Query         gi|254781219|ref|YP_003065632.1| hypothetical protein CLIBASIA_05630 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 200
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 30 06:21:06 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781219.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 COG4900 Predicted metallopepti  52.1      13 0.00033   18.6   2.6   22   92-113    68-92  (133)
  2 COG3513 Predicted CRISPR-assoc  37.9      33 0.00085   15.8   6.0   52  121-177   184-241 (1088)
  3 KOG4584 consensus               37.7      34 0.00086   15.7   5.9   17   29-45     75-99  (348)
  4 TIGR01398 FlhA flagellar biosy  33.0      24 0.00062   16.7   1.5   26  108-133   585-611 (713)
  5 TIGR00970 leuA_yeast 2-isoprop  32.8      12 0.00031   18.8  -0.0   25   15-40    165-189 (615)
  6 TIGR02941 Sigma_B RNA polymera  30.1      28 0.00072   16.3   1.5  138    6-198     4-153 (256)
  7 pfam12588 PSDC Phophatidylseri  29.5      45  0.0011   14.9   2.5   17  109-125    92-108 (140)
  8 KOG1505 consensus               29.3      43  0.0011   15.0   2.3   36   46-81    166-202 (346)
  9 pfam10220 DUF2146 Uncharacteri  27.9      48  0.0012   14.7   2.4   12  110-121   207-218 (890)
 10 COG5088 SOH1 Rad5p-binding pro  27.5      33 0.00085   15.8   1.4   19    8-31     46-64  (114)
 11 TIGR02200 GlrX_actino Glutared  26.9      30 0.00078   16.0   1.2   21  180-200    56-77  (78)
 12 PRK13762 tRNA-modifying enzyme  26.5      51  0.0013   14.5   2.8   32  166-197   142-173 (321)
 13 KOG2957 consensus               26.3      51  0.0013   14.5   4.3  149   15-176    43-218 (350)
 14 pfam00081 Sod_Fe_N Iron/mangan  25.2      25 0.00063   16.7   0.5   21  117-139    59-79  (82)
 15 KOG3220 consensus               24.0      34 0.00087   15.7   1.0   56   82-137     7-69  (225)
 16 COG4807 Uncharacterized protei  22.7      17 0.00044   17.7  -0.8   38   66-109    51-88  (155)
 17 pfam03982 DAGAT Diacylglycerol  22.5      60  0.0015   14.0   2.8   26  138-165   267-292 (297)
 18 pfam10759 DUF2587 Protein of u  22.4      60  0.0015   14.0   4.2   31  163-196    71-101 (168)
 19 KOG3189 consensus               21.9      59  0.0015   14.0   1.9   32  129-162   180-215 (252)
 20 TIGR02121 Na_Pro_sym sodium/pr  21.7      42  0.0011   15.1   1.1   11  148-158   365-375 (517)
 21 TIGR01788 Glu-decarb-GAD gluta  21.6      61  0.0016   13.9   1.9   46  123-173   328-373 (493)
 22 smart00340 HALZ homeobox assoc  21.6      63  0.0016   13.9   3.6   26   19-52      8-33  (44)
 23 TIGR01361 DAHP_synth_Bsub phos  21.3      21 0.00055   17.1  -0.5   38   36-74     66-103 (262)
 24 KOG4086 consensus               20.9      52  0.0013   14.4   1.4   19    7-30     45-63  (130)
 25 pfam08991 DUF1903 Domain of un  20.7      65  0.0017   13.8   2.3   39   34-74     16-54  (62)
 26 pfam10755 DUF2585 Protein of u  20.6      49  0.0013   14.6   1.2   76   74-152    35-116 (165)

No 1  
>COG4900 Predicted metallopeptidase [General function prediction only]
Probab=52.13  E-value=13  Score=18.56  Aligned_cols=22  Identities=55%  Similarity=0.748  Sum_probs=17.0

Q ss_pred             HHHHHCHHHHH---HHHHHHHHHHH
Q ss_conf             77641215799---87636888999
Q gi|254781219|r   92 ITEKFKPLAVA---KVVSDELLHDK  113 (200)
Q Consensus        92 itekfkplava---kvvsdellhdk  113 (200)
                      +.|||+||..+   ||+-.||||-.
T Consensus        68 ~sekF~rLs~~ekvKviiHEllHIP   92 (133)
T COG4900          68 LSEKFKRLSCAEKVKVIIHELLHIP   92 (133)
T ss_pred             EHHHCCCCCHHHHHHHHHHHHHCCC
T ss_conf             0455477873777889999886386


No 2  
>COG3513 Predicted CRISPR-associated nuclease, contains McrA/HNH-nuclease and RuvC-like nuclease domain [Defense mechanisms]
Probab=37.93  E-value=33  Score=15.76  Aligned_cols=52  Identities=33%  Similarity=0.589  Sum_probs=30.3

