Query gi|254781144|ref|YP_003065557.1| hypothetical protein CLIBASIA_05240 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 76
No_of_seqs 101 out of 111
Neff 5.1
Searched_HMMs 39220
Date Mon May 30 06:21:17 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781144.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00319 TarH Homologues of 56.0 11 0.00029 19.8 2.8 32 43-74 81-112 (135)
2 TIGR03581 EF_0839 conserved hy 54.6 15 0.00039 19.1 3.3 19 2-20 55-73 (236)
3 cd00181 TarH Taxis toward Aspa 53.6 15 0.00038 19.1 3.1 30 44-73 90-119 (140)
4 pfam01475 FUR Ferric uptake re 51.4 20 0.00051 18.4 3.5 46 15-60 8-58 (120)
5 cd07153 Fur_like Ferric uptake 49.7 21 0.00053 18.3 3.3 44 16-59 2-50 (116)
6 pfam07071 DUF1341 Protein of u 45.3 26 0.00067 17.7 3.3 19 2-20 55-73 (218)
7 pfam02203 TarH Tar ligand bind 41.5 29 0.00074 17.5 3.0 30 44-73 81-110 (133)
8 PRK09462 fur ferric uptake reg 40.0 33 0.00085 17.2 3.2 47 14-60 16-68 (148)
9 TIGR01340 aconitase_mito aconi 33.8 20 0.0005 18.5 1.1 27 49-75 373-399 (761)
10 PRK12318 methionine aminopepti 30.7 54 0.0014 16.0 6.3 61 2-66 146-206 (291)
11 TIGR00021 rpiA ribose 5-phosph 30.4 20 0.0005 18.5 0.7 14 6-19 18-31 (236)
12 cd01092 APP-like Similar to Pr 29.9 56 0.0014 15.9 6.7 57 2-62 91-147 (208)
13 cd05522 Bromo_Rsc1_2_II Bromod 28.2 32 0.00081 17.3 1.5 32 44-75 6-37 (104)
14 COG4424 Uncharacterized protei 27.9 49 0.0012 16.3 2.4 35 41-75 11-46 (250)
15 COG0735 Fur Fe2+/Zn2+ uptake r 27.6 62 0.0016 15.7 4.3 45 14-58 20-69 (145)
16 PRK11639 zinc uptake transcrip 27.1 49 0.0012 16.3 2.2 44 15-58 26-74 (169)
17 pfam09037 Sulphotransf Stf0 su 26.2 62 0.0016 15.7 2.6 26 50-75 14-40 (245)
18 pfam12040 DUF3526 Domain of un 26.1 66 0.0017 15.5 3.0 38 15-52 65-102 (158)
19 pfam05165 GGDN GGDN family. I 25.3 68 0.0017 15.5 2.9 21 2-22 205-225 (246)
20 cd07662 BAR_SNX6 The Bin/Amphi 25.2 67 0.0017 15.5 2.7 21 47-68 6-26 (218)
21 TIGR02719 repress_PhaQ poly-be 24.6 69 0.0018 15.4 2.7 26 30-57 45-70 (138)
22 cd07621 BAR_SNX5_6 The Bin/Amp 24.3 52 0.0013 16.1 2.0 23 46-68 5-27 (219)
23 pfam00356 LacI Bacterial regul 23.7 39 0.00098 16.8 1.2 22 50-71 1-24 (46)
24 cd01090 Creatinase Creatine am 23.5 74 0.0019 15.3 7.3 59 2-64 97-155 (228)
25 smart00076 IFabd Interferon al 22.8 76 0.0019 15.2 4.0 26 36-61 77-102 (117)
26 smart00342 HTH_ARAC helix_turn 21.6 72 0.0018 15.3 2.2 19 50-68 52-70 (84)
No 1
>smart00319 TarH Homologues of the ligand binding domain of Tar. Homologues of the ligand binding domain of the wild-type bacterial aspartate receptor, Tar.
