Query 033611
Match_columns 115
No_of_seqs 162 out of 1026
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 04:16:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033611.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033611hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3381 Uncharacterized conser 99.9 1.3E-23 2.9E-28 152.9 6.3 112 2-114 1-117 (161)
2 COG2151 PaaD Predicted metal-s 99.9 1.2E-22 2.5E-27 142.0 8.7 79 33-114 9-87 (111)
3 PF01883 DUF59: Domain of unkn 99.8 5.9E-19 1.3E-23 113.0 7.9 72 38-114 1-72 (72)
4 COG5133 Uncharacterized conser 99.7 1.8E-18 3.8E-23 126.2 5.8 113 2-114 1-137 (181)
5 TIGR03406 FeS_long_SufT probab 99.7 5.9E-17 1.3E-21 120.8 10.1 80 32-114 69-151 (174)
6 TIGR02945 SUF_assoc FeS assemb 99.5 2.9E-13 6.3E-18 91.4 10.0 73 38-114 3-75 (99)
7 TIGR02159 PA_CoA_Oxy4 phenylac 99.4 4.8E-13 1E-17 97.4 8.4 53 48-104 1-54 (146)
8 PRK11670 antiporter inner memb 99.3 2E-11 4.3E-16 99.7 9.9 76 34-114 10-85 (369)
9 PF01106 NifU: NifU-like domai 94.1 0.5 1.1E-05 29.9 7.3 44 68-113 22-66 (68)
10 TIGR03341 YhgI_GntY IscR-regul 92.8 0.67 1.5E-05 35.0 7.3 71 38-114 107-178 (190)
11 COG0694 Thioredoxin-like prote 91.4 1.2 2.6E-05 30.2 6.5 73 40-114 9-83 (93)
12 PRK11190 Fe/S biogenesis prote 90.1 1.4 3E-05 33.4 6.5 71 37-113 107-179 (192)
13 TIGR02000 NifU_proper Fe-S clu 89.6 2.2 4.8E-05 34.2 7.6 69 39-115 222-290 (290)
14 PF10500 SR-25: Nuclear RNA-sp 70.0 3.1 6.7E-05 32.5 1.8 25 32-56 156-183 (225)
15 PF09650 PHA_gran_rgn: Putativ 65.2 9 0.0002 25.3 3.1 35 68-104 51-85 (87)
16 TIGR02610 PHA_gran_rgn putativ 60.6 9.6 0.00021 25.6 2.6 36 68-105 54-89 (91)
17 PF09580 Spore_YhcN_YlaJ: Spor 60.2 50 0.0011 23.7 6.6 53 59-114 86-138 (177)
18 COG0858 RbfA Ribosome-binding 54.9 70 0.0015 22.3 6.9 32 47-85 25-56 (118)
19 PF13192 Thioredoxin_3: Thiore 52.6 44 0.00096 20.7 4.6 27 85-114 7-33 (76)
20 COG0735 Fur Fe2+/Zn2+ uptake r 44.0 23 0.00051 25.2 2.6 35 35-72 36-78 (145)
21 cd08499 PBP2_Ylib_like The sub 37.2 99 0.0021 25.2 5.6 57 34-95 74-131 (474)
22 PRK13818 ribosome-binding fact 34.0 1.6E+02 0.0035 20.4 7.0 33 46-85 22-54 (121)
23 PF02033 RBFA: Ribosome-bindin 33.7 1E+02 0.0022 20.3 4.3 44 39-89 11-55 (104)
24 TIGR00412 redox_disulf_2 small 33.6 1.2E+02 0.0026 18.7 4.7 27 82-109 4-30 (76)
25 PF01502 PRA-CH: Phosphoribosy 33.3 86 0.0019 20.4 3.7 24 68-91 45-68 (75)
26 PRK15413 glutathione ABC trans 32.3 1.1E+02 0.0024 25.5 5.2 57 34-95 102-159 (512)
27 cd08518 PBP2_NikA_DppA_OppA_li 32.0 92 0.002 25.5 4.6 55 34-95 73-127 (464)
28 PRK13817 ribosome-binding fact 31.9 1.8E+02 0.0038 20.2 7.1 40 38-84 13-53 (119)
29 PF02575 YbaB_DNA_bd: YbaB/Ebf 31.6 1.4E+02 0.0031 19.0 5.4 39 61-102 30-68 (93)
30 cd08514 PBP2_AppA_like The sub 30.5 1.2E+02 0.0026 24.7 5.0 57 34-95 74-132 (483)
31 PF13331 DUF4093: Domain of un 30.0 36 0.00079 22.5 1.6 32 34-65 5-44 (87)
32 PHA03001 putative virion core 28.7 1.3E+02 0.0028 21.8 4.3 39 68-107 6-44 (132)
33 cd08501 PBP2_Lpqw The substrat 28.3 1.5E+02 0.0033 24.3 5.3 56 34-94 79-138 (486)
34 cd08498 PBP2_NikA_DppA_OppA_li 26.9 1.9E+02 0.0041 23.7 5.6 56 34-94 73-128 (481)
35 PRK10503 multidrug efflux syst 26.3 1.7E+02 0.0036 27.4 5.7 70 38-114 114-186 (1040)
36 cd08515 PBP2_NikA_DppA_OppA_li 26.2 1.5E+02 0.0033 24.1 4.9 57 34-95 76-134 (460)
37 PRK00153 hypothetical protein; 24.7 1.6E+02 0.0035 19.7 4.1 39 61-102 38-80 (104)
38 PF08529 NusA_N: NusA N-termin 24.6 87 0.0019 21.5 2.8 52 48-103 65-116 (122)
39 PF07381 DUF1495: Winged helix 24.4 44 0.00096 22.4 1.2 50 35-93 36-89 (90)
40 TIGR00334 5S_RNA_mat_M5 ribonu 24.1 33 0.00072 25.8 0.6 33 31-63 91-130 (174)
41 cd08516 PBP2_NikA_DppA_OppA_li 23.5 2E+02 0.0044 23.1 5.2 57 34-95 74-131 (457)
42 cd08490 PBP2_NikA_DppA_OppA_li 23.4 2E+02 0.0044 23.2 5.2 54 34-94 72-125 (470)
43 cd08494 PBP2_NikA_DppA_OppA_li 23.3 2.2E+02 0.0049 22.8 5.3 56 34-94 75-131 (448)
44 PRK00521 rbfA ribosome-binding 23.0 2.6E+02 0.0056 19.1 6.9 39 39-84 17-56 (120)
45 PF01475 FUR: Ferric uptake re 22.5 60 0.0013 21.7 1.6 34 35-71 23-64 (120)
46 TIGR02514 type_III_yscP type I 21.8 3.1E+02 0.0068 19.7 5.4 59 49-114 42-105 (129)
47 TIGR01297 CDF cation diffusion 21.8 3.5E+02 0.0076 20.3 8.7 69 36-114 192-263 (268)
48 cd08497 PBP2_NikA_DppA_OppA_li 21.5 1.7E+02 0.0036 24.3 4.4 55 34-93 92-147 (491)
49 cd00995 PBP2_NikA_DppA_OppA_li 21.4 2.7E+02 0.0059 22.2 5.5 55 34-93 74-129 (466)
50 cd08512 PBP2_NikA_DppA_OppA_li 21.2 2E+02 0.0044 23.4 4.7 56 34-94 79-138 (476)
No 1
>KOG3381 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.89 E-value=1.3e-23 Score=152.93 Aligned_cols=112 Identities=58% Similarity=1.013 Sum_probs=98.1
Q ss_pred CCCCCCCCceEeecccccccccCCCCCCchhcCcCCHHHHHHHhcCCCCCCCCCCceeccceeeccEEEeC---CC--cE
Q 033611 2 VSGLINANPVVYEKKERRARSASSCVNDEYAAEQIDQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDD---ER--SY 76 (115)
Q Consensus 2 ~~~~~n~np~~~~~~~~~~~~~~~~~~~~~~~~~it~~~I~~aL~~V~DPEi~~~IvdLGlI~~~~I~i~~---~~--~~ 76 (115)
++.+.|+||.||...+.+.+.+ .+..|+...+..+.+.+++.+|.|.|||+|.++.+|++|+.+.|+|.+ +. ..
