Query psy281
Match_columns 162
No_of_seqs 143 out of 1039
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 17:29:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy281.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/281hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3381|consensus 100.0 7.1E-29 1.5E-33 191.8 9.7 153 5-157 1-159 (161)
2 COG2151 PaaD Predicted metal-s 99.9 3.2E-25 6.8E-30 165.0 9.5 95 34-136 9-103 (111)
3 TIGR03406 FeS_long_SufT probab 99.9 4.4E-21 9.5E-26 152.7 12.0 99 30-136 66-167 (174)
4 COG5133 Uncharacterized conser 99.8 4E-20 8.6E-25 143.0 9.4 126 31-156 48-178 (181)
5 PF01883 DUF59: Domain of unkn 99.8 1.5E-18 3.3E-23 118.4 7.4 72 39-115 1-72 (72)
6 TIGR02945 SUF_assoc FeS assemb 99.7 2.4E-17 5.2E-22 118.9 11.1 89 39-136 3-91 (99)
7 TIGR02159 PA_CoA_Oxy4 phenylac 99.7 4.5E-17 9.7E-22 126.5 9.0 86 49-146 1-87 (146)
8 PRK11670 antiporter inner memb 99.3 9.6E-12 2.1E-16 108.9 10.2 79 36-119 11-89 (369)
9 PRK11190 Fe/S biogenesis prote 94.4 0.24 5.2E-06 40.1 7.7 71 39-115 108-180 (192)
10 TIGR03341 YhgI_GntY IscR-regul 93.7 0.3 6.5E-06 39.5 7.0 71 39-115 107-178 (190)
11 PF01106 NifU: NifU-like domai 91.4 1.1 2.5E-05 30.2 6.4 48 62-113 17-65 (68)
12 PF00403 HMA: Heavy-metal-asso 89.8 0.61 1.3E-05 29.9 3.9 57 84-146 4-60 (62)
13 COG0694 Thioredoxin-like prote 88.1 3.4 7.4E-05 29.9 7.0 75 39-118 11-86 (93)
14 TIGR02000 NifU_proper Fe-S clu 75.6 15 0.00033 31.5 7.5 68 39-114 221-288 (290)
15 COG2608 CopZ Copper chaperone 73.7 12 0.00027 25.0 5.3 63 80-148 4-66 (71)
16 PF01545 Cation_efflux: Cation 68.3 34 0.00074 27.9 7.9 70 39-118 207-279 (284)
17 PF09580 Spore_YhcN_YlaJ: Spor 54.9 66 0.0014 24.7 6.9 55 61-118 87-141 (177)
18 PF10646 Germane: Sporulation 53.4 77 0.0017 22.3 7.0 51 65-118 56-109 (117)
19 COG0092 RpsC Ribosomal protein 52.7 36 0.00079 28.6 5.3 101 39-155 25-128 (233)
20 PRK10597 DNA damage-inducible 52.2 81 0.0018 22.2 6.8 53 90-144 16-69 (81)
21 PF10500 SR-25: Nuclear RNA-sp 47.5 15 0.00033 30.7 2.3 24 34-57 157-183 (225)
22 cd02975 PfPDO_like_N Pyrococcu 43.1 1E+02 0.0022 22.0 5.9 40 77-117 22-61 (113)
23 cd02973 TRX_GRX_like Thioredox 43.0 63 0.0014 20.2 4.4 32 85-117 7-38 (67)
24 TIGR01297 CDF cation diffusion 41.7 1.9E+02 0.0041 23.4 10.0 71 38-118 193-266 (268)
25 KOG1603|consensus 41.5 46 0.00099 22.2 3.6 57 77-146 6-63 (73)
26 PF09650 PHA_gran_rgn: Putativ 39.2 45 0.00098 23.5 3.4 30 75-104 55-84 (87)
27 PRK04191 rps3p 30S ribosomal p 39.1 1.5E+02 0.0032 24.2 6.9 103 37-155 12-117 (207)
28 PRK10503 multidrug efflux syst 38.7 78 0.0017 31.7 6.1 71 39-116 114-187 (1040)
29 PF13192 Thioredoxin_3: Thiore 36.6 1.2E+02 0.0025 20.0 5.0 28 86-118 7-34 (76)
30 cd02957 Phd_like Phosducin (Ph 34.4 1.2E+02 0.0025 21.4 5.0 40 78-118 25-64 (113)
31 TIGR01008 rpsC_E_A ribosomal p 33.8 1.6E+02 0.0034 24.0 6.2 103 37-155 10-115 (195)
32 PRK11657 dsbG disulfide isomer 31.6 1.4E+02 0.0031 24.7 5.8 98 10-118 55-153 (251)
33 PRK05783 hypothetical protein; 30.6 40 0.00086 23.9 1.9 48 62-117 33-81 (84)
34 TIGR02610 PHA_gran_rgn putativ 30.6 60 0.0013 23.2 2.9 31 75-105 58-88 (91)
35 TIGR00412 redox_disulf_2 small 29.6 1.2E+02 0.0027 19.9 4.2 25 83-108 4-28 (76)
36 TIGR01608 citD citrate lyase a 29.6 90 0.002 22.6 3.6 48 88-144 38-85 (92)
37 KOG4656|consensus 29.1 48 0.001 27.8 2.4 22 96-118 21-42 (247)
38 PF14480 DNA_pol3_a_NI: DNA po 28.8 1.7E+02 0.0037 19.1 7.0 71 43-118 4-75 (76)
39 cd03026 AhpF_NTD_C TRX-GRX-lik 28.4 2E+02 0.0043 19.8 5.3 31 87-118 22-52 (89)
40 cd02947 TRX_family TRX family; 28.1 1.6E+02 0.0034 18.4 4.7 39 79-118 12-50 (93)
41 cd02989 Phd_like_TxnDC9 Phosdu 28.1 2E+02 0.0043 20.5 5.4 39 79-118 24-62 (113)
42 PF06857 ACP: Malonate decarbo 28.0 1.4E+02 0.0031 21.1 4.5 56 80-144 28-84 (87)
43 TIGR00741 yfiA ribosomal subun 27.3 59 0.0013 22.2 2.4 38 83-120 4-44 (95)
44 cd00307 RuBisCO_small_like Rib 26.1 1.4E+02 0.0029 21.2 4.0 47 93-143 2-52 (84)
45 COG0735 Fur Fe2+/Zn2+ uptake r 25.5 1.2E+02 0.0026 23.1 3.9 44 37-85 37-88 (145)
46 COG2217 ZntA Cation transport 24.9 1.3E+02 0.0028 29.2 4.8 62 79-147 3-65 (713)
47 PF13098 Thioredoxin_2: Thiore 23.8 96 0.0021 21.3 3.0 22 80-101 8-29 (112)
48 TIGR02830 spore_III_AG stage I 23.8 1.3E+02 0.0028 24.4 4.0 29 90-119 57-85 (186)
49 PF05768 DUF836: Glutaredoxin- 23.6 52 0.0011 22.2 1.5 21 83-103 4-24 (81)
50 PF00101 RuBisCO_small: Ribulo 23.0 2E+02 0.0044 20.8 4.6 48 92-143 13-66 (99)
51 PF03780 Asp23: Asp23 family; 22.9 2.1E+02 0.0046 19.8 4.7 27 91-118 77-105 (108)
52 PHA02516 W baseplate wedge sub 21.7 2.6E+02 0.0056 19.9 4.9 59 39-118 16-79 (103)
53 TIGR02183 GRXA Glutaredoxin, G 21.1 1.5E+02 0.0032 20.1 3.4 35 82-117 3-37 (86)
54 TIGR03143 AhpF_homolog putativ 21.0 2.1E+02 0.0045 26.3 5.3 62 41-111 448-509 (555)
55 PF01502 PRA-CH: Phosphoribosy 20.9 1.8E+02 0.004 20.1 3.8 27 64-92 42-68 (75)
No 1
>KOG3381|consensus
Probab=99.96 E-value=7.1e-29 Score=191.77 Aligned_cols=153 Identities=57% Similarity=0.917 Sum_probs=130.0
Q ss_pred CCCcccCCceeeeccCC-CCCCcccCCCcCCCcCCHHHHHHHhccCCCCCCCCCceeecceeeeeeeeeC---CC--CeE
Q psy281 5 GDVLENINPTLYSKCED-RPVTAEDQNDYITDEFDSREIFDLIRNIYDPEHPLTLEELHVVDLSLIQVNN---ET--NQI 78 (162)
Q Consensus 5 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~t~~~I~eaL~~V~DPEl~~~IVdLGlV~~v~I~~~d---~~--~~V 78 (162)
|+.|+|+||++|.+... |..++-.-+.-..+..+.+.+++.++.|.|||.|.++-+|+.|+.-.|++.+ ++ ..|
T Consensus 1 ~s~l~N~np~v~~~~~~~~r~~~s~~d~~~~~~~~~~~~~dlir~I~DPEhP~TLeqL~VV~ee~v~V~d~~~~~~~s~V 80 (161)
T KOG3381|consen 1 GSGLQNENPLVYPTRSRERRVTASEEDELLPDSEDAEEIFDLIRDIRDPEHPLTLEQLNVVSEEGVEVDDPNVGDEESYV 80 (161)
T ss_pred CCccccCCccccccccccccccccccccccCcchhHHHHHHHHhccCCCCCCccHHHccceeecceEeecCCCCCcceEE
Confidence 44599999999984333 3333222222333556788999999999999999999999999987775332 22 479
Q ss_pred EEEEEeCCCCCchHHHHHHHHHHHHHHhCCCceeEEEEEecCCCCCchhchhhcCCHHHHHHhccccchHHHHhhhccC
Q psy281 79 KVNFTPTIPHCSMATLIGLSIRVRLIRALPARFKVVVEITPGSHSTEFAINKQLADKERVAAALENSTLIGVINQCISR 157 (162)
Q Consensus 79 ~V~ltlT~p~Cp~~~~I~~~I~~aL~~~lpgv~~V~V~i~~~~h~~~~~w~~~l~~~Erv~aalen~~~~~~~~~~~~~ 157 (162)
+|.|++|.|+|+|+..|+..||-+|.+.||.-.+|+|.+..++|..+.+.|||++|||||+|||||..|+.+|++|+..
