Query gi|254780998|ref|YP_003065411.1| hypothetical protein CLIBASIA_04495 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 146
No_of_seqs 106 out of 928
Neff 6.3
Searched_HMMs 39220
Date Mon May 30 02:49:46 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780998.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK09296 cysteine desufuration 100.0 0 0 315.7 16.3 133 3-139 6-138 (138)
2 TIGR03391 FeS_syn_CsdE cystein 100.0 0 0 311.9 15.1 129 2-134 10-138 (138)
3 pfam02657 SufE Fe-S metabolism 100.0 2.1E-44 0 297.9 14.4 124 7-135 1-124 (125)
4 COG2166 sufE Cysteine desulfur 100.0 1E-43 0 293.6 14.6 132 3-138 11-142 (144)
5 TIGR03419 NifU_clost FeS clust 95.8 0.18 4.5E-06 30.2 10.8 114 23-142 4-120 (121)
6 pfam01592 NifU_N NifU-like N t 95.7 0.21 5.4E-06 29.7 11.3 116 22-141 4-122 (126)
7 PRK11325 scaffold protein; Pro 94.5 0.47 1.2E-05 27.5 11.4 114 22-141 5-124 (127)
8 cd07348 NR_LBD_NGFI-B The liga 68.9 4.4 0.00011 21.5 2.6 119 20-143 53-179 (238)
9 cd01193 INT_IntI IntI (E2) int 60.8 11 0.00028 19.1 3.4 18 3-20 72-89 (242)
10 cd06945 NR_LBD_Nurr1_like The 59.5 6.8 0.00017 20.3 2.1 122 20-143 53-180 (239)
11 cd06954 NR_LBD_LXR The ligand 57.5 4.7 0.00012 21.3 1.0 123 20-144 55-185 (236)
12 TIGR01892 AcOrn-deacetyl acety 55.4 8.3 0.00021 19.8 2.0 70 47-136 87-160 (386)
13 COG0822 IscU NifU homolog invo 55.3 18 0.00047 17.6 9.4 120 19-141 5-144 (150)
14 cd07072 NR_LBD_DHR38_like Liga 55.2 7.5 0.00019 20.0 1.8 85 5-91 41-129 (239)
15 PRK10144 formate-dependent nit 50.2 20 0.00052 17.3 3.4 45 72-120 52-97 (126)
16 TIGR03147 cyt_nit_nrfF cytochr 48.4 22 0.00057 17.1 3.3 44 72-119 52-96 (126)
17 cd06939 NR_LBD_ROR_like The li 46.8 18 0.00047 17.6 2.7 63 6-70 48-111 (241)
18 pfam06304 DUF1048 Protein of u 46.8 21 0.00055 17.2 3.0 67 29-110 4-71 (92)
19 pfam00082 Peptidase_S8 Subtila 46.2 23 0.00058 17.1 3.1 36 66-101 231-272 (292)
20 COG4817 DNA-binding ferritin-l 42.6 22 0.00055 17.2 2.5 68 27-110 18-86 (111)
21 cd06935 NR_LBD_TR The ligand b 40.9 11 0.00029 18.9 0.9 71 20-90 64-139 (243)
22 cd06940 NR_LBD_REV_ERB The lig 40.7 10 0.00025 19.3 0.6 135 6-144 12-153 (189)
23 cd06941 NR_LBD_DmE78_like The 36.9 16 0.0004 18.0 1.1 117 20-144 14-143 (195)
24 pfam07914 DUF1679 Protein of u 36.8 36 0.00092 15.8 5.4 96 19-125 118-222 (413)
25 cd07068 NR_LBD_ER_like The lig 36.6 21 0.00053 17.3 1.7 125 18-144 37-168 (221)
26 TIGR01286 nifK nitrogenase mol 36.0 23 0.00059 17.0 1.8 84 22-119 330-416 (526)
27 pfam01466 Skp1 Skp1 family, di 34.4 36 0.00091 15.8 2.6 38 73-118 22-63 (78)
28 cd06934 NR_LBD_PXR_like The li 32.7 17 0.00042 17.9 0.6 36 21-56 48-84 (226)
29 pfam03918 CcmH Cytochrome C bi 32.6 42 0.0011 15.4 4.0 45 72-120 49-94 (145)
30 cd06937 NR_LBD_RAR The ligand 31.4 21 0.00052 17.3 0.9 123 20-144 50-179 (231)
31 cd06929 NR_LBD_F1 Ligand-bindi 30.5 18 0.00047 17.6 0.6 123 19-144 13-143 (174)
32 cd06664 IscU_like Iron-sulfur 30.3 46 0.0012 15.1 8.5 100 22-125 4-114 (123)
33 TIGR02955 TMAO_TorT TMAO reduc 30.2 46 0.0012 15.1 3.3 52 66-119 238-296 (304)
34 cd06938 NR_LBD_EcR The ligand 28.5 12 0.00032 18.7 -0.6 51 20-70 51-102 (231)
35 TIGR01690 plasmid_RAQPRD plasm 27.6 12 0.00029 18.9 -0.9 12 111-122 81-92 (107)
36 pfam06352 consensus 26.2 54 0.0014 14.7 3.1 23 1-23 1-23 (223)
37 cd06157 NR_LBD The ligand bind 25.3 46 0.0012 15.1 1.8 129 15-144 5-144 (168)
38 cd06946 NR_LBD_ERR The ligand 23.2 35 0.00089 15.9 0.9 125 18-144 37-168 (221)
39 pfam10624 TraS Plasmid conjuga 21.9 9.9 0.00025 19.3 -2.1 27 41-67 92-119 (164)
40 KOG4215 consensus 21.1 38 0.00096 15.7 0.7 72 13-91 159-246 (432)
No 1
>PRK09296 cysteine desufuration protein SufE; Provisional
Probab=100.00 E-value=0 Score=315.70 Aligned_cols=133 Identities=26% Similarity=0.516 Sum_probs=127.6
Q ss_pred CHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCHHHCCHHHHHCCCCEEEEEEEEECCCCCCCCEEEEEECCHHHHHHHH
Q ss_conf 88999998750999899999999998508999956868155022656016788730465454887999941626999999
Q gi|254780998|r 3 PINDIIEDMEMIEDLHDRYHYLIELGKKLPLFPKEYMTDQNIVAGCMSKLWMVIEWENKGDQDPIMIFYAVSDSQIVCGL 82 (146)
Q Consensus 3 ~l~~i~e~f~~~~d~~~ry~~Li~lgk~l~~l~e~~k~~~~~V~GCqS~vWl~~~~~~~~~~~~~~~f~~dSda~IvkGl 82 (146)
+.++|+++|+.|+||++||+|||++||++|++|+++|+++|+|+||||+|||+++.+ .+|+++|+|||||.|||||
T Consensus 6 ~~~~ii~~F~~~~dweery~~li~lGk~lp~l~e~~k~~~n~V~GCqS~vWl~~~~~----~~g~~~f~~dSDa~IvkGL 81 (138)
T PRK09296 6 DKEKLLRNFSRCANWEEKYLYIIELGQRLPPLTDEDRSPQNLIQGCQSQVWIVMRQN----AQGIIELQGDSDAAIVKGL 81 (138)
T ss_pred CHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCHHHCCHHHHCCCCCCCEEEEEEEC----CCCEEEEEEECCHHHHHHH
T ss_conf 399999998837999999999999986289999578285543478744504678765----8977999860608999999
Q ss_pred HHHHHHHHCCCCHHHHHHCCHHHHHHHHCCHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999975998899980798999987090431694289999999999999999999
Q gi|254780998|r 83 LYIVKSIYAHKKISEILKMDSLTILQHLGLTENLSQKRMNGLYTIVNKIQDLTQEYL 139 (146)
Q Consensus 83 ~~ll~~~~~g~t~~eI~~~d~~~f~~~lgL~~~Lt~~R~nGl~~m~~~ik~~a~~~l 139 (146)
++||+.+|||+||+||+++|+..||+++||.+||||+|+|||.+|+++||.+|++++
T Consensus 82 ~all~~~~~g~t~~eI~~~d~~~~~~~lgL~~~LSpsR~NGl~~mi~~Ik~~A~~~s 138 (138)
T PRK09296 82 IAVVFILYHQMTPQDIVNFDVRPWFEKMALTQHLTPSRSQGLEAMIRAIRAKAAALS 138 (138)
T ss_pred HHHHHHHHCCCCHHHHHHCCCHHHHHHCCHHHHCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf 999999987999999987790989987460402582188999999999999999709
No 2
>TIGR03391 FeS_syn_CsdE cysteine desulfurase, sulfur acceptor subunit CsdE. Members of this protein family are CsdE, formerly called YgdK. This protein, found as a paralog to SufE in Escherichia coli, Yersinia pestis, Photorhabdus luminescens, and related species, works together and physically interacts with CsdA (a paralog of SufS). CsdA has cysteine desulfurase activity that is enhanced by this protein (CsdE), in which Cys-61 (numbered as in E. coli) is a sulfur acceptor site. This gene pair, although involved in FeS cluster biosynthesis, is not found next to other such genes as are its paralogs from the Suf or Isc systems.
Probab=100.00 E-value=0 Score=311.90 Aligned_cols=129 Identities=32% Similarity=0.554 Sum_probs=124.2
Q ss_pred CCHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCHHHCCHHHHHCCCCEEEEEEEEECCCCCCCCEEEEEECCHHHHHHH
Q ss_conf 88899999875099989999999999850899995686815502265601678873046545488799994162699999
Q gi|254780998|r 2 IPINDIIEDMEMIEDLHDRYHYLIELGKKLPLFPKEYMTDQNIVAGCMSKLWMVIEWENKGDQDPIMIFYAVSDSQIVCG 81 (146)
Q Consensus 2 ~~l~~i~e~f~~~~d~~~ry~~Li~lgk~l~~l~e~~k~~~~~V~GCqS~vWl~~~~~~~~~~~~~~~f~~dSda~IvkG 81 (146)
||+++|+++|+.|+||++||+|||++||++|++|+++|+|+|+|+||||+|||.++.. .||+++|+|||||.||||
T Consensus 10 ~t~~eI~e~F~~~~~wedry~~LIdlGk~lp~l~~~~k~d~n~V~GC~S~vWl~~~~~----~dg~~~f~~DSDA~IvkG 85 (138)
T TIGR03391 10 ITAADLIATFAACRQWEDRYRQLILLAKQLPALPEALKTQATELTGCENRVWLGHQVL----PDGTLHFYGDSEGRIVRG 85 (138)
T ss_pred CCHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCHHHHCHHHCCCCCCCCEEEEEEEC----CCCEEEEEECCCHHHHHH
T ss_conf 7999999999826999999999999983299999789373202567633346766665----898799984460799999
Q ss_pred HHHHHHHHHCCCCHHHHHHCCHHHHHHHHCCHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 99999999759988999807989999870904316942899999999999999
Q gi|254780998|r 82 LLYIVKSIYAHKKISEILKMDSLTILQHLGLTENLSQKRMNGLYTIVNKIQDL 134 (146)
Q Consensus 82 l~~ll~~~~~g~t~~eI~~~d~~~f~~~lgL~~~Lt~~R~nGl~~m~~~ik~~ 134 (146)
|+++|+.+|||+||+||+++||.+||+++||.+||||+|+|||.+|+++||.+
T Consensus 86 L~alll~~~~g~tp~eI~~~d~~~~~~~lGL~~~LSpsR~NGl~ami~~Ik~i 138 (138)
T TIGR03391 86 LLAVLLTAVEGKTPEQLLAQDPLALFDELGLRAQLSASRSNGLAALAAAIQNI 138 (138)
T ss_pred HHHHHHHHHCCCCHHHHHHCCHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCC
T ss_conf 99999999779998999856999999885870226810889999999998539
No 3
>pfam02657 SufE Fe-S metabolism associated domain. This family consists of the SufE-related proteins. These have been implicated in Fe-S metabolism and export).