T Consensus 1 ~s~l~N~np~v~~~~~~~~r~~-~s~~d~~~~~~~~~~~~~dlir~I~DPEhP~TLeqL~VV~ee~v~V~d~~~~~~~s~ 79 (161)
T KOG3381|consen 1 GSGLQNENPLVYPTRSRERRVT-ASEEDELLPDSEDAEEIFDLIRDIRDPEHPLTLEQLNVVSEEGVEVDDPNVGDEESY 79 (161)
T ss_pred CCccccCCcccccccccccccc-ccccccccCcchhHHHHHHHHhccCCCCCCccHHHccceeecceEeecCCCCCcceE
Confidence 3669999999999877766653 334566666888999999999999999999999999999999999874 22 37
Q ss_pred EEEEEEeCCCCCChHHHHHHHHHHHHHHhCCCceeEEe
Q 033611 77 VRVTFTPTVEHCSMATVIGLCLRVKLMRSLPPRFKVRR 114 (115)
Q Consensus 77 V~V~mtlT~p~Cp~~~~I~~~v~~~L~~~~~~~~~V~v 114 (115)
|+|.||||.|||+|+..|+.+||-+|.+++|..++|+|
T Consensus 80 V~i~ftPTipHCSmaTlIGLcIrVkl~RsLp~rfkvdV 117 (161)
T KOG3381|consen 80 VRITFTPTIPHCSMATLIGLCIRVKLLRSLPPRFKVDV 117 (161)
T ss_pred EEEEeccCCCcchHHhhhhheeeeeeeecCCCceeEEE
Confidence 99999999999999999999999999999999999886
No 2
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=99.88 E-value=1.2e-22 Score=142.03 Aligned_cols=79 Identities=24% Similarity=0.433 Sum_probs=69.4
Q ss_pred cCcCCHHHHHHHhcCCCCCCCCCCceeccceeeccEEEeCCCcEEEEEEEeCCCCCChHHHHHHHHHHHHHHhCCCceeE
Q 033611 33 AEQIDQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIGLCLRVKLMRSLPPRFKV 112 (115)
Q Consensus 33 ~~~it~~~I~~aL~~V~DPEi~~~IvdLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~~I~~~v~~~L~~~~~~~~~V 112 (115)
+.+.++++|+++|++|+|||+|++|++|||||+ |.+++.++.++|+||||+||||++..|..++++++ +.+++...+
T Consensus 9 ~~~~~~~~i~~aL~~V~DPEi~idIvdLGLVy~--v~i~~~~~~v~v~mtlT~~gCP~~~~i~~~v~~al-~~~~~v~~v 85 (111)
T COG2151 9 AIKVTLEDILEALKTVIDPEIGIDIVDLGLVYE--VDIDDVDGLVKVKMTLTSPGCPLAEVIADQVEAAL-EEIPGVEDV 85 (111)
T ss_pred hhhhhHHHHHHHhhcCCCcccceeeEeeccEEE--EEEecCCceEEEEEecCCCCCCccHHHHHHHHHHH-HhcCCcceE
Confidence 345689999999999999999999999999999 99987223799999999999999999999999999 778875544
Q ss_pred Ee
Q 033611 113 RR 114 (115)
Q Consensus 113 ~v 114 (115)
+|
T Consensus 86 ~V 87 (111)
T COG2151 86 EV 87 (111)
T ss_pred EE
Confidence 43
No 3
>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=99.79 E-value=5.9e-19 Score=112.99 Aligned_cols=72 Identities=26% Similarity=0.412 Sum_probs=64.1
Q ss_pred HHHHHHHhcCCCCCCCCCCceeccceeeccEEEeCCCcEEEEEEEeCCCCCChHHHHHHHHHHHHHHhCCCceeEEe
Q 033611 38 QQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIGLCLRVKLMRSLPPRFKVRR 114 (115)
Q Consensus 38 ~~~I~~aL~~V~DPEi~~~IvdLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~~I~~~v~~~L~~~~~~~~~V~v 114 (115)
+++|+++|++|+||++|.||++||+|++ |.++++ +|+|.|++++|+||+...|..+++.+| ++++++.+|+|
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 999763 899999999999999999999999999 69999988876
No 4
>COG5133 Uncharacterized conserved protein [Function unknown]
Probab=99.75 E-value=1.8e-18 Score=126.18 Aligned_cols=113 Identities=46% Similarity=0.794 Sum_probs=94.4
Q ss_pred CCCCCCCCceEeecccccccccC----------------CCCC---CchhcCcCCHHHHHHHhcCCCCCCCCCCceeccc
Q 033611 2 VSGLINANPVVYEKKERRARSAS----------------SCVN---DEYAAEQIDQQEVFDHVRDIKDPEHPYSLEELKV 62 (115)
Q Consensus 2 ~~~~~n~np~~~~~~~~~~~~~~----------------~~~~---~~~~~~~it~~~I~~aL~~V~DPEi~~~IvdLGl 62 (115)
|+.+-|.||.|.+-++...+..+ ++.+ -+.+.+.++.++||+.++.|.|||+|+++..||+
T Consensus 1 ~a~~~nenpdi~e~NqlP~r~e~~~dlll~ss~e~~~piese~~~~~~ee~d~id~qeiydLia~I~DPEHPltL~QLsV 80 (181)
T COG5133 1 MAEFLNENPDIKEMNQLPFRAESEEDLLLGSSLEERHPIESENGVLQNEEPDLIDQQEIYDLIADIRDPEHPLTLEQLSV 80 (181)
T ss_pred CccccccCcchhhhhcCCccccchhhhhcccchhhcCcccccccccccCCCCCcCHHHHHHHHHhcCCCCCCccHhhcce
Confidence 56789999999998888554211 1111 1345567999999999999999999999999999
Q ss_pred eeeccEEEeCCC-----cEEEEEEEeCCCCCChHHHHHHHHHHHHHHhCCCceeEEe
Q 033611 63 ITEDAIEVDDER-----SYVRVTFTPTVEHCSMATVIGLCLRVKLMRSLPPRFKVRR 114 (115)
Q Consensus 63 I~~~~I~i~~~~-----~~V~V~mtlT~p~Cp~~~~I~~~v~~~L~~~~~~~~~V~v 114 (115)
|.-++|.+.++. .-|.|.+|||.|+|+|+..|+..||.+|.+.+|+.+.|+|
T Consensus 81 V~lEdi~v~D~~~~n~i~~v~v~itPTIpHCSmatlIGLcIrvrleR~lpprF~v~v 137 (181)
T COG5133 81 VSLEDISVPDGIAPNVIRCVKVVITPTIPHCSMATLIGLCIRVRLERHLPPRFHVQV 137 (181)
T ss_pred eeeccccccCCCCCCeeEEEEEEeccCCCchhHHHHhhhheeeeehhcCCCceeEEE
Confidence 999999986543 3589999999999999999999999999999999988876
No 5
>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=99.71 E-value=5.9e-17 Score=120.85 Aligned_cols=80 Identities=23% Similarity=0.361 Sum_probs=70.2
Q ss_pred hcCcCCHHHHHHHhcCCCCCCCCCCceeccceeeccEEEeC---CCcEEEEEEEeCCCCCChHHHHHHHHHHHHHHhCCC
Q 033611 32 AAEQIDQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDD---ERSYVRVTFTPTVEHCSMATVIGLCLRVKLMRSLPP 108 (115)
Q Consensus 32 ~~~~it~~~I~~aL~~V~DPEi~~~IvdLGlI~~~~I~i~~---~~~~V~V~mtlT~p~Cp~~~~I~~~v~~~L~~~~~~ 108 (115)
..+..++++|+++|++|+|||++.||++||+||+ +.+++ ++.+|+|.|++|+|+|++...|..+++.+| +.+++
T Consensus 69 ~~~~~~ee~V~eaL~tV~DPei~~nIVeLGlV~~--I~Id~~~~~~~~V~I~mtLt~p~c~~~~~L~~dV~~aL-~~l~g 145 (174)
T TIGR03406 69 ADGEDNEDQVWEQLRTVYDPEIPVNIVDLGLVYG--CRVEKLGEGQFRVDIEMTLTAPGCGMGPVLVEDVEDKV-LAVPN 145 (174)
T ss_pred ccccccHHHHHHHHcCCCCCCCCCChHHcCCeEE--EEEecccCCCCEEEEEEEeCCCCCcHHHHHHHHHHHHH-HhCCC
Confidence 3456788999999999999999999999999999 98876 323799999999999999999999999999 77888
Q ss_pred ceeEEe
Q 033611 109 RFKVRR 114 (115)
Q Consensus 109 ~~~V~v 114 (115)
..+|+|
