Query         gi|254780379|ref|YP_003064792.1| flagellar hook-basal body protein FliE [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 108
No_of_seqs    102 out of 524
Neff          6.0 
Searched_HMMs 39220
Date          Sun May 29 15:19:36 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780379.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK00253 fliE flagellar hook-b 100.0 6.3E-28 1.6E-32  185.2  13.6  102    4-108     2-105 (105)
  2 PRK00732 fliE flagellar hook-b 100.0 1.6E-27 4.1E-32  182.9  13.5  103    2-108     1-103 (103)
  3 PRK03907 fliE flagellar hook-b  99.9 3.1E-27 7.8E-32  181.2  12.4   85   24-108    15-100 (100)
  4 pfam02049 FliE Flagellar hook-  99.9 2.2E-25 5.6E-30  170.2  12.2   84   25-108    13-97  (97)
  5 PRK12728 fliE flagellar hook-b  99.9 2.4E-25 6.2E-30  170.0  11.8   77   32-108    20-97  (97)
  6 COG1677 FliE Flagellar hook-ba  99.9 8.1E-25 2.1E-29  166.8  12.3   72   37-108    33-105 (105)
  7 PRK00790 fliE flagellar hook-b  99.9   9E-25 2.3E-29  166.6  12.3   83   26-108    17-99  (99)
  8 TIGR00205 fliE flagellar hook-  99.9 9.7E-22 2.5E-26  148.6  10.8   79   30-108    34-114 (114)
  9 PRK12729 fliE flagellar hook-b  99.8 3.6E-19 9.2E-24  133.4   8.3   71   37-107    55-127 (127)
 10 PRK01699 fliE flagellar hook-b  99.6 1.8E-15 4.6E-20  111.5   9.9   69   40-108    30-99  (99)
 11 PRK01482 fliE flagellar hook-b  99.4 2.5E-12 6.5E-17   92.8   8.6   73   34-106    33-107 (108)
 12 COG1166 SpeA Arginine decarbox  31.5      21 0.00054   16.3   1.0   26   48-73    412-437 (652)
 13 KOG2280 consensus               29.0      43  0.0011   14.5   6.6   51   55-105   547-600 (829)
 14 pfam07002 Copine Copine. This   26.8      17 0.00044   16.9  -0.1   50   33-83     81-133 (145)

No 1  
>PRK00253 fliE flagellar hook-basal body protein FliE; Reviewed
Probab=99.96  E-value=6.3e-28  Score=185.25  Aligned_cols=102  Identities=18%  Similarity=0.282  Sum_probs=89.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC--CCHHHHHHHHHH
Q ss_conf             676528999966545421101367777778888665999999999999999999999999998148--989999999999
Q gi|254780379|r    4 EQIQGTNSFISHTDTIGMRYDFTQNSNEEGGSSPISFSALLQDMAKGAIGDMEKAENVSLAALQGK--TSMREAVDHIMQ   81 (108)
Q Consensus         4 ~~i~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~sF~~~L~~~i~~vn~~q~~a~~~~~~~~~G~--~dl~~vmia~~k   81 (108)
                      +.+++|++..+.++........   .+..+.+++.+|+++|+++|++||+.|++|+....+|++|+  +|||+|||+.+|
T Consensus         2 s~i~~i~~~l~qm~a~a~~a~~---~~~~~~a~~~~F~~~L~~al~~Vn~~Q~~A~~~~~~~~~G~~~v~l~~vMIa~qk   78 (105)
T PRK00253          2 SAIQGIEGVLSQLQATAMEASG---TPKPLTAPTVSFAGMLKAALDKVNDTQQAARTLAEKFELGDPGVDLNDVMIALQK   78 (105)
T ss_pred             CCHHHHHHHHHHHHHHHHHHCC---CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH
T ss_conf             5056599999999999998659---9999999999889999999999999999999999999869998879999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             999999999999999999999961889
Q gi|254780379|r   82 AERTLNLSIALRDKILSAVSEVSKMQI  108 (108)
Q Consensus        82 A~lsl~~~vqVRnK~v~AYqeImrMqV  108 (108)
                      |+++|++++|||||+|+||||||||||
T Consensus        79 A~lsfq~~~qVRNK~v~AYqEIM~MqV  105 (105)
T PRK00253         79 ASVSFQAGIQVRNKLVAAYQEIMNMQV  105 (105)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             888999999999999999999982899


No 2  
>PRK00732 fliE flagellar hook-basal body protein FliE; Reviewed
Probab=99.95  E-value=1.6e-27  Score=182.87  Aligned_cols=103  Identities=20%  Similarity=0.349  Sum_probs=88.2

