Query gi|254780510|ref|YP_003064923.1| hypothetical protein CLIBASIA_01985 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 137
No_of_seqs 10 out of 12
Neff 2.4
Searched_HMMs 39220
Date Sun May 29 23:32:36 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780510.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 pfam08717 nsp8 nsp8 replicase. 53.3 19 0.00047 17.1 5.6 23 9-31 49-71 (198)
2 pfam08362 TetR_C_3 YcdC-like p 48.5 22 0.00056 16.6 4.0 46 18-66 56-108 (143)
3 TIGR01345 malate_syn_G malate 44.8 10 0.00026 19.0 1.1 48 15-81 659-706 (726)
4 TIGR02737 caa3_CtaG cytochrome 36.5 23 0.00058 16.5 1.8 34 49-84 232-268 (286)
5 cd07627 BAR_Vps5p The Bin/Amph 35.9 34 0.00086 15.3 14.5 114 5-125 60-173 (216)
6 cd07922 CarBa CarBa is the A s 29.2 37 0.00095 15.0 2.0 32 34-66 38-69 (81)
7 PRK04199 rpl10e 50S ribosomal 29.0 9.4 0.00024 19.2 -1.1 25 81-106 93-117 (173)
8 TIGR00883 2A0106 MFS transport 25.6 45 0.0011 14.4 1.8 16 53-68 49-64 (413)
9 PRK10642 proline/glycine betai 25.2 47 0.0012 14.3 1.9 11 58-68 305-315 (490)
10 pfam04622 ERG2_Sigma1R ERG2 an 21.4 58 0.0015 13.6 1.7 23 46-69 85-107 (216)
11 pfam09254 Endonuc-FokI_C Restr 20.2 42 0.0011 14.6 0.8 46 54-99 138-183 (197)
No 1
>pfam08717 nsp8 nsp8 replicase. Viral nsp8 (non structural protein 8) forms a hexadecameric supercomplex with nsp7 that adopts a hollow cylinder-like structure. The dimensions of the central channel and positive electrostatic properties of the cylinder imply that it confers processivity on RNA-dependent RNA polymerase.
Probab=53.31 E-value=19 Score=17.10 Aligned_cols=23 Identities=13% Similarity=0.122 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999998665799999
Q gi|254780510|r 9 LYKIITAQCCIKSIAESNLAYTI 31 (137)
Q Consensus 9 LkRLv~VQrhiErmAE~~LAeT~ 31 (137)
+-|=.+|||-||||||--.+.--
T Consensus 49 ~drd~avqrKLerMAe~Amt~MY 71 (198)
T pfam08717 49 FDRDAAVQRKLERMAEQAMTQMY 71 (198)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 74778999999999999999999
No 2
>pfam08362 TetR_C_3 YcdC-like protein, C-terminal region. This family comprises proteins that belong to the TetR family of transcriptional regulators. They bear particular similarity to YcdC, a putative HTH-containing protein. This family features the C-terminal region of these sequences, which does not include the helix-turn-helix.
Probab=48.52 E-value=22 Score=16.60 Aligned_cols=46 Identities=15% Similarity=0.135 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHH-----HHHHHHHHH
Q ss_conf 99998665799999999999999999999--84111146799-----988899997
Q gi|254780510|r 18 CIKSIAESNLAYTISERKKINILREKLKD--SINSTALMNPA-----LASHYLKFY 66 (137)
Q Consensus 18 hiErmAE~~LAeT~rqR~ei~~~~e~v~~--ai~S~~pvh~a-----fs~~Ya~r~ 66 (137)
||...-..+|......++++ ++.-++ -|.+.||.|-. ..|||||+=
T Consensus 56 ~l~~~l~~~l~~~~~~k~~v---i~~Wi~~G~i~~vdP~hLif~IWA~TQhYADF~ 108 (143)
T pfam08362 56 HLPPELLGPLKELADEKAAV---IQAWIDAGKIAPVDPYHLIFTIWASTQHYADFD 108 (143)
T ss_pred CHHHHHHHHHHHHHHHHHHH---HHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCHH
T ss_conf 13899989999999999999---999998599688788999999999661031469
No 3
>TIGR01345 malate_syn_G malate synthase G; InterPro: IPR006253 These sequences represent the G isozyme of malate synthase. Malate synthase G (MSG, 723 residues) is an enzyme of the glyoxylate pathway, that catalyzes the condensation and subsequent hydrolysis of acetyl-coenzyme A (acetyl-CoA) and glyoxylate to form malate and CoA , this biochemical bypass is used by microorganisms (bacteria, yeast, and fungi) for biosynthesis under anaerobic conditions . Enzymes of the glyoxylate bypass have been implicated as virulence factors in several pathogens, including Mycobacterium tuberculosis , , . The X-ray structure of the ternary abortive complex of MSG with pyruvate (glyoxylate mimic) and acetyl-CoA has been determined and shown to have the same structure as in the complex with glyoxylate .; GO: 0004474 malate synthase activity, 0006097 glyoxylate cycle.