T Consensus 146 V~~V~V 151 (174)
T TIGR03406 146 VDEVEV 151 (174)
T ss_pred ceeEEE
Confidence 665554
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=99.50 E-value=2.9e-13 Score=91.36 Aligned_cols=73 Identities=27% Similarity=0.442 Sum_probs=65.0
Q ss_pred HHHHHHHhcCCCCCCCCCCceeccceeeccEEEeCCCcEEEEEEEeCCCCCChHHHHHHHHHHHHHHhCCCceeEEe
Q 033611 38 QQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIGLCLRVKLMRSLPPRFKVRR 114 (115)
Q Consensus 38 ~~~I~~aL~~V~DPEi~~~IvdLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~~I~~~v~~~L~~~~~~~~~V~v 114 (115)
+++|+++|++++||+++.+|+++|+|++ +.++++ +.|+|.+++++|+||....+...++.+| ..+++..+|+|
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 75 (99)
T TIGR02945 3 KDAVIEALKTVYDPEIPVNIYELGLIYD--IDVDDD-GHVDIQMTLTAPNCPVAGSMPGEVENAV-RAVPGVGSVTV 75 (99)
T ss_pred HHHHHHHHcCCCCCCCCCCeecCCCeeE--EEECCC-CeEEEEEEECCCCCChHHHHHHHHHHHH-HhCCCCceEEE
Confidence 4789999999999999999999999999 998742 3799999999999999999999999999 67887655554
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=99.44 E-value=4.8e-13 Score=97.38 Aligned_cols=53 Identities=36% Similarity=0.547 Sum_probs=49.5
Q ss_pred CCCCCCC-CCceeccceeeccEEEeCCCcEEEEEEEeCCCCCChHHHHHHHHHHHHHH
Q 033611 48 IKDPEHP-YSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIGLCLRVKLMR 104 (115)
Q Consensus 48 V~DPEi~-~~IvdLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~~I~~~v~~~L~~ 104 (115)
|.|||+| +||++||+|++ |+++++ .|+|+|+||++|||+.+.|..+++++|.+
T Consensus 1 v~DPEi~~~sIvdLG~Vr~--V~v~gd--~V~VtIt~Ty~gcpa~e~L~~~I~~aL~~ 54 (146)
T TIGR02159 1 VPDPEIPVVSVTDLGMVRE--VDVDGG--GVVVKFTPTYSGCPALEVIRQDIRDAVRA 54 (146)
T ss_pred CcCCCCCCCCchhcCCeeE--EEEECC--EEEEEEEeCCCCCchHHHHHHHHHHHHHh
Confidence 7899999 89999999999 999764 79999999999999999999999999944
No 8
>PRK11670 antiporter inner membrane protein; Provisional
Probab=99.29 E-value=2e-11 Score=99.70 Aligned_cols=76 Identities=11% Similarity=0.093 Sum_probs=68.3
Q ss_pred CcCCHHHHHHHhcCCCCCCCCCCceeccceeeccEEEeCCCcEEEEEEEeCCCCCChHHHHHHHHHHHHHHhCCCceeEE
Q 033611 34 EQIDQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIGLCLRVKLMRSLPPRFKVR 113 (115)
Q Consensus 34 ~~it~~~I~~aL~~V~DPEi~~~IvdLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~~I~~~v~~~L~~~~~~~~~V~ 113 (115)
..+++++|+++|++|.||+++.+|+++|+|++ +.++++ ++.|.+++|+++||+...+..+++++| +.+++..+++
T Consensus 10 ~~~~~~~v~~~l~~v~~p~~~~~~~~~~~v~~--~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~ 84 (369)
T PRK11670 10 PEALRAMVAGTLANFQHPTLKHNLTTLKALHH--VALLDD--TLHIELVMPFVWNSAFEELKEQCSAEL-LRITGAKAID 84 (369)
T ss_pred ccchHHHHHHHHhcCCCCCCCCChhhhCCeeE--EEEeCC--EEEEEEEECCCCchHHHHHHHHHHHHH-HhcCCCceEE
Confidence 34677999999999999999999999999999 999754 799999999999999999999999999 7788866555
Q ss_pred e
Q 033611 114 R 114 (115)
Q Consensus 114 v 114 (115)
|
T Consensus 85 ~ 85 (369)
T PRK11670 85 W 85 (369)
T ss_pred E
Confidence 4
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=94.11 E-value=0.5 Score=29.93 Aligned_cols=44 Identities=23% Similarity=0.364 Sum_probs=35.6
Q ss_pred EEEeCCCcEEEEEEEeCCCCCChHHH-HHHHHHHHHHHhCCCceeEE
Q 033611 68 IEVDDERSYVRVTFTPTVEHCSMATV-IGLCLRVKLMRSLPPRFKVR 113 (115)
Q Consensus 68 I~i~~~~~~V~V~mtlT~p~Cp~~~~-I~~~v~~~L~~~~~~~~~V~ 113 (115)
+.++++ .|+|.|+=...|||++.. +...|+++|++.+|...+|.
T Consensus 22 v~v~~~--~V~V~l~GaC~gC~~s~~Tl~~~Ie~~L~~~~~~v~~V~ 66 (68)
T PF01106_consen 22 VDVDDG--VVYVRLTGACSGCPSSDMTLKQGIEQALREAVPEVKRVV 66 (68)
T ss_dssp EEEETT--EEEEEEESSCCSSCCHHHHHHHHHHHHHHHHSTT-SEEE
T ss_pred EEecCC--EEEEEEEeCCCCCCCHHHHHHHHHHHHHHHHCCCCceEE
Confidence 456654 899999999999999854 55999999988999887775
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=92.84 E-value=0.67 Score=34.99 Aligned_cols=71 Identities=17% Similarity=0.250 Sum_probs=49.4
Q ss_pred HHHHHHHhcCCCCCCCCCCceeccceeeccEEEeCCCcEEEEEEEeCCCCCChHH-HHHHHHHHHHHHhCCCceeEEe
Q 033611 38 QQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMAT-VIGLCLRVKLMRSLPPRFKVRR 114 (115)
Q Consensus 38 ~~~I~~aL~~V~DPEi~~~IvdLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~-~I~~~v~~~L~~~~~~~~~V~v 114 (115)
.++|.++|.+-.-|-+-. +=|=|.- +.++++ +.|.|.|+=...|||++. .+...|+..|++.+|.+.+|.-
T Consensus 107 ~~~i~~~l~~~irP~l~~---dGGdiel--v~v~~~-~~v~v~l~GaC~gC~~s~~Tl~~~ie~~l~~~~p~v~~V~~ 178 (190)
T TIGR03341 107 EERINYVLQSEINPQLAS---HGGKVTL--VEITDD-GVAVLQFGGGCNGCSMVDVTLKDGVEKTLLERFPELKGVRD 178 (190)
T ss_pred HHHHHHHHHhccCHHHHh---cCCceEE--EEEcCC-CEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCCcceEEE
Confidence 455666665434455443 3444554 556544 378999999999999986 4667999999888898777653
No 11
>COG0694 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]
Probab=91.43 E-value=1.2 Score=30.24 Aligned_cols=73 Identities=15% Similarity=0.244 Sum_probs=46.4
Q ss_pred HHHHHhcCCCCCCCC-CCceeccceeeccEEEeCCCcEEEEEEEeCCCCCChHH-HHHHHHHHHHHHhCCCceeEEe
Q 033611 40 EVFDHVRDIKDPEHP-YSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMAT-VIGLCLRVKLMRSLPPRFKVRR 114 (115)
Q Consensus 40 ~I~~aL~~V~DPEi~-~~IvdLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~-~I~~~v~~~L~~~~~~~~~V~v 114 (115)
++++++..+.|-++. .=.-+=|=|.- +.++...+.|.+.+-=...|||+.. .++..|++.|+..+|+..+|..
