Query gi|254781009|ref|YP_003065422.1| hypothetical protein CLIBASIA_04555 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 750 No_of_seqs 168 out of 175 Neff 5.1 Searched_HMMs 39220 Date Mon May 30 03:20:59 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781009.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 pfam06748 DUF1217 Protein of u 100.0 0 0 360.1 14.7 150 533-688 1-150 (150) 2 pfam06748 DUF1217 Protein of u 100.0 2.7E-41 0 265.4 10.6 138 61-198 1-150 (150) 3 PHA00368 internal virion prote 85.7 1.9 4.8E-05 21.1 4.9 94 488-584 689-809 (1316) 4 TIGR01083 nth endonuclease III 69.9 3 7.6E-05 19.9 1.9 66 616-695 100-165 (192) 5 TIGR01259 comE comEA protein; 63.7 6 0.00015 18.1 2.5 21 502-522 86-106 (124) 6 PRK07209 ribonucleotide-diphos 49.3 16 0.00042 15.5 6.3 61 391-452 168-258 (391) 7 KOG1961 consensus 48.4 17 0.00043 15.4 9.5 149 423-578 436-608 (683) 8 KOG3543 consensus 45.5 19 0.00048 15.1 4.7 24 150-173 203-226 (1218) 9 COG4342 Uncharacterized protei 43.3 20 0.00052 14.9 3.5 47 509-556 69-115 (291) 10 PRK10852 thiosulfate transport 42.7 21 0.00053 14.8 3.8 25 392-417 165-189 (338) 11 COG3814 Uncharacterized protei 42.4 13 0.00034 16.0 1.4 17 155-171 8-24 (157) 12 pfam08566 Pam17 Mitochondrial 41.3 5.8 0.00015 18.2 -0.6 26 504-529 143-168 (174) 13 PRK10363 cpxP periplasmic repr 34.4 28 0.00071 14.1 3.1 58 656-713 98-155 (166) 14 pfam06599 DUF1139 Protein of u 33.3 28 0.00073 14.0 1.9 26 392-417 283-308 (309) 15 PRK11904 bifunctional proline 33.2 29 0.00074 14.0 1.9 48 383-434 430-486 (1026) 16 pfam10875 DUF2670 Protein of u 29.5 32 0.00083 13.7 1.7 32 632-664 20-51 (139) 17 PRK08032 fliD flagellar cappin 28.2 33 0.00085 13.6 1.6 27 664-697 418-444 (463) 18 pfam01216 Calsequestrin Calseq 27.8 36 0.00093 13.4 2.4 52 645-696 292-346 (350) 19 TIGR01830 3oxo_ACP_reduc 3-oxo 27.6 37 0.00093 13.4 3.1 142 513-702 56-225 (238) 20 pfam07147 PDCD9 Mitochondrial 27.3 22 0.00057 14.7 0.5 74 2-83 31-115 (423) 21 PRK11779 sbcB exonuclease I; P 25.0 34 0.00088 13.5 1.2 36 540-575 373-408 (477) 22 KOG0917 consensus 24.6 42 0.0011 13.0 3.6 40 512-551 292-331 (338) 23 TIGR02793 nikR nickel-responsi 24.1 29 0.00073 14.0 0.6 26 6-31 56-84 (130) 24 pfam07304 SRA1 Steroid recepto 23.7 43 0.0011 12.9 2.2 45 663-708 68-112 (157) 25 PRK07737 fliD flagellar cappin 21.8 44 0.0011 12.9 1.2 27 664-697 453-479 (502) No 1 >pfam06748 DUF1217 Protein of unknown function (DUF1217). This family represents a conserved region that is found within bacterial proteins, most of which are hypothetical. Some members contain multiple copies. Probab=100.00 E-value=0 Score=360.12 Aligned_cols=150 Identities=33% Similarity=0.566 Sum_probs=145.4 Q ss_pred HCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 54888544128999999622788855777521647899999761877657655677432245667999999999877888 Q gi|254781009|r 533 SKGIDSQKVREDFLCEIFKSDLKDPKSFANTYKDNRYKEIISSFNFDIHGELSHKKIGKVQDNFHIDDTCDLYKHQMIEK 612 (750) Q Consensus 533 AfGL~~~~~~~~~i~kvL~sd~~d~~slaN~l~D~ry~~la~aF~F~~~G~~~~~~~~~~q~~~~~~~i~d~Y~~qs~E~ 612 (750) ||||+++++++++|||||+||++||+||||+|+|+||++|+++|||+++|.. .+|+.+++.+|+++|++|+||. T Consensus 1 AfGLed~~~~ka~ikkvL~sd~~d~~S~aN~L~D~Ry~~lA~AF~F~~~g~~------~~q~~~~~~~iv~~Y~~~~~E~ 74 (150) T pfam06748 1 AFGLEDMIYAKAFIKKVLESDLSDPDSFANKLSDKRYREFAAAFNFGADGTL------ATQTAAQTQATVDKYLRQSLEE 74 (150) T ss_pred CCCCHHHHCCHHHHHHHHHCCCCCHHHHHHHCCCHHHHHHHHHHCCCCCCCC------CCCCHHHHHHHHHHHHHHHHHH T ss_conf 9994010220899999981599972789987088999999998489988875------4367889999999999999999 Q ss_pred HHHCCCHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHHHHHCCCHHHHCCCHHHHHHHHHHHCCHHHCCCHHHHH Q ss_conf 7300385469999998632550029987277899999999704867663199999999999621978649989999 Q gi|254781009|r 613 KEEEKDPNIALALYFKRTIPNIRNHYEILGDSKLFKVVSKKLKLSPYFAVLPERKKIRILKKHIKINDFKDSKKVE 688 (750) Q Consensus 613 ~~Ge~n~gvRLALyF~R~a~~Its~y~ILgD~aL~~V~~TAlgLP~~~a~~DiDkQa~li~~k~Di~dl~DP~kv~ 688 (750) ++|++|+||||||||+|++|+|+|||+||||++|++||+||||||++|+++|||||+++|++|+||++|+||++|+ T Consensus 75 ~~g~~n~~~rlALyf~r~~~~its~~~iL~d~~L~~v~~talgLp~~~~~~did~Q~~~i~~~ld~sdl~DP~~v~ 150 (150) T pfam06748 75 AAGEQNEGVRLALYFRRKAGTITSAYDILADPALREVALTALGLPSSVSALDIDKQAELIKKKLDLSDLSDPKSVV 150 (150) T ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCHHHCCCCHHHHHHHHHHHCCHHHCCCCCCCC T ss_conf 9735577799999999971778569999878889999999929997762489999999999852787548930129 No 2 >pfam06748 DUF1217 Protein of unknown function (DUF1217). This family represents a conserved region that is found within bacterial proteins, most of which are hypothetical. Some members contain multiple copies. Probab=100.00 E-value=2.7e-41 Score=265.40 Aligned_cols=138 Identities=33% Similarity=0.546 Sum_probs=129.1 Q ss_pred HCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHCCCHHHHHHHHHCCCCCC-CCCCCCHHHHHHHHHHH-HHHHHHHHCCCC Q ss_conf 7597244105999999982689983301332066899999998187877-76442036788998877-876775301221 Q gi|254781009|r 61 AFGLSDMSHAEKFIKKILESDLSDPKSLVNQLNSLKYQYFARSYDFSPP-PKVIQSDIQHKTIIQDY-KQSHQHKEEVAL 138 (750) Q Consensus 61 A~GLedm~~aka~~kKVLesd~~D~~s~aNkL~D~Ry~~fA~af~F~~~-~~~~~~~~~~~~~i~~y-~~~~~~~~~~~~ 138 (750) |||||||+|+|+|||||||||++||+||||||+|+||++||++|||+++ +..+|+..+++.++++| .++++...+.++ T Consensus 1 AfGLed~~~~ka~ikkvL~sd~~d~~S~aN~L~D~Ry~~lA~AF~F~~~g~~~~q~~~~~~~iv~~Y~~~~~E~~~g~~n 80 (150) T pfam06748 1 AFGLEDMIYAKAFIKKVLESDLSDPDSFANKLSDKRYREFAAAFNFGADGTLATQTAAQTQATVDKYLRQSLEEAAGEQN 80 (150) T ss_pred CCCCHHHHCCHHHHHHHHHCCCCCHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 99940102208999999815999727899870889999999984899888754367889999999999999999973557 Q ss_pred HHHH---HHHHHCCCCCCHHHHHCCHHHHHHHHHHCCCCHHHCCHH------HHHHHH-CCCCCCCHHHH Q ss_conf 0458---898511345899997243899999999739872120389------998874-18877700233 Q gi|254781009|r 139 EESK---YFRKNIHKINSVDQLFKDRRLLDYVLQSFSITPKYISLP------FLKDVL-TLGLANPKKYF 198 (750) Q Consensus 139 ~~~~---Yf~~~~~~ItsvddLL~D~~L~~vv~tAfGL~~~~~s~~------~lk~vL-tsD~sDp~S~~ 198 (750) ++++ ||+|++++|+++|+||+|++|++||+||||||+++...+ ++++.| .+|++||.+++ T Consensus 81 ~~~rlALyf~r~~~~its~~~iL~d~~L~~v~~talgLp~~~~~~did~Q~~~i~~~ld~sdl~DP~~v~ 150 (150) T pfam06748 81 EGVRLALYFRRKAGTITSAYDILADPALREVALTALGLPSSVSALDIDKQAELIKKKLDLSDLSDPKSVV 150 (150) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCHHHCCCCHHHHHHHHHHHCCHHHCCCCCCCC T ss_conf 7799999999971778569999878889999999929997762489999999999852787548930129 No 3 >PHA00368 internal virion protein D Probab=85.66 E-value=1.9 Score=21.07 Aligned_cols=94 Identities=17% Similarity=0.292 Sum_probs=49.7 Q ss_pred CCCCHHHHHHHHHHHHH-HHHHHHCCCCCCHHHHHCCHHHHHHHH-HHCCCCHH--------------------HHHHHH Q ss_conf 11102456678889899-999974156678999941489999998-75488854--------------------412899 Q gi|254781009|r 488 EQISTQKRINLEINSEV-DYYTLNINTIHSFEELLANKRILNFLL-ESKGIDSQ--------------------KVREDF 545 (750) Q Consensus 488 ~~~~~~~~~~~~~~~e~-~yf~~~i~~i~s~~dll~D~rl~~~aL-~AfGL~~~--------------------~~~~~~ 545 (750) --|-+..+.++.|...+ +|+.+.++. ++.+.+.- .+-.+|+ +|||+.-. -++--. T Consensus 689 ~SWltSY~sRpeVKaRvDe~lkE~~g~--~v~evt~e-~VekyA~dKAYGIShTd~F~~Ssvieeni~glvGiEnN~FLE 765 (1316) T PHA00368 689 KSWLTSYRSRPEVKARVDEYLKELLGI--DVKEVTPE-MVEKYAMDKAYGISHTDQFTRSSVIEENIEGLVGIENNSFLE 765 (1316) T ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHCC--CHHHHHHH-HHHHHHHHHHCCCCCHHCCCCCHHHHCCCHHHHCCCCCCHHH T ss_conf 999887302446899999999987363--41667699-999986411116661210341025541321331445540777 Q ss_pred HHHHHHCCCC-----CHHHHHHHCCCHHHHHHHHHCCCCCCCCC Q ss_conf 9999622788-----85577752164789999976187765765 Q gi|254781009|r 546 LCEIFKSDLK-----DPKSFANTYKDNRYKEIISSFNFDIHGEL 584 (750) Q Consensus 546 i~kvL~sd~~-----d~~slaN~l~D~ry~~la~aF~F~~~G~~ 584 (750) .|-.|.||.. ...=-+|-|.+-.++.+--+++=--.|.