Query         gi|254780390|ref|YP_003064803.1| nucleoside diphosphate kinase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 140
No_of_seqs    116 out of 2106
Neff          6.2 
Searched_HMMs 39220
Date          Sun May 29 16:49:06 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780390.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PTZ00093 nucleoside diphosphat 100.0       0       0  370.3  11.6  138    2-139     1-138 (149)
  2 smart00562 NDK These are enzym 100.0       0       0  361.0  12.0  135    4-138     1-135 (135)
  3 pfam00334 NDK Nucleoside dipho 100.0       0       0  360.0  12.0  135    4-138     1-135 (135)
  4 PRK00668 ndk nucleoside diphos 100.0       0       0  353.9  12.1  131    3-133     1-131 (131)
  5 cd04413 NDPk_I Nucleoside diph 100.0       0       0  351.9  12.0  130    4-133     1-130 (130)
  6 COG0105 Ndk Nucleoside diphosp 100.0       0       0  351.5  10.5  135    2-136     1-135 (135)
  7 cd04414 NDPk6 Nucleoside dipho 100.0       0       0  348.3  11.6  131    4-134     1-135 (135)
  8 cd04418 NDPk5 Nucleoside dipho 100.0       0       0  346.2  11.1  129    4-134     1-132 (132)
  9 cd00595 NDPk Nucleoside diphos 100.0       0       0  343.9  11.3  130    4-133     1-133 (133)
 10 cd04412 NDPk7B Nucleoside diph 100.0       0       0  340.2  12.0  130    4-133     1-134 (134)
 11 cd04416 NDPk_TX NDP kinase dom 100.0       0       0  339.8  11.8  129    4-133     1-132 (132)
 12 cd04415 NDPk7A Nucleoside diph 100.0       0       0  339.6  11.8  128    4-133     1-131 (131)
 13 KOG0888 consensus              100.0       0       0  316.3   7.6  137    3-139     5-144 (156)
 14 pfam04339 DUF482 Protein of un  83.1    0.54 1.4E-05   27.3   1.2   78   25-110   193-283 (370)
 15 KOG2562 consensus               54.8      21 0.00053   18.0   4.7   75   19-97    308-412 (493)
 16 TIGR01458 HAD-SF-IIA-hyp3 HAD-  40.4      35  0.0009   16.7   4.5   75   20-95     52-139 (258)
 17 cd06355 PBP1_FmdD_like Peripla  35.9      40   0.001   16.3   3.0   71    5-87    134-206 (348)
 18 COG3885 Uncharacterized conser  35.8      42  0.0011   16.2   3.5   53    5-57     40-97  (261)
 19 TIGR03407 urea_ABC_UrtA urea A  28.4      48  0.0012   15.9   2.4   73    5-89    135-212 (359)
 20 PRK13054 lipid kinase; Reviewe  27.4      58  0.0015   15.4   3.1  105    1-109     1-127 (299)
 21 pfam07576 BRAP2 BRCA1-associat  27.2      45  0.0011   16.1   2.1   53    5-59     14-79  (110)
 22 PRK09371 gas vesicle synthesis  25.8      53  0.0013   15.6   2.2   29    1-37      1-29  (72)
 23 pfam09554 RE_HaeII HaeII restr  25.7      23 0.00059   17.7   0.4   95   24-138   221-326 (338)
 24 COG2846 Regulator of cell morp  25.4      18 0.00045   18.4  -0.3   64   67-135   149-216 (221)
 25 COG2247 LytB Putative cell wal  21.4      76  0.0019   14.7   2.6   15   22-36     91-105 (337)
 26 TIGR02287 PaaY phenylacetic ac  20.1      31  0.0008   17.0   0.1   10  101-110    39-48  (193)

No 1  
>PTZ00093 nucleoside diphosphate kinase; Provisional
Probab=100.00  E-value=0  Score=370.32  Aligned_cols=138  Identities=43%  Similarity=0.784  Sum_probs=136.1

Q ss_pred             CCCEEEEEECCHHHHCCCHHHHHHHHHHCCCEEEEHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHCCCCCEEEEECCCCC
Q ss_conf             63102304552377189879999999725558921001126999999998885147421001221001115771111640
Q gi|254780390|r    2 VIEKTFSMIKPDAVKRNLIGSIVKELEDYGLCVVAAKFCWMNRKQAEDFYLIHKDRPFFPELVQAMISGPVFLQVLKGEE   81 (140)
Q Consensus         2 ~~e~Tl~iIKPDav~~~~~g~Ii~~i~~~Gf~I~~~k~~~ls~e~a~~fY~~~~~k~ff~~lv~~m~sGpv~alvl~g~n   81 (140)
                      +.||||+||||||++++++|+|+++|+++||+|+++|++++|+++|++||++|+|||||++|++||+||||+||+|+|+|
T Consensus         1 ~tErTl~iIKPDav~~~l~g~Ii~~i~~~Gf~I~~~k~~~lt~e~a~~fY~~h~gkpff~~Lv~~mtSGPvvalvleg~n   80 (149)
T PTZ00093          1 SSERTFIMVKPDGVQRGLVGEIIKRFEKKGYKLVALKFLQPTTEQAEEHYKEHKSKPFFPGLVSYISSGPVVCMVWEGKN   80 (149)
T ss_pred             CCCEEEEEECCCHHHCCCHHHHHHHHHHCCCEEEEEEEECCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCEEEEEEECCC
T ss_conf             97048999891154048879999999987998999874258999999999997188328889998678987999962788


Q ss_pred             HHHHHHHHCCCCCHHHCCCCCCCHHCCCCHHHEEEEECCCHHHHHHHHHHHCCHHHCC
Q ss_conf             1789996618899777689970001011522100440699899999998726856506
Q gi|254780390|r   82 AISKNREVMGDTDPKKALKGTIRNKYGISIGENSIHGSDSLKTALEEISYWFARNEII  139 (140)
Q Consensus        82 aV~~~R~l~Gptdp~~a~p~tiR~~fg~~~~~N~vH~Sds~e~a~rEi~~fF~~~ei~  139 (140)
                      ||+.||+|||||||.+|+|+||||+||.+.++|+||||||+|+|+|||+|||+++||+
T Consensus        81 aI~~~R~l~GpT~p~~a~p~tIR~~fg~~~~~N~vH~SDs~e~A~rEi~~fF~~~ei~  138 (149)
T PTZ00093         81 VVKSGRVLLGATNPADSAPGTIRGDFGVDVGRNVIHGSDSVESANREIALWFKPEELV  138 (149)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCHHHHHCCCCCCCCEECCCCHHHHHHHHHHCCCCCCEE
T ss_conf             8999999858999676899882888566657618578999999999999718924313


No 2  
>smart00562 NDK These are enzymes that catalyze nonsubstrate specific conversions of nucleoside diphosphates to nucleoside triphosphates. These enzymes play important roles in bacterial growth, signal transduction and pathogenicity.
Probab=100.00  E-value=0  Score=361.00  Aligned_cols=135  Identities=48%  Similarity=0.829  Sum_probs=133.7

Q ss_pred             CEEEEEECCHHHHCCCHHHHHHHHHHCCCEEEEHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHCCCCCEEEEECCCCCHH
Q ss_conf             10230455237718987999999972555892100112699999999888514742100122100111577111164017
Q gi|254780390|r    4 EKTFSMIKPDAVKRNLIGSIVKELEDYGLCVVAAKFCWMNRKQAEDFYLIHKDRPFFPELVQAMISGPVFLQVLKGEEAI   83 (140)
Q Consensus         4 e~Tl~iIKPDav~~~~~g~Ii~~i~~~Gf~I~~~k~~~ls~e~a~~fY~~~~~k~ff~~lv~~m~sGpv~alvl~g~naV   83 (140)
                      ||||+||||||++++++|+|+++|+++||+|+++|++++|+++|++||++|++||||++|++||+||||+||+|+|+|||
T Consensus         1 E~Tl~iIKPdav~~~~~g~Ii~~i~~~Gf~I~~~k~~~lt~~~a~~fY~~~~~kpff~~Lv~~m~sGp~~alvl~g~naV   80 (135)
T smart00562        1 ERTLAIIKPDAVQRGLIGEIISRFERKGFKIVAMKMLQLTEELAEEFYAEHKGKPFFNDLVEFMTSGPVVAMVLEGEDAV   80 (135)
T ss_pred             CEEEEEECCHHHHCCCHHHHHHHHHHCCCEEEEEEEECCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCEEEEEEECCCHH
T ss_conf             90699989326524788999999998699883413024899999999998844654275766434798799998569999


