Query gi|254781081|ref|YP_003065494.1| hypothetical protein CLIBASIA_04915 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 93 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Mon May 30 05:02:13 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781081.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 COG4634 Uncharacterized protei 37.0 17 0.00044 18.0 1.3 55 2-64 38-101 (113) 2 KOG3680 consensus 31.9 39 0.001 16.0 2.4 76 3-78 726-817 (830) 3 KOG1071 consensus 28.5 15 0.00039 18.2 -0.1 23 54-76 310-332 (340) 4 pfam05021 NPL4 NPL4 family. Th 26.2 41 0.0011 15.9 1.8 20 52-71 235-259 (306) 5 PRK09293 fructose-1,6-bisphosp 25.6 35 0.0009 16.3 1.3 14 62-75 238-251 (328) 6 cd04418 NDPk5 Nucleoside dipho 25.4 31 0.0008 16.5 1.0 29 62-90 98-126 (132) 7 pfam00316 FBPase Fructose-1-6- 23.6 42 0.0011 15.9 1.4 29 46-74 204-248 (325) 8 cd04414 NDPk6 Nucleoside dipho 22.3 38 0.00098 16.0 1.0 29 62-90 101-129 (135) 9 cd04416 NDPk_TX NDP kinase dom 19.4 41 0.001 15.9 0.6 29 62-90 99-127 (132) 10 cd04413 NDPk_I Nucleoside diph 18.7 59 0.0015 15.0 1.3 30 61-90 96-125 (130) No 1 >COG4634 Uncharacterized protein conserved in bacteria [Function unknown] Probab=37.01 E-value=17 Score=17.95 Aligned_cols=55 Identities=24% Similarity=0.183 Sum_probs=36.1 Q ss_pred CHHHHHHHHHHHEEEEEEEECCCCCC---------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 04678776410002467742046633---------2015778878864367786366889879999999998 Q gi|254781081|r 2 SEIMCEAYAEERYSVLLDLDFASDSD---------QITSDELSDLTQRYDYLLLNKHLLVDNLKSYLDKFGS 64 (93) Q Consensus 2 seimceayaeerysvlldldfasdsd---------qitsdelsdltqrydylllnkhllvdnlksyldkfgs 64 (93) -||+-.|++++|--|-.|.||+--+- +++...+|...+ ..+++-+|+.+.++|-+ T Consensus 38 ~EI~a~A~~~~~iivTkDsDF~~la~~~G~Ppki~wLr~gNvs~~~i--------e~l~~~~l~~~~e~le~ 101 (113) T COG4634 38 IEIWAYARRNNRIIVTKDSDFADLALTLGSPPKIVWLRCGNVSTREI--------EILIRSVLRAIGEELES 101 (113) T ss_pred HHHHHHHHHCCCEEEECCCCHHHHHHHCCCCCEEEEEEECCCCHHHH--------HHHHHHHHHHHHHHHHC T ss_conf 99999987569189971732899999708998589998368787999--------99999999999999838 No 2 >KOG3680 consensus Probab=31.89 E-value=39 Score=15.99 Aligned_cols=76 Identities=28% Similarity=0.299 Sum_probs=50.5 Q ss_pred HHHHHHHHHHHEEEEEEEECCCCCCCCCHH------HHHHHHHHHHHHHHHHH-----HH-----HHHHHHHHHHHHHHH Q ss_conf 467877641000246774204663320157------78878864367786366-----88-----987999999999898 Q gi|254781081|r 3 EIMCEAYAEERYSVLLDLDFASDSDQITSD------ELSDLTQRYDYLLLNKH-----LL-----VDNLKSYLDKFGSLI 66 (93) Q Consensus 3 eimceayaeerysvlldldfasdsdqitsd------elsdltqrydylllnkh-----ll-----vdnlksyldkfgsli 66 (93) +||-.-|...|--.-=|.-|+.|-+.-..| -|.-+-+||..-...+- .. ..+++|-+..+-+|- T Consensus 726 ~~iSaIY~~vrhrL~DdWafg~Dis~r~~D~Q~eE~~LrA~Ie~fn~RrY~~~~~~~~~~~~~a~~~~~~svlG~~~~l~ 805 (830) T KOG3680 726 KIISAIYLKVRHRLTDDWAFGNDISARPWDAQAEECALRALIEFFNSRRYDRAMESLYQFVIDAEMNCLQSVLGQRLSLP 805 (830) T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHCCCCCCCCHHHHHHHHHHHHCCCCCHH T ss_conf 89999999876515543010467787800446788999999999877642400021002210788766776640233246 Q ss_pred HHHHCCCCHHEE Q ss_conf 786207701323 Q gi|254781081|r 67 SDFHRNSESELV 78 (93) Q Consensus 67 sdfhrnseselv 78 (93) -+||+|.++-|- T Consensus 806 eyf~~ny~~wle 817 (830) T KOG3680 806 EYFHRNYESWLE 817 (830) T ss_pred HHHHHHHHHHHH T ss_conf 665543898888 No 3 >KOG1071 consensus Probab=28.51 E-value=15 Score=18.19 Aligned_cols=23 Identities=35% Similarity=0.501 Sum_probs=18.3 Q ss_pred HHHHHHHHHHHHHHHHHCCCCHH Q ss_conf 79999999998987862077013 Q gi|254781081|r 54 NLKSYLDKFGSLISDFHRNSESE 76 (93) Q Consensus 54 nlksyldkfgslisdfhrnsese 76 (93) ++|.