Query         gi|254781212|ref|YP_003065625.1| hypothetical protein CLIBASIA_05595 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 109
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 30 07:01:16 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781212.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PTZ00056 glutathione peroxidas  68.5     4.1 0.00011   22.1   2.4   34   70-103    29-65  (180)
  2 TIGR02237 recomb_radB DNA repa  61.8     6.5 0.00017   20.9   2.4   23   84-106    42-64  (223)
  3 pfam00255 GSHPx Glutathione pe  61.5     6.8 0.00017   20.8   2.4   33   71-103    12-46  (108)
  4 PRK10606 btuE putative glutath  56.5     8.4 0.00021   20.3   2.2   24   72-95     17-40  (183)
  5 KOG0475 consensus               55.9     6.2 0.00016   21.0   1.5   31   77-107   196-226 (696)
  6 PTZ00256 glutathione peroxidas  54.8      11 0.00028   19.6   2.6   32   72-103    32-67  (183)
  7 KOG1502 consensus               43.3      19 0.00048   18.3   2.3   73    7-94     18-91  (327)
  8 TIGR02540 gpx7 putative glutat  42.9      15 0.00038   18.8   1.7   23   75-97     17-39  (153)
  9 COG0386 BtuE Glutathione perox  37.7      26 0.00067   17.4   2.3   34   72-105    17-55  (162)
 10 COG4888 Uncharacterized Zn rib  37.0      15 0.00038   18.8   1.0   22   78-99     38-59  (104)
 11 cd00340 GSH_Peroxidase Glutath  29.6      24 0.00061   17.6   1.0   24   72-95     14-37  (152)
 12 pfam08423 Rad51 Rad51. Rad51 i  29.6      38 0.00097   16.5   2.0   57   46-103    24-98  (261)
 13 KOG1651 consensus               29.6      28 0.00071   17.3   1.3   23   74-96     28-50  (171)
 14 pfam03254 XG_FTase Xyloglucan   29.2      54  0.0014   15.6   3.1   50   59-108   331-380 (477)
 15 COG1052 LdhA Lactate dehydroge  28.6      22 0.00057   17.8   0.7   85    1-106   217-307 (324)
 16 KOG3220 consensus               27.2      20 0.00051   18.1   0.3   39   20-58     27-87  (225)
 17 pfam05300 DUF737 Protein of un  26.3      61  0.0016   15.3   2.9   26   21-46    129-154 (187)
 18 TIGR01754 flav_RNR ribonucleot  25.8      52  0.0013   15.7   2.2   21    3-23     13-33  (145)
 19 TIGR00457 asnS asparaginyl-tRN  20.7      60  0.0015   15.3   1.7   20   88-107   459-478 (495)
 20 pfam02826 2-Hacid_dh_C D-isome  20.6      51  0.0013   15.7   1.3   33    1-33    106-141 (176)
 21 pfam04316 FlgM Anti-sigma-28 f  20.6      77   0.002   14.7   2.2   25    9-33     31-55  (57)

No 1  
>PTZ00056 glutathione peroxidase; Provisional
Probab=68.46  E-value=4.1  Score=22.07  Aligned_cols=34  Identities=21%  Similarity=0.405  Sum_probs=24.7

Q ss_pred             CCHHEEEEECCCCEEEEEEECCCCCC---HHHHHHHH
Q ss_conf             52000101016632568873146865---99999986
Q gi|254781212|r   70 DSAHQLALLEGKRSLAVHIASNCGLS---FERIVQMY  103 (109)
Q Consensus        70 dsahqlallegkrslavhiasncgls---ferivqmy  103 (109)
                      .....|.-..||--|.|..||.||++   ++...++|
T Consensus        29 G~~~~l~~ykGkv~LIVNvAS~CG~T~q~y~~L~~L~   65 (180)
T PTZ00056         29 GNPVPMSSLKNKVLMITNSASKCGLTKSHVKQMNRLH   65 (180)
T ss_pred             CCEECHHHCCCCEEEEEEECCCCCCCHHHHHHHHHHH
T ss_conf             8993489949988999981577788666799999999