+ T Consensus 766 ARNLFDSDm~V~lpdGqtFSVNDLR~~Dm~~impaYDRRVnGDI 809 (1316) T PHA00368 766 ARNLFDSDMSVTLPDGQTFSVNDLRDFDMKKIMPAYDRRVNGDI 809 (1316) T ss_pred HHHCCCCCCCEECCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCE T ss_conf 76412567732678998200232665035541134315447744 No 4 >TIGR01083 nth endonuclease III; InterPro: IPR005759 The spectrum of DNA damage caused by reactive oxygen species includes a wide variety of modifications of purine and pyrimidine bases. Among these modified bases, 7,8-dihydro-8-oxoguanine (8-oxoG) is an important mutagenic lesion. Base excision repair is a critical mechanism for preventing mutations by removing the oxidative lesion from the DNA. Escherichia coli Nth protein (endonuclease III) has an 8-oxoG DNA glycosylase/AP lyase activity which removes 8-oxoG preferentially from 8-oxoG/G mispairs. Human hNTH1 protein, a homolog of E. coli Nth protein, has similar DNA glycosylase/AP lyase activity that removes 8-oxoG from 8-oxoG/G mispairs . ; GO: 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0006284 base-excision repair, 0005622 intracellular. Probab=69.91 E-value=3 Score=19.89 Aligned_cols=66 Identities=17% Similarity=0.228 Sum_probs=47.2 Q ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHHHHHCCCHHHHCCCHHHHHHHHHHHCCHHHCCCHHHHHHHHHHHH Q ss_conf 03854699999986325500299872778999999997048676631999999999996219786499899999999987 Q gi|254781009|r 616 EKDPNIALALYFKRTIPNIRNHYEILGDSKLFKVVSKKLKLSPYFAVLPERKKIRILKKHIKINDFKDSKKVEDFLYAAK 695 (750) Q Consensus 616 e~n~gvRLALyF~R~a~~Its~y~ILgD~aL~~V~~TAlgLP~~~a~~DiDkQa~li~~k~Di~dl~DP~kv~kli~RF~ 695 (750) .+=|.=+-+| =++|++ |-+.===|..+|||+| .+-+|.-+.-+.+|+.|+.=.||.+||+=+.+.. T Consensus 100 GeVP~~~~eL---~~LPGV-------GRKTANVVL~~aFg~P----~iAVDTHv~Rv~~Rlgl~~~~dp~~vE~~L~~l~ 165 (192) T TIGR01083 100 GEVPEDREEL---VKLPGV-------GRKTANVVLNVAFGIP----AIAVDTHVFRVSNRLGLSKGKDPDKVEEELLKLI 165 (192) T ss_pred CCCCCCHHHH---HCCCCC-------CCHHHHHHHHHHHCCC----EEEECCCHHHHHHHHCCCCCCCHHHHHHHHHHHC T ss_conf 9877553766---178998-------7114562433442687----0574143465543313577789899999998744 No 5 >TIGR01259 comE comEA protein; InterPro: IPR004787 The comE locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. comEA and comEC are required for transformability, whereas the products of comEB and of the overlapping comER, which is transcribed in the reverse direction, are dispensable . ComEA has been shown to be an integral membrane protein, as predicted from hydropathy analysis, with its C-terminal domain outside the cytoplasmic membrane. This C-terminal domain possesses a sequence with similarity to those of several proteins known to be involved in nucleic acid transactions including UvrC and a human protein that binds to the replication origin of the Human herpesvirus 4 (Epstein-Barr virus) .. Probab=63.75 E-value=6 Score=18.09 Aligned_cols=21 Identities=14% Similarity=0.196 Sum_probs=10.9 Q ss_pred HHHHHHHHHCCCCCCHHHHHC Q ss_conf 899999974156678999941 Q gi|254781009|r 502 SEVDYYTLNINTIHSFEELLA 522 (750) Q Consensus 502 ~e~~yf~~~i~~i~s~~dll~ 522 (750) .+|--||+.=|..+|+|||.+ T Consensus 86 ~aIi~YRe~nG~F~SvddL~k 106 (124) T TIGR01259 86 KAIIEYREENGAFKSVDDLTK 106 (124) T ss_pred HHHHHHHHHCCCCCCHHHHHC T ss_conf 999999985699777555003 No 6 >PRK07209 ribonucleotide-diphosphate reductase subunit beta; Validated Probab=49.26 E-value=16 Score=15.47 Aligned_cols=61 Identities=10% Similarity=0.213 Sum_probs=33.3 Q ss_pred HHHHHHHHHCCCCHHHHHHHH------------HHHHHHCCCCCCHHHHHHCCCHH------------------HHHHHH Q ss_conf 799999998098822546999------------99996338887013542014315------------------788887 Q gi|254781009|r 391 ITLQFALDAYNLNMQDLDRDQ------------LRNVLTSNPSDPDSYANKSKDDR------------------LIKLNH 440 (750) Q Consensus 391 ~ly~~AlkA~gld~~~~sk~~------------irkVLesd~~Dp~S~aN~L~D~R------------------y~~lA~ 440 (750) .-|.|.+.++|+++.+.-.++ +-+..+ .+.||.-=..+..+++ |..||- T Consensus 168 ~aYs~lleslg~d~~Eif~a~~~ipsi~~K~df~~~~~~-~l~d~~f~~~t~e~~~~f~~~Li~F~~i~EGifFysgFa~ 246 (391) T PRK07209 168 HAYQYIVESLGLDEGEIFNMYHEVPSIRAKDEFLLPFTR-ALTDPNFKTGTPEADQKLLRNLIAFYCIMEGIFFYVGFTQ 246 (391) T ss_pred HHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHH-HHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999981189889999999527889989999999999-8625454568802599999999999999879999999999 Q ss_pred HCCCCCCCCCCC Q ss_conf 448776785665 Q gi|254781009|r 441 AFNFNADGSIGP 452 (750) Q Consensus 441 AFnF~~dG~~~~ 452 (750) .