Q ss_pred             HHHHHHCCCCCHHHCCCCCCCHHCCCCHHHEEEEECCCHHHHHHHHHHHCCHHHC
Q ss_conf             8999661889977768997000101152210044069989999999872685650
Q gi|254780390|r   84 SKNREVMGDTDPKKALKGTIRNKYGISIGENSIHGSDSLKTALEEISYWFARNEI  138 (140)
Q Consensus        84 ~~~R~l~Gptdp~~a~p~tiR~~fg~~~~~N~vH~Sds~e~a~rEi~~fF~~~ei  138 (140)
                      ++||+|||||||++|+|+||||+||.+.++|+||||||+++|+||++||||++|+
T Consensus        81 ~~~R~l~Gpt~p~~a~p~siR~~fg~~~~~N~vHgSds~e~A~~Ei~~fF~~~e~  135 (135)
T smart00562       81 KTWRTLMGPTDPREAAPGTIRGDFGLDIGRNAVHGSDSPESAEREIALFFPESEI  135 (135)
T ss_pred             HHHHHHHCCCCHHHCCCCCHHHHHCCCCCCCCEECCCCHHHHHHHHHHCCCCCCC
T ss_conf             9999987889933448873578746775545957889999999999854991009


No 3  
>pfam00334 NDK Nucleoside diphosphate kinase.
Probab=100.00  E-value=0  Score=359.99  Aligned_cols=135  Identities=50%  Similarity=0.824  Sum_probs=133.6

Q ss_pred             CEEEEEECCHHHHCCCHHHHHHHHHHCCCEEEEHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHCCCCCEEEEECCCCCHH
Q ss_conf             10230455237718987999999972555892100112699999999888514742100122100111577111164017
Q gi|254780390|r    4 EKTFSMIKPDAVKRNLIGSIVKELEDYGLCVVAAKFCWMNRKQAEDFYLIHKDRPFFPELVQAMISGPVFLQVLKGEEAI   83 (140)
Q Consensus         4 e~Tl~iIKPDav~~~~~g~Ii~~i~~~Gf~I~~~k~~~ls~e~a~~fY~~~~~k~ff~~lv~~m~sGpv~alvl~g~naV   83 (140)
                      ||||+||||||++++++|+||++|+++||+|+++|++++|+++|++||++|+|||||++|++||+||||+||+|+|+|||
T Consensus         1 E~Tl~iIKPdav~~~~~g~Ii~~i~~~Gf~I~~~k~~~ls~~~a~~fY~~~~~k~ff~~lv~~mtSGpv~alvl~g~naV   80 (135)
T pfam00334         1 ERTLVIIKPDAVQRGLIGEIISRFEKKGFKIVALKMLQLTREQAEEHYAEHKGKPFFPGLVEFMTSGPVVAMVLEGENAV   80 (135)
T ss_pred             CEEEEEECCHHHHCCCHHHHHHHHHHCCCEEEEEEEECCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCEEEEEEECCCHH
T ss_conf             90699989505512788999999998699999864134899999999999843642077887652798699999659989


Q ss_pred             HHHHHHCCCCCHHHCCCCCCCHHCCCCHHHEEEEECCCHHHHHHHHHHHCCHHHC
Q ss_conf             8999661889977768997000101152210044069989999999872685650
Q gi|254780390|r   84 SKNREVMGDTDPKKALKGTIRNKYGISIGENSIHGSDSLKTALEEISYWFARNEI  138 (140)
Q Consensus        84 ~~~R~l~Gptdp~~a~p~tiR~~fg~~~~~N~vH~Sds~e~a~rEi~~fF~~~ei  138 (140)
                      .+||+|+|||||.+|+|+||||+||.+.++|++|||||+++|+||++||||++|+
T Consensus        81 ~~~R~l~Gptdp~~A~P~siR~~fg~~~~~N~vHgSds~e~A~~Ei~~fF~~~e~  135 (135)
T pfam00334        81 AVVRELMGATNPAEAAPGTIRGDFAVSIGRNAVHGSDSPESAEREIALFFPEEEI  135 (135)
T ss_pred             HHHHHHCCCCCHHHCCCCCHHHHHCCCCCCCCEECCCCHHHHHHHHHHCCCCCCC
T ss_conf             9999871899810168742678856775654857789999999999963992009


No 4  
>PRK00668 ndk nucleoside diphosphate kinase; Validated
Probab=100.00  E-value=0  Score=353.85  Aligned_cols=131  Identities=59%  Similarity=0.960  Sum_probs=130.2

Q ss_pred             CCEEEEEECCHHHHCCCHHHHHHHHHHCCCEEEEHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHCCCCCEEEEECCCCCH
Q ss_conf             31023045523771898799999997255589210011269999999988851474210012210011157711116401
Q gi|254780390|r    3 IEKTFSMIKPDAVKRNLIGSIVKELEDYGLCVVAAKFCWMNRKQAEDFYLIHKDRPFFPELVQAMISGPVFLQVLKGEEA   82 (140)
Q Consensus         3 ~e~Tl~iIKPDav~~~~~g~Ii~~i~~~Gf~I~~~k~~~ls~e~a~~fY~~~~~k~ff~~lv~~m~sGpv~alvl~g~na   82 (140)
                      ||+||+||||||++++++|+|+++|+++||+|+++|++++|+++|++||++|++||||++|++||+||||+||+|+|+||
T Consensus         1 ~E~Tl~iIKPdav~~~~~g~Ii~~i~~~Gf~I~~~k~~~lt~e~a~~~Y~~~~~k~ff~~lv~~m~sgpv~al~l~g~na   80 (131)
T PRK00668          1 IERTFSIIKPDAVKRNLIGEILARFERAGLKIVAAKMVHLSREEAEGFYAEHKGKPFFGELVEFMTSGPVVVQVLEGENA   80 (131)
T ss_pred             CCEEEEEECCHHHCCCCHHHHHHHHHHCCCEEEEEEEECCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCEEEEEEECCCH
T ss_conf             94359998950440488899999999879989884302599999999999983487537677753579879999856998


Q ss_pred             HHHHHHHCCCCCHHHCCCCCCCHHCCCCHHHEEEEECCCHHHHHHHHHHHC
Q ss_conf             789996618899777689970001011522100440699899999998726
Q gi|254780390|r   83 ISKNREVMGDTDPKKALKGTIRNKYGISIGENSIHGSDSLKTALEEISYWF  133 (140)
Q Consensus        83 V~~~R~l~Gptdp~~a~p~tiR~~fg~~~~~N~vH~Sds~e~a~rEi~~fF  133 (140)
                      |++||+|+|||||++|+|+||||+||.+.++|+||||||+++|+||++|||
T Consensus        81 V~~~R~liGptdp~~A~p~siR~~yg~~~~~N~vHgSds~e~A~rEi~~fF  131 (131)
T PRK00668         81 IARNRDLMGATNPAEAAPGTIRGDFALSIGENSVHGSDSPESAAREIAYFF  131 (131)
T ss_pred             HHHHHHHHCCCCHHHCCCCCHHHHHCCCCCCCCEECCCCHHHHHHHHHHHC
T ss_conf             999999877898212588545677467656408678899999999998539


No 5  
>cd04413 NDPk_I Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside triphosphate (NTP) donor onto a nucleoside diphosphate (NDP) acceptor through a phosphohistidine intermediate. The mammalian nm23/NDP kinase gene family can be divided into two distinct groups. The group I genes encode proteins that generally have highly homologous counterparts in other organisms and possess the classic enzymatic activity of a kinase. This group includes vertebrate NDP kinases A-D (Nm23- H1 to -H4),  and its counterparts in bacteria, archea and other eukaryotes. NDP kinases exist in two different quaternary structures; all known eukaryotic enzymes are hexamers, while some bacterial enzymes are tetramers, as in Myxococcus. They possess the NDP kinase active site motif (NXXH[G/A]SD) and the nine residues that 
Probab=100.00  E-value=0  Score=351.87  Aligned_cols=130  Identities=49%  Similarity=0.843  Sum_probs=129.3

Q ss_pred             CEEEEEECCHHHHCCCHHHHHHHHHHCCCEEEEHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHCCCCCEEEEECCCCCHH
Q ss_conf             10230455237718987999999972555892100112699999999888514742100122100111577111164017
Q gi|254780390|r    4 EKTFSMIKPDAVKRNLIGSIVKELEDYGLCVVAAKFCWMNRKQAEDFYLIHKDRPFFPELVQAMISGPVFLQVLKGEEAI   83 (140)
Q Consensus         4 e~Tl~iIKPDav~~~~~g~Ii~~i~~~Gf~I~~~k~~~ls~e~a~~fY~~~~~k~ff~~lv~~m~sGpv~alvl~g~naV   83 (140)
                      ||||+||||||++++++|+|+++|+++||+|+++|++++|+++|++||.+|++||||++|++||+||||+||+|+|+|||
T Consensus         1 E~Tl~iIKPDav~~~~~g~Ii~~i~~~Gf~I~~~k~~~ls~~~a~~fY~~~~~kpff~~lv~~m~sGpv~a~~l~g~naV   80 (130)
T cd04413           1 ERTLVIIKPDGVQRGLIGEIISRFERKGLKIVALKMLQLTEELAEEHYAEHKGKPFFPELVEFMTSGPVVAMVLEGENAV   80 (130)
T ss_pred             CCEEEEECCHHHCCCCHHHHHHHHHHCCCEEEEEEEECCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCEEEEEEECCCHH
T ss_conf             90699989405403778999999998699880301056999999999988539715475766643798799998659989