Probab=100.00 E-value=2.1e-44 Score=297.86 Aligned_cols=124 Identities=35% Similarity=0.650 Sum_probs=118.9
Q ss_pred HHHHHHCCCCHHHHHHHHHHHHHHCCCCCHHHCCHHHHHCCCCEEEEEEEEECCCCCCCCEEEEEECCHHHHHHHHHHHH
Q ss_conf 99987509998999999999985089999568681550226560167887304654548879999416269999999999
Q gi|254780998|r 7 IIEDMEMIEDLHDRYHYLIELGKKLPLFPKEYMTDQNIVAGCMSKLWMVIEWENKGDQDPIMIFYAVSDSQIVCGLLYIV 86 (146)
Q Consensus 7 i~e~f~~~~d~~~ry~~Li~lgk~l~~l~e~~k~~~~~V~GCqS~vWl~~~~~~~~~~~~~~~f~~dSda~IvkGl~~ll 86 (146)
|+++|+.|+||+|||+|||++||++|++|+++|+++|+|+||||+|||.+... .||+++|+|||||.|||||++||
T Consensus 1 iie~F~~~~dwedry~~Li~lgk~l~~l~~~~k~~~n~V~GCqS~vWl~~~~~----~dg~~~f~adSda~IvkGl~ail 76 (125)
T pfam02657 1 VVELFAEVTNWEDKYRQLLELGKELPALPDELLAQANEVQGCQSQLWLHYDVS----EDGIVHFFGDSEARIVRGLAALL 76 (125)
T ss_pred CHHHHHCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCEEEEEEEC----CCCEEEEEECCCCHHHHHHHHHH
T ss_conf 96566518999999999999882299999789505330577775568887763----79889998517429999999999
Q ss_pred HHHHCCCCHHHHHHCCHHHHHHHHCCHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9997599889998079899998709043169428999999999999999
Q gi|254780998|r 87 KSIYAHKKISEILKMDSLTILQHLGLTENLSQKRMNGLYTIVNKIQDLT 135 (146)
Q Consensus 87 ~~~~~g~t~~eI~~~d~~~f~~~lgL~~~Lt~~R~nGl~~m~~~ik~~a 135 (146)
+.+|||+||+||+++++ +|++++||.+||||+|+|||.+|+++||++|
T Consensus 77 ~~~~~g~t~~eI~~~~~-~~~~~lgL~~~LS~~R~nGl~~m~~~Ik~~A 124 (125)
T pfam02657 77 FAGYDGKTPAEILTFDP-DFFEELGLAQHLSPSRLNGLEALFARIKRKA 124 (125)
T ss_pred HHHHCCCCHHHHHHCCH-HHHHHCCCHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf 99984999999986999-9998848540048008899999999999986
No 4
>COG2166 sufE Cysteine desulfurase SufE subunit [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1e-43 Score=293.62 Aligned_cols=132 Identities=39% Similarity=0.726 Sum_probs=126.8
Q ss_pred CHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCHHHCCHHHHHCCCCEEEEEEEEECCCCCCCCEEEEEECCHHHHHHHH
Q ss_conf 88999998750999899999999998508999956868155022656016788730465454887999941626999999
Q gi|254780998|r 3 PINDIIEDMEMIEDLHDRYHYLIELGKKLPLFPKEYMTDQNIVAGCMSKLWMVIEWENKGDQDPIMIFYAVSDSQIVCGL 82 (146)
Q Consensus 3 ~l~~i~e~f~~~~d~~~ry~~Li~lgk~l~~l~e~~k~~~~~V~GCqS~vWl~~~~~~~~~~~~~~~f~~dSda~IvkGl 82 (146)
++++|+++|..+.+|++||+|||++||+||++||+.|+++|+|+||||+||++.+.++ +|.++|.|||||+|||||
T Consensus 11 ~~~~i~~~F~~~~~wedrYr~lIe~gk~Lp~lpe~~~~~en~V~GC~S~vwL~~~~~~----~~~~~F~gdSdA~ivrGL 86 (144)
T COG2166 11 TLEKIVEDFAELTNWEDRYRYLIELGKQLPPLPEELRAEENPVPGCQSQVWLVTEQND----DGTLHFFGDSDARIVRGL 86 (144)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHCCCCCCCCCCEEEEEEECC----CCEEEEECCCHHHHHHHH
T ss_conf 9999999877648989999999997620899997887242678765423368886168----863788434254999889
Q ss_pred HHHHHHHHCCCCHHHHHHCCHHHHHHHHCCHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999997599889998079899998709043169428999999999999999999
Q gi|254780998|r 83 LYIVKSIYAHKKISEILKMDSLTILQHLGLTENLSQKRMNGLYTIVNKIQDLTQEY 138 (146)
Q Consensus 83 ~~ll~~~~~g~t~~eI~~~d~~~f~~~lgL~~~Lt~~R~nGl~~m~~~ik~~a~~~ 138 (146)
++|++.+|||+||+||+++||.+||+++||.+||||+|+||+.+|+.+||+.|.+.
T Consensus 87 ~aill~~~~G~t~~eI~~~~~~~~f~~LGL~~~LSpsR~nGl~am~~~i~~~a~~~ 142 (144)
T COG2166 87 LAILLAAYSGKTAAEILAFDPLDFFEELGLAQHLSPSRSNGLEAMLKRIKRKAAQA 142 (144)
T ss_pred HHHHHHHHCCCCHHHHHCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999998599989998589789999865887659677637999999999999874
No 5
>TIGR03419 NifU_clost FeS cluster assembly scaffold protein NifU, Clostridium type. NifU and NifS form a pair of iron-sulfur (FeS) cluster biosynthesis proteins much simpler than the ISC and SUF systems. Members of this protein family are a distinct group of NifU-like proteins, found always to a NifS-like protein and restricted to species that lack a SUF system. Typically, NIF systems service a smaller number of FeS-containing proteins than do ISC or SUF. Members of this particular branch typically are found, almost half the time, near the mnmA gene, involved in the carboxymethylaminomethyl modification of U34 in some tRNAs (see GenProp0704). While other NifU proteins are associated with nitrogen fixation, this family is not.
Probab=95.85 E-value=0.18 Score=30.17 Aligned_cols=114 Identities=9% Similarity=0.056 Sum_probs=79.2
Q ss_pred HHHHHHHHCC---CCCHHHCCHHHHHCCCCEEEEEEEEECCCCCCCCEEEEEECCHHHHHHHHHHHHHHHHCCCCHHHHH
Q ss_conf 9999985089---9995686815502265601678873046545488799994162699999999999997599889998
Q gi|254780998|r 23 YLIELGKKLP---LFPKEYMTDQNIVAGCMSKLWMVIEWENKGDQDPIMIFYAVSDSQIVCGLLYIVKSIYAHKKISEIL 99 (146)
Q Consensus 23 ~Li~lgk~l~---~l~e~~k~~~~~V~GCqS~vWl~~~~~~~~~~~~~~~f~~dSda~IvkGl~~ll~~~~~g~t~~eI~ 99 (146)
.++|..+... .+++....-+..=+.|=..+=|...+++.... -+.|.+.. -.|...-++++++.+.|++.+|+.
T Consensus 4 ~ileh~~~Prn~G~l~~~~~~~~~~np~CGD~i~i~l~i~~~~I~--di~F~~~G-Cais~AsaS~~~e~i~Gk~l~ea~ 80 (121)
T TIGR03419 4 KVMDHFMNPRNVGEIENADGVGEVGNPKCGDIMKIFLKVEDDIIK--DVKFKTFG-CGAAIASSSMATEMIKGKTLEEAW 80 (121)
T ss_pred HHHHHHHCCCCCCCCCCCCEEEEECCCCCCEEEEEEEEECCCCEE--EEEEEEEC-CHHHHHHHHHHHHHHCCCCHHHHH
T ss_conf 899987697889989999967885799975189999998899678--89999655-588999999999998499499998
Q ss_pred HCCHHHHHHHHCCHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 0798999987090431694289999999999999999999633
Q gi|254780998|r 100 KMDSLTILQHLGLTENLSQKRMNGLYTIVNKIQDLTQEYLNVH 142 (146)
Q Consensus 100 ~~d~~~f~~~lgL~~~Lt~~R~nGl~~m~~~ik~~a~~~l~~~ 142 (146)
.++..+..+.+| .|+|+|..--.--+..++....+|.+++
T Consensus 81 ~i~~~~i~~~l~---~lpp~r~~CA~La~~Al~~Al~~y~~k~ 120 (121)
T TIGR03419 81 ELTNKAVAEALD---GLPPVKMHCSVLAEEAIHKAINDYREKN 120 (121)
T ss_pred HCCHHHHHHHHC---CCCCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf 635489999975---9993116699999999999999998726
No 6
>pfam01592 NifU_N NifU-like N terminal domain. This domain is found in NifU in combination with pfam01106. This domain is found on isolated in several bacterial species. The nif genes are responsible for nitrogen fixation. However this domain is found in bacteria that do not fix nitrogen, so it may have a broader significance in the cell than nitrogen fixation. These proteins appear to be scaffold proteins for iron-sulfur clusters.
Probab=95.67 E-value=0.21 Score=29.72 Aligned_cols=116 Identities=13% Similarity=0.135 Sum_probs=73.5
Q ss_pred HHHHHHHHHCC---CCCHHHCCHHHHHCCCCEEEEEEEEECCCCCCCCEEEEEECCHHHHHHHHHHHHHHHHCCCCHHHH
Q ss_conf 99999985089---999568681550226560167887304654548879999416269999999999999759988999
Q gi|254780998|r 22 HYLIELGKKLP---LFPKEYMTDQNIVAGCMSKLWMVIEWENKGDQDPIMIFYAVSDSQIVCGLLYIVKSIYAHKKISEI 98 (146)
Q Consensus 22 ~~Li~lgk~l~---~l~e~~k~~~~~V~GCqS~vWl~~~~~~~~~~~~~~~f~~dSda~IvkGl~~ll~~~~~g~t~~eI 98 (146)
+.|+|+.+... .+++....-+..-+.|=..+=|...+++....-..+.|.+.. -.|...=++++++.+.|++.+|+
T Consensus 4 e~ildh~~nPrn~G~l~~~~~~~~~~np~CGD~i~i~l~i~~~~~~I~di~F~~~G-Cais~AsaS~l~e~i~Gk~~~ea 82 (126)
T pfam01592 4 DKVLDHFKNPRNVGVLEEADAVGDVGSPACGDAMRLQIKVDEDTDRIEDAKFKTFG-CGSAIASSSALTELVKGKTLDEA 82 (126)
T ss_pred HHHHHHHHCCCCCCCCCCCCEEEEECCCCCCCEEEEEEEEECCCCEEEEEEEEEEC-CHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 89999867959899899998077747999774899999970799949998998637-68889999999999869939999
Q ss_pred HHCCHHHHHHHHCCHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 8079899998709043169428999999999999999999963
Q gi|254780998|r 99 LKMDSLTILQHLGLTENLSQKRMNGLYTIVNKIQDLTQEYLNV 141 (146)
Q Consensus 99 ~~~d~~~f~~~lgL~~~Lt~~R~nGl~~m~~~ik~~a~~~l~~ 141 (146)
.+++..++++.+| .|+|.|..--.--...++.-..+|.+.
T Consensus 83 ~~i~~~~i~~~lg---~l~~~r~~Ca~La~~al~~av~~y~~r 122 (126)
T pfam01592 83 LKITNTDIAEELG---GLPPVKMHCSVLGDDALKAAIADYKGK 122 (126)
T ss_pred HHCCHHHHHHHHC---CCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 8616999999973---799974008999999999999981761
No 7
>PRK11325 scaffold protein; Provisional
Probab=94.45 E-value=0.47 Score=27.54 Aligned_cols=114 Identities=15% Similarity=0.150 Sum_probs=72.8
Q ss_pred HHHHHHHHHCCC---CCH-HHCCHHHHH--CCCCEEEEEEEEECCCCCCCCEEEEEECCHHHHHHHHHHHHHHHHCCCCH
Q ss_conf 999999850899---995-686815502--26560167887304654548879999416269999999999999759988
Q gi|254780998|r 22 HYLIELGKKLPL---FPK-EYMTDQNIV--AGCMSKLWMVIEWENKGDQDPIMIFYAVSDSQIVCGLLYIVKSIYAHKKI 95 (146)
Q Consensus 22 ~~Li~lgk~l~~---l~e-~~k~~~~~V--~GCqS~vWl~~~~~~~~~~~~~~~f~~dSda~IvkGl~~ll~~~~~g~t~ 95 (146)
+.++|..+...- ++. ...+....+ +.|=-.+.|...+++.+.. .-+.|.+..= .|...-++++++.+.|+|.