No 2  
>TIGR02237 recomb_radB DNA repair and recombination protein RadB; InterPro: IPR011939    This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO) and DMC1 (IPR011940 from INTERPRO), and archaeal RadA (IPR011938 from INTERPRO) ,, .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=61.76  E-value=6.5  Score=20.92  Aligned_cols=23  Identities=39%  Similarity=0.408  Sum_probs=21.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHCCC
Q ss_conf             56887314686599999986268
Q gi|254781212|r   84 LAVHIASNCGLSFERIVQMYSDN  106 (109)
Q Consensus        84 lavhiasncglsferivqmysdn  106 (109)
                      .+|-|-+.-|||.||+-||.+++
T Consensus        42 ~v~YiDTEGGLS~ER~~q~~~~~   64 (223)
T TIGR02237        42 KVVYIDTEGGLSPERFKQIAEDR   64 (223)
T ss_pred             CEEEEECCCCCHHHHHHHHHHCC
T ss_conf             58999628983289999986305


No 3  
>pfam00255 GSHPx Glutathione peroxidase.
Probab=61.55  E-value=6.8  Score=20.81  Aligned_cols=33  Identities=30%  Similarity=0.558  Sum_probs=23.8

Q ss_pred             CHHEEEEECCCCEEEEEEECCCCCC--HHHHHHHH
Q ss_conf             2000101016632568873146865--99999986
Q gi|254781212|r   71 SAHQLALLEGKRSLAVHIASNCGLS--FERIVQMY  103 (109)
Q Consensus        71 sahqlallegkrslavhiasncgls--ferivqmy  103 (109)
                      ....|.-..||--|.|..||.||++  ++...++|
T Consensus        12 ~~~~l~~ykGkv~LIVNvAS~Cg~t~qy~~L~~L~   46 (108)
T pfam00255        12 EPVPLDQYRGKVLLIVNVASKCGLTPQYTELNELQ   46 (108)
T ss_pred             CEECHHHCCCCEEEEEEECCCCCCCCCHHHHHHHH
T ss_conf             99488993998899999557788970799999999


No 4  
>PRK10606 btuE putative glutathione peroxidase; Provisional
Probab=56.55  E-value=8.4  Score=20.27  Aligned_cols=24  Identities=38%  Similarity=0.624  Sum_probs=19.7

Q ss_pred             HHEEEEECCCCEEEEEEECCCCCC
Q ss_conf             000101016632568873146865
Q gi|254781212|r   72 AHQLALLEGKRSLAVHIASNCGLS   95 (109)
Q Consensus        72 ahqlallegkrslavhiasncgls   95 (109)
                      ...|.-..||--|.|..||.||++
T Consensus        17 ~~~l~~y~GKvvLIVNvAS~CG~T   40 (183)
T PRK10606         17 VTTLEKYAGNVLLIVNVASKCGLT   40 (183)
T ss_pred             EECHHHCCCCEEEEEECCCCCCCC
T ss_conf             934899399689999777557880


No 5  
>KOG0475 consensus
Probab=55.89  E-value=6.2  Score=21.04  Aligned_cols=31  Identities=39%  Similarity=0.474  Sum_probs=27.3

Q ss_pred             EECCCCEEEEEEECCCCCCHHHHHHHHCCCC
Q ss_conf             1016632568873146865999999862689
Q gi|254781212|r   77 LLEGKRSLAVHIASNCGLSFERIVQMYSDNP  107 (109)
Q Consensus        77 llegkrslavhiasncglsferivqmysdnp  107 (109)
                      |--||..--||||.+||--|++|..-|++|-
T Consensus       196 LSlGKEGP~VHiA~c~g~~~s~~f~~~~~~e  226 (696)
T KOG0475         196 LSLGKEGPSVHIATCIGNIFSKIFPKYRLNE  226 (696)
T ss_pred             CCCCCCCCCEEEEECHHHHHHHHHHHHCCCH
T ss_conf             5557778733654101036766420101223


No 6  
>PTZ00256 glutathione peroxidase; Provisional
Probab=54.83  E-value=11  Score=19.58  Aligned_cols=32  Identities=34%  Similarity=0.837  Sum_probs=22.2