Probab=44.85 E-value=10 Score=18.98 Aligned_cols=48 Identities=15% Similarity=0.102 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999866579999999999999999999984111146799988899997677673798876999
Q gi|254780510|r 15 AQCCIKSIAESNLAYTISERKKINILREKLKDSINSTALMNPALASHYLKFYHSLSQNDQKMASLQL 81 (137)
Q Consensus 15 VQrhiErmAE~~LAeT~rqR~ei~~~~e~v~~ai~S~~pvh~afs~~Ya~r~~rLs~~Dqql~giQq 81 (137)
|++-||||| +|||-=+.-||--+-++.||..-.-==-.+|=-+.|+.|
T Consensus 659 V~~slErMA-------------------kVVD~QNAGDpAYRpMA~N~~~S~AFqAA~dLif~Gtkq 706 (726)
T TIGR01345 659 VLESLERMA-------------------KVVDKQNAGDPAYRPMADNYEASVAFQAAKDLIFKGTKQ 706 (726)
T ss_pred HHHHHHHHH-------------------HEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 999975230-------------------101246777835351134588879999888888606568
No 4
>TIGR02737 caa3_CtaG cytochrome c oxidase assembly factor CtaG; InterPro: IPR014108 Members of this family are the CtaG protein required for assembly of active cytochrome c oxidase of the caa3 type, as found in Bacillus subtilis..
Probab=36.51 E-value=23 Score=16.49 Aligned_cols=34 Identities=26% Similarity=0.544 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHH--HHHHH
Q ss_conf 111146799988899997677-6737988769--99999
Q gi|254780510|r 49 NSTALMNPALASHYLKFYHSL-SQNDQKMASL--QLVQE 84 (137)
Q Consensus 49 ~S~~pvh~afs~~Ya~r~~rL-s~~Dqql~gi--Qqv~E 84 (137)
|++.+++|.+++- +.|..| +..||||.|| +=+||
T Consensus 232 g~l~~L~P~ltGP--e~f~~l~~~~DQQLGGvlMKI~QE 268 (286)
T TIGR02737 232 GTLADLSPVLTGP--EMFLSLSTLEDQQLGGVLMKIIQE 268 (286)
T ss_pred CCCCCCCCCCCCC--HHHHHCCHHHHHHHHHHHHHHHHH
T ss_conf 7666788765663--035441113346788899999999
No 5
>cd07627 BAR_Vps5p The Bin/Amphiphysin/Rvs (BAR) domain of yeast Sorting Nexin Vps5p. 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. Vsp5p is the yeast counterpart of human SNX1 and is part of the retromer complex, which functions in the endosome-to-Golgi retrieval of vacuolar protein sorting receptor Vps10p, the Golgi-resident membrane protein A-ALP, and endopeptidase Kex2. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in
Probab=35.94 E-value=34 Score=15.29 Aligned_cols=114 Identities=18% Similarity=0.177 Sum_probs=68.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 78999999999999999866579999999999999999999984111146799988899997677673798876999999
Q gi|254780510|r 5 KSRALYKIITAQCCIKSIAESNLAYTISERKKINILREKLKDSINSTALMNPALASHYLKFYHSLSQNDQKMASLQLVQE 84 (137)
Q Consensus 5 rS~kLkRLv~VQrhiErmAE~~LAeT~rqR~ei~~~~e~v~~ai~S~~pvh~afs~~Ya~r~~rLs~~Dqql~giQqv~E 84 (137)
=|..|..+-.++..+....+-. + ..+....-+.+.+-++.+..|+.+|++- ..-|..+..-.+.|..-+.-.+
T Consensus 60 ls~~l~~la~~~~~i~~~~~~~----a--~~d~~~l~~~l~eYlr~i~sVk~~f~~R-~k~~~~~~~~~~~l~kk~~~~~ 132 (216)
T cd07627 60 LSDLLAALAEVQKRIKESLERQ----A--LQDVLTLGVTLDEYIRSIGSVRAAFAQR-QKLWQYWQSAESELSKKKAQLE 132 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH----H--HHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH
T ss_conf 8999999999999999999999----8--8899999999999999999999999999-9999999999999999898899
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 89999986489999989999853475221468899988876
Q gi|254780510|r 85 NTLLSEKIKIDRLTEMKDETYLLEERQYDDENNNDNIEQRI 125 (137)
Q Consensus 85 ~r~l~Er~K~DRLeE~m~eA~~~E~ReadDn~v~D~Idq~~ 125 (137)
.-....++..|++..-..+-..+|.+-..-..-|+.|...+
T Consensus 133 Kl~~~~~~~~dK~~~~~~ei~e~e~~~~~a~~~fe~is~~i 173 (216)
T cd07627 133 KLKRQGKTQQEKLNSLLSELEEAERRASELKKEFEEVSELI 173 (216)
T ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 87646667288999999999999999999999999999999
No 6
>cd07922 CarBa CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. 2-aminophenol 1,6-dioxygenase is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, the enzyme has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=29.17 E-value=37 Score=14.97 Aligned_cols=32 Identities=28% Similarity=0.430 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999999984111146799988899997
