHHHHHHHHHHhc
Confidence 3555554431 23344455556666544 688 9999999998874444
No 25
>cd02760 MopB_Phenylacetyl-CoA-OR The MopB_Phenylacetyl-CoA-OR CD contains the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), and other related proteins. The phenylacetyl-CoA:acceptor oxidoreductase has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. Members of this CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=31.92 E-value=30 Score=31.70 Aligned_cols=24 Identities=21% Similarity=0.378 Sum_probs=19.6
Q ss_pred eEEEEEeCCCcHHHHHHHH-Hhhch
Q 038196 83 LYHIVVKPGIDQAFIAVVI-ATLDY 106 (122)
Q Consensus 83 vf~v~V~PgvD~AfimaLv-vilD~ 106 (122)
.-.|-|.||-|.||++||+ +++++
T Consensus 221 D~wlpirPGTD~AL~lam~~~Ii~e 245 (760)
T cd02760 221 AEWVPIRPKTDPAFMFAMIHVMVHE 245 (760)
T ss_pred CeEeCcCCCcHHHHHHHHHHHHHhc
Confidence 3467899999999999999 56555
No 26
>cd02770 MopB_DmsA-EC This CD (MopB_DmsA-EC) includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-terminal iron-sulfur [4Fe-4S] cluster binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=31.23 E-value=32 Score=30.19 Aligned_cols=22 Identities=27% Similarity=0.456 Sum_probs=18.5
Q ss_pred eEEEEEeCCCcHHHHHHHHHhh
Q 038196 83 LYHIVVKPGIDQAFIAVVIATL 104 (122)
Q Consensus 83 vf~v~V~PgvD~AfimaLvvil 104 (122)
.-.|.|.||-|.||++||+=++
T Consensus 217 D~~i~irPGTD~AL~lam~~~i 238 (617)
T cd02770 217 DEWIPIRPGTDAALVAAMAYVM 238 (617)
T ss_pred CEEECCCCCcHHHHHHHHHHHH
Confidence 4468899999999999999554
No 27
>COG0146 HyuB N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=29.68 E-value=37 Score=30.40 Aligned_cols=19 Identities=47% Similarity=0.646 Sum_probs=16.3
Q ss_pred CceeEEEcCCCCeEEEEee
Q 038196 52 DKYCIIVDPSGNIVAQIGV 70 (122)
Q Consensus 52 ~rsc~I~~~~g~vVAev~r 70 (122)
+.||.|+|.+|++|||...
T Consensus 39 D~scAI~d~~G~lVA~a~h 57 (563)
T COG0146 39 DFSCAIFDAEGNLVAQAPH 57 (563)
T ss_pred ceeEEEECCCCCeeccCCC
Confidence 5599999998999999854
No 28
>cd02765 MopB_4 The MopB_4 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins
Probab=28.81 E-value=41 Score=29.27 Aligned_cols=22 Identities=23% Similarity=0.365 Sum_probs=17.9
Q ss_pred eEEEEEeCCCcHHHHHHHHHhh
Q 038196 83 LYHIVVKPGIDQAFIAVVIATL 104 (122)
Q Consensus 83 vf~v~V~PgvD~AfimaLvvil 104 (122)
.-.|.|.||-|.||++||+=++
T Consensus 206 d~~l~irPGTD~al~~am~~~i 227 (567)
T cd02765 206 DQWVPIRPGTDPALALGMINYI 227 (567)
T ss_pred CEEeccCCCchHHHHHHHHHHH
Confidence 3457899999999999998433
No 29
>cd02762 MopB_1 The MopB_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=27.66 E-value=41 Score=28.90 Aligned_cols=22 Identities=36% Similarity=0.620 Sum_probs=18.8
Q ss_pred eEEEEEeCCCcHHHHHHHHHhh
Q 038196 83 LYHIVVKPGIDQAFIAVVIATL 104 (122)
Q Consensus 83 vf~v~V~PgvD~AfimaLvvil 104 (122)
...|-|.||-|.||++||+=++
T Consensus 209 D~~l~irPGtD~aL~~a~~~~i 230 (539)
T cd02762 209 DEHLFVRPGTDAWLLAAMLAVL 230 (539)
T ss_pred CEeeCcCCCcHHHHHHHHHHHH
Confidence 4678899999999999999555
No 30
>TIGR02693 arsenite_ox_L arsenite oxidase, large subunit. This model represents the large subunit of an arsenite oxidase complex. The small subunit is a Rieske protein. Homologs to both large and small subunits that score in the gray zone between the set trusted and noise bit score cutoffs for the respective models are found in Aeropyrum pernix K1 and in Sulfolobus tokodaii str. 7. This enzyme acts in energy metabolim by arsenite oxidation, rather than detoxification by reduction of arsenate to arsenite prior to export.