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             64676528999966545421101367777778888665999999999999999999999999998148989999999999
Q gi|254780379|r    2 MIEQIQGTNSFISHTDTIGMRYDFTQNSNEEGGSSPISFSALLQDMAKGAIGDMEKAENVSLAALQGKTSMREAVDHIMQ   81 (108)
Q Consensus         2 Mi~~i~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~sF~~~L~~~i~~vn~~q~~a~~~~~~~~~G~~dl~~vmia~~k   81 (108)
                      ||+++..-+++....+..+....    .++.+..++++|+++|+++++++|+.|+++|....++++|++|+||||++++|
T Consensus         1 m~t~~~Aa~AY~a~~~~~~~~~~----~~~~~~~~G~sF~~~Lk~Ai~~v~~~q~~ae~~~~a~~~G~adl~~vv~a~~~   76 (103)
T PRK00732          1 MATPLSAANAYASLARMADPSGA----GGGGGSGGGPSFGALLKDAMGSVLEAGRKSDAQTVAMASGKANVMDVVTAVAE   76 (103)
T ss_pred             CCCHHHHHHHHHHHHHHCCCCCC----CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
T ss_conf             97648999999999974165567----88888989977999999999999999999999999998489979999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             999999999999999999999961889
Q gi|254780379|r   82 AERTLNLSIALRDKILSAVSEVSKMQI  108 (108)
Q Consensus        82 A~lsl~~~vqVRnK~v~AYqeImrMqV  108 (108)
                      |+++|+++++||||+|+||||||||||
T Consensus        77 a~~~lq~~v~vRnk~v~AYqeImrMpi  103 (103)
T PRK00732         77 TDVAVSTLVSVRDRVIQAYEEIMRMPI  103 (103)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             999999999999999999999973899


No 3  
>PRK03907 fliE flagellar hook-basal body protein FliE; Reviewed
Probab=99.95  E-value=3.1e-27  Score=181.19  Aligned_cols=85  Identities=19%  Similarity=0.244  Sum_probs=76.8

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             13677777788886659999999999999999999999999981489-89999999999999999999999999999999
Q gi|254780379|r   24 DFTQNSNEEGGSSPISFSALLQDMAKGAIGDMEKAENVSLAALQGKT-SMREAVDHIMQAERTLNLSIALRDKILSAVSE  102 (108)
Q Consensus        24 ~~~~~~~~~~~~~~~sF~~~L~~~i~~vn~~q~~a~~~~~~~~~G~~-dl~~vmia~~kA~lsl~~~vqVRnK~v~AYqe  102 (108)
                      ....+.+......+++|+++|++++++||+.|..|+....++++|+. |+|+|||+++||+++|++++|||||+|+||||
T Consensus        15 ~~~~~~~~~~~~~g~~F~~~L~~ai~~VN~~Q~~ad~~~~~la~G~~~dlHevmIa~ekA~ls~ql~~qVRNK~veAYqE   94 (100)
T PRK03907         15 KSETSKSTFKEGKGGEFAKMLKQSINELNKTQEQSDKALADIATGQVKDLHQAAIAIGKAETSMKLMLEVRNKAISAYKE   94 (100)
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             57777775456887649999999999999999999999999976886769999999999888999999999999999999


Q ss_pred             HHCCCC
Q ss_conf             961889
Q gi|254780379|r  103 VSKMQI  108 (108)
Q Consensus       103 ImrMqV  108 (108)
                      ||||||
T Consensus        95 IMRMQI  100 (100)
T PRK03907         95 ILRTQI  100 (100)
T ss_pred             HHHCCC
T ss_conf             985359


No 4  
>pfam02049 FliE Flagellar hook-basal body complex protein FliE.
Probab=99.93  E-value=2.2e-25  Score=170.19  Aligned_cols=84  Identities=20%  Similarity=0.309  Sum_probs=77.0

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             367777778888665999999999999999999999999998148-9899999999999999999999999999999999
Q gi|254780379|r   25 FTQNSNEEGGSSPISFSALLQDMAKGAIGDMEKAENVSLAALQGK-TSMREAVDHIMQAERTLNLSIALRDKILSAVSEV  103 (108)
Q Consensus        25 ~~~~~~~~~~~~~~sF~~~L~~~i~~vn~~q~~a~~~~~~~~~G~-~dl~~vmia~~kA~lsl~~~vqVRnK~v~AYqeI  103 (108)
                      .....+.....++.+|+++|++++++||+.|.+++....++++|+ .|+|+|||+++||+++|++++|||||+|+||+||
T Consensus        13 ~~~~~~~~~~~~~~sF~~~l~~a~~~vn~~q~~a~~~~~~~~~G~~~~l~~vmia~~kA~~s~q~~~qVRnK~v~AYqei   92 (97)
T pfam02049        13 GASAASASAAAGGASFADVLKQALDKVNDLQQKADALAEAFATGKSVDLHEVMIAVQKASLSFQATVQVRNKLVEAYQEI   92 (97)
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             88877888899998899999999999999999999999999848988799999999999999999999999999999999