|+|+++..|-||+|---.| T Consensus 310 tv~~~l~~~~~~V~DfvR~E~Ge 332 (340) T KOG1071 310 TVKEYLDPHNVSVVDFVRFEVGE 332 (340) T ss_pred HHHHHHCCCCCCHHHHHHHHHCC T ss_conf 48777366774068889988513 No 4 >pfam05021 NPL4 NPL4 family. The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterized step in ER-associated degradation after ubiquitination of target proteins but before their recognition by the 26S proteasome. Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing. Probab=26.23 E-value=41 Score=15.87 Aligned_cols=20 Identities=40% Similarity=0.640 Sum_probs=11.6 Q ss_pred HHHHHHHHHH-----HHHHHHHHHC Q ss_conf 9879999999-----9989878620 Q gi|254781081|r 52 VDNLKSYLDK-----FGSLISDFHR 71 (93) Q Consensus 52 vdnlksyldk-----fgslisdfhr 71 (93) ...|++||.+ +...+||||- T Consensus 235 ~~~l~~yl~~~~~~~~~~~~sdFHl 259 (306) T pfam05021 235 LRALAKYLKSHKPKPFLERLSDFHL 259 (306) T ss_pred HHHHHHHHHHHCCCCHHHHHCCHHH T ss_conf 9999999986079726661024131 No 5 >PRK09293 fructose-1,6-bisphosphatase; Provisional Probab=25.61 E-value=35 Score=16.25 Aligned_cols=14 Identities=36% Similarity=0.589 Sum_probs=10.8 Q ss_pred HHHHHHHHHCCCCH Q ss_conf 99898786207701 Q gi|254781081|r 62 FGSLISDFHRNSES 75 (93) Q Consensus 62 fgslisdfhrnses 75 (93) .||++.||||+-.- T Consensus 238 ~gslVaD~hr~L~~ 251 (328) T PRK09293 238 IGSMVADVHRILLK 251 (328) T ss_pred ECCHHHHHHHHHHC T ss_conf 23224888999761 No 6 >cd04418 NDPk5 Nucleoside diphosphate kinase homolog 5 (NDP kinase homolog 5, NDPk5, NM23-H5; Inhibitor of p53-induced apoptosis-beta, IPIA-beta): In human, mRNA for NDPk5 is almost exclusively found in testis, especially in the flagella of spermatids and spermatozoa, in association with axoneme microtubules, and may play a role in spermatogenesis by increasing the ability of late-stage spermatids to eliminate reactive oxygen species. It belongs to the nm23 Group II genes and appears to differ from the other human NDPks in that it lacks two important catalytic site residues, and thus does not appear to possess NDP kinase activity. NDPk5 confers protection from cell death by Bax and alters the cellular levels of several antioxidant enzymes, including glutathione peroxidase 5 (Gpx5). Probab=25.45 E-value=31 Score=16.52 Aligned_cols=29 Identities=28% Similarity=0.188 Sum_probs=23.3 Q ss_pred HHHHHHHHHCCCCHHEEEECCCCHHHHHH Q ss_conf 99898786207701323204542056652 Q gi|254781081|r 62 FGSLISDFHRNSESELVRCSDSESEEAKE 90 (93) Q Consensus 62 fgslisdfhrnseselvrcsdseseeake 90 (93) -||+-.+|-.......|.||||.....+| T Consensus 98 P~siR~~fg~~~~~N~vH~Sds~e~A~~E 126 (132) T cd04418 98 PDSLRAIYGTDDLRNAVHGSDSFSSAERE 126 (132) T ss_pred CCCHHHHHCCCCCCCCEECCCCHHHHHHH T ss_conf 99859983899776795888999999999 No 7 >pfam00316 FBPase Fructose-1-6-bisphosphatase. Probab=23.59 E-value=42 Score=15.85 Aligned_cols=29 Identities=28% Similarity=0.413 Sum_probs=18.1 Q ss_pred HHHHHHHHHHHHHHHH----------------HHHHHHHHHCCCC Q ss_conf 6366889879999999----------------9989878620770 Q gi|254781081|r 46 LNKHLLVDNLKSYLDK----------------FGSLISDFHRNSE 74 (93) Q Consensus 46 lnkhllvdnlksyldk----------------fgslisdfhrnse 74 (93) .|..-.-+.++.|++. .||++.