++|.--|..++ T Consensus 247 il~l~RrgkM~G 258 (391) T PRK07209 247 ILSLGRQNKMTG 258 (391) T ss_pred HHHHHHHCCCCC T ss_conf 999875145757 No 7 >KOG1961 consensus Probab=48.44 E-value=17 Score=15.39 Aligned_cols=149 Identities=17% Similarity=0.134 Sum_probs=74.3 Q ss_pred CHHHHHHCCCHHHHHHHHHCCCC------CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHH Q ss_conf 01354201431578888744877------678566510111133445568899987776411222235642111024566 Q gi|254781009|r 423 PDSYANKSKDDRLIKLNHAFNFN------ADGSIGPIPMMQSRLTIRDNVKHYANRKRSIHDAENKSFNSMEQISTQKRI 496 (750) Q Consensus 423 p~S~aN~L~D~Ry~~lA~AFnF~------~dG~~~~~~~~q~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~ 496 (750) =++|-|+..-.=|-.|-..|.+. ++-+.... --.+..-.+..+|......+..-..-..+... -..- T Consensus 436 ld~y~n~v~~~LWPRFq~V~d~h~eSlR~~di~~~~~---~~d~rPHyitrRyAEf~ss~~~l~v~~~~~~~----~~~l 508 (683) T KOG1961 436 LDSYWNSVLIFLWPRFQLVMDMHCESLRKADITTLWE---KLDTRPHYITRRYAEFLSSFLMLNVTYGNEQD----VERL 508 (683) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHCCC---CCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCH----HHHH T ss_conf 1378887899998999999999988888467010346---56789629999999999999999986155220----6899 Q ss_pred HHHHHHHHHHHHHHCCC----CCCHHHHH-CCHHHHHHHH-HHCCCCH----------HHHHHHHHHHHHHCCCCCHHHH Q ss_conf 78889899999974156----67899994-1489999998-7548885----------4412899999962278885577 Q gi|254781009|r 497 NLEINSEVDYYTLNINT----IHSFEELL-ANKRILNFLL-ESKGIDS----------QKVREDFLCEIFKSDLKDPKSF 560 (750) Q Consensus 497 ~~~~~~e~~yf~~~i~~----i~s~~dll-~D~rl~~~aL-~AfGL~~----------~~~~~~~i~kvL~sd~~d~~sl 560 (750) -...+.+++-|..++.+ -+...-|| +++.+.--+| .+-+=.. ......|+.++|..+-.|--.| T Consensus 509 l~~l~~~ve~fl~rmak~~~~~K~q~vFLiNNYdlil~vL~e~~~~~~k~~~~f~e~ln~~~~~fveell~~hf~~~i~f 588 (683) T KOG1961 509 LERLQMEVESFLLRMAKLFPTRKQQLVFLINNYDLILGVLMEAEPDLSKEQEHFQELLNSNTSNFVEELLVPHFGDLIKF 588 (683) T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHH T ss_conf 99999999999999998637755642665434899999998636454657899999987338999998615776726899 Q ss_pred HHHCC--CHHHHHHHHHCCC Q ss_conf 75216--4789999976187 Q gi|254781009|r 561 ANTYK--DNRYKEIISSFNF 578 (750) Q Consensus 561 aN~l~--D~ry~~la~aF~F 578 (750) ++--. +.|+..++++|+- T Consensus 589 vk~~e~~~~~~~~LV~~F~~ 608 (683) T KOG1961 589 VKERETAENRVETLVADFGS 608 (683) T ss_pred HHHHHCCHHHHHHHHHHHHH T ss_conf 99885210668899998722 No 8 >KOG3543 consensus Probab=45.52 E-value=19 Score=15.12 Aligned_cols=24 Identities=21% Similarity=0.310 Sum_probs=15.5 Q ss_pred CCCCHHHHHCCHHHHHHHHHHCCC Q ss_conf 458999972438999999997398 Q gi|254781009|r 150 KINSVDQLFKDRRLLDYVLQSFSI 173 (750) Q Consensus 150 ~ItsvddLL~D~~L~~vv~tAfGL 173 (750) .--+.+-+|+--+|..+.+.-+|+ T Consensus 203 ~a~sad~vl~keqlyd~fq~ilgv 226 (1218) T KOG3543 203 NAMSADAVLGKEQLYDVFQQILGV 226 (1218) T ss_pred HHHHHHHHHCHHHHHHHHHHHHHH T ss_conf 012156551689999999998545 No 9 >COG4342 Uncharacterized protein conserved in archaea [Function unknown] Probab=43.32 E-value=20 Score=14.91 Aligned_cols=47 Identities=19% Similarity=0.237 Sum_probs=22.3 Q ss_pred HHCCCCCCHHHHHCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCC Q ss_conf 741566789999414899999987548885441289999996227888 Q gi|254781009|r 509 LNINTIHSFEELLANKRILNFLLESKGIDSQKVREDFLCEIFKSDLKD 556 (750) Q Consensus 509 ~~i~~i~s~~dll~D~rl~~~aL~AfGL~~~~~~~~~i~kvL~sd~~d 556 (750) --||++..-+-+.+-.|++...|..+|+.++... ..++|++...... T Consensus 69 r~ig~~~~kdKy~kA~R~f~~fl~~rgiise~~A-e~lrk~lk~k~~~ 115 (291) T COG4342 69 RPIGSVREKDKYQKAYRLFIKFLTSRGIISEEFA-EKLRKPLKVKKSN 115 (291) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHH-HHHHHHHCCCCCC T ss_conf 7644311005799999999999987041339999-9999986457678 No 10 >PRK10852 thiosulfate transporter subunit; Provisional Probab=42.66 E-value=21 Score=14.85 Aligned_cols=25 Identities=12% Similarity=-0.053 Sum_probs=17.2 Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHH Q ss_conf 99999998098822546999999963 Q gi|254781009|r 392 TLQFALDAYNLNMQDLDRDQLRNVLT 417 (750) Q Consensus 392 ly~~AlkA~gld~~~~sk~~irkVLe 417 (750) .