Query 031455
Match_columns 159
No_of_seqs 105 out of 1059
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 14:21:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031455.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031455hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3381 Uncharacterized conser 100.0 1.3E-33 2.8E-38 218.6 9.5 153 3-156 2-159 (161)
2 COG5133 Uncharacterized conser 99.9 4.6E-25 9.9E-30 170.9 9.0 125 31-155 49-178 (181)
3 COG2151 PaaD Predicted metal-s 99.9 5.2E-23 1.1E-27 153.3 9.0 96 31-130 7-103 (111)
4 TIGR03406 FeS_long_SufT probab 99.8 4.3E-18 9.3E-23 135.7 11.1 97 30-129 67-166 (174)
5 PF01883 DUF59: Domain of unkn 99.7 9.1E-18 2E-22 114.5 8.2 72 38-114 1-72 (72)
6 TIGR02945 SUF_assoc FeS assemb 99.6 1.2E-14 2.7E-19 104.6 10.2 90 38-131 3-92 (99)
7 TIGR02159 PA_CoA_Oxy4 phenylac 99.5 2.5E-14 5.5E-19 111.2 8.9 79 48-132 1-80 (146)
8 PRK11670 antiporter inner memb 99.2 7.9E-11 1.7E-15 103.0 10.4 79 35-118 11-89 (369)
9 PF01106 NifU: NifU-like domai 89.9 2.1 4.5E-05 28.9 6.7 49 61-113 17-66 (68)
10 TIGR03341 YhgI_GntY IscR-regul 88.6 2.1 4.6E-05 34.6 6.9 72 37-114 106-178 (190)
11 PRK11190 Fe/S biogenesis prote 87.6 3 6.6E-05 33.8 7.3 72 37-114 107-180 (192)
12 COG0694 Thioredoxin-like prote 80.2 10 0.00022 27.5 6.7 78 37-116 6-85 (93)
13 PF10500 SR-25: Nuclear RNA-sp 74.0 2.1 4.5E-05 35.8 1.8 26 31-56 155-183 (225)
14 PF09580 Spore_YhcN_YlaJ: Spor 73.3 15 0.00033 28.3 6.5 72 57-131 84-155 (177)
15 PRK10597 DNA damage-inducible 72.0 6.8 0.00015 27.8 3.8 51 89-141 16-67 (81)
16 TIGR02000 NifU_proper Fe-S clu 69.3 28 0.00061 29.9 7.7 68 38-113 221-288 (290)
17 TIGR01297 CDF cation diffusion 57.3 95 0.0021 25.1 8.5 75 35-118 191-267 (268)
18 PF09650 PHA_gran_rgn: Putativ 56.6 15 0.00034 25.9 3.3 34 68-103 51-84 (87)
19 PF01545 Cation_efflux: Cation 52.2 62 0.0014 26.3 6.7 74 38-120 207-282 (284)
20 COG0858 RbfA Ribosome-binding 49.9 97 0.0021 23.1 6.8 32 47-85 25-56 (118)
21 TIGR02610 PHA_gran_rgn putativ 49.6 19 0.0004 25.9 2.7 35 68-104 54-88 (91)
22 cd08499 PBP2_Ylib_like The sub 42.3 62 0.0014 28.4 5.5 57 34-95 74-131 (474)
23 cd08518 PBP2_NikA_DppA_OppA_li 38.6 56 0.0012 28.7 4.6 55 34-95 73-127 (464)
24 cd08514 PBP2_AppA_like The sub 37.9 71 0.0015 28.0 5.2 57 34-95 74-132 (483)
25 PRK15413 glutathione ABC trans 36.2 77 0.0017 28.4 5.2 56 34-94 102-158 (512)
26 PRK13818 ribosome-binding fact 34.4 2E+02 0.0042 21.5 7.0 33 46-85 22-54 (121)
27 COG0735 Fur Fe2+/Zn2+ uptake r 32.0 74 0.0016 24.2 3.8 36 34-72 35-78 (145)
28 cd08501 PBP2_Lpqw The substrat 31.9 1.1E+02 0.0023 27.0 5.3 56 34-94 79-138 (486)
29 PF00403 HMA: Heavy-metal-asso 31.8 1.3E+02 0.0027 18.7 4.4 22 95-117 13-34 (62)
30 cd08498 PBP2_NikA_DppA_OppA_li 30.5 1.3E+02 0.0028 26.5 5.6 56 34-94 73-128 (481)
31 TIGR01608 citD citrate lyase a 30.3 1.4E+02 0.003 21.7 4.7 40 77-119 29-68 (92)
32 PHA02516 W baseplate wedge sub 29.7 2.1E+02 0.0046 20.4 5.8 50 48-118 31-80 (103)
33 cd08515 PBP2_NikA_DppA_OppA_li 29.6 1.1E+02 0.0024 26.7 5.1 57 34-95 76-134 (460)
34 PF02033 RBFA: Ribosome-bindin 29.5 1.4E+02 0.003 21.1 4.7 47 38-91 10-57 (104)
35 cd08516 PBP2_NikA_DppA_OppA_li 28.9 1.3E+02 0.0028 26.0 5.3 57 34-95 74-131 (457)
36 cd08490 PBP2_NikA_DppA_OppA_li 28.3 1.3E+02 0.0027 26.2 5.1 54 34-94 72-125 (470)
37 cd08494 PBP2_NikA_DppA_OppA_li 27.2 1.5E+02 0.0033 25.5 5.4 56 34-94 75-131 (448)
38 cd00995 PBP2_NikA_DppA_OppA_li 27.1 1.6E+02 0.0034 25.3 5.5 56 34-94 74-130 (466)
39 COG1438 ArgR Arginine represso 25.2 1.6E+02 0.0035 23.1 4.7 78 36-120 21-103 (150)
40 cd08512 PBP2_NikA_DppA_OppA_li 24.5 1.4E+02 0.003 26.1 4.7 56 34-94 79-138 (476)
41 TIGR02180 GRX_euk Glutaredoxin 24.3 1.7E+02 0.0037 18.7 4.2 19 82-100 3-21 (84)
42 cd08497 PBP2_NikA_DppA_OppA_li 24.2 1.3E+02 0.0028 26.7 4.5 55 34-93 92-147 (491)
43 PRK13817 ribosome-binding fact 24.1 3E+02 0.0065 20.3 7.0 40 38-84 13-53 (119)
44 PF01475 FUR: Ferric uptake re 23.8 70 0.0015 22.9 2.3 37 33-72 21-65 (120)
45 TIGR02898 spore_YhcN_YlaJ spor 23.0 2.4E+02 0.0051 22.2 5.3 59 57-117 63-122 (158)
46 PF03780 Asp23: Asp23 family; 22.1 2.1E+02 0.0046 19.8 4.5 40 76-117 61-105 (108)
47 cd08511 PBP2_NikA_DppA_OppA_li 21.9 1.8E+02 0.0039 25.3 4.9 56 34-94 75-130 (467)
48 PRK09111 DNA polymerase III su 21.6 3.1E+02 0.0067 26.0 6.6 102 37-152 461-563 (598)
49 cd08508 PBP2_NikA_DppA_OppA_li 21.5 1.8E+02 0.004 25.5 4.9 55 34-93 80-134 (470)
50 cd08520 PBP2_NikA_DppA_OppA_li 21.0 2E+02 0.0043 25.2 5.0 56 34-94 75-130 (468)
51 PRK00521 rbfA ribosome-binding 20.9 3.4E+02 0.0075 19.8 6.1 40 39-85 17-57 (120)
No 1
>KOG3381 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.3e-33 Score=218.64 Aligned_cols=153 Identities=64% Similarity=1.071 Sum_probs=136.7
Q ss_pred CCCcCCCceEeecccccccccCCCCCCccccCcCCHHHHHHHhccCCCCCCCCCccccCceeecceEEeCC---C--ceE
Q 031455 3 SGLINANPVVYEKKERRARSASSCVNDEYAAEQIDQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDE---R--SYV 77 (159)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lt~e~I~eaL~~V~DPEl~~~IVdLGlV~~~~I~I~~~---~--~~V 77 (159)
+++.|.||.||.+.+++.+...+-+ |+-..+..+.+.+++.++.|.|||.|.++-+|+.|+.+.|+|.+. . ..|
T Consensus 2 s~l~N~np~v~~~~~~~~r~~~s~~-d~~~~~~~~~~~~~dlir~I~DPEhP~TLeqL~VV~ee~v~V~d~~~~~~~s~V 80 (161)
T KOG3381|consen 2 SGLQNENPLVYPTRSRERRVTASEE-DELLPDSEDAEEIFDLIRDIRDPEHPLTLEQLNVVSEEGVEVDDPNVGDEESYV 80 (161)
T ss_pred CccccCCcccccccccccccccccc-ccccCcchhHHHHHHHHhccCCCCCCccHHHccceeecceEeecCCCCCcceEE
Confidence 4689999999998777655544222 333447788999999999999999999999999999999998752 1 489
Q ss_pred EEEEEeCCCCCchHHHHHHHHHHHHHhhCCCceEEEEEEcCCCCcCHHHHHHHhcchhhhhcccCCccHHHHHhhhcCC
Q 031455 78 RVTFTPTVEHCSMATVIGLCLRVKLMRSLPPRFKVDIMVAPGTHATEAAVNKQLNDKERVAAALENPNLVDMVDECLAP 156 (159)
Q Consensus 78 ~V~mtlT~p~Cp~~~~I~~~V~~aL~~~v~~v~~V~V~i~~~~h~~~~~lnkql~dkErv~aa~e~~~l~~~~~~~~~~ 156 (159)
.|.||||.|+|+++..|+.+|+-+|.+++|...+|+|.|+.++|.+++++|||+||||||+||+||+.|+.++++|+.-
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 9999999999999999999999999999999999999999999999999999999999999999999999999999863
No 2
>COG5133 Uncharacterized conserved protein [Function unknown]
Probab=99.92 E-value=4.6e-25 Score=170.90 Aligned_cols=125 Identities=54% Similarity=0.897 Sum_probs=117.7
Q ss_pred cccCcCCHHHHHHHhccCCCCCCCCCccccCceeecceEEeCCC-----ceEEEEEEeCCCCCchHHHHHHHHHHHHHhh
Q 031455 31 YAAEQIDQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDER-----SYVRVTFTPTVEHCSMATVIGLCLRVKLMRS 105 (159)
Q Consensus 31 ~~~~~lt~e~I~eaL~~V~DPEl~~~IVdLGlV~~~~I~I~~~~-----~~V~V~mtlT~p~Cp~~~~I~~~V~~aL~~~ 105 (159)
...+.+++++|++.++.|.|||.|.++-.||.|.-++|.|.++. ..|.|.+|||.|+|++...|+..|+.+|.++
T Consensus 49 ee~d~id~qeiydLia~I~DPEHPltL~QLsVV~lEdi~v~D~~~~n~i~~v~v~itPTIpHCSmatlIGLcIrvrleR~ 128 (181)
T COG5133 49 EEPDLIDQQEIYDLIADIRDPEHPLTLEQLSVVSLEDISVPDGIAPNVIRCVKVVITPTIPHCSMATLIGLCIRVRLERH 128 (181)
T ss_pred CCCCCcCHHHHHHHHHhcCCCCCCccHhhcceeeeccccccCCCCCCeeEEEEEEeccCCCchhHHHHhhhheeeeehhc
Confidence 45577999999999999999999999999999999899997652 3699999999999999999999999999999
Q ss_pred CCCceEEEEEEcCCCCcCHHHHHHHhcchhhhhcccCCccHHHHHhhhcC
Q 031455 106 LPPRFKVDIMVAPGTHATEAAVNKQLNDKERVAAALENPNLVDMVDECLA 155 (159)
Q Consensus 106 v~~v~~V~V~i~~~~h~~~~~lnkql~dkErv~aa~e~~~l~~~~~~~~~ 155 (159)
+|+-+.|+|.++.++|..+.++|||+||||||+||-||..|..++++|+.