Q ss_pred             HHHHCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHHH------HHCCCHHHHHCCHHHHHHHHH
Q ss_conf             853010103643224566657899999999999998------520881542030489998875
Q gi|254781219|r  121 SVRNYSRDSGHLNRDVIFHSRYALIRYLEDFYKEIK------HTFGNPADALSPHISELADEI  177 (200)
Q Consensus       121 svrnysrdsghlnrdvifhsryaliryledfykeik------htfgnpadalsphiseladei  177 (200)
                      |..-.+|.+||... .  ...|.-|-.-+|||+|+|      ++||||.  .|-|+.|+....
T Consensus       184 s~~~~~ke~~h~rn-~--~~~Y~~~f~q~dl~~elklifeKQr~FgnPh--~~~hl~E~~~~L  241 (1088)
T COG3513         184 SAKMIEKEDTHIRN-L--PESYEEIFSQSDLYKELKLIFEKQREFGNPH--FSKHLEELVAIL  241 (1088)
T ss_pred             HHHHHHHHHHHHHC-C--CHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH--HHHHHHHHHHHH
T ss_conf             78876533202203-6--0149998639999999999999877338905--665699999999


No 3  
>KOG4584 consensus
Probab=37.70  E-value=34  Score=15.73  Aligned_cols=17  Identities=47%  Similarity=0.772  Sum_probs=9.1

Q ss_pred             CCHHHHHH--------HHHHHHHHH
Q ss_conf             18011113--------678878999
Q gi|254781219|r   29 YSPESYSN--------TYREQKLRD   45 (200)
Q Consensus        29 yspesysn--------tyreqklrd   45 (200)
                      -.|++|.+        .-|||-||.
T Consensus        75 ~~P~a~G~~~~g~~Ll~lRE~~LrE   99 (348)
T KOG4584          75 KDPEAYGGPPLGINLLRLREQILRE   99 (348)
T ss_pred             HCHHHCCCCCCHHHHHHHHHHHHHH
T ss_conf             4857408995047899999999997


No 4  
>TIGR01398 FlhA flagellar biosynthesis protein FlhA; InterPro: IPR006301   These sequences describe the flagellar biosynthesis protein FlhA, one of a large number of genes associated with the biosynthesis of functional bacterial flagella. Homologs of many such proteins, including FlhA, function in type III protein secretion systems. ; GO: 0015031 protein transport, 0016021 integral to membrane, 0019861 flagellum.
Probab=33.02  E-value=24  Score=16.72  Aligned_cols=26  Identities=23%  Similarity=0.503  Sum_probs=12.0

Q ss_pred             HHHHHHHHHHHHHH-HHHCCHHCCCCC
Q ss_conf             88899999999998-530101036432
Q gi|254781219|r  108 ELLHDKLNKILKKS-VRNYSRDSGHLN  133 (200)
Q Consensus       108 ellhdklnkilkks-vrnysrdsghln  133 (200)
                      ++|-.+.-.-|.+. ++.|..|.|.|+
T Consensus       585 ~~L~E~VR~rL~rqI~~~~~~~~g~L~  611 (713)
T TIGR01398       585 DLLVEHVRQRLGRQITQQYLDEDGVLK  611 (713)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCEEE
T ss_conf             789999999999999996448898279


No 5  
>TIGR00970 leuA_yeast 2-isopropylmalate synthase; InterPro: IPR005668    Alpha-isopropylmalate synthase (2.3.3.13 from EC) catalyses the first step in the biosynthesis of leucine, the condensation of acetyl-CoA and alpha- ketoisovalerate to form 2-isopropylmalate synthase. This model describes a family of 2-isopropylmalate synthases as found in yeasts and in a minority of studied bacteria.; GO: 0003852 2-isopropylmalate synthase activity, 0009098 leucine biosynthetic process.
Probab=32.80  E-value=12  Score=18.78  Aligned_cols=25  Identities=40%  Similarity=0.587  Sum_probs=14.0

Q ss_pred             HHHHHHHHHHHHHHCCHHHHHHHHHH
Q ss_conf             78999999998864180111136788
Q gi|254781219|r   15 EDVKFYLDKWCEALYSPESYSNTYRE   40 (200)
Q Consensus        15 edvkfyldkwcealyspesysntyre   40 (200)
                      .+.+.--..|- -=||||+||.|--|
T Consensus       165 ~a~~~~~T~W~-fEySPE~fsdTe~e  189 (615)
T TIGR00970       165 DAAKSKETRWS-FEYSPESFSDTELE  189 (615)
T ss_pred             HHHHCCCCCCC-CEECCCCCCCCCHH
T ss_conf             33415776453-10067767888547


