Query gi|254781146|ref|YP_003065559.1| hypothetical protein CLIBASIA_05265 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 122 No_of_seqs 9 out of 11 Neff 1.6 Searched_HMMs 39220 Date Mon May 30 05:19:58 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781146.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 pfam06698 DUF1192 Protein of u 61.0 12 0.0003 19.8 3.6 35 66-100 5-39 (58) 2 pfam10044 Ret_tiss Retinal tis 57.8 12 0.0003 19.7 3.2 39 73-119 50-88 (95) 3 KOG0386 consensus 53.4 12 0.0003 19.8 2.5 77 31-107 531-623 (1157) 4 KOG0652 consensus 47.4 19 0.00049 18.3 2.9 34 79-112 18-51 (424) 5 TIGR01312 XylB xylulokinase; I 43.2 16 0.00041 18.8 1.9 27 43-69 133-159 (494) 6 KOG2346 consensus 42.8 23 0.00058 17.8 2.7 38 53-99 34-71 (636) 7 KOG3221 consensus 42.6 32 0.00082 16.8 3.9 47 56-103 138-184 (199) 8 TIGR02939 RpoE_Sigma70 RNA pol 38.5 37 0.00095 16.4 3.4 47 55-101 131-192 (192) 9 TIGR01639 P_fal_TIGR01639 Plas 38.3 18 0.00045 18.6 1.5 20 78-97 7-26 (61) 10 TIGR00685 T6PP trehalose-phosp 34.8 11 0.00029 19.9 0.0 55 45-99 180-237 (290) 11 COG5398 Heme oxygenase [Inorga 34.8 42 0.0011 16.0 3.7 69 12-92 68-141 (238) 12 PRK04192 V-type ATP synthase s 34.6 43 0.0011 16.0 4.9 67 7-87 419-488 (585) 13 PRK12524 RNA polymerase sigma 31.5 29 0.00075 17.1 1.7 10 53-62 77-86 (196) 14 COG5150 Class 2 transcription 31.4 20 0.0005 18.2 0.9 15 57-71 17-31 (148) 15 pfam09628 YvfG YvfG protein. Y 30.6 50 0.0013 15.6 5.3 54 34-99 8-64 (68) 16 COG1494 GlpX Fructose-1,6-bisp 28.6 25 0.00064 17.5 1.0 66 41-107 125-191 (332) 17 KOG3284 consensus 28.5 54 0.0014 15.3 3.3 27 76-102 185-211 (213) 18 COG3962 Acetolactate synthase 27.2 33 0.00084 16.8 1.4 41 9-49 497-545 (617) 19 TIGR00608 radc DNA repair prot 24.7 41 0.0011 16.1 1.5 22 66-90 2-23 (223) 20 COG5191 Uncharacterized conser 23.8 65 0.0017 14.8 5.5 69 25-97 303-397 (435) 21 PRK12519 RNA polymerase sigma 23.3 53 0.0014 15.4 1.9 10 53-62 79-88 (194) 22 COG4451 RbcS Ribulose bisphosp 22.0 60 0.0015 15.0 1.9 30 64-94 3-32 (127) 23 PRK13919 putative RNA polymera 21.6 56 0.0014 15.2 1.7 10 54-63 75-84 (187) 24 TIGR02948 SigW_bacill RNA poly 21.5 22 0.00056 17.9 -0.4 21 39-59 75-95 (187) 25 TIGR02026 BchE magnesium-proto 21.4 42 0.0011 16.1 1.0 21 71-93 43-63 (506) 26 pfam11107 FANCF Fanconi anemia 21.2 73 0.0019 14.4 4.4 52 58-109 267-326 (343) 27 TIGR01740 pyrF orotidine 5'-ph 21.2 49 0.0013 15.6 1.3 57 53-109 9-69 (233) 28 KOG4816 consensus 20.3 65 0.0017 14.8 1.8 32 1-33 30-63 (98) No 1 >pfam06698 DUF1192 Protein of unknown function (DUF1192). This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. The function of this family is unknown. Probab=61.01 E-value=12 Score=19.75 Aligned_cols=35 Identities=29% Similarity=0.285 Sum_probs=25.4 Q ss_pred CHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 61455542454410168899999999889988887 Q gi|254781146|r 66 PREKIKQDGITNGDQLTDEQLCEIIRSLEKELQIF 100 (122) Q Consensus 66 Pkdl~~~~gin~~D~LSDEQl~erIRaLd~aiRpf 100 (122) ||-.....-...++.||-++|-+||-.|..+|--. T Consensus 5 pr~~~~~~ig~DLs~lSv~EL~~RIa~L~~EI~R~ 39 (58) T pfam06698 5 PRKKTAHEIGQDLSLLSVEELEERIALLQAEIARL 39 (58) T ss_pred CCCCCCCCCCCCCHHCCHHHHHHHHHHHHHHHHHH T ss_conf 77753002058802227999999999999999999 No 2 >pfam10044 Ret_tiss Retinal tissue protein. Rtp is a family of proteins of approximately 112 amino acids in length which is conserved from nematodes to humans. The proposed tertiary structure is of almost entirely alpha helix interrupted only by loops located at proline residues. Three sites in the protein sequence reveal two types of possible post-translation modification. A serine residue, at position 41, is