Query gi|254781157|ref|YP_003065570.1| hypothetical protein CLIBASIA_05320 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 85 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Mon May 30 05:20:38 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781157.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR01416 Rieske_proteo ubiqui 54.8 4.2 0.00011 21.3 0.4 10 65-74 154-163 (192) 2 PRK13755 putative mercury tran 35.3 19 0.00048 17.9 1.3 18 51-68 124-141 (141) 3 pfam09161 consensus 27.8 29 0.00075 16.9 1.2 27 31-57 32-58 (391) 4 cd03470 Rieske_cytochrome_bc1 27.6 21 0.00052 17.7 0.4 13 63-75 87-99 (126) 5 pfam10168 Nup88 Nuclear pore c 25.2 61 0.0016 15.2 2.5 32 3-34 504-537 (717) 6 KOG0556 consensus 24.2 52 0.0013 15.5 2.0 23 63-85 495-517 (533) 7 pfam09403 FadA Adhesion protei 20.7 65 0.0017 15.0 1.9 17 1-17 1-17 (126) 8 PRK04607 consensus 17.7 38 0.00098 16.2 0.1 12 62-73 294-305 (330) 9 PRK03877 consensus 16.7 41 0.0011 16.1 0.1 10 63-72 294-303 (328) 10 pfam01249 Ribosomal_S21e Ribos 15.9 53 0.0013 15.5 0.5 16 15-30 18-33 (81) No 1 >TIGR01416 Rieske_proteo ubiquinol-cytochrome c reductase, iron-sulfur subunit; InterPro: IPR006317 These sequences represent the Proteobacterial and mitochondrial type of the Rieske [2Fe-2S] iron-sulphur subunit as found in ubiquinol-cytochrome c reductase. Not included in this group are the Rieske iron-sulphur protein as found in the cytochrome b6-f complex of the Cyanobacteria and chloroplasts. Most members of this family have a recognizable twin-arginine translocation (tat) signal sequence (DeltaPh-dependent translocation in chloroplast) for transport across the membrane with the 2Fe-2S group already bound. These signal sequences include a motif resembling RRxFLK before the transmembrane helix. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0006118 electron transport. Probab=54.82 E-value=4.2 Score=21.32 Aligned_cols=10 Identities=60% Similarity=1.012 Sum_probs=7.7 Q ss_pred CCCCCCCCHH Q ss_conf 7334622456 Q gi|254781157|r 65 PDHGSKYDTR 74 (85) Q Consensus 65 pdhgskydtr 74 (85) |=|||+||+- T Consensus 154 PCHGS~yD~a 163 (192) T TIGR01416 154 PCHGSHYDLA 163 (192) T ss_pred CCCCCCCCCC T ss_conf 6888960555 No 2 >PRK13755 putative mercury transport protein MerC; Provisional Probab=35.34 E-value=19 Score=17.88 Aligned_cols=18 Identities=28% Similarity=0.604 Sum_probs=15.6 Q ss_pred CCCCCCCCCCCCCCCCCC Q ss_conf 555647874224897334 Q gi|254781157|r 51 VANKRCPNATKQTPPDHG 68 (85) Q Consensus 51 vankrcpnatkqtppdhg 68 (85) -++|||....-.+||.+| T Consensus 124 Pa~~rC~~~~c~~p~~~~ 141 (141) T PRK13755 124 PAHRRCGPDSCELPAKRG 141 (141) T ss_pred CCCCCCCCCCCCCCCCCC T ss_conf 632467988789986688 No 3 >pfam09161 consensus Probab=27.77 E-value=29 Score=16.85 Aligned_cols=27 Identities=33% Similarity=0.468 Sum_probs=21.3 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCC Q ss_conf 776665679999997301755556478 Q gi|254781157|r 31 EQKRKETTVGFISRLVNKRPVANKRCP 57 (85) Q Consensus 31 eqkrkettvgfisrlvnkrpvankrcp 57 (85) ..|--.+++.||..||+.||+...||- T Consensus 32 npkWL~~~~~firdLvssrPt~~gR~a 58 (391) T pfam09161 32 NPKWLPCTFSFIRDLVSSRPTPAGRAA 58 (391) T ss_pred CCCCHHHHHHHHHHHHHCCCCHHHHHH T ss_conf 997015799999998734988467789 No 4 >cd03470 Rieske_cytochrome_bc1 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including uni- and multi-cellular eukaryotes, plants (in their mitochondria) and bacteria. The cytochrome bc(1) and b6f complexes are central components of the respiratory and photosynthetic electron transport chains, respectively, which carry out similar core electron and proton transfer steps. The bc(1) and b6f complexes