T Consensus 5 e~ildH~~nPrn~G~l~~~~~~~~~~~~~nP~CGD~i~i~l~v~~~~~I-~d~~F~~~GC-~is~AsaS~~te~~~Gkt~ 82 (127)
T PRK11325 5 EKVIDHYENPRNVGSFDKNDPNVGTGMVGAPACGDVMKLQIKVNDEGII-EDAKFKTYGC-GSAIASSSLVTEWVKGKTL 82 (127)
T ss_pred HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCEE-EEEEEEECCC-HHHHHHHHHHHHHHCCCCH
T ss_conf 9999853497988888887654330213799887489999998799849-8888971285-8999999999999839979
Q ss_pred HHHHHCCHHHHHHHHCCHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9998079899998709043169428999999999999999999963
Q gi|254780998|r 96 SEILKMDSLTILQHLGLTENLSQKRMNGLYTIVNKIQDLTQEYLNV 141 (146)
Q Consensus 96 ~eI~~~d~~~f~~~lgL~~~Lt~~R~nGl~~m~~~ik~~a~~~l~~ 141 (146)
+|++.++..+..+.+| |.|.|..--.--...++.....|.++
T Consensus 83 ~ea~~i~~~~i~e~l~----lpp~r~~CA~La~~aL~~Ai~~y~~k 124 (127)
T PRK11325 83 DEALAIKNTDIAEELA----LPPVKIHCSILAEDAIKAAIADYKSK 124 (127)
T ss_pred HHHHHCCHHHHHHHCC----CCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9998555688998617----99310179999999999999999985
No 8
>cd07348 NR_LBD_NGFI-B The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors. The ligand binding domain of Nerve growth factor-induced-B (NGFI-B): NGFI-B is a member of the nuclear#steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of the embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcriptional initiation. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, NGFI-B has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LB
Probab=68.89 E-value=4.4 Score=21.51 Aligned_cols=119 Identities=18% Similarity=0.255 Sum_probs=65.3
Q ss_pred HHHHHHHHHHHCCCCCHHHCCH-HHHHCCCCEEEEEEEEECCCCCCCCEEEEEEC---CHHHHHHHHHHHHHHHHCCCCH
Q ss_conf 9999999985089999568681-55022656016788730465454887999941---6269999999999999759988
Q gi|254780998|r 20 RYHYLIELGKKLPLFPKEYMTD-QNIVAGCMSKLWMVIEWENKGDQDPIMIFYAV---SDSQIVCGLLYIVKSIYAHKKI 95 (146)
Q Consensus 20 ry~~Li~lgk~l~~l~e~~k~~-~~~V~GCqS~vWl~~~~~~~~~~~~~~~f~~d---Sda~IvkGl~~ll~~~~~g~t~ 95 (146)
-.+.++++||++|.+.+=...| ..+.++|-+.+|+..-.--....++++.|-.. +....++|+.-++-.+++=...
T Consensus 53 ~i~~IVefAK~IPGF~~L~~eDQi~LLks~~~EllvLrla~rs~~~~~~l~f~~g~~l~r~q~~~g~~~~i~~i~ef~~~ 132 (238)
T cd07348 53 SLEVIRKWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPEEGKLIFCNGVVLHRTQCVRGFGDWIDSILEFSQS 132 (238)
T ss_pred HHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCEEECHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999835998145998899999999899999999999817899948966994541999988478999999999999
Q ss_pred HHHHHCCHHHH--HHHHCCHHCCCHHHHHHH--HHHHHHHHHHHHHHHHHHH
Q ss_conf 99980798999--987090431694289999--9999999999999996331
Q gi|254780998|r 96 SEILKMDSLTI--LQHLGLTENLSQKRMNGL--YTIVNKIQDLTQEYLNVHI 143 (146)
Q Consensus 96 ~eI~~~d~~~f--~~~lgL~~~Lt~~R~nGl--~~m~~~ik~~a~~~l~~~~ 143 (146)
=.-+++|...| +..+ -.+| .| .|+ ..-++++++.....|-.++
T Consensus 133 l~~L~ld~~E~a~L~Ai---vL~s-Dr-~gL~~~~~VE~LQe~i~~aL~~yi 179 (238)
T cd07348 133 LHRMNLDVSAFSCLAAL---VIIT-DR-HGLKEPKRVEELQNRLISCLKEHV 179 (238)
T ss_pred HHHCCCCHHHHHHHHHH---HCCC-CC-CCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 99748989999998787---3067-88-887777999999999999999999
No 9
>cd01193 INT_IntI IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and a secondary target called the attC (or 59-base element) present on various mobile gene cassettes. Integron-integrases are present in many natural occurring mobile elements, including transposons and conjugative plasmids. Vibrio, Shewanella, Xanthomonas and Pseudomonas species harbor chromosomal super-integrons. All integron-integrases carry large inserts unlike the TnpF ermF-like proteins also seen in this group.
Probab=60.76 E-value=11 Score=19.06 Aligned_cols=18 Identities=11% Similarity=0.230 Sum_probs=10.2
Q ss_pred CHHHHHHHHHCCCCHHHH
Q ss_conf 889999987509998999
Q gi|254780998|r 3 PINDIIEDMEMIEDLHDR 20 (146)
Q Consensus 3 ~l~~i~e~f~~~~d~~~r 20 (146)
+.+++..-++.+++..++
T Consensus 72 t~eEi~~ll~~~~~~r~~ 89 (242)
T cd01193 72 SPEEVRRLLGALTGLKHR 89 (242)
T ss_pred CHHHHHHHHHCCCCCHHH
T ss_conf 999999999738776799
No 10
>cd06945 NR_LBD_Nurr1_like The ligand binding domain of Nurr1 and related nuclear receptor proteins, members of nuclear receptor superfamily. The ligand binding domain of nuclear receptor Nurr1_like: This family of nuclear receptors, including Nurr1, Nerve growth factor-induced-B (NGFI-B) and DHR38 are involved in the embryo development. Nurr1 is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. NGFI-B is an early immediate gene product of embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as
Probab=59.48 E-value=6.8 Score=20.32 Aligned_cols=122 Identities=19% Similarity=0.181 Sum_probs=60.9
Q ss_pred HHHHHHHHHHHCCCCCHHHCCH-HHHHCCCCEEEEEEEEECCCCCCCCEEEEEECC---HHHHHHHHHHHHHHHHCCCCH
Q ss_conf 9999999985089999568681-550226560167887304654548879999416---269999999999999759988
Q gi|254780998|r 20 RYHYLIELGKKLPLFPKEYMTD-QNIVAGCMSKLWMVIEWENKGDQDPIMIFYAVS---DSQIVCGLLYIVKSIYAHKKI 95 (146)
Q Consensus 20 ry~~Li~lgk~l~~l~e~~k~~-~~~V~GCqS~vWl~~~~~~~~~~~~~~~f~~dS---da~IvkGl~~ll~~~~~g~t~ 95 (146)
-.+.+++++|++|.+.+=...| ..+.++|-+.+|+..-.......++++.|-..- .....+|+...+-.+++=...
T Consensus 53 ~i~~iVewAK~IPgF~~L~~~DQi~LLk~~~~EllvLrla~rs~~~~~~l~f~~g~~l~~~q~~~~~~e~~~~i~~f~~~ 132 (239)
T cd06945 53 SVDVIRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPVDGKLVFCNGLVLHRLQCVRGFGEWLDSILAFSSS 132 (239)
T ss_pred HHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCEEECHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999715988245998899999999999999999999835788807867996543899998799999999999999
Q ss_pred HHHHHCCHHHHHHHHCCHHCCCHHHHHHH--HHHHHHHHHHHHHHHHHHH
Q ss_conf 99980798999987090431694289999--9999999999999996331
Q gi|254780998|r 96 SEILKMDSLTILQHLGLTENLSQKRMNGL--YTIVNKIQDLTQEYLNVHI 143 (146)
Q Consensus 96 ~eI~~~d~~~f~~~lgL~~~Lt~~R~nGl--~~m~~~ik~~a~~~l~~~~ 143 (146)
-.-+..+-..|. -+--.-.++|.| .|+ ..-++++++.....|..++
T Consensus 133 l~~L~l~~~E~~-~l~AivL~~~Dr-~gL~~~~~Ve~LQe~~~~aL~~yi 180 (239)
T cd06945 133 LQSLLLDDISAF-CCLALLLLITER-HGLKEPKKVEELQNKIISCLRDHV 180 (239)
T ss_pred HHHHCCCHHHHH-HHHHHHHHCCCC-CCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 999748738999-999999877898-887889999999999999999999
No 11
>cd06954 NR_LBD_LXR The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors. The ligand binding domain of Liver X receptors: Liver X receptors (LXRs) belong to a family of nuclear receptors of ligand-activated transcription factors. LXRs operate as cholesterol sensors which protect from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. Upon ligand binding a conformational change leads to recruitment of co-factors, which stimulates expression of target genes. Among the LXR target genes are several genes involved in cholesterol efflux from peripheral tissues such as the ATP-binding-cassette transporters ABCA1, ABCG1 and ApoE. There are two LXR isoforms in mammals, LXRalpha and LXRbeta. LXRalpha is expressed mainly in the liver, intestine, kidney, splee
Probab=57.46 E-value=4.7 Score=21.34 Aligned_cols=123 Identities=18% Similarity=0.220 Sum_probs=59.0
Q ss_pred HHHHHHHHHHHCCCCCHHHCCH-HHHHCCCCEEEEEEEEECCCCCCCCEEEEEE----CCHHHHHHHHH-HHHHHHHCCC
Q ss_conf 9999999985089999568681-5502265601678873046545488799994----16269999999-9999997599
Q gi|254780998|r 20 RYHYLIELGKKLPLFPKEYMTD-QNIVAGCMSKLWMVIEWENKGDQDPIMIFYA----VSDSQIVCGLL-YIVKSIYAHK 93 (146)
Q Consensus 20 ry~~Li~lgk~l~~l~e~~k~~-~~~V~GCqS~vWl~~~~~~~~~~~~~~~f~~----dSda~IvkGl~-~ll~~~~~g~ 93 (146)
-.+.+++++|++|.+.+=...| -.+.+||-+.||+..-.-......+.+.|.. ..+...--|.. .++-..++=.
T Consensus 55 ~iq~iVefAK~iPgF~~L~~eDQi~LLK~~~~Ev~llr~a~r~~~~~~~i~f~~~~~~~r~~~~~~g~~~~~i~~lf~f~ 134 (236)
T cd06954 55 SVQEIVDFAKQLPGFLTLTREDQIALLKASTIEVMLLETARRYNPESEAITFLKDFPYSRDDFARAGLQVEFINPIFEFS 134 (236)
T ss_pred HHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCEEEEHHHHHHHCCHHHHHHHHHHHH
T ss_conf 88755455158988145997689999998389999999999807788948865991550999988206599999999999
Q ss_pred CHHHHHHCCHHHHHHHHCCHHCCCHHHHHHH--HHHHHHHHHHHHHHHHHHHC
Q ss_conf 8899980798999987090431694289999--99999999999999963311
Q gi|254780998|r 94 KISEILKMDSLTILQHLGLTENLSQKRMNGL--YTIVNKIQDLTQEYLNVHIK 144 (146)
Q Consensus 94 t~~eI~~~d~~~f~~~lgL~~~Lt~~R~nGl--~~m~~~ik~~a~~~l~~~~~ 144 (146)
..=.-+++|...| .=+-=--.+||-| .|+ ...++++++.....|-.+++
T Consensus 135 ~~~~~L~ld~~E~-alL~AIvLfspDR-pgL~d~~~VE~lQe~~~~aL~~yi~ 185 (236)
T cd06954 135 KSMRELQLDDAEY-ALLIAINIFSADR-PNVQDHHRVERLQETYVEALHSYIK 185 (236)
T ss_pred HHHHHCCCCHHHH-HHHHHHHHHCCCC-CCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999737989999-9999999857886-5676989999999999999999999
No 12
>TIGR01892 AcOrn-deacetyl acetylornithine deacetylase (ArgE); InterPro: IPR010169 This entry represents a clade of acetylornithine deacetylases (argE) from proteobacteria, which catalyse the final step in arginine biosynthesis. The enzyme is closely related to and may share a common origin with dapE (succinyl-diaminopimelate desuccinylase), cpg2 (carboxypeptidase G2) and ACY1 (aminoacylase I), all of which are members of the metal-dependent aminoacylase family, ArgE/dapE/ACY1/CPG2/yscS .; GO: 0008270 zinc ion binding, 0008777 acetylornithine deacetylase activity, 0050897 cobalt ion binding, 0006526 arginine biosynthetic process, 0005737 cytoplasm.
Probab=55.39 E-value=8.3 Score=19.77 Aligned_cols=70 Identities=13% Similarity=0.182 Sum_probs=44.2
Q ss_pred CCCEEEEEEEEECCCCCCCCEEEEEECCHHHHHHHHHHHHHHHHCCCCHHHHHHCCHHH----HHHHHCCHHCCCHHHHH
Q ss_conf 65601678873046545488799994162699999999999997599889998079899----99870904316942899
Q gi|254780998|r 47 GCMSKLWMVIEWENKGDQDPIMIFYAVSDSQIVCGLLYIVKSIYAHKKISEILKMDSLT----ILQHLGLTENLSQKRMN 122 (146)
Q Consensus 47 GCqS~vWl~~~~~~~~~~~~~~~f~~dSda~IvkGl~~ll~~~~~g~t~~eI~~~d~~~----f~~~lgL~~~Lt~~R~n 122 (146)
++++.-|=-. .+||++|=+|..| +||++|+++...-........+ |.. +=++.| ..