a candidate for protein kinase C phosphorylation. Glycine residues at position 69 and 91 are probable sites for acetylation by covalent amide linkage of myristate via N-myristoyl transferase. Rtp is differentially expressed in the trout retina between parr and smolt developmental stages (smoltification). It is likely to be a house-keeping protein. Probab=57.79 E-value=12 Score=19.72 Aligned_cols=39 Identities=26% Similarity=0.227 Sum_probs=30.3 Q ss_pred HCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHCCHHHHHHHHHH Q ss_conf 24544101688999999998899888873110111111355666553 Q gi|254781146|r 73 DGITNGDQLTDEQLCEIIRSLEKELQIFTDFKNKDAHSRETKETTKS 119 (122) Q Consensus 73 ~gin~~D~LSDEQl~erIRaLd~aiRpf~~~k~r~~~~Rk~~~~~~~ 119 (122) .-|+.+-.||-+||++.||+|--.+-- -|++|.||-|.. T Consensus 50 ~~i~el~sLt~~~L~ekvk~L~d~aYQ--------LGleEakEMTRG 88 (95) T pfam10044 50 DKINELGSLTTSGLIAKVKKLHDLAYQ--------LGLEEAKEMTRG 88 (95) T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHH T ss_conf 999999868999999999999999999--------716999997644 No 3 >KOG0386 consensus Probab=53.39 E-value=12 Score=19.81 Aligned_cols=77 Identities=30% Similarity=0.281 Sum_probs=43.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCHHHH-----HHHHHHHCCHH----HHHHHCC-----CCC--CCCCHHHHHHHHHHHH Q ss_conf 997436899855999999974487999-----99999974614----5554245-----441--0168899999999889 Q gi|254781146|r 31 QSVLTDDFSKYGRKVIKNLREEKPEQY-----LRLISQILPRE----KIKQDGI-----TNG--DQLTDEQLCEIIRSLE 94 (122) Q Consensus 31 ~~~l~dDF~~hG~~vIarvReeKPeqY-----LKlVaSiLPkd----l~~~~gi-----n~~--D~LSDEQl~erIRaLd 94 (122) ++.|+++...|++.----+---+|-|- --+..-+||.= ..|..+- |.+ .+|++|+-.-+||-|. T Consensus 531 ~~KLt~~L~t~y~~q~RLLLTGTPLQN~LpELWaLLNFlLP~IFnS~~~FeqWFN~PFantGek~eLteEEtlLIIrRLH 610 (1157) T KOG0386 531 ICKLTDTLNTHYRAQRRLLLTGTPLQNNLPELWALLNFLLPNIFNSCKAFEQWFNQPFANTGEKVELTEEETLLIIRRLH 610 (1157) T ss_pred HHHHHHHHHCCCCCHHHHHHCCCHHHHCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHH T ss_conf 55788775025521215653288322211778999987635211047579898612666438731255227899999988 Q ss_pred HHHHHHHCCHHHH Q ss_conf 9888873110111 Q gi|254781146|r 95 KELQIFTDFKNKD 107 (122) Q Consensus 95 ~aiRpf~~~k~r~ 107 (122) .+||||+.-+.+. T Consensus 611 kVLRPFlLRRlKk 623 (1157) T KOG0386 611 KVLRPFLLRRLKK 623 (1157) T ss_pred HHHHHHHHHHHHH T ss_conf 7664788876567 No 4 >KOG0652 consensus Probab=47.36 E-value=19 Score=18.32 Aligned_cols=34 Identities=18% Similarity=0.279 Sum_probs=26.6 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCHHHHCCHHH Q ss_conf 0168899999999889988887311011111135 Q gi|254781146|r 79 DQLTDEQLCEIIRSLEKELQIFTDFKNKDAHSRE 112 (122) Q Consensus 79 D~LSDEQl~erIRaLd~aiRpf~~~k~r~~~~Rk 112 (122) -.+|-|++++|+|-||.+||++-+--.|-.|.-. T Consensus 18 ~~mste~i~~rtrlldnEirI~~sev~ri~he~~ 51 (424) T KOG0652 18 LSMSTEEIISRTRLLDNEIRIMKSEVQRINHELQ 51 (424) T ss_pred HHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 5401999999988751478999999988766788 No 5 >TIGR01312 XylB xylulokinase; InterPro: IPR006000 The ability to metabolise xylose, one of the most abundant sugars in nature, is dependent on its conversion to xylulose-5-phosphate, which then enters the non-oxidative pentose phosphate pathway . Xylulose-5-phosphate is produced from xylose by the sequential action of two enzymes; xylose isomerase, which converts xylose to xylulose, and xylulokinase, which subsequently phosphorylates xylulose. This entry represents bacterial xylulokinase. In addition to its role in xylose metabolism this enzyme may also have a biosynthetic role. 1-deoxy-D-xylulose 5-phosphate serves as a precursor for the biosynthesis of the vitamins thiamine and