T Consensus 81 ~i~ftPTipHCSmaTlIGLcIrVkl~RsLp~rfkvdV~I~~GtH~tE~~vNKQLnDKERVaAA~EN~~L~~~v~~cl~~ 159 (161)
T KOG3381|consen 81 RITFTPTIPHCSMATLIGLCIRVKLLRSLPPRFKVDVYIKPGTHATEEAVNKQLNDKERVAAALENPNLLEVVNKCLPA 159 (161)
T ss_pred EEEeccCCCcchHHhhhhheeeeeeeecCCCceeEEEEEcCCCcCCHHHHHhhhccHHHHHHHhcChHHHHHHHHHhcc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999864
No 2
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=99.92 E-value=3.2e-25 Score=164.96 Aligned_cols=95 Identities=23% Similarity=0.346 Sum_probs=88.1
Q ss_pred CCcCCHHHHHHHhccCCCCCCCCCceeecceeeeeeeeeCCCCeEEEEEEeCCCCCchHHHHHHHHHHHHHHhCCCceeE
Q psy281 34 TDEFDSREIFDLIRNIYDPEHPLTLEELHVVDLSLIQVNNETNQIKVNFTPTIPHCSMATLIGLSIRVRLIRALPARFKV 113 (162)
Q Consensus 34 ~~~~t~~~I~eaL~~V~DPEl~~~IVdLGlV~~v~I~~~d~~~~V~V~ltlT~p~Cp~~~~I~~~I~~aL~~~lpgv~~V 113 (162)
..+.++++|+++|++|+|||+|+|||+|||||++++ ++.++.++|.|++|+++||+...|..++++++ +.++|++++
T Consensus 9 ~~~~~~~~i~~aL~~V~DPEi~idIvdLGLVy~v~i--~~~~~~v~v~mtlT~~gCP~~~~i~~~v~~al-~~~~~v~~v 85 (111)
T COG2151 9 AIKVTLEDILEALKTVIDPEIGIDIVDLGLVYEVDI--DDVDGLVKVKMTLTSPGCPLAEVIADQVEAAL-EEIPGVEDV 85 (111)
T ss_pred hhhhhHHHHHHHhhcCCCcccceeeEeeccEEEEEE--ecCCceEEEEEecCCCCCCccHHHHHHHHHHH-HhcCCcceE
Confidence 345669999999999999999999999999999999 33256899999999999999999999999999 789999999
Q ss_pred EEEEecCCCCCchhchhhcCCHH
Q psy281 114 VVEITPGSHSTEFAINKQLADKE 136 (162)
Q Consensus 114 ~V~i~~~~h~~~~~w~~~l~~~E 136 (162)
+|+++ |.|+|+++++++|
T Consensus 86 ~V~l~-----~~p~Wt~~~ms~e 103 (111)
T COG2151 86 EVELT-----LSPPWTPDRMSEE 103 (111)
T ss_pred EEEEE-----EcCCCchhhcCHH
Confidence 99999 9999999999987
No 3
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=99.86 E-value=4.4e-21 Score=152.71 Aligned_cols=99 Identities=19% Similarity=0.401 Sum_probs=89.4
Q ss_pred CCcCCCcCCHHHHHHHhccCCCCCCCCCceeecceeeeeeeeeC-CCC--eEEEEEEeCCCCCchHHHHHHHHHHHHHHh
Q psy281 30 NDYITDEFDSREIFDLIRNIYDPEHPLTLEELHVVDLSLIQVNN-ETN--QIKVNFTPTIPHCSMATLIGLSIRVRLIRA 106 (162)
Q Consensus 30 ~~~~~~~~t~~~I~eaL~~V~DPEl~~~IVdLGlV~~v~I~~~d-~~~--~V~V~ltlT~p~Cp~~~~I~~~I~~aL~~~ 106 (162)
++...+..++++|+++|++|+||++++|||+||+|+++.+ ++ +++ +|+|.|+||+|+|++...|+.+++++| ++
T Consensus 66 ~~~~~~~~~ee~V~eaL~tV~DPei~~nIVeLGlV~~I~I--d~~~~~~~~V~I~mtLt~p~c~~~~~L~~dV~~aL-~~ 142 (174)
T TIGR03406 66 PENADGEDNEDQVWEQLRTVYDPEIPVNIVDLGLVYGCRV--EKLGEGQFRVDIEMTLTAPGCGMGPVLVEDVEDKV-LA 142 (174)
T ss_pred CcCccccccHHHHHHHHcCCCCCCCCCChHHcCCeEEEEE--ecccCCCCEEEEEEEeCCCCCcHHHHHHHHHHHHH-Hh
Confidence 3445566788999999999999999999999999999999 32 013 899999999999999999999999999 78
Q ss_pred CCCceeEEEEEecCCCCCchhchhhcCCHH
Q psy281 107 LPARFKVVVEITPGSHSTEFAINKQLADKE 136 (162)
Q Consensus 107 lpgv~~V~V~i~~~~h~~~~~w~~~l~~~E 136 (162)
++|+.+|+|++. |+|+|+++++|+|
T Consensus 143 l~gV~~V~V~l~-----~dp~W~~~~~s~~ 167 (174)
T TIGR03406 143 VPNVDEVEVELV-----FDPPWSREMMSEA 167 (174)
T ss_pred CCCceeEEEEEE-----ecCCCChHHCCHH
Confidence 999999999999 9999999999986
No 4
>COG5133 Uncharacterized conserved protein [Function unknown]
Probab=99.82 E-value=4e-20 Score=142.99 Aligned_cols=126 Identities=57% Similarity=0.833 Sum_probs=113.9
Q ss_pred CcCCCcCCHHHHHHHhccCCCCCCCCCceeecceeeeeeeeeCC---C--CeEEEEEEeCCCCCchHHHHHHHHHHHHHH
Q psy281 31 DYITDEFDSREIFDLIRNIYDPEHPLTLEELHVVDLSLIQVNNE---T--NQIKVNFTPTIPHCSMATLIGLSIRVRLIR 105 (162)
Q Consensus 31 ~~~~~~~t~~~I~eaL~~V~DPEl~~~IVdLGlV~~v~I~~~d~---~--~~V~V~ltlT~p~Cp~~~~I~~~I~~aL~~ 105 (162)
.++.+.++.++|++.++.|.|||.|.++-.||.|.--+|.+.|+ + ..|+|.+++|.|+|+|+..|...||-.|.+
T Consensus 48 ~ee~d~id~qeiydLia~I~DPEHPltL~QLsVV~lEdi~v~D~~~~n~i~~v~v~itPTIpHCSmatlIGLcIrvrleR 127 (181)
T COG5133 48 NEEPDLIDQQEIYDLIADIRDPEHPLTLEQLSVVSLEDISVPDGIAPNVIRCVKVVITPTIPHCSMATLIGLCIRVRLER 127 (181)
T ss_pred cCCCCCcCHHHHHHHHHhcCCCCCCccHhhcceeeeccccccCCCCCCeeEEEEEEeccCCCchhHHHHhhhheeeeehh
Confidence 35566799999999999999999999999999998666643221 1 358999999999999999999999999999
Q ss_pred hCCCceeEEEEEecCCCCCchhchhhcCCHHHHHHhccccchHHHHhhhcc
Q psy281 106 ALPARFKVVVEITPGSHSTEFAINKQLADKERVAAALENSTLIGVINQCIS 156 (162)
Q Consensus 106 ~lpgv~~V~V~i~~~~h~~~~~w~~~l~~~Erv~aalen~~~~~~~~~~~~ 156 (162)
.+|.-+.|+|.+..++|..+.+.|+|++|||||+||-||.-|..+|+.|+.
T Consensus 128 ~lpprF~v~v~ikkGtH~se~qvNKQLnDKeRVaAAcENEqLL~v~~kml~ 178 (181)
T COG5133 128 HLPPRFHVQVHIKKGTHISERQVNKQLNDKERVAAACENEQLLDVMEKMLP 178 (181)
T ss_pred cCCCceeEEEEEecCCcccHHHHhhhhchHHHHHHhhchHHHHHHHHhhhh
Confidence 999999999999999999999999999999999999999999999999985
No 5
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=99.76 E-value=1.5e-18 Score=118.41 Aligned_cols=72 Identities=28% Similarity=0.386 Sum_probs=64.5
Q ss_pred HHHHHHHhccCCCCCCCCCceeecceeeeeeeeeCCCCeEEEEEEeCCCCCchHHHHHHHHHHHHHHhCCCceeEEE
Q psy281 39 SREIFDLIRNIYDPEHPLTLEELHVVDLSLIQVNNETNQIKVNFTPTIPHCSMATLIGLSIRVRLIRALPARFKVVV 115 (162)
Q Consensus 39 ~~~I~eaL~~V~DPEl~~~IVdLGlV~~v~I~~~d~~~~V~V~ltlT~p~Cp~~~~I~~~I~~aL~~~lpgv~~V~V 115 (162)
+++|+++|++|+||++|+||++||||+++.+ + +++|+|.|++++|+|++...|+++|+++| ++++|+.+|+|
T Consensus 1 k~~V~~aL~~v~dP~~~~~iv~~g~V~~i~i---~-~~~V~v~l~l~~~~~~~~~~l~~~i~~~l-~~l~gv~~V~V 72 (72)
T PF01883_consen 1 KQAVRDALKQVKDPELGKDIVELGMVRDISI---E-GGKVSVSLELPTPACPAAEPLREEIREAL-KALPGVKSVKV 72 (72)
T ss_dssp HHHHHHHHTT-BETTTSSBTTTTTSEEEEEE---C-TCEEEEEE--SSTTHTTHHHHHHHHHHHH-HTSTT-SEEEE
T ss_pred CHHHHHHHhCCCCCCCCCCHHHcCCeeEEEE---E-CCEEEEEEEECCCCchHHHHHHHHHHHHH-HhCCCCceEeC
Confidence 5899999999999999999999999999999 3 58999999999999999999999999999 69999998876
No 6
>TIGR02945 SUF_assoc FeS assembly SUF system protein. Members of this family belong to the broader Pfam family pfam01883, or Domain of Unknown Function DUF59. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here all are found in genomes that carry the FeS assembly SUF system. For 70 % of these species, the member of this protein family is found as part of the SUF locus, usually immediately downstream of the sufS gene.
Probab=99.74 E-value=2.4e-17 Score=118.94 Aligned_cols=89 Identities=21% Similarity=0.401 Sum_probs=82.9
Q ss_pred HHHHHHHhccCCCCCCCCCceeecceeeeeeeeeCCCCeEEEEEEeCCCCCchHHHHHHHHHHHHHHhCCCceeEEEEEe
Q psy281 39 SREIFDLIRNIYDPEHPLTLEELHVVDLSLIQVNNETNQIKVNFTPTIPHCSMATLIGLSIRVRLIRALPARFKVVVEIT 118 (162)
Q Consensus 39 ~~~I~eaL~~V~DPEl~~~IVdLGlV~~v~I~~~d~~~~V~V~ltlT~p~Cp~~~~I~~~I~~aL~~~lpgv~~V~V~i~ 118 (162)
+++|+++|++|.||+++++|+++|+|+++.+ ++++.|+|.|++++|+|+....++..++++| +.++|+.+|+|++.
T Consensus 3 ~~~I~~~L~~v~dP~l~~~lv~~g~V~~i~v---~~~~~v~i~l~l~~p~~~~~~~l~~~i~~al-~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 3 KDAVIEALKTVYDPEIPVNIYELGLIYDIDV---DDDGHVDIQMTLTAPNCPVAGSMPGEVENAV-RAVPGVGSVTVELV 78 (99)
T ss_pred HHHHHHHHcCCCCCCCCCCeecCCCeeEEEE---CCCCeEEEEEEECCCCCChHHHHHHHHHHHH-HhCCCCceEEEEEE
Confidence 5789999999999999999999999999998 3236999999999999999999999999999 78999999999999
Q ss_pred cCCCCCchhchhhcCCHH
Q psy281 119 PGSHSTEFAINKQLADKE 136 (162)
Q Consensus 119 ~~~h~~~~~w~~~l~~~E 136 (162)
..++|+++++++|
T Consensus 79 -----~~~~~~~~~~~~~ 91 (99)
T TIGR02945 79 -----WDPPWTPERMSEE 91 (99)
T ss_pred -----eeCCCChHHCCHH
Confidence 8899999999975
No 7
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=99.71 E-value=4.5e-17 Score=126.47 Aligned_cols=86 Identities=24% Similarity=0.341 Sum_probs=75.6
Q ss_pred CCCCCCC-CCceeecceeeeeeeeeCCCCeEEEEEEeCCCCCchHHHHHHHHHHHHHHhCCCceeEEEEEecCCCCCchh
Q psy281 49 IYDPEHP-LTLEELHVVDLSLIQVNNETNQIKVNFTPTIPHCSMATLIGLSIRVRLIRALPARFKVVVEITPGSHSTEFA 127 (162)
Q Consensus 49 V~DPEl~-~~IVdLGlV~~v~I~~~d~~~~V~V~ltlT~p~Cp~~~~I~~~I~~aL~~~lpgv~~V~V~i~~~~h~~~~~ 127 (162)
|.|||++ +||++||+|++|++ + +++|.|+|++|+++||+.+.|+++|+++| +++ |+.+|+|++. +.|+
T Consensus 1 v~DPEi~~~sIvdLG~Vr~V~v--~--gd~V~VtIt~Ty~gcpa~e~L~~~I~~aL-~~~-Gv~~V~V~i~-----~~p~ 69 (146)
T TIGR02159 1 VPDPEIPVVSVTDLGMVREVDV--D--GGGVVVKFTPTYSGCPALEVIRQDIRDAV-RAL-GVEVVEVSTS-----LDPP 69 (146)
T ss_pred CcCCCCCCCCchhcCCeeEEEE--E--CCEEEEEEEeCCCCCchHHHHHHHHHHHH-Hhc-CCCeEEEeEe-----eCCC
Confidence 7899999 89999999999999 3 46899999999999999999999999999 566 8999999999 9999
Q ss_pred chhhcCCHHHHHHhccccc
Q psy281 128 INKQLADKERVAAALENST 146 (162)
Q Consensus 128 w~~~l~~~Erv~aalen~~ 146 (162)
|+.++++++ -++.|+..+
T Consensus 70 Wt~d~it~~-gr~~l~~~g 87 (146)
T TIGR02159 70 WTTDWITED-AREKLREYG 87 (146)
T ss_pred CChHHCCHH-HHHHHHhcC
Confidence 999999984 444454444
No 8
>PRK11670 antiporter inner membrane protein; Provisional
Probab=99.32 E-value=9.6e-12 Score=108.87 Aligned_cols=79 Identities=9% Similarity=0.056 Sum_probs=73.5
Q ss_pred cCCHHHHHHHhccCCCCCCCCCceeecceeeeeeeeeCCCCeEEEEEEeCCCCCchHHHHHHHHHHHHHHhCCCceeEEE
Q psy281 36 EFDSREIFDLIRNIYDPEHPLTLEELHVVDLSLIQVNNETNQIKVNFTPTIPHCSMATLIGLSIRVRLIRALPARFKVVV 115 (162)
Q Consensus 36 ~~t~~~I~eaL~~V~DPEl~~~IVdLGlV~~v~I~~~d~~~~V~V~ltlT~p~Cp~~~~I~~~I~~aL~~~lpgv~~V~V 115 (162)
++.+++|+++|++|.||+++++||++|||+++.+ + +++|+|.+.+|+++||....++.+++++| +.++|+.+++|
T Consensus 11 ~~~~~~v~~~l~~v~~p~~~~~~~~~~~v~~~~~--~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 85 (369)
T PRK11670 11 EALRAMVAGTLANFQHPTLKHNLTTLKALHHVAL--L--DDTLHIELVMPFVWNSAFEELKEQCSAEL-LRITGAKAIDW 85 (369)
T ss_pred cchHHHHHHHHhcCCCCCCCCChhhhCCeeEEEE--e--CCEEEEEEEECCCCchHHHHHHHHHHHHH-HhcCCCceEEE
Confidence 4568999999999999999999999999999999 3 57999999999999999999999999999 78999999999
Q ss_pred EEec
Q psy281 116 EITP 119 (162)
Q Consensus 116 ~i~~ 119 (162)
++..