T Consensus 9 ~~~e~v~~~l~~~irP~l~~dGGdve~--~~i~~~~g~V~l~l~GaC~gC~sS~~TLk~gIE~~L~~~i~ev~~V~~ 83 (93)
T COG0694 9 ELLERVEEVLDEKIRPQLAMDGGDVEL--VGIDEEDGVVYLRLGGACSGCPSSTVTLKNGIERQLKEEIPEVKEVEQ 83 (93)
T ss_pred HHHHHHHHHHHhccCcceeccCCeEEE--EEEecCCCeEEEEeCCcCCCCcccHHHHHHHHHHHHHHhCCccceEEE
Confidence 334444444442222 22334454444 5565423379999999999999986 4666799999888888777754
No 12
>PRK11190 Fe/S biogenesis protein NfuA; Provisional
Probab=90.08 E-value=1.4 Score=33.43 Aligned_cols=71 Identities=18% Similarity=0.264 Sum_probs=49.6
Q ss_pred CHHHHHHHhcCCCCCCCCCCceeccceeeccEEEeCCCcEEEEEEEeCCCCCChHHH-HHHHHHHHHHHhCC-CceeEE
Q 033611 37 DQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATV-IGLCLRVKLMRSLP-PRFKVR 113 (115)
Q Consensus 37 t~~~I~~aL~~V~DPEi~~~IvdLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~~-I~~~v~~~L~~~~~-~~~~V~ 113 (115)
..++|.++|.+-.-|-+-.+ -|=|.- +.++++ +.|.|.|+=...|||++.. +...|+..|++.+| ...+|.
T Consensus 107 ~~~~i~~~l~~~irP~l~~d---GGdiel--v~v~~~-~~v~v~l~GaC~gC~~s~~Tl~~~Ie~~l~~~~p~~i~~v~ 179 (192)
T PRK11190 107 LMERVEYVLQSQINPQLAGH---GGRVSL--MEITED-GYAILQFGGGCNGCSMVDVTLKEGIEKQLLNEFPGELKGVR 179 (192)
T ss_pred HHHHHHHHHHhccChhHHhc---CCcEEE--EEEcCC-CEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCHhhceEE
Confidence 34566777765555766544 444444 556544 3689999999999999864 66699999988888 665554
No 13
>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=89.56 E-value=2.2 Score=34.23 Aligned_cols=69 Identities=22% Similarity=0.172 Sum_probs=49.4
Q ss_pred HHHHHHhcCCCCCCCCCCceeccceeeccEEEeCCCcEEEEEEEeCCCCCChHHHHHHHHHHHHHHhCCCceeEEeC
Q 033611 39 QEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIGLCLRVKLMRSLPPRFKVRRV 115 (115)
Q Consensus 39 ~~I~~aL~~V~DPEi~~~IvdLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~~I~~~v~~~L~~~~~~~~~V~v~ 115 (115)
++|.++| +-.-|-+-.+ =|=|.- +.|++ +.|+|.|+=.-.|||+...--..|++.|+..+|+..+|.-|
T Consensus 222 ~~v~~~l-~~irP~l~~d---GGdv~l--v~v~~--~~v~v~l~GaC~gC~~s~~Tl~~Ie~~l~~~~p~~~~V~~v 290 (290)
T TIGR02000 222 QLIQKVL-EEVRPVLQAD---GGDVEL--YDVDG--KIVYVVLTGACSGCSMSTMTLKGIQQRLRERLGEFVVVEAV 290 (290)
T ss_pred HHHHHHH-HHhCchHhhc---CCcEEE--EEEeC--CEEEEEEeeCCCCCcchHHHHHHHHHHHHHhCCCceEEEeC
Confidence 4456666 3345655544 454554 55654 37999999999999998766666999998889988887654
No 14
>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=70.02 E-value=3.1 Score=32.54 Aligned_cols=25 Identities=24% Similarity=0.377 Sum_probs=20.5
Q ss_pred hcCcCCHHHH---HHHhcCCCCCCCCCC
Q 033611 32 AAEQIDQQEV---FDHVRDIKDPEHPYS 56 (115)
Q Consensus 32 ~~~~it~~~I---~~aL~~V~DPEi~~~ 56 (115)
.|-++|+++. ...++.|+|||.|.+
T Consensus 156 am~PmTkEEyearQSvIRrVvDpETGRt 183 (225)
T PF10500_consen 156 AMAPMTKEEYEARQSVIRRVVDPETGRT 183 (225)
T ss_pred hcCCCCHHHHHHHHhhheeeecCCCCce
Confidence 4678999886 456999999999965
No 15
>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=65.22 E-value=9 Score=25.32 Aligned_cols=35 Identities=17% Similarity=0.186 Sum_probs=29.8
Q ss_pred EEEeCCCcEEEEEEEeCCCCCChHHHHHHHHHHHHHH
Q 033611 68 IEVDDERSYVRVTFTPTVEHCSMATVIGLCLRVKLMR 104 (115)
Q Consensus 68 I~i~~~~~~V~V~mtlT~p~Cp~~~~I~~~v~~~L~~ 104 (115)
+.|.++ .|++.+.|.-.--|++..|...|++.|.+
T Consensus 51 l~V~~d--~v~l~v~Lg~Ll~~f~~~Ie~~I~~~Ld~ 85 (87)
T PF09650_consen 51 LDVADD--HVRLEVKLGFLLSPFKGKIEQEIEKNLDK 85 (87)
T ss_pred EEEcCC--EEEEEEEcHHHHHHHHHHHHHHHHHHHHh
Confidence 556554 79999999999999999999999999844
No 16
>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=60.63 E-value=9.6 Score=25.57 Aligned_cols=36 Identities=17% Similarity=0.170 Sum_probs=30.5
Q ss_pred EEEeCCCcEEEEEEEeCCCCCChHHHHHHHHHHHHHHh
Q 033611 68 IEVDDERSYVRVTFTPTVEHCSMATVIGLCLRVKLMRS 105 (115)
Q Consensus 68 I~i~~~~~~V~V~mtlT~p~Cp~~~~I~~~v~~~L~~~ 105 (115)
|.+.++ .|+|.+.|..---+++..|+..|++.|.+.
T Consensus 54 l~V~~d--~v~v~v~Lg~Ll~~f~~~Ie~~I~~~Ld~~ 89 (91)
T TIGR02610 54 VHLGPQ--SIRVTAELGMLLSAMSGTIKSEIERALDKA 89 (91)
T ss_pred EEEcCC--eEEEEEEhHHHHHHHHHHHHHHHHHHHHHh
Confidence 555544 799999999999999999999999998543
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=60.24 E-value=50 Score=23.72 Aligned_cols=53 Identities=11% Similarity=0.089 Sum_probs=38.2
Q ss_pred eccceeeccEEEeCCCcEEEEEEEeCCCCCChHHHHHHHHHHHHHHhCCCceeEEe
Q 033611 59 ELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIGLCLRVKLMRSLPPRFKVRR 114 (115)
Q Consensus 59 dLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~~I~~~v~~~L~~~~~~~~~V~v 114 (115)
.+.=|.+..+-+.++ .+.|.+.+... -.....|...|+.++++..|+.++|-|
T Consensus 86 ~~~~V~~A~vvv~~~--~a~Vav~~~~~-~~~~~~i~~~V~~~v~~~~p~~~~V~V 138 (177)
T PF09580_consen 86 KVPGVEDATVVVTDD--NAYVAVDLDFN-RFNTKKIKKKVEKAVKSADPRIYNVYV 138 (177)
T ss_pred cCCCceEEEEEEECC--EEEEEEEeccc-ccchhHHHHHHHHHHHHhCCCccEEEE
Confidence 344455533444443 78999999843 677899999999999776787788876
No 18
>COG0858 RbfA Ribosome-binding factor A [Translation, ribosomal structure and biogenesis]
Probab=54.89 E-value=70 Score=22.30 Aligned_cols=32 Identities=31% Similarity=0.389 Sum_probs=23.9
Q ss_pred CCCCCCCCCCceeccceeeccEEEeCCCcEEEEEEEeCC
Q 033611 47 DIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTV 85 (115)
Q Consensus 47 ~V~DPEi~~~IvdLGlI~~~~I~i~~~~~~V~V~mtlT~ 85 (115)
.|+||-++.-. |.+ |++..+-.++.|.+|+=.