Q ss_pred             HHHHHHCCCCCHHHCCCCCCCHHCCCCHHHEEEEECCCHHHHHHHHHHHC
Q ss_conf             89996618899777689970001011522100440699899999998726
Q gi|254780390|r   84 SKNREVMGDTDPKKALKGTIRNKYGISIGENSIHGSDSLKTALEEISYWF  133 (140)
Q Consensus        84 ~~~R~l~Gptdp~~a~p~tiR~~fg~~~~~N~vH~Sds~e~a~rEi~~fF  133 (140)
                      ++||++||||||++|+|+||||+||.+.++|+||||||+++|+||++|||
T Consensus        81 ~~~R~l~Gptdp~~A~p~siR~~fg~~~~~NavHgSDs~e~A~~Ei~~fF  130 (130)
T cd04413          81 KTVRKLMGATNPADAAPGTIRGDFALSIGRNIVHGSDSVESAEREIALWF  130 (130)
T ss_pred             HHHHHHHCCCCHHHCCCCCHHHHHCCCCCCCCEECCCCHHHHHHHHHHHC
T ss_conf             99998828999555697314677378756479478899999999998649


No 6  
>COG0105 Ndk Nucleoside diphosphate kinase [Nucleotide transport and metabolism]
Probab=100.00  E-value=0  Score=351.55  Aligned_cols=135  Identities=50%  Similarity=0.810  Sum_probs=133.0

Q ss_pred             CCCEEEEEECCHHHHCCCHHHHHHHHHHCCCEEEEHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHCCCCCEEEEECCCCC
Q ss_conf             63102304552377189879999999725558921001126999999998885147421001221001115771111640
Q gi|254780390|r    2 VIEKTFSMIKPDAVKRNLIGSIVKELEDYGLCVVAAKFCWMNRKQAEDFYLIHKDRPFFPELVQAMISGPVFLQVLKGEE   81 (140)
Q Consensus         2 ~~e~Tl~iIKPDav~~~~~g~Ii~~i~~~Gf~I~~~k~~~ls~e~a~~fY~~~~~k~ff~~lv~~m~sGpv~alvl~g~n   81 (140)
                      +|||||+|||||+|+|+++|+|+.+|+++||+|+++|++++++++|++||++|++||||++|++||+|||+++|+|+|+|
T Consensus         1 ~~erT~~iiKPDaV~R~LIG~IisrfE~~Glkiva~K~~~~~~e~Ae~~Y~~h~~kpFf~~Lv~fitSgPvv~~VleGe~   80 (135)
T COG0105           1 AMERTLSIIKPDAVKRGLIGEIISRFEKKGLKIVALKMVQLSRELAENHYAEHKGKPFFGELVEFITSGPVVAMVLEGEN   80 (135)
T ss_pred             CCCEEEEEECCCHHHHHHHHHHHHHHHHCCCEEEEEEEECCCHHHHHHHHHHHCCCCCCHHHHHHEECCCEEEEEEECHH
T ss_conf             96158998884266542189999999977988876440204799997778987678752877862312658999985276


Q ss_pred             HHHHHHHHCCCCCHHHCCCCCCCHHCCCCHHHEEEEECCCHHHHHHHHHHHCCHH
Q ss_conf             1789996618899777689970001011522100440699899999998726856
Q gi|254780390|r   82 AISKNREVMGDTDPKKALKGTIRNKYGISIGENSIHGSDSLKTALEEISYWFARN  136 (140)
Q Consensus        82 aV~~~R~l~Gptdp~~a~p~tiR~~fg~~~~~N~vH~Sds~e~a~rEi~~fF~~~  136 (140)
                      ||+.||+++|+|||.+|+|||||++|+.+..+|+||||||+|+|+|||+|||++.
T Consensus        81 ai~~~R~l~GaTnp~~A~pGTIRgdfa~~~~~N~vHgSDs~esA~rEIa~~F~~~  135 (135)
T COG0105          81 AISVVRKLMGATNPANAAPGTIRGDFALSVGENVVHGSDSPESAEREIALFFSKS  135 (135)
T ss_pred             HHHHHHHHHCCCCCCCCCCCEEEEEHHCCCCCCEEECCCCHHHHHHHHHHCCCCC
T ss_conf             9999999977998121799827623201467665773399788867765106799


No 7  
>cd04414 NDPk6 Nucleoside diphosphate kinase 6 (NDP kinase 6, NDPk6, NM23-H6; NME6; Inhibitor of p53-induced apoptosis-alpha, IPIA-alpha): The nm23-H6 gene encoding NDPk6 is expressed mainly in mitochondria, but also found at a lower level in most tissues. NDPk6 has all nine residues considered crucial for enzyme structure and activity, and has been found to have NDP kinase activity. It may play a role in cell growth and cell cycle progression. The nm23-H6 gene locus has been implicated in a variety of malignant tumors.
Probab=100.00  E-value=0  Score=348.30  Aligned_cols=131  Identities=36%  Similarity=0.519  Sum_probs=126.3

Q ss_pred             CEEEEEECCHHHHCCCHH-HHHHHHHHCCCEEEEHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHCCCCCEEEEECCCCCH
Q ss_conf             102304552377189879-9999997255589210011269999999988851474210012210011157711116401
Q gi|254780390|r    4 EKTFSMIKPDAVKRNLIG-SIVKELEDYGLCVVAAKFCWMNRKQAEDFYLIHKDRPFFPELVQAMISGPVFLQVLKGEEA   82 (140)
Q Consensus         4 e~Tl~iIKPDav~~~~~g-~Ii~~i~~~Gf~I~~~k~~~ls~e~a~~fY~~~~~k~ff~~lv~~m~sGpv~alvl~g~na   82 (140)
                      |+||+||||||+++++++ .|+++|+++||+|+++|++++|+++|++||++|+|||||++|++||+||||+||+|+|+||
T Consensus         1 q~Tl~iIKPDav~~~l~~~~I~~~i~~~Gf~I~~~k~~~ls~e~a~~~Y~~~~gk~ff~~Lv~~mtsGPv~a~vl~g~na   80 (135)
T cd04414           1 QLTLALIKPDAVAHPLALEAVRQLILSNGFTIVRKKELRWTTEDAERFYAEHKGKFFYDRLVSFMTSGPSWALILAHENA   80 (135)
T ss_pred             CEEEEEECHHHHHCCCCHHHHHHHHHHCCCEEEEEEEECCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCEEEEEEECCCH
T ss_conf             94899989148656983589999999879989752522389999999999975987588999996779879999836769


Q ss_pred             HHHHHHHCCCCCHHHC---CCCCCCHHCCCCHHHEEEEECCCHHHHHHHHHHHCC
Q ss_conf             7899966188997776---899700010115221004406998999999987268
Q gi|254780390|r   83 ISKNREVMGDTDPKKA---LKGTIRNKYGISIGENSIHGSDSLKTALEEISYWFA  134 (140)
Q Consensus        83 V~~~R~l~Gptdp~~a---~p~tiR~~fg~~~~~N~vH~Sds~e~a~rEi~~fF~  134 (140)
                      |++||+++|||||.+|   +|+||||+||++.++|++|||||+|+|+|||+||||
T Consensus        81 V~~~R~l~Gptdp~~a~~~~P~tIR~~fg~~~~~N~vHgSds~e~A~rEi~~fFP  135 (135)
T cd04414          81 IKTWRALMGPTKVFRARASAPDSIRGLYGLTDTRNATHGSDSPASAQREIALFFP  135 (135)
T ss_pred             HHHHHHHHCCCCCCHHHHHCCCCHHHHHCCCCCCCCEECCCCHHHHHHHHHHCCC
T ss_conf             9999997189995413450899719984787766084388999999999984198


No 8  
>cd04418 NDPk5 Nucleoside diphosphate kinase homolog 5 (NDP kinase homolog 5, NDPk5, NM23-H5; Inhibitor of p53-induced apoptosis-beta, IPIA-beta): In human, mRNA for NDPk5 is almost exclusively found in testis, especially in the flagella of spermatids and spermatozoa, in association with axoneme microtubules, and may play a role in spermatogenesis by increasing the ability of late-stage spermatids to eliminate reactive oxygen species.  It belongs to the nm23 Group II genes and appears to differ from the other human NDPks in that it lacks two important catalytic site residues, and thus does not appear to possess NDP kinase activity. NDPk5 confers protection from cell death by Bax and alters the cellular levels of several antioxidant enzymes, including glutathione peroxidase 5 (Gpx5).
Probab=100.00  E-value=0  Score=346.17  Aligned_cols=129  Identities=37%  Similarity=0.580  Sum_probs=126.4