T Consensus 129 lpprF~v~v~ikkGtH~se~qvNKQLnDKeRVaAAcENEqLL~v~~kml~ 178 (181)
T COG5133 129 LPPRFHVQVHIKKGTHISERQVNKQLNDKERVAAACENEQLLDVMEKMLP 178 (181)
T ss_pred CCCceeEEEEEecCCcccHHHHhhhhchHHHHHHhhchHHHHHHHHhhhh
Confidence 99999999999999999999999999999999999999999999999974
No 3
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=99.89 E-value=5.2e-23 Score=153.33 Aligned_cols=96 Identities=21% Similarity=0.386 Sum_probs=87.0
Q ss_pred cccCcCCHHHHHHHhccCCCCCCCCCccccCceeecceEEeC-CCceEEEEEEeCCCCCchHHHHHHHHHHHHHhhCCCc
Q 031455 31 YAAEQIDQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDD-ERSYVRVTFTPTVEHCSMATVIGLCLRVKLMRSLPPR 109 (159)
Q Consensus 31 ~~~~~lt~e~I~eaL~~V~DPEl~~~IVdLGlV~~~~I~I~~-~~~~V~V~mtlT~p~Cp~~~~I~~~V~~aL~~~v~~v 109 (159)
..+.+.++++|+++|++|.|||+|++||+|||||+ |.+++ ++ .++|+||+|+||||+...|..++++++ +.++|+
T Consensus 7 ~~~~~~~~~~i~~aL~~V~DPEi~idIvdLGLVy~--v~i~~~~~-~v~v~mtlT~~gCP~~~~i~~~v~~al-~~~~~v 82 (111)
T COG2151 7 EEAIKVTLEDILEALKTVIDPEIGIDIVDLGLVYE--VDIDDVDG-LVKVKMTLTSPGCPLAEVIADQVEAAL-EEIPGV 82 (111)
T ss_pred cchhhhhHHHHHHHhhcCCCcccceeeEeeccEEE--EEEecCCc-eEEEEEecCCCCCCccHHHHHHHHHHH-HhcCCc
Confidence 34456779999999999999999999999999999 99987 54 899999999999999999999999999 889999
Q ss_pred eEEEEEEcCCCCcCHHHHHHH
Q 031455 110 FKVDIMVAPGTHATEAAVNKQ 130 (159)
Q Consensus 110 ~~V~V~i~~~~h~~~~~lnkq 130 (159)
..++|++++.++|+...+...
T Consensus 83 ~~v~V~l~~~p~Wt~~~ms~e 103 (111)
T COG2151 83 EDVEVELTLSPPWTPDRMSEE 103 (111)
T ss_pred ceEEEEEEEcCCCchhhcCHH
Confidence 999999999999988765543
No 4
>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=99.76 E-value=4.3e-18 Score=135.65 Aligned_cols=97 Identities=20% Similarity=0.319 Sum_probs=87.4
Q ss_pred ccccCcCCHHHHHHHhccCCCCCCCCCccccCceeecceEEeC---CCceEEEEEEeCCCCCchHHHHHHHHHHHHHhhC
Q 031455 30 EYAAEQIDQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDD---ERSYVRVTFTPTVEHCSMATVIGLCLRVKLMRSL 106 (159)
Q Consensus 30 ~~~~~~lt~e~I~eaL~~V~DPEl~~~IVdLGlV~~~~I~I~~---~~~~V~V~mtlT~p~Cp~~~~I~~~V~~aL~~~v 106 (159)
+++....++++|+++|++|+||+++.+|++||+||+ |.+++ ++.+|.|+|++|+|+|++...|..+++.+| ..+
T Consensus 67 ~~~~~~~~ee~V~eaL~tV~DPei~~nIVeLGlV~~--I~Id~~~~~~~~V~I~mtLt~p~c~~~~~L~~dV~~aL-~~l 143 (174)
T TIGR03406 67 ENADGEDNEDQVWEQLRTVYDPEIPVNIVDLGLVYG--CRVEKLGEGQFRVDIEMTLTAPGCGMGPVLVEDVEDKV-LAV 143 (174)
T ss_pred cCccccccHHHHHHHHcCCCCCCCCCChHHcCCeEE--EEEecccCCCCEEEEEEEeCCCCCcHHHHHHHHHHHHH-HhC
Confidence 446677889999999999999999999999999999 99986 323799999999999999999999999999 789
Q ss_pred CCceEEEEEEcCCCCcCHHHHHH
Q 031455 107 PPRFKVDIMVAPGTHATEAAVNK 129 (159)
Q Consensus 107 ~~v~~V~V~i~~~~h~~~~~lnk 129 (159)
+++.+|+|++.++++|.++-+..
T Consensus 144 ~gV~~V~V~l~~dp~W~~~~~s~ 166 (174)
T TIGR03406 144 PNVDEVEVELVFDPPWSREMMSE 166 (174)
T ss_pred CCceeEEEEEEecCCCChHHCCH
Confidence 99999999999999998865443
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=99.74 E-value=9.1e-18 Score=114.49 Aligned_cols=72 Identities=26% Similarity=0.425 Sum_probs=64.6
Q ss_pred HHHHHHHhccCCCCCCCCCccccCceeecceEEeCCCceEEEEEEeCCCCCchHHHHHHHHHHHHHhhCCCceEEEE
Q 031455 38 QQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIGLCLRVKLMRSLPPRFKVDI 114 (159)
Q Consensus 38 ~e~I~eaL~~V~DPEl~~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~~~I~~~V~~aL~~~v~~v~~V~V 114 (159)
+++|+++|++|.||++|.||+++|||++ |.++++ +|+|+|++++|+||+...|..+++.+| ++++|+.+|+|
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 KQAVRDALKQVKDPELGKDIVELGMVRD--ISIEGG--KVSVSLELPTPACPAAEPLREEIREAL-KALPGVKSVKV 72 (72)
T ss_dssp HHHHHHHHTT-BETTTSSBTTTTTSEEE--EEECTC--EEEEEE--SSTTHTTHHHHHHHHHHHH-HTSTT-SEEEE
T ss_pred CHHHHHHHhCCCCCCCCCCHHHcCCeeE--EEEECC--EEEEEEEECCCCchHHHHHHHHHHHHH-HhCCCCceEeC
Confidence 5899999999999999999999999999 999875 999999999999999999999999999 69999988876
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=99.59 E-value=1.2e-14 Score=104.64 Aligned_cols=90 Identities=23% Similarity=0.359 Sum_probs=81.3
Q ss_pred HHHHHHHhccCCCCCCCCCccccCceeecceEEeCCCceEEEEEEeCCCCCchHHHHHHHHHHHHHhhCCCceEEEEEEc
Q 031455 38 QQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIGLCLRVKLMRSLPPRFKVDIMVA 117 (159)
Q Consensus 38 ~e~I~eaL~~V~DPEl~~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~~~I~~~V~~aL~~~v~~v~~V~V~i~ 117 (159)
+++|+++|++|.||+++.+|+++|+|++ |.+.+++ .|+|++++++|+||....+...++.+| ..++|+.+|+|++.
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 KDAVIEALKTVYDPEIPVNIYELGLIYD--IDVDDDG-HVDIQMTLTAPNCPVAGSMPGEVENAV-RAVPGVGSVTVELV 78 (99)
T ss_pred HHHHHHHHcCCCCCCCCCCeecCCCeeE--EEECCCC-eEEEEEEECCCCCChHHHHHHHHHHHH-HhCCCCceEEEEEE
Confidence 4789999999999999999999999999 9998522 899999999999999999999999999 78899999999999
Q ss_pred CCCCcCHHHHHHHh
Q 031455 118 PGTHATEAAVNKQL 131 (159)
Q Consensus 118 ~~~h~~~~~lnkql 131 (159)
....|+.+-+++..
