Query gi|254780645|ref|YP_003065058.1| hypothetical protein CLIBASIA_02660 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 91
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Sun May 29 20:42:32 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780645.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1537 PelA Predicted RNA-bin 46.6 5.7 0.00015 21.7 0.1 63 23-90 19-82 (352)
2 KOG0188 consensus 42.1 24 0.0006 18.2 2.6 61 16-83 338-405 (895)
3 KOG3925 consensus 38.2 14 0.00037 19.4 1.1 73 1-82 1-89 (371)
4 pfam10921 DUF2710 Protein of u 22.9 50 0.0013 16.3 1.7 18 44-61 14-31 (109)
5 TIGR00111 pelota probable tran 21.0 6.2 0.00016 21.5 -3.3 25 25-49 23-47 (381)
6 TIGR02035 D_Ser_am_lyase D-ser 20.7 35 0.00089 17.2 0.5 16 61-76 101-116 (431)
7 smart00806 AIP3 Actin interact 19.5 91 0.0023 14.8 3.2 48 10-62 147-194 (426)
8 cd00736 bacteriophage_lambda_l 15.6 78 0.002 15.2 1.3 19 50-69 113-131 (151)
9 TIGR00570 cdk7 CDK-activating 14.2 1.2E+02 0.0031 14.0 2.6 54 2-55 258-316 (322)
10 pfam08446 PAS_2 PAS fold. The 13.8 64 0.0016 15.7 0.5 11 59-69 2-12 (107)
No 1
>COG1537 PelA Predicted RNA-binding proteins [General function prediction only]
Probab=46.62 E-value=5.7 Score=21.70 Aligned_cols=63 Identities=35% Similarity=0.310 Sum_probs=34.5
Q ss_pred CHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHH-CCCCCCCCCEECCCCCCCCCCCCEEEEEEC
Q ss_conf 25668999998300411013456788999999863000-030167542001120023356530688722
Q gi|254780645|r 23 LQKDLNHIRQIINEGDFKSAAVKMRILVESFLRKLSEK-ESISIPGSIKARKNCWNLSTSTGAYLRIRG 90 (91)
Q Consensus 23 lqkdlnhirqiinegdfksaavkmrilvesflrklsek-esisipgsikarkncwnlststgaylrirg 90 (91)
-+.||-|+++||.+||.-+|...-| .++--.-.+.+ |-+.+-=.||.-+--+.. - ..+|||.|
T Consensus 19 ~lDDLw~L~~Ii~~GD~v~a~T~Rr--~~~~d~~r~~~~eri~m~L~IkVe~ieF~~--f-~nrLRi~G 82 (352)
T COG1537 19 TLDDLWHLYNIIEKGDKVFAKTTRR--DESSDVIRSKKGERIPMTLGIKVEKIEFDK--F-ANRLRIKG 82 (352)
T ss_pred CHHHHHHHHHHCCCCCEEEEEEEEE--CCCCCCCCCCCCEEEEEEEEEEEEEEEEEE--C-CCEEEEEE
T ss_conf 7577889987447897899999871--223565456763489999999987777430--2-66899998
No 2
>KOG0188 consensus
Probab=42.10 E-value=24 Score=18.17 Aligned_cols=61 Identities=38% Similarity=0.611 Sum_probs=44.2
Q ss_pred HHHHHCC-----CHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCCCCCCCC
Q ss_conf 3565307-----2566899999830041--101345678899999986300003016754200112002335653
Q gi|254780645|r 16 QVKENLG-----LQKDLNHIRQIINEGD--FKSAAVKMRILVESFLRKLSEKESISIPGSIKARKNCWNLSTSTG 83 (91)
Q Consensus 16 qvkenlg-----lqkdlnhirqiinegd--fksaavkmrilvesflrklsekesisipgsikarkncwnlststg 83 (91)
-|-+.|| |++|-.||+.||||-. |...--+-|-+.+.+++.+.. |-.|||. ..|+|...-|
T Consensus 338 vvv~~lgd~fPEl~~~~~~v~diineEE~~F~ktl~rg~~~f~r~~~~~~~--s~tipGd-----~~w~LydTyG 405 (895)
T KOG0188 338 VVVETLGDAFPELKRDPQHVIDIINEEEAQFLKTLDRGRKLFDRVARELGS--SKTIPGD-----VAWRLYDTYG 405 (895)
T ss_pred HHHHHHHHHCHHHHCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHCCC--CCCCCHH-----HHHHHHHHCC