Q ss_pred             HHEEEEECCCCEEE-EEEECCCCCC---HHHHHHHH
Q ss_conf             00010101663256-8873146865---99999986
Q gi|254781212|r   72 AHQLALLEGKRSLA-VHIASNCGLS---FERIVQMY  103 (109)
Q Consensus        72 ahqlallegkrsla-vhiasncgls---ferivqmy  103 (109)
                      ...|.-.+||.-|- |..||.||+.   ++...++|
T Consensus        32 ~~~L~~y~Gk~vlivVNvAS~CG~T~q~Y~~L~~L~   67 (183)
T PTZ00256         32 KTQLSKFQGKKAYICVNVACSCGLTSSNYSELVELY   67 (183)
T ss_pred             EEEHHHCCCCEEEEEEEECCCCCCCCCCHHHHHHHH
T ss_conf             952899599879999981567789836189999999


No 7  
>KOG1502 consensus
Probab=43.34  E-value=19  Score=18.26  Aligned_cols=73  Identities=27%  Similarity=0.423  Sum_probs=44.3

Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCC-CCEEEHHHHHCCCCCCCCCCCCHHEEEEECCCCEEE
Q ss_conf             9999987664225410448999775688899888777640788-605101123405300012575200010101663256
Q gi|254781212|r    7 LADMIKSKVLSRGYTVDSDALARQLEEDERRIRHYKHVYSTPE-GRFVLTDLMVEGGLLSSVSNDSAHQLALLEGKRSLA   85 (109)
Q Consensus         7 ladmikskvlsrgytvdsdalarqleederrirhykhvystpe-grfvltdlmveggllssvsndsahqlallegkrsla   85 (109)
                      +|--|-...|+|||+|-  +..|..|+ +..+.|-+..-..+| ....-.||.-++.+...+..            -.--
T Consensus        18 Igswivk~LL~rGY~V~--gtVR~~~~-~k~~~~L~~l~~a~~~l~l~~aDL~d~~sf~~ai~g------------cdgV   82 (327)
T KOG1502          18 IGSWIVKLLLSRGYTVR--GTVRDPED-EKKTEHLRKLEGAKERLKLFKADLLDEGSFDKAIDG------------CDGV   82 (327)
T ss_pred             HHHHHHHHHHHCCCEEE--EEECCCCH-HHHHHHHHHCCCCCCCCEEEECCCCCCCHHHHHHHC------------CCEE
T ss_conf             99999999986899899--99708630-565899986515754425885243551359999707------------8789


Q ss_pred             EEEECCCCC
Q ss_conf             887314686
Q gi|254781212|r   86 VHIASNCGL   94 (109)
Q Consensus        86 vhiasncgl   94 (109)
                      .|+||.+-.
T Consensus        83 fH~Asp~~~   91 (327)
T KOG1502          83 FHTASPVDF   91 (327)
T ss_pred             EEECCCCCC
T ss_conf             991766787


No 8  
>TIGR02540 gpx7 putative glutathione peroxidase Gpx7; InterPro: IPR013376    This model represents one of several families of known and probable glutathione peroxidases. It is restricted to animals and designated GPX7.; GO: 0004602 glutathione peroxidase activity, 0006979 response to oxidative stress.
Probab=42.91  E-value=15  Score=18.82  Aligned_cols=23  Identities=39%  Similarity=0.595  Sum_probs=18.9

Q ss_pred             EEEECCCCEEEEEEECCCCCCHH
Q ss_conf             10101663256887314686599
Q gi|254781212|r   75 LALLEGKRSLAVHIASNCGLSFE   97 (109)
Q Consensus        75 lallegkrslavhiasncglsfe   97 (109)
                      |.-..||-||.|.+||.|++.=.
T Consensus        17 LeKYrG~vsLVVNVAS~c~~td~   39 (153)
T TIGR02540        17 LEKYRGKVSLVVNVASECEFTDQ   39 (153)
T ss_pred             EEEECCEEEEEEEECCCCCCHHH
T ss_conf             11001107899870278810057


No 9  
>COG0386 BtuE Glutathione peroxidase [Posttranslational modification, protein turnover, chaperones]
Probab=37.73  E-value=26  Score=17.42  Aligned_cols=34  Identities=35%  Similarity=0.590  Sum_probs=24.8