T Consensus 86 ~~~~ 89 (369)
T PRK11670 86 KLSH 89 (369)
T ss_pred EEee
Confidence 8873
No 9
>PRK11190 Fe/S biogenesis protein NfuA; Provisional
Probab=94.39 E-value=0.24 Score=40.14 Aligned_cols=71 Identities=18% Similarity=0.173 Sum_probs=53.6
Q ss_pred HHHHHHHhccCCCCCCCCCceeecceeeeeeeeeCCCCeEEEEEEeCCCCCchH-HHHHHHHHHHHHHhCC-CceeEEE
Q psy281 39 SREIFDLIRNIYDPEHPLTLEELHVVDLSLIQVNNETNQIKVNFTPTIPHCSMA-TLIGLSIRVRLIRALP-ARFKVVV 115 (162)
Q Consensus 39 ~~~I~eaL~~V~DPEl~~~IVdLGlV~~v~I~~~d~~~~V~V~ltlT~p~Cp~~-~~I~~~I~~aL~~~lp-gv~~V~V 115 (162)
.+.|.++|.+-.-|-|-.+ =|-|.=++| ++++.|+|.|.=.+.+||+. ..|+..|+..|++.+| ++..|.-
T Consensus 108 ~~~i~~~l~~~irP~l~~d---GGdielv~v---~~~~~v~v~l~GaC~gC~~s~~Tl~~~Ie~~l~~~~p~~i~~v~~ 180 (192)
T PRK11190 108 MERVEYVLQSQINPQLAGH---GGRVSLMEI---TEDGYAILQFGGGCNGCSMVDVTLKEGIEKQLLNEFPGELKGVRD 180 (192)
T ss_pred HHHHHHHHHhccChhHHhc---CCcEEEEEE---cCCCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCHhhceEEE
Confidence 6778888887677877654 455555666 33568899999999999995 5677799999988888 7766543
No 10
>TIGR03341 YhgI_GntY IscR-regulated protein YhgI. IscR (TIGR02010) is an iron-sulfur cluster-binding transcriptional regulator (see Genome Property GenProp0138). Members of this protein family include YhgI, whose expression is under control of IscR, and show sequence similarity to IscA, a known protein of iron-sulfur cluster biosynthesis. These two lines of evidence strongly suggest a role as an iron-sulfur cluster biosynthesis protein. An older study designated this protein GntY and suggested a role for it and for the product of an adjacent gene, based on complementation studies, in gluconate utilization.
Probab=93.67 E-value=0.3 Score=39.47 Aligned_cols=71 Identities=17% Similarity=0.175 Sum_probs=52.6
Q ss_pred HHHHHHHhccCCCCCCCCCceeecceeeeeeeeeCCCCeEEEEEEeCCCCCchH-HHHHHHHHHHHHHhCCCceeEEE
Q psy281 39 SREIFDLIRNIYDPEHPLTLEELHVVDLSLIQVNNETNQIKVNFTPTIPHCSMA-TLIGLSIRVRLIRALPARFKVVV 115 (162)
Q Consensus 39 ~~~I~eaL~~V~DPEl~~~IVdLGlV~~v~I~~~d~~~~V~V~ltlT~p~Cp~~-~~I~~~I~~aL~~~lpgv~~V~V 115 (162)
.+.|.++|..-.-|-+-.+ =|=|.=++| + +++.|+|.|.=.+.+||+. ..++..|+..|++.+|++.+|..
T Consensus 107 ~~~i~~~l~~~irP~l~~d---GGdielv~v--~-~~~~v~v~l~GaC~gC~~s~~Tl~~~ie~~l~~~~p~v~~V~~ 178 (190)
T TIGR03341 107 EERINYVLQSEINPQLASH---GGKVTLVEI--T-DDGVAVLQFGGGCNGCSMVDVTLKDGVEKTLLERFPELKGVRD 178 (190)
T ss_pred HHHHHHHHHhccCHHHHhc---CCceEEEEE--c-CCCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCCcceEEE
Confidence 6778888875555665443 455555566 2 2468899999999999995 66788999999888998876544
No 11
>PF01106 NifU: NifU-like domain; InterPro: IPR001075 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents the C-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal (IPR002871 from INTERPRO) and a C-terminal domain []. These domains exist either together or on different polypeptides, both domains being found in organisms that do not fix nitrogen (e.g. yeast), so they have a broader significance in the cell than nitrogen fixation. ; GO: 0005506 iron ion binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly; PDB: 2JNV_A 2Z51_A 1TH5_A 1VEH_A 1XHJ_A.
Probab=91.35 E-value=1.1 Score=30.20 Aligned_cols=48 Identities=21% Similarity=0.267 Sum_probs=36.6
Q ss_pred cceeeeeeeeeCCCCeEEEEEEeCCCCCchH-HHHHHHHHHHHHHhCCCceeE
Q psy281 62 HVVDLSLIQVNNETNQIKVNFTPTIPHCSMA-TLIGLSIRVRLIRALPARFKV 113 (162)
Q Consensus 62 GlV~~v~I~~~d~~~~V~V~ltlT~p~Cp~~-~~I~~~I~~aL~~~lpgv~~V 113 (162)
|=|.=+++ + ++.|+|.|.=.+.+||+. ..++..|++.|++.+|.+.+|
T Consensus 17 Gdv~lv~v--~--~~~V~V~l~GaC~gC~~s~~Tl~~~Ie~~L~~~~~~v~~V 65 (68)
T PF01106_consen 17 GDVELVDV--D--DGVVYVRLTGACSGCPSSDMTLKQGIEQALREAVPEVKRV 65 (68)
T ss_dssp EEEEEEEE--E--TTEEEEEEESSCCSSCCHHHHHHHHHHHHHHHHSTT-SEE
T ss_pred CcEEEEEe--c--CCEEEEEEEeCCCCCCCHHHHHHHHHHHHHHHHCCCCceE
Confidence 44444556 3 459999999999999995 567799999998889987665
No 12
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=89.83 E-value=0.61 Score=29.85 Aligned_cols=57 Identities=16% Similarity=0.244 Sum_probs=38.7
Q ss_pred eCCCCCchHHHHHHHHHHHHHHhCCCceeEEEEEecCCCCCchhchhhcCCHHHHHHhccccc
Q psy281 84 PTIPHCSMATLIGLSIRVRLIRALPARFKVVVEITPGSHSTEFAINKQLADKERVAAALENST 146 (162)
Q Consensus 84 lT~p~Cp~~~~I~~~I~~aL~~~lpgv~~V~V~i~~~~h~~~~~w~~~l~~~Erv~aalen~~ 146 (162)
+.+..|+.. ...|+++| +.++||.+++|++. .+.-.-.|++...+.+.+..+++.-+
T Consensus 4 v~~m~C~~C---~~~v~~~l-~~~~GV~~v~vd~~--~~~v~v~~~~~~~~~~~i~~~i~~~G 60 (62)
T PF00403_consen 4 VPGMTCEGC---AKKVEKAL-SKLPGVKSVKVDLE--TKTVTVTYDPDKTSIEKIIEAIEKAG 60 (62)
T ss_dssp EESTTSHHH---HHHHHHHH-HTSTTEEEEEEETT--TTEEEEEESTTTSCHHHHHHHHHHTT
T ss_pred ECCcccHHH---HHHHHHHH-hcCCCCcEEEEECC--CCEEEEEEecCCCCHHHHHHHHHHhC
Confidence 344555544 35788899 78999999999876 23334466666666778888877644
No 13
>COG0694 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]
Probab=88.07 E-value=3.4 Score=29.93 Aligned_cols=75 Identities=13% Similarity=0.187 Sum_probs=51.1
Q ss_pred HHHHHHHhccCCCCCCCCCceeecceeeeeeeeeCCCCeEEEEEEeCCCCCchH-HHHHHHHHHHHHHhCCCceeEEEEE
Q psy281 39 SREIFDLIRNIYDPEHPLTLEELHVVDLSLIQVNNETNQIKVNFTPTIPHCSMA-TLIGLSIRVRLIRALPARFKVVVEI 117 (162)
Q Consensus 39 ~~~I~eaL~~V~DPEl~~~IVdLGlV~~v~I~~~d~~~~V~V~ltlT~p~Cp~~-~~I~~~I~~aL~~~lpgv~~V~V~i 117 (162)
.++|.+.|.+=.-|-+-. +=|=|.=+.| +..+|.|.+.|.=.+.+||.. -.++..|++.|+..+|++..|..-+
T Consensus 11 ~e~v~~~l~~~irP~l~~---dGGdve~~~i--~~~~g~V~l~l~GaC~gC~sS~~TLk~gIE~~L~~~i~ev~~V~~v~ 85 (93)
T COG0694 11 LERVEEVLDEKIRPQLAM---DGGDVELVGI--DEEDGVVYLRLGGACSGCPSSTVTLKNGIERQLKEEIPEVKEVEQVT 85 (93)
T ss_pred HHHHHHHHHhccCcceec---cCCeEEEEEE--ecCCCeEEEEeCCcCCCCcccHHHHHHHHHHHHHHhCCccceEEEcc
Confidence 344455555444455443 3455555556 333578999999999999994 6678889999988889887776644
Q ss_pred e
Q psy281 118 T 118 (162)
Q Consensus 118 ~ 118 (162)
.
T Consensus 86 ~ 86 (93)
T COG0694 86 E 86 (93)
T ss_pred C
Confidence 3
No 14
>TIGR02000 NifU_proper Fe-S cluster assembly protein NifU. Three different but partially homologous Fe-S cluster assembly systems have been described: Isc, Suf, and Nif. The latter is associated with donation of an Fe-S cluster to nitrogenase in a number of nitrogen-fixing species. NifU, described here, consists of an N-terminal domain (pfam01592) and a C-terminal domain (pfam01106). Homologs with an equivalent domain archictecture from Helicobacter and Campylobacter, however, are excluded from this model by a high trusted cutoff. The model, therefore, is specific for NifU involved in nitrogenase maturation. The related model TIGR01999 homologous to the N-terminus of this model describes IscU from the Isc system as in E. coli, Saccharomyces cerevisiae, and Homo sapiens.
Probab=75.62 E-value=15 Score=31.53 Aligned_cols=68 Identities=22% Similarity=0.157 Sum_probs=48.3
Q ss_pred HHHHHHHhccCCCCCCCCCceeecceeeeeeeeeCCCCeEEEEEEeCCCCCchHHHHHHHHHHHHHHhCCCceeEE
Q psy281 39 SREIFDLIRNIYDPEHPLTLEELHVVDLSLIQVNNETNQIKVNFTPTIPHCSMATLIGLSIRVRLIRALPARFKVV 114 (162)
Q Consensus 39 ~~~I~eaL~~V~DPEl~~~IVdLGlV~~v~I~~~d~~~~V~V~ltlT~p~Cp~~~~I~~~I~~aL~~~lpgv~~V~ 114 (162)
.+.|-++| +-.-|-|-.+ =|-|.=++| + ++.|+|.|.=...+||+...=-..|++.|+..+|++..|.
T Consensus 221 ~~~v~~~l-~~irP~l~~d---GGdv~lv~v--~--~~~v~v~l~GaC~gC~~s~~Tl~~Ie~~l~~~~p~~~~V~ 288 (290)
T TIGR02000 221 IQLIQKVL-EEVRPVLQAD---GGDVELYDV--D--GKIVYVVLTGACSGCSMSTMTLKGIQQRLRERLGEFVVVE 288 (290)
T ss_pred HHHHHHHH-HHhCchHhhc---CCcEEEEEE--e--CCEEEEEEeeCCCCCcchHHHHHHHHHHHHHhCCCceEEE
Confidence 46667777 4555766554 555666666 3 4799999999999999965433349999988899876553
No 15
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=73.72 E-value=12 Score=24.99 Aligned_cols=63 Identities=14% Similarity=0.226 Sum_probs=41.4
Q ss_pred EEEEeCCCCCchHHHHHHHHHHHHHHhCCCceeEEEEEecCCCCCchhchhhcCCHHHHHHhccccchH
Q psy281 80 VNFTPTIPHCSMATLIGLSIRVRLIRALPARFKVVVEITPGSHSTEFAINKQLADKERVAAALENSTLI 148 (162)
Q Consensus 80 V~ltlT~p~Cp~~~~I~~~I~~aL~~~lpgv~~V~V~i~~~~h~~~~~w~~~l~~~Erv~aalen~~~~ 148 (162)
..+.+....|.... ..|+.+| +.++|+.+|+|.+..+.. .-.......+.+.+..|++..++.
T Consensus 4 ~~l~v~~MtC~~C~---~~V~~al-~~v~gv~~v~v~l~~~~~--~V~~d~~~~~~~~i~~ai~~aGy~ 66 (71)
T COG2608 4 TTLKVEGMTCGHCV---KTVEKAL-EEVDGVASVDVDLEKGTA--TVTFDSNKVDIEAIIEAIEDAGYK 66 (71)
T ss_pred EEEEECCcCcHHHH---HHHHHHH-hcCCCeeEEEEEcccCeE--EEEEcCCcCCHHHHHHHHHHcCCC
Confidence 45566666776553 4788889 789999999999873221 112333345677888887766653
No 16
>PF01545 Cation_efflux: Cation efflux family; InterPro: IPR002524 Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are considered to be efflux pumps that remove these ions from cells [, ], however others are implicated in ion uptake []. The family has six predicted transmembrane domains. Members of the family are variable in length because of variably sized inserts, often containing low-complexity sequence.; GO: 0008324 cation transmembrane transporter activity, 0006812 cation transport, 0055085 transmembrane transport, 0016021 integral to membrane; PDB: 3BYP_B 3BYR_A 3H90_B 2QFI_B 2ZZT_A.