Q ss_pred             CEEEEEECCHHHHCCCHHHHHHHHHHCCCEEEEHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHCCCCCEEEEECCCCCHH
Q ss_conf             10230455237718987999999972555892100112699999999888514742100122100111577111164017
Q gi|254780390|r    4 EKTFSMIKPDAVKRNLIGSIVKELEDYGLCVVAAKFCWMNRKQAEDFYLIHKDRPFFPELVQAMISGPVFLQVLKGEEAI   83 (140)
Q Consensus         4 e~Tl~iIKPDav~~~~~g~Ii~~i~~~Gf~I~~~k~~~ls~e~a~~fY~~~~~k~ff~~lv~~m~sGpv~alvl~g~naV   83 (140)
                      ||||+||||||+++  .|+|+++|+++||+|+++|++++|+++|++||++|+|||||++|++||+||||+||+|+|+|||
T Consensus         1 ErTl~iIKPDav~~--~g~Il~~i~~~Gf~I~~~k~~~lt~~~a~~~Y~~~~gk~ff~~Lv~~mtSGPvvalvl~g~~aV   78 (132)
T cd04418           1 ERTLAIIKPDAVHK--AEEIEDIILESGFTIVQKRKLQLSPEQCSDFYAEHYGKMFFPHLVAYMSSGPIVAMVLARHNAI   78 (132)
T ss_pred             CCEEEEECCCHHCC--CCHHHHHHHHCCCEEEEHHHHCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCEEEEEEECCCHH
T ss_conf             92799989205335--0399999998699990021205999999999999879874787743014788799997166799


Q ss_pred             HHHHHHCCCCCHHHC---CCCCCCHHCCCCHHHEEEEECCCHHHHHHHHHHHCC
Q ss_conf             899966188997776---899700010115221004406998999999987268
Q gi|254780390|r   84 SKNREVMGDTDPKKA---LKGTIRNKYGISIGENSIHGSDSLKTALEEISYWFA  134 (140)
Q Consensus        84 ~~~R~l~Gptdp~~a---~p~tiR~~fg~~~~~N~vH~Sds~e~a~rEi~~fF~  134 (140)
                      +.||+|||||||.+|   .|+||||+||++.++|+||||||+|+|+|||+||||
T Consensus        79 ~~~R~l~Gpt~p~~A~~~~P~siR~~fg~~~~~N~vH~Sds~e~A~~Ei~~fFP  132 (132)
T cd04418          79 SYWKELLGPTNSLKAKETHPDSLRAIYGTDDLRNAVHGSDSFSSAEREIRFMFP  132 (132)
T ss_pred             HHHHHHHCCCCCHHHHHHCCCCHHHHHCCCCCCCCEECCCCHHHHHHHHHHCCC
T ss_conf             999998688992555663799859983899776795888999999999973097


No 9  
>cd00595 NDPk Nucleoside diphosphate kinases (NDP kinases, NDPks): NDP kinases, responsible for the synthesis of nucleoside triphosphates (NTPs), are involved in numerous regulatory processes associated with proliferation, development, and differentiation. They are vital for DNA/RNA synthesis, cell division, macromolecular metabolism and growth. The enzymes generate NTPs or their deoxy derivatives by terminal (gamma) phosphotransfer from an NTP such as ATP or GTP to any nucleoside diphosphate (NDP) or its deoxy derivative. The sequence of NDPk has been highly conserved through evolution. There is a single histidine residue conserved in all known NDK isozymes, which is involved in the catalytic mechanism. The first confirmed metastasis suppressor gene was the NDP kinase protein encoded by the nm23 gene. Unicellular organisms generally possess only one gene encoding NDP kinase, while most multicellular organisms possess not only an ortholog that provides most of the NDP kinase enzymatic a
Probab=100.00  E-value=0  Score=343.86  Aligned_cols=130  Identities=45%  Similarity=0.806  Sum_probs=128.3

Q ss_pred             CEEEEEECCHHHHCCCHHHHHHHHHHCCCEEEEHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHCCCCCEEEEECCCCCHH
Q ss_conf             10230455237718987999999972555892100112699999999888514742100122100111577111164017
Q gi|254780390|r    4 EKTFSMIKPDAVKRNLIGSIVKELEDYGLCVVAAKFCWMNRKQAEDFYLIHKDRPFFPELVQAMISGPVFLQVLKGEEAI   83 (140)
Q Consensus         4 e~Tl~iIKPDav~~~~~g~Ii~~i~~~Gf~I~~~k~~~ls~e~a~~fY~~~~~k~ff~~lv~~m~sGpv~alvl~g~naV   83 (140)
                      ||||+||||||++++++|+|+++|+++||+|+++|++++|+++|++||.+|+|||||++|++||+||||++|+|+|+|||
T Consensus         1 ErTl~iIKPdav~~~~~g~Ii~~i~~~Gf~I~~~k~~~lt~~~a~~~Y~~~~~k~ff~~lv~~mtsGpv~~lvl~g~naV   80 (133)
T cd00595           1 ERTLALIKPDAVAEGLLGEIIMRIEDAGFEIVAMKELHLTEEQAEEFYVEHKGRPFFPDLVQFMSSGPVVAMILEKDNAV   80 (133)
T ss_pred             CCEEEEECCCHHCCCCHHHHHHHHHHCCCEEEEEEEECCCHHHHHHHHHHHHCCCHHHHHHHHHCCCCEEEEEEECCCHH
T ss_conf             91799989315405889999999998799899875022889999999999846341778999963798499998427699


Q ss_pred             HHHHHHCCCCCHHHCC---CCCCCHHCCCCHHHEEEEECCCHHHHHHHHHHHC
Q ss_conf             8999661889977768---9970001011522100440699899999998726
Q gi|254780390|r   84 SKNREVMGDTDPKKAL---KGTIRNKYGISIGENSIHGSDSLKTALEEISYWF  133 (140)
Q Consensus        84 ~~~R~l~Gptdp~~a~---p~tiR~~fg~~~~~N~vH~Sds~e~a~rEi~~fF  133 (140)
                      ++||+|+|||||.+|.   |+||||+||++.++|++|||||+++|+||++|||
T Consensus        81 ~~~R~l~Gpt~p~~A~~~~P~siR~~yg~~~~~N~vHgSds~e~A~~Ei~~fF  133 (133)
T cd00595          81 GEWREMLGPTNPEIARHLAPGSLRADFGTDVLRNAVHGSDSVESAAREIAFFF  133 (133)
T ss_pred             HHHHHHHCCCCHHHHHHHCCCCHHHHHCCCCCCCCEECCCCHHHHHHHHHHHC
T ss_conf             99998738998278887589865777367777608447899999999998529


No 10 
>cd04412 NDPk7B Nucleoside diphosphate kinase 7 domain B (NDPk7B): The nm23-H7 class of nucleoside diphosphate kinase (NDPk7) consists of an N-terminal DM10 domain and two functional catalytic NDPk modules, NDPk7A and NDPk7B. The function of the DM10 domain, which also occurs in multiple copies in other proteins, is unknown. NDPk7 is predominantly expressed in testes, although appreciable amount are also found in liver, heart, brain, ovary, small intestine and spleen. The nm23-H7 gene is located in or near the hereditary prostrate cancer susceptibility locus. Nm23-H7 may be involved in the development of colon and gastric carcinoma, the latter possibly in a type-specific manner.
Probab=100.00  E-value=0  Score=340.20  Aligned_cols=130  Identities=32%  Similarity=0.539  Sum_probs=127.6

Q ss_pred             CEEEEEECCHHHHCCCHHHHHHHHHHCCCEEEEHHHCCCCHHHHHHHHHHHCC-CCCCCHHHHHCCCCCEEEEECCCCCH
Q ss_conf             10230455237718987999999972555892100112699999999888514-74210012210011157711116401
Q gi|254780390|r    4 EKTFSMIKPDAVKRNLIGSIVKELEDYGLCVVAAKFCWMNRKQAEDFYLIHKD-RPFFPELVQAMISGPVFLQVLKGEEA   82 (140)
Q Consensus         4 e~Tl~iIKPDav~~~~~g~Ii~~i~~~Gf~I~~~k~~~ls~e~a~~fY~~~~~-k~ff~~lv~~m~sGpv~alvl~g~na   82 (140)
                      +.||+|||||||+++++|+|+++|+++||+|+++|++++|+++|++||++|++ +|||++|++||+||||+||+|+|+||
T Consensus         1 n~Tl~iIKPdav~~~~~g~Il~~i~~~Gf~I~~~k~~~lt~~~a~~fY~~~~~~~pff~~lv~~mtsGPvval~L~g~na   80 (134)
T cd04412           1 NCTVCIIKPHAVSHGLLGEILQQILDEGFEITALQMFNLTRANAEEFLEVYKGVVPELPAMVDELTSGPCIALEIAGENA   80 (134)
T ss_pred             CCEEEEECCHHHHCCCHHHHHHHHHHCCCEEEEEECCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCEEEEEEECCCH
T ss_conf             92799989035514889999999998699997614167999999999999706543177899997169878998607459