Probab=55.97 E-value=11 Score=19.78 Aligned_cols=32 Identities=16% Similarity=0.404 Sum_probs=28.0
Q ss_pred CHHHHHHHHHHHHHHCCCCCHHHHHCCCCHHH
Q ss_conf 98999999999999808988788506988543
Q gi|254781144|r 43 STTHLYNGIARLAEAVGVQNVNEYFNNPDSEQ 74 (76)
Q Consensus 43 ~~~n~yntl~~~~e~aG~k~~~~ff~dP~~~q 74 (76)
+-+.|++.|.+++....=.+.+.||.-|.+.-
T Consensus 81 ~Y~~y~~aL~el~~~l~~g~~~~f~~~Ptq~~ 112 (135)
T smart00319 81 KFQQYITALQELIQILGNGNLGAFFDQPTQGM 112 (135)
T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHCCCHHH
T ss_conf 99999999999999987799678986870754
No 2
>TIGR03581 EF_0839 conserved hypothetical protein EF_0839/AHA_3917. Members of this family of relatively uncommon proteins are found in both Gram-positive (e.g. Enterococcus faecalis) and Gram-negative (e.g. Aeromonas hydrophila) bacteria, as part of a cluster of conserved proteins. The function is unknown.
Probab=54.64 E-value=15 Score=19.07 Aligned_cols=19 Identities=37% Similarity=0.800 Sum_probs=14.5
Q ss_pred CEEEEEECCCCCHHHHHHH
Q ss_conf 3088981147998999999
Q gi|254781144|r 2 DAKVNIGLGSGNREKDIMM 20 (76)
Q Consensus 2 Dv~V~VGLG~G~~~qk~~~ 20 (76)
|+.|+||||.|+..|--+.
T Consensus 55 ~~avSVGLGaGDp~Q~~~V 73 (236)
T TIGR03581 55 DNAVSVGLGAGDPNQSAMV 73 (236)
T ss_pred CCCEEEECCCCCHHHHHHH
T ss_conf 8856884279997999999
No 3
>cd00181 TarH Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These transmembrane signalers monitor the chemical environment by means of specific ligand-binding sites arrayed on the periplasmic side of the membrane, and in turn control cytoplasmic signals that modulate the flagellar rotational machinery. Aspartate is detected through direct binding to Tar molecules, whereas maltose is detected indirectly when complexed with the periplasmic maltose-binding protein.
Probab=53.64 E-value=15 Score=19.13 Aligned_cols=30 Identities=20% Similarity=0.518 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHCCCCCHHHHHCCCCHH
Q ss_conf 899999999999980898878850698854
Q gi|254781144|r 44 TTHLYNGIARLAEAVGVQNVNEYFNNPDSE 73 (76)
Q Consensus 44 ~~n~yntl~~~~e~aG~k~~~~ff~dP~~~ 73 (76)
-+.||+.|.+++....=.+.+.||.-|++.
T Consensus 90 Y~~~~~aL~el~~~L~~~~l~~F~~qPtq~ 119 (140)
T cd00181 90 FKQYFQALAELIQILASGNMNAFFDQPTQG 119 (140)
T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHCCCHHH
T ss_conf 999999999999998869988998387689
No 4
>pfam01475 FUR Ferric uptake regulator family. This family includes metal ion uptake regulator proteins, that bind to the operator DNA and controls transcription of metal ion-responsive genes. This family is also known as the FUR family.