pyridoxal and for the formation of isopentenyl pyrophosphate and dimethylallyl pyrophosphate via the nonmevalonate pathway of terpenoid biosynthesis. Xylulokinase catalyses the phosphorylation of 1-deoxy-D-xylulose at the hydroxy group of C-5 . This reaction therefore constitutes a potential salvage pathway for the generation of 1-deoxy-D-xylulose 5-phosphate from exogenous or endogenous 1-deoxy-D-xylulose as starting material for the biosynthesis of terpenoids, thiamine and pyridoxal. ; GO: 0004856 xylulokinase activity, 0005997 xylulose metabolic process. Probab=43.17 E-value=16 Score=18.84 Aligned_cols=27 Identities=22% Similarity=0.492 Sum_probs=23.8 Q ss_pred HHHHHHHHHHCHHHHHHHHHHHCCHHH Q ss_conf 999999974487999999999746145 Q gi|254781146|r 43 RKVIKNLREEKPEQYLRLISQILPREK 69 (122) Q Consensus 43 ~~vIarvReeKPeqYLKlVaSiLPkdl 69 (122) +-=|.=||+-+||+|=|+-.=.||||- T Consensus 133 aPKlLW~r~hePe~f~ri~~vmLPkDY 159 (494) T TIGR01312 133 APKLLWVRKHEPEVFARIAKVMLPKDY 159 (494) T ss_pred HHHHHHHHHCCHHHHHHHHHCCCCCHH T ss_conf 568999861617899876220387122 No 6 >KOG2346 consensus Probab=42.78 E-value=23 Score=17.82 Aligned_cols=38 Identities=34% Similarity=0.563 Sum_probs=19.3 Q ss_pred CHHHHHHHHHHHCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 87999999999746145554245441016889999999988998888 Q gi|254781146|r 53 KPEQYLRLISQILPREKIKQDGITNGDQLTDEQLCEIIRSLEKELQI 99 (122) Q Consensus 53 KPeqYLKlVaSiLPkdl~~~~gin~~D~LSDEQl~erIRaLd~aiRp 99 (122) -||+|+- .|||+.+.+.=+. +.++...-||+||+-++- T Consensus 34 DpEvyld----kL~REcpLaqLid-----setdMV~qIRaLDSDmqt 71 (636) T KOG2346 34 DPEVYLD----KLPRECPLAQLID-----SETDMVQQIRALDSDMQT 71 (636) T ss_pred CHHHHHH----HHHHCCCHHHHHH-----HHHHHHHHHHHHCHHHHH T ss_conf 9899999----8651298999987-----789999999874407899 No 7 >KOG3221 consensus Probab=42.63 E-value=32 Score=16.82 Aligned_cols=47 Identities=17% Similarity=0.176 Sum_probs=34.4 Q ss_pred HHHHHHHHHCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCC Q ss_conf 999999997461455542454410168899999999889988887311 Q gi|254781146|r 56 QYLRLISQILPREKIKQDGITNGDQLTDEQLCEIIRSLEKELQIFTDF 103 (122) Q Consensus 56 qYLKlVaSiLPkdl~~~~gin~~D~LSDEQl~erIRaLd~aiRpf~~~ 103 (122) +-.|++....|--.-|-..+.-+ +-++++.+++|+++-+.++|+++- T Consensus 138 ~~FkvaLklvP~r~~Fl~als~~-d~t~~~~~edi~~fl~~~~~~L~~ 184 (199) T KOG3221 138 STFKVALKLVPDRKTFLKALSAG-DETYDECIEDITSFLSLLTPILKE 184 (199) T ss_pred HHHHHHHHHCCCHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999768689999998514-312888999999999876545999 No 8 >TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE; InterPro: IPR014286 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the clade of sigma factors called RpoE. These proteins are variously annotated as sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=38.55 E-value=37 Score=16.41 Aligned_cols=47 Identities=21% Similarity=0.254 Sum_probs=35.8 Q ss_pred HHHHHHHHHHCCHHHHHHHCCCCCCCCCHHHHHH-----------HH----HHHHHHHHHHH Q ss_conf 9999999997461455542454410168899999-----------99----98899888873 Q gi|254781146|r 55 EQYLRLISQILPREKIKQDGITNGDQLTDEQLCE-----------II----RSLEKELQIFT 101 (122) Q Consensus 55 eqYLKlVaSiLPkdl~~~~gin~~D~LSDEQl~e-----------rI----RaLd~aiRpf~ 101 (122) ++|..--..-||-||-.++..--+|+||=|+|-+ || -|.+..