Q ss_pred             HHHHHHHCCCCCHHHC---CCCCCCHHCCCCHHHEEEEECCCHHHHHHHHHHHC
Q ss_conf             7899966188997776---89970001011522100440699899999998726
Q gi|254780390|r   83 ISKNREVMGDTDPKKA---LKGTIRNKYGISIGENSIHGSDSLKTALEEISYWF  133 (140)
Q Consensus        83 V~~~R~l~Gptdp~~a---~p~tiR~~fg~~~~~N~vH~Sds~e~a~rEi~~fF  133 (140)
                      |++||+|||||||.+|   +|+||||+||++.++|+||||||+++|+||++|||
T Consensus        81 V~~~R~l~Gpt~p~~A~~~~P~siR~~yG~~~~~N~vHgSds~esA~rEi~~fF  134 (134)
T cd04412          81 VKTFREFCGPFDPEIAKQLRPNTLRARYGKDKVQNAVHCTDLPEDGPLELKFFF  134 (134)
T ss_pred             HHHHHHHHCCCCHHHHHHHCCCCHHHHHCCCCCCCCEECCCCHHHHHHHHHHHC
T ss_conf             999999857998577666389965887577755518457899999999998529


No 11 
>cd04416 NDPk_TX NDP kinase domain of thioredoxin domain-containing proteins  (TXNDC3 and TXNDC6): Txl-2 (TXNDC6) and Sptrx-2 (TXNDC3) are fusion proteins of Group II N-terminal thioredoxin domains followed by one or three NDP kinase domains, respectively. Sptrx-2, which has a tissue specific distribution in human testis, has been considered as a member of the nm23 family (nm23-H8) and exhibits a high homology with sea urchin IC1 (intermediate chain-1) protein, a component of the sperm axonemal outer dynein arm complex. Txl-2 is mainly represented in close association with microtubules within tissues with cilia and flagella such as seminiferous epithelium (spermatids) and lung airway epithelium, suggesting possible role in control of microtubule stability and maintenance.
Probab=100.00  E-value=0  Score=339.79  Aligned_cols=129  Identities=36%  Similarity=0.622  Sum_probs=126.6

Q ss_pred             CEEEEEECCHHHHCCCHHHHHHHHHHCCCEEEEHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHCCCCCEEEEECCCCCHH
Q ss_conf             10230455237718987999999972555892100112699999999888514742100122100111577111164017
Q gi|254780390|r    4 EKTFSMIKPDAVKRNLIGSIVKELEDYGLCVVAAKFCWMNRKQAEDFYLIHKDRPFFPELVQAMISGPVFLQVLKGEEAI   83 (140)
Q Consensus         4 e~Tl~iIKPDav~~~~~g~Ii~~i~~~Gf~I~~~k~~~ls~e~a~~fY~~~~~k~ff~~lv~~m~sGpv~alvl~g~naV   83 (140)
                      |+||+||||||++++ +|+|+++|+++||.|+++|++++|+++|++||++|+++|||++|++|||||||+||+|+|+|||
T Consensus         1 E~Tl~iIKPDav~~~-~~~Ii~~i~~~Gf~I~~~k~~~lt~e~a~~fY~~h~~k~ff~~lv~~mtsGp~~~lvl~g~naV   79 (132)
T cd04416           1 EYTLALIKPDAVAEK-KDEILEKIKEAGFEILAQKEMVLTEEQAREFYKEHEEEDYFEDLVEFMTSGPSLILVLSKENAV   79 (132)
T ss_pred             CEEEEEECCHHHHHC-HHHHHHHHHHCCCEEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCEEEEEEECCCHH
T ss_conf             928999890677618-7899999998799899987335899999999898648731888998870598499998368878


Q ss_pred             HHHHHHCCCCCHHHC---CCCCCCHHCCCCHHHEEEEECCCHHHHHHHHHHHC
Q ss_conf             899966188997776---89970001011522100440699899999998726
Q gi|254780390|r   84 SKNREVMGDTDPKKA---LKGTIRNKYGISIGENSIHGSDSLKTALEEISYWF  133 (140)
Q Consensus        84 ~~~R~l~Gptdp~~a---~p~tiR~~fg~~~~~N~vH~Sds~e~a~rEi~~fF  133 (140)
                      ++||+|+|||||.+|   .|+||||+||++.++|+||||||+++|+|||+|||
T Consensus        80 ~~~R~l~Gptdp~~A~~~~P~siR~~fg~~~~~N~vH~SDs~e~A~rEi~~fF  132 (132)
T cd04416          80 EEWRELMGPTDPEEAKEEKPDSLRAQFARDHLSNAVHGSSSAEEAEKEIDFFF  132 (132)
T ss_pred             HHHHHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCEECCCCHHHHHHHHHHHC
T ss_conf             99998748998578733699987888568867569588999999999998649


No 12 
>cd04415 NDPk7A Nucleoside diphosphate kinase 7 domain A (NDPk7A): The nm23-H7 class of nucleoside diphosphate kinase (NDPk7) consists of an N-terminal DM10 domain and two functional catalytic NDPk modules, NDPk7A and NDPk7B. The function of the DM10 domain, which also occurs in multiple copies in other proteins, is unknown. NDPk7 is predominantly expressed in testes, although appreciable amount are also found in liver, heart, brain, ovary, small intestine and spleen. The nm23-H7 gene is located in or near the hereditary prostrate cancer susceptibility locus. Nm23-H7 may be involved in the development of colon and gastric carcinoma, the latter possibly in a type-specific manner.
Probab=100.00  E-value=0  Score=339.58  Aligned_cols=128  Identities=42%  Similarity=0.728  Sum_probs=126.0

Q ss_pred             CEEEEEECCHHHHCCCHHHHHHHHHHCCCEEEEHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHCCCCCEEEEECCCCCHH
Q ss_conf             10230455237718987999999972555892100112699999999888514742100122100111577111164017
Q gi|254780390|r    4 EKTFSMIKPDAVKRNLIGSIVKELEDYGLCVVAAKFCWMNRKQAEDFYLIHKDRPFFPELVQAMISGPVFLQVLKGEEAI   83 (140)
Q Consensus         4 e~Tl~iIKPDav~~~~~g~Ii~~i~~~Gf~I~~~k~~~ls~e~a~~fY~~~~~k~ff~~lv~~m~sGpv~alvl~g~naV   83 (140)
                      ||||+||||||+++  +|+|+++|+++||.|+++|++++|+++|++||++|+|||||+.|++||+||||+||+|+|+|||
T Consensus         1 ErTl~iIKPda~~~--~g~Ii~~i~~~Gf~I~~~k~~~lt~~~a~~~Y~~~~~k~ff~~lv~~mtsGpvvalvl~g~naV   78 (131)
T cd04415           1 EKTLALIKPDAYSK--IGKIIQIIEDAGFTITKAKMTKLSRKEAQDFYAEHQSKPFYNELVQFMTSGPIVAMELVGDDAI   78 (131)
T ss_pred             CCEEEEECCHHHHH--HHHHHHHHHHCCCEEEEEEEECCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCEEEEEEECCCHH
T ss_conf             91799989127754--9999999998799898877562899999999999669985488997814787799998277589


Q ss_pred             HHHHHHCCCCCHHHC---CCCCCCHHCCCCHHHEEEEECCCHHHHHHHHHHHC
Q ss_conf             899966188997776---89970001011522100440699899999998726
Q gi|254780390|r   84 SKNREVMGDTDPKKA---LKGTIRNKYGISIGENSIHGSDSLKTALEEISYWF  133 (140)
Q Consensus        84 ~~~R~l~Gptdp~~a---~p~tiR~~fg~~~~~N~vH~Sds~e~a~rEi~~fF  133 (140)
                      ++||+|+|||||.+|   .|+||||+||.+.++|+||||||+|+|+|||+|||
T Consensus        79 ~~~R~l~Gpt~p~~Ak~~~P~siR~~fg~~~~~N~vHgSds~e~A~~Ei~~fF  131 (131)
T cd04415          79 SEWRKLLGPTNSSVARSDAPNSIRALFGTDGTRNAAHGSDSVASAARELEFFF  131 (131)
T ss_pred             HHHHHHHCCCCHHHHCCCCCCCCHHHHCCCCCCCCEECCCCHHHHHHHHHHHC
T ss_conf             99998758898345231489987799669987558688999999999998559


No 13 
>KOG0888 consensus
Probab=100.00  E-value=0  Score=316.32  Aligned_cols=137  Identities=45%  Similarity=0.789  Sum_probs=134.8

