Query         gi|254780689|ref|YP_003065102.1| flagellar motor switch protein G [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 345
No_of_seqs    124 out of 735
Neff          6.8 
Searched_HMMs 39220
Date          Sun May 29 20:19:04 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780689.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK05686 fliG flagellar motor  100.0       0       0  625.2  40.7  323   18-343     6-332 (337)
  2 TIGR00207 fliG flagellar motor 100.0       0       0  635.4  32.2  323   20-344    14-340 (346)
  3 PRK07194 fliG flagellar motor  100.0       0       0  607.4  39.9  324   17-344     2-329 (334)
  4 COG1536 FliG Flagellar motor s 100.0       0       0  549.9  38.0  318   22-342    11-333 (339)
  5 pfam01706 FliG_C FliG C-termin 100.0 8.4E-29 2.1E-33  210.1  13.7  110  231-341     1-110 (110)
  6 PRK07194 fliG flagellar motor   99.2 3.1E-08 7.8E-13   74.2  19.8  178   14-193   112-306 (334)
  7 PRK05686 fliG flagellar motor   99.1 5.8E-08 1.5E-12   72.3  19.3  181   14-195   115-312 (337)
  8 COG1536 FliG Flagellar motor s  98.8 7.8E-06   2E-10   58.3  19.9   44  124-167   125-168 (339)
  9 TIGR00207 fliG flagellar motor  98.0  0.0014 3.5E-08   43.4  16.6  162   24-186   138-310 (346)
 10 PRK05934 type III secretion sy  97.8 4.9E-05 1.2E-09   53.0   5.8   49  129-177   290-338 (341)
 11 pfam03448 MgtE_N MgtE intracel  97.3  0.0047 1.2E-07   39.9  10.5   70  102-176    13-82  (102)
 12 pfam03448 MgtE_N MgtE intracel  96.9  0.0075 1.9E-07   38.5   8.0   95  132-248     2-96  (102)
 13 COG2239 MgtE Mg/Co/Ni transpor  96.6   0.061 1.5E-06   32.5  10.8   56   27-82     47-108 (451)
 14 COG3334 Uncharacterized conser  96.4    0.02 5.2E-07   35.7   7.4   64  123-186   123-186 (192)
 15 COG2239 MgtE Mg/Co/Ni transpor  94.7    0.37 9.4E-06   27.4  10.3   81   92-177    45-125 (451)
 16 COG3334 Uncharacterized conser  91.2    0.47 1.2E-05   26.7   4.9   48  129-176   117-164 (192)
 17 pfam09126 NaeI Restriction end  80.1     4.6 0.00012   20.1   5.4   62  279-343   162-234 (291)
 18 PHA01513 mnt Mnt                65.0      10 0.00026   17.8   6.1   60  165-226    10-70  (82)
 19 PRK09273 hypothetical protein;  60.6      12 0.00031   17.3   4.0   43  252-296   157-199 (211)
 20 COG4086 Predicted secreted pro  58.9      13 0.00034   17.1   5.9   17  126-142   111-127 (299)
 21 pfam12408 DUF3666 Ribose-5-pho  58.1      14 0.00035   17.0   3.6   34  260-295     4-37  (48)
 22 TIGR02019 BchJ bacteriochlorop  44.2      22 0.00057   15.6   6.4   80   94-173    10-91  (189)
 23 pfam11865 DUF3385 Domain of un  42.2      24 0.00061   15.4   7.6  139  142-296     6-154 (160)
 24 TIGR01737 FGAM_synth_I phospho  37.3      28 0.00072   14.9   2.7   23  319-341    73-98  (264)
 25 PRK13901 ruvA Holliday junctio  37.2      29 0.00073   14.9   9.3   54  116-170    77-130 (196)
 26 PRK12435 ferrochelatase; Provi  37.1      13 0.00032   17.2   0.6   47   25-79      3-49  (316)
 27 KOG1114 consensus               35.9      30 0.00076   14.7   7.8  104  125-243  1083-1193(1304)
 28 pfam11513 TA0956 Thermoplasma   35.0      15 0.00038   16.8   0.7   49  140-188    11-61  (110)
 29 COG4973 XerC Site-specific rec  34.5      31  0.0008   14.6   5.7  100   13-112    19-126 (299)
 30 pfam11239 DUF3040 Protein of u  33.1      33 0.00084   14.5   2.7   24  224-247     4-31  (82)
 31 pfam06070 Herpes_UL32 Herpesvi  33.1      33 0.00084   14.5   3.9  105  188-304   121-232 (777)
 32 TIGR00444 mazG MazG family pro  32.0      34 0.00087   14.4   2.2  134  136-290    79-223 (253)
 33 TIGR01398 FlhA flagellar biosy  31.8      31 0.00079   14.6   1.9   25  224-248   518-542 (713)
 34 cd07176 terB tellurite resista  31.7      35 0.00089   14.3   6.9   69   41-111    13-81  (111)
 35 COG1184 GCD2 Translation initi  30.7      36 0.00092   14.2   6.5   18  286-303   264-281 (301)
 36 COG2074 2-phosphoglycerate kin  30.0      37 0.00095   14.1   3.7   27  315-341   271-297 (299)
 37 TIGR01788 Glu-decarb-GAD gluta  27.4      41   0.001   13.8   3.1   30   83-112    41-70  (493)
 38 cd07313 terB_like_2 tellurium   26.1      43  0.0011   13.7   9.1   71   39-113     8-78  (104)
 39 TIGR02460 osmo_MPGsynth mannos  26.0     8.1 0.00021   18.5  -1.9   95  161-258    40-142 (394)
 40 pfam05099 TerB Tellurite resis  25.4      45  0.0011   13.6  10.9  103   40-148    33-136 (140)
 41 TIGR01078 arcA arginine deimin  24.7      29 0.00074   14.8   0.7   32   74-108    48-81  (421)
 42 cd07920 Pumilio Pumilio-family  24.6      46  0.0012   13.5  19.5   95  211-306   165-260 (322)
 43 pfam04499 SAPS SIT4 phosphatas  23.8      48  0.0012   13.4   8.2   11  212-222   222-232 (380)
 44 PRK12523 RNA polymerase sigma   23.4      49  0.0012   13.3   9.3   77   59-142     1-78  (172)
 45 COG2411 Uncharacterized conser  23.2      49  0.0013   13.3   2.7  102  226-338    78-188 (188)
 46 TIGR02784 addA_alphas double-s  23.0      50  0.0013   13.3   2.7   66   22-87     36-114 (1190)
 47 TIGR00455 apsK adenylylsulfate  22.9      31  0.0008   14.6   0.6   21  323-343    78-98  (187)
 48 pfam04751 DUF615 Protein of un  22.9      50  0.0013   13.3   7.2   75   24-114     6-80  (153)
 49 cd03397 PAP2_acid_phosphatase   22.9      50  0.0013   13.3   2.5   23  147-169   162-184 (232)
 50 TIGR02787 codY_Gpos GTP-sensin  22.7      46  0.0012   13.5   1.5   50  290-339   177-233 (255)
 51 pfam11625 DUF3253 Protein of u  22.4      51  0.0013   13.2   3.9   51  284-344     5-64  (83)
 52 TIGR01589 A_thal_3526 uncharac  22.3      51  0.0013   13.2   2.7   38   98-135    12-50  (57)
 53 pfam08006 DUF1700 Protein of u  21.4      53  0.0014   13.1   5.4   54   59-114    11-64  (181)
 54 PRK12514 RNA polymerase sigma   21.1      54  0.0014   13.0   9.8   35  267-306   143-177 (179)
 55 TIGR01992 PTS-IIBC-Tre PTS sys  21.0      54  0.0014   13.0   4.6   60   38-97      2-91  (489)
 56 KOG0467 consensus               21.0      54  0.0014   13.0   1.6   38  272-309   745-786 (887)
 57 pfam01984 dsDNA_bind Double-st  20.1      57  0.0014   12.9   3.4   50  177-226    47-96  (105)

No 1  
>PRK05686 fliG flagellar motor switch protein G; Validated
Probab=100.00  E-value=0  Score=625.17  Aligned_cols=323  Identities=28%  Similarity=0.480  Sum_probs=309.3

Q ss_pred             CHHHCCHHHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHH
Q ss_conf             9223686879999999838146899985199999999999986138999899999999999998510456-653488999
Q gi|254780689|r   18 SPVSLTQKDKATAILLAMEKQVSGKLLRHFTHAELKEIVASAKLLPEISPEELEDIIDEFESQFIAGIGL-TENSKNIES   96 (345)
Q Consensus        18 ~p~~Ltg~eKAAilLl~LGee~Aa~ilk~l~~~Ei~~i~~~m~~l~~i~~~~~~~vl~EF~~~~~~~~~~-~g~~~~~~~   96 (345)
                      .+.+|||+||||+||++||++.|++||+||+++||++|+++|++++.|++++++.|++||+..+.++.++ .||.+|+++
T Consensus         6 ~~~~Lsg~~KAAilLl~LGee~Aa~vlk~L~~~Ei~~i~~~m~~l~~i~~~~~~~Vl~EF~~~~~~~~~~~~g~~~~~~~   85 (337)
T PRK05686          6 DLDKLSGPEKAAILLLALGEEAAAKVLKHLTPDEVQKLSAAMANLRNVSPEQVEAVLEEFEDEFEAGAYILMGGIDYARR   85 (337)
T ss_pred             HHHHCCHHHHHHHHHHHHCHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH
T ss_conf             89875849899999999591779999863999999999999975699899999999999999998247767773899999


Q ss_pred             HHHHCCCHHHHHHHHHHHHCCCCCCCCHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHH
Q ss_conf             97611497999999754411344567567897419989999998403864788999957888999999837989999999
Q gi|254780689|r   97 ILEEGLEQNELEKLLNKSDISQENNNSIWDHLKETDPGVIADFLSKEHPQTTAYVLSMMPPSIGASVLLRFPNKIHADIM  176 (345)
Q Consensus        97 lL~~al~~d~a~~ll~~~~~~~~~~~~~~~~L~~~~~~~La~~L~~EhPQtiAlILs~L~~~~Aa~VL~~Lp~e~r~ev~  176 (345)
                      +|++++|+++++.|+++  +.++...++|++|+|++|++|++||++|||||||+|||||+|++||+||..||+++|.+|+
T Consensus        86 ~L~~alg~~~a~~il~~--i~~~~~~~~~~~L~~~dp~~La~~L~~EhPQtiAlILs~L~~~~AA~VL~~Lp~~~~~eVi  163 (337)
T PRK05686         86 LLEKALGEEKANSILER--ILESLQTSGFDFLRKMDPQQLANFIRNEHPQTIALILSYLDPDQAAEILSLLPEELRADVM  163 (337)
T ss_pred             HHHHHCCHHHHHHHHHH--HCCCCCCCHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHH
T ss_conf             99983598999999986--2156658768998659999999998724858999999809999999999869999999999


Q ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHCC---CCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH
Q ss_conf             998404899989999999999997223---44212363789999950177577999999999865999999997415789
Q gi|254780689|r  177 KRTVNLPKISPYIQKTIEKCIVEMLPQ---SNSNTSTGPEKVANLINELEKPQVDKLLTSLQEVSKEAFDKVRPKVFLFD  253 (345)
Q Consensus       177 ~Ria~l~~v~~ev~~~ie~~L~~~l~~---~~~~~~~G~~~vA~Iln~l~~~~~~~iL~~L~~~d~~la~~Ir~~mF~Fe  253 (345)
                      +|||+++.++|+++++|+++|++++..   .+..+.||++.+|+|||+++++.++++|+.|+++||+++++||++||+||
T Consensus       164 ~RiA~l~~v~p~~v~~ie~~L~~~~~~~~~~~~~~~~G~~~vA~ILN~~~~~~~~~il~~L~~~dp~la~~Ir~~mF~Fe  243 (337)
T PRK05686        164 MRIATLEGVQPEALKELEEVLEKKLSSMANADRTKMGGVKTVAEILNNLDRQTEKTIMESLEEEDPELAEKIKDLMFVFE  243 (337)
T ss_pred             HHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHCHHHHHHHHHHHEEHH
T ss_conf             99867789999999999999999974355422344553999999987476468999999998758999999998812299


Q ss_pred             HHHCCCHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             98509978999998309888999985388989999999610089999999998500589998999999999999999999
Q gi|254780689|r  254 DLITLSSHDLSIVFNNISLEVLGKALHGTSIETQNAILHCLSNRQRKIIEENIVLNDSSIAPREVAMARRSIVQEAISLL  333 (345)
Q Consensus       254 Dl~~l~~~~l~~ll~evd~~~l~~ALkga~~e~~e~il~nmS~Ra~~~l~eel~~~~g~v~~~dve~Aq~~I~~~~r~L~  333 (345)
                      ||.+++++++|.+|++|+.++|++||||++++++++||+|||+|+++|++|||+.+ |||+.+|||+||++|++++|+|+
T Consensus       244 di~~l~~~~l~~ll~~v~~~~l~~ALKga~~~~~~~il~nmS~R~a~~l~eel~~~-gpv~~~dve~Aq~~Iv~~~r~L~  322 (337)
T PRK05686        244 DLVDLDDRAIQRLLREVDNDDLALALKGADEELREKFLSNMSKRAAEMLREDLEAL-GPVRLSDVEEAQKKIVQIARRLA  322 (337)
T ss_pred             HHHCCCHHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHHHHHHC-CCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             77477999999999848999999987789899999999862899999999999863-99878999999999999999999


Q ss_pred             HCCCEECCCC
Q ss_conf             8697951888
Q gi|254780689|r  334 KTNKIELSNP  343 (345)
Q Consensus       334 ~~G~I~l~~~  343 (345)
                      ++|+|+|+..
T Consensus       323 ~~G~I~l~~~  332 (337)
T PRK05686        323 EAGEIVLGGG  332 (337)
T ss_pred             HCCCEEECCC
T ss_conf             8898885898


No 2  
>TIGR00207 fliG flagellar motor switch protein FliG; InterPro: IPR000090   The flagellar motor switch in Escherichia coli and Salmonella typhimurium regulates the direction of flagellar rotation and hence controls swimming behaviour . The switch is a complex apparatus that responds to signals transduced by the chemotaxis sensory signalling system during chemotactic behaviour . CheY, the chemotaxis response regulator, is believed to act directly on the switch to induce tumbles in the swimming pattern, but no physical interactions of CheY and switch proteins have yet been demonstrated.    The switch complex comprises at least three proteins - FliG, FliM and FliN. It has been shown that FliG interacts with FliM, FliM interacts with itself, and FliM interacts with FliN . Several residues within the middle third of FliG appear to be strongly involved in the FliG-FliM interaction, with residues near the N- or C-termini being less important . Such clustering suggests that FliG-FliM interaction plays a central role in switching.   Analysis of the FliG, FliM and FliN sequences shows that none are especially hydrophobic or appear to be integral membrane proteins . This result is consistent with other evidence suggesting that the proteins may be peripheral to the membrane, possibly mounted on the basal body M ring , . FliG is present in about 25 copies per flagellum. This structure of the C-terminal domain is known, this domain functions specifically in motor rotation .; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0006935 chemotaxis, 0009288 flagellin-based flagellum.
Probab=100.00  E-value=0  Score=635.35  Aligned_cols=323  Identities=27%  Similarity=0.444  Sum_probs=308.3