T Consensus 79 ~~~~~~~~~~~~~~ 92 (99)
T TIGR02945 79 WDPPWTPERMSEEA 92 (99)
T ss_pred eeCCCChHHCCHHH
Confidence 88888887666543
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=99.54 E-value=2.5e-14 Score=111.16 Aligned_cols=79 Identities=29% Similarity=0.403 Sum_probs=70.3
Q ss_pred CCCCCCC-CCccccCceeecceEEeCCCceEEEEEEeCCCCCchHHHHHHHHHHHHHhhCCCceEEEEEEcCCCCcCHHH
Q 031455 48 IKDPEHP-YSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIGLCLRVKLMRSLPPRFKVDIMVAPGTHATEAA 126 (159)
Q Consensus 48 V~DPEl~-~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~~~I~~~V~~aL~~~v~~v~~V~V~i~~~~h~~~~~ 126 (159)
|.|||++ ++|++||+|++ |.++++ .|.|+|++|+++||+.+.|+.+|+.+| ++. |+.+|+|++...+.|+.+-
T Consensus 1 v~DPEi~~~sIvdLG~Vr~--V~v~gd--~V~VtIt~Ty~gcpa~e~L~~~I~~aL-~~~-Gv~~V~V~i~~~p~Wt~d~ 74 (146)
T TIGR02159 1 VPDPEIPVVSVTDLGMVRE--VDVDGG--GVVVKFTPTYSGCPALEVIRQDIRDAV-RAL-GVEVVEVSTSLDPPWTTDW 74 (146)
T ss_pred CcCCCCCCCCchhcCCeeE--EEEECC--EEEEEEEeCCCCCchHHHHHHHHHHHH-Hhc-CCCeEEEeEeeCCCCChHH
Confidence 7899999 89999999999 999865 899999999999999999999999999 555 8889999999888888776
Q ss_pred HHHHhc
Q 031455 127 VNKQLN 132 (159)
Q Consensus 127 lnkql~ 132 (159)
++..-.
T Consensus 75 it~~gr 80 (146)
T TIGR02159 75 ITEDAR 80 (146)
T ss_pred CCHHHH
Confidence 655443
No 8
>PRK11670 antiporter inner membrane protein; Provisional
Probab=99.22 E-value=7.9e-11 Score=103.01 Aligned_cols=79 Identities=11% Similarity=0.114 Sum_probs=73.5
Q ss_pred cCCHHHHHHHhccCCCCCCCCCccccCceeecceEEeCCCceEEEEEEeCCCCCchHHHHHHHHHHHHHhhCCCceEEEE
Q 031455 35 QIDQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIGLCLRVKLMRSLPPRFKVDI 114 (159)
Q Consensus 35 ~lt~e~I~eaL~~V~DPEl~~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~~~I~~~V~~aL~~~v~~v~~V~V 114 (159)
.+++++|+++|++|.||+++++|+++|+|++ |.+.++ +|.|.+++|.++||....+..+++++| +.++|+.++.|
T Consensus 11 ~~~~~~v~~~l~~v~~p~~~~~~~~~~~v~~--~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 85 (369)
T PRK11670 11 EALRAMVAGTLANFQHPTLKHNLTTLKALHH--VALLDD--TLHIELVMPFVWNSAFEELKEQCSAEL-LRITGAKAIDW 85 (369)
T ss_pred cchHHHHHHHHhcCCCCCCCCChhhhCCeeE--EEEeCC--EEEEEEEECCCCchHHHHHHHHHHHHH-HhcCCCceEEE
Confidence 3567999999999999999999999999999 999865 899999999999999999999999999 78899999999
Q ss_pred EEcC
Q 031455 115 MVAP 118 (159)
Q Consensus 115 ~i~~ 118 (159)
++..
T Consensus 86 ~~~~ 89 (369)
T PRK11670 86 KLSH 89 (369)
T ss_pred EEee
Confidence 8875
No 9
>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=89.86 E-value=2.1 Score=28.92 Aligned_cols=49 Identities=20% Similarity=0.281 Sum_probs=37.7
Q ss_pred CceeecceEEeCCCceEEEEEEeCCCCCchH-HHHHHHHHHHHHhhCCCceEEE
Q 031455 61 KVITEDAIEVDDERSYVRVTFTPTVEHCSMA-TVIGLCLRVKLMRSLPPRFKVD 113 (159)
Q Consensus 61 GlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~-~~I~~~V~~aL~~~v~~v~~V~ 113 (159)
|=|.- +.++++ .|.|.|+=...+||.. .++...|+.+|++.+|++..|.
T Consensus 17 Gdv~l--v~v~~~--~V~V~l~GaC~gC~~s~~Tl~~~Ie~~L~~~~~~v~~V~ 66 (68)
T PF01106_consen 17 GDVEL--VDVDDG--VVYVRLTGACSGCPSSDMTLKQGIEQALREAVPEVKRVV 66 (68)
T ss_dssp EEEEE--EEEETT--EEEEEEESSCCSSCCHHHHHHHHHHHHHHHHSTT-SEEE
T ss_pred CcEEE--EEecCC--EEEEEEEeCCCCCCCHHHHHHHHHHHHHHHHCCCCceEE
Confidence 44454 567765 8999999999999988 4567999999988898876653
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=88.57 E-value=2.1 Score=34.57 Aligned_cols=72 Identities=15% Similarity=0.192 Sum_probs=52.2
Q ss_pred CHHHHHHHhccCCCCCCCCCccccCceeecceEEeCCCceEEEEEEeCCCCCchH-HHHHHHHHHHHHhhCCCceEEEE
Q 031455 37 DQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMA-TVIGLCLRVKLMRSLPPRFKVDI 114 (159)
Q Consensus 37 t~e~I~eaL~~V~DPEl~~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~-~~I~~~V~~aL~~~v~~v~~V~V 114 (159)
..+.|.++|.+-.-|-+. -+-|=|.- +.+++++ .|.|.|+=...|||+. .+++..|+..|++.+|++..|..
T Consensus 106 ~~~~i~~~l~~~irP~l~---~dGGdiel--v~v~~~~-~v~v~l~GaC~gC~~s~~Tl~~~ie~~l~~~~p~v~~V~~ 178 (190)
T TIGR03341 106 LEERINYVLQSEINPQLA---SHGGKVTL--VEITDDG-VAVLQFGGGCNGCSMVDVTLKDGVEKTLLERFPELKGVRD 178 (190)
T ss_pred HHHHHHHHHHhccCHHHH---hcCCceEE--EEEcCCC-EEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCCcceEEE
Confidence 456677777644445553 34555666 6666543 7899999999999987 46778999999888998876654
No 11
>PRK11190 Fe/S biogenesis protein NfuA; Provisional
Probab=87.57 E-value=3 Score=33.78 Aligned_cols=72 Identities=15% Similarity=0.200 Sum_probs=53.1
Q ss_pred CHHHHHHHhccCCCCCCCCCccccCceeecceEEeCCCceEEEEEEeCCCCCchH-HHHHHHHHHHHHhhCC-CceEEEE
Q 031455 37 DQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMA-TVIGLCLRVKLMRSLP-PRFKVDI 114 (159)
Q Consensus 37 t~e~I~eaL~~V~DPEl~~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~-~~I~~~V~~aL~~~v~-~v~~V~V 114 (159)
..+.|.++|.+-.-|-+-. +-|=|.- +.+++++ .|.|.|.=...|||.. .+|+..|+..|+..+| ++..|.-
T Consensus 107 ~~~~i~~~l~~~irP~l~~---dGGdiel--v~v~~~~-~v~v~l~GaC~gC~~s~~Tl~~~Ie~~l~~~~p~~i~~v~~ 180 (192)
T PRK11190 107 LMERVEYVLQSQINPQLAG---HGGRVSL--MEITEDG-YAILQFGGGCNGCSMVDVTLKEGIEKQLLNEFPGELKGVRD 180 (192)
T ss_pred HHHHHHHHHHhccChhHHh---cCCcEEE--EEEcCCC-EEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCHhhceEEE
Confidence 4667778887555677654 4455565 6666544 7899999999999987 4677799999988888 7766554
No 12
>COG0694 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]
Probab=80.23 E-value=10 Score=27.51 Aligned_cols=78 Identities=13% Similarity=0.223 Sum_probs=50.2
Q ss_pred CHHHHHHHhccCCCCCCC-CCccccCceeecceEEeCCCceEEEEEEeCCCCCchH-HHHHHHHHHHHHhhCCCceEEEE
Q 031455 37 DQQEVFDHVRDIKDPEHP-YSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMA-TVIGLCLRVKLMRSLPPRFKVDI 114 (159)
Q Consensus 37 t~e~I~eaL~~V~DPEl~-~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~-~~I~~~V~~aL~~~v~~v~~V~V 114 (159)
+..++++++..+.|-++. .=..+=|=|.- +.|+...+.|.+.+-=...|||.. .+++..|++.|+..+|++..|..
T Consensus 6 ~~~~~~e~v~~~l~~~irP~l~~dGGdve~--~~i~~~~g~V~l~l~GaC~gC~sS~~TLk~gIE~~L~~~i~ev~~V~~ 83 (93)
T COG0694 6 TDAELLERVEEVLDEKIRPQLAMDGGDVEL--VGIDEEDGVVYLRLGGACSGCPSSTVTLKNGIERQLKEEIPEVKEVEQ 83 (93)
T ss_pred ccHHHHHHHHHHHHhccCcceeccCCeEEE--EEEecCCCeEEEEeCCcCCCCcccHHHHHHHHHHHHHHhCCccceEEE
Confidence 334444444444443332 23345555565 566642237888888899999987 56788899999777888777666
Q ss_pred EE
Q 031455 115 MV 116 (159)
Q Consensus 115 ~i 116 (159)
..