No 6  
>TIGR02941 Sigma_B RNA polymerase sigma-B factor; InterPro: IPR014288   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 sigma factor, sigmaB. It is restricted to certain species within the order Bacillales including Staphylococcus aureus , Listeria monocytogenes  and Bacillus cereus (strain ATCC 14579 / DSM 31) ..
Probab=30.08  E-value=28  Score=16.27  Aligned_cols=138  Identities=27%  Similarity=0.439  Sum_probs=71.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH----HHHHHHHHHHHHCHHHHHHHCCCCCCHHHHHHHHH
Q ss_conf             79999988878999999998864180111136788789999----99999997654064369872899510367799999
Q gi|254781219|r    6 QKQFKNYLHEDVKFYLDKWCEALYSPESYSNTYREQKLRDK----IIELRRKFAKENGLKTVTEVCPKPKDITYSLSHFI   81 (200)
Q Consensus         6 qkqfknylhedvkfyldkwcealyspesysntyreqklrdk----iielrrkfakenglktvtevcpkpkdityslshfi   81 (200)
                      ++|-.|--.|+|-    +|-+-+-.  .-.|+--..||-++    |--+-+|+.|...         ---|+---   =.
T Consensus         4 ~sqp~n~~~e~v~----~wI~e~Q~--nP~n~eaQeklV~hY~~Lv~SiAykYSKg~~---------~HEDlvQV---GM   65 (256)
T TIGR02941         4 KSQPTNLTKEDVI----QWIKEFQK--NPKNEEAQEKLVKHYQDLVESIAYKYSKGSA---------IHEDLVQV---GM   65 (256)
T ss_pred             CCCCCCCCHHHHH----HHHHHHCC--CCCCHHHHHHHHHHHHHHHHHHHHHHCCCCC---------CCCCHHHH---HH
T ss_conf             6576557887899----99999636--9983257899999998999988754048788---------33304567---68


Q ss_pred             HHHHHHHH---HHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH---CCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99975357---777764121579987636888999999999985301010---364322456665789999999999999
Q gi|254781219|r   82 EGLIESER---SKITEKFKPLAVAKVVSDELLHDKLNKILKKSVRNYSRD---SGHLNRDVIFHSRYALIRYLEDFYKEI  155 (200)
Q Consensus        82 eglieser---skitekfkplavakvvsdellhdklnkilkksvrnysrd---sghlnrdvifhsryaliryledfykei  155 (200)
                      -||+..-|   .-+-.+|-|.||..||..              +..|-||   |=|.-|-+            .|.=-.|
T Consensus        66 ~GLlgAirRyD~s~g~~FE~FaiPTiiGE--------------IKrylRDKTWsvHVPRRI------------KelGpkI  119 (256)
T TIGR02941        66 VGLLGAIRRYDYSYGKAFEAFAIPTIIGE--------------IKRYLRDKTWSVHVPRRI------------KELGPKI  119 (256)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCHHHH--------------HHHHHCCCCCCCCCCCCH------------HCCCCCC
T ss_conf             99999986511000456566236610010--------------112111564300157411------------0037720


Q ss_pred             HHHCCCHHH--HHCCHHHHHHHHHHHHHHEEEEEECHHHHHHHHH
Q ss_conf             852088154--2030489998875225101455646028999876
Q gi|254781219|r  156 KHTFGNPAD--ALSPHISELADEIHTTCFTLQFVVNPSEAELLEK  198 (200)
Q Consensus       156 khtfgnpad--alsphiseladeihttcftlqfvvnpseaellek  198 (200)
                      |.....-.+  --||.|+|.|+.+-           -||-|.||-
T Consensus       120 kk~~dELT~~lqrSP~i~EIA~~lg-----------~SEEEVLE~  153 (256)
T TIGR02941       120 KKAVDELTDELQRSPKIAEIADRLG-----------VSEEEVLEI  153 (256)
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHCC-----------CCHHHHHHH
T ss_conf             1455664444214870654641217-----------748889877


No 7  
>pfam12588 PSDC Phophatidylserine decarboxylase. This domain family is found in bacteria and eukaryotes, and is approximately 140 amino acids in length. The family is found in association with pfam02666. Phosphatidylserine decarboxylase (PSD) is an important enzyme in the synthesis of phosphatidylethanolamine in both prokaryotes and eukaryotes.
Probab=29.54  E-value=45  Score=14.85  Aligned_cols=17  Identities=24%  Similarity=0.356  Sum_probs=8.1

Q ss_pred             HHHHHHHHHHHHHHHHC
Q ss_conf             88999999999985301
Q gi|254781219|r  109 LLHDKLNKILKKSVRNY  125 (200)
Q Consensus       109 llhdklnkilkksvrny  125 (200)
                      .+....|..|||-..-+
T Consensus        92 F~~p~vN~~lK~ILn~W  108 (140)
T pfam12588        92 FRDPAVNAQLKKILNEW  108 (140)
T ss_pred             HHCHHHHHHHHHHHHHH
T ss_conf             81889999999999999


No 8  
>KOG1505 consensus
Probab=29.29  E-value=43  Score=14.99  Aligned_cols=36  Identities=31%  Similarity=0.456  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHHHHCHHHHHHH-CCCCCCHHHHHHHHH
Q ss_conf             999999997654064369872-899510367799999
Q gi|254781219|r   46 KIIELRRKFAKENGLKTVTEV-CPKPKDITYSLSHFI   81 (200)
Q Consensus        46 kiielrrkfakenglktvtev-cpkpkdityslshfi   81 (200)
                      +.-|.-++||++|||+-...| +|.-+...++++-.-
T Consensus       166 ~~~~~S~~fa~k~GLp~l~nvLlPRt~Gf~~~l~~lr  202 (346)
T KOG1505         166 KKHERSQEFAAKNGLPHLKNVLLPRTKGFKAALEELR  202 (346)
T ss_pred             HHHHHHHHHHHHCCCCCCCCEECCCCCHHHHHHHHHC
T ss_conf             8999899999976998755242567503999999860