T Consensus 87 ~Wt~Dpf~Lt------e~dGrLYGrGt~D---mKGFlA~~L~A~pdl~~~~Lk~--Pl~~~~t~DEE~g---------~~ 146 (386)
T TIGR01892 87 AWTRDPFRLT------EKDGRLYGRGTCD---MKGFLALALAAAPDLAAEKLKK--PLHLALTADEEVG---------CA 146 (386)
T ss_pred CCCCCCCCCE------EECCCEECCCCCC---HHHHHHHHHHHHHHHHHHHCCC--CEEEEEECCHHHH---------HC
T ss_conf 8777723000------1247310476652---4789999998644676764388--4677673352321---------20
Q ss_pred HHHHHHHHHHHHHH
Q ss_conf 99999999999999
Q gi|254780998|r 123 GLYTIVNKIQDLTQ 136 (146)
Q Consensus 123 Gl~~m~~~ik~~a~ 136 (146)
|-..|++++-+.+.
T Consensus 147 Ga~~~~~~~~~~~~ 160 (386)
T TIGR01892 147 GAPKMIEALARLVL 160 (386)
T ss_pred CHHHHHHHHHHHCC
T ss_conf 24899999898517
No 13
>COG0822 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion]
Probab=55.28 E-value=18 Score=17.60 Aligned_cols=120 Identities=13% Similarity=0.123 Sum_probs=70.8
Q ss_pred HHH-HHHHHHHHHCCCCCHHHCC----HHHHHCCCCEEEEEEEEECCCCCCCCEEEEEECCHHHHHHHHHHHHHHHHCCC
Q ss_conf 999-9999998508999956868----15502265601678873046545488799994162699999999999997599
Q gi|254780998|r 19 DRY-HYLIELGKKLPLFPKEYMT----DQNIVAGCMSKLWMVIEWENKGDQDPIMIFYAVSDSQIVCGLLYIVKSIYAHK 93 (146)
Q Consensus 19 ~ry-~~Li~lgk~l~~l~e~~k~----~~~~V~GCqS~vWl~~~~~~~~~~~~~~~f~~dSda~IvkGl~~ll~~~~~g~ 93 (146)
+.| +-+++.-+.......-..- ..+--+-|-+.+=+...+++....|-++.-.|.+ |...-.+++++..-|+
T Consensus 5 ~~y~~~Ildh~~np~~~g~l~~~~~~~~~~~~~~CGD~i~l~lkv~~~~I~d~~F~~~GC~---is~ASss~~te~v~Gk 81 (150)
T COG0822 5 DLYSEKILDHYKNPRNVGVLDDADVGVGHVGAPACGDVITLYLKVDNGVIEDAKFKGFGCA---ISIASSSMMTELVKGK 81 (150)
T ss_pred HHHHHHHHHHHCCCCCCCCCCCCCHHCCCCCCCCCCCEEEEEEEECCCEEEEEEEEECCCH---HHHHHHHHHHHHHCCC
T ss_conf 8999999998519776785675221102558987555479999971998999886414808---9999999999997699
Q ss_pred CHHHHHHCC--HHHHHHHHCC-------------HHCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 889998079--8999987090-------------43169428999999999999999999963
Q gi|254780998|r 94 KISEILKMD--SLTILQHLGL-------------TENLSQKRMNGLYTIVNKIQDLTQEYLNV 141 (146)
Q Consensus 94 t~~eI~~~d--~~~f~~~lgL-------------~~~Lt~~R~nGl~~m~~~ik~~a~~~l~~ 141 (146)
|.+|++++. ..+..+.+|- ...+.|.|.+=..--..-++.-..++..+
T Consensus 82 ti~EAl~i~~~~~~m~~~~~~~~~~~l~d~~~l~~v~~~p~r~~C~~L~~~al~~ai~~~~~~ 144 (150)
T COG0822 82 TLDEALKITEAFTDMAKELGGDPDDRLGDLVALAGVALPPARIKCSLLAWDALKAAIKDYKGK 144 (150)
T ss_pred CHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCCCCCHHCCHHHHHHHHHHHHCC
T ss_conf 799999999999999997278864203566764201246110420640599999999986433
No 14
>cd07072 NR_LBD_DHR38_like Ligand binding domain of DHR38_like proteins, members of the nuclear receptor superfamily. The ligand binding domain of nuclear receptor DHR38_like proteins: DHR38 is a member of the steroid receptor superfamily in Drosophila. DHR38 interacts with the USP component of the ecdysone receptor complex, suggesting that DHR38 might modulate ecdysone-triggered signals in the fly, in addition to the ECR/USP pathway. At least four differentially expressed mRNA isoforms have been detected during development. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR38 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=55.15 E-value=7.5 Score=20.04 Aligned_cols=85 Identities=12% Similarity=0.166 Sum_probs=51.2
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCHHHCCH-HHHHCCCCEEEEEEEEECCCCCCCCEEEEEE---CCHHHHHH
Q ss_conf 9999987509998999999999985089999568681-5502265601678873046545488799994---16269999
Q gi|254780998|r 5 NDIIEDMEMIEDLHDRYHYLIELGKKLPLFPKEYMTD-QNIVAGCMSKLWMVIEWENKGDQDPIMIFYA---VSDSQIVC 80 (146)
Q Consensus 5 ~~i~e~f~~~~d~~~ry~~Li~lgk~l~~l~e~~k~~-~~~V~GCqS~vWl~~~~~~~~~~~~~~~f~~---dSda~Ivk 80 (146)
.++.+.|..+-++ -.+.+++++|++|.+.+=...| ..+.++|-..+|+..-.-.....++++.|-. .......+
T Consensus 41 ~~~~~~f~~l~t~--~i~~iVefAK~IPGF~~L~~~DQi~LLK~~~~Ell~Lrla~rs~~~~~~l~f~~g~~l~r~q~~~ 118 (239)
T cd07072 41 AEKVQQFYSLLTS--SIDVIKTFAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAPEDTKLTFCNGVVLHKQQCQR 118 (239)
T ss_pred HHHHHHHHHHHHH--HHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCEECHHHHHH
T ss_conf 9999999998779--99999999736988257997799999999899999999999805689948853990423999999
Q ss_pred HHHHHHHHHHC
Q ss_conf 99999999975
Q gi|254780998|r 81 GLLYIVKSIYA 91 (146)
Q Consensus 81 Gl~~ll~~~~~ 91 (146)
|+..++-.++.
T Consensus 119 ~~g~~~~~i~e 129 (239)
T cd07072 119 SFGDWLHAILE 129 (239)
T ss_pred HHHHHHHHHHH
T ss_conf 88999999999
No 15
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=50.24 E-value=20 Score=17.33 Aligned_cols=45 Identities=16% Similarity=0.101 Sum_probs=34.6
Q ss_pred ECCHHHHHHHHHHHHHH-HHCCCCHHHHHHCCHHHHHHHHCCHHCCCHHH
Q ss_conf 41626999999999999-97599889998079899998709043169428
Q gi|254780998|r 72 AVSDSQIVCGLLYIVKS-IYAHKKISEILKMDSLTILQHLGLTENLSQKR 120 (146)
Q Consensus 72 ~dSda~IvkGl~~ll~~-~~~g~t~~eI~~~d~~~f~~~lgL~~~Lt~~R 120 (146)
++|+|.+.+-+-..+.+ +-+|+|.+||.++ +.+..|=.-...|..
T Consensus 52 ~~S~s~iA~dmR~~Ir~~i~~G~sd~eI~~~----l~~rYG~~Il~~Pp~ 97 (126)
T PRK10144 52 LESNAPVAVSMRHQVYSMVAEGKSEVEIIGW----MTERYGDFVRYNPPL 97 (126)
T ss_pred HHCCHHHHHHHHHHHHHHHHCCCCHHHHHHH----HHHHCCCEEEEECCC
T ss_conf 1157799999999999999869999999999----998648849861899
No 16
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=48.39 E-value=22 Score=17.11 Aligned_cols=44 Identities=20% Similarity=0.150 Sum_probs=33.9
Q ss_pred ECCHHHHHHHHHHHHHH-HHCCCCHHHHHHCCHHHHHHHHCCHHCCCHH
Q ss_conf 41626999999999999-9759988999807989999870904316942
Q gi|254780998|r 72 AVSDSQIVCGLLYIVKS-IYAHKKISEILKMDSLTILQHLGLTENLSQK 119 (146)
Q Consensus 72 ~dSda~IvkGl~~ll~~-~~~g~t~~eI~~~d~~~f~~~lgL~~~Lt~~ 119 (146)
++|+|.+.+-+-..+.. +-+|+|.+||.++ +.+..|=.-.+.|.
T Consensus 52 ~~S~a~~A~dmR~~I~~~i~~G~sd~eI~~~----l~~RYG~~Il~~Pp 96 (126)
T TIGR03147 52 VESNSPIAYDLRHEVYSMVNEGKSNQQIIDF----MTARFGDFVLYNPP 96 (126)
T ss_pred HHCCHHHHHHHHHHHHHHHHCCCCHHHHHHH----HHHHCCCEEEECCC
T ss_conf 0076199999999999999859998999999----99970882875399
No 17
>cd06939 NR_LBD_ROR_like The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily. The ligand binding domain (LBD) of Retinoid-related orphan receptors (RORs): Retinoid-related orphan receptors (RORs) are transcription factors belonging to the nuclear receptor superfamily. RORs are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. Transcription regulation by RORs is mediated through certain corepressors, as well as coactivators. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma that differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum, particularly in the regulation of the maturation and survival of Purkinje cells. RORbeta expression is largely r
Probab=46.84 E-value=18 Score=17.64 Aligned_cols=63 Identities=13% Similarity=0.164 Sum_probs=38.5
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHCCCCCHHHCCH-HHHHCCCCEEEEEEEEECCCCCCCCEEEE
Q ss_conf 999987509998999999999985089999568681-55022656016788730465454887999
Q gi|254780998|r 6 DIIEDMEMIEDLHDRYHYLIELGKKLPLFPKEYMTD-QNIVAGCMSKLWMVIEWENKGDQDPIMIF 70 (146)
Q Consensus 6 ~i~e~f~~~~d~~~ry~~Li~lgk~l~~l~e~~k~~-~~~V~GCqS~vWl~~~~~~~~~~~~~~~f 70 (146)
++-+.|...-++ --+++|+++|++|.+.+=...| -.++++|-..||+..-.-.-...++.+.|
T Consensus 48 ~lW~~fa~~~t~--~Iq~VVeFAK~IPGF~~L~~eDQi~LLK~~~~Ev~llr~a~~~~~~~~~v~~ 111 (241)
T cd06939 48 EMWQLCAEKITE--AIQYVVEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNPSNNTVLF 111 (241)
T ss_pred HHHHHHHHHHHH--HHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEE
T ss_conf 999999999489--9999999981399713489878999998668999999999982666796876
No 18
>pfam06304 DUF1048 Protein of unknown function (DUF1048). This family consists of several hypothetical bacterial proteins of unknown function.
Probab=46.79 E-value=21 Score=17.20 Aligned_cols=67 Identities=15% Similarity=0.230 Sum_probs=49.0
Q ss_pred HHCCCCCHHHCCHHHHHCCCCEEEEEEEEECCCCCCCCEEEEEECCHHHHHHHHHHHHHH-HHCCCCHHHHHHCCHHHHH
Q ss_conf 508999956868155022656016788730465454887999941626999999999999-9759988999807989999
Q gi|254780998|r 29 KKLPLFPKEYMTDQNIVAGCMSKLWMVIEWENKGDQDPIMIFYAVSDSQIVCGLLYIVKS-IYAHKKISEILKMDSLTIL 107 (146)
Q Consensus 29 k~l~~l~e~~k~~~~~V~GCqS~vWl~~~~~~~~~~~~~~~f~~dSda~IvkGl~~ll~~-~~~g~t~~eI~~~d~~~f~ 107 (146)
.+...||++|++.-..++.- +|-..- +.+.+--.|-.|++-|+-. +-+|++..||.--|+..|-
T Consensus 4 aRvk~LP~dY~~a~~~iqkY---l~~~g~------------~~g~~~~~il~~lldLfEe~AadG~~V~ev~GeDva~F~ 68 (92)
T pfam06304 4 ARAKALPEDYYQAYKEIQKY---LWNFGA------------TDGADMKPILTDILDLFEEAAADGKSVLEVTGEDVAAFC 68 (92)
T ss_pred HHHHHCCHHHHHHHHHHHHH---HHHCCC------------CCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCHHHHH
T ss_conf 88877888899999999997---542289------------866888999999999999988669972476177899999
Q ss_pred HHH
Q ss_conf 870
Q gi|254780998|r 108 QHL 110 (146)
Q Consensus 108 ~~l 110 (146)
+++
T Consensus 69 d~l 71 (92)
T pfam06304 69 DEL 71 (92)
T ss_pred HHH
T ss_conf 999
No 19
>pfam00082 Peptidase_S8 Subtilase family. Subtilases are a family of serine proteases. They appear to have independently and convergently evolved an Asp/Ser/His catalytic triad, like that found in the trypsin serine proteases (see pfam00089). Structure is an alpha/beta fold containing a 7-stranded parallel beta sheet, order 2314567.
