Query gi|254781126|ref|YP_003065539.1| hypothetical protein CLIBASIA_05140 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 85
No_of_seqs 2 out of 4
Neff 1.2
Searched_HMMs 39220
Date Mon May 30 04:59:26 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781126.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01686 FkbH FkbH domain; In 52.4 20 0.0005 17.7 3.5 55 8-64 279-333 (337)
2 TIGR01802 CM_pl-yst chorismate 51.8 5.5 0.00014 20.8 0.6 16 4-19 146-161 (273)
3 pfam09633 DUF2023 Protein of u 36.2 23 0.00058 17.3 1.8 30 1-30 51-80 (101)
4 KOG4682 consensus 32.4 25 0.00064 17.1 1.5 19 52-70 172-190 (488)
5 pfam06878 Pkip-1 Pkip-1 protei 24.7 62 0.0016 14.8 3.6 59 15-84 94-155 (163)
6 pfam10464 Peptidase_U40 Peptid 22.5 45 0.0011 15.6 1.4 18 21-38 25-42 (212)
7 COG5275 BRCT domain type II [G 21.4 7.5 0.00019 20.0 -2.8 46 8-53 154-209 (276)
8 pfam12599 DUF3768 Protein of u 21.2 48 0.0012 15.5 1.3 21 17-37 1-21 (84)
9 TIGR00993 3a0901s04IAP86 chlor 18.9 52 0.0013 15.3 1.1 17 20-36 426-442 (772)
10 pfam10904 DUF2694 Protein of u 17.6 88 0.0022 14.0 2.4 19 4-22 50-68 (101)
No 1
>TIGR01686 FkbH FkbH domain; InterPro: IPR010037 This entry describes a domain of unknown function. One of proteins with this domain is a modular polyketide synthase, which is 4800 amino acids in length from Streptomyces avermilitis, where the domain is the C-terminal segment. By contrast, the FkbH protein from Streptomyces hygroscopicus (Q84G18 from SWISSPROT) apparently contains only this domain. The remaining members of the family all contain an additional N-terminal domain of between 200 and 275 amino acids, which show less than 20 0dentity to one another. It seems likely then that these proteins are involved in disparate functions, probably the biosynthesis of different natural products. For instance, the FkbH gene is found in a gene cluster believed to be responsible for the biosynthesis of unusual 'PKS extender units' in the ascomycin pathway . This domain is composed of two parts, the first of which is a member of subfamily IIIC of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. All of the characterised enzymes within subfamily III are phosphatases, and all of the active site residues characteristic of HAD-superfamily phosphatases are present in this domain. The C-terminal portion of this domain is unique to this family (by BLAST)..
Probab=52.38 E-value=20 Score=17.66 Aligned_cols=55 Identities=25% Similarity=0.348 Sum_probs=44.9
Q ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 899999999997766524836789999878767751686732012218999986320
Q gi|254781126|r 8 ISCLRALVFVITRGVARLPKDQKKAFFRHEKKVADHLNYNAGDRKSNIDKLYKARCK 64 (85)
Q Consensus 8 isclralvfvITR~~~~L~~~~KKAFF~HEKKV~~~LNYNA~DRK~NI~~~Y~AR~K 64 (85)
+|| |++-+-+-..+-++--++-+.||+- +--.--+.|.-++|-.-...||++-|+
T Consensus 279 ~SC-R~l~r~~e~~~L~~l~d~A~hff~~-g~~~~~~~y~~T~rN~~~~~~~~~~g~ 333 (337)
T TIGR01686 279 MSC-RVLGRGVEERLLRWLVDQAKHFFEL-GAHKVRLIYRRTERNVPVESFYEELGF 333 (337)
T ss_pred HHH-HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHEEEEECCCCCCHHHHHHHHHHCC
T ss_conf 640-1410116799999999988999984-135403100689877689999998531
No 2
>TIGR01802 CM_pl-yst chorismate mutase; InterPro: IPR008238 Chorismate mutase (CM; 5.4.99.5 from EC) catalyses the reaction at the branch point of the biosynthetic pathway leading to the three aromatic amino acids, phenylalanine, tryptophan and tyrosine (chorismic acid is the last common intermediate, and CM leads to the L-phenylalanine/L-tyrosine branch). It is part of the shikimate pathway, which is present only in bacteria, fungi and plants. Members of this family, which are restricted to plants and fungi, contain a chorismate mutase domain of the AroQ class (eukaryotic type) and have an all-helical structure. The monomer consists of a catalytic and a regulatory domain covalently linked by a loop, which functions as a molecular hinge. They are monofunctional, allosteric enzymes and are subject to allosteric inhibition by tyrosine and activation by tryptophan. The three types of CM are AroQ class, prokaryotic type (e.g., IPR008239 from INTERPRO and others); AroQ class, eukaryotic type; and AroH class (IPR008243 from INTERPRO). They fall into two structural folds (AroQ class and AroH class) which are completely unrelated . The two types of the AroQ structural class (the Escherichia coli CM dimer and the yeast CM monomer) can be structurally superimposed, and the topology of the four-helix bundle forming the active site is conserved . For additional information please see , , , , , , , .; GO: 0004106 chorismate mutase activity, 0009073 aromatic amino acid family biosynthetic process.