Probab=51.39 E-value=20 Score=18.43 Aligned_cols=46 Identities=22% Similarity=0.245 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHH-----HHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf 99999999999999-----99996038888866989999999999998089
Q gi|254781144|r 15 EKDIMMVSHLLALQ-----KEILATFGLNNPFVSTTHLYNGIARLAEAVGV 60 (76)
Q Consensus 15 ~qk~~~L~~i~~~Q-----~q~lq~~G~~nplV~~~n~yntl~~~~e~aG~ 60 (76)
.+|.+.|.-+.+.. +++.......+|-+++.-+|++|..+.+..=+
T Consensus 8 ~qR~~Il~~l~~~~~~~ta~~i~~~l~~~~~~i~~~TVYR~L~~L~~~gli 58 (120)
T pfam01475 8 PQRLKILEVLEKSDEHLSAEEIYRELLEEDPNISLATVYRTLKLLEEAGIV 58 (120)
T ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCE
T ss_conf 899999999982799989999999999658998789999999999967946
No 5
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=49.66 E-value=21 Score=18.33 Aligned_cols=44 Identities=23% Similarity=0.312 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHH-----HHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCC
Q ss_conf 999999999999-----99999603888886698999999999999808
Q gi|254781144|r 16 KDIMMVSHLLAL-----QKEILATFGLNNPFVSTTHLYNGIARLAEAVG 59 (76)
Q Consensus 16 qk~~~L~~i~~~-----Q~q~lq~~G~~nplV~~~n~yntl~~~~e~aG 59 (76)
||.+.|.-+... -++++..+-..+|-+++..+|++|..+++..=
T Consensus 2 qR~~Il~~l~~~~~h~sa~eI~~~l~~~~~~i~~~TVYR~L~~l~~~gl 50 (116)
T cd07153 2 QRLAILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGL 50 (116)
T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCC
T ss_conf 5899999998379898999999999975899988899999999996895
No 6
>pfam07071 DUF1341 Protein of unknown function (DUF1341). This family consists of several hypothetical bacterial proteins of around 220 residues in length. The function of this family is unknown.
Probab=45.29 E-value=26 Score=17.75 Aligned_cols=19 Identities=32% Similarity=0.795 Sum_probs=14.3
Q ss_pred CEEEEEECCCCCHHHHHHH
Q ss_conf 3088981147998999999
Q gi|254781144|r 2 DAKVNIGLGSGNREKDIMM 20 (76)
Q Consensus 2 Dv~V~VGLG~G~~~qk~~~ 20 (76)
|..|+||||.|+..|--+.
T Consensus 55 ~~~vSVGLGaGDp~Q~~~V 73 (218)
T pfam07071 55 DNAISVGLGAGDPNQSAMV 73 (218)
T ss_pred CCCEEEECCCCCHHHHHHH
T ss_conf 9856884289997999999
No 7
>pfam02203 TarH Tar ligand binding domain homologue.
Probab=41.47 E-value=29 Score=17.51 Aligned_cols=30 Identities=17% Similarity=0.479 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHCCCCCHHHHHCCCCHH
Q ss_conf 899999999999980898878850698854
Q gi|254781144|r 44 TTHLYNGIARLAEAVGVQNVNEYFNNPDSE 73 (76)
Q Consensus 44 ~~n~yntl~~~~e~aG~k~~~~ff~dP~~~ 73 (76)
-++|+++|.+++....=.+.+.||.-|...
T Consensus 81 y~~y~~aL~el~~~l~~~~~~~F~~~Ptq~ 110 (133)
T pfam02203 81 YKQYISALAELIQILEAGNIDAFFDQPTQK 110 (133)
T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHCCHHH
T ss_conf 999999999999998779857898687376
No 8
>PRK09462 fur ferric uptake regulator; Provisional
Probab=40.03 E-value=33 Score=17.18 Aligned_cols=47 Identities=9% Similarity=0.067 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHH------HHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf 89999999999999------999996038888866989999999999998089
Q gi|254781144|r 14 REKDIMMVSHLLAL------QKEILATFGLNNPFVSTTHLYNGIARLAEAVGV 60 (76)
Q Consensus 14 ~~qk~~~L~~i~~~------Q~q~lq~~G~~nplV~~~n~yntl~~~~e~aG~ 60 (76)
-.+|.+.|.-+... -+++....-..+|-+++.-+|+||..+.+..=+
T Consensus 16 T~qR~~Il~~L~~~~~~hlsaeeI~~~l~~~~~~is~aTVYRtL~~L~e~Glv 68 (148)
T PRK09462 16 TLPRLKILEVLQEPDNHHVSAEDLYKKLIDMGEEIGLATVYRVLNQFDDAGIV 68 (148)
T ss_pred CHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCE
T ss_conf 99999999999817999999999999999758998666299999999868967
No 9