Probab=27.46 E-value=46 Score=30.60 Aligned_cols=21 Identities=19% Similarity=0.384 Sum_probs=18.6
Q ss_pred eEEEEEeCCCcHHHHHHHHHh
Q 038196 83 LYHIVVKPGIDQAFIAVVIAT 103 (122)
Q Consensus 83 vf~v~V~PgvD~AfimaLvvi 103 (122)
+..|-|.||-|.||++||+=+
T Consensus 291 ~~~l~i~PGTD~aL~~a~~~~ 311 (806)
T TIGR02693 291 VLHLRINLGTDYALFNALATY 311 (806)
T ss_pred ceEeccCCCcHHHHHHHHHHH
Confidence 588999999999999999843
No 31
>PF01167 Tub: Tub family; InterPro: IPR000007 Tubby, an autosomal recessive mutation, mapping to mouse chromosome 7, was recently found to be the result of a splicing defect in a novel gene with unknown function. This mutation maps to the tub gene [, ]. The mouse tubby mutation is the cause of maturity-onset obesity, insulin resistance and sensory deficits. By contrast with the rapid juvenile-onset weight gain seen in diabetes (db) and obese (ob) mice, obesity in tubby mice develops gradually, and strongly resembles the late-onset obesity observed in the human population. Excessive deposition of adipose tissue culminates in a two-fold increase of body weight. Tubby mice also suffer retinal degeneration and neurosensory hearing loss. The tripartite character of the tubby phenotype is highly similar to human obesity syndromes, such as Alstrom and Bardet-Biedl. Although these phenotypes indicate a vital role for tubby proteins, no biochemical function has yet been ascribed to any family member [], although it has been suggested that the phenotypic features of tubby mice may be the result of cellular apoptosis triggered by expression of the mutated tub gene. TUB is the founding-member of the tubby-like proteins, the TULPs. TULPs are found in multicellular organisms from both the plant and animal kingdoms. Ablation of members of this protein family cause disease phenotypes that are indicative of their importance in nervous-system function and development []. Mammalian TUB is a hydrophilic protein of ~500 residues. The N-terminal (IPR005398 from INTERPRO) portion of the protein is conserved neither in length nor sequence, but, in TUB, contains the nuclear localisation signal and may have transcriptional-activation activity. The C-terminal 250 residues are highly conserved. The C-terminal extremity contains a cysteine residue that might play an important role in the normal functioning of these proteins. The crystal structure of the C-terminal core domain from mouse tubby has been determined to 1.9A resolution. This domain is arranged as a 12-stranded, all anti-parallel, closed beta-barrel that surrounds a central alpha helix, (which is at the extreme carboxyl terminus of the protein) that forms most of the hydrophobic core. Structural analyses suggest that TULPs constitute a unique family of bipartite transcription factors [].; PDB: 3C5N_B 2FIM_A 1I7E_A 1C8Z_A 1S31_A.