||||+-- T Consensus 204 ~n~~~w~~~~~~yi~~~~~~~~~~~k~y~~Ry~GsmVaD~HR~L~ 248 (325) T pfam00316 204 GNYRHWDPPVRKYIDDCKAGAEGPRRPYNMRYIGSMVADVHRILL 248 (325) T ss_pred CCHHHCCHHHHHHHHHHHCCCCCCCCCCCEEEECCHHHHHHHHHH T ss_conf 003323688999999986557677887433442321588999987 No 8 >cd04414 NDPk6 Nucleoside diphosphate kinase 6 (NDP kinase 6, NDPk6, NM23-H6; NME6; Inhibitor of p53-induced apoptosis-alpha, IPIA-alpha): The nm23-H6 gene encoding NDPk6 is expressed mainly in mitochondria, but also found at a lower level in most tissues. NDPk6 has all nine residues considered crucial for enzyme structure and activity, and has been found to have NDP kinase activity. It may play a role in cell growth and cell cycle progression. The nm23-H6 gene locus has been implicated in a variety of malignant tumors. Probab=22.27 E-value=38 Score=16.04 Aligned_cols=29 Identities=17% Similarity=0.138 Sum_probs=23.2 Q ss_pred HHHHHHHHHCCCCHHEEEECCCCHHHHHH Q ss_conf 99898786207701323204542056652 Q gi|254781081|r 62 FGSLISDFHRNSESELVRCSDSESEEAKE 90 (93) Q Consensus 62 fgslisdfhrnseselvrcsdseseeake 90 (93) -||+-.+|-.+.-...|.||||..+-.+| T Consensus 101 P~tIR~~fg~~~~~N~vHgSds~e~A~rE 129 (135) T cd04414 101 PDSIRGLYGLTDTRNATHGSDSPASAQRE 129 (135) T ss_pred CCCHHHHHCCCCCCCCEECCCCHHHHHHH T ss_conf 99719984787766084388999999999 No 9 >cd04416 NDPk_TX NDP kinase domain of thioredoxin domain-containing proteins (TXNDC3 and TXNDC6): Txl-2 (TXNDC6) and Sptrx-2 (TXNDC3) are fusion proteins of Group II N-terminal thioredoxin domains followed by one or three NDP kinase domains, respectively. Sptrx-2, which has a tissue specific distribution in human testis, has been considered as a member of the nm23 family (nm23-H8) and exhibits a high homology with sea urchin IC1 (intermediate chain-1) protein, a component of the sperm axonemal outer dynein arm complex. Txl-2 is mainly represented in close association with microtubules within tissues with cilia and flagella such as seminiferous epithelium (spermatids) and lung airway epithelium, suggesting possible role in control of microtubule stability and maintenance. Probab=19.43 E-value=41 Score=15.89 Aligned_cols=29 Identities=38% Similarity=0.365 Sum_probs=22.8 Q ss_pred HHHHHHHHHCCCCHHEEEECCCCHHHHHH Q ss_conf 99898786207701323204542056652 Q gi|254781081|r 62 FGSLISDFHRNSESELVRCSDSESEEAKE 90 (93) Q Consensus 62 fgslisdfhrnseselvrcsdseseeake 90 (93) -||+-.+|-.+.....|.||||...-.+| T Consensus 99 P~siR~~fg~~~~~N~vH~SDs~e~A~rE 127 (132) T cd04416 99 PDSLRAQFARDHLSNAVHGSSSAEEAEKE 127 (132) T ss_pred CCCCHHHHCCCCCCCCEECCCCHHHHHHH T ss_conf 99878885688675695889999999999 No 10 >cd04413 NDPk_I Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside triphosphate (NTP) donor onto a nucleoside diphosphate (NDP) acceptor through a phosphohistidine intermediate. The mammalian nm23/NDP kinase gene family can be divided into two distinct groups. The group I genes encode proteins that generally have highly homologous counterparts in other organisms and possess the classic enzymatic activity of a kinase. This group includes vertebrate NDP kinases A-D (Nm23- H1 to -H4), and its counterparts in bacteria, archea and other eukaryotes. NDP kinases exist in two different quaternary structures; all known eukaryotic enzymes are hexamers, while some bacterial enzymes are tetramers, as in Myxococcus. They possess the NDP kinase active site motif (NXXH[G/A]SD) and the nine residues that Probab=18.71 E-value=59 Score=15.03 Aligned_cols=30 Identities=27% Similarity=0.347 Sum_probs=23.6 Q ss_pred HHHHHHHHHHCCCCHHEEEECCCCHHHHHH Q ss_conf 999898786207701323204542056652 Q gi|254781081|r 61 KFGSLISDFHRNSESELVRCSDSESEEAKE 90 (93) Q Consensus 61 kfgslisdfhrnseselvrcsdseseeake 90 (93) +-||+-.+|-.+.....|.||||...-.+| T Consensus 96 ~p~siR~~fg~~~~~NavHgSDs~e~A~~E 125 (130) T cd04413 96 APGTIRGDFALSIGRNIVHGSDSVESAERE 125 (130) T ss_pred CCCCHHHHHCCCCCCCCEECCCCHHHHHHH T ss_conf 973146773787564794788999999999 Done!