Q ss_pred             HHEEEEECCCCEEEEEEECCCCCC-----HHHHHHHHCC
Q ss_conf             000101016632568873146865-----9999998626
Q gi|254781212|r   72 AHQLALLEGKRSLAVHIASNCGLS-----FERIVQMYSD  105 (109)
Q Consensus        72 ahqlallegkrslavhiasncgls-----ferivqmysd  105 (109)
                      .-.|.-..||--|-|..||.||+.     +|.+-+-|.|
T Consensus        17 ~~~l~~y~GkVlLIVNtASkCGfTpQYegLe~Ly~ky~~   55 (162)
T COG0386          17 PVSLSDYKGKVLLIVNTASKCGFTPQYEGLEALYKKYKD   55 (162)
T ss_pred             CCCHHHHCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             824899299689999745446886758999999999864


No 10 
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=37.00  E-value=15  Score=18.81  Aligned_cols=22  Identities=32%  Similarity=0.625  Sum_probs=17.7

Q ss_pred             ECCCCEEEEEEECCCCCCHHHH
Q ss_conf             0166325688731468659999
Q gi|254781212|r   78 LEGKRSLAVHIASNCGLSFERI   99 (109)
Q Consensus        78 legkrslavhiasncglsferi   99 (109)
                      +.-+-..++-+-+|||||||--
T Consensus        38 vkk~~~~g~~~Cg~CGls~e~e   59 (104)
T COG4888          38 VKKTVNIGTAVCGNCGLSFECE   59 (104)
T ss_pred             EEECCCEEEEECCCCCCEEEEE
T ss_conf             9742745689714575537882


No 11 
>cd00340 GSH_Peroxidase Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per subunit, which is involved in catalysis. Different isoenzymes are known in mammals,which are involved in protection against reactive oxygen species, redox regulation of many metabolic processes, peroxinitrite scavenging, and modulation of inflammatory processes.
Probab=29.63  E-value=24  Score=17.64  Aligned_cols=24  Identities=38%  Similarity=0.643  Sum_probs=18.3

Q ss_pred             HHEEEEECCCCEEEEEEECCCCCC
Q ss_conf             000101016632568873146865
Q gi|254781212|r   72 AHQLALLEGKRSLAVHIASNCGLS   95 (109)
Q Consensus        72 ahqlallegkrslavhiasncgls   95 (109)
                      ...|.-..||-.|.|..||.||.+
T Consensus        14 ~~~l~~y~GkvvLiVNvAS~Cg~t   37 (152)
T cd00340          14 PVSLSKYKGKVLLIVNVASKCGFT   37 (152)
T ss_pred             EECHHHCCCCEEEEEECCCCCCCC
T ss_conf             945899399789999667788887


No 12 
>pfam08423 Rad51 Rad51. Rad51 is a DNA repair and recombination protein and is a homologue of the bacterial ATPase RecA protein.
Probab=29.56  E-value=38  Score=16.48  Aligned_cols=57  Identities=25%  Similarity=0.359  Sum_probs=32.8

Q ss_pred             CCCCCCEEEHHHHHCCCCCCCC---------C--CCCHHEEEE-------ECCCCEEEEEEECCCCCCHHHHHHHH
Q ss_conf             0788605101123405300012---------5--752000101-------01663256887314686599999986
Q gi|254781212|r   46 STPEGRFVLTDLMVEGGLLSSV---------S--NDSAHQLAL-------LEGKRSLAVHIASNCGLSFERIVQMY  103 (109)
Q Consensus        46 stpegrfvltdlmveggllssv---------s--ndsahqlal-------legkrslavhiasncglsferivqmy  103 (109)
                      .-|-|-..|.+++- ||+-...         |  ..-+|||++       +.|.-.-++-|-+.-+++-||+.||-
T Consensus        24 ~isTg~~~LD~lLg-GGi~~g~ITEi~G~~gsGKTQlc~qlav~~qlp~~~gg~~g~vvyIDTEg~f~~eRl~qia   98 (261)
T pfam08423        24 RITTGSKELDKLLG-GGIETGSITEVFGEFRTGKTQLCHTLCVTCQLPLEMGGGEGKALYIDTEGTFRPERIVAIA   98 (261)
T ss_pred             EECCCCHHHHHHHC-CCCCCCEEEEEECCCCCCHHHHHHHHHHHHHCHHHHCCCCCEEEEEECCCCCCHHHHHHHH
T ss_conf             57789878998737-9866772999989988878999999999940709656999728999368886989999999