Probab=26.84 E-value=1.1e+02 Score=24.09 Aligned_cols=49 Identities=20% Similarity=0.325 Sum_probs=30.2
Q ss_pred CCCeeEEEEEcCCCcccccccceEEEEEcCC---CCcceE--EEEeecCCceeEEEcC
Q 038196 8 RSKKLVFTLKEPPNSSCLVRNSSIRISTETT---ARSNNF--EVKGYFPDKYCIIVDP 60 (122)
Q Consensus 8 ~~~~~lFtvkrs~~~~i~~~k~~~~V~~~~~---~~~~~~--~i~G~~~~rsc~I~~~ 60 (122)
+.++.|...||... ...+..-+.+..+ .....| +|+.++.+..+.|||.
T Consensus 34 ~~~kfLLaArK~~~----s~~s~YiIS~~~~dlsr~s~~yvGKLrsNf~GT~F~iyD~ 87 (246)
T PF01167_consen 34 ENGKFLLAARKRKR----SKTSNYIISLDPDDLSRSSNNYVGKLRSNFLGTEFTIYDN 87 (246)
T ss_dssp TTSEEEEEEEEECS----SSSEEEEEESSHHHHCTT---ESEEEEE-TTSSEEEEEES
T ss_pred CCCcEEEeeeeccc----CCCcceEEecCCCccccCCCceeeeeccccceeEEEEECC
Confidence 45688888887541 2234455555433 133456 8999999999999993
No 32
>cd02754 MopB_Nitrate-R-NapA-like Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. Members of the MopB_Nitrate-R-NapA CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=26.06 E-value=51 Score=28.35 Aligned_cols=22 Identities=27% Similarity=0.560 Sum_probs=18.8
Q ss_pred eEEEEEeCCCcHHHHHHHHHhh
Q 038196 83 LYHIVVKPGIDQAFIAVVIATL 104 (122)
Q Consensus 83 vf~v~V~PgvD~AfimaLvvil 104 (122)
...|.|.||-|.||++||+-++
T Consensus 206 d~~l~i~PGtD~al~la~~~~i 227 (565)
T cd02754 206 DLHLPIRPGTDLALLNGLLHVL 227 (565)
T ss_pred CeeeCCCCCccHHHHHHHHHHH
Confidence 3568899999999999999665
No 33
>cd02758 MopB_Tetrathionate-Ra The MopB_Tetrathionate-Ra CD contains tetrathionate reductase, subunit A, (TtrA) and other related proteins. The Salmonella enterica tetrathionate reductase catalyses the reduction of trithionate but not sulfur or thiosulfate. Members of this CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=24.56 E-value=81 Score=28.76 Aligned_cols=26 Identities=23% Similarity=0.487 Sum_probs=20.3
Q ss_pred eeeeEEEEEeCCCcHHHHHHHHH-hhc
Q 038196 80 SKDLYHIVVKPGIDQAFIAVVIA-TLD 105 (122)
Q Consensus 80 G~dvf~v~V~PgvD~AfimaLvv-ilD 105 (122)
.+-...|-|.||-|.||++||+= +++
T Consensus 262 ~~Ad~wlpIrPGTD~AL~lam~~~Iie 288 (735)
T cd02758 262 GENIRWVPIKPGGDGALAMAMIRWIIE 288 (735)
T ss_pred ccCCEEECCCCCcHHHHHHHHHHHHHH
Confidence 34456788999999999999994 443
No 34
>COG4385 gpI Bacteriophage P2-related tail formation protein [General function prediction only]
Probab=24.22 E-value=1.8e+02 Score=22.80 Aligned_cols=40 Identities=23% Similarity=0.181 Sum_probs=29.5
Q ss_pred eeEEEEE---eCCCcHHHHHHHHHhhchhcCCCc--eeeEEEEee
Q 038196 82 DLYHIVV---KPGIDQAFIAVVIATLDYIYGEYT--RCWSIRIFT 121 (122)
Q Consensus 82 dvf~v~V---~PgvD~AfimaLvvilD~i~~~~~--~~~~~~~~~ 121 (122)
.+|++.| .+|+|..+..-|....|+...-.+ --.|++|++