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 59999987433 778 888877777877777644
No 19
>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=52.58 E-value=44 Score=20.68 Aligned_cols=27 Identities=15% Similarity=0.171 Sum_probs=17.2
Q ss_pred CCCCChHHHHHHHHHHHHHHhCCCceeEEe
Q 033611 85 VEHCSMATVIGLCLRVKLMRSLPPRFKVRR 114 (115)
Q Consensus 85 ~p~Cp~~~~I~~~v~~~L~~~~~~~~~V~v 114 (115)
+++||.=..+...++.++ ... + .++++
T Consensus 7 ~~~C~~C~~~~~~~~~~~-~~~-~-i~~ei 33 (76)
T PF13192_consen 7 SPGCPYCPELVQLLKEAA-EEL-G-IEVEI 33 (76)
T ss_dssp CSSCTTHHHHHHHHHHHH-HHT-T-EEEEE
T ss_pred CCCCCCcHHHHHHHHHHH-Hhc-C-CeEEE
Confidence 555776677777788877 444 3 44444
No 20
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=44.05 E-value=23 Score=25.24 Aligned_cols=35 Identities=20% Similarity=0.570 Sum_probs=28.9
Q ss_pred cCCHHHHHHHhcCCCCCCCCC-C-------ceeccceeeccEEEeC
Q 033611 35 QIDQQEVFDHVRDIKDPEHPY-S-------LEELKVITEDAIEVDD 72 (115)
Q Consensus 35 ~it~~~I~~aL~~V~DPEi~~-~-------IvdLGlI~~~~I~i~~ 72 (115)
+++.++|++.|++ .+|.++. + +.++|+|.. +...+
T Consensus 36 ~~sAeei~~~l~~-~~p~islaTVYr~L~~l~e~Glv~~--~~~~~ 78 (145)
T COG0735 36 HLSAEELYEELRE-EGPGISLATVYRTLKLLEEAGLVHR--LEFEG 78 (145)
T ss_pred CCCHHHHHHHHHH-hCCCCCHhHHHHHHHHHHHCCCEEE--EEeCC
Confidence 3899999999999 7899873 2 578999999 87754
No 21
>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=37.16 E-value=99 Score=25.24 Aligned_cols=57 Identities=19% Similarity=0.283 Sum_probs=38.6
Q ss_pred CcCCHHHHHHHhcCCCCCCCCCCce-eccceeeccEEEeCCCcEEEEEEEeCCCCCChHHHHH
Q 033611 34 EQIDQQEVFDHVRDIKDPEHPYSLE-ELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIG 95 (115)
Q Consensus 34 ~~it~~~I~~aL~~V~DPEi~~~Iv-dLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~~I~ 95 (115)
.++|.++|...++.+.+|+.+.... -++-|.. |+..++ -+|++++..|..++...+.
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 4699999999999999998653321 2344556 776543 4667777777666655543
No 22
>PRK13818 ribosome-binding factor A; Provisional
Probab=34.00 E-value=1.6e+02 Score=20.44 Aligned_cols=33 Identities=27% Similarity=0.480 Sum_probs=23.8
Q ss_pred cCCCCCCCCCCceeccceeeccEEEeCCCcEEEEEEEeCC
Q 033611 46 RDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTV 85 (115)
Q Consensus 46 ~~V~DPEi~~~IvdLGlI~~~~I~i~~~~~~V~V~mtlT~ 85 (115)
+.++||-++ +--|.+ |++..+...+.|.++...
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 679999985 223456 778777777888887763
No 23
>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=33.71 E-value=1e+02 Score=20.32 Aligned_cols=44 Identities=25% Similarity=0.343 Sum_probs=29.3
Q ss_pred HHHHHHhcC-CCCCCCCCCceeccceeeccEEEeCCCcEEEEEEEeCCCCCC
Q 033611 39 QEVFDHVRD-IKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCS 89 (115)
Q Consensus 39 ~~I~~aL~~-V~DPEi~~~IvdLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp 89 (115)
+.|-++|.. +.||.+ .+=-|.+ |++..+...+.|.+++...+..
T Consensus 11 ~~i~~il~~~~~d~~l-----~~vtIt~--V~ls~Dl~~a~Vy~~~~~~~~~ 55 (104)
T PF02033_consen 11 REISEILQREIKDPRL-----KLVTITR--VELSPDLSHAKVYVSILGDEEE 55 (104)
T ss_dssp HHHHHHHCTCTSSCGH-----HCEEEEE--EEECTTSSEEEEEEEESSSHHH
T ss_pred HHHHHHHHhhccCcCc-----ceEEEEE--EEECCCCCEEEEEEEEecCchh
Confidence 456666766 889987 1222345 7887777789999988654433
No 24
>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=33.62 E-value=1.2e+02 Score=18.71 Aligned_cols=27 Identities=7% Similarity=0.030 Sum_probs=20.4
Q ss_pred EeCCCCCChHHHHHHHHHHHHHHhCCCc
Q 033611 82 TPTVEHCSMATVIGLCLRVKLMRSLPPR 109 (115)
Q Consensus 82 tlT~p~Cp~~~~I~~~v~~~L~~~~~~~ 109 (115)
.+.+++||.-..+...+++.+ ++.+..
T Consensus 4 ~~~a~~C~~C~~~~~~~~~~~-~e~~~~ 30 (76)
T TIGR00412 4 QIYGTGCANCQMTEKNVKKAV-EELGID 30 (76)
T ss_pred EEECCCCcCHHHHHHHHHHHH-HHcCCC
Confidence 345699999999999888888 555543
No 25
>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=33.34 E-value=86 Score=20.43 Aligned_cols=24 Identities=13% Similarity=0.195 Sum_probs=18.8
Q ss_pred EEEeCCCcEEEEEEEeCCCCCChH
Q 033611 68 IEVDDERSYVRVTFTPTVEHCSMA 91 (115)
Q Consensus 68 I~i~~~~~~V~V~mtlT~p~Cp~~ 91 (115)
|.++-+++.+.+.+.+..|.|..+
T Consensus 45 i~~DCD~D~ll~~V~~~G~aCHtg 68 (75)
T PF01502_consen 45 IRLDCDGDALLFKVEQVGPACHTG 68 (75)
T ss_dssp EEE-TTSSEEEEEEEESS-SSTTS
T ss_pred EEecCCCCeEEEEEEeCCCCccCC
Confidence 777777779999999999999764
No 26
>PRK15413 glutathione ABC transporter substrate-binding protein GsiB; Provisional
Probab=32.31 E-value=1.1e+02 Score=25.54 Aligned_cols=57 Identities=14% Similarity=0.227 Sum_probs=39.7
Q ss_pred CcCCHHHHHHHhcCCCCCCCCCC-ceeccceeeccEEEeCCCcEEEEEEEeCCCCCChHHHHH
Q 033611 34 EQIDQQEVFDHVRDIKDPEHPYS-LEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIG 95 (115)
Q Consensus 34 ~~it~~~I~~aL~~V~DPEi~~~-IvdLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~~I~ 95 (115)
+++|.++|...+....+|..+.. ...++-|.. |+..++ -+|+|+++.|..++...+.
T Consensus 102 ~pvTA~DV~~s~~r~~~~~~~~~~~~~~~~i~~--v~~~D~---~Tv~~~l~~p~~~~~~~l~ 159 (512)
T PRK15413 102 TDFNAAAVKANLDRASNPDNHLKRYNLYKNIAK--TEAVDP---TTVKITLKQPFSAFINILA 159 (512)
T ss_pred CCccHHHHHHHHHHhhCcccccccccccccceE--EEecCC---CEEEEEECCCChHHHHHHh
Confidence 56999999999999999886422 223444555 776543 5778888888777665553
No 27
>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=32.00 E-value=92 Score=25.46 Aligned_cols=55 Identities=20% Similarity=0.312 Sum_probs=39.4
Q ss_pred CcCCHHHHHHHhcCCCCCCCCCCceeccceeeccEEEeCCCcEEEEEEEeCCCCCChHHHHH
Q 033611 34 EQIDQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIG 95 (115)
Q Consensus 34 ~~it~~~I~~aL~~V~DPEi~~~IvdLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~~I~ 95 (115)
+++|.++|...+..+.+|...... ++-|.. |+..++ -+|+|++..|.-++...+.