Q ss_pred             CCEEEEEECCHHHHCCCHHHHHHHHHHCCCEEEEHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHCCCCCEEEEECCCCCH
Q ss_conf             31023045523771898799999997255589210011269999999988851474210012210011157711116401
Q gi|254780390|r    3 IEKTFSMIKPDAVKRNLIGSIVKELEDYGLCVVAAKFCWMNRKQAEDFYLIHKDRPFFPELVQAMISGPVFLQVLKGEEA   82 (140)
Q Consensus         3 ~e~Tl~iIKPDav~~~~~g~Ii~~i~~~Gf~I~~~k~~~ls~e~a~~fY~~~~~k~ff~~lv~~m~sGpv~alvl~g~na   82 (140)
                      +|+||++||||+|+++++++|+.+|+++||+|+++|+++++++.+++||.+|+++|||+.||.||+|||++||+|+|.||
T Consensus         5 ~e~tfi~iKpd~v~~~li~~ii~r~~~~gF~i~~~k~~~~s~~~~e~~Y~~~~~k~Ff~~Lv~~m~SGPv~amv~~g~~~   84 (156)
T KOG0888           5 LERTFILIKPDGVQRGLIGEIIKRFEDKGFKIVALKLVQLSKELLEEHYSDLKSKPFFPGLVEYMSSGPVVAMVLEGDNV   84 (156)
T ss_pred             HHHHHHEECCCHHHHHHHHHHHHHHHHCCCCHHHHEEECCCHHHHHHHHHHHCCCCCHHHHHHHHHCCCCEEHHHCCCCH
T ss_conf             55566305723544203379999998717506552002179999999999863786389999998338610041217779


Q ss_pred             HHHHHHHCCCCCHHHC---CCCCCCHHCCCCHHHEEEEECCCHHHHHHHHHHHCCHHHCC
Q ss_conf             7899966188997776---89970001011522100440699899999998726856506
Q gi|254780390|r   83 ISKNREVMGDTDPKKA---LKGTIRNKYGISIGENSIHGSDSLKTALEEISYWFARNEII  139 (140)
Q Consensus        83 V~~~R~l~Gptdp~~a---~p~tiR~~fg~~~~~N~vH~Sds~e~a~rEi~~fF~~~ei~  139 (140)
                      |+.||.++|||||..|   .|+|||++||.+.+||++|||||.++|+|||++|||++|++
T Consensus        85 V~~~r~llG~t~~~~a~~~~pgsir~~f~~~~~rn~~HgSDs~~sA~rEi~~~F~~~e~~  144 (156)
T KOG0888          85 VQYWRALLGPTNPAAARAAAPGSIRGDFGVDDGRNSIHGSDSVESAEREIKLWFPEFELV  144 (156)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHH
T ss_conf             999999838888431223589874300113677775546776777778988626613410


No 14 
>pfam04339 DUF482 Protein of unknown function, DUF482. This family contains several proteins of uncharacterized function.
Probab=83.10  E-value=0.54  Score=27.30  Aligned_cols=78  Identities=15%  Similarity=0.254  Sum_probs=53.6

Q ss_pred             HHHHHCCCEEEEHHHCCCCHHHHHHHHHHHC------------CCCCCCHHHHHCCCCCEEEEECCCCCHHHHHHHHCCC
Q ss_conf             9997255589210011269999999988851------------4742100122100111577111164017899966188
Q gi|254780390|r   25 KELEDYGLCVVAAKFCWMNRKQAEDFYLIHK------------DRPFFPELVQAMISGPVFLQVLKGEEAISKNREVMGD   92 (140)
Q Consensus        25 ~~i~~~Gf~I~~~k~~~ls~e~a~~fY~~~~------------~k~ff~~lv~~m~sGpv~alvl~g~naV~~~R~l~Gp   92 (140)
                      +++.+.|+.|....=-.++++....||.-|.            .+.||..|.+.|....++++.-.+...|.-.-.+.  
T Consensus       193 ~~v~~~gI~~~~l~G~~I~~~~w~~fy~fY~~Ty~kr~g~~YLn~~FF~~l~~~m~~~i~lv~A~~~~~~IA~al~~~--  270 (370)
T pfam04339       193 RKVAEQGITIRWLTGDEITPEHWDAFYRFYQDTYLRKWGSPYLTRAFFSLLAERMPDRILLVLAERDGRPIAGALNLI--  270 (370)
T ss_pred             HHHHHCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEEEEC--
T ss_conf             999986977999727889999999999999999998758804349999999986744739999996894589999963--


Q ss_pred             CCHHHCCCCCCCHHC-CCC
Q ss_conf             997776899700010-115
Q gi|254780390|r   93 TDPKKALKGTIRNKY-GIS  110 (140)
Q Consensus        93 tdp~~a~p~tiR~~f-g~~  110 (140)
                            ..+||-|+| |..
T Consensus       271 ------~~~~LYGRYWG~~  283 (370)
T pfam04339       271 ------GGDTLYGRYWGCL  283 (370)
T ss_pred             ------CCCEEEEEECCCC
T ss_conf             ------6876775310534


No 15 
>KOG2562 consensus
Probab=54.80  E-value=21  Score=18.00  Aligned_cols=75  Identities=27%  Similarity=0.307  Sum_probs=51.0

Q ss_pred             CHHHHHHHHHH---CCCEEEEHHHCCCCHHHHHHHHHHHCCC---------------------------CCCCHHHHHCC
Q ss_conf             87999999972---5558921001126999999998885147---------------------------42100122100
Q gi|254780390|r   19 LIGSIVKELED---YGLCVVAAKFCWMNRKQAEDFYLIHKDR---------------------------PFFPELVQAMI   68 (140)
Q Consensus        19 ~~g~Ii~~i~~---~Gf~I~~~k~~~ls~e~a~~fY~~~~~k---------------------------~ff~~lv~~m~   68 (140)
                      +..-|++||-.   .|+.+..  .-+|+-+..-.|--...+|                           .||.+....|-
T Consensus       308 lt~~ivdRIFs~v~r~~~~~~--eGrmdykdFv~FilA~e~k~t~~SleYwFrclDld~~G~Lt~~el~~fyeeq~~rm~  385 (493)
T KOG2562         308 LTERIVDRIFSQVPRGFTVKV--EGRMDYKDFVDFILAEEDKDTPASLEYWFRCLDLDGDGILTLNELRYFYEEQLQRME  385 (493)
T ss_pred             HHHHHHHHHHHHCCCCCEEEE--CCCCCHHHHHHHHHHHCCCCCCCCHHHHEEEEECCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             056899999754146645630--475669999999998605889603122224661168873549999999999999898


Q ss_pred             CCCEEEEECCCCCHHHHHHHHCCCCCHHH
Q ss_conf             11157711116401789996618899777
Q gi|254780390|r   69 SGPVFLQVLKGEEAISKNREVMGDTDPKK   97 (140)
Q Consensus        69 sGpv~alvl~g~naV~~~R~l~Gptdp~~   97 (140)
                      ++-.-++..  +|+..+.|+|+||.|+-+
T Consensus       386 ~~~~e~l~f--ed~l~qi~DMvkP~~~~k  412 (493)
T KOG2562         386 CMGQEALPF--EDALCQIRDMVKPEDENK  412 (493)
T ss_pred             HCCCCCCCH--HHHHHHHHHHHCCCCCCC
T ss_conf             648876538--999999999748567784


No 16 
>TIGR01458 HAD-SF-IIA-hyp3 HAD-superfamily subfamily IIA hydrolase, TIGR01458; InterPro: IPR006355   These sequences are all members of the IIA subfamily of the haloacid dehalogenase superfamily of aspartate-nucleophile hydrolases. .
Probab=40.42  E-value=35  Score=16.66  Aligned_cols=75  Identities=16%  Similarity=0.216  Sum_probs=49.6

Q ss_pred             HHHHHHHHHHCCCEEEEHHHCCCCHHHHHHHHHHHCCCCC---CCHHHHHC----CCCC-EEEEECCCC-----CHHHHH
Q ss_conf             7999999972555892100112699999999888514742---10012210----0111-577111164-----017899
Q gi|254780390|r   20 IGSIVKELEDYGLCVVAAKFCWMNRKQAEDFYLIHKDRPF---FPELVQAM----ISGP-VFLQVLKGE-----EAISKN   86 (140)
Q Consensus        20 ~g~Ii~~i~~~Gf~I~~~k~~~ls~e~a~~fY~~~~~k~f---f~~lv~~m----~sGp-v~alvl~g~-----naV~~~   86 (140)
                      -.+++.++++-||.|.-...+ -+-.-|.+...+.+=+|+   -++...++    ||.| ||+|-..+|     +-=..+
T Consensus        52 ~~~l~~rLqrLgfdisE~ev~-tpapaa~q~l~e~~lRP~Llv~D~vl~~FdgIdTS~PNcVV~g~a~E~Fsyq~~N~AF  130 (258)
T TIGR01458        52 KRDLVERLQRLGFDISEEEVI-TPAPAAAQLLKEKKLRPYLLVDDDVLEEFDGIDTSDPNCVVMGEAEESFSYQRLNRAF  130 (258)
T ss_pred             HHHHHHHHHHCCCCCCHHHHC-CCHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHH
T ss_conf             799999987707732144210-6778999999746899516777685532575667898758982578873488888899