T Consensus 113 ~tF~l~v~~~~~G~de~~~~~le~li~~~kpv~R~~~~ls~~i~~ 157 (206)
T COG4385 113 GTFRLEVGVSDQGIDEPTVAELERLIDDAKPVSRHLTGLSIFIEP 157 (206)
T ss_pred ceEEEEEEeeccCcChhHHHHHHHHHHhhccccccccceeEEEEe
Confidence 4677754 699999999999999999876532 334555553
No 35
>cd02766 MopB_3 The MopB_3 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins
Probab=23.76 E-value=51 Score=28.18 Aligned_cols=21 Identities=38% Similarity=0.586 Sum_probs=17.9
Q ss_pred EEEEEeCCCcHHHHHHHHHhh
Q 038196 84 YHIVVKPGIDQAFIAVVIATL 104 (122)
Q Consensus 84 f~v~V~PgvD~AfimaLvvil 104 (122)
..|-|.||-|.||++||+-++
T Consensus 205 ~~l~i~PGtD~al~~al~~~i 225 (501)
T cd02766 205 LHIQIRPGTDGALALGVAKVL 225 (501)
T ss_pred eeeccCCCcHHHHHHHHHHHH
Confidence 467899999999999998654
No 36
>PRK15102 trimethylamine N-oxide reductase I catalytic subunit; Provisional
Probab=23.28 E-value=55 Score=29.90 Aligned_cols=19 Identities=26% Similarity=0.483 Sum_probs=17.1
Q ss_pred EEEEeCCCcHHHHHHHHHh
Q 038196 85 HIVVKPGIDQAFIAVVIAT 103 (122)
Q Consensus 85 ~v~V~PgvD~AfimaLvvi 103 (122)
.|-|.||-|.||++||+=+
T Consensus 275 ~l~irPGTD~AL~lam~~~ 293 (825)
T PRK15102 275 HLYVNPQTDVPLMLALAHT 293 (825)
T ss_pred eecccCCcHHHHHHHHHHH
Confidence 7889999999999999843
No 37
>cd03444 Thioesterase_II_repeat1 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP) domains, respectively. TEII has two tandem asymmetric hot dog folds that are structurally similar to one found in PaaI thioesterase, 4-hydroxybenzoyl-CoA thioesterase (4HBT) and beta-hydroxydecanoyl-ACP dehydratase and thus, the TEII monomer is equivalent to the homodimeric form of the latter three enzymes. Human TEII is expressed in T cells and has been shown to bind the product of the HIV-1 Nef gene.
Probab=22.48 E-value=98 Score=20.73 Aligned_cols=20 Identities=20% Similarity=0.177 Sum_probs=16.5
Q ss_pred CceeEEEcCCCCeEEEEeee
Q 038196 52 DKYCIIVDPSGNIVAQIGVK 71 (122)
Q Consensus 52 ~rsc~I~~~~g~vVAev~rK 71 (122)
...++|++++|++||-+.+.
T Consensus 82 ~~~~~l~~~~G~LvAs~~Q~ 101 (104)
T cd03444 82 LVEGRIFTRDGELVASVAQE 101 (104)
T ss_pred EEEEEEECCCCCEEEEEEEe
Confidence 34679999999999999774
No 38
>TIGR02166 dmsA_ynfE anaerobic dimethyl sulfoxide reductase, A subunit, DmsA/YnfE family. Members of this family include known and probable dimethyl sulfoxide reductase (DMSO reductase) A chains. In E. coli, dmsA encodes the canonical anaerobic DMSO reductase A chain. The paralog ynfE, as part of ynfFGH expressed from a multicopy plasmid, could complement a dmsABC deletion, suggesting a similar function and some overlap in specificity, although YnfE could not substitute for DmsA in a mixed complex.