Probab=46.22 E-value=23 Score=17.06 Aligned_cols=36 Identities=14% Similarity=0.044 Sum_probs=28.3
Q ss_pred CEEEEEECCHH-HHHHHHHHHHHHHHCCC-----CHHHHHHC
Q ss_conf 87999941626-99999999999997599-----88999807
Q gi|254780998|r 66 PIMIFYAVSDS-QIVCGLLYIVKSIYAHK-----KISEILKM 101 (146)
Q Consensus 66 ~~~~f~~dSda-~IvkGl~~ll~~~~~g~-----t~~eI~~~ 101 (146)
+...+.|.|=| ++|-|.++||.+.+-.. ||.||++.
T Consensus 231 ~y~~~sGTS~AaP~VaG~aALl~~~~P~l~~~~~t~~qv~~~ 272 (292)
T pfam00082 231 GYASHSGTSMAAPHVAGVAALLLSANPSLHLIVLTAAELRAA 272 (292)
T ss_pred EEEECCEEEHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHH
T ss_conf 587789934718999999999998693667778999999999
No 20
>COG4817 DNA-binding ferritin-like protein (Dps family) [General function prediction only]
Probab=42.62 E-value=22 Score=17.18 Aligned_cols=68 Identities=19% Similarity=0.301 Sum_probs=50.9
Q ss_pred HHHHCCCCCHHHCCHHHHHCCCCEEEEEEEEECCCCCCCCEEEEEECCHHHHHHHHHHHHHH-HHCCCCHHHHHHCCHHH
Q ss_conf 98508999956868155022656016788730465454887999941626999999999999-97599889998079899
Q gi|254780998|r 27 LGKKLPLFPKEYMTDQNIVAGCMSKLWMVIEWENKGDQDPIMIFYAVSDSQIVCGLLYIVKS-IYAHKKISEILKMDSLT 105 (146)
Q Consensus 27 lgk~l~~l~e~~k~~~~~V~GCqS~vWl~~~~~~~~~~~~~~~f~~dSda~IvkGl~~ll~~-~~~g~t~~eI~~~d~~~ 105 (146)
+-.+...||++|++.--.| |+-+|... +.+.-+-.|-.+++-++-. ..+|+++.+++--|...
T Consensus 18 ~e~RakkLPkdY~~aykeI---qkYlw~~g-------------~t~~~~~~Il~~iLelfE~aaadgk~v~dv~GdDvA~ 81 (111)
T COG4817 18 FENRAKKLPKDYYTAYKEI---QKYLWKSG-------------PTGWNEMKILGNILELFEEAAADGKEVTDVLGDDVAT 81 (111)
T ss_pred HHHHHHHCCHHHHHHHHHH---HHHHHHCC-------------CCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCHHHH
T ss_conf 9999987829899999999---99999717-------------6404788889999999998773365589985634999
Q ss_pred HHHHH
Q ss_conf 99870
Q gi|254780998|r 106 ILQHL 110 (146)
Q Consensus 106 f~~~l 110 (146)
|.+.|
T Consensus 82 F~D~L 86 (111)
T COG4817 82 FCDAL 86 (111)
T ss_pred HHHHH
T ss_conf 99999
No 21
>cd06935 NR_LBD_TR The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear receptors. The ligand binding domain (LBD) of thyroid hormone receptors: Thyroid hormone receptors are members of a superfamily of nuclear receptors. Thyroid hormone receptors (TR) mediate the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the heart to regulate heart rate and rhythm and TRbeta is active in the liver and other tissues. The unliganded TRs function as transcription repressors, by binding to thyroid hormone response elements (TRE) predominantly as homodimers, or as heterodimers with retinoid X-receptors (RXR), a
Probab=40.87 E-value=11 Score=18.94 Aligned_cols=71 Identities=15% Similarity=0.268 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHCCCCCHHHCCH-HHHHCCCCEEEEEEEEECCCCCCCCEEEEEEC----CHHHHHHHHHHHHHHHH
Q ss_conf 9999999985089999568681-55022656016788730465454887999941----62699999999999997
Q gi|254780998|r 20 RYHYLIELGKKLPLFPKEYMTD-QNIVAGCMSKLWMVIEWENKGDQDPIMIFYAV----SDSQIVCGLLYIVKSIY 90 (146)
Q Consensus 20 ry~~Li~lgk~l~~l~e~~k~~-~~~V~GCqS~vWl~~~~~~~~~~~~~~~f~~d----Sda~IvkGl~~ll~~~~ 90 (146)
--+.+++++|++|.+.+=...| -.+.++|-..+|+..-.-.....++++.|.++ .+..-.-|+..++-.+|
T Consensus 64 ~Iq~IVeFAK~IPGF~~L~~eDQi~LLK~~~~Evl~Lr~a~r~~~~~~~l~~~~~~~~~~~~~~~~g~~~l~~~if 139 (243)
T cd06935 64 AITRVVDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLSGEMAVTREQLKNGGLGVVSDAIF 139 (243)
T ss_pred HHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCEEECHHHHHHCCHHHHHHHHH
T ss_conf 9999999980598713599889999999878999999999983666897997599777299997547588999999
No 22
>cd06940 NR_LBD_REV_ERB The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily. The ligand binding domain (LBD) of REV-ERB receptors: REV-ERBs are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. The LBD domain of REV-ERB is unusual in the nuclear receptor family by lacking the AF-2 region that is responsible for coactivator interaction. REV-ERBs act as constitutive repressors because of their inability to bind coactivators. REV-ERB receptors can bind to two classes of DNA response elements as either a monomer or heterodimer, indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target gene. The porphyrin heme has been demonstrated to function as a ligand for REV-ERB. Like other members of
Probab=40.75 E-value=10 Score=19.27 Aligned_cols=135 Identities=17% Similarity=0.191 Sum_probs=61.6
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHCCCCCHHHCCH-HHHHCCCCEEEEEEEEECCCCCCCCEEEEEECC----HHHHHH
Q ss_conf 999987509998999999999985089999568681-550226560167887304654548879999416----269999
Q gi|254780998|r 6 DIIEDMEMIEDLHDRYHYLIELGKKLPLFPKEYMTD-QNIVAGCMSKLWMVIEWENKGDQDPIMIFYAVS----DSQIVC 80 (146)
Q Consensus 6 ~i~e~f~~~~d~~~ry~~Li~lgk~l~~l~e~~k~~-~~~V~GCqS~vWl~~~~~~~~~~~~~~~f~~dS----da~Ivk 80 (146)
++-+.|...-+ .--+.+|+++|++|.+.+=...| -.++++|-..+|+..-..--....+.+.|..+. |..-.-
T Consensus 12 ~~~~~f~~~~t--~~I~~iVefAK~IPgF~~L~~~DQi~LLk~~~~ElllL~~a~~~~~~~~~l~~~~~~~~~~~~~~~~ 89 (189)
T cd06940 12 EIWEEFSMSFT--PAVREVVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFDAKERSVTFLSGQKYSVDDLHSM 89 (189)
T ss_pred HHHHHHHHHHH--HHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCEECHHHHHHC
T ss_conf 99999999979--9999999999709896689977899999987899999999998077999588469946639999774
Q ss_pred HHHHHHHHHHCCCCHHHHHHCCHHHHHHHHCCHHCCCHHHHHHH--HHHHHHHHHHHHHHHHHHHC
Q ss_conf 99999999975998899980798999987090431694289999--99999999999999963311
Q gi|254780998|r 81 GLLYIVKSIYAHKKISEILKMDSLTILQHLGLTENLSQKRMNGL--YTIVNKIQDLTQEYLNVHIK 144 (146)
Q Consensus 81 Gl~~ll~~~~~g~t~~eI~~~d~~~f~~~lgL~~~Lt~~R~nGl--~~m~~~ik~~a~~~l~~~~~ 144 (146)
|...++-..++=...=.-+.+|...| .-+.---.++|-|. |+ ..-++++++.....|..+++
T Consensus 90 ~~~~l~~~~~~f~~~~~~L~ld~~E~-alL~AivLfspDr~-gL~~~~~Ve~lQe~~~~aL~~y~~ 153 (189)
T cd06940 90 GAGDLLNSMFDFSEKLNSLQLSDEEM-GLFTAVVLVSADRS-GLENVNLVEALQETLIRALRTLIA 153 (189)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCHHHH-HHHHHHHHHCCCCC-CCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 74999999999999998638999999-99999998368878-998999999999999999999999
No 23
>cd06941 NR_LBD_DmE78_like The ligand binding domain of Drosophila ecdysone-induced protein 78, a member of the nuclear receptor superfamily. The ligand binding domain (LBD) of Drosophila ecdysone-induced protein 78 (E78) like: Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. Two isoforms of E78, E78A and E78B, are expressed from two nested transcription units. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. SmE78 may be involved in transduction of an ecdysone signal in S. mansoni, consistent with its function in Drosophila. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, E78-like receptors ha
Probab=36.89 E-value=16 Score=18.03 Aligned_cols=117 Identities=22% Similarity=0.298 Sum_probs=54.1
Q ss_pred HHHHHHHHHHHCCCCCHHHCCH-HHHHCCCCEEEEEEEEECCCCCCCCEEEEEECCHHHHHHHHHHHHHHHHCCCCHHHH
Q ss_conf 9999999985089999568681-550226560167887304654548879999416269999999999999759988999
Q gi|254780998|r 20 RYHYLIELGKKLPLFPKEYMTD-QNIVAGCMSKLWMVIEWENKGDQDPIMIFYAVSDSQIVCGLLYIVKSIYAHKKISEI 98 (146)
Q Consensus 20 ry~~Li~lgk~l~~l~e~~k~~-~~~V~GCqS~vWl~~~~~~~~~~~~~~~f~~dSda~IvkGl~~ll~~~~~g~t~~eI 98 (146)
--+.+|+++|++|.+.+=...| ..++++|-+.+++..-.-.....++.+.+. .+-.+.+..+.... ...-.+.+
T Consensus 14 ~I~~iV~fAK~IPgF~~L~~~DQi~LLk~~~~Ellll~~a~~~~~~~~~~~~~--~~~~~~~~~~~~~~---~~~~~~~i 88 (195)
T cd06941 14 SVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRISRLINSKSGSITFD--DGISISRQQLDIIY---DSDFVKAL 88 (195)
T ss_pred HHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEC--CCEEECHHHHHHCC---CHHHHHHH
T ss_conf 99999999915988135998899999998699999999998705788848746--99200499998703---49999999
Q ss_pred HHCCHHHHHHHHCCH----------HCCCHHHHHHH--HHHHHHHHHHHHHHHHHHHC
Q ss_conf 807989999870904----------31694289999--99999999999999963311
Q gi|254780998|r 99 LKMDSLTILQHLGLT----------ENLSQKRMNGL--YTIVNKIQDLTQEYLNVHIK 144 (146)
Q Consensus 99 ~~~d~~~f~~~lgL~----------~~Lt~~R~nGl--~~m~~~ik~~a~~~l~~~~~ 144 (146)
.++ . .-+.++++. -.++|-|. |+ ..-++++++.....|..+++
T Consensus 89 ~~f-~-~~~~~L~ld~~E~alL~AivLf~pDr~-gL~~~~~Ve~lQe~~~~aL~~~~~ 143 (195)
T cd06941 89 FEF-S-DSFNSLGLSDTEVALFCAVVLLSPDRI-GLSEPKKVAILQDRVLEALKVQVS 143 (195)
T ss_pred HHH-H-HHHHHCCCCHHHHHHHHHHHEECCCCC-CCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 999-9-999981898899998877420368876-788879999999999999999999
No 24
>pfam07914 DUF1679 Protein of unknown function (DUF1679). The region featured in this family is found in a number of C. elegans proteins, in one case as a repeat. In many of the family members, this region is associated with the CHK region described by SMART as being found in ZnF_C4 and HLH domain-containing kinases. In fact, one member of this family is annotated as being a member of the nuclear hormone receptor family, and contains regions typical of such proteins (Interpro:IPR000536, Interpro:IPR008946, and Interpro:IPR001628).