share a common core structure of three catalytic subunits: cyt b, the Rieske ISP, and either a cyt c1 in the bc(1) complex or cyt f in the b6f complex, which are arranged in an integral membrane-bound dimeric complex. While the core of the b6f complex is similar to that of the bc(1) complex, the domain arrangement outside the core and the complement of prosthetic groups are strikingly different. Probab=27.57 E-value=21 Score=17.68 Aligned_cols=13 Identities=46% Similarity=0.682 Sum_probs=9.4 Q ss_pred CCCCCCCCCCHHH Q ss_conf 8973346224566 Q gi|254781157|r 63 TPPDHGSKYDTRE 75 (85) Q Consensus 63 tppdhgskydtre 75 (85) --|=|||+||+-. T Consensus 87 ~CPCHGS~yD~aG 99 (126) T cd03470 87 FCPCHGSHYDASG 99 (126) T ss_pred ECCCCCCCCCCCC T ss_conf 0357687417888 No 5 >pfam10168 Nup88 Nuclear pore component. Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumour cells. Probab=25.19 E-value=61 Score=15.18 Aligned_cols=32 Identities=31% Similarity=0.385 Sum_probs=22.4 Q ss_pred HHHHHHHHHHHHHCCCCCE--ECCCCCHHHHHHH Q ss_conf 6799999999743258722--1354202457766 Q gi|254781157|r 3 KFVVRIMFLLSAISSNPIL--AANEHSSVSEQKR 34 (85) Q Consensus 3 kfvvrimfllsaissnpil--aanehssvseqkr 34 (85) -|...|--+|---++|||| .++..+|.+.|.. T Consensus 504 ~F~~~Ik~lL~R~~sqPIL~~~~dk~~sps~~E~ 537 (717) T pfam10168 504 SFEDHIRSILQRSVNNPILLRSADKDSSPPPEEC 537 (717) T ss_pred CHHHHHHHHHHCCCCCCHHHHCCCCCCCCCHHHH T ss_conf 7899999997267877421203677779998999 No 6 >KOG0556 consensus Probab=24.23 E-value=52 Score=15.55 Aligned_cols=23 Identities=43% Similarity=0.762 Sum_probs=17.1 Q ss_pred CCCCCCCCCCHHHHHHHHCCCCC Q ss_conf 89733462245668973605689 Q gi|254781157|r 63 TPPDHGSKYDTREVLMLFGGLNN 85 (85) Q Consensus 63 tppdhgskydtrevlmlfgglnn 85 (85) .||.-|.-..-..|.|||-||+| T Consensus 495 ~PPHaGgGIGLERvvmlyl~L~n 517 (533) T KOG0556 495 APPHAGGGIGLERVVMLYLGLNN 517 (533) T ss_pred CCCCCCCCCCHHHHHHHHHCCCC T ss_conf 99877875159999999816775 No 7 >pfam09403 FadA Adhesion protein FadA. FadA (Fusobacterium adhesin A) is an adhesin which forms two alpha helices. Probab=20.72 E-value=65 Score=15.02 Aligned_cols=17 Identities=35% Similarity=0.544 Sum_probs=15.1 Q ss_pred CHHHHHHHHHHHHHHCC Q ss_conf 92679999999974325 Q gi|254781157|r 1 MSKFVVRIMFLLSAISS 17 (85) Q Consensus 1 mskfvvrimfllsaiss 17 (85) |-||.+-+|.++|++|- T Consensus 1 MkK~ll~~~llls~~s~ 17 (126) T pfam09403 1 MKKILLCSMLILSSLSY 17 (126) T ss_pred CHHHHHHHHHHHHHHHH T ss_conf 91699999999999998 No 8 >PRK04607 consensus Probab=17.70 E-value=38 Score=16.25 Aligned_cols=12 Identities=33% Similarity=0.623 Sum_probs=7.3 Q ss_pred CCCCCCCCCCCH Q ss_conf 489733462245 Q gi|254781157|r 62 QTPPDHGSKYDT 73 (85) Q Consensus 62 qtppdhgskydt 73 (85) .|-||||.-||- T Consensus 294 RtS~dHGTa~dI 305 (330) T PRK04607 294 RTSVDHGTALEL 305 (330) T ss_pred EECCCCCCHHHH T ss_conf 778998704666 No 9 >PRK03877 consensus Probab=16.75 E-value=41 Score=16.06 Aligned_cols=10 Identities=50% Similarity=0.976 Sum_probs=5.6 Q ss_pred CCCCCCCCCC Q ss_conf 8973346224 Q gi|254781157|r 63 TPPDHGSKYD 72 (85) Q Consensus 63 tppdhgskyd 72 (85) |-||||.-|| T Consensus 294 tSpdHGta~d 303 (328) T PRK03877 294 TSVDHGTAFD 303 (328) T ss_pred ECCCCCCHHH T ss_conf 7899870566 No 10 >pfam01249 Ribosomal_S21e Ribosomal protein S21e. Probab=15.92 E-value=53 Score=15.52 Aligned_cols=16 Identities=31% Similarity=0.596 Sum_probs=13.6 Q ss_pred HCCCCCEECCCCCHHH Q ss_conf 3258722135420245 Q gi|254781157|r 15 ISSNPILAANEHSSVS 30 (85) Q Consensus 15 issnpilaanehssvs 30 (85) -.||.|++|.+|.||. T Consensus 18 SatNriI~AKDHaSvQ 33 (81) T pfam01249 18 SATNRLIGAKDHASVQ 33 (81) T ss_pred CCCCCCEECCCCCEEE T ss_conf 2227624047732378 Done!