No 9  
>pfam10220 DUF2146 Uncharacterized conserved protein (DUF2146). This is a family of proteins conserved from plants to humans. In Dictyostelium it is annotated as Mss11p but this could not be confirmed. Mss11p is required for the activation of pseudo-hyphal and invasive growth by Ste12p in yeast.
Probab=27.85  E-value=48  Score=14.66  Aligned_cols=12  Identities=50%  Similarity=0.794  Sum_probs=4.7

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             899999999998
Q gi|254781219|r  110 LHDKLNKILKKS  121 (200)
Q Consensus       110 lhdklnkilkks  121 (200)
                      |.|....||+++
T Consensus       207 lEdQIy~iLR~~  218 (890)
T pfam10220       207 LEDQIYDILRKS  218 (890)
T ss_pred             HHHHHHHHHHHC
T ss_conf             999999999875


No 10 
>COG5088 SOH1 Rad5p-binding protein [General function prediction only]
Probab=27.45  E-value=33  Score=15.77  Aligned_cols=19  Identities=53%  Similarity=1.046  Sum_probs=13.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCH
Q ss_conf             999988878999999998864180
Q gi|254781219|r    8 QFKNYLHEDVKFYLDKWCEALYSP   31 (200)
Q Consensus         8 qfknylhedvkfyldkwcealysp   31 (200)
                      .|+|||.     ||.-||+.-||.
T Consensus        46 ~F~~YL~-----YlEYWr~PeYs~   64 (114)
T COG5088          46 NFKNYLK-----YLEYWRNPEYSQ   64 (114)
T ss_pred             HHHHHHH-----HHHHHHCCCCCC
T ss_conf             8999999-----999861876300


No 11 
>TIGR02200 GlrX_actino Glutaredoxin-like protein; InterPro: IPR011915   Glutaredoxins , , , also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system .    Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond . It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond.   Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed  that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro.    This family of glutaredoxin-like proteins is limited to the Actinobacteria and contains the conserved CxxC motif..
Probab=26.86  E-value=30  Score=16.02  Aligned_cols=21  Identities=33%  Similarity=0.509  Sum_probs=15.4

Q ss_pred             HHHEE-EEEECHHHHHHHHHHC
Q ss_conf             51014-5564602899987629
Q gi|254781219|r  180 TCFTL-QFVVNPSEAELLEKVA  200 (200)
Q Consensus       180 tcftl-qfvvnpseaellekva  200 (200)
                      --|.= .|.+|||-++.++|++
T Consensus        56 V~~~DGs~~tnPSa~~v~~klq   77 (78)
T TIGR02200        56 VKFADGSFLTNPSAAQVKAKLQ   77 (78)
T ss_pred             EEECCCCCCCCCCHHHHHHHHC
T ss_conf             8747994443867789999843


No 12 
>PRK13762 tRNA-modifying enzyme; Provisional
Probab=26.53  E-value=51  Score=14.50  Aligned_cols=32  Identities=38%  Similarity=0.615  Sum_probs=12.6

Q ss_pred             HCCHHHHHHHHHHHHHHEEEEEECHHHHHHHH
Q ss_conf             03048999887522510145564602899987
Q gi|254781219|r  166 LSPHISELADEIHTTCFTLQFVVNPSEAELLE  197 (200)
Q Consensus       166 lsphiseladeihttcftlqfvvnpseaelle  197 (200)
                      +-|+|.||-++.|..-+|--.|.|-...+.|+
T Consensus       142 lYP~l~eLi~~~h~r~~stFLVTNg~~P~~l~  173 (321)
T PRK13762        142 LYPRLPELIEEFHKRGFTTFLVTNGTRPDVLE  173 (321)
T ss_pred             CCHHHHHHHHHHHHCCCCEEEEECCCCHHHHH
T ss_conf             20218999999985798379982898989998


No 13 
>KOG2957 consensus
Probab=26.34  E-value=51  Score=14.48  Aligned_cols=149  Identities=28%  Similarity=0.421  Sum_probs=74.1