Probab=68.29 E-value=34 Score=27.94 Aligned_cols=70 Identities=24% Similarity=0.240 Sum_probs=43.2
Q ss_pred HHHHHHHhccCCCCCCCCCceeecceeeeeeeeeCCCCeEEEEEEeC-CCCCch--HHHHHHHHHHHHHHhCCCceeEEE
Q psy281 39 SREIFDLIRNIYDPEHPLTLEELHVVDLSLIQVNNETNQIKVNFTPT-IPHCSM--ATLIGLSIRVRLIRALPARFKVVV 115 (162)
Q Consensus 39 ~~~I~eaL~~V~DPEl~~~IVdLGlV~~v~I~~~d~~~~V~V~ltlT-~p~Cp~--~~~I~~~I~~aL~~~lpgv~~V~V 115 (162)
.+++.+.+++ .|+. .+ +++++++-.+ .+...+.+.+. .+.++. ...+.+++++.++++++++.++.|
T Consensus 207 ~~~i~~~i~~--~~~v----~~---v~~~~~~~~g-~~~~~v~i~v~v~~~~~v~~~~~i~~~i~~~l~~~~~~i~~v~I 276 (284)
T PF01545_consen 207 VEKIRRIIES--VPGV----IE---VHDLRVWQVG-RNKYVVEIHVQVDPDMSVEEAHEIRERIEKRLREKFPGIYDVTI 276 (284)
T ss_dssp HHHHHHHHHH--TSS-----SE---EEEEEEEEET-T-EEEEEEEEEETTTSBHHHHHHHHHHHHHHHHHHSTTCEEEEE
T ss_pred hhHHHHhhcc--CCce----Ee---ccceEEEEec-CCcEEEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhCCCcEEEEE
Confidence 4677777766 2221 12 3444443112 22444444444 344555 467899999999888999999999
Q ss_pred EEe
Q psy281 116 EIT 118 (162)
Q Consensus 116 ~i~ 118 (162)
++.
T Consensus 277 ~~~ 279 (284)
T PF01545_consen 277 HIE 279 (284)
T ss_dssp EEE
T ss_pred EEE
Confidence 887
No 17
>PF09580 Spore_YhcN_YlaJ: Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ); InterPro: IPR019076 This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Probab=54.89 E-value=66 Score=24.74 Aligned_cols=55 Identities=15% Similarity=0.081 Sum_probs=40.5
Q ss_pred ecceeeeeeeeeCCCCeEEEEEEeCCCCCchHHHHHHHHHHHHHHhCCCceeEEEEEe
Q psy281 61 LHVVDLSLIQVNNETNQIKVNFTPTIPHCSMATLIGLSIRVRLIRALPARFKVVVEIT 118 (162)
Q Consensus 61 LGlV~~v~I~~~d~~~~V~V~ltlT~p~Cp~~~~I~~~I~~aL~~~lpgv~~V~V~i~ 118 (162)
+.=|.+..+-+. +..+.|-+.+... -.....|+..|+.+++...|++.+|.|.-+
T Consensus 87 ~~~V~~A~vvv~--~~~a~Vav~~~~~-~~~~~~i~~~V~~~v~~~~p~~~~V~Vs~D 141 (177)
T PF09580_consen 87 VPGVEDATVVVT--DDNAYVAVDLDFN-RFNTKKIKKKVEKAVKSADPRIYNVYVSTD 141 (177)
T ss_pred CCCceEEEEEEE--CCEEEEEEEeccc-ccchhHHHHHHHHHHHHhCCCccEEEEEcC
Confidence 444565555323 5789999988844 677899999999999777888888888543
No 18
>PF10646 Germane: Sporulation and spore germination; InterPro: IPR019606 The GerMN domain is a region of approximately 100 residues that is found, duplicated, in the Bacillus GerM protein and is implicated in both sporulation and spore germination. It is also found in lipoprotein LpqB. The domain is present in a number of different bacterial species both alone and in association with other domains such as Gmad1 and Gmad2. It is predicted to have a novel alpha-beta fold.
Probab=53.44 E-value=77 Score=22.30 Aligned_cols=51 Identities=20% Similarity=0.282 Sum_probs=36.8
Q ss_pred eeeeeeeeCCCCeEEEEEEeCC---CCCchHHHHHHHHHHHHHHhCCCceeEEEEEe
Q psy281 65 DLSLIQVNNETNQIKVNFTPTI---PHCSMATLIGLSIRVRLIRALPARFKVVVEIT 118 (162)
Q Consensus 65 ~~v~I~~~d~~~~V~V~ltlT~---p~Cp~~~~I~~~I~~aL~~~lpgv~~V~V~i~ 118 (162)
.++.+ + +++.++|+|.-.. .+-.....+..+|..-+.+.++++.+|++.+.
T Consensus 56 ~~v~~--~-~~~~~~Vd~s~~~~~~~~~~~~~~~~~~i~~Tl~~~~~~v~~V~i~vd 109 (117)
T PF10646_consen 56 NSVTV--D-DGNTLTVDFSSEFLNFLGSSQEALLLAQIVNTLTEQFPGVKKVQILVD 109 (117)
T ss_pred eeEEE--C-CCCEEEEECCHHHhhcCChHHHHHHHHHHHHHHHHhcCCccEEEEEEC
Confidence 36666 3 3558888886643 34445677888888888448999999999876
No 19
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=52.67 E-value=36 Score=28.60 Aligned_cols=101 Identities=16% Similarity=0.209 Sum_probs=62.0
Q ss_pred HHHHHHHhccCCCCCCCCCceeecceeeeeeeeeCCCCeEEEEEEeCCCCCchH--HHHHHHHHHHHHHhCCCceeEEEE
Q psy281 39 SREIFDLIRNIYDPEHPLTLEELHVVDLSLIQVNNETNQIKVNFTPTIPHCSMA--TLIGLSIRVRLIRALPARFKVVVE 116 (162)
Q Consensus 39 ~~~I~eaL~~V~DPEl~~~IVdLGlV~~v~I~~~d~~~~V~V~ltlT~p~Cp~~--~~I~~~I~~aL~~~lpgv~~V~V~ 116 (162)
...|.+.|.+ .+...| +..++|. -....+.|.+...-|+--.+ -.=-+.++..| +.+.|..+|+|+
T Consensus 25 d~kIre~l~k--------~l~~Ag-~s~veIe--R~~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l-~k~~g~~~v~I~ 92 (233)
T COG0092 25 DLKIREFLEK--------ELSNAG-ISGVEIE--RTPKGTRVTIHAARPGLVIGKKGSNIEKLRKEL-EKLFGKENVQIN 92 (233)
T ss_pred HHHHHHHHHH--------HHHhCC-cceEEEE--ecCCceEEEEEeCCCcceEcCCCccHHHHHHHH-HHHhCCCCceEE
Confidence 4455666653 223344 3456663 22457888888888876552 22233445555 444566678888
Q ss_pred EecCCCCCchhchhhcCCHHHHHHhcccc-chHHHHhhhc
Q psy281 117 ITPGSHSTEFAINKQLADKERVAAALENS-TLIGVINQCI 155 (162)
Q Consensus 117 i~~~~h~~~~~w~~~l~~~Erv~aalen~-~~~~~~~~~~ 155 (162)
+. .-..|..+.++... +++.+||+. +.|+++.+.+
T Consensus 93 i~---EV~~peL~A~lvA~-~IA~qLErrv~FRRA~k~ai 128 (233)
T COG0092 93 IE---EVKKPELDAQLVAE-SIAQQLERRVSFRRAMKRAI 128 (233)
T ss_pred EE---EcCCCCcCHHHHHH-HHHHHHHcccHHHHHHHHHH
Confidence 76 33677888888877 999999986 4666666554
No 20
>PRK10597 DNA damage-inducible protein I; Provisional
Probab=52.17 E-value=81 Score=22.22 Aligned_cols=53 Identities=19% Similarity=0.288 Sum_probs=32.9
Q ss_pred chHHHHHHHHHHHHHHhCCCce-eEEEEEecCCCCCchhchhhcCCHHHHHHhccc
Q psy281 90 SMATLIGLSIRVRLIRALPARF-KVVVEITPGSHSTEFAINKQLADKERVAAALEN 144 (162)
Q Consensus 90 p~~~~I~~~I~~aL~~~lpgv~-~V~V~i~~~~h~~~~~w~~~l~~~Erv~aalen 144 (162)
...+.|..++..+|...+|... .|.|+.....+-. --.-.-.+|+++...||.
T Consensus 16 ga~~AL~~EL~kRl~~~fPd~~~~v~Vr~~s~n~ls--v~g~~k~dK~~i~eiLqE 69 (81)
T PRK10597 16 GAIDALAGELSRRIQYAFPDNEGHVSVRYAAANNLS--VIGATKEDKDRISEILQE 69 (81)
T ss_pred hHHHHHHHHHHHHHHhhCCCCCccEEEeecCCCceE--ecCCCcchHHHHHHHHHH
Confidence 4567799999999988888764 5777766322211 001112267888777764
No 21
>PF10500 SR-25: Nuclear RNA-splicing-associated protein; InterPro: IPR019532 SR-25, otherwise known as ADP-ribosylation factor-like factor 6-interacting protein 4, is expressed in virtually all tissue types. At the N terminus there is a repeat of serine-arginine (SR repeat), and towards the middle of the protein there are clusters of both serines and of basic amino acids. The presence of many nuclear localisation signals strongly implies that this is a nuclear protein that may contribute to RNA splicing []. SR-25 is also implicated, along with heat-shock-protein-27, as a mediator in the Rac1 (GTPase ras-related C3 botulinum toxin substrate 1; also see IPR019093 from INTERPRO) signalling pathway [].
Probab=47.52 E-value=15 Score=30.68 Aligned_cols=24 Identities=29% Similarity=0.398 Sum_probs=19.0
Q ss_pred CCcCCHHHH---HHHhccCCCCCCCCC
Q psy281 34 TDEFDSREI---FDLIRNIYDPEHPLT 57 (162)
Q Consensus 34 ~~~~t~~~I---~eaL~~V~DPEl~~~ 57 (162)
+.++|+++. ...++.|+|||.|+.
T Consensus 157 m~PmTkEEyearQSvIRrVvDpETGRt 183 (225)
T PF10500_consen 157 MAPMTKEEYEARQSVIRRVVDPETGRT 183 (225)
T ss_pred cCCCCHHHHHHHHhhheeeecCCCCce
Confidence 446888776 467899999999984
No 22
>cd02975 PfPDO_like_N Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO)-like family, N-terminal TRX-fold subdomain; composed of proteins with similarity to PfPDO, a redox active thermostable protein believed to be the archaeal counterpart of bacterial DsbA and eukaryotic protein disulfide isomerase (PDI), which are both involved in oxidative protein folding. PfPDO contains two redox active CXXC motifs in two contiguous TRX-fold subdomains. The active site in the N-terminal TRX-fold subdomain is required for isomerase but not for reductase activity of PfPDO. The exclusive presence of PfPDO-like proteins in extremophiles may suggest that they have a special role in adaptation to extreme conditions.
Probab=43.15 E-value=1e+02 Score=22.03 Aligned_cols=40 Identities=3% Similarity=-0.028 Sum_probs=26.6
Q ss_pred eEEEEEEeCCCCCchHHHHHHHHHHHHHHhCCCceeEEEEE
Q psy281 77 QIKVNFTPTIPHCSMATLIGLSIRVRLIRALPARFKVVVEI 117 (162)
Q Consensus 77 ~V~V~ltlT~p~Cp~~~~I~~~I~~aL~~~lpgv~~V~V~i 117 (162)
.+.+.+.++.++|+....++.-+++.. +..+.+.=+.|++
T Consensus 22 ~~~vvv~f~a~wC~~C~~~~~~l~~la-~~~~~i~~~~vd~ 61 (113)
T cd02975 22 PVDLVVFSSKEGCQYCEVTKQLLEELS-ELSDKLKLEIYDF 61 (113)
T ss_pred CeEEEEEeCCCCCCChHHHHHHHHHHH-HhcCceEEEEEeC
Confidence 455667778899999988888887766 4444443334443
No 23
>cd02973 TRX_GRX_like Thioredoxin (TRX)-Glutaredoxin (GRX)-like family; composed of archaeal and bacterial proteins that show similarity to both TRX and GRX, including the C-terminal TRX-fold subdomain of Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). All members contain a redox-active CXXC motif and may function as PDOs. The archaeal proteins Mj0307 and Mt807 show structures more similar to GRX, but activities more similar to TRX. Some members of the family are similar to PfPDO in that they contain a second CXXC motif located in a second TRX-fold subdomain at the N-terminus; the superimposable N- and C-terminal TRX subdomains form a compact structure. PfPDO is postulated to be the archaeal counterpart of bacterial DsbA and eukaryotic protein disulfide isomerase (PDI). The C-terminal CXXC motif of PfPDO is required for its oxidase, reductase and isomerase activities. Also included in the family is the C-terminal TRX-fold subdomain of the N-terminal domain (NTD) of bacteri
Probab=43.01 E-value=63 Score=20.22 Aligned_cols=32 Identities=9% Similarity=0.051 Sum_probs=18.7
Q ss_pred CCCCCchHHHHHHHHHHHHHHhCCCceeEEEEE
Q psy281 85 TIPHCSMATLIGLSIRVRLIRALPARFKVVVEI 117 (162)
Q Consensus 85 T~p~Cp~~~~I~~~I~~aL~~~lpgv~~V~V~i 117 (162)
+.++||....+..-+++.. ...+++.-..+++
T Consensus 7 ~~~~C~~C~~~~~~l~~l~-~~~~~i~~~~id~ 38 (67)
T cd02973 7 VSPTCPYCPDAVQAANRIA-ALNPNISAEMIDA 38 (67)
T ss_pred ECCCCCCcHHHHHHHHHHH-HhCCceEEEEEEc
Confidence 5678888777776666554 3344444444443
No 24
>TIGR01297 CDF cation diffusion facilitator family transporter. This model describes a broadly distributed family of transporters, a number of which have been shown to transport divalent cations of cobalt, cadmium and/or zinc. The family has six predicted transmembrane domains. Members of the family are variable in length because of variably sized inserts, often containing low-complexity sequence.