T Consensus 84 v~ 85 (93)
T COG0694 84 VT 85 (93)
T ss_pred cc
Confidence 43
No 13
>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=73.98 E-value=2.1 Score=35.77 Aligned_cols=26 Identities=23% Similarity=0.341 Sum_probs=21.8
Q ss_pred cccCcCCHHHH---HHHhccCCCCCCCCC
Q 031455 31 YAAEQIDQQEV---FDHVRDIKDPEHPYS 56 (159)
Q Consensus 31 ~~~~~lt~e~I---~eaL~~V~DPEl~~~ 56 (159)
-||-|+|+|+. ...++.|+|||.|++
T Consensus 155 ~am~PmTkEEyearQSvIRrVvDpETGRt 183 (225)
T PF10500_consen 155 QAMAPMTKEEYEARQSVIRRVVDPETGRT 183 (225)
T ss_pred hhcCCCCHHHHHHHHhhheeeecCCCCce
Confidence 36889999887 567899999999964
No 14
>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=73.26 E-value=15 Score=28.35 Aligned_cols=72 Identities=10% Similarity=0.135 Sum_probs=48.4
Q ss_pred ccccCceeecceEEeCCCceEEEEEEeCCCCCchHHHHHHHHHHHHHhhCCCceEEEEEEcCCCCcCHHHHHHHh
Q 031455 57 LEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIGLCLRVKLMRSLPPRFKVDIMVAPGTHATEAAVNKQL 131 (159)
Q Consensus 57 IVdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~~~I~~~V~~aL~~~v~~v~~V~V~i~~~~h~~~~~lnkql 131 (159)
+..+.-|.+..+-+.++ .+.|-+.+... -.....|+..|+.++++..|++..|.|-=..+.-+.-..+...+
T Consensus 84 v~~~~~V~~A~vvv~~~--~a~Vav~~~~~-~~~~~~i~~~V~~~v~~~~p~~~~V~Vs~D~~~~~ri~~~~~~~ 155 (177)
T PF09580_consen 84 VKKVPGVEDATVVVTDD--NAYVAVDLDFN-RFNTKKIKKKVEKAVKSADPRIYNVYVSTDPDIFDRIRNLANRI 155 (177)
T ss_pred HhcCCCceEEEEEEECC--EEEEEEEeccc-ccchhHHHHHHHHHHHHhCCCccEEEEEcCHHHHHHHHHHHHHH
Confidence 34455567655556655 89999999844 67789999999999977678878888854332223333444444
No 15
>PRK10597 DNA damage-inducible protein I; Provisional
Probab=72.05 E-value=6.8 Score=27.75 Aligned_cols=51 Identities=18% Similarity=0.270 Sum_probs=30.5
Q ss_pred chHHHHHHHHHHHHHhhCCCce-EEEEEEcCCCCcCHHHHHHHhcchhhhhccc
Q 031455 89 SMATVIGLCLRVKLMRSLPPRF-KVDIMVAPGTHATEAAVNKQLNDKERVAAAL 141 (159)
Q Consensus 89 p~~~~I~~~V~~aL~~~v~~v~-~V~V~i~~~~h~~~~~lnkql~dkErv~aa~ 141 (159)
.+.+.|..++..+|...+|... .|.|+.......+-.-..| .||+++...|
T Consensus 16 ga~~AL~~EL~kRl~~~fPd~~~~v~Vr~~s~n~lsv~g~~k--~dK~~i~eiL 67 (81)
T PRK10597 16 GAIDALAGELSRRIQYAFPDNEGHVSVRYAAANNLSVIGATK--EDKDRISEIL 67 (81)
T ss_pred hHHHHHHHHHHHHHHhhCCCCCccEEEeecCCCceEecCCCc--chHHHHHHHH
Confidence 4567899999999988777653 5777655333322111122 2677765544
No 16
>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=69.28 E-value=28 Score=29.87 Aligned_cols=68 Identities=21% Similarity=0.168 Sum_probs=48.2
Q ss_pred HHHHHHHhccCCCCCCCCCccccCceeecceEEeCCCceEEEEEEeCCCCCchHHHHHHHHHHHHHhhCCCceEEE
Q 031455 38 QQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIGLCLRVKLMRSLPPRFKVD 113 (159)
Q Consensus 38 ~e~I~eaL~~V~DPEl~~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~~~I~~~V~~aL~~~v~~v~~V~ 113 (159)
.+.|-++| +-.-|-+-.+ =|-|.- +.|+++ .|.|.|.=...|||....=-..|+..|+..+|++..|.
T Consensus 221 ~~~v~~~l-~~irP~l~~d---GGdv~l--v~v~~~--~v~v~l~GaC~gC~~s~~Tl~~Ie~~l~~~~p~~~~V~ 288 (290)
T TIGR02000 221 IQLIQKVL-EEVRPVLQAD---GGDVEL--YDVDGK--IVYVVLTGACSGCSMSTMTLKGIQQRLRERLGEFVVVE 288 (290)
T ss_pred HHHHHHHH-HHhCchHhhc---CCcEEE--EEEeCC--EEEEEEeeCCCCCcchHHHHHHHHHHHHHhCCCceEEE
Confidence 35666777 3345666543 566666 667653 89999999999999985443449999988888776553
No 17
>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=57.28 E-value=95 Score=25.11 Aligned_cols=75 Identities=17% Similarity=0.283 Sum_probs=44.5
Q ss_pred cCCHHHHHHHhccCCCCCCCCCccccCceeecceEEeCCCceEEEEEEeCCCCCchH--HHHHHHHHHHHHhhCCCceEE
Q 031455 35 QIDQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMA--TVIGLCLRVKLMRSLPPRFKV 112 (159)
Q Consensus 35 ~lt~e~I~eaL~~V~DPEl~~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~--~~I~~~V~~aL~~~v~~v~~V 112 (159)
....+++.+.+..+ |+. .++.++..-+ ...+...+.+.+.+ .++++.. ..+...++++++++.+++.+|
T Consensus 191 ~~~~~~i~~~i~~~--~~v-~~v~~~~~~~-----~G~~~~~v~~~v~v-~~~~~~~~ah~i~~~i~~~i~~~~~~v~~v 261 (268)
T TIGR01297 191 EEDLEEIKKAILSI--PGV-KGVHDLHIWR-----IGPGKLFLDVHVVV-DPDLDLKQAHDIALEIEREILKRHPGIEHV 261 (268)
T ss_pred cccHHHHHHHHhcC--CCc-ccceEeEEEE-----cCCCCEEEEEEEEE-CCCCChhHHHHHHHHHHHHHHHhcCCCCeE
Confidence 34567777777643 444 3444432211 11112234555555 4566665 578888988887778899888
Q ss_pred EEEEcC
Q 031455 113 DIMVAP 118 (159)
Q Consensus 113 ~V~i~~ 118 (159)
.|.+.+
T Consensus 262 ~ih~ep 267 (268)
T TIGR01297 262 TIQVEP 267 (268)
T ss_pred EEEeCC
Confidence 887763
No 18
>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=56.60 E-value=15 Score=25.89 Aligned_cols=34 Identities=18% Similarity=0.165 Sum_probs=30.1
Q ss_pred eEEeCCCceEEEEEEeCCCCCchHHHHHHHHHHHHH
Q 031455 68 IEVDDERSYVRVTFTPTVEHCSMATVIGLCLRVKLM 103 (159)
Q Consensus 68 I~I~~~~~~V~V~mtlT~p~Cp~~~~I~~~V~~aL~ 103 (159)
+.|.++ .|.|.+.|...--|++..|+..|+..|.
T Consensus 51 l~V~~d--~v~l~v~Lg~Ll~~f~~~Ie~~I~~~Ld 84 (87)
T PF09650_consen 51 LDVADD--HVRLEVKLGFLLSPFKGKIEQEIEKNLD 84 (87)
T ss_pred EEEcCC--EEEEEEEcHHHHHHHHHHHHHHHHHHHH
Confidence 667665 8999999999999999999999999884
No 19
>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=52.22 E-value=62 Score=26.33 Aligned_cols=74 Identities=16% Similarity=0.257 Sum_probs=44.0
Q ss_pred HHHHHHHhccCCCCCCCCCccccCceeecceEEeCCCceEEEEEEeCCCCCchH--HHHHHHHHHHHHhhCCCceEEEEE
Q 031455 38 QQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMA--TVIGLCLRVKLMRSLPPRFKVDIM 115 (159)
Q Consensus 38 ~e~I~eaL~~V~DPEl~~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~--~~I~~~V~~aL~~~v~~v~~V~V~ 115 (159)
.+++.+.+++ .|+. .++.++..-+ +..+...+.+.+.. .++++.. ..+...+++.++++++++.++.|+
T Consensus 207 ~~~i~~~i~~--~~~v-~~v~~~~~~~-----~g~~~~~v~i~v~v-~~~~~v~~~~~i~~~i~~~l~~~~~~i~~v~I~ 277 (284)
T PF01545_consen 207 VEKIRRIIES--VPGV-IEVHDLRVWQ-----VGRNKYVVEIHVQV-DPDMSVEEAHEIRERIEKRLREKFPGIYDVTIH 277 (284)
T ss_dssp HHHHHHHHHH--TSS--SEEEEEEEEE-----ETT-EEEEEEEEEE-TTTSBHHHHHHHHHHHHHHHHHHSTTCEEEEEE
T ss_pred hhHHHHhhcc--CCce-EeccceEEEE-----ecCCcEEEEEEEEe-CCCCCHHHHHHHHHHHHHHHHHhCCCcEEEEEE
Confidence 4667777766 3332 2333332222 22112244455552 4556554 568999999998889999999998
Q ss_pred EcCCC
Q 031455 116 VAPGT 120 (159)
Q Consensus 116 i~~~~ 120 (159)
+.+..
T Consensus 278 ~~p~~ 282 (284)
T PF01545_consen 278 IEPDE 282 (284)
T ss_dssp EEECG
T ss_pred EEecC
Confidence 88654
No 20
>COG0858 RbfA Ribosome-binding factor A [Translation, ribosomal structure and biogenesis]
Probab=49.94 E-value=97 Score=23.12 Aligned_cols=32 Identities=31% Similarity=0.389 Sum_probs=24.4
Q ss_pred cCCCCCCCCCccccCceeecceEEeCCCceEEEEEEeCC
Q 031455 47 DIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTV 85 (159)
Q Consensus 47 ~V~DPEl~~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT~ 85 (159)
.|+||-++--. |.+ |++..|..++.|.+++=.