Q ss_pred             HHHHHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHH---HHHHHHHHCHHHHHHHCCCCCCHHHHHHHHHHHHH---
Q ss_conf             789999999988641801---111367887899999999---99976540643698728995103677999999997---
Q gi|254781219|r   15 EDVKFYLDKWCEALYSPE---SYSNTYREQKLRDKIIEL---RRKFAKENGLKTVTEVCPKPKDITYSLSHFIEGLI---   85 (200)
Q Consensus        15 edvkfyldkwcealyspe---sysntyreqklrdkiiel---rrkfakenglktvtevcpkpkdityslshfiegli---   85 (200)
                      ||+|.-|.+---.++-..   +-+-+--+.++|+|...-   -|.-|- .++.|.-+      -|||+  |.|...+   
T Consensus        43 EDlki~Ls~Tdyg~fl~n~~s~lt~s~I~~~l~ekL~~ef~h~R~~a~-epl~tfld------yity~--ymIdNv~lLi  113 (350)
T KOG2957          43 EDLKIHLSSTDYGNFLANEPSPLTVSVIDEKLREKLVDEFDHIRDQAD-EPLSTFLD------YITYG--YMIDNVILLI  113 (350)
T ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC-CCHHHHHH------HHHHH--HHHHHHHHHH
T ss_conf             998776402542211036888875799999999999999999986043-31889999------99878--8886899987


Q ss_pred             -----HHHHHHHHHHHCHH------HHHHHHHH--HH-----HHHHHHHHHHHHHHHCCHHCCCCCHHHHHHHHHHHHHH
Q ss_conf             -----53577777641215------79987636--88-----89999999999853010103643224566657899999
Q gi|254781219|r   86 -----ESERSKITEKFKPL------AVAKVVSD--EL-----LHDKLNKILKKSVRNYSRDSGHLNRDVIFHSRYALIRY  147 (200)
Q Consensus        86 -----eserskitekfkpl------avakvvsd--el-----lhdklnkilkksvrnysrdsghlnrdvifhsryaliry  147 (200)
                           ...-+.+-+|-.||      ..-+|.++  ||     ....|-+-.+..++  ..|-..+|-.+|-..-|-  -|
T Consensus       114 tgtl~~r~~~ell~kChpLG~F~~l~ai~vA~n~~ely~~vlvdTpla~~F~dc~~--~~dld~mniEIiRn~lYK--ay  189 (350)
T KOG2957         114 TGTLHDRDVGELLEKCHPLGSFDQLEAIKVASNPAELYNAVLVDTPLAPYFEDCLS--EEDLDEMNIEIIRNTLYK--AY  189 (350)
T ss_pred             HCCCCCCCHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHCC--HHHHHHHHHHHHHHHHHH--HH
T ss_conf             24236977899998557767643311456518889998789746842677875358--745555419999999999--99


Q ss_pred             HHHHHHHHHHHCCCHHHHHCCHHHHHHHH
Q ss_conf             99999999852088154203048999887
Q gi|254781219|r  148 LEDFYKEIKHTFGNPADALSPHISELADE  176 (200)
Q Consensus       148 ledfykeikhtfgnpadalsphiselade  176 (200)
                      |||||+-.+.--|+.|+...|-.+=-||.
T Consensus       190 lE~fY~fc~~~g~~tae~M~~iL~fEaDR  218 (350)
T KOG2957         190 LEDFYNFCKKLGGATAEVMCEILAFEADR  218 (350)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHCCCC
T ss_conf             99999999865886599999987310351


No 14 
>pfam00081 Sod_Fe_N Iron/manganese superoxide dismutases, alpha-hairpin domain. superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplasmic Cu/Zn SOD, and a mitochondrial Mn/Fe SOD. N-terminal domain is a long alpha antiparallel hairpin. A small fragment of YTRE_LEPBI matches well - sequencing error?
Probab=25.22  E-value=25  Score=16.65  Aligned_cols=21  Identities=24%  Similarity=0.393  Sum_probs=10.4

Q ss_pred             HHHHHHHHCCHHCCCCCHHHHHH
Q ss_conf             99998530101036432245666
Q gi|254781219|r  117 ILKKSVRNYSRDSGHLNRDVIFH  139 (200)
Q Consensus       117 ilkksvrnysrdsghlnrdvifh  139 (200)
                      .+++.|||-  -+||.|-+.-|.
T Consensus        59 ~~~~~v~nN--agg~~NH~lfW~   79 (82)
T pfam00081        59 ALLGALFNN--GGGHWNHSFFWK   79 (82)
T ss_pred             HHHHHHHHH--HHHHHHHHHHHH
T ss_conf             989998871--027988999987


No 15 
>KOG3220 consensus
Probab=24.02  E-value=34  Score=15.70  Aligned_cols=56  Identities=21%  Similarity=0.413  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHH-------HHHHHHHHHCCHHCCCCCHHHH
Q ss_conf             9997535777776412157998763688899999-------9999985301010364322456
Q gi|254781219|r   82 EGLIESERSKITEKFKPLAVAKVVSDELLHDKLN-------KILKKSVRNYSRDSGHLNRDVI  137 (200)
Q Consensus        82 eglieserskitekfkplavakvvsdellhdkln-------kilkksvrnysrdsghlnrdvi  137 (200)
                      .|-|.|..|.+..-|+.+..+-+-+|-+-++-+.       +|.+---..+--.+|++||+++
T Consensus         7 TGgiatGKStVs~~f~~~G~~vIDaD~vaR~vv~PG~p~~~~ive~FG~eiLl~~G~inR~~L   69 (225)
T KOG3220           7 TGGIATGKSTVSQVFKALGIPVIDADVVAREVVEPGTPAYRRIVEAFGTEILLEDGEINRKVL   69 (225)
T ss_pred             ECCCCCCHHHHHHHHHHCCCCEECHHHHHHHHHCCCCHHHHHHHHHHCCEEECCCCCCCHHHH
T ss_conf             056566737999999974995762789999985599807899999848400056884168998