No 13 
>KOG1651 consensus
Probab=29.55  E-value=28  Score=17.27  Aligned_cols=23  Identities=43%  Similarity=0.678  Sum_probs=18.9

Q ss_pred             EEEEECCCCEEEEEEECCCCCCH
Q ss_conf             01010166325688731468659
Q gi|254781212|r   74 QLALLEGKRSLAVHIASNCGLSF   96 (109)
Q Consensus        74 qlallegkrslavhiasncglsf   96 (109)
                      .|.-..||-.|-|.+||-||+.-
T Consensus        28 ~l~~yrGkV~LiVNVAS~Cg~T~   50 (171)
T KOG1651          28 SLSQYRGKVVLIVNVASQCGLTE   50 (171)
T ss_pred             CHHHHCCEEEEEEECCCCCCCCH
T ss_conf             67891873999997100105651


No 14 
>pfam03254 XG_FTase Xyloglucan fucosyltransferase. Plant cell walls are crucial for development, signal transduction, and disease resistance in plants. Cell walls are made of cellulose, hemicelluloses, and pectins. Xyloglucan (XG), the principal load-bearing hemicellulose of dicotyledonous plants, has a terminal fucosyl residue. This fucosyltransferase adds this residue.
Probab=29.15  E-value=54  Score=15.58  Aligned_cols=50  Identities=24%  Similarity=0.326  Sum_probs=34.4

Q ss_pred             HCCCCCCCCCCCCHHEEEEECCCCEEEEEEECCCCCCHHHHHHHHCCCCC
Q ss_conf             40530001257520001010166325688731468659999998626899
Q gi|254781212|r   59 VEGGLLSSVSNDSAHQLALLEGKRSLAVHIASNCGLSFERIVQMYSDNPR  108 (109)
Q Consensus        59 veggllssvsndsahqlallegkrslavhiasncglsferivqmysdnpr  108 (109)
                      .+-.||..|...+.--..-....++-||-|+|--.--+|+|-.||-.+|.
T Consensus       331 ~~e~LLPev~~~~~~~~~~~~~~~~kAVLVtSL~~~Yye~lr~mY~~~pt  380 (477)
T pfam03254       331 QKEKLLPEVDTQEPSVASASRNQKSKAVLVTSLYSEYYEKIKNMYWEHPT  380 (477)
T ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCHHHHHHHHHHHHCCCC
T ss_conf             64345888666677777767788547999995878999999998850777


No 15 
>COG1052 LdhA Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]
Probab=28.56  E-value=22  Score=17.84  Aligned_cols=85  Identities=28%  Similarity=0.375  Sum_probs=49.4

Q ss_pred             CCCHHHHHHHHHHHHH---HCCCCCCHHHHHHHHHHHHHHHHHHH-HHHCCCCCCEEEHHHHHCCCCCCCCCCCCHHEEE
Q ss_conf             9639999999987664---22541044899977568889988877-7640788605101123405300012575200010
Q gi|254781212|r    1 MVNFRKLADMIKSKVL---SRGYTVDSDALARQLEEDERRIRHYK-HVYSTPEGRFVLTDLMVEGGLLSSVSNDSAHQLA   76 (109)
Q Consensus         1 mvnfrkladmikskvl---srgytvdsdalarqleederrirhyk-hvystpegrfvltdlmveggllssvsndsahqla   76 (109)
                      |+|-..|+.|-+.-+|   +||-.||.+||.+-|++.  .|..+- .||..-.-.+                 |.  .|.
T Consensus       217 Lin~~~l~~mk~ga~lVNtaRG~~VDe~ALi~AL~~g--~i~gaglDV~e~Ep~~~-----------------d~--~l~  275 (324)
T COG1052         217 LINAEELAKMKPGAILVNTARGGLVDEQALIDALKSG--KIAGAGLDVFENEPALF-----------------DH--PLL  275 (324)
T ss_pred             HCCHHHHHHCCCCEEEEECCCCCEECHHHHHHHHHCC--CCCEEEECCCCCCCCCC-----------------CH--HHH
T ss_conf             3299999756897699964874216599999999809--74226701167888778-----------------80--676