T Consensus 25 eikDprl~~~~-----Vt~--V~vS~Dl~~A~Vyvt~l~ 56 (118)
T COG0858 25 EIKDPRLGLVT-----VTD--VEVSKDLSHAKVYVTVLG 56 (118)
T ss_pred HccCCCcCceE-----EEE--EEEcCCCceEEEEEEecC
Confidence 59999987332 788 999888778888888644
No 21
>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=49.56 E-value=19 Score=25.86 Aligned_cols=35 Identities=17% Similarity=0.165 Sum_probs=30.8
Q ss_pred eEEeCCCceEEEEEEeCCCCCchHHHHHHHHHHHHHh
Q 031455 68 IEVDDERSYVRVTFTPTVEHCSMATVIGLCLRVKLMR 104 (159)
Q Consensus 68 I~I~~~~~~V~V~mtlT~p~Cp~~~~I~~~V~~aL~~ 104 (159)
|.|.++ .|.|.+.|..-.-+++..|+..|+..|.+
T Consensus 54 l~V~~d--~v~v~v~Lg~Ll~~f~~~Ie~~I~~~Ld~ 88 (91)
T TIGR02610 54 VHLGPQ--SIRVTAELGMLLSAMSGTIKSEIERALDK 88 (91)
T ss_pred EEEcCC--eEEEEEEhHHHHHHHHHHHHHHHHHHHHH
Confidence 666665 89999999999999999999999999844
No 22
>cd08499 PBP2_Ylib_like The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding component of an uncharacterized ATP-binding cassette (ABC)-type peptide transport system YliB. Although the ligand specificity of Ylib protein is not known, it shares significant sequence similarity to the ABC-type dipeptide and oligopeptide binding proteins. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling
Probab=42.34 E-value=62 Score=28.35 Aligned_cols=57 Identities=19% Similarity=0.283 Sum_probs=38.8
Q ss_pred CcCCHHHHHHHhccCCCCCCCCCcc-ccCceeecceEEeCCCceEEEEEEeCCCCCchHHHHH
Q 031455 34 EQIDQQEVFDHVRDIKDPEHPYSLE-ELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIG 95 (159)
Q Consensus 34 ~~lt~e~I~eaL~~V~DPEl~~~IV-dLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~~~I~ 95 (159)
.++|.++|...+..+.+|+.+.... -++-|.+ |+..++ -+|++++..|..++...+.
T Consensus 74 ~p~tA~Dv~~s~~~~~~~~~~~~~~~~~~~i~~--v~~~d~---~tv~i~l~~p~~~~~~~l~ 131 (474)
T cd08499 74 TPFNAEAVKANLDRVLDPETASPRASLFSMIEE--VEVVDD---YTVKITLKEPFAPLLAHLA 131 (474)
T ss_pred CCCCHHHHHHHHHhhcCCccCcccccccceeee--EEEcCC---CeEEEEECCCChHHHHHHh
Confidence 5799999999999999998653322 2344666 777654 4566677777666655543
No 23
>cd08518 PBP2_NikA_DppA_OppA_like_19 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=38.63 E-value=56 Score=28.66 Aligned_cols=55 Identities=20% Similarity=0.312 Sum_probs=39.9
Q ss_pred CcCCHHHHHHHhccCCCCCCCCCccccCceeecceEEeCCCceEEEEEEeCCCCCchHHHHH
Q 031455 34 EQIDQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIG 95 (159)
Q Consensus 34 ~~lt~e~I~eaL~~V~DPEl~~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~~~I~ 95 (159)
.++|.++|...+..+.+|..+... ++-|.+ |+..++ -+|++++..|..++...+.
T Consensus 73 ~p~TA~Dv~~s~~r~~~~~~~~~~--~~~i~~--v~~~d~---~Tv~i~l~~p~~~~~~~l~ 127 (464)
T cd08518 73 EPLTAEDVAFTYNTAKDPGSASDI--LSNLED--VEAVDD---YTVKFTLKKPDSTFLDKLA 127 (464)
T ss_pred cCCchHHhhehHHHhhCCCCCccc--ccceeE--EEecCC---CEEEEEEcCCCchHHHHhh
Confidence 579999999999999999876443 555677 777654 4566677777666665554
No 24
>cd08514 PBP2_AppA_like The substrate-binding component of the oligopeptide-binding protein, AppA, from Bacillus subtilis contains the type 2 periplasmic-binding fold. This family represents the substrate-binding domain of the oligopeptide-binding protein, AppA, from Bacillus subtilis and its closest homologs from other bacteria and archaea. Bacillus subtilis has three ABC-type peptide transport systems, a dipeptide-binding protein (DppA) and two oligopeptide-binding proteins (OppA and AppA) with overlapping specificity. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and also is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains correspondin
Probab=37.92 E-value=71 Score=28.01 Aligned_cols=57 Identities=19% Similarity=0.205 Sum_probs=38.9
Q ss_pred CcCCHHHHHHHhccCCCCCCCCCcc--ccCceeecceEEeCCCceEEEEEEeCCCCCchHHHHH
Q 031455 34 EQIDQQEVFDHVRDIKDPEHPYSLE--ELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIG 95 (159)
Q Consensus 34 ~~lt~e~I~eaL~~V~DPEl~~~IV--dLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~~~I~ 95 (159)
.++|.++|...+....+|..+-... .+..|.+ |+..++ -+|+++++.|..++...+.
T Consensus 74 ~pvtA~Dv~~s~~r~~~~~~~~~~~~~~~~~i~~--v~~~d~---~tv~i~l~~p~~~~~~~l~ 132 (483)
T cd08514 74 EPLTADDVKFTYKAIADPKYAGPRASGDYDEIKG--VEVPDD---YTVVFHYKEPYAPALESWA 132 (483)
T ss_pred cCcCHHHHHhHHHHHhCCCCCCccccccccceeE--EEEccC---ceEEEEECCCCchhHHHhh
Confidence 4799999999999999987653221 2445667 777654 4566777777766655543
No 25
>PRK15413 glutathione ABC transporter substrate-binding protein GsiB; Provisional
Probab=36.20 E-value=77 Score=28.38 Aligned_cols=56 Identities=14% Similarity=0.228 Sum_probs=39.5
Q ss_pred CcCCHHHHHHHhccCCCCCCCCC-ccccCceeecceEEeCCCceEEEEEEeCCCCCchHHHH
Q 031455 34 EQIDQQEVFDHVRDIKDPEHPYS-LEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVI 94 (159)
Q Consensus 34 ~~lt~e~I~eaL~~V~DPEl~~~-IVdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~~~I 94 (159)
.++|.++|...+....+|..+.. .-.++-|.. |+..++ -+|+++++.|..++...+
T Consensus 102 ~pvTA~DV~~s~~r~~~~~~~~~~~~~~~~i~~--v~~~D~---~Tv~~~l~~p~~~~~~~l 158 (512)
T PRK15413 102 TDFNAAAVKANLDRASNPDNHLKRYNLYKNIAK--TEAVDP---TTVKITLKQPFSAFINIL 158 (512)
T ss_pred CCccHHHHHHHHHHhhCcccccccccccccceE--EEecCC---CEEEEEECCCChHHHHHH
Confidence 57999999999999999986422 223444666 777654 567778888877766555
No 26
>PRK13818 ribosome-binding factor A; Provisional
Probab=34.40 E-value=2e+02 Score=21.47 Aligned_cols=33 Identities=27% Similarity=0.480 Sum_probs=24.3
Q ss_pred ccCCCCCCCCCccccCceeecceEEeCCCceEEEEEEeCC
Q 031455 46 RDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTV 85 (159)
Q Consensus 46 ~~V~DPEl~~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT~ 85 (159)
+.++||-++ +--|.+ |.+..|..++.|.++...
T Consensus 22 ~ei~Dprl~-----~vtVt~--V~lS~Dl~~AkVyvs~~~ 54 (121)
T PRK13818 22 KNIRDPRLS-----DVTITA--VECTNDLSYATVYYSLLT 54 (121)
T ss_pred HhCcCCCcC-----ceEEeE--EEECCCCCEEEEEEEeCC
Confidence 678999985 223566 888877778888887764
No 27
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=32.04 E-value=74 Score=24.25 Aligned_cols=36 Identities=19% Similarity=0.547 Sum_probs=29.6
Q ss_pred CcCCHHHHHHHhccCCCCCCCC-C-------ccccCceeecceEEeC
Q 031455 34 EQIDQQEVFDHVRDIKDPEHPY-S-------LEELKVITEDAIEVDD 72 (159)
Q Consensus 34 ~~lt~e~I~eaL~~V~DPEl~~-~-------IVdLGlV~~~~I~I~~ 72 (159)
++++.++|++.|++ .+|.++. + +.++|+|.. +...+
T Consensus 35 ~~~sAeei~~~l~~-~~p~islaTVYr~L~~l~e~Glv~~--~~~~~ 78 (145)
T COG0735 35 GHLSAEELYEELRE-EGPGISLATVYRTLKLLEEAGLVHR--LEFEG 78 (145)
T ss_pred CCCCHHHHHHHHHH-hCCCCCHhHHHHHHHHHHHCCCEEE--EEeCC
Confidence 34999999999999 7899973 3 568999999 87764
No 28
>cd08501 PBP2_Lpqw The substrate-binding domain of mycobacterial lipoprotein Lpqw contains type 2 periplasmic binding fold. LpqW is one of key players in synthesis and transport of the unique components of the mycobacterial cell wall which is a complex structure rich in two related lipoglycans, the phosphatidylinositol mannosides (PIMs) and lipoarabinomannans (LAMs). Lpqw is a highly conserved lipoprotein that transport intermediates from a pathway for mature PIMs production into a pathway for LAMs biosynthesis, thus controlling the relative abundance of these two essential components of cell wall. LpqW is thought to have been adapted by the cell-wall biosynthesis machinery of mycobacteria and other closely related pathogens, evolving to play an important role in PIMs/LAMs biosynthesis. Most of periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the LpqW protein. The structural topology of these domains is most similar to
Probab=31.89 E-value=1.1e+02 Score=27.01 Aligned_cols=56 Identities=13% Similarity=0.105 Sum_probs=37.3
Q ss_pred CcCCHHHHHHHhccCCCCCCCCCcc---ccCceeecceEEeC-CCceEEEEEEeCCCCCchHHHH
Q 031455 34 EQIDQQEVFDHVRDIKDPEHPYSLE---ELKVITEDAIEVDD-ERSYVRVTFTPTVEHCSMATVI 94 (159)
Q Consensus 34 ~~lt~e~I~eaL~~V~DPEl~~~IV---dLGlV~~~~I~I~~-~~~~V~V~mtlT~p~Cp~~~~I 94 (159)
+++|.++|...++.+.+|.-+.... .+.-|.+ |++.+ + -+|++++..|...+...+
T Consensus 79 ~~~TA~DV~~s~~~~~~~~~~~~~~~~~~~~~i~~--i~~~d~~---~tv~~~l~~p~~~~~~~l 138 (486)
T cd08501 79 TPITAADFEYLWKAMSGEPGTYDPASTDGYDLIES--VEKGDGG---KTVVVTFKQPYADWRALF 138 (486)
T ss_pred CcCcHHHHHHHHHHhcCCCCccccccCcchheeee--eeccCCC---cEEEEEEcCCCccHHHHh
Confidence 5799999999999999987653322 2344666 77765 4 455666666665554444
No 29
>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=31.82 E-value=1.3e+02 Score=18.72 Aligned_cols=22 Identities=18% Similarity=0.157 Sum_probs=17.0
Q ss_pred HHHHHHHHHhhCCCceEEEEEEc
Q 031455 95 GLCLRVKLMRSLPPRFKVDIMVA 117 (159)
Q Consensus 95 ~~~V~~aL~~~v~~v~~V~V~i~ 117 (159)
...|+++| ..++|+.++.+.+.