>TIGR01340 aconitase_mito aconitate hydratase, mitochondrial; InterPro: IPR006248 Aconitase (aconitate hydratase; 4.2.1.3 from EC) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop , . Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is small than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) . Below is a description of some of the multi-functional activities associated with different aconitases. Eukaryotic mAcn catalyses the second step of the mitochondrial TCA cycle, which is important for energy production, providing high energy electrons in the form of NADH and FADH2 to the mitochondrial oxidative phosphorylation pathway . The TCA cycle also provides precursors for haem and amino acid production. This enzyme has a second, non-catalytic but essential role in mitochondrial DNA (mtDNA) maintenance: mAcn acts to stabilise mtDNA, forming part of mtDNA protein-DNA complexes known as nucleoids. mAcn is thought to reversibly model nucleoids to directly influence mitochondrial gene expression in response to changes in the cellular environment. Therefore, mAcn can influence the expression of components of the oxidative phosphorylation pathway encoded in mtDNA. Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) , . As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated . IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis . Although IRP2 is homologous to IRP1, IPR2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes . In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system. Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica , . In S.enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress. This entry represents mitochondrial aconitase (mAcn), as well as close homologues such as certain bacterial aconitase A (AcnA) enzymes. More information about these proteins can be found at Protein of the Month: Aconitase .; GO: 0003994 aconitate hydratase activity, 0051539 4 iron 4 sulfur cluster binding, 0006099 tricarboxylic acid cycle.
Probab=33.77 E-value=20 Score=18.47 Aligned_cols=27 Identities=33% Similarity=0.463 Sum_probs=23.1
Q ss_pred HHHHHHHHHCCCCCHHHHHCCCCHHHC
Q ss_conf 999999998089887885069885433
Q gi|254781144|r 49 NGIARLAEAVGVQNVNEYFNNPDSEQW 75 (76)
Q Consensus 49 ntl~~~~e~aG~k~~~~ff~dP~~~q~ 75 (76)
.-+.|-++.+|+|....||..|.+||-
T Consensus 373 ~si~k~A~~~G~K~~~~F~vTPGSEqI 399 (761)
T TIGR01340 373 ASIVKDAEKAGLKPKIPFFVTPGSEQI 399 (761)
T ss_pred HHHHHHHHHCCCCCCCCCEECCCCCCC
T ss_conf 999999994889755673246886210
No 10
>PRK12318 methionine aminopeptidase; Provisional
Probab=30.75 E-value=54 Score=16.00 Aligned_cols=61 Identities=16% Similarity=0.167 Sum_probs=46.7
Q ss_pred CEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHH
Q ss_conf 30889811479989999999999999999996038888866989999999999998089887885
Q gi|254781144|r 2 DAKVNIGLGSGNREKDIMMVSHLLALQKEILATFGLNNPFVSTTHLYNGIARLAEAVGVQNVNEY 66 (76)
Q Consensus 2 Dv~V~VGLG~G~~~qk~~~L~~i~~~Q~q~lq~~G~~nplV~~~n~yntl~~~~e~aG~k~~~~f 66 (76)
|++-++.+|.-+++++ ..+.....-|+.++..-.|.. ....+.....+.++..||.-+..|
T Consensus 146 D~tRT~~vG~~s~~~~-~l~~~v~~A~~~aI~~ikpG~---~~~dI~~ai~~~~~~~G~~~~~~~ 206 (291)
T PRK12318 146 DCSRMVMIGEVSEIKK-KVCQASLECLNAAIAILKPNL---PLYEIGEVIENCADTYGFSVVDQF 206 (291)
T ss_pred CCCCEEECCCCCHHHH-HHHHHHHHHHHHHHHHHCCCC---CHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf 2131453488989999-999999999999999807996---477999999999998499117680
No 11
>TIGR00021 rpiA ribose 5-phosphate isomerase A; InterPro: IPR004788 Ribose 5-phosphate isomerase (5.3.1.6 from EC), also known as phosphoriboisomerase, catalyses the conversion of D-ribose 5-phosphate to D-ribulose 5-phosphate in the non-oxidative branch of the pentose phosphate pathway.; GO: 0004751 ribose-5-phosphate isomerase activity, 0009052 pentose-phosphate shunt non-oxidative branch.