Probab=36.79 E-value=36 Score=15.80 Aligned_cols=96 Identities=15% Similarity=0.168 Sum_probs=57.0
Q ss_pred HHHHHHHHHHHHCCCCCHHH----CCHHHHHCCCCEEEEE-----EEEECCCCCCCCEEEEEECCHHHHHHHHHHHHHHH
Q ss_conf 99999999985089999568----6815502265601678-----87304654548879999416269999999999999
Q gi|254780998|r 19 DRYHYLIELGKKLPLFPKEY----MTDQNIVAGCMSKLWM-----VIEWENKGDQDPIMIFYAVSDSQIVCGLLYIVKSI 89 (146)
Q Consensus 19 ~ry~~Li~lgk~l~~l~e~~----k~~~~~V~GCqS~vWl-----~~~~~~~~~~~~~~~f~~dSda~IvkGl~~ll~~~ 89 (146)
+-|+.|.-+-...-|+|.-| -.++|..+||.--=++ ..-+++ +.++-=-+|+||++.+-..+
T Consensus 118 n~Ykil~k~n~~~i~~pKVY~~kkfd~en~~KG~IimE~v~ni~~~~~y~n---------i~~deL~~vv~~iA~fqA~~ 188 (413)
T pfam07914 118 NFYKILEKFNHPDIPYTKVYFLKKFDDENDLKGYIIMEYVPNIHTRHMYEN---------IPADELIPVLRAIATFQALG 188 (413)
T ss_pred HHHHHHHHCCCCCCCCCCEEEECCCCCCCCCCCEEEEEECCCCEEEECCCC---------CCHHHHHHHHHHHHHHHHHH
T ss_conf 999999970687898740123024565677777788882488468725489---------89899999999999999864
Q ss_pred HCCCCHHHHHHCCHHHHHHHHCCHHCCCHHHHHHHH
Q ss_conf 759988999807989999870904316942899999
Q gi|254780998|r 90 YAHKKISEILKMDSLTILQHLGLTENLSQKRMNGLY 125 (146)
Q Consensus 90 ~~g~t~~eI~~~d~~~f~~~lgL~~~Lt~~R~nGl~ 125 (146)
+ ..|.+|...+...+|++. .++..++.....|+.
T Consensus 189 ~-~LseEE~k~i~g~df~~~-~~~~~~~~~~~~~~f 222 (413)
T pfam07914 189 E-SLSEEEKKSANGADFLEQ-MFETFMSEEGLKGIF 222 (413)
T ss_pred C-CCCHHHHHHCCCHHHHHH-HHHHHHHHHHHHHHH
T ss_conf 3-499899753567579999-999872367799999
No 25
>cd07068 NR_LBD_ER_like The ligand binding domain of estrogen receptor and estrogen receptor-related receptors. The ligand binding domain of estrogen receptor (ER) and estrogen receptor-related receptors (ERRs): Estrogen receptors are a group of receptors which are activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. ERRs are closely related to the estrogen receptor (ER) family. But, it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signalin
Probab=36.64 E-value=21 Score=17.26 Aligned_cols=125 Identities=14% Similarity=0.080 Sum_probs=57.6
Q ss_pred HHHHHHHHHHHHHCCCCCHHHCCH-HHHHCCCCEEEEEEEEECCCCCCCCEEEEEEC----CHHHHHHHHHHHHHHHHCC
Q ss_conf 999999999985089999568681-55022656016788730465454887999941----6269999999999999759
Q gi|254780998|r 18 HDRYHYLIELGKKLPLFPKEYMTD-QNIVAGCMSKLWMVIEWENKGDQDPIMIFYAV----SDSQIVCGLLYIVKSIYAH 92 (146)
Q Consensus 18 ~~ry~~Li~lgk~l~~l~e~~k~~-~~~V~GCqS~vWl~~~~~~~~~~~~~~~f~~d----Sda~IvkGl~~ll~~~~~g 92 (146)
......+|+++|++|.+.+=...| -.+.++|-+.+++..-.-.....++.+.|..+ -+..-.-|+..++...+.=
T Consensus 37 ~r~L~~~VewAK~iPgF~~L~~~DQi~LLk~~w~ElllL~~a~rs~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~e~ 116 (221)
T cd07068 37 DRELVHIISWAKHIPGFSDLSLNDQMHLLQSAWLEILMLGLVWRSLPHPGKLVFAPDLLLDREQARVEGLLEIFDMLLQL 116 (221)
T ss_pred HHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCEEECHHHHHHCCHHHHHHHHHHH
T ss_conf 99999999999839653067988999999998899999999997057888278418853357765022699999999999
Q ss_pred CCHHHHHHCCHHHHHHHHCCHHCCCHHHHHHH--HHHHHHHHHHHHHHHHHHHC
Q ss_conf 98899980798999987090431694289999--99999999999999963311
Q gi|254780998|r 93 KKISEILKMDSLTILQHLGLTENLSQKRMNGL--YTIVNKIQDLTQEYLNVHIK 144 (146)
Q Consensus 93 ~t~~eI~~~d~~~f~~~lgL~~~Lt~~R~nGl--~~m~~~ik~~a~~~l~~~~~ 144 (146)
...=.-+++|...| .-+.---.++|.|. |+ ..-+++++..+...|..++.
T Consensus 117 ~~~~~~L~ld~~E~-a~LkAivLf~pD~~-gL~~~~~Ve~lQ~~~~~aL~~y~~ 168 (221)
T cd07068 117 VRRFRELGLQREEY-VCLKAIILANSDVR-HLEDREAVQQLRDAILDALVDVEA 168 (221)
T ss_pred HHHHHHHCCCHHHH-HHHHHHHHHCCCCC-CCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999808989999-99999998388888-887999999999999999999999
No 26
>TIGR01286 nifK nitrogenase molybdenum-iron protein beta chain; InterPro: IPR005976 The enzyme responsible for nitrogen fixation, the nitrogenase, shows a high degree of conservation of structure, function, and amino acid sequence across wide phylogenetic ranges. All known Mo-nitrogenases consist of two components, component I (also called dinitrogenase, or Fe-Mo protein), an alpha2beta2 tetramer encoded by the nifD and nifK genes, and component II (dinitrogenase reductase, or Fe protein) a homodimer encoded by the nifH gene , . Two operons, nifDK and nifEN, encode a tetrameric (alpha2beta2 and N2E2) enzymatic complex. Nitrogenase contains two unusual rare metal clusters; one of them is the iron molybdenum cofactor (FeMo-co), which is considered to be the site of dinitrogen reduction and whose biosynthesis requires the products of nifNE and of some other nif genes . It has been proposed that NifNE might serve as a scaffold upon which FeMo-co is built and then inserted into component I .; GO: 0016163 nitrogenase activity, 0009399 nitrogen fixation, 0016612 molybdenum-iron nitrogenase complex.
Probab=35.97 E-value=23 Score=17.00 Aligned_cols=84 Identities=15% Similarity=0.252 Sum_probs=58.5
Q ss_pred HHHHHHHHHC-CCCCHHHCCHHHHHCC--CCEEEEEEEEECCCCCCCCEEEEEECCHHHHHHHHHHHHHHHHCCCCHHHH
Q ss_conf 9999998508-9999568681550226--560167887304654548879999416269999999999999759988999
Q gi|254780998|r 22 HYLIELGKKL-PLFPKEYMTDQNIVAG--CMSKLWMVIEWENKGDQDPIMIFYAVSDSQIVCGLLYIVKSIYAHKKISEI 98 (146)
Q Consensus 22 ~~Li~lgk~l-~~l~e~~k~~~~~V~G--CqS~vWl~~~~~~~~~~~~~~~f~~dSda~IvkGl~~ll~~~~~g~t~~eI 98 (146)
++||..++=. .|+|++.+.+-=|.-- -=|+.||.. .++-..||-| .|=||+.-+++. |..|--|
T Consensus 330 eFLm~vs~isg~eiP~~l~~eRGRlVDamtDs~awlHG---------Kr~Ai~GDPD--lV~al~~F~LEl--G~ePvHi 396 (526)
T TIGR01286 330 EFLMKVSEISGQEIPAELTIERGRLVDAMTDSQAWLHG---------KRVAIYGDPD--LVMALVRFVLEL--GIEPVHI 396 (526)
T ss_pred HHHHHHHHHCCCCCHHHHHHHCCCHHHHHHHHHHHHHH---------CCEEEECCCH--HHHHHHHHHHHH--CCCCEEE
T ss_conf 99999998507876278885103302555543343400---------3045405815--899999999981--8975589
Q ss_pred HHCCHHHHHHHHCCHHCCCHH
Q ss_conf 807989999870904316942
Q gi|254780998|r 99 LKMDSLTILQHLGLTENLSQK 119 (146)
Q Consensus 99 ~~~d~~~f~~~lgL~~~Lt~~ 119 (146)
+.-+...-+++- .+..|+.|
T Consensus 397 l~~N~~~~f~~~-~~~~LAAS 416 (526)
T TIGR01286 397 LATNGTKEFKAE-MKALLAAS 416 (526)
T ss_pred EEECCCHHHHHH-HHHHHHCC
T ss_conf 841888589999-99986026
No 27
>pfam01466 Skp1 Skp1 family, dimerization domain.
Probab=34.38 E-value=36 Score=15.83 Aligned_cols=38 Identities=18% Similarity=0.288 Sum_probs=24.7
Q ss_pred CCHHHHHHHHHHHHHHH----HCCCCHHHHHHCCHHHHHHHHCCHHCCCH
Q ss_conf 16269999999999999----75998899980798999987090431694
Q gi|254780998|r 73 VSDSQIVCGLLYIVKSI----YAHKKISEILKMDSLTILQHLGLTENLSQ 118 (146)
Q Consensus 73 dSda~IvkGl~~ll~~~----~~g~t~~eI~~~d~~~f~~~lgL~~~Lt~ 118 (146)
.++-+-++||+-+.|.. ..|+||+||+++ +|+..-+||
T Consensus 22 AAnyL~I~~Lldl~c~~vA~~ikgKt~eEiR~~--------f~I~~D~t~ 63 (78)
T pfam01466 22 AANYLNIKGLLDLACQKVADMIKGKTPEEIREI--------FGIENDFTP 63 (78)
T ss_pred HHHHHCCHHHHHHHHHHHHHHHCCCCHHHHHHH--------HCCCCCCCH
T ss_conf 998718488999999999999849999999999--------699999999
No 28
>cd06934 NR_LBD_PXR_like The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor. The ligand binding domain of xenobiotic receptors: This xenobiotic receptor family includes pregnane X receptor (PXR), constitutive androstane receptor (CAR) and other related nuclear receptors. They function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The nuclear receptor pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. The ligand binding domain of PXR shows remarkable flexibility to accommodate both large and small molecules. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and elimination of
Probab=32.73 E-value=17 Score=17.91 Aligned_cols=36 Identities=19% Similarity=0.381 Sum_probs=26.1
Q ss_pred HHHHHHHHHHCCCCCHHHCCH-HHHHCCCCEEEEEEE
Q ss_conf 999999985089999568681-550226560167887
Q gi|254780998|r 21 YHYLIELGKKLPLFPKEYMTD-QNIVAGCMSKLWMVI 56 (146)
Q Consensus 21 y~~Li~lgk~l~~l~e~~k~~-~~~V~GCqS~vWl~~ 56 (146)
.+.+++++|++|.+.+=...| -.+.+||...|++..
T Consensus 48 Iq~iVeFAK~iPGF~~L~~eDQI~LLK~~~~Ev~~LR 84 (226)
T cd06934 48 IKQIIKFAKDLPYFRSLPIEDQISLLKGATFEICQIR 84 (226)
T ss_pred HHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999757987025998899999999899999999
No 29
>pfam03918 CcmH Cytochrome C biogenesis protein. Members of this family include NrfF, CcmH, CycL, Ccl2.