No 16 
>COG4807 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.67  E-value=17  Score=17.74  Aligned_cols=38  Identities=32%  Similarity=0.588  Sum_probs=26.4

Q ss_pred             HCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHH
Q ss_conf             28995103677999999997535777776412157998763688
Q gi|254781219|r   66 VCPKPKDITYSLSHFIEGLIESERSKITEKFKPLAVAKVVSDEL  109 (200)
Q Consensus        66 vcpkpkdityslshfieglieserskitekfkplavakvvsdel  109 (200)
                      -||.     --|++|..|||-..|.| .|++...+|..+.+...
T Consensus        51 ~cpd-----~~l~~fL~GLI~qkRGk-de~~P~p~ve~~inNNi   88 (155)
T COG4807          51 RCPD-----IVLSSFLNGLIYQKRGK-DESAPAPEVERRINNNI   88 (155)
T ss_pred             HCCH-----HHHHHHHCCHHEEECCC-CCCCCCCCCEEEECCHH
T ss_conf             5848-----79999843011101266-67898997413304304


No 17 
>pfam03982 DAGAT Diacylglycerol acyltransferase. The terminal step of triacylglycerol (TAG) formation is catalysed by the enzyme diacylglycerol acyltransferase (DAGAT).
Probab=22.47  E-value=60  Score=13.99  Aligned_cols=26  Identities=35%  Similarity=0.805  Sum_probs=21.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCHHHH
Q ss_conf             6657899999999999998520881542
Q gi|254781219|r  138 FHSRYALIRYLEDFYKEIKHTFGNPADA  165 (200)
Q Consensus       138 fhsryaliryledfykeikhtfgnpada  165 (200)
                      .|.+|  +.-|++.|.+-|+.||.|.|.
T Consensus       267 ~H~~Y--i~~L~~LFe~~K~~yG~~~~~  292 (297)
T pfam03982       267 LHGQY--MEALRELFEEHKTKFGVPPDT  292 (297)
T ss_pred             HHHHH--HHHHHHHHHHHHHHCCCCCCC
T ss_conf             99999--999999999978756999997


No 18 
>pfam10759 DUF2587 Protein of unknown function (DUF2587). This is a bacterial family of proteins with no known function.
Probab=22.40  E-value=60  Score=13.98  Aligned_cols=31  Identities=35%  Similarity=0.530  Sum_probs=16.1

Q ss_pred             HHHHCCHHHHHHHHHHHHHHEEEEEECHHHHHHH
Q ss_conf             5420304899988752251014556460289998
Q gi|254781219|r  163 ADALSPHISELADEIHTTCFTLQFVVNPSEAELL  196 (200)
Q Consensus       163 adalsphiseladeihttcftlqfvvnpseaell  196 (200)
                      .|+|||   ||.+|.+.-.....--..||+|||-
T Consensus        71 ~~gLsp---eL~~EL~rlslPF~~~~~Ps~aELR  101 (168)
T pfam10759        71 EDGLAP---ELVEELERLSLPFTEDAVPSDAELR  101 (168)
T ss_pred             HHHCCH---HHHHHHHHHCCCCCCCCCCCHHHHH
T ss_conf             863488---9999999825887899998579999


No 19 
>KOG3189 consensus
Probab=21.88  E-value=59  Score=14.04  Aligned_cols=32  Identities=34%  Similarity=0.681  Sum_probs=17.1

Q ss_pred             CCCCCHHHH---HHHHHHHHHHHHHH-HHHHHHHCCCH
Q ss_conf             364322456---66578999999999-99998520881
Q gi|254781219|r  129 SGHLNRDVI---FHSRYALIRYLEDF-YKEIKHTFGNP  162 (200)
Q Consensus       129 sghlnrdvi---fhsryaliryledf-ykeikhtfgnp  162 (200)
                      .|...-||.   +..+|.| +|+|.- +++| |-||+-
T Consensus       180 GGQISfDvFP~GWDKtyCL-qhle~dgf~~I-hFFGDk  215 (252)
T KOG3189         180 GGQISFDVFPKGWDKTYCL-QHLEKDGFDTI-HFFGDK  215 (252)
T ss_pred             CCEEEEEECCCCCCHHHHH-HHHHHCCCCEE-EEECCC
T ss_conf             7868885357874266899-88402477468-871566


No 20 
>TIGR02121 Na_Pro_sym sodium/proline symporter; InterPro: IPR011851    This family consists of the sodium/proline symporter (proline permease) from a number of Gram-negative and Gram-positive bacteria and from the archaeal genus Methanosarcina. ; GO: 0005298 proline:sodium symporter activity, 0031402 sodium ion binding, 0006814 sodium ion transport, 0015824 proline transport, 0016021 integral to membrane.
Probab=21.70  E-value=42  Score=15.07  Aligned_cols=11  Identities=45%  Similarity=0.745  Sum_probs=8.7