Q ss_pred             HHHCCCCCH
Q ss_conf             966188997
Q gi|254780390|r   87 REVMGDTDP   95 (140)
Q Consensus        87 R~l~Gptdp   95 (140)
                      |-|+--..|
T Consensus       131 r~L~d~~kP  139 (258)
T TIGR01458       131 RVLLDLEKP  139 (258)
T ss_pred             HHHHCCCCC
T ss_conf             887428896


No 17 
>cd06355 PBP1_FmdD_like Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF). This group includes the periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF), found in Methylophilus methylotrophus, and its homologs from other bacteria. FmdD, a type I periplasmic binding protein, is induced by short-chain amides and urea and repressed by excess ammonia, while FmdE and FmdF are hydrophobic transmembrane proteins. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two transmembrane proteins present in various hydrophobic amino acid-binding transport systems.
Probab=35.91  E-value=40  Score=16.32  Aligned_cols=71  Identities=18%  Similarity=0.276  Sum_probs=38.5

Q ss_pred             EEEEEECCHH-HHCCCHHHHHHHHHHCCCEEEEHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHCCCCC-EEEEECCCCCH
Q ss_conf             0230455237-718987999999972555892100112699999999888514742100122100111-57711116401
Q gi|254780390|r    5 KTFSMIKPDA-VKRNLIGSIVKELEDYGLCVVAAKFCWMNRKQAEDFYLIHKDRPFFPELVQAMISGP-VFLQVLKGEEA   82 (140)
Q Consensus         5 ~Tl~iIKPDa-v~~~~~g~Ii~~i~~~Gf~I~~~k~~~ls~e~a~~fY~~~~~k~ff~~lv~~m~sGp-v~alvl~g~na   82 (140)
                      +++++|-+|. .-+.......+.+++.|.+|+........            ..+|-+.|.+-..++| ++.+.+-+.+.
T Consensus       134 k~vaii~~d~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~g------------~~Dfs~~l~ki~~a~pD~v~~~~~g~~~  201 (348)
T cd06355         134 KRFYLVGSDYVYPRTANKILKAQLESLGGEVVGEEYLPLG------------HTDFQSIINKIKAAKPDVVVSTVNGDSN  201 (348)
T ss_pred             CEEEEEECCCHHHHHHHHHHHHHHHHCCCEEEEEEECCCC------------CCCHHHHHHHHHHCCCCEEEEECCCCCH
T ss_conf             8799991685134899999999999859989999813799------------7567999999997699999994765124


Q ss_pred             HHHHH
Q ss_conf             78999
Q gi|254780390|r   83 ISKNR   87 (140)
Q Consensus        83 V~~~R   87 (140)
                      +.-+|
T Consensus       202 ~~~~~  206 (348)
T cd06355         202 VAFFK  206 (348)
T ss_pred             HHHHH
T ss_conf             89999


No 18 
>COG3885 Uncharacterized conserved protein [Function unknown]
Probab=35.84  E-value=42  Score=16.23  Aligned_cols=53  Identities=21%  Similarity=0.230  Sum_probs=37.2

Q ss_pred             EEEEEECCHHHH-CCCHHHHHHHHHHC----CCEEEEHHHCCCCHHHHHHHHHHHCCC
Q ss_conf             023045523771-89879999999725----558921001126999999998885147
Q gi|254780390|r    5 KTFSMIKPDAVK-RNLIGSIVKELEDY----GLCVVAAKFCWMNRKQAEDFYLIHKDR   57 (140)
Q Consensus         5 ~Tl~iIKPDav~-~~~~g~Ii~~i~~~----Gf~I~~~k~~~ls~e~a~~fY~~~~~k   57 (140)
                      -|+++|-|+++. ..+++-|......-    +-...-.+...-+++.|...|..-++.
T Consensus        40 eT~VvIsPHgi~ldd~iaviys~~l~g~~~~~k~~~i~~ey~~dreLa~~I~~~a~g~   97 (261)
T COG3885          40 ETYVVISPHGIRLDDYIAVIYSEYLSGLPYRTKHHPIRKEYKNDRELADKIYEEAKGQ   97 (261)
T ss_pred             CEEEEECCCCEEEECHHHHHHHHHHCCCCCCCCCCCCHHHHHCCHHHHHHHHHHHCCC
T ss_conf             6189985785256101467768765366456656750143320088999999984367


No 19 
>TIGR03407 urea_ABC_UrtA urea ABC transporter, urea binding protein. Members of this protein family are ABC transporter substrate-binding proteins associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity. Members of this protein family tend to have the twin-arginine signal for Sec-independent transport across the plasma membrane.
Probab=28.42  E-value=48  Score=15.89  Aligned_cols=73  Identities=21%  Similarity=0.288  Sum_probs=38.2

Q ss_pred             EEEEEECCHHH-HCCCHHHHHHHHHHCCCEEEEHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHCCCCC-EEEEECCCCCH
Q ss_conf             02304552377-18987999999972555892100112699999999888514742100122100111-57711116401
Q gi|254780390|r    5 KTFSMIKPDAV-KRNLIGSIVKELEDYGLCVVAAKFCWMNRKQAEDFYLIHKDRPFFPELVQAMISGP-VFLQVLKGEEA   82 (140)
Q Consensus         5 ~Tl~iIKPDav-~~~~~g~Ii~~i~~~Gf~I~~~k~~~ls~e~a~~fY~~~~~k~ff~~lv~~m~sGp-v~alvl~g~na   82 (140)
                      +++++|-+|-. -+.....+.+.+++.|.+|+.........            ..|=+.|.+-..++| ++.+.+-+.++
T Consensus       135 k~vaii~~d~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~g~------------~Dfs~~l~kik~a~pD~v~~~~~~~~~  202 (359)
T TIGR03407       135 KRFFLLGSDYVFPRTANKIIKAYLKSLGGTVVGEDYTPLGH------------TDFQTIINKIKAFKPDVVFNTLNGDSN  202 (359)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCC------------CCHHHHHHHHHHCCCCEEEEECCCCCH
T ss_conf             87999945873058999999999997599737788257987------------558999999997699999993746205


Q ss_pred             H---HHHHHH
Q ss_conf             7---899966
Q gi|254780390|r   83 I---SKNREV   89 (140)
Q Consensus        83 V---~~~R~l   89 (140)
                      +   +++|++
T Consensus       203 ~~~~kq~~~~  212 (359)
T TIGR03407       203 VAFFKQLKNA  212 (359)
T ss_pred             HHHHHHHHHH
T ss_conf             7999999982


No 20 
>PRK13054 lipid kinase; Reviewed
Probab=27.38  E-value=58  Score=15.38  Aligned_cols=105  Identities=14%  Similarity=0.114  Sum_probs=56.8

Q ss_pred             CCCCEEEEEECCHHHHCCCHHHHHHHHHHCCCEEEEHHHCCCCHHHHHHHHHHHCCC-----------CCCCHHHHHCC-
Q ss_conf             963102304552377189879999999725558921001126999999998885147-----------42100122100-
Q gi|254780390|r    1 MVIEKTFSMIKPDAVKRNLIGSIVKELEDYGLCVVAAKFCWMNRKQAEDFYLIHKDR-----------PFFPELVQAMI-   68 (140)
Q Consensus         1 m~~e~Tl~iIKPDav~~~~~g~Ii~~i~~~Gf~I~~~k~~~ls~e~a~~fY~~~~~k-----------~ff~~lv~~m~-   68 (140)
                      |.|+|.|.|+-|-.=-.....++++.++++|+++.-...-.  +-.|+++-.+-...           --.++.++-|. 
T Consensus         1 ~~~~k~lli~N~~~~g~~~~~~~~~~l~~~~~~~~~~~T~~--~gda~~la~~a~~~g~d~vv~~GGDGTv~evvngl~~   78 (299)
T PRK13054          1 MEFPKSLLILNGKSAGNEELREAVGLLREEGHTLHVRVTWE--KGDAARYVEEALALGVATVIAGGGDGTLNEVATALAQ   78 (299)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHCCCEEEEEECCC--CCHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHH
T ss_conf             99856999981700050689999999997698799996489--7459999999987799899998772299999999974


Q ss_pred             -CC---CEEEEECCCC-CHHHHHHHHCCCCCHHHCC----C-CCCCHHCCC
Q ss_conf             -11---1577111164-0178999661889977768----9-970001011
Q gi|254780390|r   69 -SG---PVFLQVLKGE-EAISKNREVMGDTDPKKAL----K-GTIRNKYGI  109 (140)
Q Consensus        69 -sG---pv~alvl~g~-naV~~~R~l~Gptdp~~a~----p-~tiR~~fg~  109 (140)
                       .+   |.++++=.|- |-.  .|.+=-|.||++|.    . .+.+-+.|.
T Consensus        79 ~~~~~~~~LgiiP~GTgNdf--AR~lgip~d~~~a~~~i~~g~~~~iDlg~  127 (299)
T PRK13054         79 LEGDDRPSLGILPLGTANDF--ATAAGIPLEPDKALKLAIEGNAQPIDLAR  127 (299)
T ss_pred             CCCCCCCEEEEECCCCHHHH--HHHCCCCCCHHHHHHHHHCCCEEEEEEEE
T ss_conf             78877863999638756899--99829998999999778469879985999


