Query gi|254780230|ref|YP_003064643.1| hypothetical protein CLIBASIA_00575 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 96
No_of_seqs 103 out of 553
Neff 5.6
Searched_HMMs 39220
Date Tue May 24 00:06:23 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780230.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 pfam02325 YGGT YGGT family. Th 99.8 6.7E-20 1.7E-24 124.8 8.8 74 8-93 1-74 (75)
2 COG0762 Predicted integral mem 99.7 1.2E-17 3.1E-22 112.9 10.3 78 7-95 13-90 (96)
3 TIGR00801 ncs2 uracil-xanthine 37.5 28 0.00071 15.7 2.4 42 46-94 129-175 (480)
4 TIGR02978 phageshock_pspC phag 36.2 33 0.00085 15.3 4.4 58 4-61 33-95 (128)
5 pfam10859 DUF2660 Protein of u 34.6 29 0.00074 15.6 2.1 18 44-61 47-64 (86)
6 pfam03428 RP-C Replication pro 31.2 21 0.00053 16.4 0.9 12 70-81 124-135 (177)
7 PRK10697 DNA-binding transcrip 30.6 42 0.0011 14.8 4.4 33 4-36 39-71 (119)
8 TIGR00354 polC DNA polymerase 29.8 39 0.001 14.9 2.1 33 46-81 930-962 (1173)
9 pfam02077 SURF4 SURF4 family. 29.6 43 0.0011 14.7 3.2 17 51-67 10-26 (267)
10 pfam04898 Glu_syn_central Glut 29.6 18 0.00045 16.8 0.4 28 35-62 44-71 (288)
11 PRK13824 replication initiatio 27.2 28 0.00071 15.7 1.0 12 70-81 136-147 (404)
12 PRK09463 fadE acyl-CoA dehydro 24.5 50 0.0013 14.4 1.9 17 51-67 27-43 (761)
13 PRK13026 acyl-CoA dehydrogenas 23.6 53 0.0014 14.2 1.9 17 51-67 26-42 (771)
14 COG2233 UraA Xanthine/uracil p 20.6 65 0.0017 13.7 2.0 26 44-69 114-140 (451)
15 TIGR03616 RutG pyrimidine util 20.2 67 0.0017 13.7 2.3 33 46-78 120-161 (429)
No 1
>pfam02325 YGGT YGGT family. This family consists of a repeat found in conserved hypothetical integral membrane proteins. The function of this region and the proteins which possess it is unknown.
Probab=99.81 E-value=6.7e-20 Score=124.84 Aligned_cols=74 Identities=41% Similarity=0.665 Sum_probs=64.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 99999999999999999998635887876548999999999999778999999862765775532017999999999999
Q gi|254780230|r 8 LLLLLELYANIVITRIVFSFLYTYDIINPLNFFVQTARQLLYSFTEPFLIPIRRFTPSLGVEWKRIDLSPIILLTVIYIL 87 (96)
Q Consensus 8 l~~~l~iy~~~li~rvIlsW~~~f~~~n~~n~~v~~i~~~l~~lTeP~L~piRr~iPplg~g~~giDlSpiv~~l~l~~l 87 (96)
++.++++|.+++++|+++||+++ +.+ |+ ..++++++|||+++|+||++|++| |+|+||++++++++++
T Consensus 1 l~~~l~i~~~~iiir~ilsW~~~-~~~---~~----~~~~i~~~teP~l~p~Rr~iP~~g----giD~Spiv~~~~l~~l 68 (75)
T pfam02325 1 LSTLLNIYIFLLIIRVILSWVPA-DPY---NP----IVQFLYRLTEPLLRPFRRVIPPIG----GIDLSPIVAFLLLQFL 68 (75)
T ss_pred CHHHHHHHHHHHHHHHHHHHCCC-CCC---CC----HHHHHHHHHHHHHHHHHHHCCCCC----CCCHHHHHHHHHHHHH
T ss_conf 98699999999999999996677-888---86----999999987988999998778967----6559999999999999
Q ss_pred HHHHHH
Q ss_conf 999998
Q gi|254780230|r 88 QCFLKF 93 (96)
Q Consensus 88 ~~~l~~ 93 (96)
+.++..