Q ss_pred             EEC--CCCEEEEEEECCCCCCHHHHHHHHCCC
Q ss_conf             101--663256887314686599999986268
Q gi|254781212|r   77 LLE--GKRSLAVHIASNCGLSFERIVQMYSDN  106 (109)
Q Consensus        77 lle--gkrslavhiasncglsferivqmysdn  106 (109)
                      -+.  .+-.+.-||||--.-+.+++++.--+|
T Consensus       276 ~l~~~~~vvltPHia~at~ea~~~m~~~~~~n  307 (324)
T COG1052         276 RLDNFPNVVLTPHIASATEEARKAMAELALEN  307 (324)
T ss_pred             HCCCCCCEEEECCCCCCCHHHHHHHHHHHHHH
T ss_conf             36689987970441302099999999999999


No 16 
>KOG3220 consensus
Probab=27.18  E-value=20  Score=18.12  Aligned_cols=39  Identities=33%  Similarity=0.470  Sum_probs=26.8

Q ss_pred             CCCCHHHHHHHHHH--------------HH--------HHHHHHHHHHCCCCCCEEEHHHH
Q ss_conf             41044899977568--------------88--------99888777640788605101123
Q gi|254781212|r   20 YTVDSDALARQLEE--------------DE--------RRIRHYKHVYSTPEGRFVLTDLM   58 (109)
Q Consensus        20 ytvdsdalarqlee--------------de--------rrirhykhvystpegrfvltdlm   58 (109)
                      ..+|+|.+||+.-+              +|        .|-.--+-|++.|+-|-.|++.|
T Consensus        27 ~vIDaD~vaR~vv~PG~p~~~~ive~FG~eiLl~~G~inR~~LG~~vF~~~~~r~~Ln~It   87 (225)
T KOG3220          27 PVIDADVVAREVVEPGTPAYRRIVEAFGTEILLEDGEINRKVLGKRVFSDPKKRQALNKIT   87 (225)
T ss_pred             CEECHHHHHHHHHCCCCHHHHHHHHHHCCEEECCCCCCCHHHHHHHHHCCHHHHHHHHHCC
T ss_conf             5762789999985599807899999848400056884168998678708988999987313


No 17 
>pfam05300 DUF737 Protein of unknown function (DUF737). This family consists of several uncharacterized mammalian proteins of unknown function.
Probab=26.29  E-value=61  Score=15.27  Aligned_cols=26  Identities=35%  Similarity=0.543  Sum_probs=20.1

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             10448999775688899888777640
Q gi|254781212|r   21 TVDSDALARQLEEDERRIRHYKHVYS   46 (109)
Q Consensus        21 tvdsdalarqleederrirhykhvys   46 (109)
                      -..++.||||||+-|+-+++-.-.|-
T Consensus       129 r~ka~~lArqLE~kEaELkr~daFYK  154 (187)
T pfam05300       129 RQKAKHLARQLEEKEAELKRLDAFYK  154 (187)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999988999998999999


No 18 
>TIGR01754 flav_RNR ribonucleotide reductase-associated flavodoxin, putative; InterPro: IPR010088   This entry represents a family of proteins found immediately downstream of ribonucleotide reductase genes in Xyella fastidiosa and some Gram-positive bacteria. It appears to be a highly divergent flavodoxin of the short chain type, more like the flavodoxins of the sulphate-reducing genus Desulfovibrio than like the NifF flavodoxins associated with nitrogen fixation..
Probab=25.84  E-value=52  Score=15.69  Aligned_cols=21  Identities=33%  Similarity=0.528  Sum_probs=19.9

Q ss_pred             CHHHHHHHHHHHHHHCCCCCC
Q ss_conf             399999999876642254104
Q gi|254781212|r    3 NFRKLADMIKSKVLSRGYTVD   23 (109)
Q Consensus         3 nfrkladmikskvlsrgytvd   23 (109)
                      |-+..|+||+...-++|..||
T Consensus        13 NT~eVA~~I~~~l~~~G~eVD   33 (145)
T TIGR01754        13 NTKEVADIIRDILEKDGHEVD   33 (145)
T ss_pred             CHHHHHHHHHHHHHHCCCEEE
T ss_conf             778999999999984797767