Probab=32.55 E-value=42 Score=15.37 Aligned_cols=45 Identities=18% Similarity=0.143 Sum_probs=34.4
Q ss_pred ECCHHHHHHHHHHHHHH-HHCCCCHHHHHHCCHHHHHHHHCCHHCCCHHH
Q ss_conf 41626999999999999-97599889998079899998709043169428
Q gi|254780998|r 72 AVSDSQIVCGLLYIVKS-IYAHKKISEILKMDSLTILQHLGLTENLSQKR 120 (146)
Q Consensus 72 ~dSda~IvkGl~~ll~~-~~~g~t~~eI~~~d~~~f~~~lgL~~~Lt~~R 120 (146)
+||+|.|.+-+-..+.+ +-+|+|-+||.++ +.+..|=.-.+.|..
T Consensus 49 ~dS~a~iA~dmR~~i~~~i~~G~sd~eI~~~----~~~rYG~~Vl~~Pp~ 94 (145)
T pfam03918 49 ADSNAPLARDLRLEVREMLVEGKSDEEIIDY----MVARYGDFVLYKPPL 94 (145)
T ss_pred HCCCHHHHHHHHHHHHHHHHCCCCHHHHHHH----HHHHCCCCEEECCCC
T ss_conf 0077799999999999999859999999999----998638615555999
No 30
>cd06937 NR_LBD_RAR The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily. The ligand binding domain (LBD) of retinoic acid receptor (RAR): Retinoic acid receptors are members of the nuclear receptor (NR) superfamily of ligand-regulated transcription factors. RARs mediate the biological effect of retinoids, including both naturally dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RARs function as heterodimers with retinoic X receptors by binding to specific RAR response elements (RAREs) found in the promoter regions of retinoid target genes. In the absence of ligand, the RAR-RXR heterodimer recruits the corepressor proteins NCoR or AMRT, and associated factors such as histone deacetylases or DNA-methyltransferases, leading to
Probab=31.36 E-value=21 Score=17.32 Aligned_cols=123 Identities=17% Similarity=0.185 Sum_probs=58.2
Q ss_pred HHHHHHHHHHHCCCCCHHHCCH-HHHHCCCCEEEEEEEEECCCCCCCCEEEEEE----CCHHHHHHHHHHHHHHHHCCCC
Q ss_conf 9999999985089999568681-5502265601678873046545488799994----1626999999999999975998
Q gi|254780998|r 20 RYHYLIELGKKLPLFPKEYMTD-QNIVAGCMSKLWMVIEWENKGDQDPIMIFYA----VSDSQIVCGLLYIVKSIYAHKK 94 (146)
Q Consensus 20 ry~~Li~lgk~l~~l~e~~k~~-~~~V~GCqS~vWl~~~~~~~~~~~~~~~f~~----dSda~IvkGl~~ll~~~~~g~t 94 (146)
-.+.+++++|++|.+.+=...| ..++++|-..+|+..-..-....++.+.|.. +.+..-..|+..++-.+++=..
T Consensus 50 ~i~~IVewAK~IPgF~~L~~~DQi~LLk~~~~Ell~Lr~a~r~~~~~~~l~f~~g~~l~r~~~~~~g~~~l~~~i~~f~~ 129 (231)
T cd06937 50 CIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVFTFAN 129 (231)
T ss_pred HHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCEEECHHHHHHCCHHHHHHHHHHHHH
T ss_conf 99999999815988247987799999999899999999999826678857844981442999866473999999999999
Q ss_pred HHHHHHCCHHHHHHHHCCHHCCCHHHHHHH--HHHHHHHHHHHHHHHHHHHC
Q ss_conf 899980798999987090431694289999--99999999999999963311
Q gi|254780998|r 95 ISEILKMDSLTILQHLGLTENLSQKRMNGL--YTIVNKIQDLTQEYLNVHIK 144 (146)
Q Consensus 95 ~~eI~~~d~~~f~~~lgL~~~Lt~~R~nGl--~~m~~~ik~~a~~~l~~~~~ 144 (146)
.=.-+++|...| .=+.---.++|-| .|+ ..-++++++.....|..+++
T Consensus 130 ~l~~L~ld~~E~-alL~AivL~spDr-~gL~~~~~Ve~lQe~i~~aL~~yi~ 179 (231)
T cd06937 130 QLLPLEMDDTEI-GLLSAICLICGDR-QDLEEPDRVEKLQEPLLEALKIYAR 179 (231)
T ss_pred HHHHCCCCHHHH-HHHHHHHHCCCCC-CCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 999808999999-9999999728776-7888999999999999999999999
No 31
>cd06929 NR_LBD_F1 Ligand-binding domain of nuclear receptor family 1. Ligand-binding domain (LBD) of nuclear receptor (NR) family 1: This is one of the major subfamily of nuclear receptors, including thyroid receptor, retinoid acid receptor, ecdysone receptor, farnesoid X receptor, vitamin D receptor, and other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=30.50 E-value=18 Score=17.62 Aligned_cols=123 Identities=18% Similarity=0.217 Sum_probs=54.6
Q ss_pred HHHHHHHHHHHHCCCCCHHHCCH-HHHHCCCCEEEEEEEEECCCCCCCCEEEEEECC-----HHHHHHHHHHHHHHHHCC
Q ss_conf 99999999985089999568681-550226560167887304654548879999416-----269999999999999759
Q gi|254780998|r 19 DRYHYLIELGKKLPLFPKEYMTD-QNIVAGCMSKLWMVIEWENKGDQDPIMIFYAVS-----DSQIVCGLLYIVKSIYAH 92 (146)
Q Consensus 19 ~ry~~Li~lgk~l~~l~e~~k~~-~~~V~GCqS~vWl~~~~~~~~~~~~~~~f~~dS-----da~IvkGl~~ll~~~~~g 92 (146)
.-.+.+|+++|++|.+.+=...| -.++++|-..+++..-........+.+.+ ++. +..-..|...++...+.=
T Consensus 13 ~~i~~iV~waK~iP~F~~L~~~DQ~~LLk~~~~El~~l~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 91 (174)
T cd06929 13 VAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPEKNSLTF-GDGKGNSRDVLLNGGFGEFIEPLFEF 91 (174)
T ss_pred HHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEE-CCCCCCCHHHHHHCCHHHHHHHHHHH
T ss_conf 99999999980698814599999999999989999999999993678884661-79840059988702379999999999
Q ss_pred CCHHHHHHCCHHHHHHHHCCHHCCCHHHHHHH--HHHHHHHHHHHHHHHHHHHC
Q ss_conf 98899980798999987090431694289999--99999999999999963311
Q gi|254780998|r 93 KKISEILKMDSLTILQHLGLTENLSQKRMNGL--YTIVNKIQDLTQEYLNVHIK 144 (146)
Q Consensus 93 ~t~~eI~~~d~~~f~~~lgL~~~Lt~~R~nGl--~~m~~~ik~~a~~~l~~~~~ 144 (146)
...=.-+++|...| .=+.---.++|-|. |+ ...++++++.+...|..+++
T Consensus 92 ~~~~~~L~l~~~E~-alLkaivLf~pd~~-gL~~~~~Ve~lQ~~~~~aL~~y~~ 143 (174)
T cd06929 92 AEKMNKLQLDDNEY-ALLTAIVLFSPDRP-GLQDVDTVEKLQERLLEALQRYLK 143 (174)
T ss_pred HHHHHHHCCCHHHH-HHHHHHHHCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999818999999-99999997078888-987899999999999999999999
No 32
>cd06664 IscU_like Iron-sulfur cluster scaffold-like proteins. IscU_like and NifU_like proteins. IscU and NifU function as a scaffold for the assembly of [2Fe-2S] clusters before they are transferred to apo target proteins. They are highly conserved and play vital roles in the ISC and NIF systems of Fe-S protein maturation. NIF genes participate in nitrogen fixation in several isolated bacterial species. The NifU domain, however, is also found in bacteria that do not fix nitrogen, so it may have wider significance in the cell. Human IscU interacts with frataxin, the Friedreich ataxia gene product, and incorrectly spliced IscU has been shown to disrupt iron homeostasis in skeletal muscle and cause myopathy.
Probab=30.25 E-value=46 Score=15.14 Aligned_cols=100 Identities=12% Similarity=0.047 Sum_probs=63.2
Q ss_pred HHHHHHHHHC---CCCCHHHCCHHHHHCCCCEEEEEEEEECCCCCCCCEEEEEECCHHHHHHHHHHHHHHHHCCCCHHHH
Q ss_conf 9999998508---9999568681550226560167887304654548879999416269999999999999759988999
Q gi|254780998|r 22 HYLIELGKKL---PLFPKEYMTDQNIVAGCMSKLWMVIEWENKGDQDPIMIFYAVSDSQIVCGLLYIVKSIYAHKKISEI 98 (146)
Q Consensus 22 ~~Li~lgk~l---~~l~e~~k~~~~~V~GCqS~vWl~~~~~~~~~~~~~~~f~~dSda~IvkGl~~ll~~~~~g~t~~eI 98 (146)
+.|+++.+.. ..++.....-...=+-|-.++=|....++... ..+.|.+..= .|...=++++.+...|++.+|+
T Consensus 4 ~~Il~h~~np~~~g~l~~~~~~~~~~np~CGD~i~l~l~i~~~~I--~~i~f~~~GC-ai~~Asas~~~~~~~g~~i~e~ 80 (123)
T cd06664 4 EIILDHYRNPRNVGRLEDADGTGEVGNPLCGDEITLYLKVEDGRI--TDAKFQGFGC-AISIASASLLTELIKGKTLDEA 80 (123)
T ss_pred HHHHHHHHCCCCCCCCCCCCEEEEECCCCCCCEEEEEEEECCCEE--EEEEEEECCC-HHHHHHHHHHHHHHCCCCHHHH
T ss_conf 999999759888897999987988689998557999999808957--7889995377-5549999999999859989999
Q ss_pred HHCCHHHHHHHHCC--------HHCCCHHHHHHHH
Q ss_conf 80798999987090--------4316942899999
Q gi|254780998|r 99 LKMDSLTILQHLGL--------TENLSQKRMNGLY 125 (146)
Q Consensus 99 ~~~d~~~f~~~lgL--------~~~Lt~~R~nGl~ 125 (146)
.++. ..+...+.- ....-|+|.+-..
T Consensus 81 ~~l~-~~~~~~~~~~~~l~~~~~v~~~p~R~~Ca~ 114 (123)
T cd06664 81 LKLL-NKDIAMLDGKEELAALAGVGLPPARIHCAL 114 (123)
T ss_pred HHHH-HHHHHHHCCCCCHHHHHCCCCCCCCCHHHH
T ss_conf 9999-999998637631346403467866572998
No 33
>TIGR02955 TMAO_TorT TMAO reductase system periplasmic protein TorT; InterPro: IPR014301 Members of this entry are the periplasmic protein TorT that, together with the TorS/TorR histidine kinase/response regulator system, regulates expression of the torCAD operon for trimethylamine N-oxide reductase (TMAO reductase). It appears to bind an inducer for TMAO reductase and shows homology to a periplasmic D-ribose binding protein..
Probab=30.23 E-value=46 Score=15.13 Aligned_cols=52 Identities=23% Similarity=0.281 Sum_probs=41.9
Q ss_pred CEEEEEECCHHHHHHHHHHHHHH--HHCCCCHH-----HHHHCCHHHHHHHHCCHHCCCHH
Q ss_conf 87999941626999999999999--97599889-----99807989999870904316942
Q gi|254780998|r 66 PIMIFYAVSDSQIVCGLLYIVKS--IYAHKKIS-----EILKMDSLTILQHLGLTENLSQK 119 (146)
Q Consensus 66 ~~~~f~~dSda~IvkGl~~ll~~--~~~g~t~~-----eI~~~d~~~f~~~lgL~~~Lt~~ 119 (146)
+|+-| +.||-.+-+|=+||=.+ .+.+.+++ .|..++|. .+++-.+..+|||+
T Consensus 238 ~kvlf-a~~D~MV~QG~Lai~QAv~yL~~~~~~~~~aP~I~~lTp~-~~~r~~~~~SLSPa 296 (304)
T TIGR02955 238 GKVLF-APTDQMVLQGKLAIDQAVRYLEGKPVSFDLAPKIEALTPQ-HLPREVIEDSLSPA 296 (304)
T ss_pred CCEEE-CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHH-HCCHHHHHHHCCCC
T ss_conf 73566-5752689999999999999962898041258743104855-41456675404766
No 34
>cd06938 NR_LBD_EcR The ligand binding domain (LBD) of the Ecdysone receptor, a member of the nuclear receptors super family. The ligand binding domain (LBD) of the ecdysone receptor: The ecdysone receptor (EcR) belongs to the superfamily of nuclear receptors (NRs) of ligand-dependent transcription factors. Ecdysone receptor is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. ECR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of ecdysone receptor are ecdysteroids#the endogenous steroidal hormones found in invertebrates. In addition, insecticide bisacylhydrazine used against pests has shown to act on EcR. EcR must be dimerised with a USP for high-affinity ligand binding to occur. The ligand binding triggers a conformational change in the C-terminal part of the EcR ligand-binding domain that leads to transcript
Probab=28.48 E-value=12 Score=18.68 Aligned_cols=51 Identities=22% Similarity=0.384 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHCCCCCHHHCCH-HHHHCCCCEEEEEEEEECCCCCCCCEEEE
Q ss_conf 9999999985089999568681-55022656016788730465454887999
Q gi|254780998|r 20 RYHYLIELGKKLPLFPKEYMTD-QNIVAGCMSKLWMVIEWENKGDQDPIMIF 70 (146)
Q Consensus 20 ry~~Li~lgk~l~~l~e~~k~~-~~~V~GCqS~vWl~~~~~~~~~~~~~~~f 70 (146)
-.+.+|+++|++|.+.+=...| -.+.+||-+.||+..-.--....++.+.|
T Consensus 51 ~iq~IVefAK~iPgF~~L~~eDQi~LLK~~~~Ev~~Lr~a~~~~~~~~~~~f 102 (231)
T cd06938 51 TVQLIVEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAKTDSIVF 102 (231)
T ss_pred HHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEE
T ss_conf 9999999983698813599879999999989999999999985578996995
No 35
>TIGR01690 plasmid_RAQPRD plasmid conserved hypothetical protein, RAQPRD family; InterPro: IPR010040 This entry identifies a family of proteins, which are about 100 amino acids in length, including a predicted signal sequence and a perfectly conserved motif RAQPRD towards the C terminus. Members are found in the Pseudomonas putida TOL plasmid pWW0 and in cryptic plasmid regions of Salmonella enterica subsp. enterica serovar Typhi and Pseudomonas syringae DC3000. The function of these proteins are unknown..