Probab=30.37 E-value=20 Score=18.48 Aligned_cols=14 Identities=29% Similarity=0.603 Sum_probs=10.3
Q ss_pred EEECCCCCHHHHHH
Q ss_conf 98114799899999
Q gi|254781144|r 6 NIGLGSGNREKDIM 19 (76)
Q Consensus 6 ~VGLG~G~~~qk~~ 19 (76)
.|||||||--.=+.
T Consensus 18 ~~GlGTGST~~~~i 31 (236)
T TIGR00021 18 VVGLGTGSTVAYFI 31 (236)
T ss_pred EEEECCHHHHHHHH
T ss_conf 89824504689999
No 12
>cd01092 APP-like Similar to Prolidase and Aminopeptidase P. The members of this subfamily presumably catalyse hydrolysis of Xaa-Pro dipeptides and/or release of any N-terminal amino acid, including proline, that is linked with proline.
Probab=29.92 E-value=56 Score=15.92 Aligned_cols=57 Identities=14% Similarity=0.212 Sum_probs=43.7
Q ss_pred CEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf 3088981147998999999999999999999603888886698999999999999808988
Q gi|254781144|r 2 DAKVNIGLGSGNREKDIMMVSHLLALQKEILATFGLNNPFVSTTHLYNGIARLAEAVGVQN 62 (76)
Q Consensus 2 Dv~V~VGLG~G~~~qk~~~L~~i~~~Q~q~lq~~G~~nplV~~~n~yntl~~~~e~aG~k~ 62 (76)
|++-.+-+|.-+++++ .....+...|+.++....|. ++...+++...+.++..||.+
T Consensus 91 D~~Rt~~vG~~~~~~~-~~~~~~~~~~~~~i~~~kpG---~~~~dv~~~~~~~~~~~g~~~ 147 (208)
T cd01092 91 DITRTVAVGEPSDELK-EIYEIVLEAQQAAIKAVKPG---VTAKEVDKAARDVIEEAGYGE 147 (208)
T ss_pred CCCCCCCCCCCCHHHH-HHHHHHHHHHHHHHHHCCCC---CCHHHHHHHHHHHHHHCCCCE
T ss_conf 0303334898899999-99999999999999723799---909999999999999759870
No 13
>cd05522 Bromo_Rsc1_2_II Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=28.21 E-value=32 Score=17.29 Aligned_cols=32 Identities=13% Similarity=0.199 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHHCCCCCHHHHHCCCCHHHC
Q ss_conf 89999999999998089887885069885433
Q gi|254781144|r 44 TTHLYNGIARLAEAVGVQNVNEYFNNPDSEQW 75 (76)
Q Consensus 44 ~~n~yntl~~~~e~aG~k~~~~ff~dP~~~q~ 75 (76)
++++++++.+..+..|-.=++.|..-|+..+|
T Consensus 6 ~~~il~~l~~~~d~~G~~la~~F~~lP~r~~~ 37 (104)
T cd05522 6 IKNILKGLRKERDENGRLLTLHFEKLPDKARE 37 (104)
T ss_pred HHHHHHHHHHHCCCCCCCCCHHHHHCCCCCCC
T ss_conf 99999999976288989803977309895237
No 14
>COG4424 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.94 E-value=49 Score=16.25 Aligned_cols=35 Identities=17% Similarity=0.457 Sum_probs=25.1
Q ss_pred CCCHHHHHHHHHHHHHHCCC-CCHHHHHCCCCHHHC
Q ss_conf 66989999999999998089-887885069885433
Q gi|254781144|r 41 FVSTTHLYNGIARLAEAVGV-QNVNEYFNNPDSEQW 75 (76)
Q Consensus 41 lV~~~n~yntl~~~~e~aG~-k~~~~ff~dP~~~q~ 75 (76)
+.+++.=.+.|-+++...|. .++.+||.-|..-+|
T Consensus 11 lt~pRSGStlLckllaatG~sG~p~sff~rp~~sEW 46 (250)
T COG4424 11 LTTPRSGSTLLCKLLAATGCSGEPQSFFQRPQPSEW 46 (250)
T ss_pred ECCCCCCCHHHHHHHHHCCCCCCCHHHHCCCCHHHH
T ss_conf 547887536999999841778995043138887899
No 15
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=27.64 E-value=62 Score=15.69 Aligned_cols=45 Identities=20% Similarity=0.308 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHHHH-----HHHHHCCCCCCCCCCHHHHHHHHHHHHHHC
Q ss_conf 899999999999999-----999960388888669899999999999980
Q gi|254781144|r 14 REKDIMMVSHLLALQ-----KEILATFGLNNPFVSTTHLYNGIARLAEAV 58 (76)
Q Consensus 14 ~~qk~~~L~~i~~~Q-----~q~lq~~G~~nplV~~~n~yntl~~~~e~a 58 (76)
-.+|++.|.-+++.. +++....-...|=+++..+|+||..+.|..