Q ss_pred             HHCCHHHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHH
Q ss_conf             23686879999999838146899985199999999999986138999899999999999998510456-65348899997
Q gi|254780689|r   20 VSLTQKDKATAILLAMEKQVSGKLLRHFTHAELKEIVASAKLLPEISPEELEDIIDEFESQFIAGIGL-TENSKNIESIL   98 (345)
Q Consensus        20 ~~Ltg~eKAAilLl~LGee~Aa~ilk~l~~~Ei~~i~~~m~~l~~i~~~~~~~vl~EF~~~~~~~~~~-~g~~~~~~~lL   98 (345)
                      -.|||.||+||||+++|+|.+++|||||+.+||++|+.+|+++..|+......||.||...+....++ .||.+|+|.+|
T Consensus        14 ~~Ltg~~K~aILL~~iG~d~~a~vfkhL~~~ei~~Ls~~i~~l~~i~~~~~~~VL~EF~~~~~~~~yi~~gg~~YaR~lL   93 (346)
T TIGR00207        14 DELTGKQKAAILLISIGEDVSAEVFKHLSQEEIEELSAEIAKLEQIDKQQKDDVLEEFEEIAEAQEYINKGGLDYARELL   93 (346)
T ss_pred             HHCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHH
T ss_conf             42104567888877722214557864178889999999988532234888789999999999999988506378999998


Q ss_pred             HHCCCHHHHHHHHHHHHCCCCCCCCHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHH
Q ss_conf             61149799999975441134456756789741998999999840386478899995788899999983798999999999
Q gi|254780689|r   99 EEGLEQNELEKLLNKSDISQENNNSIWDHLKETDPGVIADFLSKEHPQTTAYVLSMMPPSIGASVLLRFPNKIHADIMKR  178 (345)
Q Consensus        99 ~~al~~d~a~~ll~~~~~~~~~~~~~~~~L~~~~~~~La~~L~~EhPQtiAlILs~L~~~~Aa~VL~~Lp~e~r~ev~~R  178 (345)
                      +|+||+++|..+|+++. ..-...+.|+++.+++|.++++||++|||||||+|||||+|.+||.||+.||+++|++|+.|
T Consensus        94 ~kaLG~e~A~~~l~~l~-~slq~~~~f~~~~~~~P~~~~dfI~~EHPQtiAlIL~hL~~~~Aa~iLs~l~~e~~~~v~~R  172 (346)
T TIGR00207        94 EKALGEEKAKKILNKLT-SSLQTKPGFEFLRKAEPQQIADFIQQEHPQTIALILSHLDPAQAAEILSLLPEEVQAEVARR  172 (346)
T ss_pred             HHHCCHHHHHHHHHHHH-HHHCCCCCHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHCHHHHHHHHHCCCHHHHHHHHHH
T ss_conf             86141589999999888-75316311567631586889987750586799999985183047888730685689999999


Q ss_pred             HHHCCCCCHHHHHHHHHHHHHHHCCCCC---CCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHH
Q ss_conf             8404899989999999999997223442---1236378999995017757799999999986599999999741578998
Q gi|254780689|r  179 TVNLPKISPYIQKTIEKCIVEMLPQSNS---NTSTGPEKVANLINELEKPQVDKLLTSLQEVSKEAFDKVRPKVFLFDDL  255 (345)
Q Consensus       179 ia~l~~v~~ev~~~ie~~L~~~l~~~~~---~~~~G~~~vA~Iln~l~~~~~~~iL~~L~~~d~~la~~Ir~~mF~FeDl  255 (345)
                      ||.|+.++|+++.+|+++|..+|.+..+   .+.||+..||+|+|.+++.+++.+|++++..||+||++|+++||+||||
T Consensus       173 iA~~g~~sP~vv~ev~~VLe~kL~s~~~~~~~~~GGv~~vaEi~N~~~~~~ek~~l~~~e~~D~~LA~~Ik~~MF~FEdi  252 (346)
T TIGR00207       173 IAVMGRTSPEVVKEVERVLEKKLESLTSEDYTKVGGVRAVAEIINLLDRKTEKTILESLEEVDPELAEEIKKKMFVFEDI  252 (346)
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHCCCCCCHHHHHHHHHHHHCHHHHHHHHHHCCCHHHH
T ss_conf             98507867899999999997762244212355416257899987357871599999999831847899999723640115


Q ss_pred             HCCCHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             50997899999830988899998538898999999961008999999999850058999899999999999999999986
Q gi|254780689|r  256 ITLSSHDLSIVFNNISLEVLGKALHGTSIETQNAILHCLSNRQRKIIEENIVLNDSSIAPREVAMARRSIVQEAISLLKT  335 (345)
Q Consensus       256 ~~l~~~~l~~ll~evd~~~l~~ALkga~~e~~e~il~nmS~Ra~~~l~eel~~~~g~v~~~dve~Aq~~I~~~~r~L~~~  335 (345)
                      +.||+|++|+||++||.+.|.+|||+++.+++++||.|||+||+++++|||+.+ ||||.+|||.+|+.|+.++|+|++.
T Consensus       253 V~lDdraIqr~L~~vd~~~L~~ALK~~~~~l~ek~l~NMS~Raa~~l~edm~fl-Gpvr~kdVe~~Q~~I~~iVr~L~E~  331 (346)
T TIGR00207       253 VKLDDRAIQRVLREVDKEDLLLALKTAEKPLREKFLNNMSQRAAEILKEDMEFL-GPVRLKDVEEAQKKIVSIVRKLEEK  331 (346)
T ss_pred             HHHCCHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf             430308999999984335567785126624788986315489999999988726-8844024589999999999866117


Q ss_pred             CCEECCCCC
Q ss_conf             979518888
Q gi|254780689|r  336 NKIELSNPI  344 (345)
Q Consensus       336 G~I~l~~~~  344 (345)
                      |+|+|++-.
T Consensus       332 GEiVI~~Gg  340 (346)
T TIGR00207       332 GEIVIQRGG  340 (346)
T ss_pred             CCEEEECCC
T ss_conf             605760478


No 3  
>PRK07194 fliG flagellar motor switch protein G; Reviewed
Probab=100.00  E-value=0  Score=607.44  Aligned_cols=324  Identities=21%  Similarity=0.359  Sum_probs=306.9

Q ss_pred             CCHHHCCHHHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCC-CCHHHHH
Q ss_conf             792236868799999998381468999851999999999999861389998999999999999985104566-5348899
Q gi|254780689|r   17 ISPVSLTQKDKATAILLAMEKQVSGKLLRHFTHAELKEIVASAKLLPEISPEELEDIIDEFESQFIAGIGLT-ENSKNIE   95 (345)
Q Consensus        17 ~~p~~Ltg~eKAAilLl~LGee~Aa~ilk~l~~~Ei~~i~~~m~~l~~i~~~~~~~vl~EF~~~~~~~~~~~-g~~~~~~   95 (345)
                      -.|.+|||.||||+||++||++.|++||+||+++||++|+.+|+++++|++++++.|++||+..+..++++. ||.+|++
T Consensus         2 ~d~~~Lsg~~KAAilll~LGee~Aa~ilk~L~~~Ei~~l~~~m~~l~~v~~~~~~~Vl~EF~~~~~~~~~l~~g~~~~~~   81 (334)
T PRK07194          2 SDTKGMSNLEQAAILLLSMGEEAAAMVMQHLSREEVQRLSQKMARLSGIKVDQARQVLQRFFQDYREQSGINGASRSYLQ   81 (334)
T ss_pred             CCCCCCCHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH
T ss_conf             99754588999999999979277999987499999999999998269989999999999999998725775535399999


Q ss_pred             HHHHHCCCHHHHHHHHHHHHCCCCCCCCHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHH
Q ss_conf             99761149799999975441134456756789741998999999840386478899995788899999983798999999
Q gi|254780689|r   96 SILEEGLEQNELEKLLNKSDISQENNNSIWDHLKETDPGVIADFLSKEHPQTTAYVLSMMPPSIGASVLLRFPNKIHADI  175 (345)
Q Consensus        96 ~lL~~al~~d~a~~ll~~~~~~~~~~~~~~~~L~~~~~~~La~~L~~EhPQtiAlILs~L~~~~Aa~VL~~Lp~e~r~ev  175 (345)
                      ++|++++|+++++.++++  +.+....++|++|+|++|++|++||++|||||||+|||||+|++||+||..||++.|.+|
T Consensus        82 ~~L~~alg~~~a~~il~~--i~~~~~~~~~~~L~~~dp~~La~~L~~EhPQtiAlILs~L~~~~AA~VL~~Lp~~~~~ev  159 (334)
T PRK07194         82 RTLNKALGGDIAKSLINS--IYGDEIRHKMQRLQWVDPQQLARLIANEHLQMQAVFLAFLPPESAAAVLKYLPEDRQDDI  159 (334)
T ss_pred             HHHHHHCCHHHHHHHHHH--HHCCCCCCHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHH
T ss_conf             999985373789999998--606664567899867999999999873485799999980899999999997899989999


Q ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHCC---CCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCH
Q ss_conf             9998404899989999999999997223---4421236378999995017757799999999986599999999741578
Q gi|254780689|r  176 MKRTVNLPKISPYIQKTIEKCIVEMLPQ---SNSNTSTGPEKVANLINELEKPQVDKLLTSLQEVSKEAFDKVRPKVFLF  252 (345)
Q Consensus       176 ~~Ria~l~~v~~ev~~~ie~~L~~~l~~---~~~~~~~G~~~vA~Iln~l~~~~~~~iL~~L~~~d~~la~~Ir~~mF~F  252 (345)
                      ++|||+++.++|+++..|+++|.+++..   ....+.+|++.+|+|||+++++. +++|+.|++.||+++++||++||||
T Consensus       160 i~Ria~l~~v~p~~i~~i~~~L~~~~~~~~~~~~~~~~G~~~~A~IlN~~~~~~-~~il~~L~~~d~~la~~Ir~~mF~F  238 (334)
T PRK07194        160 LYRIAQLDDVDRDVVDELDELIERCLAMVLEEHGTKVIGVKQAADIINRFPGDR-QQLMEMLKEHDEEVVNEIEDNMYDF  238 (334)
T ss_pred             HHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCHHH-HHHHHHHHHHCHHHHHHHHHHCEEH
T ss_conf             999974478999999999999999987433445566662899999982585259-9999999863999999999871127


Q ss_pred             HHHHCCCHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             99850997899999830988899998538898999999961008999999999850058999899999999999999999
Q gi|254780689|r  253 DDLITLSSHDLSIVFNNISLEVLGKALHGTSIETQNAILHCLSNRQRKIIEENIVLNDSSIAPREVAMARRSIVQEAISL  332 (345)
Q Consensus       253 eDl~~l~~~~l~~ll~evd~~~l~~ALkga~~e~~e~il~nmS~Ra~~~l~eel~~~~g~v~~~dve~Aq~~I~~~~r~L  332 (345)
                      |||.++++++++.+|++|+.++|++||||++++++++||+|||+|+++|+++||+.+ |||+.+|||+||+.|++++|+|
T Consensus       239 edl~~l~~~~~~~ll~~v~~~~l~~ALkga~~e~~~~il~nmS~R~a~~l~eel~~~-gpv~~~dve~Aq~~Iv~~~r~L  317 (334)
T PRK07194        239 FILSRQSEETLQRLMDEVPMELWAIALKGTEPALRQAILRVMPKRQAQALETQIERT-GPVPLSRVEQARKEIMALVREL  317 (334)
T ss_pred             HHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCHHHHHHHHHHHHHHHHHH
T ss_conf             875338937899998628998999998469899999999876699999999999853-9986899999999999999999


Q ss_pred             HHCCCEECCCCC
Q ss_conf             986979518888
Q gi|254780689|r  333 LKTNKIELSNPI  344 (345)
Q Consensus       333 ~~~G~I~l~~~~  344 (345)
                      +++|+|+|..--
T Consensus       318 ~~~G~I~L~~~~  329 (334)
T PRK07194        318 AEAGEIELQLFE  329 (334)
T ss_pred             HHCCCEEECCCC
T ss_conf             988998835787


No 4  
>COG1536 FliG Flagellar motor switch protein [Cell motility and secretion]
Probab=100.00  E-value=0  Score=549.87  Aligned_cols=318  Identities=27%  Similarity=0.494  Sum_probs=304.5

Q ss_pred             CCHHHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCC-CCHHHHHHHHHH
Q ss_conf             6868799999998381468999851999999999999861389998999999999999985104566-534889999761
Q gi|254780689|r   22 LTQKDKATAILLAMEKQVSGKLLRHFTHAELKEIVASAKLLPEISPEELEDIIDEFESQFIAGIGLT-ENSKNIESILEE  100 (345)
Q Consensus        22 Ltg~eKAAilLl~LGee~Aa~ilk~l~~~Ei~~i~~~m~~l~~i~~~~~~~vl~EF~~~~~~~~~~~-g~~~~~~~lL~~  100 (345)
                      |||.+|||++|++||++.|++||+||+++|+++++.+|++++.|+++..+.++.||++.+..+.++. |+.+|.+.+|++
T Consensus        11 Lt~~~KaAilLlslGe~~aa~vlk~l~~~eiq~l~~~~a~lk~v~~~~~~~il~eF~~~~~~~~~i~~~~~~~~~~lL~k   90 (339)
T COG1536          11 LTGTEKAAILLLALGEEIAAEVLKHLSPEEIQRLSTEMATLKTVSPEEKEQVLEEFEELFTEQAGINKGADEYARELLEK   90 (339)
T ss_pred             CCHHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
T ss_conf             65767999999980979999999858998999999999855589999999999999999985000123719999999998


Q ss_pred             CCCHHHHHHHHHHHHCCCCCC-CCHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHH
Q ss_conf             149799999975441134456-7567897419989999998403864788999957888999999837989999999998
Q gi|254780689|r  101 GLEQNELEKLLNKSDISQENN-NSIWDHLKETDPGVIADFLSKEHPQTTAYVLSMMPPSIGASVLLRFPNKIHADIMKRT  179 (345)
Q Consensus       101 al~~d~a~~ll~~~~~~~~~~-~~~~~~L~~~~~~~La~~L~~EhPQtiAlILs~L~~~~Aa~VL~~Lp~e~r~ev~~Ri  179 (345)
                      ++|+++++.+++++.  +... ..+|+++.|++|.+|++||.+|||||||+|||||+|++||.||..||+++|.+|++||
T Consensus        91 alg~~~a~~i~~~i~--~~~~~~~~~~~l~~~~p~~l~~~i~~EhPQtia~iLs~L~~~~aa~vL~~l~~e~r~~v~~Ri  168 (339)
T COG1536          91 ALGEEKAESLLERIT--GSAIQTSPFDLLRKLDPSQLADLIKNEHPQTIALILSYLPPDQAAEILSTLPEELRADVVKRI  168 (339)
T ss_pred             HCCHHHHHHHHHHHH--HCCCCCCHHHHHHHCCHHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHH
T ss_conf             576768999997754--201213277775017899999998712518899999815877789999859998999999998


Q ss_pred             HHCCCCCHHHHHHHHHHHHHHHCCC---CCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH
Q ss_conf             4048999899999999999972234---4212363789999950177577999999999865999999997415789985
Q gi|254780689|r  180 VNLPKISPYIQKTIEKCIVEMLPQS---NSNTSTGPEKVANLINELEKPQVDKLLTSLQEVSKEAFDKVRPKVFLFDDLI  256 (345)
Q Consensus       180 a~l~~v~~ev~~~ie~~L~~~l~~~---~~~~~~G~~~vA~Iln~l~~~~~~~iL~~L~~~d~~la~~Ir~~mF~FeDl~  256 (345)
                      ++++.++|++++.++++|+.++...   ...+.||++.+|+|+|++++..++.++++|+..||+++++|+++||+||||+
T Consensus       169 a~l~~v~p~al~~i~~~l~~~l~~~~~~~~~~~gg~~~~aeIlN~~d~~~e~~il~~l~~~~~~la~~I~~kmF~Fedi~  248 (339)
T COG1536         169 ATLEGVSPEALAELENVLEKKLQSLVNEDYSKLGGIKAAAEILNLLDRGTEKTILESLEEEDPELAEEIKEKMFVFEDIV  248 (339)
T ss_pred             HHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH
T ss_conf             71126998999999999999987520300002563868999998444668999999876328878999999872199887