T Consensus 13 ~~~v~~~l-~~~~GV~~v~vd~~ 34 (62)
T PF00403_consen 13 AKKVEKAL-SKLPGVKSVKVDLE 34 (62)
T ss_dssp HHHHHHHH-HTSTTEEEEEEETT
T ss_pred HHHHHHHH-hcCCCCcEEEEECC
Confidence 34578888 78899988888664
No 30
>cd08498 PBP2_NikA_DppA_OppA_like_2 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=30.46 E-value=1.3e+02 Score=26.50 Aligned_cols=56 Identities=18% Similarity=0.223 Sum_probs=37.6
Q ss_pred CcCCHHHHHHHhccCCCCCCCCCccccCceeecceEEeCCCceEEEEEEeCCCCCchHHHH
Q 031455 34 EQIDQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVI 94 (159)
Q Consensus 34 ~~lt~e~I~eaL~~V~DPEl~~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~~~I 94 (159)
+++|.++|...+..+.+|..+....-+.-|.+ |+..++ -+|+++++.|...+...+
T Consensus 73 ~pltA~Dv~~s~~~~~~~~~~~~~~~~~~i~~--v~~~d~---~tv~i~l~~p~~~~~~~l 128 (481)
T cd08498 73 SPFTAEDVVFSLERARDPPSSPASFYLRTIKE--VEVVDD---YTVDIKTKGPNPLLPNDL 128 (481)
T ss_pred CcCCHHHHHhHHhhhhCCCcccccccccceeE--EEEecC---CEEEEEECCCChHHHHHH
Confidence 58999999999999999876533212334566 776654 456677777765555444
No 31
>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=30.29 E-value=1.4e+02 Score=21.73 Aligned_cols=40 Identities=10% Similarity=0.062 Sum_probs=27.9
Q ss_pred EEEEEEeCCCCCchHHHHHHHHHHHHHhhCCCceEEEEEEcCC
Q 031455 77 VRVTFTPTVEHCSMATVIGLCLRVKLMRSLPPRFKVDIMVAPG 119 (159)
Q Consensus 77 V~V~mtlT~p~Cp~~~~I~~~V~~aL~~~v~~v~~V~V~i~~~ 119 (159)
+.|.+.- +-.+.++..|+..|+..| +++ |+..+.|.+...
T Consensus 29 i~iel~S-~V~kQfG~~Ir~~v~etL-~~l-gV~~~~v~v~Dk 68 (92)
T TIGR01608 29 IEIDLVS-DVKKQFGDDIESTVKETL-KLL-GVENAVVKVVDK 68 (92)
T ss_pred EEEEEEE-HHHHHHhHHHHHHHHHHH-HHc-CCceEEEEEEeC
Confidence 5455444 234667788888888888 555 899999988743
No 32
>PHA02516 W baseplate wedge subunit; Provisional
Probab=29.72 E-value=2.1e+02 Score=20.42 Aligned_cols=50 Identities=16% Similarity=0.101 Sum_probs=34.0
Q ss_pred CCCCCCCCCccccCceeecceEEeCCCceEEEEEEeCCCCCchHHHHHHHHHHHHHhhCCCceEEEEEEcC
Q 031455 48 IKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIGLCLRVKLMRSLPPRFKVDIMVAP 118 (159)
Q Consensus 48 V~DPEl~~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~~~I~~~V~~aL~~~v~~v~~V~V~i~~ 118 (159)
+.+|++|.+|-+| +-.. ..-.....|...|+.+|.+--|-+.-++|.+..
T Consensus 31 ~~~p~fG~~l~dl-~~~~--------------------~~~~~~~~i~~~i~~aI~~~EPRi~~~~V~v~~ 80 (103)
T PHA02516 31 VMRREYGSLLPDL-IDQP--------------------QNPALRLQIYAACAMALMRWEPRITLTRVQIER 80 (103)
T ss_pred ccCcccccchHHH-hCCC--------------------CCHHHHHHHHHHHHHHHHhcCCCcEEEEEEEEE
Confidence 8899999999888 1111 011247788999999995555666666666553
No 33
>cd08515 PBP2_NikA_DppA_OppA_like_10 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=29.57 E-value=1.1e+02 Score=26.66 Aligned_cols=57 Identities=11% Similarity=0.196 Sum_probs=40.1
Q ss_pred CcCCHHHHHHHhccCCCCCCCCC--ccccCceeecceEEeCCCceEEEEEEeCCCCCchHHHHH
Q 031455 34 EQIDQQEVFDHVRDIKDPEHPYS--LEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIG 95 (159)
Q Consensus 34 ~~lt~e~I~eaL~~V~DPEl~~~--IVdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~~~I~ 95 (159)
.++|.++|...++...+|..+-. ---++-|.+ |++.++ -+|.+++..|.+++...+.
T Consensus 76 ~pvtA~Dv~~s~~r~~~~~~~~~~~~~~~~~i~~--v~~~d~---~tv~i~l~~p~~~~~~~l~ 134 (460)
T cd08515 76 SPMTAEDVVFTFNRVRDPDSKAPRGRQNFNWLDK--VEKVDP---YTVRIVTKKPDPAALERLA 134 (460)
T ss_pred CcCCHHHhhehHhhhhCCccCCcchhhhccceeE--EEEccC---CeEEEEECCCCchHHHHHH
Confidence 57999999999999998876432 112344666 777654 4677777888777766664
No 34
>PF02033 RBFA: Ribosome-binding factor A; InterPro: IPR000238 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosome-binding factor A [] (gene rbfA) is a bacterial protein that associates with free 30S ribosomal subunits. It does not associate with 30S subunits that are part of 70S ribosomes or polysomes. It is essential for efficient processing of 16S rRNA. Ribosome-binding factor A is a protein of from 13 to 15 Kd which is found in most bacteria. A putative chloroplastic form seems to exist in plants.; GO: 0006364 rRNA processing; PDB: 2R1C_A 2DYJ_B 2KZF_A 2E7G_A 1JOS_A 1KKG_A 1PA4_A.
Probab=29.52 E-value=1.4e+02 Score=21.12 Aligned_cols=47 Identities=26% Similarity=0.333 Sum_probs=30.8
Q ss_pred HHHHHHHhcc-CCCCCCCCCccccCceeecceEEeCCCceEEEEEEeCCCCCchH
Q 031455 38 QQEVFDHVRD-IKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMA 91 (159)
Q Consensus 38 ~e~I~eaL~~-V~DPEl~~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~ 91 (159)
.+.|-+.|.. +.||.+ .+=-|.. |.+..|...+.|.+++..+.....
T Consensus 10 ~~~i~~il~~~~~d~~l-----~~vtIt~--V~ls~Dl~~a~Vy~~~~~~~~~~~ 57 (104)
T PF02033_consen 10 QREISEILQREIKDPRL-----KLVTITR--VELSPDLSHAKVYVSILGDEEEQE 57 (104)
T ss_dssp HHHHHHHHCTCTSSCGH-----HCEEEEE--EEECTTSSEEEEEEEESSSHHHHH
T ss_pred HHHHHHHHHhhccCcCc-----ceEEEEE--EEECCCCCEEEEEEEEecCchhHH
Confidence 3455666666 888887 2222445 888877778999998866554443
No 35
>cd08516 PBP2_NikA_DppA_OppA_like_11 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=28.91 E-value=1.3e+02 Score=26.03 Aligned_cols=57 Identities=16% Similarity=0.295 Sum_probs=36.9
Q ss_pred CcCCHHHHHHHhccCCCCCCCCCc-cccCceeecceEEeCCCceEEEEEEeCCCCCchHHHHH
Q 031455 34 EQIDQQEVFDHVRDIKDPEHPYSL-EELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIG 95 (159)
Q Consensus 34 ~~lt~e~I~eaL~~V~DPEl~~~I-VdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~~~I~ 95 (159)
+++|.++|...+....+|..+... -.+.-|.+ |+..++ -+|+++++.|...+...+.