No 21 
>pfam07576 BRAP2 BRCA1-associated protein 2. These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening. These proteins share a region of sequence similarity at their N terminus. They also have pfam02148 at the C terminus.
Probab=27.22  E-value=45  Score=16.07  Aligned_cols=53  Identities=11%  Similarity=0.175  Sum_probs=29.6

Q ss_pred             EEEEEECCHHHHCCCHHHHHHHHHHCCCEEEEHHHC-------------CCCHHHHHHHHHHHCCCCC
Q ss_conf             023045523771898799999997255589210011-------------2699999999888514742
Q gi|254780390|r    5 KTFSMIKPDAVKRNLIGSIVKELEDYGLCVVAAKFC-------------WMNRKQAEDFYLIHKDRPF   59 (140)
Q Consensus         5 ~Tl~iIKPDav~~~~~g~Ii~~i~~~Gf~I~~~k~~-------------~ls~e~a~~fY~~~~~k~f   59 (140)
                      .|++|+-+.+.-.  ..+++.-+...-=.|...|.+             --+.+.|.+||..+-||+|
T Consensus        14 ~~lcil~VPa~~~--~~dll~f~a~~~~~i~h~Riird~~~nrymvLikFr~~~~A~~Fy~~fNGk~F   79 (110)
T pfam07576        14 FVLCLAAVPALLN--SDDILFFVAPIQKVIDHIRIRRDGMPNQYMVLIKFRDQEDADTFYEEFNGKQF   79 (110)
T ss_pred             CEEEEEECCCCCC--HHHHHHHHHHHHHHEEEEEEEECCCCCEEEEEEEECCHHHHHHHHHHHCCCCC
T ss_conf             2899981575255--88989874457510059999707998717999998988999999998489806


No 22 
>PRK09371 gas vesicle synthesis protein GvpA; Provisional
Probab=25.79  E-value=53  Score=15.64  Aligned_cols=29  Identities=34%  Similarity=0.571  Sum_probs=19.8

Q ss_pred             CCCCEEEEEECCHHHHCCCHHHHHHHHHHCCCEEEEH
Q ss_conf             9631023045523771898799999997255589210
Q gi|254780390|r    1 MVIEKTFSMIKPDAVKRNLIGSIVKELEDYGLCVVAA   37 (140)
Q Consensus         1 m~~e~Tl~iIKPDav~~~~~g~Ii~~i~~~Gf~I~~~   37 (140)
                      |++|++     |+   ..-..+|++++.++|..|-+-
T Consensus         1 mav~~s-----~~---sssLadvldriLDKGiVI~~~   29 (72)
T PRK09371          1 MAVEKT-----PD---SSSLAEVIDRILDKGIVVDAW   29 (72)
T ss_pred             CCCCCC-----CC---CCCHHHHHHHHHCCCEEEEEE
T ss_conf             961117-----89---651999999972477599878


No 23 
>pfam09554 RE_HaeII HaeII restriction endonuclease. This family includes the HaeII (recognizes and cleaves RGCGC^Y) restriction endonuclease.
Probab=25.69  E-value=23  Score=17.72  Aligned_cols=95  Identities=21%  Similarity=0.272  Sum_probs=55.3

Q ss_pred             HHHHHHCCCEEEEHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHCCCCCEEEEECCCC-CHHHHHHHHCCCCCHHH-----
Q ss_conf             999972555892100112699999999888514742100122100111577111164-01789996618899777-----
Q gi|254780390|r   24 VKELEDYGLCVVAAKFCWMNRKQAEDFYLIHKDRPFFPELVQAMISGPVFLQVLKGE-EAISKNREVMGDTDPKK-----   97 (140)
Q Consensus        24 i~~i~~~Gf~I~~~k~~~ls~e~a~~fY~~~~~k~ff~~lv~~m~sGpv~alvl~g~-naV~~~R~l~Gptdp~~-----   97 (140)
                      +++--.-|. .++.|.+.+++++|+             ++|+..+|..++..|=..+ ..|...-+-+|=..--+     
T Consensus       221 LDMWANFG~-aiQiKHLSL~e~laE-------------~IVssitaDrIVIVCkdaE~~vI~sLLnQIGWksrIqsIite  286 (338)
T pfam09554       221 LDMWANFGS-AVQIKHLSLDEELAE-------------NIVSSITADRIVIVCKSAEEEVIVSLLNQIGWKSRIQSIITE  286 (338)
T ss_pred             HHHHHCCCH-HHEEEEECCCHHHHH-------------HHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHHHHHCCH
T ss_conf             667860461-424432033588998-------------888650357389996640489999999874368778776139


Q ss_pred             C---C--CCCCCHHCCCCHHHEEEEECCCHHHHHHHHHHHCCHHHC
Q ss_conf             6---8--997000101152210044069989999999872685650
Q gi|254780390|r   98 A---L--KGTIRNKYGISIGENSIHGSDSLKTALEEISYWFARNEI  138 (140)
Q Consensus        98 a---~--p~tiR~~fg~~~~~N~vH~Sds~e~a~rEi~~fF~~~ei  138 (140)
                      .   +  .-.|||+|..-.      |..--+.-..||..=||+.|.
T Consensus       287 ~~Li~WY~KaLrGk~s~~i------g~~ll~~l~eei~~EFPs~e~  326 (338)
T pfam09554       287 DDLIDWYDKALRGKYSELL------GEKLIETLSEEIKNEFPSVEN  326 (338)
T ss_pred             HHHHHHHHHHHCCCHHHHH------HHHHHHHHHHHHHHHCCCCCC
T ss_conf             9999999998713047888------899999999999986887550


No 24 
>COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]
Probab=25.40  E-value=18  Score=18.43  Aligned_cols=64  Identities=19%  Similarity=0.269  Sum_probs=38.7

Q ss_pred             CCCCCEEEEECCCCC---HHHHHHHHCCCCCHHHCCCCCCCHHC-CCCHHHEEEEECCCHHHHHHHHHHHCCH
Q ss_conf             001115771111640---17899966188997776899700010-1152210044069989999999872685
Q gi|254780390|r   67 MISGPVFLQVLKGEE---AISKNREVMGDTDPKKALKGTIRNKY-GISIGENSIHGSDSLKTALEEISYWFAR  135 (140)
Q Consensus        67 m~sGpv~alvl~g~n---aV~~~R~l~Gptdp~~a~p~tiR~~f-g~~~~~N~vH~Sds~e~a~rEi~~fF~~  135 (140)
                      ..+||+.+|+-+.+.   .+.+.+.+--.-.|-..+=+|.|+.| |.+...     -|..+.--.|-++.||.
T Consensus       149 ~a~~pI~vm~~EHde~g~~l~~lk~lT~n~tpP~~AC~tWkalY~gl~~~~-----dDl~~HIHLENnvLFpr  216 (221)
T COG2846         149 QAAGPISVMESEHDEAGELLEVLKHLTNNYTPPEEACGTWKALYNGLNEFI-----DDLMEHIHLENNVLFPR  216 (221)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHCCCCCH
T ss_conf             657547999987898877999999984478898577658999998899999-----99998877651102011


No 25 
>COG2247 LytB Putative cell wall-binding domain [Cell envelope biogenesis, outer membrane]
Probab=21.40  E-value=76  Score=14.69  Aligned_cols=15  Identities=20%  Similarity=0.330  Sum_probs=7.5

Q ss_pred             HHHHHHHHCCCEEEE
Q ss_conf             999999725558921
Q gi|254780390|r   22 SIVKELEDYGLCVVA   36 (140)
Q Consensus        22 ~Ii~~i~~~Gf~I~~   36 (140)
                      ..-+.+++-|+.+.+
T Consensus        91 ~yE~~Lks~GitV~R  105 (337)
T COG2247          91 NYENALKSLGITVKR  105 (337)
T ss_pred             HHHHHHHHCCCEEEE
T ss_conf             589999857957999


No 26 
>TIGR02287 PaaY phenylacetic acid degradation protein PaaY; InterPro: IPR011974    Members of this family are located next to other genes organised into apparent operons for phenylacetic acid degradation . PaaY is located near the end of these gene clusters and often next to PaaX, a transcriptional regulator..
Probab=20.05  E-value=31  Score=16.95  Aligned_cols=10  Identities=20%  Similarity=0.597  Sum_probs=7.7

Q ss_pred             CCCCHHCCCC
Q ss_conf             9700010115
Q gi|254780390|r  101 GTIRNKYGIS  110 (140)
Q Consensus       101 ~tiR~~fg~~  110 (140)
                      -|||||||.=
T Consensus        39 ASLRGDFGrI   48 (193)
T TIGR02287        39 ASLRGDFGRI   48 (193)
T ss_pred             CCCCCCCCCE
T ss_conf             3135775725


Done!