Probab=27.61 E-value=12 Score=18.88 Aligned_cols=12 Identities=25% Similarity=0.504 Sum_probs=9.7
Q ss_pred CCHHCCCHHHHH
Q ss_conf 904316942899
Q gi|254780998|r 111 GLTENLSQKRMN 122 (146)
Q Consensus 111 gL~~~Lt~~R~n 122 (146)
|+..||||+|.+
T Consensus 81 Giq~YL~PsRAQ 92 (107)
T TIGR01690 81 GIQAYLTPSRAQ 92 (107)
T ss_pred HHHHHCCCCCCC
T ss_conf 788645788887
No 36
>pfam06352 consensus
Probab=26.23 E-value=54 Score=14.69 Aligned_cols=23 Identities=13% Similarity=0.348 Sum_probs=18.8
Q ss_pred CCCHHHHHHHHHCCCCHHHHHHH
Q ss_conf 98889999987509998999999
Q gi|254780998|r 1 MIPINDIIEDMEMIEDLHDRYHY 23 (146)
Q Consensus 1 M~~l~~i~e~f~~~~d~~~ry~~ 23 (146)
|||++++.++++.+.++.-|--|
T Consensus 1 mmt~eevmaeLe~Lg~~~tkki~ 23 (223)
T pfam06352 1 MITFDQLDAELQALENPNTIKIF 23 (223)
T ss_pred CCCHHHHHHHHHHCCCHHHHHHH
T ss_conf 97789999999981786589999
No 37
>cd06157 NR_LBD The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators. Ligand-binding domain (LBD) of nuclear receptor (NR): Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=25.29 E-value=46 Score=15.14 Aligned_cols=129 Identities=16% Similarity=0.082 Sum_probs=59.2
Q ss_pred CCHHHHHHHHHHHHHHCCCCCHHHCC-HHHHHCCCCEEEEEEEEEC--CCCCCCCEEEEEE-----CCHHHHHHHHHHHH
Q ss_conf 99899999999998508999956868-1550226560167887304--6545488799994-----16269999999999
Q gi|254780998|r 15 EDLHDRYHYLIELGKKLPLFPKEYMT-DQNIVAGCMSKLWMVIEWE--NKGDQDPIMIFYA-----VSDSQIVCGLLYIV 86 (146)
Q Consensus 15 ~d~~~ry~~Li~lgk~l~~l~e~~k~-~~~~V~GCqS~vWl~~~~~--~~~~~~~~~~f~~-----dSda~IvkGl~~ll 86 (146)
+-+......+++++|.+|.+.+=... ...++++|-+.+|+....- .....+..+.+.+ ..+....++....+
T Consensus 5 ~~~~~~l~~~ve~ak~lp~F~~L~~~DQ~~Llk~~~~e~~~L~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 84 (168)
T cd06157 5 ELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHTDDDKEDEMKLLLKGEL 84 (168)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCCCHHHHHHHHCCHHH
T ss_conf 99999999999998629784318999999999998899999999999761289826724876555434888764110899
Q ss_pred HHHHCCC-CHHHHHHCCHHHHHHHHCCHHCCCHHHHHHH--HHHHHHHHHHHHHHHHHHHC
Q ss_conf 9997599-8899980798999987090431694289999--99999999999999963311
Q gi|254780998|r 87 KSIYAHK-KISEILKMDSLTILQHLGLTENLSQKRMNGL--YTIVNKIQDLTQEYLNVHIK 144 (146)
Q Consensus 87 ~~~~~g~-t~~eI~~~d~~~f~~~lgL~~~Lt~~R~nGl--~~m~~~ik~~a~~~l~~~~~ 144 (146)
...++.- .|=.-+++|...| .-+.---.++|.|.+|+ ...++.+++...+.|..++.
T Consensus 85 ~~~~~~~~~~~~~L~l~~~E~-~lLkai~l~~pd~~~s~~~~~~i~~~q~~~~~aL~~y~~ 144 (168)
T cd06157 85 IRLLFEFVNPLRALKLDDEEY-ALLKAIVLFSPDRKESLEDRKIVEELQERLLEALQDYLR 144 (168)
T ss_pred HHHHHHHHHHHHHHCCCHHHH-HHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999999999839999999-999999980899988602299999999999999999999
No 38
>cd06946 NR_LBD_ERR The ligand binding domain of estrogen receptor-related nuclear receptors. The ligand binding domain of estrogen receptor-related receptors (ERRs): The family of estrogen receptor-related receptors (ERRs), a subfamily of nuclear receptors, is closely related to the estrogen receptor (ER) family, but it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signaling pathway, positively or negatively. ERRs share target genes, co-regulators and promoters with the estrogen receptor (ER) family. There are three subtypes of ERRs: alpha, beta and gamma. ERRs bind at least two types of DNA sequence, the estrogen response element and another site, originally characterized as SF-1 (steroidogenic factor 1) response element. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ERR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-
Probab=23.19 E-value=35 Score=15.87 Aligned_cols=125 Identities=12% Similarity=0.080 Sum_probs=62.4
Q ss_pred HHHHHHHHHHHHHCCCCCHHHCCH-HHHHCCCCEEEEEEEEECCCCCCCCEEEEEEC----CHHHHHHHHHHHHHHHHCC
Q ss_conf 999999999985089999568681-55022656016788730465454887999941----6269999999999999759
Q gi|254780998|r 18 HDRYHYLIELGKKLPLFPKEYMTD-QNIVAGCMSKLWMVIEWENKGDQDPIMIFYAV----SDSQIVCGLLYIVKSIYAH 92 (146)
Q Consensus 18 ~~ry~~Li~lgk~l~~l~e~~k~~-~~~V~GCqS~vWl~~~~~~~~~~~~~~~f~~d----Sda~IvkGl~~ll~~~~~g 92 (146)
....-.+|+|+|++|.+.+=...| -.+.++|-+.+++..-.......++.+.|..+ .+..-..|+..+....+.=
T Consensus 37 ~r~L~~~V~WAK~iPgF~~L~~~DQi~LLk~~w~El~iL~~a~rs~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~e~ 116 (221)
T cd06946 37 DRELVVIIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFRSLPFNGELVFAEDFILDEELAREAGLLELYSACLQL 116 (221)
T ss_pred HHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCEEECHHHHHHCCHHHHHHHHHHH
T ss_conf 99999999999609970015857899999999899999999997067888257238801067875023699999999999
Q ss_pred CCHHHHHHCCHHHHHHHHCCHHCCCHHHHHHH--HHHHHHHHHHHHHHHHHHHC
Q ss_conf 98899980798999987090431694289999--99999999999999963311
Q gi|254780998|r 93 KKISEILKMDSLTILQHLGLTENLSQKRMNGL--YTIVNKIQDLTQEYLNVHIK 144 (146)
Q Consensus 93 ~t~~eI~~~d~~~f~~~lgL~~~Lt~~R~nGl--~~m~~~ik~~a~~~l~~~~~ 144 (146)
...=.-+++|...| .=+.---.++|-| .|+ ..-++++++.+...|..+++
T Consensus 117 ~~~~~~L~ld~~E~-a~LkAivLf~pD~-~gL~~~~~Ve~LQe~~~~aL~~yi~ 168 (221)
T cd06946 117 VRRLQRLRLEKEEY-VLLKALALANSDS-VHIEDVEAVRQLRDALLEALSDYEA 168 (221)
T ss_pred HHHHHHCCCCHHHH-HHHHHHHHCCCCC-CCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999818999999-9999999707875-4554789999999999999999998
No 39
>pfam10624 TraS Plasmid conjugative transfer entry exclusion protein TraS. Entry exclusion (Eex) is a process which prevents redundant transfer of DNA between donor cells. TraS is a protein involved in Eex. It blocks redundant conjugative DNA synthesis and transport between donor cells, and it is suggested that TraS interferes with a signalling pathway that is required to trigger DNA transfer. TraS on the recipient cell is known to form an interaction with TraG on the donor cell.
Probab=21.89 E-value=9.9 Score=19.30 Aligned_cols=27 Identities=30% Similarity=0.651 Sum_probs=13.3
Q ss_pred HHHHHCCCCE-EEEEEEEECCCCCCCCE
Q ss_conf 1550226560-16788730465454887
Q gi|254780998|r 41 DQNIVAGCMS-KLWMVIEWENKGDQDPI 67 (146)
Q Consensus 41 ~~~~V~GCqS-~vWl~~~~~~~~~~~~~ 67 (146)
+-.+|.||.| +-|+.+++++..++|-.
T Consensus 92 elrrvsgcisikew~q~q~~dq~~ed~~ 119 (164)
T pfam10624 92 ELRRISGCISIKEWMKCQLDDQTDEDLG 119 (164)
T ss_pred HHHHHHCCEEHHHHHHHHHHCCCCCCCC
T ss_conf 8887404245999998665111362117
No 40
>KOG4215 consensus
Probab=21.14 E-value=38 Score=15.68 Aligned_cols=72 Identities=17% Similarity=0.226 Sum_probs=39.6
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCCHHHCC----------HHHHHCC------CCEEEEEEEEECCCCCCCCEEEEEECCHH
Q ss_conf 0999899999999998508999956868----------1550226------56016788730465454887999941626
Q gi|254780998|r 13 MIEDLHDRYHYLIELGKKLPLFPKEYMT----------DQNIVAG------CMSKLWMVIEWENKGDQDPIMIFYAVSDS 76 (146)
Q Consensus 13 ~~~d~~~ry~~Li~lgk~l~~l~e~~k~----------~~~~V~G------CqS~vWl~~~~~~~~~~~~~~~f~~dSda 76 (146)
.++.-...+-+++||+|.+|++++--.. .++.|-| |-++|.+.. + +-.++-.+.--.
T Consensus 159 v~eSm~qqLlllVEWAK~i~~F~el~l~DqvaLLk~~a~~hllLg~a~RSm~l~~v~ll~---N----~~v~~~~~~~~~ 231 (432)
T KOG4215 159 VCESMKQQLLLLVEWAKYIPPFCELPLDDQVALLKAHAGQHLLLGAAFRSMHLKDVCLLN---N----TYVLHRHAPDLP 231 (432)
T ss_pred HHHHHHHHHHHHHHHHHHCCCHHCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCEEEEC---C----CEEECCCCCCHH
T ss_conf 999999999999999985651202771148999872551452345554032303548856---8----566125789727
Q ss_pred HHHHHHHHHHHHHHC
Q ss_conf 999999999999975
Q gi|254780998|r 77 QIVCGLLYIVKSIYA 91 (146)
Q Consensus 77 ~IvkGl~~ll~~~~~ 91 (146)
-|.+-...|+=++++
T Consensus 232 eis~v~~RIiDElv~ 246 (432)
T KOG4215 232 EISRVAPRIIDELVN 246 (432)
T ss_pred HHHHHHHHHHHHHHH
T ss_conf 777888999999861
Done!