T ss_conf 999987554544422878999874679999999998889999999986688--8867617-----8777776128
No 3
>KOG3925 consensus
Probab=38.20 E-value=14 Score=19.40 Aligned_cols=73 Identities=30% Similarity=0.268 Sum_probs=41.2
Q ss_pred CCCCCCCCCCCCCCHH------HHHH------CCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHH----HHHCCCC
Q ss_conf 9754588742222113------5653------0725668999998300411013456788999999863----0000301
Q gi|254780645|r 1 MHYDFTPPSKKSKGAQ------VKEN------LGLQKDLNHIRQIINEGDFKSAAVKMRILVESFLRKL----SEKESIS 64 (91)
Q Consensus 1 mhydftppskkskgaq------vken------lglqkdlnhirqiinegdfksaavkmrilvesflrkl----sekesis 64 (91)
||-|-.|+.++++|-. +||. .-.++.|.|-++++++.. |--..++-..+. .-.-||.
T Consensus 1 ~~~~~~~~~~~~~~i~~k~~~~~~eek~~~~~~~k~~klk~e~~~~kqae-------~~~~~k~e~~~~~~~~~~t~SIa 73 (371)
T KOG3925 1 MRGDKRPCGKGENGIRHKWKQQKKEEKKKWKVKKKEKKLKKEEKQAKQAE-------EAGKAKSEKEKKDESRPYTYSIA 73 (371)
T ss_pred CCCCCCCCCCCCCCCCHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHCCCCCCCEEEEEE
T ss_conf 98766788876566224555417688877776667888888998888898-------87677766641688896689997
Q ss_pred CCCCCEECCCCCCCCCCC
Q ss_conf 675420011200233565
Q gi|254780645|r 65 IPGSIKARKNCWNLSTST 82 (91)
Q Consensus 65 ipgsikarkncwnlstst 82 (91)
|||||- .||-||+--|
T Consensus 74 iPgsil--~n~~nlel~T 89 (371)
T KOG3925 74 IPGSIL--NNAQNLELAT 89 (371)
T ss_pred ECHHHH--HHHHHHHHHH
T ss_conf 256787--6533267777
No 4
>pfam10921 DUF2710 Protein of unknown function (DUF2710). This family of proteins with unknown function appears to be restricted to Mycobacteriaceae.
Probab=22.94 E-value=50 Score=16.29 Aligned_cols=18 Identities=50% Similarity=0.551 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHHHHHHHC
Q ss_conf 567889999998630000
Q gi|254780645|r 44 VKMRILVESFLRKLSEKE 61 (91)
Q Consensus 44 vkmrilvesflrklseke 61 (91)
..-+-+|||.||.|||..
T Consensus 14 lsdkdlvesvlr~lseaa 31 (109)
T pfam10921 14 LSDKDLVESVLRDLSEAA 31 (109)
T ss_pred CCHHHHHHHHHHHHHHHH
T ss_conf 662889999999999988
No 5
>TIGR00111 pelota probable translation factor pelota; InterPro: IPR004405 The Drosophila melanogaster protein pelota is proposed to act in protein translation. It can replace the budding yeast protein DOM34, and is closely related to a set of archaeal proteins. This family contains a proposed RNA binding motif, and is homologous to a family of peptide chain release factors. In Drosophila melanogaster it is required prior to the first meiotic division for spindle formation and nuclear envelope breakdown during spermatogenesis. It is also required for normal eye patterning and for mitotic divisions in the ovary. The meiotic defect in pelota mutants may be a complex result of a protein translation defect, as suggested in yeast by ribosomal protein RPS30A being a multicopy suppressor, and by an altered polyribosome profile in DOM34 mutants rescued by RPS30A.; GO: 0006412 translation, 0005634 nucleus.