T Consensus 74 ~~~tA~Dv~~s~~~~~~~~~~~~~~~~~~~i~~--v~~~d~---~tv~i~l~~p~~~~~~~l~ 131 (457)
T cd08516 74 DPVTAADVKYSFNRIADPDSGAPLRALFQEIES--VEAPDD---ATVVIKLKQPDAPLLSLLA 131 (457)
T ss_pred CCCCHHHhhhhhhhhhCCCCCccchhhhcceeE--EEeCCC---CeEEEEeCCCCHHHHHHHh
Confidence 579999999999999998754322 12344566 766544 4556666666555554443
No 36
>cd08490 PBP2_NikA_DppA_OppA_like_3 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=28.34 E-value=1.3e+02 Score=26.22 Aligned_cols=54 Identities=11% Similarity=0.035 Sum_probs=35.5
Q ss_pred CcCCHHHHHHHhccCCCCCCCCCccccCceeecceEEeCCCceEEEEEEeCCCCCchHHHH
Q 031455 34 EQIDQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVI 94 (159)
Q Consensus 34 ~~lt~e~I~eaL~~V~DPEl~~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~~~I 94 (159)
+++|.++|...++.+.+|..+... ...+.+ |+..++ -+|.+++..|...+...+
T Consensus 72 ~plTA~Dv~~s~~~~~~~~~~~~~--~~~~~~--v~~~d~---~tv~i~l~~p~~~~~~~l 125 (470)
T cd08490 72 TPLTAEAVKASLERALAKSPRAKG--GALIIS--VIAVDD---YTVTITTKEPYPALPARL 125 (470)
T ss_pred CCCCHHHHHHHHHHHhccCccccc--cccceE--EEecCC---CEEEEEeCCCChhHHHHH
Confidence 579999999999999988755332 344556 776654 345566666654444443
No 37
>cd08494 PBP2_NikA_DppA_OppA_like_6 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=27.23 E-value=1.5e+02 Score=25.51 Aligned_cols=56 Identities=18% Similarity=0.173 Sum_probs=37.1
Q ss_pred CcCCHHHHHHHhccCCCCCCCCCc-cccCceeecceEEeCCCceEEEEEEeCCCCCchHHHH
Q 031455 34 EQIDQQEVFDHVRDIKDPEHPYSL-EELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVI 94 (159)
Q Consensus 34 ~~lt~e~I~eaL~~V~DPEl~~~I-VdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~~~I 94 (159)
.++|.++|...+..+.+|..+-.- -.+.-|.+ |+..++ -+|++++..|..++...+
T Consensus 75 ~pvTA~Dv~~s~~~~~~~~~~~~~~~~~~~i~~--v~~~d~---~tv~i~l~~p~~~~~~~l 131 (448)
T cd08494 75 TPFDAADVKFSLQRARAPDSTNADKALLAAIAS--VEAPDA---HTVVVTLKHPDPSLLFNL 131 (448)
T ss_pred CCCCHHHHHhHHHHHhCCCCCccccchhcceeE--EEecCC---CEEEEEECCCChhHHHHH
Confidence 579999999999999988765322 12344666 777554 456666666655554444
No 38
>cd00995 PBP2_NikA_DppA_OppA_like The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding domain of nickel/dipeptide/oligopeptide transport systems, which function in the import of nickel and peptides, and other closely related proteins. The oligopeptide-binding protein OppA is a periplasmic component of an ATP-binding cassette (ABC) transport system OppABCDEF consisting of five subunits: two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and is inv
Probab=27.15 E-value=1.6e+02 Score=25.27 Aligned_cols=56 Identities=18% Similarity=0.277 Sum_probs=36.2
Q ss_pred CcCCHHHHHHHhccCCCCCCCCCcc-ccCceeecceEEeCCCceEEEEEEeCCCCCchHHHH
Q 031455 34 EQIDQQEVFDHVRDIKDPEHPYSLE-ELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVI 94 (159)
Q Consensus 34 ~~lt~e~I~eaL~~V~DPEl~~~IV-dLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~~~I 94 (159)
.++|.++|...+..+.+|..+.... .+.-|.+ |++.++ -+|+++++.|.-.+...+
T Consensus 74 ~p~TA~Dv~~s~~~~~~~~~~~~~~~~~~~i~~--v~~~d~---~tv~i~l~~p~~~~~~~l 130 (466)
T cd00995 74 TPLTAEDVVFSFERLADPKNASPSAGKADEIEG--VEVVDD---YTVTITLKEPDAPFLALL 130 (466)
T ss_pred CCcCHHHHHhHHHHhcCCccCCcccccccceee--EEecCC---CeEEEEECCCCchHHHHh
Confidence 4799999999999999998764432 2344566 777654 345555555544444333
No 39
>COG1438 ArgR Arginine repressor [Transcription]
Probab=25.23 E-value=1.6e+02 Score=23.08 Aligned_cols=78 Identities=14% Similarity=0.198 Sum_probs=51.7
Q ss_pred CCHHHHHHHhcc----CCCCCCCCCccccCceeecceEEeCCCceEEEEEEeCCCCCchHHHHHHHHHHHHHhhCCCc-e
Q 031455 36 IDQQEVFDHVRD----IKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIGLCLRVKLMRSLPPR-F 110 (159)
Q Consensus 36 lt~e~I~eaL~~----V~DPEl~~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~~~I~~~V~~aL~~~v~~v-~ 110 (159)
-|++++.+.|.+ |.=.-+.++|-+||+|+ |..+. .-.+...+...+-|.......-+...+ -.+..+ .
T Consensus 21 ~TQ~Elv~~L~~~Gi~vTQaTvSRDlkelglvK---v~~~~---g~~~Y~l~~~~~~~~~~~~~~~~~~~v-~~vd~~~~ 93 (150)
T COG1438 21 STQEELVELLQEEGIEVTQATVSRDLKELGLVK---VRNEK---GTYVYSLPAELGVPPTSKLKRYLKDLV-LSIDRNGN 93 (150)
T ss_pred CCHHHHHHHHHHcCCeEehHHHHHHHHHcCCEE---ecCCC---CcEEEEeCCccCCCchhhHHHHHHHHh-eeeccCCc
Confidence 467888888865 66667779999999999 55433 366777888888888877775566655 333332 2
Q ss_pred EEEEEEcCCC
Q 031455 111 KVDIMVAPGT 120 (159)
Q Consensus 111 ~V~V~i~~~~ 120 (159)
-+-++..++.
T Consensus 94 ~ivlkT~PG~ 103 (150)
T COG1438 94 LIVLKTSPGA 103 (150)
T ss_pred EEEEEeCCch
Confidence 4444444443
No 40
>cd08512 PBP2_NikA_DppA_OppA_like_7 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=24.50 E-value=1.4e+02 Score=26.10 Aligned_cols=56 Identities=13% Similarity=0.121 Sum_probs=36.5
Q ss_pred CcCCHHHHHHHhccCCCCCCCCCcc----ccCceeecceEEeCCCceEEEEEEeCCCCCchHHHH
Q 031455 34 EQIDQQEVFDHVRDIKDPEHPYSLE----ELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVI 94 (159)
Q Consensus 34 ~~lt~e~I~eaL~~V~DPEl~~~IV----dLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~~~I 94 (159)
+++|.++|...+..+.+|..+.... .+.-+.+ |+..++ -+|++++..|...+...+
T Consensus 79 ~p~TA~Dv~~s~~~~~~~~~~~~~~~~~~~~~~i~~--v~~~d~---~tv~i~l~~p~~~~~~~l 138 (476)
T cd08512 79 NPVTAEDVKYSFERALKLNKGPAFILTQTSLNVPET--IKAVDD---YTVVFKLDKPPALFLSTL 138 (476)
T ss_pred CcCCHHHhHhHHHHHhccCCCCcceeecccccccee--EEEcCC---CeEEEEECCCcHHHHHHh
Confidence 4799999999999999887653322 1344566 776554 455666666655554444
No 41
>TIGR02180 GRX_euk Glutaredoxin. This model represents eukaryotic glutaredoxins and includes sequences from fungi, plants and metazoans as well as viruses.
Probab=24.28 E-value=1.7e+02 Score=18.69 Aligned_cols=19 Identities=11% Similarity=0.011 Sum_probs=12.2
Q ss_pred EeCCCCCchHHHHHHHHHH
Q 031455 82 TPTVEHCSMATVIGLCLRV 100 (159)
Q Consensus 82 tlT~p~Cp~~~~I~~~V~~ 100 (159)
..+.++||.-..+..-+..
T Consensus 3 ~f~~~~Cp~C~~~~~~L~~ 21 (84)
T TIGR02180 3 VFSKSYCPYCKKAKEILAK 21 (84)
T ss_pred EEECCCChhHHHHHHHHHH
Confidence 3567889887775544433
No 42
>cd08497 PBP2_NikA_DppA_OppA_like_14 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=24.18 E-value=1.3e+02 Score=26.73 Aligned_cols=55 Identities=16% Similarity=0.238 Sum_probs=35.9
Q ss_pred CcCCHHHHHHHhccCCCCCCCCCccccCceeecceEEeCCCceEEEEEEeCC-CCCchHHH
Q 031455 34 EQIDQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTV-EHCSMATV 93 (159)
Q Consensus 34 ~~lt~e~I~eaL~~V~DPEl~~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT~-p~Cp~~~~ 93 (159)
+++|.++|...++.+.+|.-+....-++-|.+ |+..++ -+|+++++. |.+.+...
T Consensus 92 ~p~tA~DV~~s~~~~~~~~~~~~~~~~~~i~~--v~~~d~---~tv~i~l~~~p~~~~~~~ 147 (491)
T cd08497 92 TPVTAEDVVFSFETLKSKGPPYYRAYYADVEK--VEALDD---HTVRFTFKEKANRELPLI 147 (491)
T ss_pred CcccHhHhhhHHHHHhCCCCchhhhhhhceeE--EEEECC---CEEEEEECCCCCcchhhh
Confidence 36999999999999999872222222345667 777654 456677777 55555444
No 43
>PRK13817 ribosome-binding factor A; Provisional
Probab=24.13 E-value=3e+02 Score=20.35 Aligned_cols=40 Identities=10% Similarity=0.294 Sum_probs=27.2
Q ss_pred HHHHHHHh-ccCCCCCCCCCccccCceeecceEEeCCCceEEEEEEeC
Q 031455 38 QQEVFDHV-RDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPT 84 (159)
Q Consensus 38 ~e~I~eaL-~~V~DPEl~~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT 84 (159)
.++|-++| +.+.||-++ +--|.+ |.+..|...++|.+++-
T Consensus 13 ~reis~il~~ei~dp~l~-----~vtVt~--V~vS~Dl~~AkVyvs~~ 53 (119)
T PRK13817 13 HQQLAELLKKEVRDSRLS-----KISLTA--VSISPDLKQAKVFYSLL 53 (119)
T ss_pred HHHHHHHHHHhccCCCCC-----ceEEeE--EEECCCCCEEEEEEEEC
Confidence 34455555 579999986 222556 88887777888877665
No 44
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=23.76 E-value=70 Score=22.95 Aligned_cols=37 Identities=35% Similarity=0.652 Sum_probs=28.0
Q ss_pred cCcCCHHHHHHHhccCCCCCCCCC--------ccccCceeecceEEeC
Q 031455 33 AEQIDQQEVFDHVRDIKDPEHPYS--------LEELKVITEDAIEVDD 72 (159)
Q Consensus 33 ~~~lt~e~I~eaL~~V~DPEl~~~--------IVdLGlV~~~~I~I~~ 72 (159)
..++|.++|++.|+. .+|.++.+ +++.|+|.. +...+
T Consensus 21 ~~~~ta~ei~~~l~~-~~~~is~~TVYR~L~~L~e~Gli~~--~~~~~ 65 (120)
T PF01475_consen 21 PEHLTAEEIYDKLRK-KGPRISLATVYRTLDLLEEAGLIRK--IEFGD 65 (120)
T ss_dssp SSSEEHHHHHHHHHH-TTTT--HHHHHHHHHHHHHTTSEEE--EEETT
T ss_pred CCCCCHHHHHHHhhh-ccCCcCHHHHHHHHHHHHHCCeEEE--EEcCC
Confidence 347999999999995 67887744 679999999 87763
No 45
>TIGR02898 spore_YhcN_YlaJ sporulation lipoprotein, YhcN/YlaJ family. YhcN and YlaJ 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 that is not included in the seed alignment for this model. A portion of the low-complexity region between the lipoprotein signal sequence and the main conserved region of the protein family was also excised from the seed alignment.