Q ss_pred             CCCHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             09978999998309888999985388989999999610089999999998500589998999999999999999999869
Q gi|254780689|r  257 TLSSHDLSIVFNNISLEVLGKALHGTSIETQNAILHCLSNRQRKIIEENIVLNDSSIAPREVAMARRSIVQEAISLLKTN  336 (345)
Q Consensus       257 ~l~~~~l~~ll~evd~~~l~~ALkga~~e~~e~il~nmS~Ra~~~l~eel~~~~g~v~~~dve~Aq~~I~~~~r~L~~~G  336 (345)
                      .++++++|.+|++|+.++|++||||++++++++||+|||+|+++|+++|++.+ |||+.+||+.||+.|++++|+|++.|
T Consensus       249 ~ldd~~iq~lL~~v~~~~La~aLkg~~~~lrekilsnmskR~~e~i~~el~~~-gpi~~~dve~aq~~il~~~r~l~~~G  327 (339)
T COG1536         249 LLDDRSIQRLLREVDKEDLAIALKGASEELREKILSNMSKRAAEMLKEELEFL-GPVRLSDVETAQKAILNIVRRLAESG  327 (339)
T ss_pred             HCCHHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHHHHHCC-CCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             45689999999873878999998179889999999844599999999876503-88538888999999999999999779


Q ss_pred             CEECCC
Q ss_conf             795188
Q gi|254780689|r  337 KIELSN  342 (345)
Q Consensus       337 ~I~l~~  342 (345)
                      +|.|..
T Consensus       328 ~I~i~~  333 (339)
T COG1536         328 EIVIKR  333 (339)
T ss_pred             CEEECC
T ss_conf             877367


No 5  
>pfam01706 FliG_C FliG C-terminal domain. FliG is a component of the flageller rotor, present in about 25 copies per flagellum. This domain functions specifically in motor rotation.
Probab=99.96  E-value=8.4e-29  Score=210.12  Aligned_cols=110  Identities=28%  Similarity=0.457  Sum_probs=107.0

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHHHHHHCC
Q ss_conf             99999865999999997415789985099789999983098889999853889899999996100899999999985005
Q gi|254780689|r  231 LTSLQEVSKEAFDKVRPKVFLFDDLITLSSHDLSIVFNNISLEVLGKALHGTSIETQNAILHCLSNRQRKIIEENIVLND  310 (345)
Q Consensus       231 L~~L~~~d~~la~~Ir~~mF~FeDl~~l~~~~l~~ll~evd~~~l~~ALkga~~e~~e~il~nmS~Ra~~~l~eel~~~~  310 (345)
                      |++|++.||+++++|+++||+||||.+++++++|.++++|+.++|++||||++++++++||+|||+|+++++++||+.+ 
T Consensus         1 l~~L~~~d~~la~~I~~~mf~Fedl~~l~~~~l~~ll~~v~~~~L~~ALkga~~~~~~~il~nms~R~~~~i~~e~~~~-   79 (110)
T pfam01706         1 LEALEERDPELAEEIRKLMFTFEDLVRLDDRDIQRLLREVDKDVLALALKGASEELREKILSNMSKRAAEMLREELEAL-   79 (110)
T ss_pred             CCHHHHHCHHHHHHHHHHHCCHHHHHCCCHHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHHHHHHC-
T ss_conf             9038775999999999860039868557999999999849999999988679899999999876899999999999863-


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHCCCEECC
Q ss_conf             8999899999999999999999986979518
Q gi|254780689|r  311 SSIAPREVAMARRSIVQEAISLLKTNKIELS  341 (345)
Q Consensus       311 g~v~~~dve~Aq~~I~~~~r~L~~~G~I~l~  341 (345)
                      |||+.+||++||+.|++.+|+|+++|+|+|.
T Consensus        80 g~v~~~dve~Aq~~i~~~~r~l~~~G~I~l~  110 (110)
T pfam01706        80 GPVRLSDVEAAQKEIVAIVRELAEEGEIELG  110 (110)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHCCCEECC
T ss_conf             9988999999999999999999987696049


No 6  
>PRK07194 fliG flagellar motor switch protein G; Reviewed
Probab=99.16  E-value=3.1e-08  Score=74.17  Aligned_cols=178  Identities=10%  Similarity=0.147  Sum_probs=136.2

Q ss_pred             HHCCCHHHCC------HHHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHH---HHHHHHHHHHC
Q ss_conf             4037922368------68799999998381468999851999999999999861389998999999---99999998510
Q gi|254780689|r   14 YKEISPVSLT------QKDKATAILLAMEKQVSGKLLRHFTHAELKEIVASAKLLPEISPEELEDI---IDEFESQFIAG   84 (345)
Q Consensus        14 ~~~~~p~~Lt------g~eKAAilLl~LGee~Aa~ilk~l~~~Ei~~i~~~m~~l~~i~~~~~~~v---l~EF~~~~~~~   84 (345)
                      .+.+.|..|.      .||=+|++|.-|.++.|++||.+|+++....|...|++++.|+|+.++.|   |..........
T Consensus       112 L~~~dp~~La~~L~~EhPQtiAlILs~L~~~~AA~VL~~Lp~~~~~evi~Ria~l~~v~p~~i~~i~~~L~~~~~~~~~~  191 (334)
T PRK07194        112 LQWVDPQQLARLIANEHLQMQAVFLAFLPPESAAAVLKYLPEDRQDDILYRIAQLDDVDRDVVDELDELIERCLAMVLEE  191 (334)
T ss_pred             HHCCCHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCC
T ss_conf             86799999999987348579999998089999999999789998999999997447899999999999999998743344


Q ss_pred             CC-CCCCHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCC-------CCHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHCC
Q ss_conf             45-66534889999761149799999975441134456-------75678974199899999984038647889999578
Q gi|254780689|r   85 IG-LTENSKNIESILEEGLEQNELEKLLNKSDISQENN-------NSIWDHLKETDPGVIADFLSKEHPQTTAYVLSMMP  156 (345)
Q Consensus        85 ~~-~~g~~~~~~~lL~~al~~d~a~~ll~~~~~~~~~~-------~~~~~~L~~~~~~~La~~L~~EhPQtiAlILs~L~  156 (345)
                      .+ -.||.+.+..+|+.. +.++ +.+++.+.-..+..       --.|+-|..+++..+..+++.=++.++++-|-.-+
T Consensus       192 ~~~~~~G~~~~A~IlN~~-~~~~-~~il~~L~~~d~~la~~Ir~~mF~Fedl~~l~~~~~~~ll~~v~~~~l~~ALkga~  269 (334)
T PRK07194        192 HGTKVIGVKQAADIINRF-PGDR-QQLMEMLKEHDEEVVNEIEDNMYDFFILSRQSEETLQRLMDEVPMELWAIALKGTE  269 (334)
T ss_pred             CCCCCCCHHHHHHHHCCC-CHHH-HHHHHHHHHHCHHHHHHHHHHCEEHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCC
T ss_conf             556666289999998258-5259-99999998639999999998711278753389378999986289989999984698


Q ss_pred             HHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf             8899999983798999999999840489998999999
Q gi|254780689|r  157 PSIGASVLLRFPNKIHADIMKRTVNLPKISPYIQKTI  193 (345)
Q Consensus       157 ~~~Aa~VL~~Lp~e~r~ev~~Ria~l~~v~~ev~~~i  193 (345)
                      ++....+|..++...+..+---|..++++...-++.-
T Consensus       270 ~e~~~~il~nmS~R~a~~l~eel~~~gpv~~~dve~A  306 (334)
T PRK07194        270 PALRQAILRVMPKRQAQALETQIERTGPVPLSRVEQA  306 (334)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH
T ss_conf             9999999987669999999999985399868999999


No 7  
>PRK05686 fliG flagellar motor switch protein G; Validated
Probab=99.11  E-value=5.8e-08  Score=72.33  Aligned_cols=181  Identities=12%  Similarity=0.195  Sum_probs=141.4

Q ss_pred             HHCCCHHHCC------HHHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH----
Q ss_conf             4037922368------687999999983814689998519999999999998613899989999999999999851----
Q gi|254780689|r   14 YKEISPVSLT------QKDKATAILLAMEKQVSGKLLRHFTHAELKEIVASAKLLPEISPEELEDIIDEFESQFIA----   83 (345)
Q Consensus        14 ~~~~~p~~Lt------g~eKAAilLl~LGee~Aa~ilk~l~~~Ei~~i~~~m~~l~~i~~~~~~~vl~EF~~~~~~----   83 (345)
                      .+.+.|..|.      .||=+|++|.-|.++.|++||.+|+++....|...|++++.++|+.+..|=+--...+..    
T Consensus       115 L~~~dp~~La~~L~~EhPQtiAlILs~L~~~~AA~VL~~Lp~~~~~eVi~RiA~l~~v~p~~v~~ie~~L~~~~~~~~~~  194 (337)
T PRK05686        115 LRKMDPQQLANFIRNEHPQTIALILSYLDPDQAAEILSLLPEELRADVMMRIATLEGVQPEALKELEEVLEKKLSSMANA  194 (337)
T ss_pred             HHCCCHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCC
T ss_conf             86599999999987248589999998099999999998699999999999986778999999999999999997435542


Q ss_pred             CCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCC-------CCHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHCC
Q ss_conf             04566534889999761149799999975441134456-------75678974199899999984038647889999578
Q gi|254780689|r   84 GIGLTENSKNIESILEEGLEQNELEKLLNKSDISQENN-------NSIWDHLKETDPGVIADFLSKEHPQTTAYVLSMMP  156 (345)
Q Consensus        84 ~~~~~g~~~~~~~lL~~al~~d~a~~ll~~~~~~~~~~-------~~~~~~L~~~~~~~La~~L~~EhPQtiAlILs~L~  156 (345)
                      +..-.||.+.+.++|+.. +.+..+.+|+.++...+..       --.|+-|.++++..+..+++.=.++++++-|-.-+
T Consensus       195 ~~~~~~G~~~vA~ILN~~-~~~~~~~il~~L~~~dp~la~~Ir~~mF~Fedi~~l~~~~l~~ll~~v~~~~l~~ALKga~  273 (337)
T PRK05686        195 DRTKMGGVKTVAEILNNL-DRQTEKTIMESLEEEDPELAEKIKDLMFVFEDLVDLDDRAIQRLLREVDNDDLALALKGAD  273 (337)
T ss_pred             CCCCCCCHHHHHHHHHHC-CHHHHHHHHHHHHHHCHHHHHHHHHHHEEHHHHHCCCHHHHHHHHHHCCHHHHHHHHCCCC
T ss_conf             234455399999998747-6468999999998758999999998812299774779999999998489999999877898


Q ss_pred             HHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf             889999998379899999999984048999899999999
Q gi|254780689|r  157 PSIGASVLLRFPNKIHADIMKRTVNLPKISPYIQKTIEK  195 (345)
Q Consensus       157 ~~~Aa~VL~~Lp~e~r~ev~~Ria~l~~v~~ev~~~ie~  195 (345)
                      .+..-.||..+|...+.-+--.|..++++...-++.--+
T Consensus       274 ~~~~~~il~nmS~R~a~~l~eel~~~gpv~~~dve~Aq~  312 (337)
T PRK05686        274 EELREKFLSNMSKRAAEMLREDLEALGPVRLSDVEEAQK  312 (337)
T ss_pred             HHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHH
T ss_conf             999999998628999999999998639987899999999


No 8  
>COG1536 FliG Flagellar motor switch protein [Cell motility and secretion]
Probab=98.77  E-value=7.8e-06  Score=58.28  Aligned_cols=44  Identities=34%  Similarity=0.459  Sum_probs=24.4

Q ss_pred             HHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHC
Q ss_conf             67897419989999998403864788999957888999999837
Q gi|254780689|r  124 IWDHLKETDPGVIADFLSKEHPQTTAYVLSMMPPSIGASVLLRF  167 (345)
Q Consensus       124 ~~~~L~~~~~~~La~~L~~EhPQtiAlILs~L~~~~Aa~VL~~L  167 (345)
                      .|++|.+=.|+.++-+|..=+|.-.|-||++++.+...+|+.++
T Consensus       125 l~~~i~~EhPQtia~iLs~L~~~~aa~vL~~l~~e~r~~v~~Ri  168 (339)
T COG1536         125 LADLIKNEHPQTIALILSYLPPDQAAEILSTLPEELRADVVKRI  168 (339)
T ss_pred             HHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHH
T ss_conf             99998712518899999815877789999859998999999998


No 9  
>TIGR00207 fliG flagellar motor switch protein FliG; InterPro: IPR000090   The flagellar motor switch in Escherichia coli and Salmonella typhimurium regulates the direction of flagellar rotation and hence controls swimming behaviour . The switch is a complex apparatus that responds to signals transduced by the chemotaxis sensory signalling system during chemotactic behaviour . CheY, the chemotaxis response regulator, is believed to act directly on the switch to induce tumbles in the swimming pattern, but no physical interactions of CheY and switch proteins have yet been demonstrated.    The switch complex comprises at least three proteins - FliG, FliM and FliN. It has been shown that FliG interacts with FliM, FliM interacts with itself, and FliM interacts with FliN . Several residues within the middle third of FliG appear to be strongly involved in the FliG-FliM interaction, with residues near the N- or C-termini being less important . Such clustering suggests that FliG-FliM interaction plays a central role in switching.   Analysis of the FliG, FliM and FliN sequences shows that none are especially hydrophobic or appear to be integral membrane proteins . This result is consistent with other evidence suggesting that the proteins may be peripheral to the membrane, possibly mounted on the basal body M ring , . FliG is present in about 25 copies per flagellum. This structure of the C-terminal domain is known, this domain functions specifically in motor rotation .; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0006935 chemotaxis, 0009288 flagellin-based flagellum.
Probab=98.05  E-value=0.0014  Score=43.44  Aligned_cols=162  Identities=10%  Similarity=0.148  Sum_probs=87.0

Q ss_pred             HHHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH---CCC-CCCCHHHHHHHHH
Q ss_conf             687999999983814689998519999999999998613899989999999999999851---045-6653488999976
Q gi|254780689|r   24 QKDKATAILLAMEKQVSGKLLRHFTHAELKEIVASAKLLPEISPEELEDIIDEFESQFIA---GIG-LTENSKNIESILE   99 (345)
Q Consensus        24 g~eKAAilLl~LGee~Aa~ilk~l~~~Ei~~i~~~m~~l~~i~~~~~~~vl~EF~~~~~~---~~~-~~g~~~~~~~lL~   99 (345)
                      .||=.|.+|.-|.+..|+.+|..|++.=-..|+.-||.|+.++|+.+.+|-+=....+.+   ... -.||.+.+-.+++
T Consensus       138 HPQtiAlIL~hL~~~~Aa~iLs~l~~e~~~~v~~RiA~~g~~sP~vv~ev~~VLe~kL~s~~~~~~~~~GGv~~vaEi~N  217 (346)
T TIGR00207       138 HPQTIALILSHLDPAQAAEILSLLPEEVQAEVARRIAVMGRTSPEVVKEVERVLEKKLESLTSEDYTKVGGVRAVAEIIN  217 (346)
T ss_pred             CHHHHHHHHHHHCHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHC
T ss_conf             86799999985183047888730685689999999985078678999999999977622442123554162578999873


Q ss_pred             HCCCHHHHHHHHHHHHCCCCC-------CCCHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHCCHHHH
Q ss_conf             114979999997544113445-------6756789741998999999840386478899995788899999983798999
Q gi|254780689|r  100 EGLEQNELEKLLNKSDISQEN-------NNSIWDHLKETDPGVIADFLSKEHPQTTAYVLSMMPPSIGASVLLRFPNKIH  172 (345)
Q Consensus       100 ~al~~d~a~~ll~~~~~~~~~-------~~~~~~~L~~~~~~~La~~L~~EhPQtiAlILs~L~~~~Aa~VL~~Lp~e~r  172 (345)
                      .. +....+.++..++...+.       .--.|+-+=.+|...+-.+|+.=.-+-.++=|=--+.+..=++|..+.....
T Consensus       218 ~~-~~~~ek~~l~~~e~~D~~LA~~Ik~~MF~FEdiV~lDdraIqr~L~~vd~~~L~~ALK~~~~~l~ek~l~NMS~Raa  296 (346)
T TIGR00207       218 LL-DRKTEKTILESLEEVDPELAEEIKKKMFVFEDIVKLDDRAIQRVLREVDKEDLLLALKTAEKPLREKFLNNMSQRAA  296 (346)
T ss_pred             CC-CCCHHHHHHHHHHHHCHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             57-87159999999983184789999972364011543030899999998433556778512662478898631548999