Probab=41.71 E-value=1.9e+02 Score=23.40 Aligned_cols=71 Identities=18% Similarity=0.229 Sum_probs=42.4
Q ss_pred CHHHHHHHhccCCCCCCCCCceeecceeeeeeeeeCCCCeEEEEEEeC-CCCCchH--HHHHHHHHHHHHHhCCCceeEE
Q psy281 38 DSREIFDLIRNIYDPEHPLTLEELHVVDLSLIQVNNETNQIKVNFTPT-IPHCSMA--TLIGLSIRVRLIRALPARFKVV 114 (162)
Q Consensus 38 t~~~I~eaL~~V~DPEl~~~IVdLGlV~~v~I~~~d~~~~V~V~ltlT-~p~Cp~~--~~I~~~I~~aL~~~lpgv~~V~ 114 (162)
..+++.+.+.++ |+. .++.+ ++++-.+ .+...+++.+. .+.++.. ..+...+++++++.++++.+|.
T Consensus 193 ~~~~i~~~i~~~--~~v-~~v~~------~~~~~~G-~~~~~v~~~v~v~~~~~~~~ah~i~~~i~~~i~~~~~~v~~v~ 262 (268)
T TIGR01297 193 DLEEIKKAILSI--PGV-KGVHD------LHIWRIG-PGKLFLDVHVVVDPDLDLKQAHDIALEIEREILKRHPGIEHVT 262 (268)
T ss_pred cHHHHHHHHhcC--CCc-ccceE------eEEEEcC-CCCEEEEEEEEECCCCChhHHHHHHHHHHHHHHHhcCCCCeEE
Confidence 467788887743 433 23333 3332112 22444444333 3456654 6788899998877789999888
Q ss_pred EEEe
Q psy281 115 VEIT 118 (162)
Q Consensus 115 V~i~ 118 (162)
|++.
T Consensus 263 ih~e 266 (268)
T TIGR01297 263 IQVE 266 (268)
T ss_pred EEeC
Confidence 8875
No 25
>KOG1603|consensus
Probab=41.53 E-value=46 Score=22.21 Aligned_cols=57 Identities=14% Similarity=0.211 Sum_probs=38.9
Q ss_pred eEEEEEEeCCCCCchHHHHHHHHHHHHHHhCCCceeEEEEEecCCCCCchhch-hhcCCHHHHHHhccccc
Q psy281 77 QIKVNFTPTIPHCSMATLIGLSIRVRLIRALPARFKVVVEITPGSHSTEFAIN-KQLADKERVAAALENST 146 (162)
Q Consensus 77 ~V~V~ltlT~p~Cp~~~~I~~~I~~aL~~~lpgv~~V~V~i~~~~h~~~~~w~-~~l~~~Erv~aalen~~ 146 (162)
.+...+.+++.+|.- .|+..+ +.+.||.++.+.+.. ...+ ..-+++..+.+.+++.+
T Consensus 6 ~~v~kv~~~C~gc~~------kV~~~l-~~~~GV~~v~id~~~------~kvtV~g~~~p~~vl~~l~k~~ 63 (73)
T KOG1603|consen 6 TVVLKVNMHCEGCAR------KVKRVL-QKLKGVESVDIDIKK------QKVTVKGNVDPVKLLKKLKKTG 63 (73)
T ss_pred EEEEEECcccccHHH------HHHHHh-hccCCeEEEEecCCC------CEEEEEEecCHHHHHHHHHhcC
Confidence 455667778888854 678888 789999999888751 1111 22267778887777644
No 26
>PF09650 PHA_gran_rgn: Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn); InterPro: IPR013433 Proteins in this entry are encoded by genes involved in either polyhydroxyalkanoic acid (PHA) biosynthesis or utilisation, including proteins at found at the surface of PHA granules. These proteins have so far been predominantly found in the Pseudomonadales, Xanthomonadales, and Vibrionales, all of which belong to the Gammaproteobacteria.
Probab=39.17 E-value=45 Score=23.45 Aligned_cols=30 Identities=10% Similarity=0.102 Sum_probs=27.1
Q ss_pred CCeEEEEEEeCCCCCchHHHHHHHHHHHHH
Q psy281 75 TNQIKVNFTPTIPHCSMATLIGLSIRVRLI 104 (162)
Q Consensus 75 ~~~V~V~ltlT~p~Cp~~~~I~~~I~~aL~ 104 (162)
++.|.|.+.|+-..-|++..|+..|+..|.
T Consensus 55 ~d~v~l~v~Lg~Ll~~f~~~Ie~~I~~~Ld 84 (87)
T PF09650_consen 55 DDHVRLEVKLGFLLSPFKGKIEQEIEKNLD 84 (87)
T ss_pred CCEEEEEEEcHHHHHHHHHHHHHHHHHHHH
Confidence 579999999999999999999999999884
No 27
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=39.11 E-value=1.5e+02 Score=24.18 Aligned_cols=103 Identities=11% Similarity=0.014 Sum_probs=59.7
Q ss_pred CCHHHHHHHhccCCCCCCCCCceeecceeeeeeeeeCCCCeEEEEEEeCCCCCchH--HHHHHHHHHHHHHhCCCceeEE
Q psy281 37 FDSREIFDLIRNIYDPEHPLTLEELHVVDLSLIQVNNETNQIKVNFTPTIPHCSMA--TLIGLSIRVRLIRALPARFKVV 114 (162)
Q Consensus 37 ~t~~~I~eaL~~V~DPEl~~~IVdLGlV~~v~I~~~d~~~~V~V~ltlT~p~Cp~~--~~I~~~I~~aL~~~lpgv~~V~ 114 (162)
+....|.+.|++...+. -|..|+|. ...+.+.|.+....|+--.+ ..=-..++..| +...+..++.
T Consensus 12 ~~~~~irefi~~~~~~A---------gIs~IeI~--Rt~~~i~I~I~ta~PGivIGk~G~~I~klk~~L-kk~~~~~~v~ 79 (207)
T PRK04191 12 LKKVMIDEYLAKELYRA---------GYGGMEIK--KTPLGTRITIYAERPGMVIGRGGKNIRELTEIL-EKKFGLENPQ 79 (207)
T ss_pred hHHHHHHHHHHhhhhhc---------ceeEEEEE--EcCCcEEEEEEECCCCeEECCCchhHHHHHHHH-HHHhCCCcee
Confidence 45677788887644332 35566663 21346777777777764331 11124445555 3344555566
Q ss_pred EEEecCCCCCchhchhhcCCHHHHHHhccccc-hHHHHhhhc
Q psy281 115 VEITPGSHSTEFAINKQLADKERVAAALENST-LIGVINQCI 155 (162)
Q Consensus 115 V~i~~~~h~~~~~w~~~l~~~Erv~aalen~~-~~~~~~~~~ 155 (162)
+++. .-..|..++++... +++.+||++- .|+++++++
T Consensus 80 I~v~---ev~~p~~~a~~vA~-~ia~qLe~r~~fRra~k~~i 117 (207)
T PRK04191 80 IDVK---EVENPELNARVVAF-RLANALERGWHFRRAAHSAI 117 (207)
T ss_pred EEEE---EEeCCCcCHHHHHH-HHHHHHHccchHHHHHHHHH
Confidence 6654 22456666766555 8999999876 666666654
No 28
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=38.74 E-value=78 Score=31.73 Aligned_cols=71 Identities=10% Similarity=0.054 Sum_probs=43.3
Q ss_pred HHHHHHHhccCCCCCCCCCceeecceeeeeeeeeCCCCeEEEEEEeCCCCCc---hHHHHHHHHHHHHHHhCCCceeEEE
Q psy281 39 SREIFDLIRNIYDPEHPLTLEELHVVDLSLIQVNNETNQIKVNFTPTIPHCS---MATLIGLSIRVRLIRALPARFKVVV 115 (162)
Q Consensus 39 ~~~I~eaL~~V~DPEl~~~IVdLGlV~~v~I~~~d~~~~V~V~ltlT~p~Cp---~~~~I~~~I~~aL~~~lpgv~~V~V 115 (162)
.++|.+++.++. +++|.+..+--.+..+.. ...-.+.+.+++.+-+ +....+.+++.+| +.+|||.+|++
T Consensus 114 ~~ev~~~i~~~~-~~LP~~~~~~p~~~~~~~-----~~~pv~~~~l~~~~~~~~~L~~~~~~~l~~~L-~~i~gV~~V~~ 186 (1040)
T PRK10503 114 EQEVQAAINAAT-NLLPSDLPNPPVYSKVNP-----ADPPIMTLAVTSTAMPMTQVEDMVETRVAQKI-SQVSGVGLVTL 186 (1040)
T ss_pred HHHHHHHHHHHH-HhCCCccCCCCEEEEeCC-----CCCceEEEEEEcCCCCHHHHHHHHHHHHHHHh-cCCCCceEEEe
Confidence 577888888875 677766433334443322 2222334444444333 3455567899999 79999998776
Q ss_pred E
Q psy281 116 E 116 (162)
Q Consensus 116 ~ 116 (162)
.
T Consensus 187 ~ 187 (1040)
T PRK10503 187 S 187 (1040)
T ss_pred c
Confidence 4
No 29
>PF13192 Thioredoxin_3: Thioredoxin domain; PDB: 1ZYP_B 1ZYN_A 1HYU_A 1ILO_A 1J08_F 2YWM_B 2AYT_B 2HLS_B 1A8L_A 2K8S_B ....
Probab=36.56 E-value=1.2e+02 Score=20.05 Aligned_cols=28 Identities=21% Similarity=0.335 Sum_probs=18.7
Q ss_pred CCCCchHHHHHHHHHHHHHHhCCCceeEEEEEe
Q psy281 86 IPHCSMATLIGLSIRVRLIRALPARFKVVVEIT 118 (162)
Q Consensus 86 ~p~Cp~~~~I~~~I~~aL~~~lpgv~~V~V~i~ 118 (162)
+++||....+.+.+++++ ... + +++++.
T Consensus 7 ~~~C~~C~~~~~~~~~~~-~~~-~---i~~ei~ 34 (76)
T PF13192_consen 7 SPGCPYCPELVQLLKEAA-EEL-G---IEVEII 34 (76)
T ss_dssp CSSCTTHHHHHHHHHHHH-HHT-T---EEEEEE
T ss_pred CCCCCCcHHHHHHHHHHH-Hhc-C---CeEEEE
Confidence 556777778888888888 444 3 444544
No 30
>cd02957 Phd_like Phosducin (Phd)-like family; composed of Phd and Phd-like proteins (PhLP), characterized as cytosolic regulators of G protein functions. Phd and PhLPs specifically bind G protein betagamma (Gbg)-subunits with high affinity, resulting in the solubilization of Gbg from the plasma membrane and impeding G protein-mediated signal transduction by inhibiting the formation of a functional G protein trimer (G protein alphabetagamma). Phd also inhibits the GTPase activity of G protein alpha. Phd can be phosphorylated by protein kinase A and G protein-coupled receptor kinase 2, leading to its inactivation. Phd was originally isolated from the retina, where it is highly expressed and has been implicated to play an important role in light adaptation. It is also found in the pineal gland, liver, spleen, striated muscle and the brain. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-te
Probab=34.44 E-value=1.2e+02 Score=21.41 Aligned_cols=40 Identities=10% Similarity=0.046 Sum_probs=30.8
Q ss_pred EEEEEEeCCCCCchHHHHHHHHHHHHHHhCCCceeEEEEEe
Q psy281 78 IKVNFTPTIPHCSMATLIGLSIRVRLIRALPARFKVVVEIT 118 (162)
Q Consensus 78 V~V~ltlT~p~Cp~~~~I~~~I~~aL~~~lpgv~~V~V~i~ 118 (162)
-.+.+.+..++|+....+...+++.. +..+++.=++|+..