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 469999999999999998866443 555666 776543 4667777787766665553
No 28
>PRK13817 ribosome-binding factor A; Provisional
Probab=31.90 E-value=1.8e+02 Score=20.18 Aligned_cols=40 Identities=10% Similarity=0.294 Sum_probs=26.9
Q ss_pred HHHHHHHh-cCCCCCCCCCCceeccceeeccEEEeCCCcEEEEEEEeC
Q 033611 38 QQEVFDHV-RDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPT 84 (115)
Q Consensus 38 ~~~I~~aL-~~V~DPEi~~~IvdLGlI~~~~I~i~~~~~~V~V~mtlT 84 (115)
.++|-++| +.++||-++ +--|.+ |++..+...+.|.++.-
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 122456 88877777788877765
No 29
>PF02575 YbaB_DNA_bd: YbaB/EbfC DNA-binding family; InterPro: IPR004401 The function of this protein is unknown. It is restricted to bacteria and a few plants, such as Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A crystal structure of one member, YbaB from Haemophilus influenzae, revealed a core structure consisting of two layers, alpha/beta; YbaB forms a tight dimer with a 3-layer structure, beta/alpha/beta []. YbaB is co-transcribed with RecR, which appears to protect DNA strands of the replilcation fork when it is blocked by DNA damage. A deletion of the YbaB operon resulted in increased sensitivity to DNA-damaging agents compared with the wild-type strain.; PDB: 1PUG_B 3F42_B 1YBX_B 1J8B_A.
Probab=31.58 E-value=1.4e+02 Score=19.05 Aligned_cols=39 Identities=10% Similarity=0.130 Sum_probs=21.8
Q ss_pred cceeeccEEEeCCCcEEEEEEEeCCCCCChHHHHHHHHHHHH
Q 033611 61 KVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIGLCLRVKL 102 (115)
Q Consensus 61 GlI~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~~I~~~v~~~L 102 (115)
|+|. |.+++.|.-+.|.|.+....---...|...|..++
T Consensus 30 g~V~---V~v~g~g~v~~i~i~~~~~~~~~~~~L~~~I~~A~ 68 (93)
T PF02575_consen 30 GLVT---VTVNGNGEVVDIEIDPSALRPLDPEELEDLIVEAV 68 (93)
T ss_dssp CTEE---EEEETTS-EEEEEE-GGGGCTS-HHHHHHHHHHHH
T ss_pred CEEE---EEEecCceEEEEEEehHhhccCCHHHHHHHHHHHH
Confidence 4555 77887777788888887665233344444444444
No 30
>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=30.49 E-value=1.2e+02 Score=24.75 Aligned_cols=57 Identities=19% Similarity=0.205 Sum_probs=38.4
Q ss_pred CcCCHHHHHHHhcCCCCCCCCCCce--eccceeeccEEEeCCCcEEEEEEEeCCCCCChHHHHH
Q 033611 34 EQIDQQEVFDHVRDIKDPEHPYSLE--ELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIG 95 (115)
Q Consensus 34 ~~it~~~I~~aL~~V~DPEi~~~Iv--dLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~~I~ 95 (115)
.++|.+++...++...+|..+-... .+..|.. |+..++ -+|+++++.|..++...+.
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 4699999999998888887553211 2344666 776543 4677788888777665543
No 31
>PF13331 DUF4093: Domain of unknown function (DUF4093)
Probab=30.01 E-value=36 Score=22.54 Aligned_cols=32 Identities=16% Similarity=0.269 Sum_probs=22.7
Q ss_pred CcCCHHHHHHHhcCCCCCCCC--------CCceeccceee
Q 033611 34 EQIDQQEVFDHVRDIKDPEHP--------YSLEELKVITE 65 (115)
Q Consensus 34 ~~it~~~I~~aL~~V~DPEi~--------~~IvdLGlI~~ 65 (115)
++.+.+.|++||+.+.-+... .++.++||+-.
T Consensus 5 E~A~~e~I~~AL~~~~~~~~~~~~~~it~~dL~~~GL~g~ 44 (87)
T PF13331_consen 5 EHASPEAIREALENARTEDEEPKESEITWEDLIELGLIGG 44 (87)
T ss_pred cCCCHHHHHHHHHHhCccccCCccCcCCHHHHHHCCCCCC
Confidence 567899999999998765443 24566666654
No 32
>PHA03001 putative virion core protein; Provisional
Probab=28.72 E-value=1.3e+02 Score=21.75 Aligned_cols=39 Identities=13% Similarity=0.209 Sum_probs=29.1
Q ss_pred EEEeCCCcEEEEEEEeCCCCCChHHHHHHHHHHHHHHhCC
Q 033611 68 IEVDDERSYVRVTFTPTVEHCSMATVIGLCLRVKLMRSLP 107 (115)
Q Consensus 68 I~i~~~~~~V~V~mtlT~p~Cp~~~~I~~~v~~~L~~~~~ 107 (115)
|-.+.+.++|.+.+..+.+.||-...+..++..-| +.+.
T Consensus 6 IfLEsd~grvkl~~~~~~~~~~~~~~~~ka~~~fl-~~L~ 44 (132)
T PHA03001 6 IFLETDAGRVKLAIENPDKVCATKAEMRKAINKFL-ELLK 44 (132)
T ss_pred EEEeccCCceEEEEcCCCccccccchHHHHHHHHH-HHHH
Confidence 55554556899999999999999777777777766 4443
No 33
>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=28.32 E-value=1.5e+02 Score=24.25 Aligned_cols=56 Identities=13% Similarity=0.105 Sum_probs=37.7
Q ss_pred CcCCHHHHHHHhcCCCCCCCCCCce---eccceeeccEEEeC-CCcEEEEEEEeCCCCCChHHHH
Q 033611 34 EQIDQQEVFDHVRDIKDPEHPYSLE---ELKVITEDAIEVDD-ERSYVRVTFTPTVEHCSMATVI 94 (115)
Q Consensus 34 ~~it~~~I~~aL~~V~DPEi~~~Iv---dLGlI~~~~I~i~~-~~~~V~V~mtlT~p~Cp~~~~I 94 (115)
.++|.++|...++.+.+|.-+.... .+.-|.. |++.+ + -+|++++..|...+...+
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 5699999999999999987653322 3344556 77654 3 466777777766555444
No 34
>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=26.94 E-value=1.9e+02 Score=23.69 Aligned_cols=56 Identities=18% Similarity=0.223 Sum_probs=37.3
Q ss_pred CcCCHHHHHHHhcCCCCCCCCCCceeccceeeccEEEeCCCcEEEEEEEeCCCCCChHHHH
Q 033611 34 EQIDQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVI 94 (115)
Q Consensus 34 ~~it~~~I~~aL~~V~DPEi~~~IvdLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~~I 94 (115)
+++|.+++...++...+|..+..-.-+.-|.. |+.-++ -+|+|+++.|...+...+
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 46999999999999988876532212333555 766543 467788888866555444
No 35
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=26.28 E-value=1.7e+02 Score=27.45 Aligned_cols=70 Identities=14% Similarity=0.093 Sum_probs=41.9
Q ss_pred HHHHHHHhcCCCCCCCCCCceeccceeeccEEEeCCCcEEEEEEEeCCCCCC---hHHHHHHHHHHHHHHhCCCceeEEe
Q 033611 38 QQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCS---MATVIGLCLRVKLMRSLPPRFKVRR 114 (115)
Q Consensus 38 ~~~I~~aL~~V~DPEi~~~IvdLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp---~~~~I~~~v~~~L~~~~~~~~~V~v 114 (115)
..++++++.++. +++|.+..+--.+.+ +. .. ..-...+.+++++-+ +.......++.+| +.+||+.+|++
T Consensus 114 ~~ev~~~i~~~~-~~LP~~~~~~p~~~~--~~--~~-~~pv~~~~l~~~~~~~~~L~~~~~~~l~~~L-~~i~gV~~V~~ 186 (1040)
T PRK10503 114 EQEVQAAINAAT-NLLPSDLPNPPVYSK--VN--PA-DPPIMTLAVTSTAMPMTQVEDMVETRVAQKI-SQVSGVGLVTL 186 (1040)
T ss_pred HHHHHHHHHHHH-HhCCCccCCCCEEEE--eC--CC-CCceEEEEEEcCCCCHHHHHHHHHHHHHHHh-cCCCCceEEEe
Confidence 467888888775 777766433333333 22 11 122344555555444 3344557899999 88999998876
No 36
>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=26.19 E-value=1.5e+02 Score=24.06 Aligned_cols=57 Identities=11% Similarity=0.196 Sum_probs=39.6
Q ss_pred CcCCHHHHHHHhcCCCCCCCCCC--ceeccceeeccEEEeCCCcEEEEEEEeCCCCCChHHHHH
Q 033611 34 EQIDQQEVFDHVRDIKDPEHPYS--LEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIG 95 (115)
Q Consensus 34 ~~it~~~I~~aL~~V~DPEi~~~--IvdLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~~I~ 95 (115)
.++|.+++...++...+|..+-. -..++-|.. |+..++ -+|++++..|.+++...+.