Q ss_pred             HHHHHHHHHCCCCC
Q ss_conf             99999984048999
Q gi|254780689|r  173 ADIMKRTVNLPKIS  186 (345)
Q Consensus       173 ~ev~~Ria~l~~v~  186 (345)
                      .-..--|..+++|-
T Consensus       297 ~~l~edm~flGpvr  310 (346)
T TIGR00207       297 EILKEDMEFLGPVR  310 (346)
T ss_pred             HHHHHHHHHCCCCC
T ss_conf             99999887268844


No 10 
>PRK05934 type III secretion system protein; Validated
Probab=97.81  E-value=4.9e-05  Score=53.02  Aligned_cols=49  Identities=20%  Similarity=0.472  Sum_probs=46.3

Q ss_pred             HCCCHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             4199899999984038647889999578889999998379899999999
Q gi|254780689|r  129 KETDPGVIADFLSKEHPQTTAYVLSMMPPSIGASVLLRFPNKIHADIMK  177 (345)
Q Consensus       129 ~~~~~~~La~~L~~EhPQtiAlILs~L~~~~Aa~VL~~Lp~e~r~ev~~  177 (345)
                      +.++...|..+++.|.|.-||+|||||||.+|-+++.+||++++..|++
T Consensus       290 qgINI~KLiEi~qkESPEKi~lILSYLDpkKAeelln~LPEd~khqVLK  338 (341)
T PRK05934        290 QGINIPKLIEIMQKESPEKIALILSYLDPKKAEELLNKLPEDMKHQVLK  338 (341)
T ss_pred             CCCCHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHCHHHHHHHHHH
T ss_conf             0388799999986418687658988438175999998690989887884


No 11 
>pfam03448 MgtE_N MgtE intracellular N domain. This domain is found at the N-terminus of eubacterial magnesium transporters of the MgtE family pfam01769. This domain is an intracellular domain that has an alpha-helical structure. The crystal structure of the MgtE transporter shows two of 5 magnesium ions are in the interface between the N domain and the CBS domains. In the absence of magnesium there is a large shift between the N and CBS domains.
Probab=97.33  E-value=0.0047  Score=39.87  Aligned_cols=70  Identities=24%  Similarity=0.338  Sum_probs=36.3

Q ss_pred             CCHHHHHHHHHHHHCCCCCCCCHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHH
Q ss_conf             497999999754411344567567897419989999998403864788999957888999999837989999999
Q gi|254780689|r  102 LEQNELEKLLNKSDISQENNNSIWDHLKETDPGVIADFLSKEHPQTTAYVLSMMPPSIGASVLLRFPNKIHADIM  176 (345)
Q Consensus       102 l~~d~a~~ll~~~~~~~~~~~~~~~~L~~~~~~~La~~L~~EhPQtiAlILs~L~~~~Aa~VL~~Lp~e~r~ev~  176 (345)
                      ++++....+++.+.     .....+.|..++++....++..=++.-++-++++|+++-++.+|..||++.+..|+
T Consensus        13 l~~~~r~~~~~~l~-----~~~~~~il~~l~~~~~~~il~~l~~~~~~~il~~m~~Dd~~dll~~L~~~~~~~iL   82 (102)
T pfam03448        13 LPPEERLALLRLLP-----PERAAEVLEELDEDVQAELLEALPPEELAELLEELDPDDAADLLEELPEEVREELL   82 (102)
T ss_pred             CCHHHHHHHHHHCC-----HHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHCCHHHHHHHH
T ss_conf             99999999998789-----65599999817999999999868989899999818927899999879999999999


No 12 
>pfam03448 MgtE_N MgtE intracellular N domain. This domain is found at the N-terminus of eubacterial magnesium transporters of the MgtE family pfam01769. This domain is an intracellular domain that has an alpha-helical structure. The crystal structure of the MgtE transporter shows two of 5 magnesium ions are in the interface between the N domain and the CBS domains. In the absence of magnesium there is a large shift between the N and CBS domains.
Probab=96.88  E-value=0.0075  Score=38.54  Aligned_cols=95  Identities=23%  Similarity=0.430  Sum_probs=53.4

Q ss_pred             CHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCH
Q ss_conf             98999999840386478899995788899999983798999999999840489998999999999999722344212363
Q gi|254780689|r  132 DPGVIADFLSKEHPQTTAYVLSMMPPSIGASVLLRFPNKIHADIMKRTVNLPKISPYIQKTIEKCIVEMLPQSNSNTSTG  211 (345)
Q Consensus       132 ~~~~La~~L~~EhPQtiAlILs~L~~~~Aa~VL~~Lp~e~r~ev~~Ria~l~~v~~ev~~~ie~~L~~~l~~~~~~~~~G  211 (345)
                      .|..+|.++..=.|+-...++..++++.++.|+..++++.+.+++..+      ++.-+..+=..+             .
T Consensus         2 hp~diA~~le~l~~~~r~~~~~~l~~~~~~~il~~l~~~~~~~il~~l------~~~~~~~il~~m-------------~   62 (102)
T pfam03448         2 HPADIAELLEELPPEERLALLRLLPPERAAEVLEELDEDVQAELLEAL------PPEELAELLEEL-------------D   62 (102)
T ss_pred             CHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHC------CHHHHHHHHHHC-------------C
T ss_conf             889999999819999999999878965599999817999999999868------989899999818-------------9


Q ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             7899999501775779999999998659999999974
Q gi|254780689|r  212 PEKVANLINELEKPQVDKLLTSLQEVSKEAFDKVRPK  248 (345)
Q Consensus       212 ~~~vA~Iln~l~~~~~~~iL~~L~~~d~~la~~Ir~~  248 (345)
                      ..-+|+|++.++.+..+.+|..+...+   .+.|++.
T Consensus        63 ~Dd~~dll~~L~~~~~~~iL~~l~~~~---r~~i~~l   96 (102)
T pfam03448        63 PDDAADLLEELPEEVREELLSLLDPEE---REEIREL   96 (102)
T ss_pred             CHHHHHHHHHCCHHHHHHHHHCCCHHH---HHHHHHH
T ss_conf             278999998799999999998599999---9999998


No 13 
>COG2239 MgtE Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]
Probab=96.58  E-value=0.061  Score=32.55  Aligned_cols=56  Identities=14%  Similarity=0.293  Sum_probs=26.0

Q ss_pred             HHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHH------CCCCCHHHHHHHHHHHHHHHH
Q ss_conf             99999998381468999851999999999999861------389998999999999999985
Q gi|254780689|r   27 KATAILLAMEKQVSGKLLRHFTHAELKEIVASAKL------LPEISPEELEDIIDEFESQFI   82 (345)
Q Consensus        27 KAAilLl~LGee~Aa~ilk~l~~~Ei~~i~~~m~~------l~~i~~~~~~~vl~EF~~~~~   82 (345)
                      +..+++..++++.++++|.+++++--..|...|..      +...+++++-.+++|+-....
T Consensus        47 ~r~~v~~ll~~~~~~~v~~~l~~~~~~~ii~~~~~~~~~~~ie~m~~Dd~~~ll~elp~~~~  108 (451)
T COG2239          47 ERVVVWRLLPKEDAAEVLGELDDEVREEIIEALSDEELAAAIEELDIDDAADLLDELPDEVR  108 (451)
T ss_pred             HHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHCCHHHH
T ss_conf             88888873887677899983298689999985599999999872692778999986877789


No 14 
>COG3334 Uncharacterized conserved protein [Function unknown]
Probab=96.38  E-value=0.02  Score=35.67  Aligned_cols=64  Identities=14%  Similarity=0.187  Sum_probs=59.2

Q ss_pred             CHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCC
Q ss_conf             5678974199899999984038647889999578889999998379899999999984048999
Q gi|254780689|r  123 SIWDHLKETDPGVIADFLSKEHPQTTAYVLSMMPPSIGASVLLRFPNKIHADIMKRTVNLPKIS  186 (345)
Q Consensus       123 ~~~~~L~~~~~~~La~~L~~EhPQtiAlILs~L~~~~Aa~VL~~Lp~e~r~ev~~Ria~l~~v~  186 (345)
                      ..-+..+.|+|+-.|..|.+=+|+..+-|+..|+|.+++.||+.++++....++.+|+.....+
T Consensus       123 klv~iY~~Mkp~~aA~~le~l~~e~Aa~Il~~L~~r~~~~ILakMdPekAA~lt~~i~~~~~~~  186 (192)
T COG3334         123 KLVKIYSKMKPDAAAAILENLPDEEAAAILMKLKPRKLGLILAKMDPEKAATLTELIASPPRNN  186 (192)
T ss_pred             HHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHCCCHHHHHHHHHHHHCCCCCC
T ss_conf             7999998079166899998389888999998388218999987389888999999986578766


No 15 
>COG2239 MgtE Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]
Probab=94.70  E-value=0.37  Score=27.38  Aligned_cols=81  Identities=12%  Similarity=0.139  Sum_probs=47.4

Q ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHCCHHH
Q ss_conf             88999976114979999997544113445675678974199899999984038647889999578889999998379899
Q gi|254780689|r   92 KNIESILEEGLEQNELEKLLNKSDISQENNNSIWDHLKETDPGVIADFLSKEHPQTTAYVLSMMPPSIGASVLLRFPNKI  171 (345)
Q Consensus        92 ~~~~~lL~~al~~d~a~~ll~~~~~~~~~~~~~~~~L~~~~~~~La~~L~~EhPQtiAlILs~L~~~~Aa~VL~~Lp~e~  171 (345)
                      ...+.++-+.++.+.+..++...+  ..   .-++.+..++++.++..+..=+|--.+-++.-+|.+...++|..++++.
T Consensus        45 ~~~r~~v~~ll~~~~~~~v~~~l~--~~---~~~~ii~~~~~~~~~~~ie~m~~Dd~~~ll~elp~~~~~~lL~~l~~~~  119 (451)
T COG2239          45 GRERVVVWRLLPKEDAAEVLGELD--DE---VREEIIEALSDEELAAAIEELDIDDAADLLDELPDEVRDELLSLLDPEE  119 (451)
T ss_pred             HHHHHHHHHHCCHHHHHHHHHHCC--HH---HHHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHCCHHH
T ss_conf             998888887388767789998329--86---8999998559999999987269277899998687778999998189999


Q ss_pred             HHHHHH
Q ss_conf             999999
Q gi|254780689|r  172 HADIMK  177 (345)
Q Consensus       172 r~ev~~  177 (345)
                      |..+-.
T Consensus       120 r~~v~~  125 (451)
T COG2239         120 RARVRQ  125 (451)
T ss_pred             HHHHHH
T ss_conf             999998


No 16 
>COG3334 Uncharacterized conserved protein [Function unknown]
Probab=91.23  E-value=0.47  Score=26.65  Aligned_cols=48  Identities=23%  Similarity=0.432  Sum_probs=28.8

Q ss_pred             HCCCHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHH
Q ss_conf             419989999998403864788999957888999999837989999999
Q gi|254780689|r  129 KETDPGVIADFLSKEHPQTTAYVLSMMPPSIGASVLLRFPNKIHADIM  176 (345)
Q Consensus       129 ~~~~~~~La~~L~~EhPQtiAlILs~L~~~~Aa~VL~~Lp~e~r~ev~  176 (345)
                      ..-..+-|....++=.|--+|-+|..|+++.|+.|+..|++.....|+
T Consensus       117 ~qae~~klv~iY~~Mkp~~aA~~le~l~~e~Aa~Il~~L~~r~~~~IL  164 (192)
T COG3334         117 KQAEDGKLVKIYSKMKPDAAAAILENLPDEEAAAILMKLKPRKLGLIL  164 (192)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHH
T ss_conf             786562799999807916689999838988899999838821899998


No 17 
>pfam09126 NaeI Restriction endonuclease NaeI. Members of this family adopt a secondary structure consisting of nine alpha-helices, six 3-10 helices and 13 beta-strands. They bind two GCC-CGG recognition sequences to cleave DNA into blunt-ended products.
Probab=80.09  E-value=4.6  Score=20.13  Aligned_cols=62  Identities=15%  Similarity=0.128  Sum_probs=47.6

Q ss_pred             HCCCCHHHHHHHHHHCCH--HHHHHHHHHHHHCCCCCCHHHHH--HHHHHHHHHHH-------HHHHCCCEECCCC
Q ss_conf             538898999999961008--99999999985005899989999--99999999999-------9998697951888
Q gi|254780689|r  279 LHGTSIETQNAILHCLSN--RQRKIIEENIVLNDSSIAPREVA--MARRSIVQEAI-------SLLKTNKIELSNP  343 (345)
Q Consensus       279 Lkga~~e~~e~il~nmS~--Ra~~~l~eel~~~~g~v~~~dve--~Aq~~I~~~~r-------~L~~~G~I~l~~~  343 (345)
                      |.+.+++.+++||++=|.  |.++.++.=-  . -||....|+  +-|++.+..+|       .|..+|-|.|+.-
T Consensus       162 Ll~l~~~~r~~Ifa~~sG~~R~~eLFR~~q--g-~~I~R~vv~tVa~Q~D~mrRVR~~ggaR~~L~~EGIlilgg~  234 (291)
T pfam09126       162 LLHLPDDVREAIFAPKSGNARMAELFRRVQ--G-RPIPRDVVEAVARQQDFMRRVRSDGGARDVLRPEGILLLGGQ  234 (291)
T ss_pred             HHCCCHHHHHHHHCCCCHHHHHHHHHHHHH--C-CCCCHHHHHHHHHCCHHHHHHHCCCCHHHHHCCCCEEEECCC
T ss_conf             324998899998548616799999999984--8-566689999988121065564237755666263747997477


No 18 
>PHA01513 mnt Mnt
Probab=64.96  E-value=10  Score=17.79  Aligned_cols=60  Identities=12%  Similarity=0.221  Sum_probs=41.1

Q ss_pred             HHCCHHHHHHHHHHHH-HCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCHHH
Q ss_conf             8379899999999984-0489998999999999999722344212363789999950177577
Q gi|254780689|r  165 LRFPNKIHADIMKRTV-NLPKISPYIQKTIEKCIVEMLPQSNSNTSTGPEKVANLINELEKPQ  226 (345)
Q Consensus       165 ~~Lp~e~r~ev~~Ria-~l~~v~~ev~~~ie~~L~~~l~~~~~~~~~G~~~vA~Iln~l~~~~  226 (345)
                      -+||.+++..+-.|-- +=.+++.++++.+++.|.+-  +..+.-.+-.+++||.....-+..
T Consensus        10 lRlP~elk~Ki~~RAk~NgRSmNaEivqiv~dalskp--spvsgYrddaERlAd~qse~~k~~   70 (82)
T PHA01513         10 LRLPYELKEKVKQRAKANGRSLNAELVQIVADSLEKP--TPVIGYRDDAEREADIVSREIQEL   70 (82)
T ss_pred             CCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCC--CCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             4787999999999998758511199999999985189--987433228999889999999999


No 19 
>PRK09273 hypothetical protein; Provisional
Probab=60.65  E-value=12  Score=17.29  Aligned_cols=43  Identities=16%  Similarity=0.247  Sum_probs=28.3