|.|+++++|=++. -++.||++++. T Consensus 165 Awg~a~~~~gg~e~-~a~~fv~~l~~ 189 (338) T PRK10852 165 AWGAADKADGGDKA-KTEQFMTQFLK 189 (338) T ss_pred HHHHHHHHCCCCHH-HHHHHHHHHHH T ss_conf 99999986499989-99999999983 No 11 >COG3814 Uncharacterized protein conserved in bacteria [Function unknown] Probab=42.40 E-value=13 Score=16.03 Aligned_cols=17 Identities=12% Similarity=0.155 Sum_probs=9.0 Q ss_pred HHHHCCHHHHHHHHHHC Q ss_conf 99724389999999973 Q gi|254781009|r 155 DQLFKDRRLLDYVLQSF 171 (750) Q Consensus 155 ddLL~D~~L~~vv~tAf 171 (750) |++|+...||.||...+ T Consensus 8 Y~~laqealrgvvkkvL 24 (157) T COG3814 8 YDILAQEALRGVVKKVL 24 (157) T ss_pred HHHHHHHHHHHHHHHHH T ss_conf 99999999999999999 No 12 >pfam08566 Pam17 Mitochondrial import protein Pam17. The presequence translocase-associated motor (PAM) drives the completion of preprotein translocation into the mitochondrial matrix. The Pam17 subunit is required for formation of a stable complex between cochaperones Pam16 and Pam18 and promotes the association of Pam16-Pam18 with the presequence translocase. Mitochondria lacking Pam17 are selectively impaired in the import of matrix proteins. Probab=41.26 E-value=5.8 Score=18.16 Aligned_cols=26 Identities=27% Similarity=0.562 Sum_probs=20.5 Q ss_pred HHHHHHHCCCCCCHHHHHCCHHHHHH Q ss_conf 99999741566789999414899999 Q gi|254781009|r 504 VDYYTLNINTIHSFEELLANKRILNF 529 (750) Q Consensus 504 ~~yf~~~i~~i~s~~dll~D~rl~~~ 529 (750) -+||-|+|+++..=-+-|.|.+.++= T Consensus 143 PDYYGEKI~Sl~~YRQWLRDq~a~~r 168 (174) T pfam08566 143 PDYYGEKIGSLAGYRQWLRDQRAFNR 168 (174) T ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHH T ss_conf 97443302228999999999899998 No 13 >PRK10363 cpxP periplasmic repressor CpxP; Reviewed Probab=34.44 E-value=28 Score=14.07 Aligned_cols=58 Identities=10% Similarity=-0.047 Sum_probs=47.9 Q ss_pred CCHHHHCCCHHHHHHHHHHHCCHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC Q ss_conf 8676631999999999996219786499899999999987531101111124567866 Q gi|254781009|r 656 LSPYFAVLPERKKIRILKKHIKINDFKDSKKVEDFLYAAKAMDHQSIDYKKALFSSPN 713 (750) Q Consensus 656 LP~~~a~~DiDkQa~li~~k~Di~dl~DP~kv~kli~RF~Am~~~~yD~~n~~~~s~~ 713 (750) +-+.+++.-+++|+++.+.+=.+=.+-.|+.-.+|-.+|--==.+-||+.+-+-+||- T Consensus 98 q~ekm~~~~~~r~Vem~~~~nqmy~lLTPEQK~~~~~~~qqRm~q~~~~~~~~~~~~~ 155 (166) T PRK10363 98 QAEKMAQEQVARQVEMAKVRNQMYRLLTPEQQAVLNEKHQQRMEQLRDVAQWQKSSSL 155 (166) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCH T ss_conf 9999999999999999999989998279999999999999999999999862547710 No 14 >pfam06599 DUF1139 Protein of unknown function (DUF1139). This family consists of several hypothetical Fijivirus proteins of unknown function. Probab=33.29 E-value=28 Score=14.02 Aligned_cols=26 Identities=8% Similarity=0.172 Sum_probs=16.7 Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHH Q ss_conf 99999998098822546999999963 Q gi|254781009|r 392 TLQFALDAYNLNMQDLDRDQLRNVLT 417 (750) Q Consensus 392 ly~~AlkA~gld~~~~sk~~irkVLe 417 (750) -|...||+.--..|.+.|..+|++|. T Consensus 283 WY~lfmrtlvfksm~~TK~lik~iLn 308 (309) T pfam06599 283 WYTLFMRTLIFRSMKYTKRLIKNLLN 308 (309) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 99999999999999999999999746 No 15 >PRK11904 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed Probab=33.22 E-value=29 Score=13.98 Aligned_cols=48 Identities=19% Similarity=0.168 Sum_probs=34.2 Q ss_pred CCCCCCHHHHHHHHHHHCCCCHHH---------HHHHHHHHHHHCCCCCCHHHHHHCCCHH Q ss_conf 122210047999999980988225---------4699999996338887013542014315 Q gi|254781009|r 383 PNSAEEPIITLQFALDAYNLNMQD---------LDRDQLRNVLTSNPSDPDSYANKSKDDR 434 (750) Q Consensus 383 ~~~~~~~~~ly~~AlkA~gld~~~---------~sk~~irkVLesd~~Dp~S~aN~L~D~R 434 (750) .-.|.++ ||+.+++.+|.--.. .-.+.+||.||-| -.