T Consensus 25 ~~vvv~F~a~~c~~C~~l~~~l~~la-~~~~~v~f~~vd~~ 64 (113)
T cd02957 25 TRVVVHFYEPGFPRCKILDSHLEELA-AKYPETKFVKINAE 64 (113)
T ss_pred CEEEEEEeCCCCCcHHHHHHHHHHHH-HHCCCcEEEEEEch
Confidence 45666788999999999999998877 67777655666554
No 31
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=33.83 E-value=1.6e+02 Score=24.00 Aligned_cols=103 Identities=14% Similarity=0.100 Sum_probs=59.7
Q ss_pred CCHHHHHHHhccCCCCCCCCCceeecceeeeeeeeeCCCCeEEEEEEeCCCCCchH--HHHHHHHHHHHHHhCCCceeEE
Q psy281 37 FDSREIFDLIRNIYDPEHPLTLEELHVVDLSLIQVNNETNQIKVNFTPTIPHCSMA--TLIGLSIRVRLIRALPARFKVV 114 (162)
Q Consensus 37 ~t~~~I~eaL~~V~DPEl~~~IVdLGlV~~v~I~~~d~~~~V~V~ltlT~p~Cp~~--~~I~~~I~~aL~~~lpgv~~V~ 114 (162)
+.+..|.+.|.+- +.+.| +..++|+-. .+.+.|.+..+-|+--.. ..--..+++.| +...+..++.
T Consensus 10 ~~~~~ire~l~k~--------~~~ag-is~ieI~r~--~~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l-~k~~~~~~~~ 77 (195)
T TIGR01008 10 LKRTLIDEFLKKE--------LREAG-YSGVDVRVT--PLGTKVIIFAERPGLVIGRGGRRIRELTEKL-QKKFGLENPQ 77 (195)
T ss_pred hHHHHHHHHHHHH--------HHhCC-eeEEEEEEc--CCcEEEEEEECCCceEECCCchHHHHHHHHH-HHHhCCCceE
Confidence 4566777777641 22233 556777322 457888888888874331 11224455555 3333433455
Q ss_pred EEEecCCCCCchhchhhcCCHHHHHHhccccc-hHHHHhhhc
Q psy281 115 VEITPGSHSTEFAINKQLADKERVAAALENST-LIGVINQCI 155 (162)
Q Consensus 115 V~i~~~~h~~~~~w~~~l~~~Erv~aalen~~-~~~~~~~~~ 155 (162)
|++. .-..|..+.++... +++.+||+.- .|+++++.+
T Consensus 78 I~v~---ev~~p~l~A~lvA~-~Ia~qLe~rv~fRra~k~ai 115 (195)
T TIGR01008 78 IDVE---EVENPELNAQVQAE-RIARSLERGLHFRRAAYTAV 115 (195)
T ss_pred EEEE---EEeCCCcCHHHHHH-HHHHHHHccccHHHHHHHHH
Confidence 5554 12456777777655 9999999876 666665543
No 32
>PRK11657 dsbG disulfide isomerase/thiol-disulfide oxidase; Provisional
Probab=31.56 E-value=1.4e+02 Score=24.68 Aligned_cols=98 Identities=11% Similarity=0.095 Sum_probs=51.4
Q ss_pred cCCc-eeeeccCCCCCCcccCCCcCCCcCCHHHHHHHhccCCCCCCCCCceeecceeeeeeeeeCCCCeEEEEEEeCCCC
Q psy281 10 NINP-TLYSKCEDRPVTAEDQNDYITDEFDSREIFDLIRNIYDPEHPLTLEELHVVDLSLIQVNNETNQIKVNFTPTIPH 88 (162)
Q Consensus 10 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~t~~~I~eaL~~V~DPEl~~~IVdLGlV~~v~I~~~d~~~~V~V~ltlT~p~ 88 (162)
+-++ ++|....-||+..-+.=|-....+|.+.+.+... -|.-...+-.|..-..+.. ..++.=.+...+|.|.
T Consensus 55 ~~~~~i~Y~t~dg~y~i~G~l~d~~~~nlT~~~~~~~~~---~~~~~~~~~~l~~~~~i~~---g~~~ak~~I~vFtDp~ 128 (251)
T PRK11657 55 QDMGVTIYLTPDGKHAISGYMYDEKGENLSEALLEKEVY---APMGREMWQRLEQSHWILD---GKADAPRIVYVFADPN 128 (251)
T ss_pred CCCceEEEEcCCCCEEEEEEEEcCCCCccCHHHHHHHhc---CCccHHHHHHhhccCCccc---cCCCCCeEEEEEECCC
Confidence 4455 6788887788765443343334667665554321 1211111222221111211 1112223344589999
Q ss_pred CchHHHHHHHHHHHHHHhCCCceeEEEEEe
Q psy281 89 CSMATLIGLSIRVRLIRALPARFKVVVEIT 118 (162)
Q Consensus 89 Cp~~~~I~~~I~~aL~~~lpgv~~V~V~i~ 118 (162)
||+...+..+++..+ +. | +|+|++.
T Consensus 129 CpyC~kl~~~l~~~~-~~--g--~V~v~~i 153 (251)
T PRK11657 129 CPYCKQFWQQARPWV-DS--G--KVQLRHI 153 (251)
T ss_pred ChhHHHHHHHHHHHh-hc--C--ceEEEEE
Confidence 999999999988777 32 2 4566544
No 33
>PRK05783 hypothetical protein; Provisional
Probab=30.62 E-value=40 Score=23.88 Aligned_cols=48 Identities=17% Similarity=0.084 Sum_probs=24.5
Q ss_pred cceeeeeeeeeCCCCeEEEEEEeCCCCCchHHHHHHHHHHH-HHHhCCCceeEEEEE
Q psy281 62 HVVDLSLIQVNNETNQIKVNFTPTIPHCSMATLIGLSIRVR-LIRALPARFKVVVEI 117 (162)
Q Consensus 62 GlV~~v~I~~~d~~~~V~V~ltlT~p~Cp~~~~I~~~I~~a-L~~~lpgv~~V~V~i 117 (162)
|.|.++++ +..+.+.+.-++.. -+...+.+-+++. | +=|-+.++.|.+
T Consensus 33 ~~V~~VRv-----GK~iel~l~~~~~e-~a~~~v~~mc~~LrL--aNpVIe~y~i~~ 81 (84)
T PRK05783 33 GNIIEVRA-----GKYLVFKIEANSPE-EAKELALKIAREGRL--YNPIVHKIVVRV 81 (84)
T ss_pred CCcceEEe-----eEEEEEEEcCCCHH-HHHHHHHHHHHhcCc--CCceeEEEEEEE
Confidence 34777777 23444444333221 2245555555554 4 346667766654
No 34
>TIGR02610 PHA_gran_rgn putative polyhydroxyalkanoic acid system protein. All members of this family are encoded by genes polyhydroxyalkanoic acid (PHA) biosynthesis and utilization genes, including proteins at found at the surface of PHA granules. Examples so far are found in the Pseudomonales, Xanthomonadales, and Vibrionales, all of which belong to the Gammaproteobacteria.
Probab=30.61 E-value=60 Score=23.17 Aligned_cols=31 Identities=19% Similarity=0.153 Sum_probs=27.8
Q ss_pred CCeEEEEEEeCCCCCchHHHHHHHHHHHHHH
Q psy281 75 TNQIKVNFTPTIPHCSMATLIGLSIRVRLIR 105 (162)
Q Consensus 75 ~~~V~V~ltlT~p~Cp~~~~I~~~I~~aL~~ 105 (162)
++.|.|.+.|+-..-+++..|+..|+..|.+
T Consensus 58 ~d~v~v~v~Lg~Ll~~f~~~Ie~~I~~~Ld~ 88 (91)
T TIGR02610 58 PQSIRVTAELGMLLSAMSGTIKSEIERALDK 88 (91)
T ss_pred CCeEEEEEEhHHHHHHHHHHHHHHHHHHHHH
Confidence 5799999999999999999999999998843
No 35
>TIGR00412 redox_disulf_2 small redox-active disulfide protein 2. This small protein is found in three archaeal species so far (Methanococcus jannaschii, Archeoglobus fulgidus, and Methanobacterium thermoautotrophicum) as well as in Anabaena PCC7120. It is homologous to thioredoxins, glutaredoxins, and protein disulfide isomerases, and shares with them a redox-active disulfide. The redox active disulfide region CXXC motif resembles neither thioredoxin nor glutaredoxin. A closely related protein found in the same three Archaea, described by redox_disulf_1, has a glutaredoxin-like CP[YH]C sequence; it has been characterized in functional assays as redox-active but unlikely to be a thioredoxin or glutaredoxin.
Probab=29.62 E-value=1.2e+02 Score=19.94 Aligned_cols=25 Identities=8% Similarity=0.121 Sum_probs=20.1
Q ss_pred EeCCCCCchHHHHHHHHHHHHHHhCC
Q psy281 83 TPTIPHCSMATLIGLSIRVRLIRALP 108 (162)
Q Consensus 83 tlT~p~Cp~~~~I~~~I~~aL~~~lp 108 (162)
.+.+++||....+...+++.+ ++++
T Consensus 4 ~~~a~~C~~C~~~~~~~~~~~-~e~~ 28 (76)
T TIGR00412 4 QIYGTGCANCQMTEKNVKKAV-EELG 28 (76)
T ss_pred EEECCCCcCHHHHHHHHHHHH-HHcC
Confidence 334699999999999999988 5654
No 36
>TIGR01608 citD citrate lyase acyl carrier protein. This is a model of the acyl carrier protein (aka gamma subunit) of the holoenzyme citrate lyase (EC 4.1.3.6) composed of alpha (EC 2.8.3.10), beta (EC 4.1.3.34), and acyl carrier protein subunits in a stoichiometric relationship of 6:6:6. Citrate lyase is an enzyme which converts citrate to oxaloacetate. In bacteria, this reaction is involved in citrate fermentation. The acyl carrier protein covalently binds the coenzyme of citrate lyase. The seed contains an experimentally characterized member from Leuconostoc mesenteroides. The model covers a wide range of Gram positive bacteria. For Gram negative bacteria, it appears that only gamma proteobacteria hit this model. The model is quite robust with queries scoring either quite well or quite poorly against the model. There are currently no hits in-between the noise cutoff and trusted cutoff.
Probab=29.58 E-value=90 Score=22.61 Aligned_cols=48 Identities=21% Similarity=0.222 Sum_probs=29.1
Q ss_pred CCchHHHHHHHHHHHHHHhCCCceeEEEEEecCCCCCchhchhhcCCHHHHHHhccc
Q psy281 88 HCSMATLIGLSIRVRLIRALPARFKVVVEITPGSHSTEFAINKQLADKERVAAALEN 144 (162)
Q Consensus 88 ~Cp~~~~I~~~I~~aL~~~lpgv~~V~V~i~~~~h~~~~~w~~~l~~~Erv~aalen 144 (162)
.+-++.+|++-|++.| +.+ ||.++.|.+..+.. |.= -=+.|+.+|+..
T Consensus 38 ~kQfG~~Ir~~v~etL-~~l-gV~~~~v~v~DkGA-----LDc--~IrAR~~tAv~R 85 (92)
T TIGR01608 38 KKQFGDDIESTVKETL-KLL-GVENAVVKVVDKGA-----LNC--VIKARTLAAVQR 85 (92)
T ss_pred HHHHhHHHHHHHHHHH-HHc-CCceEEEEEEeCCh-----HHH--HHHHHHHHHHHH
Confidence 3455677777777777 444 89999999884332 111 114577766643
No 37
>KOG4656|consensus
Probab=29.14 E-value=48 Score=27.81 Aligned_cols=22 Identities=18% Similarity=0.312 Sum_probs=18.7
Q ss_pred HHHHHHHHHHhCCCceeEEEEEe
Q psy281 96 GLSIRVRLIRALPARFKVVVEIT 118 (162)
Q Consensus 96 ~~~I~~aL~~~lpgv~~V~V~i~ 118 (162)
..++|++| +.++|+.+|+|.+.
T Consensus 21 vnavk~~L-~~V~Gi~~vevdle 42 (247)
T KOG4656|consen 21 VNAVKACL-KGVPGINSVEVDLE 42 (247)
T ss_pred HHHHHHHh-ccCCCcceEEEEhh
Confidence 56788899 78999999999875
No 38
>PF14480 DNA_pol3_a_NI: DNA polymerase III polC-type N-terminus I
Probab=28.84 E-value=1.7e+02 Score=19.13 Aligned_cols=71 Identities=13% Similarity=0.163 Sum_probs=41.1
Q ss_pred HHHhccCCCCCCC-CCceeecceeeeeeeeeCCCCeEEEEEEeCCCCCchHHHHHHHHHHHHHHhCCCceeEEEEEe
Q psy281 43 FDLIRNIYDPEHP-LTLEELHVVDLSLIQVNNETNQIKVNFTPTIPHCSMATLIGLSIRVRLIRALPARFKVVVEIT 118 (162)
Q Consensus 43 ~eaL~~V~DPEl~-~~IVdLGlV~~v~I~~~d~~~~V~V~ltlT~p~Cp~~~~I~~~I~~aL~~~lpgv~~V~V~i~ 118 (162)
...|.++.=|+-- .+..+-|.|..|.+. .......+.+..+..- ....-..+.+.|++++.++.+|++.+.