T Consensus 69 ~~~l~~ 74 (75)
T pfam02325 69 QILLLG 74 (75)
T ss_pred HHHHHC
T ss_conf 999714
No 2
>COG0762 Predicted integral membrane protein [Function unknown]
Probab=99.75 E-value=1.2e-17 Score=112.90 Aligned_cols=78 Identities=38% Similarity=0.676 Sum_probs=69.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 99999999999999999999863588787654899999999999977899999986276577553201799999999999
Q gi|254780230|r 7 ILLLLLELYANIVITRIVFSFLYTYDIINPLNFFVQTARQLLYSFTEPFLIPIRRFTPSLGVEWKRIDLSPIILLTVIYI 86 (96)
Q Consensus 7 il~~~l~iy~~~li~rvIlsW~~~f~~~n~~n~~v~~i~~~l~~lTeP~L~piRr~iPplg~g~~giDlSpiv~~l~l~~ 86 (96)
++..+++.|.+.++++..+||+++.+..| ++.++++++|||+++|+||++||+| |+|+||+++++++++
T Consensus 13 ~l~~~i~~~~~~~ii~~~lsw~~~~~~~~-------~i~~~l~~lteP~L~p~Rr~ip~lg----giD~Spiv~iliL~~ 81 (96)
T COG0762 13 VLLILIGVYIFLLLIRALLSWFPPAGETN-------PIGRLLAQLTEPLLRPFRRLIPPLG----GIDFSPIVALLILQF 81 (96)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCCC-------CHHHHHHHHHHHHHHHHHHCCCCCC----CCHHHHHHHHHHHHH
T ss_conf 99999999999999999998467877535-------5999999973286899998089867----700659999999999
Q ss_pred HHHHHHHHC
Q ss_conf 999999854
Q gi|254780230|r 87 LQCFLKFLI 95 (96)
Q Consensus 87 l~~~l~~ll 95 (96)
+|.++.+..
T Consensus 82 l~~~l~~~~ 90 (96)
T COG0762 82 LQFFLIRLL 90 (96)
T ss_pred HHHHHHHHH
T ss_conf 999999999
No 3
>TIGR00801 ncs2 uracil-xanthine permease; InterPro: IPR006042 A number of transport proteins which are involved in the uptake of xanthine or uracil are evolutionary related . They are proteins of from 430 to 595 residues that seem to contain 12 transmembrane domains.; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane.
Probab=37.53 E-value=28 Score=15.70 Aligned_cols=42 Identities=19% Similarity=0.429 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHH-----HHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999778999-----9998627657755320179999999999999999985
Q gi|254780230|r 46 QLLYSFTEPFLI-----PIRRFTPSLGVEWKRIDLSPIILLTVIYILQCFLKFL 94 (96)
Q Consensus 46 ~~l~~lTeP~L~-----piRr~iPplg~g~~giDlSpiv~~l~l~~l~~~l~~l 94 (96)
..+|.+.|...+ .+||++||+= ..|.|..+++++++.-+++.
T Consensus 129 G~~~~l~~~~~~k~~~~~l~~lfPPvV-------~G~VV~~IGLsL~~~a~~~~ 175 (480)
T TIGR00801 129 GLVYTLLALLIKKLGTRWLRRLFPPVV-------TGPVVMLIGLSLIPVAVKMA 175 (480)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCE-------EEHHHHHHHHHHHHHHHHHH
T ss_conf 999999999998888999998659902-------44212314255899999874
No 4
>TIGR02978 phageshock_pspC phage shock protein C; InterPro: IPR014320 All members of this protein are the phage shock protein PspC. The phage shock regulon is restricted to the Proteobacteria and somewhat sparsely distributed there. It is expressed, under positive control of a sigma-54-dependent transcription factor; PspF, which binds and is modulated by PspA. Stresses that induce the psp regulon include phage secretin over expression, ethanol, heat shock and protein export defects..
Probab=36.16 E-value=33 Score=15.30 Aligned_cols=58 Identities=10% Similarity=0.062 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHH----HHHHHHHHHHHHH-HHHHHHH
Q ss_conf 99999999999999999999999863588787654899----9999999999778-9999998
Q gi|254780230|r 4 LFKILLLLLELYANIVITRIVFSFLYTYDIINPLNFFV----QTARQLLYSFTEP-FLIPIRR 61 (96)
Q Consensus 4 i~~il~~~l~iy~~~li~rvIlsW~~~f~~~n~~n~~v----~~i~~~l~~lTeP-~L~piRr 61 (96)
+..+...++...++++.||+++.++--..|.+.+..-- |..-+-.+|-.+| +=+-+|+
T Consensus 33 il~v~~~lfg~~~~~~~AYia~~~~L~k~P~~~~~~~~~~~~~~vk~k~Wq~g~~~p~~~L~~ 95 (128)
T TIGR02978 33 ILVVSALLFGGGFFVLVAYIALWLLLDKKPVNLYEDDDTSKEHEVKSKFWQAGQTSPKQALRE 95 (128)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHCCCCCCCCHHHHCCCHHHHHHH
T ss_conf 999999999879999999999999635446332345301110114541002205788899999
No 5
>pfam10859 DUF2660 Protein of unknown function (DUF2660). This is a family of proteins with unknown function.