+||+|++-|+. T Consensus 430 LhGMGe~--ly~~~~~~~~~~~RiYAPVG~h~dLLpYLVRRLLENg--ANsSFv~~~~d~~ 486 (1026) T PRK11904 430 LHGMGEA--LYDALLDAPGIPCRIYAPVGSHKDLLPYLVRRLLENG--ANSSFVHRLVDPD 486 (1026) T ss_pred ECCCCHH--HHHHHHHCCCCCEEEECCCCCHHHHHHHHHHHHHHCC--CCHHHHHHHHCCC T ss_conf 2157899--9999985379843897767867888999999987258--8488997760489 No 16 >pfam10875 DUF2670 Protein of unknown function (DUF2670). This bacterial family of proteins has no known function. Probab=29.54 E-value=32 Score=13.68 Aligned_cols=32 Identities=19% Similarity=0.256 Sum_probs=24.2 Q ss_pred CCCHHHHHHHCCHHHHHHHHHHHCCCHHHHCCC Q ss_conf 550029987277899999999704867663199 Q gi|254781009|r 632 PNIRNHYEILGDSKLFKVVSKKLKLSPYFAVLP 664 (750) Q Consensus 632 ~~Its~y~ILgD~aL~~V~~TAlgLP~~~a~~D 664 (750) +-|+.||=|++-..|-..+-|++||-. +|.+| T Consensus 20 siitkwyliiavaslitlyytvlglkk-igfid 51 (139) T pfam10875 20 SIITKWYLIIAVASLITLYYTVLGLKK-IGFID 51 (139) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-HCHHH T ss_conf 999999999999999999999970466-25145 No 17 >PRK08032 fliD flagellar capping protein; Reviewed Probab=28.20 E-value=33 Score=13.60 Aligned_cols=27 Identities=11% Similarity=0.130 Sum_probs=21.0 Q ss_pred CHHHHHHHHHHHCCHHHCCCHHHHHHHHHHHHHH Q ss_conf 9999999999621978649989999999998753 Q gi|254781009|r 664 PERKKIRILKKHIKINDFKDSKKVEDFLYAAKAM 697 (750) Q Consensus 664 DiDkQa~li~~k~Di~dl~DP~kv~kli~RF~Am 697 (750) +|++|.+-+++|++ .+.+.+.++|++| T Consensus 418 ~l~~~i~~l~~rl~-------~~e~~~~~QFtam 444 (463) T PRK08032 418 KLTKQYNAVSDSID-------ATVARYKAQFTQL 444 (463) T ss_pred HHHHHHHHHHHHHH-------HHHHHHHHHHHHH T ss_conf 99999999999999-------9999999999999 No 18 >pfam01216 Calsequestrin Calsequestrin. Probab=27.78 E-value=36 Score=13.39 Aligned_cols=52 Identities=15% Similarity=0.206 Sum_probs=38.9 Q ss_pred HHHHHHHHHHCC---CHHHHCCCHHHHHHHHHHHCCHHHCCCHHHHHHHHHHHHH Q ss_conf 999999997048---6766319999999999962197864998999999999875 Q gi|254781009|r 645 KLFKVVSKKLKL---SPYFAVLPERKKIRILKKHIKINDFKDSKKVEDFLYAAKA 696 (750) Q Consensus 645 aL~~V~~TAlgL---P~~~a~~DiDkQa~li~~k~Di~dl~DP~kv~kli~RF~A 696 (750) -|..+++-++|| |.+++..+|..-.....+--+=+++-.++.+++||+++.. T Consensus 292 ~i~~y~~~~~~i~L~~~qi~vv~v~d~~~~~~~~~~~~d~~tae~l~~wiedvL~ 346 (350) T pfam01216 292 LLVPYWEKTFKIDLSKPQIGVVNVTDADSVWMEMDDEEDLPTAEELEDWIEDVLE 346 (350) T ss_pred HHHHHHHHHCCCCCCCCCCCEEEEECCHHCCCCCCCHHCCCCHHHHHHHHHHHHC T ss_conf 6889999853778775547756422322100358870004789999999999866 No 19 >TIGR01830 3oxo_ACP_reduc 3-oxoacyl-(acyl-carrier-protein) reductase; InterPro: IPR011284 This entry represents 3-oxoacyl-[ACP] reductase, also called 3-ketoacyl-acyl carrier protein reductase, an enzyme of fatty acid biosynthesis found in many plant and bacterial species. This enzyme is involved in type II fatty acid biosynthesis, where the individual metabolic transformations are carried out by different enzymes rather than by a single enzyme as occurs in type I fatty acid biosynthesis . Structural studies show that the enzyme is a tetramer which forms a typical Rossman fold , . Unlike other members of the short-chain dehydrogenase/reductase superfamily, the enzyme undergoes a marked conformational change upon binding of the NADP(H)cofactor. This conformational change aligns the side chains of the catalytic triad at the active site in an active conformation and increases the affinity of the enzyme for its substrate.; GO: 0004316 3-oxoacyl-[acyl-carrier-protein] reductase activity, 0051287 NAD binding, 0006633 fatty acid biosynthetic process. Probab=27.60 E-value=37 Score=13.37 Aligned_cols=142 Identities=18% Similarity=0.234 Sum_probs=77.7 Q ss_pred CCCCHHHHHCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCC Q ss_conf 66789999414899999987548885441289999996227888557775216478999997618776576556774322 Q gi|254781009|r 513 TIHSFEELLANKRILNFLLESKGIDSQKVREDFLCEIFKSDLKDPKSFANTYKDNRYKEIISSFNFDIHGELSHKKIGKV 592 (750) Q Consensus 513 ~i~s~~dll~D~rl~~~aL~AfGL~~~~~~~~~i~kvL~sd~~d~~slaN~l~D~ry~~la~aF~F~~~G~~~~~~~~~~ 592 (750) +|+..