T Consensus 20 T~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~G 69 (145)
T COG0735 20 TPQRLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAG 69 (145)
T ss_pred CHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCC
T ss_conf 88899999999966899999999999997489998879999999999889
No 16
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=27.13 E-value=49 Score=16.26 Aligned_cols=44 Identities=11% Similarity=0.175 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHH-----HHHHHHCCCCCCCCCCHHHHHHHHHHHHHHC
Q ss_conf 9999999999999-----9999960388888669899999999999980
Q gi|254781144|r 15 EKDIMMVSHLLAL-----QKEILATFGLNNPFVSTTHLYNGIARLAEAV 58 (76)
Q Consensus 15 ~qk~~~L~~i~~~-----Q~q~lq~~G~~nplV~~~n~yntl~~~~e~a 58 (76)
.+|.+.|.-++.. -++++..+-..+|=+++..+|.||.-++|..
T Consensus 26 ~qR~~VL~~l~~~~~~lsA~eI~~~l~~~~~~is~aTVYRtL~~L~e~G 74 (169)
T PRK11639 26 PQRLEVLRLMSLQDGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQG 74 (169)
T ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCC
T ss_conf 8999999999957999999999999997589988277999999999789
No 17
>pfam09037 Sulphotransf Stf0 sulphotransferase. Members of this family are essential for the biosynthesis of sulpholipid-1 in prokaryotes. They adopt a structure that belongs to the sulphotransferase superfamily, consisting of a single domain with a core four-stranded parallel beta-sheet flanked by alpha-helices.
Probab=26.23 E-value=62 Score=15.69 Aligned_cols=26 Identities=31% Similarity=0.713 Sum_probs=9.3
Q ss_pred HHHHHHHHCCC-CCHHHHHCCCCHHHC
Q ss_conf 99999998089-887885069885433
Q gi|254781144|r 50 GIARLAEAVGV-QNVNEYFNNPDSEQW 75 (76)
Q Consensus 50 tl~~~~e~aG~-k~~~~ff~dP~~~q~ 75 (76)
.|.++++..|. ..|+.||..|...+|
T Consensus 14 lL~~lL~~Tgv~G~P~E~f~~~~~~~w 40 (245)
T pfam09037 14 LLCELLRATGVAGEPQEFFQRPQPREW 40 (245)
T ss_pred HHHHHHHHCCCCCCCHHHHCCCCHHHH
T ss_conf 999999966578899788488867799
No 18
>pfam12040 DUF3526 Domain of unknown function (DUF3526). This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is typically between 149 to 170 amino acids in length. This domain has a single completely conserved residue P that may be functionally important.
Probab=26.09 E-value=66 Score=15.53 Aligned_cols=38 Identities=18% Similarity=0.218 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHH
Q ss_conf 99999999999999999960388888669899999999
Q gi|254781144|r 15 EKDIMMVSHLLALQKEILATFGLNNPFVSTTHLYNGIA 52 (76)
Q Consensus 15 ~qk~~~L~~i~~~Q~q~lq~~G~~nplV~~~n~yntl~ 52 (76)
++....+.++.++|..+....|.-+|.+.++...+.|+
T Consensus 65 ~~~~~~~~~~~~~Q~~~~~~~~~lsP~~alq~~s~~lA 102 (158)
T pfam12040 65 APLAEALDQALLAQQRLARRFGLLSPTLALQRASMALA 102 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH
T ss_conf 99999999999999999998889096999999999986
No 19
>pfam05165 GGDN GGDN family. I have named this protein family of unknown function GGDN after the most conserved motif. The proteins are 200-270 amino acids in length.