Q ss_pred             HHHHHHHHHHH
Q ss_conf             99999999852
Q gi|254781219|r  148 LEDFYKEIKHT  158 (200)
Q Consensus       148 ledfykeikht  158 (200)
                      -|||||.+.+.
T Consensus       365 tEDfYK~~~~~  375 (517)
T TIGR02121       365 TEDFYKAFLKK  375 (517)
T ss_pred             HHHHHHHHHCC
T ss_conf             99999875230


No 21 
>TIGR01788 Glu-decarb-GAD glutamate decarboxylase; InterPro: IPR010107   This entry represents Glutamate decarboxylase (gad;) it is a pyridoxal 5'-phosphate (PLP)-dependent enzyme, which catalyses the irreversible alpha-decarboxylation of L-glutamate to gamma-aminobutyrate (GABA). This enzyme is widely distributed amongst eukaryotes and prokaryotes, but its function varies in different organisms .   Gad has a crucial role in the vertebrate central nervous system where it is responsible for the synthesis of GABA, the major inhibitory neurotransmitter. In the majority of vertebrates Gad occurs in two isoforms, GAD65 and GAD67, both active at neutral pH . Gad isoforms (GadA and GadB) have also been reported in some bacterial species, including the Gram-negative bacterium  and Gram-positive bacterium .   A unique feature of plant and yeast Gad is the presence of a calmodulin (CaM)-binding domain in the C-terminal region. In Saccharomyces cerevisiae, Gad expression is required for normal oxidative stress tolerance . In plants, Gad is thought to be a stress-adapter chaperonin sensing Ca2+ signals.; GO: 0004351 glutamate decarboxylase activity, 0030170 pyridoxal phosphate binding, 0006536 glutamate metabolic process.
Probab=21.64  E-value=61  Score=13.95  Aligned_cols=46  Identities=24%  Similarity=0.423  Sum_probs=37.4

Q ss_pred             HHCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHCCHHHHH
Q ss_conf             301010364322456665789999999999999852088154203048999
Q gi|254781219|r  123 RNYSRDSGHLNRDVIFHSRYALIRYLEDFYKEIKHTFGNPADALSPHISEL  173 (200)
Q Consensus       123 rnysrdsghlnrdvifhsryaliryledfykeikhtfgnpadalsphisel  173 (200)
                      -|+||-+++     |.+--|-+||+=-+=|+.|-.+.-.-|..|+-.|.++
T Consensus       328 LNFSrp~~q-----ViaQYYnFlRLG~~GYr~i~q~~~~vA~~La~~~~~~  373 (493)
T TIGR01788       328 LNFSRPANQ-----VIAQYYNFLRLGREGYRKIMQNLLDVAQYLAEEIAKL  373 (493)
T ss_pred             CCCCCCCCC-----HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             135576231-----1364466885040134899998999999999999986


No 22 
>smart00340 HALZ homeobox associated leucin zipper.
Probab=21.60  E-value=63  Score=13.87  Aligned_cols=26  Identities=31%  Similarity=0.558  Sum_probs=16.7

Q ss_pred             HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999998864180111136788789999999999
Q gi|254781219|r   19 FYLDKWCEALYSPESYSNTYREQKLRDKIIELRR   52 (200)
Q Consensus        19 fyldkwcealyspesysntyreqklrdkiielrr   52 (200)
                      -||.+|||.|-        -....|...+-|||.
T Consensus         8 e~LKrcce~Lt--------eeNrRL~kE~~eLra   33 (44)
T smart00340        8 ELLKRCCESLT--------EENRRLQKEVQELRA   33 (44)
T ss_pred             HHHHHHHHHHH--------HHHHHHHHHHHHHHH
T ss_conf             99999999986--------988999999999985


No 23 
>TIGR01361 DAHP_synth_Bsub phospho-2-dehydro-3-deoxyheptonate aldolase; InterPro: IPR006268   These sequences are one of at least three types of phospho-2-dehydro-3-deoxyheptonate aldolase (DAHP synthase). This enzyme catalyzes the first of 7 steps in the biosynthesis of chorismate, that last common precursor of all three aromatic amino acids and of PABA, ubiquinone and menaquinone. Some members of this family, including an experimentally characterised member from Bacillus subtilis, are bifunctional, with a chorismate mutase domain N-terminal to this region. The member of this family from Synechocystis PCC 6803, CcmA, was shown to be essential for carboxysome formation. However, no other candidate for this enzyme is present in that species, chorismate biosynthesis does occur, other species having this protein lack carboxysomes but appear to make chorismate, and a requirement of CcmA for carboxysome formation does not prohibit a role in chorismate biosynthesis.; GO: 0016832 aldehyde-lyase activity, 0009073 aromatic amino acid family biosynthetic process.
Probab=21.30  E-value=21  Score=17.08  Aligned_cols=38  Identities=39%  Similarity=0.579  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCHH
Q ss_conf             367887899999999999765406436987289951036
Q gi|254781219|r   36 NTYREQKLRDKIIELRRKFAKENGLKTVTEVCPKPKDIT   74 (200)
Q Consensus        36 ntyreqklrdkiielrrkfakenglktvtevcpkpkdit   74 (200)
                      +-|-=|-|-.+-+++-|+-+.+-||-+||||-- |.|..
T Consensus        66 SPYsFQGlg~~gl~~l~~A~~~~GL~~vTEvmd-~~d~e  103 (262)
T TIGR01361        66 SPYSFQGLGEEGLKLLRRAADETGLPVVTEVMD-PRDVE  103 (262)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEC-HHHHH
T ss_conf             884124741899999999998609948988636-25677