|||++ T Consensus 131 ~~~v~~a~~aLPE~Lr~Ai~LREleGLSYe~IA~~MdCPvGTVRSRIFRAREAi~~~lrPLL 192 (192) T TIGR02939 131 EQTVNKALEALPEDLRTAITLRELEGLSYEDIAEIMDCPVGTVRSRIFRAREAIAKRLRPLL 192 (192) T ss_pred HHHHHHHHHHCCHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCC T ss_conf 99999998617267874544651268787888733069988621146775899998624679 No 9 >TIGR01639 P_fal_TIGR01639 Plasmodium falciparum uncharacterized domain TIGR01639; InterPro: IPR006526 These sequences contain a conserved sequence region of about 60 amino acids found in over 40 predicted proteins of Plasmodium falciparum. It is not curently found elsewhere, even in closely related Plasmodium species. No member of this family has been functionally characterised. . Probab=38.30 E-value=18 Score=18.59 Aligned_cols=20 Identities=35% Similarity=0.529 Sum_probs=16.8 Q ss_pred CCCCCHHHHHHHHHHHHHHH Q ss_conf 10168899999999889988 Q gi|254781146|r 78 GDQLTDEQLCEIIRSLEKEL 97 (122) Q Consensus 78 ~D~LSDEQl~erIRaLd~ai 97 (122) -+++|+|||-+.|++|+... T Consensus 7 ~~~~s~Eel~~~i~~L~~~~ 26 (61) T TIGR01639 7 SKKLSKEELNELINSLDEIP 26 (61) T ss_pred CCCCCHHHHHHHHHHHCCCC T ss_conf 41047789999977314887 No 10 >TIGR00685 T6PP trehalose-phosphatase; InterPro: IPR003337 Trehalose-phosphatases 3.1.3.12 from EC catalyse the de-phosphorylation of trehalose-6-phosphate to trehalose and orthophosphate. Trehalose is a common disaccharide of bacteria, fungi and invertebrates that appears to play a major role in desiccation tolerance. A pathway for trehalose biosynthesis may also exist in plants . The trehalose-phosphatase signature is found in the C-terminus of trehalose-6-phosphate synthase 2.4.1.15 from EC adjacent to the trehalose-6-phosphate synthase domain (see IPR001830 from INTERPRO). It would appear that the two equivalent genes in the Escherichia coli otsBA operon: otsA, the trehalose-6-phosphate synthase and otsB, trehalose-phosphatase (this family) have undergone gene fusion in most eukaryotes .; GO: 0003824 catalytic activity, 0005992 trehalose biosynthetic process. Probab=34.80 E-value=11 Score=19.91 Aligned_cols=55 Identities=27% Similarity=0.454 Sum_probs=44.0 Q ss_pred HHHHHHHHC---HHHHHHHHHHHCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 999997448---7999999999746145554245441016889999999988998888 Q gi|254781146|r 45 VIKNLREEK---PEQYLRLISQILPREKIKQDGITNGDQLTDEQLCEIIRSLEKELQI 99 (122) Q Consensus 45 vIarvReeK---PeqYLKlVaSiLPkdl~~~~gin~~D~LSDEQl~erIRaLd~aiRp 99 (122) .|+++=++. |...||-++.-||||-.-.+-+-=+|++|||.--..||..|+.-.- T Consensus 180 ~v~~~l~~~~~~gqdmlkG~s~~lPkdemP~~~vyLGDD~TDed~F~~v~tietCWke 237 (290) T TIGR00685 180 IVKKLLEHAPVSGQDMLKGISAKLPKDEMPDVVVYLGDDITDEDAFRVVRTIETCWKE 237 (290) T ss_pred HHHHHHHHCCCCCCHHHCCCCCCCCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHH T ss_conf 9999997378986232136788887544674468707876704678888777765530 No 11 >COG5398 Heme oxygenase [Inorganic ion transport and metabolism] Probab=34.80 E-value=42 Score=16.02 Aligned_cols=69 Identities=22% Similarity=0.307 Sum_probs=46.8 Q ss_pred CCCHHHHHCHHHHHHHHHHHHHHHHHHHHH--HHHHHHH---HHHHCHHHHHHHHHHHCCHHHHHHHCCCCCCCCCHHHH Q ss_conf 080123201256689999999743689985--5999999---97448799999999974614555424544101688999 Q gi|254781146|r 12 KYPCINRLSHKEISLQYLYQSVLTDDFSKY--GRKVIKN---LREEKPEQYLRLISQILPREKIKQDGITNGDQLTDEQL 86 (122) Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~l~dDF~~h--G~~vIar---vReeKPeqYLKlVaSiLPkdl~~~~gin~~D~LSDEQl 86 (122) -+|-.||+..-|-.++|.|-+-.+++...- +..-+.| +-+.+|+ ++|++-+-|- +.+||.-|+ T Consensus 68 ~fp~lnr~~tle~dl~~yyg~nwre~I~~sp~t~~yv~rv~~iaa~ap~---lLIah~ytRy---------LGdlsggq~ 135 (238) T COG5398 68 YFPELNRKATLEKDLLYYYGNNWRENIQPSPATIAYVDRVRYIAATAPE---LLIAHNYTRY---------LGDLSGGQI 135 (238) T ss_pred CCHHHHHHHHHHCCHHHHHCCCHHHHCCCCHHHHHHHHHHHHHHHCCCC---HHHHHHHHHH---------HHCCCCCHH T ss_conf 3610326877634878773251988648474689999999999962860---4578888988---------704887189 Q ss_pred HHHHHH Q ss_conf 999998 Q gi|254781146|r 87 CEIIRS 92 (122) Q Consensus 87 ~erIRa 92 (122) +++|-- T Consensus 136 l~ki~q 141 (238) T COG5398 136 