Q ss_pred             HHHHHCCCHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHCCH
Q ss_conf             899850997899999830988899998538898999999961008
Q gi|254780689|r  252 FDDLITLSSHDLSIVFNNISLEVLGKALHGTSIETQNAILHCLSN  296 (345)
Q Consensus       252 FeDl~~l~~~~l~~ll~evd~~~l~~ALkga~~e~~e~il~nmS~  296 (345)
                      +.++-.+..+++-.+|+.+|++.+-.|++|  +.+++.||.|=..
T Consensus       157 L~~vk~~t~k~~~~iLk~iD~~llk~ai~g--e~F~e~ff~n~q~  199 (211)
T PRK09273        157 LNEVKAATYKDYLDILKAIDQELLKTAISG--ERFQEYFFANCQD  199 (211)
T ss_pred             HHHHHHHHCCCHHHHHHHCCHHHHHHHHCC--HHHHHHHHHCCCH
T ss_conf             999999863659999986299999998642--7799999964873


No 20 
>COG4086 Predicted secreted protein [Function unknown]
Probab=58.85  E-value=13  Score=17.09  Aligned_cols=17  Identities=18%  Similarity=0.303  Sum_probs=11.9

Q ss_pred             HHHHCCCHHHHHHHHHC
Q ss_conf             89741998999999840
Q gi|254780689|r  126 DHLKETDPGVIADFLSK  142 (345)
Q Consensus       126 ~~L~~~~~~~La~~L~~  142 (345)
                      +...|+.|++.++-|..
T Consensus       111 ~nI~~vt~eMYanAL~T  127 (299)
T COG4086         111 GNITVVTPEMYANALVT  127 (299)
T ss_pred             EEEEEECHHHHHHHHHH
T ss_conf             31788778999999986


No 21 
>pfam12408 DUF3666 Ribose-5-phosphate isomerase. This domain family is found in bacteria, and is approximately 50 amino acids in length. The family is found in association with pfam02502. There are two completely conserved residues (D and F) that may be functionally important.
Probab=58.11  E-value=14  Score=17.01  Aligned_cols=34  Identities=18%  Similarity=0.231  Sum_probs=26.9

Q ss_pred             HHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHCC
Q ss_conf             789999983098889999853889899999996100
Q gi|254780689|r  260 SHDLSIVFNNISLEVLGKALHGTSIETQNAILHCLS  295 (345)
Q Consensus       260 ~~~l~~ll~evd~~~l~~ALkga~~e~~e~il~nmS  295 (345)
                      -+++-.+|+++|++-+-.|+.|  +.+++.||.|=-
T Consensus         4 ~kdll~iLk~iDqdLvK~AvsG--e~Fqe~FF~ncq   37 (48)
T pfam12408         4 YKDLLDILKAIDQDLVKGAVSG--ERFQECFFANCQ   37 (48)
T ss_pred             HHHHHHHHHHHCHHHHHHHHCH--HHHHHHHHHCCC
T ss_conf             4569999999689999988431--999999984388


No 22 
>TIGR02019 BchJ bacteriochlorophyll 4-vinyl reductase; InterPro: IPR010249   This entry represents the component of bacteriochlorophyll synthetase responsible for reduction of the B-ring pendant ethylene (4-vinyl) group. It appears that this step must precede the reduction of ring D, at least by the 'dark' protochlorophyllide reductase enzymes BchN, BchB and BchL . This family appears to be present in photosynthetic bacteria except for the cyanobacterial clade. Cyanobacteria must use a non-orthologous gene to carry out this required step for the biosynthesis of both bacteriochlorophyll and chlorophyll.; GO: 0015979 photosynthesis, 0030494 bacteriochlorophyll biosynthetic process.
Probab=44.17  E-value=22  Score=15.58  Aligned_cols=80  Identities=24%  Similarity=0.182  Sum_probs=60.2

Q ss_pred             HHHHHHHCCCHHHHHHHHHHHHCCCCCCCCHHHHHHCCCHHHHHHHHHCCCHH-HHHHHHHHCCHHHHHHHHHH-CCHHH
Q ss_conf             99997611497999999754411344567567897419989999998403864-78899995788899999983-79899
Q gi|254780689|r   94 IESILEEGLEQNELEKLLNKSDISQENNNSIWDHLKETDPGVIADFLSKEHPQ-TTAYVLSMMPPSIGASVLLR-FPNKI  171 (345)
Q Consensus        94 ~~~lL~~al~~d~a~~ll~~~~~~~~~~~~~~~~L~~~~~~~La~~L~~EhPQ-tiAlILs~L~~~~Aa~VL~~-Lp~e~  171 (345)
                      .--.|+-++|++.++++|.+.--.-..+.-+=+.|..-+-..|...|+++||. -.|-||..---..|-.||.. .|.-.
T Consensus        10 ~v~aleaayG~~a~~~~L~~~G~G~l~~~~ps~MlpEs~f~~L~~~Lr~~lge~aaa~~L~esG~~Ta~Y~l~~RiP~p~   89 (189)
T TIGR02019        10 TVAALEAAYGKEAVEKLLKKIGRGYLLEALPSEMLPESKFSALVAALRKELGESAAADVLKESGEATAKYVLKNRIPVPI   89 (189)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCHHH
T ss_conf             99998613685689999998388855887875567600178999999975695401689999878898887760698778


Q ss_pred             HH
Q ss_conf             99
Q gi|254780689|r  172 HA  173 (345)
Q Consensus       172 r~  173 (345)
                      |.
T Consensus        90 q~   91 (189)
T TIGR02019        90 QR   91 (189)
T ss_pred             HH
T ss_conf             99


No 23 
>pfam11865 DUF3385 Domain of unknown function (DUF3385). This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 160 to 172 amino acids in length. This domain is found associated with pfam00454, pfam02260, pfam02985, pfam02259 and pfam08771.
Probab=42.20  E-value=24  Score=15.38  Aligned_cols=139  Identities=13%  Similarity=0.165  Sum_probs=76.4

Q ss_pred             CCCHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCC
Q ss_conf             03864788999957888999999837989999999998404899989999999999997223442123637899999501
Q gi|254780689|r  142 KEHPQTTAYVLSMMPPSIGASVLLRFPNKIHADIMKRTVNLPKISPYIQKTIEKCIVEMLPQSNSNTSTGPEKVANLINE  221 (345)
Q Consensus       142 ~EhPQtiAlILs~L~~~~Aa~VL~~Lp~e~r~ev~~Ria~l~~v~~ev~~~ie~~L~~~l~~~~~~~~~G~~~vA~Iln~  221 (345)
                      .+||+-..+++.-|..++        ...+|.|+++-++.++.++|-..+.+.........   ....+......-..+.
T Consensus         6 ~~YP~LL~~L~~iLk~e~--------s~~iR~E~lr~lGiLGALDP~~~k~~~~~~~~~~~---~~~~~~~~~~~l~~~~   74 (160)
T pfam11865         6 LDYPELLGVLLNILKTET--------SWEVRRETLKLLGILGALDPYKHKEIERNLSDGQS---AESTNKCTDILLLMKG   74 (160)
T ss_pred             HHHHHHHHHHHHHHHCCC--------CHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCCCCC---CCCCCCCCCHHHHHCC
T ss_conf             777899999999986078--------78899999999877057677999872145787665---3456887428888536


Q ss_pred             CCHHHHH----HHHHHHHH--HHHHHH----HHHHHHCCCHHHHHCCCHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHH
Q ss_conf             7757799----99999998--659999----9999741578998509978999998309888999985388989999999
Q gi|254780689|r  222 LEKPQVD----KLLTSLQE--VSKEAF----DKVRPKVFLFDDLITLSSHDLSIVFNNISLEVLGKALHGTSIETQNAIL  291 (345)
Q Consensus       222 l~~~~~~----~iL~~L~~--~d~~la----~~Ir~~mF~FeDl~~l~~~~l~~ll~evd~~~l~~ALkga~~e~~e~il  291 (345)
                      +....++    -.+..|-.  +||.+.    .-|+..||.|--+   .-+. -..|..|-+ .+.-.++.+++.++|.+|
T Consensus        75 ~~~~~eeyyptvvi~~Lm~IL~D~sLs~~h~~vvqai~~Ifksl---g~~c-v~~l~qiiP-~~l~virt~~~~l~e~~~  149 (160)
T pfam11865        75 LSPSSDEYYPTVVINSLLKILKDPSLSSHHTAVVQAIMNIFKSL---GLKC-VPFLPQVIP-PFLSVIRTLPASLLEFYF  149 (160)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHC---CCCC-HHHHHHHHH-HHHHHHHHCCHHHHHHHH
T ss_conf             89838889999999999999838337889999999999999806---7430-210788889-999999709916899999


Q ss_pred             HHCCH
Q ss_conf             61008
Q gi|254780689|r  292 HCLSN  296 (345)
Q Consensus       292 ~nmS~  296 (345)
                      ..++.
T Consensus       150 ~qL~~  154 (160)
T pfam11865       150 QQLST  154 (160)
T ss_pred             HHHHH
T ss_conf             99998


No 24 
>TIGR01737 FGAM_synth_I phosphoribosylformylglycinamidine synthase I; InterPro: IPR010075   In some species, phosphoribosylformylglycinamidine synthase is composed of a single polypeptide chain. This entry describes the PurQ protein of Bacillus subtilis (where PurL, PurQ, and PurS are required for phosphoribosylformylglycinamidine synthase activity) and functionally equivalent proteins from other bacteria and archaea.; GO: 0004642 phosphoribosylformylglycinamidine synthase activity, 0006189 'de novo' IMP biosynthetic process, 0005737 cytoplasm.
Probab=37.31  E-value=28  Score=14.89  Aligned_cols=23  Identities=26%  Similarity=0.209  Sum_probs=19.5

Q ss_pred             HHHH---HHHHHHHHHHHHCCCEECC
Q ss_conf             9999---9999999999986979518
Q gi|254780689|r  319 AMAR---RSIVQEAISLLKTNKIELS  341 (345)
Q Consensus       319 e~Aq---~~I~~~~r~L~~~G~I~l~  341 (345)
                      -+|+   ..|++.+++++++|+.+|+
T Consensus        73 IAa~rvk~p~~~~V~~~A~~G~pVLG   98 (264)
T TIGR01737        73 IAALRVKSPIMQEVREFAEKGKPVLG   98 (264)
T ss_pred             HHHHHCCHHHHHHHHHHHHCCCEEEE
T ss_conf             99875030889999999955982899


No 25 
>PRK13901 ruvA Holliday junction DNA helicase motor protein; Provisional
Probab=37.22  E-value=29  Score=14.88  Aligned_cols=54  Identities=11%  Similarity=0.155  Sum_probs=27.6

Q ss_pred             CCCCCCCCHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHCCHH
Q ss_conf             1344567567897419989999998403864788999957888999999837989
Q gi|254780689|r  116 ISQENNNSIWDHLKETDPGVIADFLSKEHPQTTAYVLSMMPPSIGASVLLRFPNK  170 (345)
Q Consensus       116 ~~~~~~~~~~~~L~~~~~~~La~~L~~EhPQtiAlILs~L~~~~Aa~VL~~Lp~e  170 (345)
                      +.+-.+...+..|+.++|+.++..+.++.+.+..-| .-+-+..|.+|+-.|-..
T Consensus        77 VsGIGpk~Al~iLs~~~~~~l~~aI~~~D~~~L~~v-pGIG~KtA~rIi~ELk~K  130 (196)
T PRK13901         77 VDGIGPRAALRVLSGIKYNEFRDAIDREDIELISKV-KGIGNKMAGKIFLKLRGK  130 (196)
T ss_pred             CCCCCHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHC-CCCCHHHHHHHHHHHHHH
T ss_conf             588268999999757999999999992899998319-995899999999999765


No 26 
>PRK12435 ferrochelatase; Provisional
Probab=37.07  E-value=13  Score=17.21  Aligned_cols=47  Identities=19%  Similarity=0.284  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf             8799999998381468999851999999999999861389998999999999999
Q gi|254780689|r   25 KDKATAILLAMEKQVSGKLLRHFTHAELKEIVASAKLLPEISPEELEDIIDEFES   79 (345)
Q Consensus        25 ~eKAAilLl~LGee~Aa~ilk~l~~~Ei~~i~~~m~~l~~i~~~~~~~vl~EF~~   79 (345)
                      .+|.|+||++||-..        +.++|+.--..+..-+.++.+.+..+...|..
T Consensus         3 k~K~gVLL~nlG~P~--------s~~dV~pyL~~i~~gr~p~~~~l~~~~~~Y~~   49 (316)
T PRK12435          3 KKKIGLLVMAYGTPE--------SLDDVEAYYTHIRHGRKPSEEALEDLIGRYKA   49 (316)
T ss_pred             CCCEEEEEEECCCCC--------CHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH
T ss_conf             885899998789999--------87689999999706899989999999999998


No 27 
>KOG1114 consensus
Probab=35.91  E-value=30  Score=14.75  Aligned_cols=104  Identities=13%  Similarity=0.185  Sum_probs=62.3

Q ss_pred             HHHHHCCC---HHHHHHHHHCCCH---HHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHH-HH
Q ss_conf             78974199---8999999840386---47889999578889999998379899999999984048999899999999-99
Q gi|254780689|r  125 WDHLKETD---PGVIADFLSKEHP---QTTAYVLSMMPPSIGASVLLRFPNKIHADIMKRTVNLPKISPYIQKTIEK-CI  197 (345)
Q Consensus       125 ~~~L~~~~---~~~La~~L~~EhP---QtiAlILs~L~~~~Aa~VL~~Lp~e~r~ev~~Ria~l~~v~~ev~~~ie~-~L  197 (345)
                      .++|.+++   -+.+.++++.+||   -...+.|.+|        +...  +...+...|+-.+=+....+++.++. .|
T Consensus      1083 v~~l~kl~~e~~~k~~~~l~s~ypd~lpll~~~l~kl--------~~~s--D~~kE~~~ki~eIl~~A~~Vi~~~D~eaL 1152 (1304)
T KOG1114        1083 VSWLSKLADEEAEKIYNYLKSSYPDYLPLLEVRLAKL--------MQKS--DAVKETNKKIEEILSAADSVIQEIDTEAL 1152 (1304)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH--------HHHC--CCCHHHHHHHHHHHHHHHHHHHHHCHHHH
T ss_conf             8999876189999999999876765340799999874--------0010--12357788899999887888876068999


Q ss_pred             HHHHCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9972234421236378999995017757799999999986599999
Q gi|254780689|r  198 VEMLPQSNSNTSTGPEKVANLINELEKPQVDKLLTSLQEVSKEAFD  243 (345)
Q Consensus       198 ~~~l~~~~~~~~~G~~~vA~Iln~l~~~~~~~iL~~L~~~d~~la~  243 (345)
                      ...+.-    +.+....++.|.+.|+... +.+++.|-+.-.-++.
T Consensus      1153 ~~y~~~----k~D~r~da~klk~~me~qk-~tli~AL~kKg~a~ak 1193 (1304)
T KOG1114        1153 ARYYAL----KEDTRPDAVKLKKKMEKQK-DTLIDALVKKGEAFAK 1193 (1304)
T ss_pred             HHHHHC----CCCCCCHHHHHHHHHHHHH-HHHHHHHHHHHHHHHH
T ss_conf             999861----4677641889988888888-9999999973068766


No 28 
>pfam11513 TA0956 Thermoplasma acidophilum protein TA0956. TA0956 is a protein from Thermoplasma acidophilum which currently has no known function however the structure has been determined. The protein has a two-layered alpha/beta-sandwich topology and is a putative Elongation factor 1-alpha binding motif.
Probab=35.00  E-value=15  Score=16.78  Aligned_cols=49  Identities=20%  Similarity=0.253  Sum_probs=32.2

Q ss_pred             HHCCCHHHHHHHHHHCCHHHHH--HHHHHCCHHHHHHHHHHHHHCCCCCHH
Q ss_conf             8403864788999957888999--999837989999999998404899989
Q gi|254780689|r  140 LSKEHPQTTAYVLSMMPPSIGA--SVLLRFPNKIHADIMKRTVNLPKISPY  188 (345)
Q Consensus       140 L~~EhPQtiAlILs~L~~~~Aa--~VL~~Lp~e~r~ev~~Ria~l~~v~~e  188 (345)
                      +++-||-||-+++++..-..+.  .|+..-..+.--+.+.|-|+.+.+-|+
T Consensus        11 m~~~HPtTICVvm~kF~dSf~elidv~~~~~~Del~dFI~~yARTDEImPE   61 (110)
T pfam11513        11 MKEQHPTTICVVMDKFLDSFKELIDVVTSPDIDELMDFISRYARTDEIMPE   61 (110)
T ss_pred             ECCCCCCEEEEEHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCC
T ss_conf             056688348886898899999999873388878999999986321325777