No 24 
>KOG4086 consensus
Probab=20.90  E-value=52  Score=14.40  Aligned_cols=19  Identities=47%  Similarity=0.987  Sum_probs=12.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             999998887899999999886418
Q gi|254781219|r    7 KQFKNYLHEDVKFYLDKWCEALYS   30 (200)
Q Consensus         7 kqfknylhedvkfyldkwcealys   30 (200)
                      ..|+|||.     ||.-||+.-|+
T Consensus        45 e~F~nYLk-----YLeYWk~PeYa   63 (130)
T KOG4086          45 EAFVNYLK-----YLEYWKEPEYA   63 (130)
T ss_pred             HHHHHHHH-----HHHHHCCCCHH
T ss_conf             89999999-----99986082078


No 25 
>pfam08991 DUF1903 Domain of unknown function (DUF1903). Members of this family adopt a coiled coil structure, with two antiparallel alpha-helices that are tightly strapped together by two disulfide bridges at each end. The protein sequence shows a cysteine motif, required for the stabilisation of the coiled-coil-like structure. Additional inter-helix hydrophobic contacts impart stability to this scaffold. The precise function of this eukaryotic domain is, as yet, unknown.
Probab=20.73  E-value=65  Score=13.75  Aligned_cols=39  Identities=36%  Similarity=0.457  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCHH
Q ss_conf             11367887899999999999765406436987289951036
Q gi|254781219|r   34 YSNTYREQKLRDKIIELRRKFAKENGLKTVTEVCPKPKDIT   74 (200)
Q Consensus        34 ysntyreqklrdkiielrrkfakenglktvtevcpkpkdit   74 (200)
                      -.|.|.|.|-.+-|-+|++=-++-+  ...+-.||+|....
T Consensus        16 q~n~y~EskC~~~id~Ly~CC~kf~--~~~S~cCp~~~ll~   54 (62)
T pfam08991        16 QKNGYDESKCEDVIEDLYRCCAKFN--DARSVCCPGPSLLE   54 (62)
T ss_pred             HHCCCCHHHHHHHHHHHHHHHHHCC--CCCCCCCCCCHHHH
T ss_conf             9859888999999999999996125--56887789807999


No 26 
>pfam10755 DUF2585 Protein of unknown function (DUF2585). This family is conserved in Proteobacteria. The function is not known.
Probab=20.56  E-value=49  Score=14.60  Aligned_cols=76  Identities=24%  Similarity=0.270  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCH----HHHHHHHHH--HHHHHHHHHHHHHHHHHCCHHCCCCCHHHHHHHHHHHHHH
Q ss_conf             6779999999975357777764121----579987636--8889999999999853010103643224566657899999
Q gi|254781219|r   74 TYSLSHFIEGLIESERSKITEKFKP----LAVAKVVSD--ELLHDKLNKILKKSVRNYSRDSGHLNRDVIFHSRYALIRY  147 (200)
Q Consensus        74 tyslshfieglieserskitekfkp----lavakvvsd--ellhdklnkilkksvrnysrdsghlnrdvifhsryaliry  147 (200)
                      -|++||.|.|++-----..--...|    |++|-.+..  |++... .-|... -| -...|...+.|-|..|.-..+--
T Consensus        35 WYt~SHiiHGflFy~~~~l~~~r~p~~~rL~~A~liE~aWEivENs-p~II~r-YR-~aTis~~Y~GDSvlNSv~D~~~m  111 (165)
T pfam10755        35 WYTPSHIIHGFLFYALGWLIFPRLPLGWRLALAVLIEAAWEILENS-PFIIDR-YR-AATISLDYYGDSVLNSVSDTLAM  111 (165)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCC-HHHHHH-HH-HHHHHCCCCCHHHHHHHHHHHHH
T ss_conf             5668999999999999999825887228999999997667766078-789999-98-76220244532888878899999


Q ss_pred             HHHHH
Q ss_conf             99999
Q gi|254781219|r  148 LEDFY  152 (200)
Q Consensus       148 ledfy  152 (200)
                      +-.|.
T Consensus       112 ~~GF~  116 (165)
T pfam10755       112 LLGFL  116 (165)
T ss_pred             HHHHH
T ss_conf             99999


Done!