Probab=25.35 E-value=68 Score=15.45 Aligned_cols=21 Identities=19% Similarity=0.490 Sum_probs=10.2
Q ss_pred CEEEEEECCCCCHHHHHHHHH
Q ss_conf 308898114799899999999
Q gi|254781144|r 2 DAKVNIGLGSGNREKDIMMVS 22 (76)
Q Consensus 2 Dv~V~VGLG~G~~~qk~~~L~ 22 (76)
|+.++||+|.|..-+....+.
T Consensus 205 ~i~lkvGIG~g~ta~~A~~~A 225 (246)
T pfam05165 205 DVDLKAGIGIAPTAEDALALA 225 (246)
T ss_pred CCEEEEEECCCCCHHHHHHHH
T ss_conf 952785145688889999999
No 20
>cd07662 BAR_SNX6 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 6. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX6 forms a stable complex with SNX1 and may be a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting as a mammalian equivalent of yeast Vsp17p. It interacts with the receptor serine/threonine kinases from the transforming growth factor-beta family. It also plays
Probab=25.18 E-value=67 Score=15.48 Aligned_cols=21 Identities=19% Similarity=0.555 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHCCCCCHHHHHC
Q ss_conf 9999999999808988788506
Q gi|254781144|r 47 LYNGIARLAEAVGVQNVNEYFN 68 (76)
Q Consensus 47 ~yntl~~~~e~aG~k~~~~ff~ 68 (76)
+..+.-++. .+|+||+|.||.
T Consensus 6 l~ks~de~l-~s~~KDvDefFe 26 (218)
T cd07662 6 VVKSADGVI-VSGVKDVDDFFE 26 (218)
T ss_pred HHHHHHHHH-HHCCCCHHHHHH
T ss_conf 777558999-944663688999
No 21
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor; InterPro: IPR014091 Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family..
Probab=24.62 E-value=69 Score=15.40 Aligned_cols=26 Identities=19% Similarity=0.423 Sum_probs=19.1
Q ss_pred HHHHCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 9996038888866989999999999998
Q gi|254781144|r 30 EILATFGLNNPFVSTTHLYNGIARLAEA 57 (76)
Q Consensus 30 q~lq~~G~~nplV~~~n~yntl~~~~e~ 57 (76)
|.+...|- -=|+-.|+|.|||++=+.
T Consensus 45 Q~LM~~GF--~SVDQGNVYRTLR~LEK~ 70 (138)
T TIGR02719 45 QQLMDIGF--SSVDQGNVYRTLRKLEKD 70 (138)
T ss_pred HHHHHCCC--CCCCCCHHHHHHHHHHHH
T ss_conf 99986167--532310377898887665
No 22
>cd07621 BAR_SNX5_6 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins 5 and 6. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. Members of this subfamily include SNX5, SNX6, the mammalian SNX32, and similar proteins. SNX5 and SNX6 may be components of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting as a mammalian equivalent of yeast Vsp17p. The function of SNX32 is still unknown. BAR domain
Probab=24.26 E-value=52 Score=16.09 Aligned_cols=23 Identities=17% Similarity=0.338 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHCCCCCHHHHHC
Q ss_conf 99999999999808988788506
Q gi|254781144|r 46 HLYNGIARLAEAVGVQNVNEYFN 68 (76)
Q Consensus 46 n~yntl~~~~e~aG~k~~~~ff~ 68 (76)
++..+.-+.+-.+|.||+|.||-
T Consensus 5 ~~~k~~d~~~~~s~~kd~D~~Fe 27 (219)
T cd07621 5 SISKSADEELLLSGQKDVDEFFE 27 (219)
T ss_pred HHHHHHHHHHHHCCCCCCHHHHH
T ss_conf 42330018998558885268899
No 23
>pfam00356 LacI Bacterial regulatory proteins, lacI family.
