Query gi|254780912|ref|YP_003065325.1| hypothetical protein CLIBASIA_04055 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 68
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Mon May 30 00:29:53 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780912.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0348 consensus 58.9 8.8 0.00022 19.9 2.7 40 21-60 220-275 (708)
2 TIGR02431 pcaR_pcaU beta-ketoa 25.7 63 0.0016 15.2 2.7 36 12-51 2-44 (252)
3 KOG4083 consensus 16.4 76 0.0019 14.7 1.4 15 21-35 169-183 (192)
4 PRK11562 nitrite transporter N 13.8 1.2E+02 0.003 13.7 3.0 17 51-67 20-36 (268)
5 KOG4587 consensus 13.7 1.2E+02 0.003 13.6 2.8 46 18-63 342-387 (605)
6 TIGR00632 vsr DNA mismatch end 13.2 1.2E+02 0.003 13.7 1.7 21 25-45 28-48 (143)
7 KOG0900 consensus 12.9 99 0.0025 14.1 1.2 33 14-47 26-59 (121)
8 pfam01114 Colipase Colipase, N 12.1 67 0.0017 15.0 0.2 15 21-35 10-24 (40)
9 cd00228 eu-GS Eukaryotic Gluta 12.0 77 0.002 14.7 0.4 22 45-66 345-366 (471)
10 cd04756 Commd8 COMM_Domain con 11.6 1.4E+02 0.0035 13.3 2.3 29 25-55 81-109 (176)
No 1
>KOG0348 consensus
Probab=58.92 E-value=8.8 Score=19.90 Aligned_cols=40 Identities=40% Similarity=0.514 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHH----------------HHHHHHHHHHHHHHHHHHCCCHHHHH
Q ss_conf 99999999999974----------------22002278765432231018289999
Q gi|254780912|r 21 SLELCSQIMQCVSK----------------EKNTINKASVRAGARNAISNPGKYVI 60 (68)
Q Consensus 21 slelcsqimqcvsk----------------ekntinkasvragarnaisnpgkyvi 60 (68)
.-|||.||...+.| ||..-.||-.|-|..--|+.||..|-
T Consensus 220 TREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRKGiNILIgTPGRLvD 275 (708)
T KOG0348 220 TRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRKGINILIGTPGRLVD 275 (708)
T ss_pred HHHHHHHHHHHHHHHHCCCEEEEECEEECCCCCCCHHHHHHCCCEEEECCCHHHHH
T ss_conf 19999999999998725743773021223633101788875485489758427889
No 2
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; InterPro: IPR012794 Members of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0045941 positive regulation of transcription, 0046278 protocatechuate metabolic process.
Probab=25.75 E-value=63 Score=15.19 Aligned_cols=36 Identities=31% Similarity=0.510 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHH
Q ss_conf 999999999999999999999742200227876-------5432231
Q gi|254780912|r 12 PSFMKSLLRSLELCSQIMQCVSKEKNTINKASV-------RAGARNA 51 (68)
Q Consensus 12 psfmksllrslelcsqimqcvskekntinkasv-------ragarna 51 (68)
++||.||-|.|- +||+.+.++...+=+.| ||+||-.
T Consensus 2 ~d~v~sLarGLa----Vi~aF~~~~~~ltl~~vA~~TGL~RAaARR~ 44 (252)
T TIGR02431 2 RDFVASLARGLA----VIEAFGEERPRLTLTDVAEATGLTRAAARRF 44 (252)
T ss_pred CHHHHHHHHHHH----HHHHHCCCCCCCCHHHHHHHHCCCCHHHHHH
T ss_conf 305678999999----9997310378989899998758994798889
No 3
>KOG4083 consensus
Probab=16.40 E-value=76 Score=14.73 Aligned_cols=15 Identities=33% Similarity=0.538 Sum_probs=8.0
Q ss_pred HHHHHHHHHHHHHHH
Q ss_conf 999999999999742
Q gi|254780912|r 21 SLELCSQIMQCVSKE 35 (68)
Q Consensus 21 slelcsqimqcvske 35 (68)
-.+|..|+|+||+--
T Consensus 169 C~~lv~af~~Cv~~~ 183 (192)
T KOG4083 169 CSPLVAAFMKCVSLA 183 (192)
T ss_pred CCHHHHHHHHHHHHH
T ss_conf 408999999999899
No 4
>PRK11562 nitrite transporter NirC; Provisional
Probab=13.75 E-value=1.2e+02 Score=13.65 Aligned_cols=17 Identities=24% Similarity=0.438 Sum_probs=9.8
Q ss_pred HHCCCHHHHHHHHHHHH
Q ss_conf 10182899999998542
Q gi|254780912|r 51 AISNPGKYVISGLLEGL 67 (68)
Q Consensus 51 aisnpgkyvisgllegl 67 (68)
-.++|++|.++..+-|.