T Consensus 4 ~~ll~ql~~~~~~~~~~f~~~~I~kv~v~--k~~~~w~f~l~~~~~l---~~~~~~~~~~~l~~~F~~ia~v~~~i~ 75 (76)
T PF14480_consen 4 FELLKQLQIPDELDNPLFEDAEIEKVTVH--KKSRKWRFHLSSPHIL---PFEVYQKFEEKLKKQFSHIAKVELIIE 75 (76)
T ss_pred HHHHHHcCCCchhhhhhhcccEEEEEEEE--ccCCEEEEEEEeCCcC---CHHHHHHHHHHHHHHhCCcCeEEEEEE
Confidence 3445555545444 567788999999994 3356777777766542 222333344444444455556666553
No 39
>cd03026 AhpF_NTD_C TRX-GRX-like family, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) subfamily, C-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which then reduces hydrogen peroxide and organic hydroperoxides. AhpF contains an NTD containing two contiguous TRX-fold subdomains similar to Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). It also contains a catalytic core similar to TRX reductase containing FAD and NADH binding domains with an active site disulfide. The proposed mechanism of action of AhpF is similar to a TRX/TRX reductase system. The flow of reducing equivalents goes from NADH - catalytic core of AhpF - NTD of AhpF - AhpC - peroxide substrates. The catalytic CXXC motif of the NTD of AhpF is contained in its C-terminal TRX subdomain.
Probab=28.44 E-value=2e+02 Score=19.80 Aligned_cols=31 Identities=6% Similarity=0.019 Sum_probs=15.8
Q ss_pred CCCchHHHHHHHHHHHHHHhCCCceeEEEEEe
Q psy281 87 PHCSMATLIGLSIRVRLIRALPARFKVVVEIT 118 (162)
Q Consensus 87 p~Cp~~~~I~~~I~~aL~~~lpgv~~V~V~i~ 118 (162)
++|+....+..-+++.. +..+++.-..++++
T Consensus 22 ~~C~~C~~~~~~~~~l~-~~~~~i~~~~vd~~ 52 (89)
T cd03026 22 LSCHNCPDVVQALNLMA-VLNPNIEHEMIDGA 52 (89)
T ss_pred CCCCCcHHHHHHHHHHH-HHCCCceEEEEEhH
Confidence 55555555555555555 44555444444443
No 40
>cd02947 TRX_family TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox state of target proteins via the reversible oxidation of an active site dithiol, present in a CXXC motif, partially exposed at the protein's surface. TRX reduces protein disulfide bonds, resulting in a disulfide bond at its active site. Oxidized TRX is converted to the active form by TRX reductase, using reducing equivalents derived from either NADPH or ferredoxins. By altering their redox state, TRX regulates the functions of at least 30 target proteins, some of which are enzymes and transcription factors. It also plays an important role in the defense against oxidative stress by directly reducing hydrogen peroxide and certain radicals, and by serving as a reductant for peroxiredoxins. At least two major types of functio
Probab=28.10 E-value=1.6e+02 Score=18.40 Aligned_cols=39 Identities=18% Similarity=0.150 Sum_probs=27.2
Q ss_pred EEEEEeCCCCCchHHHHHHHHHHHHHHhCCCceeEEEEEe
Q psy281 79 KVNFTPTIPHCSMATLIGLSIRVRLIRALPARFKVVVEIT 118 (162)
Q Consensus 79 ~V~ltlT~p~Cp~~~~I~~~I~~aL~~~lpgv~~V~V~i~ 118 (162)
.+-+.+++++|+....+...+++.. +..+++.-+.++..
T Consensus 12 ~~ll~~~~~~C~~C~~~~~~~~~~~-~~~~~~~~~~i~~~ 50 (93)
T cd02947 12 PVVVDFWAPWCGPCKAIAPVLEELA-EEYPKVKFVKVDVD 50 (93)
T ss_pred cEEEEEECCCChhHHHhhHHHHHHH-HHCCCceEEEEECC
Confidence 3566778899999999998888877 44455444455443
No 41
>cd02989 Phd_like_TxnDC9 Phosducin (Phd)-like family, Thioredoxin (TRX) domain containing protein 9 (TxnDC9) subfamily; composed of predominantly uncharacterized eukaryotic proteins, containing a TRX-like domain without the redox active CXXC motif. The gene name for the human protein is TxnDC9. The two characterized members are described as Phd-like proteins, PLP1 of Saccharomyces cerevisiae and PhLP3 of Dictyostelium discoideum. Gene disruption experiments show that both PLP1 and PhLP3 are non-essential proteins. Unlike Phd and most Phd-like proteins, members of this group do not contain the Phd N-terminal helical domain which is implicated in binding to the G protein betagamma subunit.
Probab=28.06 E-value=2e+02 Score=20.51 Aligned_cols=39 Identities=8% Similarity=0.005 Sum_probs=29.6
Q ss_pred EEEEEeCCCCCchHHHHHHHHHHHHHHhCCCceeEEEEEe
Q psy281 79 KVNFTPTIPHCSMATLIGLSIRVRLIRALPARFKVVVEIT 118 (162)
Q Consensus 79 ~V~ltlT~p~Cp~~~~I~~~I~~aL~~~lpgv~~V~V~i~ 118 (162)
.|.+.+..++|+....+.-.+++.. +..+++.=++|++.
T Consensus 24 ~vvV~f~a~~c~~C~~~~p~l~~la-~~~~~i~f~~Vd~~ 62 (113)
T cd02989 24 RVVCHFYHPEFFRCKIMDKHLEILA-KKHLETKFIKVNAE 62 (113)
T ss_pred cEEEEEECCCCccHHHHHHHHHHHH-HHcCCCEEEEEEcc
Confidence 3555667899999999888888877 67788766677655
No 42
>PF06857 ACP: Malonate decarboxylase delta subunit (MdcD); InterPro: IPR023439 This family consists of the acyl carrier protein found in malonate decarboxylase and citrate lyase. This subunit has the same covalently bound prosthetic group, derived from and similar to coenzyme A, as does citrate lyase, although this protein and the acyl carrier protein of citrate lyase do not show significant sequence similarity. Both malonyl and acetyl groups are transferred to the prosthetic group for catalysis.
Probab=27.97 E-value=1.4e+02 Score=21.09 Aligned_cols=56 Identities=21% Similarity=0.161 Sum_probs=34.4
Q ss_pred EEEEeCCC-CCchHHHHHHHHHHHHHHhCCCceeEEEEEecCCCCCchhchhhcCCHHHHHHhccc
Q psy281 80 VNFTPTIP-HCSMATLIGLSIRVRLIRALPARFKVVVEITPGSHSTEFAINKQLADKERVAAALEN 144 (162)
Q Consensus 80 V~ltlT~p-~Cp~~~~I~~~I~~aL~~~lpgv~~V~V~i~~~~h~~~~~w~~~l~~~Erv~aalen 144 (162)
+.+.++++ ..-+...|++-+++.| +.+ |+..+.|.+.++... +... +-|+..|++.
T Consensus 28 i~i~l~S~v~~~fg~~i~~vi~~~l-~~~-~i~~~~v~i~D~GAl---d~vi----~aRl~~A~~r 84 (87)
T PF06857_consen 28 IEIELESSVVKQFGDQIRAVIRETL-EEL-GIEDAKVEINDKGAL---DCVI----RARLEQALER 84 (87)
T ss_pred EEEEEEchHHhhhHHHHHHHHHHHH-Hhc-CCCceEEEEEeCCCC---HHHH----HHHHHHHHHH
Confidence 33444455 6667888888888888 444 778888888743321 1111 3477777654
No 43
>TIGR00741 yfiA ribosomal subunit interface protein. The member of this family from E. coli is now recognized as a protein at the interace between ribosomal large and small subunits, with about 1/3 as many copies per cell as the number of ribosomes.
Probab=27.25 E-value=59 Score=22.24 Aligned_cols=38 Identities=13% Similarity=0.084 Sum_probs=23.3
Q ss_pred EeCCCCCchHHHHHHHHHHHH---HHhCCCceeEEEEEecC
Q psy281 83 TPTIPHCSMATLIGLSIRVRL---IRALPARFKVVVEITPG 120 (162)
Q Consensus 83 tlT~p~Cp~~~~I~~~I~~aL---~~~lpgv~~V~V~i~~~ 120 (162)
.+++.++++.+.+++.|++.+ .+-++.+..++|.+...
T Consensus 4 ~i~~~~~~~t~~l~~~i~~k~~kl~k~~~~i~~~~V~l~~e 44 (95)
T TIGR00741 4 NITGKNVEITEALREYVEEKLARLERYFTHIINVDVVLSKE 44 (95)
T ss_pred EEEEeccccCHHHHHHHHHHHHHHHHhcCCCceEEEEEEEe
Confidence 345566666666666666655 23356677788887643
No 44
>cd00307 RuBisCO_small_like Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit and related proteins. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits. This superfamily also contains specific proteins from cyanobacteria. CcmM plays a role in a CO2 concentrating mechanism, which cyanobacteria need to to overcome t
Probab=26.12 E-value=1.4e+02 Score=21.15 Aligned_cols=47 Identities=19% Similarity=0.204 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHhCCCceeEEEEEecCCCCCchhchh--hc--CCHHHHHHhcc
Q psy281 93 TLIGLSIRVRLIRALPARFKVVVEITPGSHSTEFAINK--QL--ADKERVAAALE 143 (162)
Q Consensus 93 ~~I~~~I~~aL~~~lpgv~~V~V~i~~~~h~~~~~w~~--~l--~~~Erv~aale 143 (162)
..|.++|+..|.+ | ..+.+++....++|..-|-+ .. .+...|.+.|+
T Consensus 2 ~~i~~QI~yll~q---G-~~~~iE~~d~~rywt~w~lp~f~~~~~~~~~Vl~el~ 52 (84)
T cd00307 2 EDVVEQVRQLLAQ---G-YKIGLEHADARRFRTSSWQSCGPIEGRSEAQVLAALE 52 (84)
T ss_pred HHHHHHHHHHHHC---C-CEeEEEECCCCccHhhhcCCCCCCCCCCHHHHHHHHH
Confidence 4678889998843 2 68899998888887777766 22 34445554443
No 45
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=25.48 E-value=1.2e+02 Score=23.09 Aligned_cols=44 Identities=18% Similarity=0.330 Sum_probs=30.9
Q ss_pred CCHHHHHHHhccCCCCCCCC--------CceeecceeeeeeeeeCCCCeEEEEEEeC
Q psy281 37 FDSREIFDLIRNIYDPEHPL--------TLEELHVVDLSLIQVNNETNQIKVNFTPT 85 (162)
Q Consensus 37 ~t~~~I~eaL~~V~DPEl~~--------~IVdLGlV~~v~I~~~d~~~~V~V~ltlT 85 (162)
++.++|++.|++ .+|.++. -++++|+|..+.. . ++.......-.
T Consensus 37 ~sAeei~~~l~~-~~p~islaTVYr~L~~l~e~Glv~~~~~---~-~~~~~y~~~~~ 88 (145)
T COG0735 37 LSAEELYEELRE-EGPGISLATVYRTLKLLEEAGLVHRLEF---E-GGKTRYELNSE 88 (145)
T ss_pred CCHHHHHHHHHH-hCCCCCHhHHHHHHHHHHHCCCEEEEEe---C-CCEEEEecCCC
Confidence 678888888887 7777764 2578999999987 2 34454444433
No 46
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=24.86 E-value=1.3e+02 Score=29.25 Aligned_cols=62 Identities=15% Similarity=0.187 Sum_probs=40.7
Q ss_pred EEEEEeCCCCCchHHHHHHHHHHHHHHhCCCceeEEEEEecCCCCCchhchhhcCC-HHHHHHhccccch
Q psy281 79 KVNFTPTIPHCSMATLIGLSIRVRLIRALPARFKVVVEITPGSHSTEFAINKQLAD-KERVAAALENSTL 147 (162)
Q Consensus 79 ~V~ltlT~p~Cp~~~~I~~~I~~aL~~~lpgv~~V~V~i~~~~h~~~~~w~~~l~~-~Erv~aalen~~~ 147 (162)
++.+.+....|......-+ +| .+++|+.++.|++. ++...-.|.+...+ .+.+..+.+..++
T Consensus 3 ~~~l~v~Gm~Ca~C~~~ie----~l-~~~~gV~~~~vn~~--t~~~~v~~~~~~~~~~~~~~~~v~~~gy 65 (713)
T COG2217 3 ETSLSVEGMTCAACASRIE----AL-NKLPGVEEARVNLA--TERATVVYDPEEVDLPADIVAAVEKAGY 65 (713)
T ss_pred eeEEeecCcCcHHHHHHHH----HH-hcCCCeeEEEeecc--cceEEEEecccccccHHHHHHHHHhcCc
Confidence 4567777888887654333 78 78999999999987 33344455554444 4566666555544
No 47
>PF13098 Thioredoxin_2: Thioredoxin-like domain; PDB: 1T3B_A 2L57_A 1EEJ_B 1TJD_A 1JZD_B 1JZO_A 1G0T_B 3GV1_A 1V58_A 2H0H_A ....