Probab=34.57 E-value=29 Score=15.61 Aligned_cols=18 Identities=33% Similarity=0.534 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHHHHH
Q ss_conf 999999997789999998
Q gi|254780230|r 44 ARQLLYSFTEPFLIPIRR 61 (96)
Q Consensus 44 i~~~l~~lTeP~L~piRr 61 (96)
-|.++|.+||-+|+.+-|
T Consensus 47 SWkFLYdiTe~ILnkFsk 64 (86)
T pfam10859 47 SWQFLYDITETILNKFSK 64 (86)
T ss_pred HHHHHHHHHHHHHHHHCH
T ss_conf 899999899999987168
No 6
>pfam03428 RP-C Replication protein C N-terminal domain. Replication protein C is involved in the early stages of viral DNA replication.
Probab=31.23 E-value=21 Score=16.39 Aligned_cols=12 Identities=25% Similarity=0.354 Sum_probs=9.4
Q ss_pred CCCCHHHHHHHH
Q ss_conf 532017999999
Q gi|254780230|r 70 WKRIDLSPIILL 81 (96)
Q Consensus 70 ~~giDlSpiv~~ 81 (96)
..|+|+||+++=
T Consensus 124 A~GfdLsPL~~R 135 (177)
T pfam03428 124 AFGFDLAPLLAR 135 (177)
T ss_pred EECCCHHHHHHH
T ss_conf 446473899988
No 7
>PRK10697 DNA-binding transcriptional activator PspC; Provisional
Probab=30.57 E-value=42 Score=14.79 Aligned_cols=33 Identities=18% Similarity=0.293 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 999999999999999999999998635887876
Q gi|254780230|r 4 LFKILLLLLELYANIVITRIVFSFLYTYDIINP 36 (96)
Q Consensus 4 i~~il~~~l~iy~~~li~rvIlsW~~~f~~~n~ 36 (96)
+..++..++..+.+.+++++++.|+....+.+.
T Consensus 39 ~~~vl~~f~g~~~~~~~aYii~~~~l~p~P~~~ 71 (119)
T PRK10697 39 IIVVLSIFFGLFFFTLVAYIILSFVLDPMPDNM 71 (119)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf 999999999606899999999999807787532
No 8
>TIGR00354 polC DNA polymerase II, large subunit DP2; InterPro: IPR004475 This family represents the large subunit, DP2, of a two subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0006308 DNA catabolic process.
Probab=29.78 E-value=39 Score=14.93 Aligned_cols=33 Identities=18% Similarity=0.383 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHH
Q ss_conf 999999778999999862765775532017999999
Q gi|254780230|r 46 QLLYSFTEPFLIPIRRFTPSLGVEWKRIDLSPIILL 81 (96)
Q Consensus 46 ~~l~~lTeP~L~piRr~iPplg~g~~giDlSpiv~~ 81 (96)
+..-=+-|-.||+-|+|+|.=+.| ..| +|+|+-
T Consensus 930 DsfmLLLDalLNFSkkfLPdkRGG--qMD-APLVLt 962 (1173)
T TIGR00354 930 DSFMLLLDALLNFSKKFLPDKRGG--QMD-APLVLT 962 (1173)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCCC--CCC-CHHHHH
T ss_conf 689999988873236547787879--756-324530
No 9
>pfam02077 SURF4 SURF4 family.
Probab=29.63 E-value=43 Score=14.70 Aligned_cols=17 Identities=24% Similarity=0.604 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHCCCCC
Q ss_conf 97789999998627657
Q gi|254780230|r 51 FTEPFLIPIRRFTPSLG 67 (96)
Q Consensus 51 lTeP~L~piRr~iPplg 67 (96)
.+|-+.+|.|+++|.+|
T Consensus 10 ~~d~~~r~~k~~LP~ia 26 (267)
T pfam02077 10 YAETFARKTKPYLPTLA 26 (267)
T ss_pred HHHHHHHCCCCCCHHHH
T ss_conf 89999861555664899
No 10
>pfam04898 Glu_syn_central Glutamate synthase central domain. The central domain of glutamate synthase connects the amino terminal amidotransferase domain with the FMN-binding domain and has an alpha / beta overall topology. This domain appears to be a rudimentary form of the FMN-binding TIM barrel according to SCOP.