Probab=21.04 E-value=6.2 Score=21.50 Aligned_cols=25 Identities=44% Similarity=0.567 Sum_probs=20.5
Q ss_pred HHHHHHHHHHCCCCCCHHHHHHHHH
Q ss_conf 6689999983004110134567889
Q gi|254780645|r 25 KDLNHIRQIINEGDFKSAAVKMRIL 49 (91)
Q Consensus 25 kdlnhirqiinegdfksaavkmril 49 (91)
.||-|++|||.+||.-+|.-+-|+-
T Consensus 23 dDLw~l~~Iie~gD~~~a~t~r~~q 47 (381)
T TIGR00111 23 DDLWHLYQIIEKGDVVFAVTKRRVQ 47 (381)
T ss_pred CCCEEEEEEEECCCEEEEEEEEEEC
T ss_conf 1103575457438779998510101
No 6
>TIGR02035 D_Ser_am_lyase D-serine ammonia-lyase; InterPro: IPR011780 This family consists of D-serine ammonia-lyases, pyridoxal-phosphate enzymes that convert D-serine to pyruvate and NH3. These enzyme are also called D-serine dehydratase and D-serine deaminase and was previously designated 4.2.1.14 from EC. It is homologous to an enzyme that acts on threonine and may itself act weakly on threonine.; GO: 0008721 D-serine ammonia-lyase activity, 0030170 pyridoxal phosphate binding, 0046416 D-amino acid metabolic process.
Probab=20.68 E-value=35 Score=17.18 Aligned_cols=16 Identities=44% Similarity=0.688 Sum_probs=11.6
Q ss_pred CCCCCCCCCEECCCCC
Q ss_conf 0301675420011200
Q gi|254780645|r 61 ESISIPGSIKARKNCW 76 (91)
Q Consensus 61 esisipgsikarkncw 76 (91)
....|-||||||--.+
T Consensus 101 shLPisGSIKARGGiY 116 (431)
T TIGR02035 101 SHLPISGSIKARGGIY 116 (431)
T ss_pred CCCCCCCCEECCCCHH
T ss_conf 6788443110465077
No 7
>smart00806 AIP3 Actin interacting protein 3. Aip3p/Bud6p is a regulator of cell and cytoskeletal polarity in Saccharomyces cerevisiae that was previously identified as an actin-interacting protein. Actin-interacting protein 3 (Aip3p) localizes at the cell cortex where cytoskeleton assembly must be achieved to execute polarized cell growth, and deletion of AIP3 causes gross defects in cell and cytoskeletal polarity. Aip3p localization is mediated by the secretory pathway, mutations in early- or late-acting components of the secretory apparatus lead to Aip3p mislocalization PUBMED:10679021.
Probab=19.49 E-value=91 Score=14.80 Aligned_cols=48 Identities=25% Similarity=0.268 Sum_probs=29.4
Q ss_pred CCCCCHHHHHHCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 22221135653072566899999830041101345678899999986300003
Q gi|254780645|r 10 KKSKGAQVKENLGLQKDLNHIRQIINEGDFKSAAVKMRILVESFLRKLSEKES 62 (91)
Q Consensus 10 kkskgaqvkenlglqkdlnhirqiinegdfksaavkmrilvesflrklsekes 62 (91)
.+..+.+.+|--.|+.||.-+||+-++. ++ .+.-.+.+++.|+..-.+
T Consensus 147 ~~~~~~~~~el~~lrrdLavlrQ~~~~~--~~---~i~~sm~~i~~k~~~~k~ 194 (426)
T smart00806 147 DKLNKEQRAELKSLQRELAVLRQTHNSF--FT---EIKESIKDILEKIDKFKS 194 (426)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHH--HH---HHHHHHHHHHHHHHHHHH
T ss_conf 4443555999999999999999999988--98---999999999999999988
No 8
>cd00736 bacteriophage_lambda_lysozyme The lysozyme from bacteriophage lambda hydrolyses the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc), as do other lysozymes. But unlike other lysozymes, bacteriophage lambda does not produce a reducing end upon cleavage of the peptidoglycan but rather uses the 6-OH of the same MurNAc residue to produce a 1,6-anhydromuramic acid terminal residue and is therefore a lytic transglycosylase. An identical 1,6-anhydro bond is formed in bacterial peptidoglycans by the action of the lytic transglycosylases of E. coli. However, they differ structurally.