Probab=23.69 E-value=39 Score=16.83 Aligned_cols=22 Identities=36% Similarity=0.599 Sum_probs=13.0
Q ss_pred HHHHHHHHCCC--CCHHHHHCCCC
Q ss_conf 99999998089--88788506988
Q gi|254781144|r 50 GIARLAEAVGV--QNVNEYFNNPD 71 (76)
Q Consensus 50 tl~~~~e~aG~--k~~~~ff~dP~ 71 (76)
|++++.+.+|+ ..++++|+++.
T Consensus 1 Ti~DIA~~agVS~~TVSr~ln~~~ 24 (46)
T pfam00356 1 TIKDVARLAGVSKATVSRVLNNPE 24 (46)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCC
T ss_conf 999999998979999999987979
No 24
>cd01090 Creatinase Creatine amidinohydrolase. E.C.3.5.3.3. Hydrolyzes creatine to sarcosine and urea.
Probab=23.53 E-value=74 Score=15.25 Aligned_cols=59 Identities=5% Similarity=-0.057 Sum_probs=46.8
Q ss_pred CEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCCCHH
Q ss_conf 308898114799899999999999999999960388888669899999999999980898878
Q gi|254781144|r 2 DAKVNIGLGSGNREKDIMMVSHLLALQKEILATFGLNNPFVSTTHLYNGIARLAEAVGVQNVN 64 (76)
Q Consensus 2 Dv~V~VGLG~G~~~qk~~~L~~i~~~Q~q~lq~~G~~nplV~~~n~yntl~~~~e~aG~k~~~ 64 (76)
|++=++-+|.-+++++ -....+..-|+.++...-| =++.+.+....++.++..||....
T Consensus 97 d~~RT~~vG~~s~~~~-~~~~~~~ea~~~a~~~ikP---G~~~~dv~~~~~~~~~~~g~~~~~ 155 (228)
T cd01090 97 ALERTLFLDEVSDAHL-KIWEANVAVHERGLELIKP---GARCKDIAAELNEMYREHDLLRYR 155 (228)
T ss_pred CCEEEEECCCCCHHHH-HHHHHHHHHHHHHHHHHCC---CCCHHHHHHHHHHHHHHCCCCCCC
T ss_conf 7635897268999999-9999999999999998169---984999999999999974986204
No 25
>smart00076 IFabd Interferon alpha, beta and delta. Interferons produce antiviral and antiproliferative responses in cells. They are classified into five groups, all of them related but gamma-interferon.
Probab=22.82 E-value=76 Score=15.17 Aligned_cols=26 Identities=8% Similarity=0.029 Sum_probs=20.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf 88888669899999999999980898
Q gi|254781144|r 36 GLNNPFVSTTHLYNGIARLAEAVGVQ 61 (76)
Q Consensus 36 G~~nplV~~~n~yntl~~~~e~aG~k 61 (76)
++.++...+++||+.+..+++.-.|-
T Consensus 77 ~~~~~~L~lkkYF~rI~~yLk~K~yS 102 (117)
T smart00076 77 LPRNTHLALRKYFQRIQLYLKEKKYS 102 (117)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHCCCC
T ss_conf 87764269999998999999847996
No 26
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=21.56 E-value=72 Score=15.32 Aligned_cols=19 Identities=16% Similarity=0.296 Sum_probs=16.7
Q ss_pred HHHHHHHHCCCCCHHHHHC
Q ss_conf 9999999808988788506
Q gi|254781144|r 50 GIARLAEAVGVQNVNEYFN 68 (76)
Q Consensus 50 tl~~~~e~aG~k~~~~ff~ 68 (76)
++.++.+..||.|++.|..
T Consensus 52 ~i~~ia~~~Gy~~~s~f~r 70 (84)
T smart00342 52 SVTEIALRVGFSSQSYFSR 70 (84)
T ss_pred HHHHHHHHCCCCCHHHHHH
T ss_conf 4999988819999999999
Done!