No 29 
>COG4973 XerC Site-specific recombinase XerC [DNA replication, recombination, and repair]
Probab=34.54  E-value=31  Score=14.60  Aligned_cols=100  Identities=19%  Similarity=0.233  Sum_probs=72.9

Q ss_pred             HHHCCCHHHCCHHHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHCCCC--CHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             44037922368687999999983814689998519999999999998613899--9899999999999998510456653
Q gi|254780689|r   13 LYKEISPVSLTQKDKATAILLAMEKQVSGKLLRHFTHAELKEIVASAKLLPEI--SPEELEDIIDEFESQFIAGIGLTEN   90 (345)
Q Consensus        13 ~~~~~~p~~Ltg~eKAAilLl~LGee~Aa~ilk~l~~~Ei~~i~~~m~~l~~i--~~~~~~~vl~EF~~~~~~~~~~~g~   90 (345)
                      +-+.++|-+++.-++-=--+++++.+.+...+..+++..++.+...-.+=+--  |-...-..++.|++-+...+-+..+
T Consensus        19 ~Er~lS~hTl~~Y~rqL~~l~~~~~q~~~~~w~~ld~~~vr~~~a~~~~~Gl~a~SlA~rLSa~R~f~~wLv~~g~l~~n   98 (299)
T COG4973          19 VERQLSPHTLANYRRQLEALIALLAQMGLGSWQQLDPADVRAFVARSHRRGLSARSLARRLSALRSFYDWLVKQGELKAN   98 (299)
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             86146888899999999999999997276566656999999999998318855778999999999999999872764668


Q ss_pred             H-H-----HHHHHHHHCCCHHHHHHHHH
Q ss_conf             4-8-----89999761149799999975
Q gi|254780689|r   91 S-K-----NIESILEEGLEQNELEKLLN  112 (345)
Q Consensus        91 ~-~-----~~~~lL~~al~~d~a~~ll~  112 (345)
                      . .     ...+-|.++++.|++..+++
T Consensus        99 Pa~GvsaPK~~r~LPk~ld~d~~~~ll~  126 (299)
T COG4973          99 PAKGVSAPKQPRHLPKNLDVDEANRLLD  126 (299)
T ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHC
T ss_conf             6456889887443777689999999966


No 30 
>pfam11239 DUF3040 Protein of unknown function (DUF3040). Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed.
Probab=33.13  E-value=33  Score=14.46  Aligned_cols=24  Identities=13%  Similarity=0.159  Sum_probs=15.7

Q ss_pred             HHHHHHHHHHHH----HHHHHHHHHHHH
Q ss_conf             577999999999----865999999997
Q gi|254780689|r  224 KPQVDKLLTSLQ----EVSKEAFDKVRP  247 (345)
Q Consensus       224 ~~~~~~iL~~L~----~~d~~la~~Ir~  247 (345)
                      ++.|+++|++||    ++||+++..++.
T Consensus         4 Se~Eqr~L~eiE~~L~~eDP~fa~~~~~   31 (82)
T pfam11239         4 SEHEQRRLEEIERALYAEDPKFAAAVRS   31 (82)
T ss_pred             CHHHHHHHHHHHHHHHHCCHHHHHHHCC
T ss_conf             8899999999999998439799997515


No 31 
>pfam06070 Herpes_UL32 Herpesvirus large structural phosphoprotein UL32. The large phosphorylated protein (UL32-like) of herpes viruses is the polypeptide most frequently reactive in immuno-blotting analyses with antisera when compared with other viral proteins.
Probab=33.07  E-value=33  Score=14.45  Aligned_cols=105  Identities=16%  Similarity=0.169  Sum_probs=66.4

Q ss_pred             HHHHHHHHHHHHHHCCC--CCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH-CCCHH---
Q ss_conf             99999999999972234--4212363789999950177577999999999865999999997415789985-09978---
Q gi|254780689|r  188 YIQKTIEKCIVEMLPQS--NSNTSTGPEKVANLINELEKPQVDKLLTSLQEVSKEAFDKVRPKVFLFDDLI-TLSSH---  261 (345)
Q Consensus       188 ev~~~ie~~L~~~l~~~--~~~~~~G~~~vA~Iln~l~~~~~~~iL~~L~~~d~~la~~Ir~~mF~FeDl~-~l~~~---  261 (345)
                      ...+.+++.|.. |+..  ...-..|.  ...-+|- -.....+|-++|+        .++++||.|.-+- +++-.   
T Consensus       121 ~~~~vvlr~l~~-La~~~~~~~l~~G~--~~~FVNL-r~ee~~~le~NL~--------~a~~NMl~ytv~~l~d~r~eN~  188 (777)
T pfam06070       121 PDVDVVLRALVS-LARLSECQPLAWGT--EIGFVNL-RAEEVQELEENLR--------AARNNMLVYTVLDLNDPRNENG  188 (777)
T ss_pred             CHHHHHHHHHHH-HHHHCCCCCCCCCC--CCCEEEC-CHHHHHHHHHHHH--------HHHHCCEEEEEECCCCCCCCCC
T ss_conf             189999999999-88613688876666--3221425-7899999999999--------9985626899741367001364


Q ss_pred             -HHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             -9999983098889999853889899999996100899999999
Q gi|254780689|r  262 -DLSIVFNNISLEVLGKALHGTSIETQNAILHCLSNRQRKIIEE  304 (345)
Q Consensus       262 -~l~~ll~evd~~~l~~ALkga~~e~~e~il~nmS~Ra~~~l~e  304 (345)
                       -+..+.+=|=.-.|++||+++=.++.++.|..+-+..+..+++
T Consensus       189 ~LV~avNKLvYLGrli~al~~SW~eLek~cL~rI~e~~k~Lvk~  232 (777)
T pfam06070       189 PLVNAVNKLVYLGRLILALSTSWRELEKKCLDRINELCKRLVKE  232 (777)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             28888888999889999987689999999999999999999999


No 32 
>TIGR00444 mazG MazG family protein; InterPro: IPR011551   This group of prokaryotic proteins has no known function. It includes the uncharacterised protein MazG in Escherichia coli..
Probab=32.00  E-value=34  Score=14.35  Aligned_cols=134  Identities=12%  Similarity=0.197  Sum_probs=68.3

Q ss_pred             HHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHHHHCC--CCCHHHHHHHHHHHHH-----HHCCCCCCC
Q ss_conf             999984038647889999578889999998379899999999984048--9998999999999999-----722344212
Q gi|254780689|r  136 IADFLSKEHPQTTAYVLSMMPPSIGASVLLRFPNKIHADIMKRTVNLP--KISPYIQKTIEKCIVE-----MLPQSNSNT  208 (345)
Q Consensus       136 La~~L~~EhPQtiAlILs~L~~~~Aa~VL~~Lp~e~r~ev~~Ria~l~--~v~~ev~~~ie~~L~~-----~l~~~~~~~  208 (345)
                      |+.=|..-||++=    +--...-+.+||++=..=...|   |-.+-+  ++-...++.|-++|=.     ++. ..+.+
T Consensus        79 is~KlvRRHPHVF----~d~~v~d~~evlA~W~~iK~~E---k~~~~~~tPllss~Ld~~p~tLPaL~~A~Klq-kkaA~  150 (253)
T TIGR00444        79 ISEKLVRRHPHVF----ADVKVEDEEEVLARWEEIKAKE---KALKEEETPLLSSLLDSVPRTLPALMRAAKLQ-KKAAK  150 (253)
T ss_pred             HHHHHHCCCCCCC----CCCCCCCHHHHHHHHHHHHHHH---HCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHH-HHHHC
T ss_conf             8752212788605----6542145476785099999997---25783333368887741466563456866776-88732


Q ss_pred             CC-HHHHHHHHHCCCCHHHHHHHHHHHHHHHH---HHHHHHHHHCCCHHHHHCCCHHHHHHHHHCCCHHHHHHHHCCCCH
Q ss_conf             36-37899999501775779999999998659---999999974157899850997899999830988899998538898
Q gi|254780689|r  209 ST-GPEKVANLINELEKPQVDKLLTSLQEVSK---EAFDKVRPKVFLFDDLITLSSHDLSIVFNNISLEVLGKALHGTSI  284 (345)
Q Consensus       209 ~~-G~~~vA~Iln~l~~~~~~~iL~~L~~~d~---~la~~Ir~~mF~FeDl~~l~~~~l~~ll~evd~~~l~~ALkga~~  284 (345)
                      +| -=..|.+|...+ ...-+++...+...+.   ++-+++-.++|+.=+|.|-=         .++++   .||++||+
T Consensus       151 VGFdW~~v~~v~~Kv-~EEl~E~~~e~~~~~~~~~Kl~~E~GDLLFalvNlAR~y---------~~~ae---~AL~~aN~  217 (253)
T TIGR00444       151 VGFDWEDVSPVWDKV-SEELEEVKSEVSEADVEHNKLEAELGDLLFALVNLARHY---------KLDAE---EALRKANE  217 (253)
T ss_pred             CCCCCCCCCHHHHHH-HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH---------CCCHH---HHHHHHHH
T ss_conf             789866432157877-888899999985260357899999707999999999871---------89887---99988549


Q ss_pred             HHHHHH
Q ss_conf             999999
Q gi|254780689|r  285 ETQNAI  290 (345)
Q Consensus       285 e~~e~i  290 (345)
                      .++.+|
T Consensus       218 kF~rRf  223 (253)
T TIGR00444       218 KFERRF  223 (253)
T ss_pred             HHHHHH
T ss_conf             999999


No 33 
>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=31.83  E-value=31  Score=14.62  Aligned_cols=25  Identities=24%  Similarity=0.445  Sum_probs=11.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5779999999998659999999974
Q gi|254780689|r  224 KPQVDKLLTSLQEVSKEAFDKVRPK  248 (345)
Q Consensus       224 ~~~~~~iL~~L~~~d~~la~~Ir~~  248 (345)
                      ++..+++|+.+.+.+|.+.+++...
T Consensus       518 r~ev~~LLd~l~~~~PklVee~~P~  542 (713)
T TIGR01398       518 RQEVQNLLDRLKEEYPKLVEELIPD  542 (713)
T ss_pred             HHHHHHHHHHHHHHCCEEHHHCCCC
T ss_conf             8999999986013267400113889


No 34 
>cd07176 terB tellurite resistance protein terB. This family contains uncharacterized bacterial proteins involved in tellurium resistance. The prototype of this CD is the Kp-terB protein from Klebsiella pneumoniae, whose 3D structure was recently determined. The biological function of terB and the mechanism responsible for tellurium resistance are unknown.
Probab=31.73  E-value=35  Score=14.31  Aligned_cols=69  Identities=19%  Similarity=0.109  Sum_probs=45.6

Q ss_pred             HHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCHHHHHHHH
Q ss_conf             99985199999999999986138999899999999999998510456653488999976114979999997
Q gi|254780689|r   41 GKLLRHFTHAELKEIVASAKLLPEISPEELEDIIDEFESQFIAGIGLTENSKNIESILEEGLEQNELEKLL  111 (345)
Q Consensus        41 a~ilk~l~~~Ei~~i~~~m~~l~~i~~~~~~~vl~EF~~~~~~~~~~~g~~~~~~~lL~~al~~d~a~~ll  111 (345)
                      +..=++++++|.+.|...+...+..++.....+..-|...+..-  -..|...+.+.+...++++.....+
T Consensus        13 A~ADG~i~~~E~~~i~~~l~~~~~l~~~~~~~l~~~~~~~~~~~--~~~~~~~l~~~i~~~~~~~~~~~~~   81 (111)
T cd07176          13 AAADGDIDDAELQAIEALLRSLPVLSGFDRERLIALLDKLLALL--RPEGLAALLKAAAKLLPPELRETAF   81 (111)
T ss_pred             HHHCCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHCCHHHHHHHH
T ss_conf             98647999999999999986384468777999999999999872--7576999999999866887899999


No 35 
>COG1184 GCD2 Translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]
Probab=30.69  E-value=36  Score=14.20  Aligned_cols=18  Identities=11%  Similarity=0.052  Sum_probs=5.9

Q ss_pred             HHHHHHHHCCHHHHHHHH
Q ss_conf             999999610089999999
Q gi|254780689|r  286 TQNAILHCLSNRQRKIIE  303 (345)
Q Consensus       286 ~~e~il~nmS~Ra~~~l~  303 (345)
                      ++...|---|.|-.+.+-
T Consensus       264 v~Np~fD~TP~~~Id~iI  281 (301)
T COG1184         264 VRNPAFDVTPPEYIDAII  281 (301)
T ss_pred             CCCCCCCCCCHHHHHEEE
T ss_conf             344265789588743123


No 36 
>COG2074 2-phosphoglycerate kinase [Carbohydrate transport and metabolism]
Probab=30.03  E-value=37  Score=14.12  Aligned_cols=27  Identities=7%  Similarity=0.003  Sum_probs=17.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCEECC
Q ss_conf             899999999999999999986979518
Q gi|254780689|r  315 PREVAMARRSIVQEAISLLKTNKIELS  341 (345)
Q Consensus       315 ~~dve~Aq~~I~~~~r~L~~~G~I~l~  341 (345)
                      -.|++++.+.|+..+++-..+|.-.+.
T Consensus       271 n~di~etv~~il~~i~~~~~r~~~~~~  297 (299)
T COG2074         271 NDDIDETVDRILEDIRKRTVRGLSLLE  297 (299)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             531999999999999999888765026


No 37 
>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=27.38  E-value=41  Score=13.83  Aligned_cols=30  Identities=20%  Similarity=0.203  Sum_probs=14.1

Q ss_pred             HCCCCCCCHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf             104566534889999761149799999975
Q gi|254780689|r   83 AGIGLTENSKNIESILEEGLEQNELEKLLN  112 (345)
Q Consensus        83 ~~~~~~g~~~~~~~lL~~al~~d~a~~ll~  112 (345)
                      ....+-|+...--...=.+.-+++|.+||.
T Consensus        41 DEL~LDGNprLNLAsFV~Twme~EA~KLm~   70 (493)
T TIGR01788        41 DELSLDGNPRLNLASFVTTWMEPEAEKLMD   70 (493)
T ss_pred             HHCCCCCCHHHHHHCCCCCCCCHHHHHHHH
T ss_conf             540457762223213247877767899997


No 38 
>cd07313 terB_like_2 tellurium resistance terB-like protein, subgroup 2. This family includes several uncharacterized bacterial proteins. Protein sequence homology analysis shows they are similar to tellurium resistance protein terB, but the function of this family is unknown.
Probab=26.12  E-value=43  Score=13.68  Aligned_cols=71  Identities=14%  Similarity=0.098  Sum_probs=52.7

Q ss_pred             HHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             689998519999999999998613899989999999999999851045665348899997611497999999754
Q gi|254780689|r   39 VSGKLLRHFTHAELKEIVASAKLLPEISPEELEDIIDEFESQFIAGIGLTENSKNIESILEEGLEQNELEKLLNK  113 (345)
Q Consensus        39 ~Aa~ilk~l~~~Ei~~i~~~m~~l~~i~~~~~~~vl~EF~~~~~~~~~~~g~~~~~~~lL~~al~~d~a~~ll~~  113 (345)
                      ..+..=.++++.|...|.....+.-.+++++.+.++............    .....+.+...++.+.=-.++..
T Consensus         8 eva~aDg~~~~~E~~~i~~~l~~~f~l~~~~~~~l~~~a~~~~~~~~~----l~~ft~~in~~~~~~~R~~li~~   78 (104)
T cd07313           8 EVARADGEYDEEERAAIDRLLAERFGLDAEEAAELLAEAEALEEEAPD----LYEFTSLIKEHFDYEERLELVEA   78 (104)
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCC----HHHHHHHHHHCCCHHHHHHHHHH
T ss_conf             999877487999999999999998785789999999999998865734----99999987333898999999999