LKKIAQ 141 (238) T ss_pred HHHHHH T ss_conf 999999 No 12 >PRK04192 V-type ATP synthase subunit A; Provisional Probab=34.59 E-value=43 Score=16.00 Aligned_cols=67 Identities=27% Similarity=0.375 Sum_probs=32.1 Q ss_pred CCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHCHHHHHHHHHHHCCHH--HHHHHCCCCCCCCCH Q ss_conf 11000080123201256689999999743689985-599999997448799999999974614--555424544101688 Q gi|254781146|r 7 LPIRKKYPCINRLSHKEISLQYLYQSVLTDDFSKY-GRKVIKNLREEKPEQYLRLISQILPRE--KIKQDGITNGDQLTD 83 (122) Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~dDF~~h-G~~vIarvReeKPeqYLKlVaSiLPkd--l~~~~gin~~D~LSD 83 (122) |.-++.||.||.|.--- +|...+.+-|.++ ++.-. +.|+ -...||-++ +.--+.+-+.|.|+| T Consensus 419 lA~~rhfPainwl~SyS-----~y~~~~~~~~~~~~~~~~~-~~r~--------~~~~iL~~e~~l~eiv~lvG~d~l~~ 484 (585) T PRK04192 419 LAYRRHYPAINWLTSYS-----LYLDDVADWWEENVSPDWR-ELRD--------EAMSLLQREAELQEIVRLVGEDALSE 484 (585) T ss_pred HHHCCCCCCCCHHHHHH-----HHHHHHHHHHHHHCCCHHH-HHHH--------HHHHHHHHHHHHHHHHHHHCCCCCCH T ss_conf 77556688667024367-----7888899999874181599-9999--------99999872689999998647755898 Q ss_pred HHHH Q ss_conf 9999 Q gi|254781146|r 84 EQLC 87 (122) Q Consensus 84 EQl~ 87 (122) +|-. T Consensus 485 ~~~l 488 (585) T PRK04192 485 EDRL 488 (585) T ss_pred HHHH T ss_conf 8978 No 13 >PRK12524 RNA polymerase sigma factor; Provisional Probab=31.48 E-value=29 Score=17.09 Aligned_cols=10 Identities=10% Similarity=0.245 Sum_probs=4.3 Q ss_pred CHHHHHHHHH Q ss_conf 8799999999 Q gi|254781146|r 53 KPEQYLRLIS 62 (122) Q Consensus 53 KPeqYLKlVa 62 (122) ++..||.-|+ T Consensus 77 ~~~tWL~~Ia 86 (196) T PRK12524 77 RVSTWLYRVV 86 (196) T ss_pred HHHHHHHHHH T ss_conf 7999999999 No 14 >COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription] Probab=31.38 E-value=20 Score=18.25 Aligned_cols=15 Identities=27% Similarity=0.600 Sum_probs=9.1 Q ss_pred HHHHHHHHCCHHHHH Q ss_conf 999999974614555 Q gi|254781146|r 57 YLRLISQILPREKIK 71 (122) Q Consensus 57 YLKlVaSiLPkdl~~ 71 (122) --|.|++|||+|+.+ T Consensus 17 VqKMvS~iLp~dl~f 31 (148) T COG5150 17 VQKMVSSILPKDLVF 31 (148) T ss_pred HHHHHHHHCCCCCCC T ss_conf 999999856522245 No 15 >pfam09628 YvfG YvfG protein. Yvfg is a hypothetical protein of 71 residues expressed in some bacteria. The monomer consists of two parallel alpha helices, and the protein crystallises as a homo-dimer. Probab=30.64 E-value=50 Score=15.58 Aligned_cols=54 Identities=15% Similarity=0.269 Sum_probs=31.4 Q ss_pred HHHHHHHHHHHHHHHHHHHC---HHHHHHHHHHHCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 43689985599999997448---7999999999746145554245441016889999999988998888 Q gi|254781146|r 34 LTDDFSKYGRKVIKNLREEK---PEQYLRLISQILPREKIKQDGITNGDQLTDEQLCEIIRSLEKELQI 99 (122) Q Consensus 34 l~dDF~~hG~~vIarvReeK---PeqYLKlVaSiLPkdl~~~~gin~~D~LSDEQl~erIRaLd~aiRp 99 (122) +-++|.+|-.---+ -|+| -..|.|.|+|-+-.|-++. .--++-|||-||.|-+- T Consensus 8 fi~Nfk~hi~mn~~--yedKIhA~NaYYksV~~si~~Dqi~K----------NA~~ikRiqHLdEAY~K 64 (68) T pfam09628 8 FIENFKEHIEMNEA--YEDKIHALNAYYKSVAGSILADQIAK----------NADLIKRIQHLDEAYNK 64 (68) T ss_pred HHHHHHHHHHHCCH--HHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHH T ss_conf 99989999985700--88899999999999999999999985----------08999999989999998 No 16 >COG1494 GlpX Fructose-1,6-bisphosphatase/sedoheptulose 1,7-bisphosphatase and related proteins [Carbohydrate transport and metabolism] Probab=28.58 E-value=25 Score=17.54 Aligned_cols=66 Identities=14% Similarity=0.130 Sum_probs=49.2 Q ss_pred HHHHHHHHHHHHC-HHHHHHHHHHHCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHH Q ss_conf 5599999997448-799999999974614555424544101688999999998899888873110111 Q gi|254781146|r 41 YGRKVIKNLREEK-PEQYLRLISQILPREKIKQDGITNGDQLTDEQLCEIIRSLEKELQIFTDFKNKD 107 (122) Q Consensus 41 hG~~vIarvReeK-PeqYLKlVaSiLPkdl~~~~gin~~D~LSDEQl~erIRaLd~aiRpf~~~k~r~ 107 (122) -||.