Probab=23.83 E-value=96 Score=21.26 Aligned_cols=22 Identities=14% Similarity=0.166 Sum_probs=15.7
Q ss_pred EEEEeCCCCCchHHHHHHHHHH
Q psy281 80 VNFTPTIPHCSMATLIGLSIRV 101 (162)
Q Consensus 80 V~ltlT~p~Cp~~~~I~~~I~~ 101 (162)
+.+.++.++||....+...+..
T Consensus 8 ~v~~F~~~~C~~C~~~~~~~~~ 29 (112)
T PF13098_consen 8 IVVVFTDPWCPYCKKLEKELFP 29 (112)
T ss_dssp EEEEEE-TT-HHHHHHHHHHHH
T ss_pred EEEEEECCCCHHHHHHHHHHHH
Confidence 3444579999999999998885
No 48
>TIGR02830 spore_III_AG stage III sporulation protein AG. CC A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is found in a spore formation operon and is designated stage III sporulation protein AG.
Probab=23.78 E-value=1.3e+02 Score=24.39 Aligned_cols=29 Identities=10% Similarity=0.024 Sum_probs=24.8
Q ss_pred chHHHHHHHHHHHHHHhCCCceeEEEEEec
Q psy281 90 SMATLIGLSIRVRLIRALPARFKVVVEITP 119 (162)
Q Consensus 90 p~~~~I~~~I~~aL~~~lpgv~~V~V~i~~ 119 (162)
.+...++..+++.| +.+.|+.+|+|.+..
T Consensus 57 ~Ye~~lE~~L~~iL-~~I~GvG~V~VmItl 85 (186)
T TIGR02830 57 DYEKQYENELKEIL-EKIEGVGDVTVMVNL 85 (186)
T ss_pred HHHHHHHHHHHHHH-HhccCcceeEEEEEE
Confidence 35778999999999 789999999999873
No 49
>PF05768 DUF836: Glutaredoxin-like domain (DUF836); InterPro: IPR008554 Glutaredoxins [, , ], also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system []. Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond []. It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed [] that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This family contains several viral glutaredoxins, and many related bacterial and eukaryotic proteins of unknown function. The best characterised member of this family is G4L (P68460 from SWISSPROT) from Vaccinia virus (strain Western Reserve/WR) (VACV), which is necessary for virion morphogenesis and virus replication []. This is a cytomplasmic protein which functions as a shuttle in a redox pathway between membrane-associated E10R and L1R or F9L []. ; PDB: 1TTZ_A 1XPV_A 2FGX_A 2G2Q_C 1WJK_A.
Probab=23.63 E-value=52 Score=22.17 Aligned_cols=21 Identities=14% Similarity=0.091 Sum_probs=15.6
Q ss_pred EeCCCCCchHHHHHHHHHHHH
Q psy281 83 TPTIPHCSMATLIGLSIRVRL 103 (162)
Q Consensus 83 tlT~p~Cp~~~~I~~~I~~aL 103 (162)
-+|.++|++.......++...
T Consensus 4 l~~k~~C~LC~~a~~~L~~~~ 24 (81)
T PF05768_consen 4 LYTKPGCHLCDEAKEILEEVA 24 (81)
T ss_dssp EEE-SSSHHHHHHHHHHHHCC
T ss_pred EEcCCCCChHHHHHHHHHHHH
Confidence 357899999998887777644
No 50
>PF00101 RuBisCO_small: Ribulose bisphosphate carboxylase, small chain; InterPro: IPR000894 RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a bifunctional enzyme that catalyses both the carboxylation and oxygenation of ribulose-1,5-bisphosphate (RuBP) [], thus fixing carbon dioxide as the first step of the Calvin cycle. RuBisCO is the major protein in the stroma of chloroplasts, and in higher plants exists as a complex of 8 large and 8 small subunits. The function of the small subunit is unknown []. While the large subunit is coded for by a single gene, the small subunit is coded for by several different genes, which are distributed in a tissue specific manner. They are transcriptionally regulated by light receptor phytochrome [], which results in RuBisCO being more abundant during the day when it is required. The RuBisCo small subunit consists of a central four-stranded beta-sheet, with two helices packed against it [].; PDB: 1BWV_W 1IWA_P 3AXM_X 1WDD_S 3AXK_T 1IR2_K 1RBL_N 1UZH_J 1RSC_P 1UW9_C ....
Probab=22.96 E-value=2e+02 Score=20.81 Aligned_cols=48 Identities=19% Similarity=0.132 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHhCCCceeEEEEEecCCCCCchhch----hh--cCCHHHHHHhcc
Q psy281 92 ATLIGLSIRVRLIRALPARFKVVVEITPGSHSTEFAIN----KQ--LADKERVAAALE 143 (162)
Q Consensus 92 ~~~I~~~I~~aL~~~lpgv~~V~V~i~~~~h~~~~~w~----~~--l~~~Erv~aale 143 (162)
...|.++|+..|.+ | ..+.++.....|.....|. +. -.+...|.++|+
T Consensus 13 ~~~i~~Qv~~ll~q---G-~~i~iE~ad~r~~r~~~W~mW~~p~~~~~~~~~Vl~el~ 66 (99)
T PF00101_consen 13 DEEIAKQVRYLLSQ---G-WIIGIEHADPRRFRTSYWQMWKLPMFGCTDPAQVLAELE 66 (99)
T ss_dssp HHHHHHHHHHHHHT---T--EEEEEEESCGGSTSSS-EEESSEBTTBSSHHHHHHHHH
T ss_pred HHHHHHHHHhhhhc---C-ceeeEEecCCCCCCCCEeecCCCCCcCCCCHHHHHHHHH
Confidence 67899999999953 2 5889999988888777777 32 235656766665
No 51
>PF03780 Asp23: Asp23 family; InterPro: IPR005531 This entry represents the alkaline shock protein 23 family. These small proteins are involved in alkaline pH tolerance of Staphylococcus aureus [,].
Probab=22.90 E-value=2.1e+02 Score=19.83 Aligned_cols=27 Identities=15% Similarity=0.178 Sum_probs=18.2
Q ss_pred hHHHHHHHHHHHHHHhCCCc--eeEEEEEe
Q psy281 91 MATLIGLSIRVRLIRALPAR--FKVVVEIT 118 (162)
Q Consensus 91 ~~~~I~~~I~~aL~~~lpgv--~~V~V~i~ 118 (162)
....++..|+++| +.+-|. .+|+|.+.
T Consensus 77 v~~~iq~~V~~~v-~~~tg~~v~~V~V~V~ 105 (108)
T PF03780_consen 77 VAEEIQEKVKEAV-EEMTGIEVSEVNVHVE 105 (108)
T ss_pred HHHHHHHHHHHHH-HHHHCCeeEEEEEEEE
Confidence 3677888888888 566664 45666554
No 52
>PHA02516 W baseplate wedge subunit; Provisional
Probab=21.67 E-value=2.6e+02 Score=19.91 Aligned_cols=59 Identities=20% Similarity=0.166 Sum_probs=38.6
Q ss_pred HHHHHHHhcc-----CCCCCCCCCceeecceeeeeeeeeCCCCeEEEEEEeCCCCCchHHHHHHHHHHHHHHhCCCceeE
Q psy281 39 SREIFDLIRN-----IYDPEHPLTLEELHVVDLSLIQVNNETNQIKVNFTPTIPHCSMATLIGLSIRVRLIRALPARFKV 113 (162)
Q Consensus 39 ~~~I~eaL~~-----V~DPEl~~~IVdLGlV~~v~I~~~d~~~~V~V~ltlT~p~Cp~~~~I~~~I~~aL~~~lpgv~~V 113 (162)
.+.|...|.+ +.+|++|.+|-+| +.. .. .-.....|...|+.+|.+--|-+.-.
T Consensus 16 ~qsI~~iL~T~~Ger~~~p~fG~~l~dl--~~~-~~------------------~~~~~~~i~~~i~~aI~~~EPRi~~~ 74 (103)
T PHA02516 16 RQSIGDILLTPLGSRVMRREYGSLLPDL--IDQ-PQ------------------NPALRLQIYAACAMALMRWEPRITLT 74 (103)
T ss_pred HHHHHHHHcCCCcccccCcccccchHHH--hCC-CC------------------CHHHHHHHHHHHHHHHHhcCCCcEEE
Confidence 3444444543 8899999998887 221 11 11257888999999996666767666
Q ss_pred EEEEe
Q psy281 114 VVEIT 118 (162)
Q Consensus 114 ~V~i~ 118 (162)
+|.+.
T Consensus 75 ~V~v~ 79 (103)
T PHA02516 75 RVQIE 79 (103)
T ss_pred EEEEE
Confidence 66665
No 53
>TIGR02183 GRXA Glutaredoxin, GrxA family. This model includes the E. coli glyutaredoxin GrxA which appears to have primary responsibility for the reduction of ribonucleotide reductase.
Probab=21.12 E-value=1.5e+02 Score=20.08 Aligned_cols=35 Identities=9% Similarity=-0.102 Sum_probs=21.0
Q ss_pred EEeCCCCCchHHHHHHHHHHHHHHhCCCceeEEEEE
Q psy281 82 FTPTIPHCSMATLIGLSIRVRLIRALPARFKVVVEI 117 (162)
Q Consensus 82 ltlT~p~Cp~~~~I~~~I~~aL~~~lpgv~~V~V~i 117 (162)
...+.++||+....++-+.+.- ...+++.-..+++
T Consensus 3 ~vys~~~Cp~C~~ak~~L~~~~-~~~~~i~~~~idi 37 (86)
T TIGR02183 3 VIFGRPGCPYCVRAKQLAEKLA-IERADFEFRYIDI 37 (86)
T ss_pred EEEeCCCCccHHHHHHHHHHhC-cccCCCcEEEEEC
Confidence 3467889999988777766643 2223444334443
No 54
>TIGR03143 AhpF_homolog putative alkyl hydroperoxide reductase F subunit. This family of thioredoxin reductase homologs is found adjacent to alkylhydroperoxide reductase C subunit predominantly in cases where there is only one C subunit in the genome and that genome is lacking the F subunit partner (also a thioredcxin reductase homolog) that is usually found (TIGR03140).
Probab=20.95 E-value=2.1e+02 Score=26.33 Aligned_cols=62 Identities=18% Similarity=0.169 Sum_probs=31.8
Q ss_pred HHHHHhccCCCCCCCCCceeecceeeeeeeeeCCCCeEEEEEEeCCCCCchHHHHHHHHHHHHHHhCCCce
Q psy281 41 EIFDLIRNIYDPEHPLTLEELHVVDLSLIQVNNETNQIKVNFTPTIPHCSMATLIGLSIRVRLIRALPARF 111 (162)
Q Consensus 41 ~I~eaL~~V~DPEl~~~IVdLGlV~~v~I~~~d~~~~V~V~ltlT~p~Cp~~~~I~~~I~~aL~~~lpgv~ 111 (162)
.++.+|-++-=++.+.+=-.+..|+.++ ..-+++|-+.+++|.||.... .++... ...|++.
T Consensus 448 s~i~~i~~~~~~~~~l~~~~~~~i~~~~-----~~~~i~v~~~~~C~~Cp~~~~---~~~~~~-~~~~~i~ 509 (555)
T TIGR03143 448 SFILALYNAAGPGQPLGEELLEKIKKIT-----KPVNIKIGVSLSCTLCPDVVL---AAQRIA-SLNPNVE 509 (555)
T ss_pred HHHHHHHHhcCCCCCCCHHHHHHHHhcC-----CCeEEEEEECCCCCCcHHHHH---HHHHHH-HhCCCce
Confidence 3455666665444444333333455442 133566666888888875444 344444 3445443
No 55
>PF01502 PRA-CH: Phosphoribosyl-AMP cyclohydrolase; InterPro: IPR002496 Phosphoribosyl-AMP cyclohydrolase 3.5.4.19 from EC catalyses the third step in the histidine biosynthetic pathway: 5-phosphoribosyl-AMP + H2O = 5-(5-phospho-D-ribosylaminoformimino)-1-(5-phospho-ribosyl) imidazole-4-carboxamide It requires Zn2+ ions for activity [].; GO: 0004635 phosphoribosyl-AMP cyclohydrolase activity, 0000105 histidine biosynthetic process; PDB: 1ZPS_B.
Probab=20.88 E-value=1.8e+02 Score=20.14 Aligned_cols=27 Identities=11% Similarity=0.192 Sum_probs=19.4
Q ss_pred eeeeeeeeeCCCCeEEEEEEeCCCCCchH
Q psy281 64 VDLSLIQVNNETNQIKVNFTPTIPHCSMA 92 (162)
Q Consensus 64 V~~v~I~~~d~~~~V~V~ltlT~p~Cp~~ 92 (162)
|.+|.+ +.+.+.+.+.+.+..|.|+..
T Consensus 42 v~~i~~--DCD~D~ll~~V~~~G~aCHtg 68 (75)
T PF01502_consen 42 VVEIRL--DCDGDALLFKVEQVGPACHTG 68 (75)
T ss_dssp EEEEEE---TTSSEEEEEEEESS-SSTTS
T ss_pred EEEEEe--cCCCCeEEEEEEeCCCCccCC
Confidence 445555 566789999999999999853
Done!