Probab=22.10 E-value=63 Score=29.17 Aligned_cols=21 Identities=29% Similarity=0.457 Sum_probs=17.9
Q ss_pred eEEEEEeCCCcHHHHHHHHHh
Q 038196 83 LYHIVVKPGIDQAFIAVVIAT 103 (122)
Q Consensus 83 vf~v~V~PgvD~AfimaLvvi 103 (122)
...|-|.||-|.||++||+=+
T Consensus 266 d~~l~irPGtD~al~~a~~~~ 286 (797)
T TIGR02166 266 DEWIPIRPGTDAALVAAIAYV 286 (797)
T ss_pred CEEECCCCCCHHHHHHHHHHH
Confidence 457889999999999999843
No 39
>cd02759 MopB_Acetylene-hydratase The MopB_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. Members of this CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=22.09 E-value=61 Score=27.36 Aligned_cols=22 Identities=18% Similarity=0.397 Sum_probs=18.5
Q ss_pred eEEEEEeCCCcHHHHHHHHHhh
Q 038196 83 LYHIVVKPGIDQAFIAVVIATL 104 (122)
Q Consensus 83 vf~v~V~PgvD~AfimaLvvil 104 (122)
...|.|.||-|.||++||+-++
T Consensus 208 d~~l~i~PGtD~al~~al~~~i 229 (477)
T cd02759 208 DLWLPIRPGTDAALALGMLNVI 229 (477)
T ss_pred CeeeccCCCcHHHHHHHHHHHH
Confidence 3568899999999999998654
No 40
>TIGR01706 NAPA periplasmic nitrate reductase, large subunit. The enzymes from Alicagenes eutrophus and Paracoccus pantotrophus have been characterized. In E. coli (as well as other organisms) this gene is part of a large nitrate reduction operon (napFDAGHBC).
Probab=21.98 E-value=61 Score=29.74 Aligned_cols=21 Identities=24% Similarity=0.400 Sum_probs=17.6
Q ss_pred EEEEEeCCCcHHHHHHHHHhh
Q 038196 84 YHIVVKPGIDQAFIAVVIATL 104 (122)
Q Consensus 84 f~v~V~PgvD~AfimaLvvil 104 (122)
-.|-|.||-|.||++||+=++
T Consensus 256 ~~l~irPGTD~AL~lam~~~i 276 (830)
T TIGR01706 256 IGIIFKPQTDLAILNYIANYI 276 (830)
T ss_pred eeeccCCCCHHHHHHHHHHHH
Confidence 457899999999999998443
No 41
>cd02751 MopB_DMSOR-like The MopB_DMSOR-like CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Also included in this group is the pyrogallol-phloroglucinol transhydroxylase from Pelobacter acidigallici. Members of the MopB_DMSOR-like CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=20.93 E-value=70 Score=27.99 Aligned_cols=21 Identities=29% Similarity=0.452 Sum_probs=17.9
Q ss_pred eEEEEEeCCCcHHHHHHHHHh
Q 038196 83 LYHIVVKPGIDQAFIAVVIAT 103 (122)
Q Consensus 83 vf~v~V~PgvD~AfimaLvvi 103 (122)
...|-|.||-|.||++||+=+
T Consensus 225 D~~l~irPGtD~aL~lam~~~ 245 (609)
T cd02751 225 AEWIPIRPGTDVALMLAMAHT 245 (609)
T ss_pred CEEECCCCCcHHHHHHHHHHH
Confidence 456789999999999999944
No 42
>PRK13532 nitrate reductase catalytic subunit; Provisional
Probab=20.91 E-value=74 Score=29.13 Aligned_cols=23 Identities=17% Similarity=0.294 Sum_probs=18.5
Q ss_pred EEEEEeCCCcHHHHHHHH-Hhhch
Q 038196 84 YHIVVKPGIDQAFIAVVI-ATLDY 106 (122)
Q Consensus 84 f~v~V~PgvD~AfimaLv-vilD~ 106 (122)
-.|-|.||-|.||++||+ +++++
T Consensus 256 ~~l~irPGtD~al~~am~~~ii~~ 279 (830)
T PRK13532 256 NGIIFTPQTDLAILNYIANYIIQN 279 (830)
T ss_pred eeeccCCCCcHHHHHHHHHHHHHC
Confidence 457899999999999998 44443
No 43
>PF12863 DUF3821: Domain of unknown function (DUF3821); InterPro: IPR024277 This is a domain largely confined to sequences from Methanomicrobiales. It is found in putative lipases but the function is unknown.