+--.|.-++ ++.-|+.||.-|-|+++--+-+. +|---..|+|+.||.+-+.++-+.|+---+ T Consensus 125 VgP~a~g~IDl~~p~~~Nl~~vAkalgk~~~dl~vvi-ldrpRH~~lI~~ir~~GarV~li~DGDVa~ 191 (332) T COG1494 125 VGPEAKGVIDLDAPLADNLRAVAKALGKSLSDLTVVI-LDRPRHAELIAEIRAAGARVRLIPDGDVAA 191 (332) T ss_pred CCCCCCCEEECCCCHHHHHHHHHHHHCCCHHHEEEEE-ECCHHHHHHHHHHHHHCCEEEEECCCCHHH T ss_conf 0755464662689979999999987299878928999-537029999999997297799836874434 No 17 >KOG3284 consensus Probab=28.55 E-value=54 Score=15.34 Aligned_cols=27 Identities=26% Similarity=0.490 Sum_probs=22.5 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHC Q ss_conf 441016889999999988998888731 Q gi|254781146|r 76 TNGDQLTDEQLCEIIRSLEKELQIFTD 102 (122) Q Consensus 76 n~~D~LSDEQl~erIRaLd~aiRpf~~ 102 (122) +-.|+|+|.|.++-+--||+|-.-|-. T Consensus 185 ~asDeL~e~q~RqllfDLEsAY~~f~~ 211 (213) T KOG3284 185 SASDELTEQQVRQLLFDLESAYNSFNA 211 (213) T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 633324699999999879999999986 No 18 >COG3962 Acetolactate synthase [Amino acid transport and metabolism] Probab=27.18 E-value=33 Score=16.78 Aligned_cols=41 Identities=24% Similarity=0.305 Sum_probs=25.0 Q ss_pred CCCCCCHHHHHCHHH--HHHHHHHHHHH------HHHHHHHHHHHHHHH Q ss_conf 000080123201256--68999999974------368998559999999 Q gi|254781146|r 9 IRKKYPCINRLSHKE--ISLQYLYQSVL------TDDFSKYGRKVIKNL 49 (122) Q Consensus 9 ~~~~~~~~~~~~~~~--~~~~~~~~~~l------~dDF~~hG~~vIarv 49 (122) -..-|-|||||.-.. -|..-+|..-. .-||++|-.+-=++. T Consensus 497 DN~GyGCIn~LQm~~Gg~sf~~~~r~~~~e~~~~~vDfA~~A~s~Ga~~ 545 (617) T COG3962 497 DNRGYGCINRLQMATGGASFNNLLRDTDHEEEILQVDFAAHAESYGAKA 545 (617) T ss_pred CCCCCCHHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHCCCEE T ss_conf 7887513655555407602313565403557877663898886548625 No 19 >TIGR00608 radc DNA repair protein RadC; InterPro: IPR001405 RadC is a DNA repair protein found in many bacteria. They share a region of similarity at the C-terminus that contains two perfectly conserved histidine residues.; GO: 0006281 DNA repair. Probab=24.69 E-value=41 Score=16.09 Aligned_cols=22 Identities=41% Similarity=0.661 Sum_probs=19.1 Q ss_pred CHHHHHHHCCCCCCCCCHHHHHHHH Q ss_conf 6145554245441016889999999 Q gi|254781146|r 66 PREKIKQDGITNGDQLTDEQLCEII 90 (122) Q Consensus 66 Pkdl~~~~gin~~D~LSDEQl~erI 90 (122) |||+-...|. ..|||.+|...| T Consensus 2 PREkLLk~Ga---~~L~d~ELLAi~ 23 (223) T TIGR00608 2 PREKLLKFGA---EALSDYELLAIL 23 (223) T ss_pred CHHHHHHCCH---HCCCCHHHHHHH T ss_conf 5032333163---005646799999 No 20 >COG5191 Uncharacterized conserved protein, contains HAT (Half-A-TPR) repeat [General function prediction only] Probab=23.80 E-value=65 Score=14.78 Aligned_cols=69 Identities=30% Similarity=0.512 Sum_probs=51.4 Q ss_pred HHHHHHHHH-----HHHHHHHHHHHHHH--------------HHHHHCHHHHHHHHHH-------HCCHHHHHHHCCCCC Q ss_conf 899999997-----43689985599999--------------9974487999999999-------746145554245441 Q gi|254781146|r 25 SLQYLYQSV-----LTDDFSKYGRKVIK--------------NLREEKPEQYLRLISQ-------ILPREKIKQDGITNG 78 (122) Q Consensus 25 ~~~~~~~~~-----l~dDF~~hG~~vIa--------------rvReeKPeqYLKlVaS-------iLPkdl~~~~gin~~ 78 (122) .+||+||.- +||.|-..+.+-|- .+|.+-|+-|+|.|.- -.|++++--+ - T Consensus 303 ~lnYlfsEsl~~~~~~~E~~~~E~~~l~~~vL~~W~~~~~~lsLR~~~P~~~~~~~~~~I~~~~r~~P~~~~~i~----q 378 (435) T COG5191 303 TLNYLFSESLRYIKLFDEFLDLERDYLINHVLQFWKNDMYDLSLRKDLPELYLKTVMIDITLNIRYMPVEKLDID----Q 378 (435) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHCCHHCCEEEEECCCCHHHHHHH----C T ss_conf 999999876699999899870121279999999987668878761135165424101020211215716776664----1 Q ss_pred CCCCHHHHHHHHHHHHHHH Q ss_conf 0168899999999889988 Q gi|254781146|r 79 DQLTDEQLCEIIRSLEKEL 97 (122) Q Consensus 79 D~LSDEQl~erIRaLd~ai 97 (122) |+++-+.