Probab=22.98 E-value=2.4e+02 Score=22.20 Aligned_cols=59 Identities=10% Similarity=0.043 Sum_probs=42.0
Q ss_pred ccccCceeecceEEeCCCceEEEEEEeCCCC-CchHHHHHHHHHHHHHhhCCCceEEEEEEc
Q 031455 57 LEELKVITEDAIEVDDERSYVRVTFTPTVEH-CSMATVIGLCLRVKLMRSLPPRFKVDIMVA 117 (159)
Q Consensus 57 IVdLGlV~~~~I~I~~~~~~V~V~mtlT~p~-Cp~~~~I~~~V~~aL~~~v~~v~~V~V~i~ 117 (159)
+..+.-|.+..+-+.++ ++.|-+.+.... -.....|+..|..++++..|....|-|-=.
T Consensus 63 v~~v~~V~dA~vvVtg~--~A~Vgv~~~~~~~~~~~~~iK~~Va~~Vk~~dp~~~~VyVsaD 122 (158)
T TIGR02898 63 AAKVKGVKDATVVITGN--YAYVGVDLTNGLEGSVTDELKEKVAETVKSTDNRIANVYVSAD 122 (158)
T ss_pred HhcCCCCceEEEEEECC--EEEEEEEcCCCcchhhHHHHHHHHHHHHHhhCCCcceEEEEcC
Confidence 45566677755666655 788888876554 556789999999999554787778887433
No 46
>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=22.06 E-value=2.1e+02 Score=19.84 Aligned_cols=40 Identities=13% Similarity=0.091 Sum_probs=21.6
Q ss_pred eEEEEEEeCCCCCch---HHHHHHHHHHHHHhhCCCc--eEEEEEEc
Q 031455 76 YVRVTFTPTVEHCSM---ATVIGLCLRVKLMRSLPPR--FKVDIMVA 117 (159)
Q Consensus 76 ~V~V~mtlT~p~Cp~---~~~I~~~V~~aL~~~v~~v--~~V~V~i~ 117 (159)
.|.+.+.+. .|+++ ...++..|+.+| +.+-|. .+|+|.+.
T Consensus 61 ~v~l~v~v~-~g~~i~~v~~~iq~~V~~~v-~~~tg~~v~~V~V~V~ 105 (108)
T PF03780_consen 61 TVDLHVVVE-YGVNIPEVAEEIQEKVKEAV-EEMTGIEVSEVNVHVE 105 (108)
T ss_pred EEEEEEEEE-CCccHHHHHHHHHHHHHHHH-HHHHCCeeEEEEEEEE
Confidence 444444442 33444 456677777777 444454 46666554
No 47
>cd08511 PBP2_NikA_DppA_OppA_like_5 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This family represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is mos
Probab=21.90 E-value=1.8e+02 Score=25.31 Aligned_cols=56 Identities=18% Similarity=0.222 Sum_probs=34.8
Q ss_pred CcCCHHHHHHHhccCCCCCCCCCccccCceeecceEEeCCCceEEEEEEeCCCCCchHHHH
Q 031455 34 EQIDQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVI 94 (159)
Q Consensus 34 ~~lt~e~I~eaL~~V~DPEl~~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~~~I 94 (159)
+++|.++|...+..+.+|.-...--.+..|.. |+..++ -+|+++++.|...+...+
T Consensus 75 ~pvTA~Dv~~s~~~~~~~~~~~~~~~~~~i~~--v~~~d~---~tv~i~l~~p~~~~~~~l 130 (467)
T cd08511 75 TPFDAAAVKANLERLLTLPGSNRKSELASVES--VEVVDP---ATVRFRLKQPFAPLLAVL 130 (467)
T ss_pred CCCCHHHHHHHHHHHhCCCCcccccccceeeE--EEecCC---CeEEEEeCCCCHHHHHHH
Confidence 47999999999999888753211122345666 766544 455666666654454444
No 48
>PRK09111 DNA polymerase III subunits gamma and tau; Validated
Probab=21.58 E-value=3.1e+02 Score=25.96 Aligned_cols=102 Identities=15% Similarity=0.199 Sum_probs=65.8
Q ss_pred CHHHHHHHhccCCCCCCCCCccccCceeecceEEeCCCceEEEEEEeCCCCCchHHHHHHHHHHHHHhhCCC-ceEEEEE
Q 031455 37 DQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIGLCLRVKLMRSLPP-RFKVDIM 115 (159)
Q Consensus 37 t~e~I~eaL~~V~DPEl~~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~~~I~~~V~~aL~~~v~~-v~~V~V~ 115 (159)
+=+++.+.+++-.|..+...+-.- |+- |..+.+ ++.+.++.. +...+..++..+| ..+.| -|.|.+.
T Consensus 461 ~~~~~~~~~~~~~~~~l~~~~~~~--~~~--~~~~~g--~~~~~~~~~-----~~~~~~~~l~~~l-~~~t~~~w~v~~~ 528 (598)
T PRK09111 461 SFEDIVALAEEKRDIKLKAAVERD--VRL--VRFEPG--RLEFALAPG-----APRDLAQRLARKL-EEWTGRRWVVSVS 528 (598)
T ss_pred CHHHHHHHHHhcCcHHHHHHHHhc--ceE--EeecCC--eEEEEECCC-----CChHHHHHHHHHH-HHHhCCceEEEEe
Confidence 458999999999998887766652 344 445543 777776665 4456777788888 45544 4677774
Q ss_pred EcCCCCcCHHHHHHHhcchhhhhcccCCccHHHHHhh
Q 031455 116 VAPGTHATEAAVNKQLNDKERVAAALENPNLVDMVDE 152 (159)
Q Consensus 116 i~~~~h~~~~~lnkql~dkErv~aa~e~~~l~~~~~~ 152 (159)
-..+.++-.+.-+. ..+++...+.+++.++.++..
T Consensus 529 ~~~~~~t~~e~~~~--~~~~~~~~~~~~p~v~~~l~~ 563 (598)
T PRK09111 529 REGGQPTLAEQEAA--AREEREAAAEADPLVAAVLAA 563 (598)
T ss_pred cCCCCCCHHHHHHH--HHHHHHHHHhhCcHHHHHHHh
Confidence 44444443332222 227788888888888877654
No 49
>cd08508 PBP2_NikA_DppA_OppA_like_1 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=21.45 E-value=1.8e+02 Score=25.50 Aligned_cols=55 Identities=16% Similarity=0.232 Sum_probs=34.7
Q ss_pred CcCCHHHHHHHhccCCCCCCCCCccccCceeecceEEeCCCceEEEEEEeCCCCCchHHH
Q 031455 34 EQIDQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATV 93 (159)
Q Consensus 34 ~~lt~e~I~eaL~~V~DPEl~~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~~~ 93 (159)
.++|.++|...+..+.+|+.+-..-.+.-|.. |+..++ -+|++++..|...+...
T Consensus 80 ~plTA~Dv~~s~~~~~~~~~~~~~~~~~~i~~--v~~~d~---~tv~i~l~~p~~~~~~~ 134 (470)
T cd08508 80 GEVTAEDVVFSLERAADPKRSSFSADFAALKE--VEAHDP---YTVRITLSRPVPSFLGL 134 (470)
T ss_pred CceeHHHhHhHHHhhhCCCCCcccccccccee--EEecCC---CeEEEEECCCCchHHHH
Confidence 56999999999999999883221222444666 776654 34555665654444333
No 50
>cd08520 PBP2_NikA_DppA_OppA_like_21 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=21.03 E-value=2e+02 Score=25.20 Aligned_cols=56 Identities=20% Similarity=0.170 Sum_probs=34.2
Q ss_pred CcCCHHHHHHHhccCCCCCCCCCccccCceeecceEEeCCCceEEEEEEeCCCCCchHHHH
Q 031455 34 EQIDQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVI 94 (159)
Q Consensus 34 ~~lt~e~I~eaL~~V~DPEl~~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT~p~Cp~~~~I 94 (159)
.++|.++|...+..+.++.....-..+..|.+ |+..++ -+|.+++..|..++...+
T Consensus 75 ~pvtA~Dv~~s~~r~~~~~~~~~~~~~~~i~~--v~~~d~---~tv~i~l~~p~~~~~~~l 130 (468)
T cd08520 75 EPLTAEDVAFTFDYMKKHPYVWVDIELSIIER--VEALDD---YTVKITLKRPYAPFLEKI 130 (468)
T ss_pred CCccHHHHHHHHHHHhhCCCCcccccccceee--EEecCC---cEEEEEEccCCchHHHHh
Confidence 47999999999988776543321112344666 777654 345555666655554444
No 51
>PRK00521 rbfA ribosome-binding factor A; Validated
Probab=20.88 E-value=3.4e+02 Score=19.81 Aligned_cols=40 Identities=28% Similarity=0.417 Sum_probs=26.3
Q ss_pred HHHHHHh-ccCCCCCCCCCccccCceeecceEEeCCCceEEEEEEeCC
Q 031455 39 QEVFDHV-RDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTV 85 (159)
Q Consensus 39 e~I~eaL-~~V~DPEl~~~IVdLGlV~~~~I~I~~~~~~V~V~mtlT~ 85 (159)
++|-++| +.+.||.++ +--|.. |.+..|...+.|.+.+-.
T Consensus 17 ~~is~il~~~i~d~~~~-----~vtIt~--V~vS~Dl~~AkVyvs~~~ 57 (120)
T PRK00521 17 RELAEILQREIKDPRLG-----MVTVTD--VEVSPDLAHAKVYVTVLG 57 (120)
T ss_pred HHHHHHHHHHccCCCCC-----eeEEEE--EEECCCCCEEEEEEEECC
Confidence 3444455 378999985 122445 788777778888888743
Done!