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 46999999999988888876432 112344556 766543 4778888888887776664
No 37
>PRK00153 hypothetical protein; Validated
Probab=24.73 E-value=1.6e+02 Score=19.67 Aligned_cols=39 Identities=13% Similarity=0.276 Sum_probs=22.9
Q ss_pred cceeeccEEEeCCCcEEEEEEEeCCCCCC----hHHHHHHHHHHHH
Q 033611 61 KVITEDAIEVDDERSYVRVTFTPTVEHCS----MATVIGLCLRVKL 102 (115)
Q Consensus 61 GlI~~~~I~i~~~~~~V~V~mtlT~p~Cp----~~~~I~~~v~~~L 102 (115)
|+|+ |.+++++.-..|++.+..-.-. +.+.|..++..|+
T Consensus 38 G~V~---V~v~G~~~v~~i~Id~~ll~~~d~e~LedlI~~A~n~A~ 80 (104)
T PRK00153 38 GLVK---VTMTGKKEVKRVKIDPSLVDPEDVEMLEDLILAAFNDAL 80 (104)
T ss_pred CeEE---EEEecCceEEEEEECHHHcCCcCHHHHHHHHHHHHHHHH
Confidence 5665 7777776677777777654322 4444444444444
No 38
>PF08529 NusA_N: NusA N-terminal domain; InterPro: IPR013735 This entry represents the N-terminal RNA polymerase-binding domain of bacterial transcription factors such as NusA (N-utilising substance A). NusA is involved in transcriptional pausing, termination and anti-termination. NusA from Thermotoga maritima contains an N-terminal domain and three RNA-binding domains (one S1 domain and two KH domains). The N-terminal domain consists of a bifurcated coiled beta-sheet within an alpha/beta(3)/alpha/beta/alpha fold, which can be divided into two subdomains: a globular head and a helical body. The globular head subdomain may interact with RNA polymerase, while the helical body displays a similar structure to that of the helical domain in sigma70 [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0031554 regulation of transcription termination, DNA-dependent; PDB: 1K0R_B 1HH2_P 1L2F_A 2KWP_A.
Probab=24.57 E-value=87 Score=21.55 Aligned_cols=52 Identities=23% Similarity=0.215 Sum_probs=32.8
Q ss_pred CCCCCCCCCceeccceeeccEEEeCCCcEEEEEEEeCCCCCChHHHHHHHHHHHHH
Q 033611 48 IKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIGLCLRVKLM 103 (115)
Q Consensus 48 V~DPEi~~~IvdLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~~I~~~v~~~L~ 103 (115)
+.||..-++|.+..-+. +++++ |..+.+.++|...|--++..+.+.+.++|+
T Consensus 65 ~~d~~~eI~l~eAk~~~-~~~~v---GD~i~~~i~~~~fgR~aa~~akq~i~qkir 116 (122)
T PF08529_consen 65 VEDPDTEISLSEAKKID-PNAEV---GDEIEEEIDPEDFGRIAAQTAKQVIIQKIR 116 (122)
T ss_dssp -S-TTTEEEHHHHHCCC-TT--T---TCEEEEE---TTCCCCCHHHHHHHHHHHHH
T ss_pred ccCccceeeHHHHHhhC-CCCcc---CCEEEecCChhhcCHHHHHHHHHHHHHHHH
Confidence 44555555555554443 33554 347999999999999999999999999984
No 39
>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length. The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.
Probab=24.40 E-value=44 Score=22.42 Aligned_cols=50 Identities=22% Similarity=0.193 Sum_probs=32.4
Q ss_pred cCCHHHHHHHhcCC---CCCCCCCCceeccce-eeccEEEeCCCcEEEEEEEeCCCCCChHHH
Q 033611 35 QIDQQEVFDHVRDI---KDPEHPYSLEELKVI-TEDAIEVDDERSYVRVTFTPTVEHCSMATV 93 (115)
Q Consensus 35 ~it~~~I~~aL~~V---~DPEi~~~IvdLGlI-~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~~ 93 (115)
..+...|+-||+.. +..| .+|+.|||| .. +.. .+ .+ ..++|-.|+.+.+.
T Consensus 36 ~~~~snV~GaL~G~g~rY~~e--~SLv~lGLV~~~--~~~--~g--~k-~Y~lT~~G~~~~~~ 89 (90)
T PF07381_consen 36 GSDYSNVLGALRGDGKRYNKE--DSLVGLGLVEEE--EEK--GG--FK-YYRLTEKGKRIAEM 89 (90)
T ss_pred CCCHHHHHHHHhcCCCCcCcc--hhHHHcCCeeEe--eec--CC--ee-EEEeChhhhhHHhc
Confidence 36677788887763 4444 599999999 44 332 22 22 67788888766543
No 40
>TIGR00334 5S_RNA_mat_M5 ribonuclease M5. This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases.
Probab=24.13 E-value=33 Score=25.79 Aligned_cols=33 Identities=15% Similarity=0.311 Sum_probs=24.9
Q ss_pred hhcCcCCHHHHHHHhcCCCCC------CCC-CCceeccce
Q 033611 31 YAAEQIDQQEVFDHVRDIKDP------EHP-YSLEELKVI 63 (115)
Q Consensus 31 ~~~~~it~~~I~~aL~~V~DP------Ei~-~~IvdLGlI 63 (115)
-.-++.+.++|++||+++.-+ ++. -++.++||+
T Consensus 91 iGVE~As~e~I~~AL~~~~~~~~~~~~~it~~dl~~~gL~ 130 (174)
T TIGR00334 91 IGVEEASVEAIIAALENVHEETKAQQSDISWEDLLELGLI 130 (174)
T ss_pred cccCCCCHHHHHHHHHHhcccccCcccccCHHHHHHCCCC
Confidence 355778999999999999865 344 466777776
No 41
>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=23.54 E-value=2e+02 Score=23.10 Aligned_cols=57 Identities=16% Similarity=0.295 Sum_probs=36.4
Q ss_pred CcCCHHHHHHHhcCCCCCCCCCCc-eeccceeeccEEEeCCCcEEEEEEEeCCCCCChHHHHH
Q 033611 34 EQIDQQEVFDHVRDIKDPEHPYSL-EELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIG 95 (115)
Q Consensus 34 ~~it~~~I~~aL~~V~DPEi~~~I-vdLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~~I~ 95 (115)
+++|.+++...+....+|+.+... ..+.-|.. |+..++ -+|+++++.|...+...+.
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 469999999999999888754322 12334555 666443 4567777776655554443
No 42
>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=23.41 E-value=2e+02 Score=23.20 Aligned_cols=54 Identities=11% Similarity=0.035 Sum_probs=35.2
Q ss_pred CcCCHHHHHHHhcCCCCCCCCCCceeccceeeccEEEeCCCcEEEEEEEeCCCCCChHHHH
Q 033611 34 EQIDQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVI 94 (115)
Q Consensus 34 ~~it~~~I~~aL~~V~DPEi~~~IvdLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~~I 94 (115)
+++|.++|...++...+|..+... ...+.. |+..++ -+|.+++..|...+...+
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 469999999999988888754322 344555 766543 356677777754444443
No 43
>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=23.27 E-value=2.2e+02 Score=22.81 Aligned_cols=56 Identities=18% Similarity=0.173 Sum_probs=36.6
Q ss_pred CcCCHHHHHHHhcCCCCCCCCCCc-eeccceeeccEEEeCCCcEEEEEEEeCCCCCChHHHH
Q 033611 34 EQIDQQEVFDHVRDIKDPEHPYSL-EELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVI 94 (115)
Q Consensus 34 ~~it~~~I~~aL~~V~DPEi~~~I-vdLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~~I 94 (115)
+++|.+++...+....+|..+-.. ..+.-|.. |+..++ -+|++++..|..++...+
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 569999999999988888765322 12344556 766543 466777777665554443
No 44
>PRK00521 rbfA ribosome-binding factor A; Validated
Probab=23.01 E-value=2.6e+02 Score=19.13 Aligned_cols=39 Identities=28% Similarity=0.456 Sum_probs=25.6
Q ss_pred HHHHHHh-cCCCCCCCCCCceeccceeeccEEEeCCCcEEEEEEEeC
Q 033611 39 QEVFDHV-RDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPT 84 (115)
Q Consensus 39 ~~I~~aL-~~V~DPEi~~~IvdLGlI~~~~I~i~~~~~~V~V~mtlT 84 (115)
.+|-++| +.+.||.++ +--|.. |++..+...+.|.++.-
T Consensus 17 ~~is~il~~~i~d~~~~-----~vtIt~--V~vS~Dl~~AkVyvs~~ 56 (120)
T PRK00521 17 RELAEILQREIKDPRLG-----MVTVTD--VEVSPDLAHAKVYVTVL 56 (120)
T ss_pred HHHHHHHHHHccCCCCC-----eeEEEE--EEECCCCCEEEEEEEEC
Confidence 3444555 379999985 122345 77777777888888864
No 45
>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=22.53 E-value=60 Score=21.73 Aligned_cols=34 Identities=32% Similarity=0.625 Sum_probs=26.5
Q ss_pred cCCHHHHHHHhcCCCCCCCCCC--------ceeccceeeccEEEe
Q 033611 35 QIDQQEVFDHVRDIKDPEHPYS--------LEELKVITEDAIEVD 71 (115)
Q Consensus 35 ~it~~~I~~aL~~V~DPEi~~~--------IvdLGlI~~~~I~i~ 71 (115)
++|.++|++.|+. .+|.++.+ +++.|+|.. +...