No 39 
>TIGR02460 osmo_MPGsynth mannosyl-3-phosphoglycerate synthase; InterPro: IPR012812    This family consists of examples of mannosyl-3-phosphoglycerate synthase (MPGS), which together with mannosyl-3-phosphoglycerate phosphatase (MPGP), comprises a two-step pathway for mannosylglycerate biosynthesis. Mannosylglycerate is a compatible solute that tends to be restricted to extreme thermophiles of archaea and bacteria. Note that in Rhodothermus marinus, this pathway is one of two; the other is condensation of GDP-mannose with D-glycerate by mannosylglycerate synthase.; GO: 0050504 mannosyl-3-phosphoglycerate synthase activity, 0051479 mannosylglycerate biosynthetic process, 0005737 cytoplasm.
Probab=26.00  E-value=8.1  Score=18.50  Aligned_cols=95  Identities=12%  Similarity=0.178  Sum_probs=73.3

Q ss_pred             HHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH--------HCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             9999837989999999998404899989999999999997--------22344212363789999950177577999999
Q gi|254780689|r  161 ASVLLRFPNKIHADIMKRTVNLPKISPYIQKTIEKCIVEM--------LPQSNSNTSTGPEKVANLINELEKPQVDKLLT  232 (345)
Q Consensus       161 a~VL~~Lp~e~r~ev~~Ria~l~~v~~ev~~~ie~~L~~~--------l~~~~~~~~~G~~~vA~Iln~l~~~~~~~iL~  232 (345)
                      ..-|..+|.+.-.|++.++|=.=++--|=+..+|.+|+.-        .+++.....+-.+.=.|++..+..-+.++|+ 
T Consensus        40 ~~~l~~~d~~~L~d~~~~~aivvP~knE~L~llegVL~~IP~e~li~vvSnS~Re~vdRF~~EveL~r~f~~~~~~~i~-  118 (394)
T TIGR02460        40 AVSLKALDREELEDVLEKTAIVVPVKNEKLKLLEGVLSGIPHECLIIVVSNSKREPVDRFKMEVELVREFSRLTERKIL-  118 (394)
T ss_pred             CCCCCCCCHHHHHHHHHCCEEEEECCCCCHHHHHHHHHCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHCCCEE-
T ss_conf             4431206836799885085788711147414331134227883768888667489985667899999999986189518-


Q ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHCC
Q ss_conf             99986599999999741578998509
Q gi|254780689|r  233 SLQEVSKEAFDKVRPKVFLFDDLITL  258 (345)
Q Consensus       233 ~L~~~d~~la~~Ir~~mF~FeDl~~l  258 (345)
                      -+-+.||.+|+..|+-  -+.+++.-
T Consensus       119 i~hQ~DP~LA~Al~~~--~y~~~~~~  142 (394)
T TIGR02460       119 IIHQKDPALAEALKEV--GYESILGE  142 (394)
T ss_pred             EEECCCHHHHHHHHCC--CCCCCCCC
T ss_conf             9972887899997338--88675579


No 40 
>pfam05099 TerB Tellurite resistance protein TerB. This family contains the TerB tellurite resistance proteins from a a number of bacteria.
Probab=25.38  E-value=45  Score=13.59  Aligned_cols=103  Identities=14%  Similarity=0.131  Sum_probs=65.6

Q ss_pred             HHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHH-HCCC
Q ss_conf             899985199999999999986138999899999999999998510456653488999976114979999997544-1134
Q gi|254780689|r   40 SGKLLRHFTHAELKEIVASAKLLPEISPEELEDIIDEFESQFIAGIGLTENSKNIESILEEGLEQNELEKLLNKS-DISQ  118 (345)
Q Consensus        40 Aa~ilk~l~~~Ei~~i~~~m~~l~~i~~~~~~~vl~EF~~~~~~~~~~~g~~~~~~~lL~~al~~d~a~~ll~~~-~~~~  118 (345)
                      .++.=+++++.|++.+...+...-.++++..+.++..|........+    .....+.+...++.+....++.-. .+.-
T Consensus        33 vA~aDG~i~~~E~~~i~~~l~~~~~l~~~~~~~l~~~~~~~~~~~~~----l~~~~~~i~~~~~~~~r~~ll~~lw~va~  108 (140)
T pfam05099        33 VAKADGQVDEEERQAIRRLLRSRFGLDPEEAAALIELAEEAEQEAPD----LYEFTRAIKDHFDYEQRLALLEALWEVAL  108 (140)
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCC----HHHHHHHHHHHCCHHHHHHHHHHHHHHHH
T ss_conf             99877898999999999999998689999999999999998745557----99999999997699999999999999999


Q ss_pred             CCCCCHHHHHHCCCHHHHHHHHHCCCHHHH
Q ss_conf             456756789741998999999840386478
Q gi|254780689|r  119 ENNNSIWDHLKETDPGVIADFLSKEHPQTT  148 (345)
Q Consensus       119 ~~~~~~~~~L~~~~~~~La~~L~~EhPQti  148 (345)
                      .++  .++..+.-=-..++++|.=.|-+-+
T Consensus       109 ADG--~~d~~E~~~irria~lL~i~~~~f~  136 (140)
T pfam05099       109 ADG--ELDEYEDALIRRVAELLGLSHADFI  136 (140)
T ss_pred             HCC--CCCHHHHHHHHHHHHHCCCCHHHHH
T ss_conf             847--9999999999999988398999999


No 41 
>TIGR01078 arcA arginine deiminase; InterPro: IPR003876 This is a family of arginine deiminases, 3.5.3.6 from EC. The aligned region corresponds to the C-terminal of the protein. These enzymes catalyse the conversion of arginine + H2O to citrulline + NH3. Also found in this family is the Streptococcus anti tumor glycoprotein .; GO: 0016990 arginine deiminase activity, 0006527 arginine catabolic process.
Probab=24.67  E-value=29  Score=14.82  Aligned_cols=32  Identities=22%  Similarity=0.228  Sum_probs=17.9

Q ss_pred             HHHHHHHHHHCCCCCCCHHHHHHHHHHCCCHH--HHH
Q ss_conf             99999998510456653488999976114979--999
Q gi|254780689|r   74 IDEFESQFIAGIGLTENSKNIESILEEGLEQN--ELE  108 (345)
Q Consensus        74 l~EF~~~~~~~~~~~g~~~~~~~lL~~al~~d--~a~  108 (345)
                      -++|.+.++.++-   ..-++.+|+..++..-  .|+
T Consensus        48 Hd~Fa~~Lr~~g~---eVl~L~dL~~E~l~~~~qea~   81 (421)
T TIGR01078        48 HDQFANTLRDNGV---EVLYLEDLLAETLALPSQEAK   81 (421)
T ss_pred             HHHHHHHHHHCCC---CEEEHHHHHHHHHHHHHHHHH
T ss_conf             8999999987897---287444599999850289999


No 42 
>cd07920 Pumilio Pumilio-family RNA binding domain. Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canon
Probab=24.63  E-value=46  Score=13.50  Aligned_cols=95  Identities=16%  Similarity=0.247  Sum_probs=40.3

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHCC-CHHHHHHHHHCCCHHHHHHHHCCCCHHHHHH
Q ss_conf             378999995017757799999999986599999999741578998509-9789999983098889999853889899999
Q gi|254780689|r  211 GPEKVANLINELEKPQVDKLLTSLQEVSKEAFDKVRPKVFLFDDLITL-SSHDLSIVFNNISLEVLGKALHGTSIETQNA  289 (345)
Q Consensus       211 G~~~vA~Iln~l~~~~~~~iL~~L~~~d~~la~~Ir~~mF~FeDl~~l-~~~~l~~ll~evd~~~l~~ALkga~~e~~e~  289 (345)
                      |-..+=.+|.+.+.+....+++.|-..-..++..=-.+ ++.=.++.. ++.....++..+-.....+++.--..-+.|+
T Consensus       165 GCrViQr~le~~~~~~~~~l~~~I~~~~~~L~~dq~GN-YVVQ~ile~g~~~~~~~I~~~l~~~~~~LS~~Kf~SnVVEk  243 (322)
T cd07920         165 GCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGN-YVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNVVEK  243 (322)
T ss_pred             CHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCHH-HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             04899999971999999999999999799996174115-99999998099889999999999999999833776699999


Q ss_pred             HHHHCCHHHHHHHHHHH
Q ss_conf             99610089999999998
Q gi|254780689|r  290 ILHCLSNRQRKIIEENI  306 (345)
Q Consensus       290 il~nmS~Ra~~~l~eel  306 (345)
                      .+..-++..+..+-+++
T Consensus       244 cl~~~~~~~~~~ii~el  260 (322)
T cd07920         244 CLKHASKEERELIIDEI  260 (322)
T ss_pred             HHHHCCHHHHHHHHHHH
T ss_conf             99869999999999998


No 43 
>pfam04499 SAPS SIT4 phosphatase-associated protein. This family includes a conserved region from a group of yeast proteins that associate with the SIT4 phosphatase. This association is required for SIT4's role in G1 cyclin transcription and for bud formation. This family also includes homologous regions from other eukaryotes.
Probab=23.77  E-value=48  Score=13.39  Aligned_cols=11  Identities=27%  Similarity=0.274  Sum_probs=5.5

Q ss_pred             HHHHHHHHCCC
Q ss_conf             78999995017
Q gi|254780689|r  212 PEKVANLINEL  222 (345)
Q Consensus       212 ~~~vA~Iln~l  222 (345)
                      .+-+|++|+--
T Consensus       222 ~eLia~LL~~s  232 (380)
T pfam04499       222 VELIAELLHCS  232 (380)
T ss_pred             HHHHHHHHHCC
T ss_conf             99999999268


No 44 
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=23.40  E-value=49  Score=13.35  Aligned_cols=77  Identities=10%  Similarity=0.148  Sum_probs=31.0

Q ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHCC-CCCCCHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCHHHHHHCCCHHHHH
Q ss_conf             861389998999999999999985104-5665348899997611497999999754411344567567897419989999
Q gi|254780689|r   59 AKLLPEISPEELEDIIDEFESQFIAGI-GLTENSKNIESILEEGLEQNELEKLLNKSDISQENNNSIWDHLKETDPGVIA  137 (345)
Q Consensus        59 m~~l~~i~~~~~~~vl~EF~~~~~~~~-~~~g~~~~~~~lL~~al~~d~a~~ll~~~~~~~~~~~~~~~~L~~~~~~~La  137 (345)
                      |++-+....+.+..+.++++..+..-. ...|..+.+..++..++=     .+++..  ......++..+|-.+--..+.
T Consensus         1 ~~~~~~p~~~~~~~Ly~~~~~~L~~~~~r~~~~~e~AEDivQd~Fl-----rl~~~~--~~~~~~~~~a~Lf~iarNl~~   73 (172)
T PRK12523          1 MSSAQSPHSELVGALYRDHRGWLLAWLRRNLACRQRAEDLSQDTFV-----RLLGRP--ELPTPREPRAFLAAVAKGLMF   73 (172)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH-----HHHHCC--CCCCCCCHHHHHHHHHHHHHH
T ss_conf             9999997399999999999999999999994988689999999999-----998277--656734599999999999999


Q ss_pred             HHHHC
Q ss_conf             99840
Q gi|254780689|r  138 DFLSK  142 (345)
Q Consensus       138 ~~L~~  142 (345)
                      ++++.
T Consensus        74 D~~Rr   78 (172)
T PRK12523         74 DHFRR   78 (172)
T ss_pred             HHHHH
T ss_conf             99998


No 45 
>COG2411 Uncharacterized conserved protein [Function unknown]
Probab=23.17  E-value=49  Score=13.32  Aligned_cols=102  Identities=21%  Similarity=0.245  Sum_probs=57.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHCCCHHHHHH-HHCCCCHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             7999999999865999999997415789985099789999983098889999-853889899999996100899999999
Q gi|254780689|r  226 QVDKLLTSLQEVSKEAFDKVRPKVFLFDDLITLSSHDLSIVFNNISLEVLGK-ALHGTSIETQNAILHCLSNRQRKIIEE  304 (345)
Q Consensus       226 ~~~~iL~~L~~~d~~la~~Ir~~mF~FeDl~~l~~~~l~~ll~evd~~~l~~-ALkga~~e~~e~il~nmS~Ra~~~l~e  304 (345)
                      ..+++++.|....+++-..----.+-|+++-.++......-....|+-.+|- ||..         |.|+|.|-...++.
T Consensus        78 sreELi~~LkriYg~lr~ed~VTIi~Fe~v~~~d~~i~~~~y~g~dp~eIA~laLe~---------l~~Ls~~~~~iL~~  148 (188)
T COG2411          78 SREELIEELKRIYGELRDEDIVTIIEFEVVEKLDKPILDLPYEGRDPIEIARLALEH---------LDNLSERDKRILEL  148 (188)
T ss_pred             CHHHHHHHHHHHCCCCCCCCEEEEEEEEEEHHCCCHHHHCCCCCCCHHHHHHHHHHH---------CCCCCHHHHHHHHH
T ss_conf             599999999998286788963899998870102625564557899989999999874---------32589889999999


Q ss_pred             HHHH--------CCCCCCHHHHHHHHHHHHHHHHHHHHCCCE
Q ss_conf             9850--------058999899999999999999999986979
Q gi|254780689|r  305 NIVL--------NDSSIAPREVAMARRSIVQEAISLLKTNKI  338 (345)
Q Consensus       305 el~~--------~~g~v~~~dve~Aq~~I~~~~r~L~~~G~I  338 (345)
                      =++.        ..|++..+  -.-|+-.-.....|-.+|-|
T Consensus       149 ~~~~gslRkaA~klgg~~kr--~~ir~vLrKay~~L~~rGli  188 (188)
T COG2411         149 FVEEGSLRKAAKKLGGLEKR--GRIRRVLRKAYHELKKRGLI  188 (188)
T ss_pred             HHHCCCHHHHHHHHCCCCHH--HHHHHHHHHHHHHHHHCCCC
T ss_conf             99759299999995584120--38999999999999864479


No 46 
>TIGR02784 addA_alphas double-strand break repair helicase AddA; InterPro: IPR014151   AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologues between the alphaproteobacteria and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species..
Probab=22.97  E-value=50  Score=13.29  Aligned_cols=66  Identities=14%  Similarity=0.226  Sum_probs=33.8

Q ss_pred             CCHHHHHHHHHHHHCCHHHHH----HHHH------CC-HHHHHHHHHHHH--HCCCCCHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             686879999999838146899----9851------99-999999999986--138999899999999999998510456
Q gi|254780689|r   22 LTQKDKATAILLAMEKQVSGK----LLRH------FT-HAELKEIVASAK--LLPEISPEELEDIIDEFESQFIAGIGL   87 (345)
Q Consensus        22 Ltg~eKAAilLl~LGee~Aa~----ilk~------l~-~~Ei~~i~~~m~--~l~~i~~~~~~~vl~EF~~~~~~~~~~   87 (345)
                      |+|.+=.+||-++--+-+||+    ||+.      |+ |.+++.=-.++.  .-+.++.+.+...=.=|..-+.+=+|+
T Consensus        36 L~G~~P~~ILCLTYTKAAAAeMq~RvF~rL~~Wa~L~nD~~L~~~l~~LeGe~~~~~da~~L~~AR~LFArALETPGGL  114 (1190)
T TIGR02784        36 LAGTEPSKILCLTYTKAAAAEMQNRVFKRLGEWAVLDNDADLRARLEALEGEAGKRPDAAKLAEARRLFARALETPGGL  114 (1190)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHCCCCCC
T ss_conf             1787831000205558999999999875510444388868899999984254688888889999989999974178776