Probab=51.82 E-value=5.5 Score=20.79 Aligned_cols=16 Identities=31% Similarity=0.482 Sum_probs=11.9
Q ss_pred EHHHHHHHHHHHHHHH
Q ss_conf 0114899999999997
Q gi|254781126|r 4 FVRDISCLRALVFVIT 19 (85)
Q Consensus 4 fvrdisclralvfvIT 19 (85)
-||||+||.||-==|-
T Consensus 146 AtcD~~CLQ~LSRRIH 161 (273)
T TIGR01802 146 ATCDVECLQSLSRRIH 161 (273)
T ss_pred EEHHHHHHHHHCCCCC
T ss_conf 5324357533301102
No 3
>pfam09633 DUF2023 Protein of unknown function (DUF2023). This protein of approx.120 residues consists of three beta strands and five alpha helices, thought to fold into a homo-dimer. It is expressed in bacteria.
Probab=36.22 E-value=23 Score=17.30 Aligned_cols=30 Identities=20% Similarity=0.562 Sum_probs=26.0
Q ss_pred CCEEHHHHHHHHHHHHHHHHHHHHCCHHHH
Q ss_conf 942011489999999999776652483678
Q gi|254781126|r 1 MNIFVRDISCLRALVFVITRGVARLPKDQK 30 (85)
Q Consensus 1 mnifvrdisclralvfvITR~~~~L~~~~K 30 (85)
.|+|--+-.|+.++-..+++-++.|+..|.
T Consensus 51 vNlFFG~~~Ci~~ir~~~~~pL~~ltpEED 80 (101)
T pfam09633 51 INVFFGRPECVEVIRHIVTRPLNQLTPEED 80 (101)
T ss_pred EEEEECCHHHHHHHHHHHCCCHHHCCCHHH
T ss_conf 888768889999999991695443890998
No 4
>KOG4682 consensus
Probab=32.39 E-value=25 Score=17.06 Aligned_cols=19 Identities=37% Similarity=0.513 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q ss_conf 2218999986320133778
Q gi|254781126|r 52 KSNIDKLYKARCKYRKESK 70 (85)
Q Consensus 52 K~NI~~~Y~AR~KYRkesk 70 (85)
-.++-+||+|-|||.-|+-
T Consensus 172 pkta~~yYea~ckYgle~v 190 (488)
T KOG4682 172 PKTACGYYEAACKYGLESV 190 (488)
T ss_pred HHHHHHHHHHHHHHHHHHH
T ss_conf 0546778788877416888
No 5
>pfam06878 Pkip-1 Pkip-1 protein. This family consists of several Pkip-1 proteins which seem to be specific to Nucleopolyhedroviruses. The function of this family is unknown although it has been found that Pkip-1 is not essential for virus replication in cell culture or by in vivo intrahaemocoelic injection.
Probab=24.66 E-value=62 Score=14.83 Aligned_cols=59 Identities=31% Similarity=0.361 Sum_probs=42.7
Q ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHCEEECC
Q ss_conf 9999776652483678999987876775168673201221899998632013377---898742310210014
Q gi|254781126|r 15 VFVITRGVARLPKDQKKAFFRHEKKVADHLNYNAGDRKSNIDKLYKARCKYRKES---KLQKLSKSKIFSIKH 84 (85)
Q Consensus 15 vfvITR~~~~L~~~~KKAFF~HEKKV~~~LNYNA~DRK~NI~~~Y~AR~KYRkes---klqklskskifsikh 84 (85)
.|..--+..++|+.-.++|-.+-++...++ -||-.+|+-|||.. -|+.|-..|---|||
T Consensus 94 ~l~~ky~a~~~~~~~~~~~~~n~~~F~kvl-----------~qFv~Krn~~rk~~~~~lL~ELV~LKs~lIKH 155 (163)
T pfam06878 94 YLLKKYNAAKLLEAIQKAFDKNAKKFLKVL-----------EQFIDKRNAYRKNENNALLDELVLLKSNLIKH 155 (163)
T ss_pred HHHHHCCHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_conf 998753620115899999998628899999-----------99999999986386477999999999999999
No 6
>pfam10464 Peptidase_U40 Peptidase U40. This family contains P5 murein endopeptidase from bacteriophage phi-6. P5 murein endopeptidase has lytic activity against several gram-negative bacteria. It is thought that the enzyme cleaves the cell wall peptide bridge formed by meso-2,6-diaminopimelic acid and D-Ala
Probab=22.52 E-value=45 Score=15.62 Aligned_cols=18 Identities=33% Similarity=0.534 Sum_probs=14.5
Q ss_pred HHHHCCHHHHHHHHHHHH
Q ss_conf 665248367899998787
Q gi|254781126|r 21 GVARLPKDQKKAFFRHEK 38 (85)
Q Consensus 21 ~~~~L~~~~KKAFF~HEK 38 (85)
.+..||+|||||..+-..