T Consensus 23 ~~ta~ei~~~l~~-~~~~is~~TVYR~L~~L~e~Gli~~--~~~~ 64 (120)
T PF01475_consen 23 HLTAEEIYDKLRK-KGPRISLATVYRTLDLLEEAGLIRK--IEFG 64 (120)
T ss_dssp SEEHHHHHHHHHH-TTTT--HHHHHHHHHHHHHTTSEEE--EEET
T ss_pred CCCHHHHHHHhhh-ccCCcCHHHHHHHHHHHHHCCeEEE--EEcC
Confidence 7899999999994 67777744 789999999 8775
No 46
>TIGR02514 type_III_yscP type III secretion system needle length determinant. Members of this family include YscP of the Yersinia type III secretion system and equivalent proteins in other animal pathogen bacterial type III secretion systems. The model describes the conserved C-terminal region. N-terminal regions are poorly conserved and variable in length with some low-complexity sequence.
Probab=21.81 E-value=3.1e+02 Score=19.69 Aligned_cols=59 Identities=14% Similarity=0.220 Sum_probs=36.1
Q ss_pred CCCCCCCCceeccceeeccEEEeCCCcEEEEEEEeCCCCCChHHHHHHHHHHHHHHh----CCC-ceeEEe
Q 033611 49 KDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVIGLCLRVKLMRS----LPP-RFKVRR 114 (115)
Q Consensus 49 ~DPEi~~~IvdLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~~I~~~v~~~L~~~----~~~-~~~V~v 114 (115)
.-||+.++|-.||=.. |+|..+.+...|+|.-+ |+...|-.+.|..|... .|+ .+.+++
T Consensus 42 ~~~evrL~LpqLg~~e---I~I~~~~g~l~Vei~a~----~~~~qiL~qaR~eL~eRLqRl~p~q~vrl~i 105 (129)
T TIGR02514 42 RPAELRLTLPQLGGLE---IRIARDSGGLQVEILAS----PASSQLLQQARQELLERLQRLYPGQPVRLDL 105 (129)
T ss_pred CCcEEEEecCCCCCeE---EEEEccCCeEEEEEecC----hhHHHHHHHHHHHHHHHHHhhCCCCceEEEe
Confidence 5567777787888665 66654445688888733 66666666655554332 243 355554
No 47
>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=21.79 E-value=3.5e+02 Score=20.26 Aligned_cols=69 Identities=14% Similarity=0.224 Sum_probs=38.8
Q ss_pred CCHHHHHHHhcCCCCCCCCCCceeccceeeccEEEeCC-CcEEEEEEEeCCCCCChH--HHHHHHHHHHHHHhCCCceeE
Q 033611 36 IDQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDE-RSYVRVTFTPTVEHCSMA--TVIGLCLRVKLMRSLPPRFKV 112 (115)
Q Consensus 36 it~~~I~~aL~~V~DPEi~~~IvdLGlI~~~~I~i~~~-~~~V~V~mtlT~p~Cp~~--~~I~~~v~~~L~~~~~~~~~V 112 (115)
...+++.+.+.++ |+. .++.++..-+ . +. ...+.+.+.+ .++++.. ..+...++++++++.|+..+|
T Consensus 192 ~~~~~i~~~i~~~--~~v-~~v~~~~~~~-----~-G~~~~~v~~~v~v-~~~~~~~~ah~i~~~i~~~i~~~~~~v~~v 261 (268)
T TIGR01297 192 EDLEEIKKAILSI--PGV-KGVHDLHIWR-----I-GPGKLFLDVHVVV-DPDLDLKQAHDIALEIEREILKRHPGIEHV 261 (268)
T ss_pred ccHHHHHHHHhcC--CCc-ccceEeEEEE-----c-CCCCEEEEEEEEE-CCCCChhHHHHHHHHHHHHHHHhcCCCCeE
Confidence 4567777777743 443 3444432111 1 22 2234444444 4566665 678888988887777776555
Q ss_pred Ee
Q 033611 113 RR 114 (115)
Q Consensus 113 ~v 114 (115)
.|
T Consensus 262 ~i 263 (268)
T TIGR01297 262 TI 263 (268)
T ss_pred EE
Confidence 43
No 48
>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=21.49 E-value=1.7e+02 Score=24.25 Aligned_cols=55 Identities=16% Similarity=0.238 Sum_probs=35.7
Q ss_pred CcCCHHHHHHHhcCCCCCCCCCCceeccceeeccEEEeCCCcEEEEEEEeCC-CCCChHHH
Q 033611 34 EQIDQQEVFDHVRDIKDPEHPYSLEELKVITEDAIEVDDERSYVRVTFTPTV-EHCSMATV 93 (115)
Q Consensus 34 ~~it~~~I~~aL~~V~DPEi~~~IvdLGlI~~~~I~i~~~~~~V~V~mtlT~-p~Cp~~~~ 93 (115)
+++|.+++...++...+|..+....-++-|.. |+..++ -+|+|+++. |.+.+...
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 35999999999998888873222222344666 776543 467788888 55555444
No 49
>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=21.44 E-value=2.7e+02 Score=22.20 Aligned_cols=55 Identities=18% Similarity=0.265 Sum_probs=35.3
Q ss_pred CcCCHHHHHHHhcCCCCCCCCCCce-eccceeeccEEEeCCCcEEEEEEEeCCCCCChHHH
Q 033611 34 EQIDQQEVFDHVRDIKDPEHPYSLE-ELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATV 93 (115)
Q Consensus 34 ~~it~~~I~~aL~~V~DPEi~~~Iv-dLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~~ 93 (115)
.++|.++|...++...+|..+.... .+.-+.. |+..++ -+|+++++.|.-.+...
T Consensus 74 ~p~TA~Dv~~s~~~~~~~~~~~~~~~~~~~i~~--v~~~d~---~tv~i~l~~p~~~~~~~ 129 (466)
T cd00995 74 TPLTAEDVVFSFERLADPKNASPSAGKADEIEG--VEVVDD---YTVTITLKEPDAPFLAL 129 (466)
T ss_pred CCcCHHHHHhHHHHhcCCccCCcccccccceee--EEecCC---CeEEEEECCCCchHHHH
Confidence 4699999999999999988764432 2344555 766543 35566666654433333
No 50
>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=21.18 E-value=2e+02 Score=23.39 Aligned_cols=56 Identities=13% Similarity=0.121 Sum_probs=36.2
Q ss_pred CcCCHHHHHHHhcCCCCCCCCCCce----eccceeeccEEEeCCCcEEEEEEEeCCCCCChHHHH
Q 033611 34 EQIDQQEVFDHVRDIKDPEHPYSLE----ELKVITEDAIEVDDERSYVRVTFTPTVEHCSMATVI 94 (115)
Q Consensus 34 ~~it~~~I~~aL~~V~DPEi~~~Iv----dLGlI~~~~I~i~~~~~~V~V~mtlT~p~Cp~~~~I 94 (115)
+++|.+++...++...+|..+.... .+.-+.. |+..++ -+|++++..|...+...+
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 4699999999999888887653322 1344555 766543 456777777755454444
Done!