Probab=29.61 E-value=18 Score=16.75 Aligned_cols=28 Identities=25% Similarity=0.316 Sum_probs=19.9
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 7654899999999999977899999986
Q gi|254780230|r 35 NPLNFFVQTARQLLYSFTEPFLIPIRRF 62 (96)
Q Consensus 35 n~~n~~v~~i~~~l~~lTeP~L~piRr~ 62 (96)
+.|+....-.-+-..|+|.|+..|+|--
T Consensus 44 ~~~~~l~~yFkQ~FAQVTNPPID~iRE~ 71 (288)
T pfam04898 44 EKPRLLYDYFKQLFAQVTNPPIDPIREE 71 (288)
T ss_pred CCCCCHHHHHHHHHHCCCCCCCCHHHHH
T ss_conf 8975278998764200578986387776
No 11
>PRK13824 replication initiation protein RepC; Provisional
Probab=27.23 E-value=28 Score=15.72 Aligned_cols=12 Identities=17% Similarity=0.238 Sum_probs=9.4
Q ss_pred CCCCHHHHHHHH
Q ss_conf 532017999999
Q gi|254780230|r 70 WKRIDLSPIILL 81 (96)
Q Consensus 70 ~~giDlSpiv~~ 81 (96)
..|||+||+++=
T Consensus 136 AyGFDLsPL~~R 147 (404)
T PRK13824 136 AFGFSLAPLLAR 147 (404)
T ss_pred EECCCHHHHHHH
T ss_conf 646367999999
No 12
>PRK09463 fadE acyl-CoA dehydrogenase; Reviewed
Probab=24.45 E-value=50 Score=14.35 Aligned_cols=17 Identities=18% Similarity=0.499 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHCCCCC
Q ss_conf 97789999998627657
Q gi|254780230|r 51 FTEPFLIPIRRFTPSLG 67 (96)
Q Consensus 51 lTeP~L~piRr~iPplg 67 (96)
+|.|+++.+||++|++.
T Consensus 27 ~t~~~~~~~~~~lP~~s 43 (761)
T PRK09463 27 ISAPLFKWFRKVLPPMS 43 (761)
T ss_pred HHHHHHHHHHHHCCCCC
T ss_conf 14999999986489998
No 13
>PRK13026 acyl-CoA dehydrogenase; Reviewed
Probab=23.55 E-value=53 Score=14.22 Aligned_cols=17 Identities=24% Similarity=0.497 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHCCCCC
Q ss_conf 97789999998627657
Q gi|254780230|r 51 FTEPFLIPIRRFTPSLG 67 (96)
Q Consensus 51 lTeP~L~piRr~iPplg 67 (96)
+|.|+++.+||.+|++.
T Consensus 26 ~t~~~~~~~~k~lP~iS 42 (771)
T PRK13026 26 ITRPVFKFFKKVLPPLS 42 (771)
T ss_pred HHHHHHHHHHHHCCCCC
T ss_conf 04899999996489998
No 14
>COG2233 UraA Xanthine/uracil permeases [Nucleotide transport and metabolism]
Probab=20.64 E-value=65 Score=13.75 Aligned_cols=26 Identities=23% Similarity=0.424 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHHH-HHHHHCCCCCCC
Q ss_conf 99999999778999-999862765775
Q gi|254780230|r 44 ARQLLYSFTEPFLI-PIRRFTPSLGVE 69 (96)
Q Consensus 44 i~~~l~~lTeP~L~-piRr~iPplg~g 69 (96)
...++|-+-.|..+ .++|+.||.=.|
T Consensus 114 ~ag~~~~li~~~~~~~l~rlfpPvVtG 140 (451)
T COG2233 114 AAGLVYFLISPIVKIRLARLFPPVVTG 140 (451)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCEEE
T ss_conf 999999999999999999858984677
No 15
>TIGR03616 RutG pyrimidine utilization transport protein G. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the uracil-xanthine permease family defined by TIGR00801. As well as the The Nucleobase:Cation Symporter-2 (NCS2) Family (TC 2.A.40).
Probab=20.22 E-value=67 Score=13.70 Aligned_cols=33 Identities=24% Similarity=0.388 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHH-----HHHHHCCCCCCCC----CCCHHHHH
Q ss_conf 999999778999-----9998627657755----32017999
Q gi|254780230|r 46 QLLYSFTEPFLI-----PIRRFTPSLGVEW----KRIDLSPI 78 (96)
Q Consensus 46 ~~l~~lTeP~L~-----piRr~iPplg~g~----~giDlSpi 78 (96)
..++.+-.+... .+||+.||+=.|+ +|+.+.|.
T Consensus 120 g~~~~~~~~~~~~~~~~~i~r~fPPvVtG~vV~lIGlsL~pv 161 (429)
T TIGR03616 120 GLVYAAIGLVVMRTGTRWIERLMPPVVTGAVVMAIGLNLAPI 161 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHEEEEECCCHHHH
T ss_conf 999999999999850888887289602002231454100887
Done!