Probab=20.69 E-value=88 Score=24.43 Aligned_cols=20 Identities=15% Similarity=0.433 Sum_probs=14.6
Q ss_pred CcCCcCCCCeeEEEEEcCCC
Q 038196 2 YAFDYERSKKLVFTLKEPPN 21 (122)
Q Consensus 2 y~~d~~~~~~~lFtvkrs~~ 21 (122)
|.++......+.|.|+.++.
T Consensus 65 Y~~~~~~~~~~aF~V~~Psl 84 (209)
T PF12863_consen 65 YQWNGTPKGDVAFYVQDPSL 84 (209)
T ss_pred EecCCCCCcceEEEEeCCce
Confidence 45555545599999999984
No 44
>PF13860 FlgD_ig: FlgD Ig-like domain; PDB: 3C12_A 3OSV_A.
Probab=20.32 E-value=2.4e+02 Score=17.86 Aligned_cols=18 Identities=28% Similarity=0.458 Sum_probs=13.4
Q ss_pred eeEEEcCCCCeEEEEeee
Q 038196 54 YCIIVDPSGNIVAQIGVK 71 (122)
Q Consensus 54 sc~I~~~~g~vVAev~rK 71 (122)
...|+|.+|++|.++.-.
T Consensus 28 ~v~I~d~~G~~V~t~~~~ 45 (81)
T PF13860_consen 28 TVTIYDSNGQVVRTISLG 45 (81)
T ss_dssp EEEEEETTS-EEEEEEEE
T ss_pred EEEEEcCCCCEEEEEEcC
Confidence 567889889999888764
No 45
>COG0243 BisC Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]
Probab=20.27 E-value=60 Score=29.25 Aligned_cols=20 Identities=25% Similarity=0.479 Sum_probs=17.6
Q ss_pred EEEEeCCCcHHHHHHHHHhh
Q 038196 85 HIVVKPGIDQAFIAVVIATL 104 (122)
Q Consensus 85 ~v~V~PgvD~AfimaLvvil 104 (122)
.|-|.||-|.||++||+=+|
T Consensus 251 ~l~irPGTD~Al~~gi~~~l 270 (765)
T COG0243 251 WLPIRPGTDAALALGIAHVL 270 (765)
T ss_pred ccccCCCcHHHHHHHHHHHH
Confidence 78899999999999998554
No 46
>TIGR03876 cas_csaX CRISPR-associated protein, CsaX family. This family comprises a minor CRISPR-associated protein family. It occurs only in the context of the (strictly archaeal) Apern subtype of CRISPR/Cas system, and is further restricted to the Sulfolobales, including Metallosphaera sedula DSM 5348 and multiple species of the genus Sulfolobus.
Probab=20.01 E-value=2.1e+02 Score=23.01 Aligned_cols=44 Identities=14% Similarity=0.236 Sum_probs=32.3
Q ss_pred eeeeeeEEEEE-------------eCCCcHHHHHHHHHhhchhcCCCceeeEEEEee
Q 038196 78 MESKDLYHIVV-------------KPGIDQAFIAVVIATLDYIYGEYTRCWSIRIFT 121 (122)
Q Consensus 78 ~~G~dvf~v~V-------------~PgvD~AfimaLvvilD~i~~~~~~~~~~~~~~ 121 (122)
-.|-.+|++++ -||+-+.-+..|.++.--+.......++|||++
T Consensus 142 ~vGvnvFt~t~~~lys~~~n~~g~ipG~kPeTAF~lwlA~~vvss~~~~~S~~riY~ 198 (281)
T TIGR03876 142 RVGVNVFTVTVDRLYSVLPNLSGLIPGFKPETAFLLWLAYQVVSSKAEIRSGIRIYA 198 (281)
T ss_pred eeEEEEEEeehhhhhhhcccccccCCCcCcchHHHHHHHHHHHhccCCcceeEEEEE
Confidence 34778888875 488876666677777766666667788999985
Done!