+-..|--|+++- T Consensus 379 ~~~~V~~~~A~i~K~~S~S 397 (435) T COG5191 379 LQLSVKKYFAYISKLDSAS 397 (435) T ss_pred CCCHHHHHHHHHHHHHHHH T ss_conf 3000999999999873166 No 21 >PRK12519 RNA polymerase sigma factor; Provisional Probab=23.34 E-value=53 Score=15.37 Aligned_cols=10 Identities=20% Similarity=0.361 Sum_probs=4.6 Q ss_pred CHHHHHHHHH Q ss_conf 8799999999 Q gi|254781146|r 53 KPEQYLRLIS 62 (122) Q Consensus 53 KPeqYLKlVa 62 (122) ....||-.|+ T Consensus 79 ~~~~wL~~ia 88 (194) T PRK12519 79 SLSSYLLTLT 88 (194) T ss_pred CHHHHHHHHH T ss_conf 2999999999 No 22 >COG4451 RbcS Ribulose bisphosphate carboxylase small subunit [Energy production and conversion] Probab=22.03 E-value=60 Score=15.00 Aligned_cols=30 Identities=37% Similarity=0.526 Sum_probs=17.4 Q ss_pred HCCHHHHHHHCCCCCCCCCHHHHHHHHHHHH Q ss_conf 7461455542454410168899999999889 Q gi|254781146|r 64 ILPREKIKQDGITNGDQLTDEQLCEIIRSLE 94 (122) Q Consensus 64 iLPkdl~~~~gin~~D~LSDEQl~erIRaLd 94 (122) ++|++ +-.-+-+-.-.|||+|+.+-+|.|= T Consensus 3 ~~P~~-~~~~~~s~lp~Ltd~qi~~QVrylL 32 (127) T COG4451 3 ILPKN-SRYKTLSSLPPLTDEQIAEQVRYLL 32 (127) T ss_pred CCCCC-CCCCCEECCCCCCHHHHHHHHHHHH T ss_conf 36888-7645343378676799999999998 No 23 >PRK13919 putative RNA polymerase sigma E protein; Provisional Probab=21.63 E-value=56 Score=15.20 Aligned_cols=10 Identities=10% Similarity=0.351 Sum_probs=4.6 Q ss_pred HHHHHHHHHH Q ss_conf 7999999999 Q gi|254781146|r 54 PEQYLRLISQ 63 (122) Q Consensus 54 PeqYLKlVaS 63 (122) ...||--|+. T Consensus 75 ~~~wL~~ia~ 84 (187) T PRK13919 75 ARAFLLTLGH 84 (187) T ss_pred HHHHHHHHHH T ss_conf 9999999999 No 24 >TIGR02948 SigW_bacill RNA polymerase sigma-W factor; InterPro: IPR014294 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents sigmaW, which is restricted to certain lineages of the order Bacillales.. Probab=21.48 E-value=22 Score=17.92 Aligned_cols=21 Identities=33% Similarity=0.479 Sum_probs=15.9 Q ss_pred HHHHHHHHHHHHHHCHHHHHH Q ss_conf 985599999997448799999 Q gi|254781146|r 39 SKYGRKVIKNLREEKPEQYLR 59 (122) Q Consensus 39 ~~hG~~vIarvReeKPeqYLK 59 (122) +--.--.|-++|--|||.||. T Consensus 75 RIATNl~IDrlRKrKPD~yLd 95 (187) T TIGR02948 75 RIATNLTIDRLRKRKPDFYLD 95 (187) T ss_pred HHHHHHHHHHHHCCCCCCCCC T ss_conf 999877886541348886436 No 25 >TIGR02026 BchE magnesium-protoporphyrin IX monomethyl ester anaerobic oxidative cyclase; InterPro: IPR011772 This entry respresents the cobalamin-dependent oxidative cyclase responsible for forming the distinctive E-ring of the chlorin ring system under anaerobic conditions . This step is essential in the biosynthesis of both bacteriochlorophyll and chlorophyll under anaerobic conditions (a separate enzyme, AcsF, acts under aerobic conditions). This entry identifies two clades of sequences, one from photosynthetic, non-cyanobacterial bacteria and another including Synechocystis and several non-photosynthetic bacteria. The function of the Synechocystis gene is supported by gene clustering with other photosynthetic genes, so the purpose of the gene in the non-photosynthetic bacteria is uncertain. Note that homologues of this gene are not found in plants which rely solely on the aerobic cyclase.; GO: 0016709 oxidoreductase activity acting on paired donors with incorporation or reduction of molecular oxygen NADH or NADPH as one donor and incorporation of one atom of oxygen, 0050661 NADP binding, 0015995 chlorophyll biosynthetic process. Probab=21.42 E-value=42 Score=16.08 Aligned_cols=21 Identities=48% Similarity=0.604 Sum_probs=14.6 Q ss_pred HHHCCCCCCCCCHHHHHHHHHHH Q ss_conf 54245441016889999999988 Q gi|254781146|r 71 KQDGITNGDQLTDEQLCEIIRSL 93 (122) Q Consensus 71 ~~~gin~~D~LSDEQl~erIRaL 93 (122) +-++-+ |.