Q gi|254780510|r 34 RKKINILREKLKDSINSTALMNPALASHYLKFY 66 (137)
Q Consensus 34 R~ei~~~~e~v~~ai~S~~pvh~afs~~Ya~r~ 66 (137)
..|..+..+--+.|+.+.+ |||.+-+||+-.-
T Consensus 38 ~~E~~AL~eg~~gaL~~iG-Vhp~l~MHy~m~~ 69 (81)
T cd07922 38 PAERAALREGTFGALTSIG-VHPILQMHYLMYT 69 (81)
T ss_pred HHHHHHHHCCCHHHHHHCC-CCHHHHHHHHHHC
T ss_conf 8999998638864677367-3699999999981
No 7
>PRK04199 rpl10e 50S ribosomal protein L10e; Reviewed
Probab=29.03 E-value=9.4 Score=19.19 Aligned_cols=25 Identities=16% Similarity=0.280 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99998999998648999998999985
Q gi|254780510|r 81 LVQENTLLSEKIKIDRLTEMKDETYL 106 (137)
Q Consensus 81 qv~E~r~l~Er~K~DRLeE~m~eA~~ 106 (137)
-+-||++++- +.||||+++|--|.+
T Consensus 93 VlReNKm~s~-AGADRlq~GMR~aFG 117 (173)
T PRK04199 93 VLRENKMATG-AGADRVSDGMRLAFG 117 (173)
T ss_pred EEEECHHHCC-CCHHHHHCCCCCCCC
T ss_conf 2564122202-213455203433357
No 8
>TIGR00883 2A0106 MFS transporter, metabolite:H+ symporter (MHS) family protein; InterPro: IPR004736 Recent genome-sequencing data and a wealth of biochemical and molecular genetic investigations have revealed the occurrence of dozens of families of primary and secondary transporters. Two such families have been found to occur ubiquitously in all classifications of living organisms. These are the ATP-binding cassette (ABC) superfamily and the major facilitator superfamily (MFS), also called the uniporter-symporter-antiporter family. While ABC family permeases are in general multicomponent primary active transporters, capable of transporting both small molecules and macromolecules in response to ATP hydrolysis the MFS transporters are single-polypeptide secondary carriers capable only of transporting small solutes in response to chemiosmotic ion gradients. Although well over 100 families of transporters have now been recognized and classified, the ABC superfamily and MFS account for nearly half of the solute transporters encoded within the genomes of microorganisms. They are also prevalent in higher organisms. The importance of these two families of transport systems to living organisms can therefore not be overestimated . The MFS was originally believed to function primarily in the uptake of sugars but subsequent studies revealed that drug efflux systems, Krebs cycle metabolites, organophosphate:phosphate exchangers, oligosaccharide:H1 symport permeases, and bacterial aromatic acid permeases were all members of the MFS. These observations led to the probability that the MFS is far more widespread in nature and far more diverse in function than had been thought previously. 17 subgroups of the MFS have been identified . Evidence suggests that the MFS permeases arose by a tandem intragenic duplication event in the early prokaryotes. This event generated a 2-transmembrane-spanner (TMS) protein topology from a primordial 6-TMS unit. Surprisingly, all currently recognized MFS permeases retain the two six-TMS units within a single polypeptide chain, although in 3 of the 17 MFS families, an additional two TMSs are found . Moreover, the well-conserved MFS specific motif between TMS2 and TMS3 and the related but less well conserved motif between TMS8 and TMS9 prove to be a characteristic of virtually all of the more than 300 MFS proteins identified. This entry represents the metabolite-H(+) symport (MHS) subfamily of the MFS. Members include citrate-proton symporters , alpha-ketoglutarate permease , shikimate transporters , and the proline/betaine transporter ProP .; GO: 0005215 transporter activity, 0006810 transport, 0016021 integral to membrane.