No 47 
>TIGR00455 apsK adenylylsulfate kinase; InterPro: IPR002891 Enzyme that catalyses the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulphate. This domain contains an ATP binding P-loop motif .; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity transferring phosphorus-containing groups, 0000103 sulfate assimilation.
Probab=22.90  E-value=31  Score=14.60  Aligned_cols=21  Identities=29%  Similarity=0.249  Sum_probs=13.5

Q ss_pred             HHHHHHHHHHHHCCCEECCCC
Q ss_conf             999999999998697951888
Q gi|254780689|r  323 RSIVQEAISLLKTNKIELSNP  343 (345)
Q Consensus       323 ~~I~~~~r~L~~~G~I~l~~~  343 (345)
                      |.|..+++-|.+.|.|+|.+-
T Consensus        78 RRigEVa~L~~~~G~i~ltsf   98 (187)
T TIGR00455        78 RRIGEVAKLLVRNGVIVLTSF   98 (187)
T ss_pred             CEEHHHHHHHHHCCEEEEEEE
T ss_conf             353264677764793899842


No 48 
>pfam04751 DUF615 Protein of unknown function (DUF615). This family of bacterial proteins has no known function.
Probab=22.90  E-value=50  Score=13.28  Aligned_cols=75  Identities=16%  Similarity=0.264  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCC
Q ss_conf             68799999998381468999851999999999999861389998999999999999985104566534889999761149
Q gi|254780689|r   24 QKDKATAILLAMEKQVSGKLLRHFTHAELKEIVASAKLLPEISPEELEDIIDEFESQFIAGIGLTENSKNIESILEEGLE  103 (345)
Q Consensus        24 g~eKAAilLl~LGee~Aa~ilk~l~~~Ei~~i~~~m~~l~~i~~~~~~~vl~EF~~~~~~~~~~~g~~~~~~~lL~~al~  103 (345)
                      ..-|.|.-+-.||++     |-.|++.++.++        ++|. .+...+.+|... .++++...-..|+.+++... +
T Consensus         6 q~KRe~~~lq~LG~~-----L~~L~~~ql~~l--------~l~e-~L~~AI~~~~~i-~~~~A~rRQlqyIGKlmR~~-D   69 (153)
T pfam04751         6 ELKREAEALQDLGEE-----LVELSKDQLAKL--------PLDE-ELRDAIAEARRI-TKHEARRRQLQYIGKLMREE-D   69 (153)
T ss_pred             HHHHHHHHHHHHHHH-----HHHCCHHHHHCC--------CCCH-HHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHC-C
T ss_conf             999999999999999-----982999999629--------9988-999999997503-40068999999999998656-8


Q ss_pred             HHHHHHHHHHH
Q ss_conf             79999997544
Q gi|254780689|r  104 QNELEKLLNKS  114 (345)
Q Consensus       104 ~d~a~~ll~~~  114 (345)
                      .+....-++.+
T Consensus        70 ~e~i~~~l~~~   80 (153)
T pfam04751        70 PEAIRAALDKL   80 (153)
T ss_pred             HHHHHHHHHHH
T ss_conf             99999999987


No 49 
>cd03397 PAP2_acid_phosphatase PAP2, bacterial acid phosphatase or class A non-specific acid phosphatases. These enzymes catalyze phosphomonoester hydrolysis, with optimal activity in low pH conditions. They are secreted into the periplasmic space, and their physiological role remains to be determined.
Probab=22.86  E-value=50  Score=13.28  Aligned_cols=23  Identities=22%  Similarity=0.280  Sum_probs=17.9

Q ss_pred             HHHHHHHHCCHHHHHHHHHHCCH
Q ss_conf             78899995788899999983798
Q gi|254780689|r  147 TTAYVLSMMPPSIGASVLLRFPN  169 (345)
Q Consensus       147 tiAlILs~L~~~~Aa~VL~~Lp~  169 (345)
                      ..|+||+++-|+++..++.+=-+
T Consensus       162 ~~a~~la~~~P~~~~~~~~r~~~  184 (232)
T cd03397         162 AWALILAELVPERADEILARGSE  184 (232)
T ss_pred             HHHHHHHHHCHHHHHHHHHHHHH
T ss_conf             99999998787449999999999


No 50 
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY; InterPro: IPR014154   This entry represents pleiotropic repressors in Bacillus subtilis, CodY, and other Firmicutes (low-GC Gram-positive bacteria) that respond to intracellular levels of GTP and branched chain amino acids. All have a C-terminal helix-turn-helix DNA-binding region..
Probab=22.74  E-value=46  Score=13.50  Aligned_cols=50  Identities=24%  Similarity=0.253  Sum_probs=30.5

Q ss_pred             HHHHCCH---HHHHHHHHHHHHCCCCCCHH----HHHHHHHHHHHHHHHHHHCCCEE
Q ss_conf             9961008---99999999985005899989----99999999999999999869795
Q gi|254780689|r  290 ILHCLSN---RQRKIIEENIVLNDSSIAPR----EVAMARRSIVQEAISLLKTNKIE  339 (345)
Q Consensus       290 il~nmS~---Ra~~~l~eel~~~~g~v~~~----dve~Aq~~I~~~~r~L~~~G~I~  339 (345)
                      -.+++|=   +|.+.|=+||+=.-|-+--|    .|==.|.=||+..|+|+.+|-|+
T Consensus       177 Ai~TLSYSEL~AV~aIf~ELdG~EG~LvAS~IAD~vGITRSVIVNALRKlESAGvIE  233 (255)
T TIGR02787       177 AINTLSYSELEAVEAIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIE  233 (255)
T ss_pred             HHHHCCHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHCCEEE
T ss_conf             987202889999999984228996627753020712660335545434442076413


No 51 
>pfam11625 DUF3253 Protein of unknown function (DUF3253). This bacterial family of proteins has no known function.
Probab=22.45  E-value=51  Score=13.23  Aligned_cols=51  Identities=31%  Similarity=0.378  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCHHHHHHHH---------HHHHHHHHHHHHCCCEECCCCC
Q ss_conf             899999996100899999999985005899989999999---------9999999999986979518888
Q gi|254780689|r  284 IETQNAILHCLSNRQRKIIEENIVLNDSSIAPREVAMAR---------RSIVQEAISLLKTNKIELSNPI  344 (345)
Q Consensus       284 ~e~~e~il~nmS~Ra~~~l~eel~~~~g~v~~~dve~Aq---------~~I~~~~r~L~~~G~I~l~~~~  344 (345)
                      ..+.+.|+.-+.+|..          ..++-+|||..|-         ..+=..+++|+.+|+|++.-++
T Consensus         5 ~~ie~~Il~ll~~R~~----------~~ticPsevARal~~~~WR~lm~~vR~aA~~L~~~G~i~ItqkG   64 (83)
T pfam11625         5 AEIEAAILRLLAARGP----------GKSICPSEVARALAPDDWRPLMPPVRRAARRLAEAGEVEITQKG   64 (83)
T ss_pred             HHHHHHHHHHHHHCCC----------CCCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCEEEEECC
T ss_conf             9999999999996599----------89809899998868472798869999999999878968997799


No 52 
>TIGR01589 A_thal_3526 uncharacterized plant-specific domain TIGR01589; InterPro: IPR006476   This plant-specific family of proteins are defined by an uncharacterised region 57 residues in length. It is found toward the N terminus of most proteins that contain it. Examples include at least several proteins from Arabidopsis thaliana and Oryza sativa. The function of the proteins are unknown..
Probab=22.29  E-value=51  Score=13.21  Aligned_cols=38  Identities=21%  Similarity=0.425  Sum_probs=26.5

Q ss_pred             HHHCCCH-HHHHHHHHHHHCCCCCCCCHHHHHHCCCHHH
Q ss_conf             7611497-9999997544113445675678974199899
Q gi|254780689|r   98 LEEGLEQ-NELEKLLNKSDISQENNNSIWDHLKETDPGV  135 (345)
Q Consensus        98 L~~al~~-d~a~~ll~~~~~~~~~~~~~~~~L~~~~~~~  135 (345)
                      |..-++. +-++.|.++..+.+.-...+|..|.+-+++=
T Consensus        12 l~~YMS~eE~~~~l~~~~~i~~~~T~~vW~~L~keN~dF   50 (57)
T TIGR01589        12 LQLYMSKEETVEFLLENAKISPKFTKLVWKKLEKENADF   50 (57)
T ss_pred             HHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCHHH
T ss_conf             731488899999998752689453327889998846888


No 53 
>pfam08006 DUF1700 Protein of unknown function (DUF1700). This family contains many hypothetical bacterial proteins and two putative membrane proteins.
Probab=21.45  E-value=53  Score=13.09  Aligned_cols=54  Identities=22%  Similarity=0.303  Sum_probs=32.0

Q ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             86138999899999999999998510456653488999976114979999997544
Q gi|254780689|r   59 AKLLPEISPEELEDIIDEFESQFIAGIGLTENSKNIESILEEGLEQNELEKLLNKS  114 (345)
Q Consensus        59 m~~l~~i~~~~~~~vl~EF~~~~~~~~~~~g~~~~~~~lL~~al~~d~a~~ll~~~  114 (345)
                      -..|+.+|+++.++++++|.+.+..+..--.+.+++-+  +=.-|.+-|+++....
T Consensus        11 ~~~L~~lp~~e~~~il~~y~e~f~~~~~~G~se~ei~~--~LG~P~~iA~ei~a~~   64 (181)
T pfam08006        11 ESSLKKLPEEERKDILYDYEEHFYEGEEEGKSEEEIIK--ELGNPKTIAKELKADY   64 (181)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHH--HHCCHHHHHHHHHHHH
T ss_conf             99886599999999999999999987668999999998--8299999999999874


No 54 
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=21.10  E-value=54  Score=13.05  Aligned_cols=35  Identities=11%  Similarity=0.076  Sum_probs=17.8

Q ss_pred             HHCCCHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHHHH
Q ss_conf             8309888999985388989999999610089999999998
Q gi|254780689|r  267 FNNISLEVLGKALHGTSIETQNAILHCLSNRQRKIIEENI  306 (345)
Q Consensus       267 l~evd~~~l~~ALkga~~e~~e~il~nmS~Ra~~~l~eel  306 (345)
                      +.+.+.+.++-.|.-....++.++.     |+...|++-|
T Consensus       143 ~eg~s~~EIA~~l~is~~tVk~~l~-----rA~~~Lr~~L  177 (179)
T PRK12514        143 LEGLSYKELAERHDVPLNTMRTWLR-----RSLLKLRECL  177 (179)
T ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHH-----HHHHHHHHHH
T ss_conf             0699899999988909999999999-----9999999985


No 55 
>TIGR01992 PTS-IIBC-Tre PTS system, trehalose-specific IIBC component; InterPro: IPR011296   This entry represents the fused enzyme II B and C components of the trehalose-specific PTS sugar transporter system . Trehalose is converted to trehalose-6-phosphate in the process of translocation into the cell. These transporters lack their own IIA domains and instead use the glucose IIA protein (IIAglc or Crr) . The exceptions to this rule are Staphylococci and Streptococci which contain their own A domain as a C-terminal fusion. This family is closely related to the sucrose transporting PTS IIBC enzymes described by the IIB component and the IIC component (IPR004719 from INTERPRO), respectively. In Escherichia coli, Bacillus subtilis and Pseudomonas fluorescens the presence of this gene is associated with the presence of trehalase which degrades T6P to glucose and glucose-6-P. Trehalose may also be transported (in Salmonella) via the mannose PTS or galactose permease systems , or (in Sinorhizobium, Thermococcus and Sulfolobus, for instance) by ABC transporters , , .; GO: 0015574 trehalose transmembrane transporter activity, 0015771 trehalose transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=21.05  E-value=54  Score=13.04  Aligned_cols=60  Identities=18%  Similarity=0.317  Sum_probs=42.8

Q ss_pred             HHHHHHHHHCC-HHHHHHHHHHHHHCCC-------CCHHHHHHH---------------------HHHHHHHHHHCCCCC
Q ss_conf             46899985199-9999999999861389-------998999999---------------------999999985104566
Q gi|254780689|r   38 QVSGKLLRHFT-HAELKEIVASAKLLPE-------ISPEELEDI---------------------IDEFESQFIAGIGLT   88 (345)
Q Consensus        38 e~Aa~ilk~l~-~~Ei~~i~~~m~~l~~-------i~~~~~~~v---------------------l~EF~~~~~~~~~~~   88 (345)
                      +.|.+++.+.. .+=|+..++|++||+-       ++++.++++                     +++||+++.+.+++.
T Consensus         2 ~da~~l~e~iGG~eNi~~atHCvTRLRfvL~D~~~v~~~~l~~~~~VKG~F~~~GQFQVvIGpg~V~~~Y~~l~~~tG~~   81 (489)
T TIGR01992         2 KDAKALLEAIGGKENIEAATHCVTRLRFVLKDPSKVDVEALEQIDLVKGSFTTAGQFQVVIGPGDVEKVYAELIKETGIA   81 (489)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCCEEECCCEEEEEECCCCHHHHHHHHHHHHCCC
T ss_conf             14789998527820166875688888886168133785676368822441424852799863798799999999741711


Q ss_pred             CCHH-HHHHH
Q ss_conf             5348-89999
Q gi|254780689|r   89 ENSK-NIESI   97 (345)
Q Consensus        89 g~~~-~~~~l   97 (345)
                      +.++ .+++-
T Consensus        82 ~~~K~~vK~a   91 (489)
T TIGR01992        82 EVTKEEVKKA   91 (489)
T ss_pred             CCCHHHHHHH
T ss_conf             3678999998


No 56 
>KOG0467 consensus
Probab=21.02  E-value=54  Score=13.04  Aligned_cols=38  Identities=21%  Similarity=0.234  Sum_probs=28.1

Q ss_pred             HHHHHHHHC----CCCHHHHHHHHHHCCHHHHHHHHHHHHHC
Q ss_conf             889999853----88989999999610089999999998500
Q gi|254780689|r  272 LEVLGKALH----GTSIETQNAILHCLSNRQRKIIEENIVLN  309 (345)
Q Consensus       272 ~~~l~~ALk----ga~~e~~e~il~nmS~Ra~~~l~eel~~~  309 (345)
                      ...|+.|+-    .++.++--++|..+|+|..+.|.|||...
T Consensus       745 ~pRl~~aMYsC~I~t~~e~LGkvYAVlskR~gkVLsEem~Eg  786 (887)
T KOG0467         745 SPRIMAAMYSCDIQTASEVLGKVYAVLSKRHGKVLSEEMKEG  786 (887)
T ss_pred             CHHHHHHHEEEEEEEHHHHHHHHHHHHHHHCCHHHHHHHHCC
T ss_conf             877766656434532387755678544220132101566378


No 57 
>pfam01984 dsDNA_bind Double-stranded DNA-binding domain. This domain is believed to bind double-stranded DNA of 20 bases length.
Probab=20.10  E-value=57  Score=12.91  Aligned_cols=50  Identities=8%  Similarity=0.263  Sum_probs=25.4

Q ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCHHH
Q ss_conf             99840489998999999999999722344212363789999950177577
Q gi|254780689|r  177 KRTVNLPKISPYIQKTIEKCIVEMLPQSNSNTSTGPEKVANLINELEKPQ  226 (345)
Q Consensus       177 ~Ria~l~~v~~ev~~~ie~~L~~~l~~~~~~~~~G~~~vA~Iln~l~~~~  226 (345)
                      .|++++.-|-|+....||..|......+.-...-.-..+..||+.+....
T Consensus        47 eRL~ri~lvkPe~A~~VE~~Liqlaq~G~l~~kise~~L~~iL~~is~~~   96 (105)
T pfam01984        47 ERLNRIRLVKPERAEAVENQLIQLAQSGRIRGKITEEQLKEILEQIAPQK   96 (105)
T ss_pred             HHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCC
T ss_conf             99980220388889999999999998599889849999999999974510


Done!