No 19 
>TIGR00457 asnS asparaginyl-tRNA synthetase; InterPro: IPR004522   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   AsparaginyltRNA synthetase (6.1.1.22 from EC) is an alpha2 dimer that belongs to class IIb. There is a striking similarity between asparaginyl-tRNA synthetases and archaeal/eukaryotic type aspartyl-tRNA synthetases (IPR004523 from INTERPRO) and a striking divergence of bacterial type aspartyl-tRNA synthetases (IPR004524 from INTERPRO). This family, AsnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.; GO: 0000166 nucleotide binding, 0004816 asparagine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006421 asparaginyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=20.74  E-value=60  Score=15.31  Aligned_cols=20  Identities=35%  Similarity=0.466  Sum_probs=15.6

Q ss_pred             EECCCCCCHHHHHHHHCCCC
Q ss_conf             73146865999999862689
Q gi|254781212|r   88 IASNCGLSFERIVQMYSDNP  107 (109)
Q Consensus        88 iasncglsferivqmysdnp  107 (109)
                      -.|.-||.|||+|+--++.+
T Consensus       459 PH~GFGLGfERl~ay~~G~~  478 (495)
T TIGR00457       459 PHSGFGLGFERLVAYITGLE  478 (495)
T ss_pred             CCCCCCHHHHHHHHHHHCCC
T ss_conf             64664324899999981787


No 20 
>pfam02826 2-Hacid_dh_C D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain. This domain is inserted into the catalytic domain, the large dehydrogenase and D-lactate dehydrogenase families in SCOP. N-terminal portion of which is represented by family pfam00389.
Probab=20.62  E-value=51  Score=15.73  Aligned_cols=33  Identities=36%  Similarity=0.472  Sum_probs=20.4

Q ss_pred             CCCHHHHHHHHHHHH---HHCCCCCCHHHHHHHHHH
Q ss_conf             963999999998766---422541044899977568
Q gi|254781212|r    1 MVNFRKLADMIKSKV---LSRGYTVDSDALARQLEE   33 (109)
Q Consensus         1 mvnfrkladmikskv---lsrgytvdsdalarqlee   33 (109)
                      |+|...+.-|-+.-+   .+||-.||.+||...|++
T Consensus       106 li~~~~l~~mk~~a~lIN~sRG~ivde~aL~~aL~~  141 (176)
T pfam02826       106 LINAERLALMKPGAILINTARGGLVDEDALIAALKS  141 (176)
T ss_pred             CCCHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHH
T ss_conf             346999985189988998067551289999999980


No 21 
>pfam04316 FlgM Anti-sigma-28 factor, FlgM. FlgM binds and inhibits the activity of the transcription factor sigma 28. Inhibition of sigma 28 prevents the expression of genes from flagellar transcriptional class 3, which include genes for the filament and chemotaxis. Correctly assembled basal body-hook structures export FlgM, relieving inhibition of sigma 28 and allowing expression of class 3 genes. NMR studies show that free FlgM is mostly unfolded, which may facilitate its export. The C terminal half of FlgM adopts a tertiary structure when it binds to sigma 28. All mutations in FlgM that prevent sigma 28 inhibition affect the C-terminal domain and is the region thought to constitute the binding domain. A minimal binding domain has been identified between Glu 64 and Arg 88 in Salmonella typhimurium. The N-terminal portion remains unstructured and may be necessary for recognition by the export machinery.
Probab=20.60  E-value=77  Score=14.71  Aligned_cols=25  Identities=24%  Similarity=0.501  Sum_probs=20.6

Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHH
Q ss_conf             9998766422541044899977568
Q gi|254781212|r    9 DMIKSKVLSRGYTVDSDALARQLEE   33 (109)
Q Consensus         9 dmikskvlsrgytvdsdalarqlee   33 (109)
                      .-||..+-+-.|.||++.+|..+-+
T Consensus        31 ~~iK~~I~~G~Y~vd~~~iA~kml~   55 (57)
T pfam04316        31 EEIKAAIANGSYKVDAEKIADKMLN   55 (57)
T ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHC
T ss_conf             9999999869988899999999883


Done!