Probab=25.58 E-value=45 Score=14.41 Aligned_cols=16 Identities=6% Similarity=0.004 Sum_probs=7.6
Q ss_pred HHHHHHHHHHHHHHHH
Q ss_conf 4679998889999767
Q gi|254780510|r 53 LMNPALASHYLKFYHS 68 (137)
Q Consensus 53 pvh~afs~~Ya~r~~r 68 (137)
|+=.++=+||.||+||
T Consensus 49 P~Gg~~FG~~GDr~GR 64 (413)
T TIGR00883 49 PLGGIVFGHFGDRIGR 64 (413)
T ss_pred HHHHHHHHHHHHHHHH
T ss_conf 8999999886323546
No 9
>PRK10642 proline/glycine betaine transporter; Provisional
Probab=25.25 E-value=47 Score=14.27 Aligned_cols=11 Identities=0% Similarity=-0.049 Sum_probs=5.8
Q ss_pred HHHHHHHHHHH
Q ss_conf 98889999767
Q gi|254780510|r 58 LASHYLKFYHS 68 (137)
Q Consensus 58 fs~~Ya~r~~r 68 (137)
+.+..+||+||
T Consensus 305 l~G~LSDriGR 315 (490)
T PRK10642 305 VMGLLSDRFGR 315 (490)
T ss_pred HHHHHHHHHCC
T ss_conf 99999988264
No 10
>pfam04622 ERG2_Sigma1R ERG2 and Sigma1 receptor like protein. This family consists of the fungal C-8 sterol isomerase and mammalian sigma1 receptor. C-8 sterol isomerase (delta-8--delta-7 sterol isomerase), catalyses a reaction in ergosterol biosynthesis, which results in unsaturation at C-7 in the B ring of sterols. Sigma 1 receptor is a low molecular mass mammalian protein located in the endoplasmic reticulum, which interacts with endogenous steroid hormones, such as progesterone and testosterone. It also binds the sigma ligands, which are are a set of chemically unrelated drugs including haloperidol, pentazocine, and ditolylguanidine. Sigma1 effectors are not well understood, but sigma1 agonists have been observed to affect NMDA receptor function, the alpha-adrenergic system and opioid analgesia.
Probab=21.41 E-value=58 Score=13.62 Aligned_cols=23 Identities=9% Similarity=0.426 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 984111146799988899997677
Q gi|254780510|r 46 DSINSTALMNPALASHYLKFYHSL 69 (137)
Q Consensus 46 ~ai~S~~pvh~afs~~Ya~r~~rL 69 (137)
.|||||-++|..|+ -|.-.||.-
T Consensus 85 GaMGsM~ilHaS~t-EYli~FGTa 107 (216)
T pfam04622 85 GAMGAMYILHASFT-EYLILFGTA 107 (216)
T ss_pred CHHHHHHHHHHHHH-HHHHHHCCC
T ss_conf 40342477887799-999995687
No 11
>pfam09254 Endonuc-FokI_C Restriction endonuclease FokI, C terminal. Members of this family are predominantly found in prokaryotic restriction endonuclease FokI, and adopt a structure consisting of an alpha/beta/alpha core containing a five-stranded beta-sheet. They recognize the double-stranded DNA sequence 5'-GGATG-3' and cleave DNA phosphodiester groups 9 base pairs away on this strand and 13 base pairs away on the complementary strand.
Probab=20.22 E-value=42 Score=14.59 Aligned_cols=46 Identities=13% Similarity=0.212 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 6799988899997677673798876999999899999864899999
Q gi|254780510|r 54 MNPALASHYLKFYHSLSQNDQKMASLQLVQENTLLSEKIKIDRLTE 99 (137)
Q Consensus 54 vh~afs~~Ya~r~~rLs~~Dqql~giQqv~E~r~l~Er~K~DRLeE 99 (137)
|--.|.++|-.++.++++..+-+-|.-.|-+--++-|..|+-+|+-
T Consensus 138 VSg~F~g~fk~qL~~~~~~T~~~GaAl~v~~LLl~Ae~ik~G~l~~ 183 (197)
T pfam09254 138 VSGHFKGNYKAQLQKFNHDTNCLGAALEFEELLIGAEMIKAGKLSK 183 (197)
T ss_pred EEEEECCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCH
T ss_conf 9513245289999998875167610000999987589987187609
Done!