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!