T Consensus 20 l~~~~~~yfv~a~lAGa 36 (268)
T PRK11562 20 SANNPLGFWVSSAMAGA 36 (268)
T ss_pred HHCCHHHHHHHHHHHHH
T ss_conf 84585999999999999
No 5
>KOG4587 consensus
Probab=13.69 E-value=1.2e+02 Score=13.64 Aligned_cols=46 Identities=35% Similarity=0.405 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999999999999997422002278765432231018289999999
Q gi|254780912|r 18 LLRSLELCSQIMQCVSKEKNTINKASVRAGARNAISNPGKYVISGL 63 (68)
Q Consensus 18 llrslelcsqimqcvskekntinkasvragarnaisnpgkyvisgl 63 (68)
.+|.+-.-...||-|..-.+-||..+-|+..+..+...|.||-+-+
T Consensus 342 ~~~tll~P~~l~~~v~~vr~~i~~~~~~~~~~ke~~~~Ge~vY~~l 387 (605)
T KOG4587 342 SLRTLLPPADLMQDVKRVRAQINRNSERAQETKEAATDGEYVYSFL 387 (605)
T ss_pred HHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 8512278299999999999997115888777686324607899999
No 6
>TIGR00632 vsr DNA mismatch endonuclease Vsr; InterPro: IPR004603 This entry represents VSR (very short patch repair) endonucleases, which occur in a variety of bacteria. VSR recognises a TG mismatched base pair, generated after spontaneous deamination of methylated cytosines, and cleaves the phosphate backbone on the 5' side of the thymine . GT mismatches can lead to C-to-T transition mutations if not repaired. VSR repairs the mismatches in favour of the G-containing strand. In Escherichia coli, this endonuclease nicks double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next to the thymidine residue, which is mismatched to 2'-deoxyguanosine . The incision is mismatch-dependent and strand specific. The structure of VSR is similar to the core structure of restriction endonucleases, which have a 3-layer alpha/beta/alpha topology . ; GO: 0004519 endonuclease activity, 0006298 mismatch repair.
Probab=13.22 E-value=1.2e+02 Score=13.69 Aligned_cols=21 Identities=33% Similarity=0.333 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999997422002278765
Q gi|254780912|r 25 CSQIMQCVSKEKNTINKASVR 45 (68)
Q Consensus 25 csqimqcvskekntinkasvr 45 (68)
=+..||-+|+.|+|--.+.+|
T Consensus 28 R~~~M~a~s~~~~T~pE~~l~ 48 (143)
T TIGR00632 28 RSKNMQAVSRSKGTKPEKALA 48 (143)
T ss_pred HHHHHHHHHCCCCCHHHHHHH
T ss_conf 447788764157981789999
No 7
>KOG0900 consensus
Probab=12.89 E-value=99 Score=14.08 Aligned_cols=33 Identities=33% Similarity=0.511 Sum_probs=22.6
Q ss_pred HHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999-999999999742200227876543
Q gi|254780912|r 14 FMKSLLRSLE-LCSQIMQCVSKEKNTINKASVRAG 47 (68)
Q Consensus 14 fmksllrsle-lcsqimqcvskekntinkasvrag 47 (68)
|+.+.+|||| .|.+|.. -.||+|---|..||.-
T Consensus 26 ~~~~~~kslekvC~dl~~-~ak~~nl~~kg~vr~P 59 (121)
T KOG0900 26 LTSQKVKSLEKVCADLVR-GAKEKNLKVKGPVRLP 59 (121)
T ss_pred EEHHHHHHHHHHHHHHHH-HHHHCCCCCCCCCCCC
T ss_conf 327778789999999998-8764277415764588
No 8
>pfam01114 Colipase Colipase, N-terminal domain. SCOP reports duplication of common fold with Colipase C-terminal domain.
Probab=12.13 E-value=67 Score=15.02 Aligned_cols=15 Identities=40% Similarity=0.514 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHHH
Q ss_conf 999999999999742
Q gi|254780912|r 21 SLELCSQIMQCVSKE 35 (68)
Q Consensus 21 slelcsqimqcvske 35 (68)
.-|||-+-+||-|+-
T Consensus 10 ~GElClnSaQCkS~C 24 (40)
T pfam01114 10 DGELCLNSAQCKSSC 24 (40)
T ss_pred CCCCHHHHHHHCCCC
T ss_conf 870003245542121
No 9
>cd00228 eu-GS Eukaryotic Glutathione Synthetase (eu-GS); catalyses the production of glutathione from gamma-glutamylcysteine and glycine in an ATP-dependent manner. Belongs to the ATP-grasp superfamily.
Probab=11.96 E-value=77 Score=14.68 Aligned_cols=22 Identities=27% Similarity=0.424 Sum_probs=15.1
Q ss_pred HHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 5432231018289999999854
Q gi|254780912|r 45 RAGARNAISNPGKYVISGLLEG 66 (68)
Q Consensus 45 ragarnaisnpgkyvisglleg 66 (68)
+.+.+.|+.+|.+||.---.||
T Consensus 345 ~~~~~~A~~~P~~yVLKPQREG 366 (471)
T cd00228 345 DEIVRKALEKPELFVLKPQREG 366 (471)
T ss_pred HHHHHHHHHCHHHEEECCCCCC
T ss_conf 8999998839131256474657
No 10
>cd04756 Commd8 COMM_Domain containing protein 8. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=11.60 E-value=1.4e+02 Score=13.28 Aligned_cols=29 Identities=31% Similarity=0.527 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 9999999974220022787654322310182
Q gi|254780912|r 25 CSQIMQCVSKEKNTINKASVRAGARNAISNP 55 (68)
Q Consensus 25 csqimqcvskekntinkasvragarnaisnp 55 (68)
-..||+|+.-.++-|.+|-+ ...|+||.+
T Consensus 81 q~aIl~cL~~Rk~EI~~aL~--~~~~siss~ 109 (176)
T cd04756 81 QEALLKCVKSRKEEIRQALV--NKTNSISSA 109 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHH--HHHHCCCCC
T ss_conf 99999999983699999999--997323521
Done!