Probab=15.62 E-value=78 Score=15.17 Aligned_cols=19 Identities=37% Similarity=0.459 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHCCCCCCCCC
Q ss_conf 99999863000030167542
Q gi|254780645|r 50 VESFLRKLSEKESISIPGSI 69 (91)
Q Consensus 50 vesflrklsekesisipgsi 69 (91)
.+..+.||+- |=-|+|||-
T Consensus 113 ~~~ai~kl~~-~WASlPgs~ 131 (151)
T cd00736 113 IEQAIAKLSN-IWASLPGAG 131 (151)
T ss_pred HHHHHHHHCC-CCCCCCCCC
T ss_conf 9999998421-101589877
No 9
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1; InterPro: IPR004575 MAT1 (menage a trois 1) is a RING finger protein with a characteristic C3HC4 motif located in the N-terminal domain. MAT1 stabilises the cyclin H-CDK7 complex to form a functional CDK-activating kinase (CAK) enzymatic complex which then goes on to activate many of the CDK enzymes intimately involved in the cell cycle . CDK7 forms a stable complex with cyclin H and MAT1 in vivo only when phosphorylated on either one of two residues (Ser164 or Thr170) in its T-loop. The requirement for MAT1 for the activation of CAK can be by-passed by the phosphorylation of CDK7 on the T-loop. The two mechanisms for CDK7 complex stabilisation and activation (MAT1 addition and T-loop phosphorylation), which can operate independently in vitro, actually cooperate under physiological conditions to maintain complex integrity. With prolonged exposure to elevated temperature, dissociation to monomeric subunits occurs in vivo when CDK7 is dephosphorylated, even in the presence of MAT1 . The Cyclin H-MAT1-CDK7 complex also forms part of TFIIH, a multiprotein complex required for both transcription and DNA repair.; GO: 0007049 cell cycle, 0005634 nucleus.
Probab=14.20 E-value=1.2e+02 Score=14.03 Aligned_cols=54 Identities=31% Similarity=0.446 Sum_probs=42.3
Q ss_pred CCCCCCCCCCCCCHHHH--HHCCCHHHHHHHHHHH---CCCCCCHHHHHHHHHHHHHHH
Q ss_conf 75458874222211356--5307256689999983---004110134567889999998
Q gi|254780645|r 2 HYDFTPPSKKSKGAQVK--ENLGLQKDLNHIRQII---NEGDFKSAAVKMRILVESFLR 55 (91)
Q Consensus 2 hydftppskkskgaqvk--enlglqkdlnhirqii---negdfksaavkmrilvesflr 55 (91)
-|.|+|-.-.+-|.++- +.++-+.-++|+|.-- +.|.|.|+-.-.|.|-|.|--
T Consensus 258 l~~Y~P~~~~~~gP~~P~~~~~~~~~Y~~hvr~~~pq~~AgGy~~~lAc~RaLqeAf~G 316 (322)
T TIGR00570 258 LFEYEPLNIETEGPQVPTLEELVRQGYLNHVRAASPQDIAGGYTSNLACERALQEAFSG 316 (322)
T ss_pred CCCCCCCCCCCCCCCCCCCCHHCCCCHHHHHHHHCCCHHHCCHHHHHHHHHHHHHHHHC
T ss_conf 50115656455678888600000124024435416510203135789999999998511
No 10
>pfam08446 PAS_2 PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.
Probab=13.85 E-value=64 Score=15.66 Aligned_cols=11 Identities=45% Similarity=0.519 Sum_probs=0.0
Q ss_pred HHCCCCCCCCC
Q ss_conf 00030167542
Q gi|254780645|r 59 EKESISIPGSI 69 (91)
Q Consensus 59 ekesisipgsi 69 (91)
++|-|.|||+|
T Consensus 2 drEPIHipG~I 12 (107)
T pfam08446 2 YLEPIQRPGLI 12 (107)
T ss_pred CCCCCCCCCCC
T ss_conf 75555567844
Done!