T Consensus 25 aldalpenqkkaivelqa 42 (212)
T pfam10464 25 ALDALPENQKKAIVELQA 42 (212)
T ss_pred HHHHCCHHHHHHHHHHHH
T ss_conf 885375123668898987
No 7
>COG5275 BRCT domain type II [General function prediction only]
Probab=21.36 E-value=7.5 Score=20.02 Aligned_cols=46 Identities=33% Similarity=0.499 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHHH-HHHHHH---------HCCCCCCHHHH
Q ss_conf 89999999999776652483678999987-876775---------16867320122
Q gi|254781126|r 8 ISCLRALVFVITRGVARLPKDQKKAFFRH-EKKVAD---------HLNYNAGDRKS 53 (85)
Q Consensus 8 isclralvfvITR~~~~L~~~~KKAFF~H-EKKV~~---------~LNYNA~DRK~ 53 (85)
-.||..++||+|--+.+|+.++-++.... --+|+. -|.-|||-+|-
T Consensus 154 ~~cL~G~~fVfTG~l~TlsR~~a~~lvk~yGgrvT~~pSskTtflvlGdnaGP~K~ 209 (276)
T COG5275 154 RECLKGKVFVFTGDLKTLSRDDAKTLVKVYGGRVTAVPSSKTTFLVLGDNAGPSKM 209 (276)
T ss_pred CCCCCCCEEEEECCCCCCCCHHHHHHHHHHCCEEECCCCCCEEEEEECCCCCHHHH
T ss_conf 64325617999424300032038889998687344056654158996588881787
No 8
>pfam12599 DUF3768 Protein of unknown function (DUF3768). This family of proteins is found in bacteria. Proteins in this family are typically between 108 and 129 amino acids in length. There are two conserved sequence motifs: NDP and RVLT.
Probab=21.16 E-value=48 Score=15.46 Aligned_cols=21 Identities=43% Similarity=0.657 Sum_probs=16.9
Q ss_pred HHHHHHHHCCHHHHHHHHHHH
Q ss_conf 997766524836789999878
Q gi|254781126|r 17 VITRGVARLPKDQKKAFFRHE 37 (85)
Q Consensus 17 vITR~~~~L~~~~KKAFF~HE 37 (85)
|||+|++.|+.+.-.+.++.-
T Consensus 1 v~T~gv~aLg~~~~~~il~~V 21 (84)
T pfam12599 1 VITQGVAALGEDDQQELLRAV 21 (84)
T ss_pred CCCHHHHHCCHHHHHHHHHHH
T ss_conf 925778774999999999999
No 9
>TIGR00993 3a0901s04IAP86 chloroplast protein import component Toc86/159, G and M domains; InterPro: IPR005690 Two integral outer envelope GTPases, Toc34 and Toc86, are proposed to regulate the recognition and translocation of nuclear-encoded preproteins during the early stages of protein import into chloroplasts. The long precursor of the 86K protein is proposed to have three domains. The N-terminal A-domain is acidic, repetitive, weakly conserved, readily removed by proteolysis during chloroplast isolation, and not required for protein translocation . The other domains are designated G (GTPase) and M (membrane anchor); this family includes most of the G domain and all of M.; GO: 0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity, 0006886 intracellular protein transport, 0009707 chloroplast outer membrane.
Probab=18.92 E-value=52 Score=15.25 Aligned_cols=17 Identities=35% Similarity=0.677 Sum_probs=14.3
Q ss_pred HHHHHCCHHHHHHHHHH
Q ss_conf 76652483678999987
Q gi|254781126|r 20 RGVARLPKDQKKAFFRH 36 (85)
Q Consensus 20 R~~~~L~~~~KKAFF~H 36 (85)
--+|+|++.|+|++|+.
T Consensus 426 ~Q~A~L~~~Q~K~Yl~E 442 (772)
T TIGR00993 426 AQLAKLSKEQRKAYLEE 442 (772)
T ss_pred HHHHHHHHHHHHHHHHH
T ss_conf 88876305654556456
No 10
>pfam10904 DUF2694 Protein of unknown function (DUF2694). This family of proteins with unknown function appears to be restricted to Mycobacterium spp.
Probab=17.63 E-value=88 Score=13.97 Aligned_cols=19 Identities=42% Similarity=0.600 Sum_probs=13.3
Q ss_pred EHHHHHHHHHHHHHHHHHH
Q ss_conf 0114899999999997766
Q gi|254781126|r 4 FVRDISCLRALVFVITRGV 22 (85)
Q Consensus 4 fvrdisclralvfvITR~~ 22 (85)
...|+|||.||.-|-..-+
T Consensus 50 ltadvsclkallevrdeiv 68 (101)
T pfam10904 50 LTADVSCLKALLEVRDEIV 68 (101)
T ss_pred HHCCHHHHHHHHHHHHHHH
T ss_conf 1212999999999899999
Done!