||||+|.|++|++ T Consensus 43 f~DA~~--~~l~de~l~e~lr~~ 63 (506) T TIGR02026 43 FLDAMT--DPLTDEKLVERLRAH 63 (506) T ss_pred EEECCC--CCCCHHHHHHHHHHC T ss_conf 762236--888748999999725 No 26 >pfam11107 FANCF Fanconi anemia group F protein (FANCF). FANCF regulates its own expression by methylation at both mRNA and protein levels. Methylation-induced inactivation of FANCF has an important role on the occurrence of ovarian cancers by disrupting the FA-BRCA pathway. Probab=21.20 E-value=73 Score=14.44 Aligned_cols=52 Identities=23% Similarity=0.294 Sum_probs=29.9 Q ss_pred HHHHHHHCCHHHHHHHCCCCCCCCCHHHHHHHHHHHH--------HHHHHHHCCHHHHCC Q ss_conf 9999997461455542454410168899999999889--------988887311011111 Q gi|254781146|r 58 LRLISQILPREKIKQDGITNGDQLTDEQLCEIIRSLE--------KELQIFTDFKNKDAH 109 (122) Q Consensus 58 LKlVaSiLPkdl~~~~gin~~D~LSDEQl~erIRaLd--------~aiRpf~~~k~r~~~ 109 (122) |+...|-+--|...-.-++.--+++=|++|||+|+|- .+.+.+-+.|-.||. T Consensus 267 L~~wg~~l~yD~~~G~Wv~~e~~~~~eeL~erf~~L~~~~~~Lke~~~~~L~~lk~qDGD 326 (343) T pfam11107 267 LKVWGQWMIYDVFEGLWVGLEAAGSFDELCERFRSLTQGSPPLKDATLTALEDLKRQDGD 326 (343) T ss_pred HHHHHHHHHCCCCCCCEECCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCC T ss_conf 999987612050026100566667899999999998569877899999999999985489 No 27 >TIGR01740 pyrF orotidine 5'-phosphate decarboxylase; InterPro: IPR014732 Orotidine 5'-phosphate decarboxylase (OMPdecase) (4.1.1.23 from EC) , catalyzes the last step in the de novo biosynthesis of pyrimidines, the decarboxylation of OMP into UMP. In higher eukaryotes OMPdecase is part, with orotate phosphoribosyltransferase, of a bifunctional enzyme, while the prokaryotic and fungal OMPdecases are monofunctional proteins. Some parts of the sequence of OMPdecase are well conserved across species. The best conserved region is located in the N-terminal half of OMPdecases and is centred around a lysine residue which is essential for the catalytic function of the enzyme.. Probab=21.19 E-value=49 Score=15.60 Aligned_cols=57 Identities=26% Similarity=0.273 Sum_probs=43.3 Q ss_pred CHHHHHHHHHHHCCHHH--HHHHCCCCCCCCCHHHHHHHHHHHHH--HHHHHHCCHHHHCC Q ss_conf 87999999999746145--55424544101688999999998899--88887311011111 Q gi|254781146|r 53 KPEQYLRLISQILPREK--IKQDGITNGDQLTDEQLCEIIRSLEK--ELQIFTDFKNKDAH 109 (122) Q Consensus 53 KPeqYLKlVaSiLPkdl--~~~~gin~~D~LSDEQl~erIRaLd~--aiRpf~~~k~r~~~ 109 (122) -++..|+++.++=|-.- ..-+|+.=...-+|+++++.+-.+.+ -+++|+|+|=-|=+ T Consensus 9 ~~~e~l~~a~~~~~~~~v~~~Kvg~~l~~~~~~~~~~~~L~~~~~KHNf~if~D~Kf~DIp 69 (233) T TIGR01740 9 TKEEALKLADSLGPEIDVLVIKVGIDLLLSGGYEKIIEELAKLNKKHNFLIFLDLKFADIP 69 (233) T ss_pred CHHHHHHHHHHHCCEEEEEEEECCHHHHHCCCCHHHHHHHHHHHCCCCCEEEECCEECCCC T ss_conf 9899999997504627777775142333327848899999997456882032120313661 No 28 >KOG4816 consensus Probab=20.32 E-value=65 Score=14.79 Aligned_cols=32 Identities=38% Similarity=0.545 Sum_probs=22.7 Q ss_pred CCCCEECCCCCCCCHH--HHHCHHHHHHHHHHHHH Q ss_conf 9871221100008012--32012566899999997 Q gi|254781146|r 1 MSPLTLLPIRKKYPCI--NRLSHKEISLQYLYQSV 33 (122) Q Consensus 1 ~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~ 33 (122) |-|-+.+|.| .||-- ---..+.|-|.||||-. T Consensus 30 ~rPsvYlPTr-eyPseQiIvTEktNILlRylhQqw 63 (98) T KOG4816 30 MRPSVYLPTR-EYPSEQIIVTEKTNILLRYLHQQW 63 (98) T ss_pred CCCCCCCCCC-CCCCHHEEEEHHHHHHHHHHHHHH T ss_conf 6764005666-798133454024689999999999 Done!