|+. ..+++-+...|| =|=.++.|-|- .|.|.-|.+|+.|-+.-+. ++... T Consensus 56 dvs~~~~~---~~~~~~~~~~~G-iDiLVNNAGIT---------rD~Ll~RMk~edWd~Vi~~------------NL~g~ 110 (238) T TIGR01830 56 DVSDREDV---KALVEEAEEELG-IDILVNNAGIT---------RDNLLMRMKEEDWDAVINV------------NLKGV 110 (238) T ss_pred CCCCHHHH---HHHHHHHHHHHC-CEEEEECCCCC---------CCCHHCCCCHHHHHHHHHH------------HHHHH T ss_conf 38888999---999999999829-90899787413---------4301004885568999986------------12668 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH--CCCCHHHHHHHCCHHHHHHHHHHH---CCCHHHH----C- Q ss_conf 45667999999999877888730038546999999863--255002998727789999999970---4867663----1- Q gi|254781009|r 593 QDNFHIDDTCDLYKHQMIEKKEEEKDPNIALALYFKRT--IPNIRNHYEILGDSKLFKVVSKKL---KLSPYFA----V- 662 (750) Q Consensus 593 q~~~~~~~i~d~Y~~qs~E~~~Ge~n~gvRLALyF~R~--a~~Its~y~ILgD~aL~~V~~TAl---gLP~~~a----~- 662 (750) - ..+..=+++... +|. +=+|+|.=.++|++==....=+-= ||-.+++ . T Consensus 111 F------~~t~~v~~~M~K----------------~R~GrIINisSVVG~~GN~GQaNYaASKAG~IGftKSlAkElasR 168 (238) T TIGR01830 111 F------NLTQAVLRPMIK----------------QRSGRIINISSVVGLMGNAGQANYAASKAGVIGFTKSLAKELASR 168 (238) T ss_pred H------HHHHHHHHHHHH----------------HCCCCEEEEEEHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 7------888998898875----------------067434861002000068742678888755899999999860368 Q ss_pred -----------CC-------HHHHHHHHHHHCCHHHCCCHHHHHHHHHHHHHHHHCCC Q ss_conf -----------99-------99999999962197864998999999999875311011 Q gi|254781009|r 663 -----------LP-------ERKKIRILKKHIKINDFKDSKKVEDFLYAAKAMDHQSI 702 (750) Q Consensus 663 -----------~D-------iDkQa~li~~k~Di~dl~DP~kv~kli~RF~Am~~~~y 702 (750) ++ -|+|.+-+.+.+=|.-|-.||.|-..+ .|+|=|+++| T Consensus 169 nItVNaVAPGFI~TdMT~~L~e~~~~~~l~~IPLgR~G~pEeVA~~v-~FLASd~AsY 225 (238) T TIGR01830 169 NITVNAVAPGFIETDMTDKLSEKVKKAMLSQIPLGRFGTPEEVANAV-AFLASDEASY 225 (238) T ss_pred CCEEEEECCCCCCCCCCHHCCHHHHHHHHHCCCCCCCCCHHHHHHHH-HHHCCCCCCC T ss_conf 70588874899897000216988999998527723267765699999-9732512474 No 20 >pfam07147 PDCD9 Mitochondrial 28S ribosomal protein S30 (PDCD9). This family consists of several eukaryotic mitochondrial 28S ribosomal protein S30 (or programmed cell death protein 9 PDCD9) sequences. The exact function of this family is unknown although it is known to be a component of the mitochondrial ribosome and a component in cellular apoptotic signaling pathways. Probab=27.31 E-value=22 Score=14.65 Aligned_cols=74 Identities=20% Similarity=0.162 Sum_probs=48.6 Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHCHHHHHHHHHHHHHCCCCCCHHHHHCCH----HHHHHHHHHCCCHHHH-------HH Q ss_conf 752021001254147999887608656889999998507758898996668----9999999975972441-------05 Q gi|254781009|r 2 IPSHVAPFPSKDIQSKLFSTVSKDPIVSCEERYYRERIKHISTIDEFIKDK----RLFSYALKAFGLSDMS-------HA 70 (750) Q Consensus 2 ~~~~~~~~~~rd~~~~~~~~~a~~p~V~r~~~yy~~~I~~v~svDdll~D~----rl~~yamkA~GLedm~-------~a 70 (750) +|.|--+++++|+..+. ++ .|..+-+-+.|.++.||+|=|.=. +-.-|.-|+|++.+.+ .. T Consensus 31 ~p~YpPi~~s~~~~~ka----~k----~r~~~ew~~~i~~~ptVeEKl~~~~~~~~p~Y~~yK~~~~~p~~~~~nal~~~ 102 (423) T pfam07147 31 SPRYPPIVYSRTFKSKA----AK----RRRAEEFHEMVHAAPTVEEKIRLITPVQRPKYVVYKANIIPPQTFALNALRWY 102 (423) T ss_pred CCCCCCCCCCCCCCCHH----HH----HHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCEEEEEEECCCCCCEECCCCHHH T ss_conf 87799853456778266----65----43589999998548989998876532166412136521038862344531465 Q ss_pred HHHHHHHHHCCCC Q ss_conf 9999999826899 Q gi|254781009|r 71 EKFIKKILESDLS 83 (750) Q Consensus 71 ka~~kKVLesd~~ 83 (750) ..+-|-||++++- T Consensus 103 Q~~TkTv~~~gLP 115 (423) T pfam07147 103 QYLTKTVFVSGLP 115 (423) T ss_pred HHHHEEEECCCCC T ss_conf 6410013204688 No 21 >PRK11779 sbcB exonuclease I; Provisional Probab=25.02 E-value=34 Score=13.53 Aligned_cols=36 Identities=14% Similarity=0.262 Sum_probs=28.4 Q ss_pred HHHHHHHHHHHHCCCCCHHHHHHHCCCHHHHHHHHH Q ss_conf 412899999962278885577752164789999976 Q gi|254781009|r 540 KVREDFLCEIFKSDLKDPKSFANTYKDNRYKEIISS 575 (750) Q Consensus 540 ~~~~~~i~kvL~sd~~d~~slaN~l~D~ry~~la~a 575 (750) ...+..|.++-...+.+...+.+.+.|+|+++|.-- T Consensus 373 ~~Dk~lm~~fh~a~~~el~~~~~~F~D~RL~eLlfR 408 (477) T PRK11779 373 DADRRLMKIIRETEPENLAALDLTFDDPRLEELLFR 408 (477) T ss_pred HHHHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH T ss_conf 899999999981999999840457878218999999 No 22 >KOG0917 consensus Probab=24.57 E-value=42 Score=13.03 Aligned_cols=40 Identities=8% Similarity=0.067 Sum_probs=31.3 Q ss_pred CCCCCHHHHHCCHHHHHHHHHHCCCCHHHHHHHHHHHHHH Q ss_conf 5667899994148999999875488854412899999962 Q gi|254781009|r 512 NTIHSFEELLANKRILNFLLESKGIDSQKVREDFLCEIFK 551 (750) Q Consensus 512 ~~i~s~~dll~D~rl~~~aL~AfGL~~~~~~~~~i~kvL~ 551 (750) |.+-+.|+|-.-+++-+||+.|...|+-.-...-++|.|+ T Consensus 292 g~qptpE~faea~K~~kyA~sAl~yedVstavenL~KaL~ 331 (338) T KOG0917 292 GVQPTPEDFAEAQKYCKYAGSALQYEDVSTAVENLQKALK 331 (338) T ss_pred CCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH T ss_conf 8756879999999999876311016889999999999999 No 23 >TIGR02793 nikR nickel-responsive transcriptional regulator NikR; InterPro: IPR014160 The members of this entry from Escherichia coli, Pseudomonas putida, and Brucella melitensis, are found associated with a nickel ABC transporter operon that acts to import nickel for use as a cofactor in urease or hydrogenase. These proteins, with characterised nickel-binding and DNA-binding domains, act as nickel-responsive transcriptional regulators. In the larger family of full-length homologues, most others both lack proximity to the nickel ABC transporter operon and form a separate clade. Several of the homologues not in this entry have been shown to bind nickel, copper, or both, and to regulate genes in response to nickel.. Probab=24.06 E-value=29 Score=13.99 Aligned_cols=26 Identities=15% Similarity=0.144 Sum_probs=14.7 Q ss_pred CCCCC---CCCHHHHHHHHHHHCHHHHHH Q ss_conf 21001---254147999887608656889 Q gi|254781009|r 6 VAPFP---SKDIQSKLFSTVSKDPIVSCE 31 (750) Q Consensus 6 ~~~~~---~rd~~~~~~~~~a~~p~V~r~ 31 (750) ++|+| +||+++||.++.=..=+++|. T Consensus 56 lsY~YdHs~RdL~~rL~~t~H~HHdLs~a 84 (130) T TIGR02793 56 LSYTYDHSKRDLPRRLTQTLHHHHDLSRA 84 (130) T ss_pred EEEEECCCCCHHHHHHHHCCCCCCHHHHH T ss_conf 98731175311345551014320011142 No 24 >pfam07304 SRA1 Steroid receptor RNA activator (SRA1). This family consists of several hypothetical mammalian steroid receptor RNA activator proteins. SRA-RNAs likely to encode stable proteins are widely expressed in breast cancer cell lines. SRA-RNA is a steroid receptor co-activator which acts as a functional RNA and is classified as belonging to the growing family of functional non-coding RNAs. Probab=23.70 E-value=43 Score=12.93 Aligned_cols=45 Identities=9% Similarity=0.157 Sum_probs=33.3 Q ss_pred CCHHHHHHHHHHHCCHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCC Q ss_conf 9999999999962197864998999999999875311011111245 Q gi|254781009|r 663 LPERKKIRILKKHIKINDFKDSKKVEDFLYAAKAMDHQSIDYKKAL 708 (750) Q Consensus 663 ~DiDkQa~li~~k~Di~dl~DP~kv~kli~RF~Am~~~~yD~~n~~ 708 (750) -|++|+..++.+++.=.+|..| .++++..--.+|....||.++.. T Consensus 68 ~D~~kRL~iL~d~ln~~~Ls~p-v~~kl~~La~aL~~~dy~~A~~I 112 (157) T pfam07304 68 KDISRRLKLLEDMWMGGKLSKP-VKKRMIKLVKELDDGQWDAADNI 112 (157) T ss_pred HHHHHHHHHHHHHHHCCCCCHH-HHHHHHHHHHHHHHCCHHHHHHH T ss_conf 9999999999999846886679-99999999999983688899999 No 25 >PRK07737 fliD flagellar capping protein; Validated Probab=21.82 E-value=44 Score=12.87 Aligned_cols=27 Identities=15% Similarity=0.257 Sum_probs=18.3 Q ss_pred CHHHHHHHHHHHCCHHHCCCHHHHHHHHHHHHHH Q ss_conf 9999999999621978649989999999998753 Q gi|254781009|r 664 PERKKIRILKKHIKINDFKDSKKVEDFLYAAKAM 697 (750) Q Consensus 664 DiDkQa~li~~k~Di~dl~DP~kv~kli~RF~Am 697 (750) ++++|.+-+++|++ .+.+.+.++|++| T Consensus 453 ~~~~~i~~l~~rl~-------~~e~rl~~QFtam 479 (502) T PRK07737 453 SIETRISRMQDRLK-------QIEDRYYKKFSAM 479 (502) T ss_pred HHHHHHHHHHHHHH-------HHHHHHHHHHHHH T ss_conf 99999999999999-------9999999999999 Done!