Q ss_pred             HCCCC
Q ss_conf             61889
Q gi|254780379|r  104 SKMQI  108 (108)
Q Consensus       104 mrMqV  108 (108)
                      |||||
T Consensus        93 mrMqv   97 (97)
T pfam02049        93 MRMQI   97 (97)
T ss_pred             HCCCC
T ss_conf             81889


No 5  
>PRK12728 fliE flagellar hook-basal body protein FliE; Provisional
Probab=99.93  E-value=2.4e-25  Score=169.96  Aligned_cols=77  Identities=22%  Similarity=0.396  Sum_probs=72.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             78888665999999999999999999999999998148-989999999999999999999999999999999961889
Q gi|254780379|r   32 EGGSSPISFSALLQDMAKGAIGDMEKAENVSLAALQGK-TSMREAVDHIMQAERTLNLSIALRDKILSAVSEVSKMQI  108 (108)
Q Consensus        32 ~~~~~~~sF~~~L~~~i~~vn~~q~~a~~~~~~~~~G~-~dl~~vmia~~kA~lsl~~~vqVRnK~v~AYqeImrMqV  108 (108)
                      .+...+.+|+++|++++++||+.|..|+....+|++|+ .|+|+|||+.+||+++|++++|||||+|+||+|||||||
T Consensus        20 ~p~~~~~sF~~~L~~al~~Vn~~Q~~a~~~~~~~~~G~~~~lhevmia~qkA~ls~q~~~qVRNK~v~AYqEIMrMqv   97 (97)
T PRK12728         20 TPSEKQVSFSDFLKEALNKVNDKQVEADNSTEALIKGEDVDLHDVMIAAQKASISLQLAVQVRNKVVEAYQEIMRMQL   97 (97)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             999998889999999999999999999999999984898889999999999999999999999999999999982889


No 6  
>COG1677 FliE Flagellar hook-basal body protein [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=99.92  E-value=8.1e-25  Score=166.84  Aligned_cols=72  Identities=28%  Similarity=0.417  Sum_probs=69.6

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             6659999999999999999999999999981489-89999999999999999999999999999999961889
Q gi|254780379|r   37 PISFSALLQDMAKGAIGDMEKAENVSLAALQGKT-SMREAVDHIMQAERTLNLSIALRDKILSAVSEVSKMQI  108 (108)
Q Consensus        37 ~~sF~~~L~~~i~~vn~~q~~a~~~~~~~~~G~~-dl~~vmia~~kA~lsl~~~vqVRnK~v~AYqeImrMqV  108 (108)
                      +.+|+++|+++++++|+.|+.|+..+.+|++|+. ++|||||+++||+++|+++++||||+|+||||||||||
T Consensus        33 ~~sF~~~L~~ai~~vn~~Q~~a~~~~~~~~~G~~~~l~dVmia~~KAs~sLq~ai~VRnKlV~AYqEImrmqi  105 (105)
T COG1677          33 GASFAEVLKNAIDDVNDTQKKAEKASEAFILGQAGDLHDVMIAMQKASVSLQTAIQVRNKLVSAYQEIMRMQI  105 (105)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             3339999999999999999999999999984896409999999999999999999999999999999986769


No 7  
>PRK00790 fliE flagellar hook-basal body protein FliE; Reviewed
Probab=99.92  E-value=9e-25  Score=166.58  Aligned_cols=83  Identities=33%  Similarity=0.517  Sum_probs=76.8

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             67777778888665999999999999999999999999998148989999999999999999999999999999999961
Q gi|254780379|r   26 TQNSNEEGGSSPISFSALLQDMAKGAIGDMEKAENVSLAALQGKTSMREAVDHIMQAERTLNLSIALRDKILSAVSEVSK  105 (108)
Q Consensus        26 ~~~~~~~~~~~~~sF~~~L~~~i~~vn~~q~~a~~~~~~~~~G~~dl~~vmia~~kA~lsl~~~vqVRnK~v~AYqeImr  105 (108)
                      ..++...+.+++.+|+++|+++++++++.++++|..+.++++|++|+|+||+++++|+++|+++++||||+|+|||||||
T Consensus        17 ~~~pa~~~~a~g~sF~~~l~~a~~~~~~t~~~aE~~s~~~~~Gkad~~~vv~a~~~Ae~slq~~v~VRdKvv~AYqEI~R   96 (99)
T PRK00790         17 ASAPAAAPAAPGASFASVLGQAAGDAVQTLKAAEATSIAAIKGKADPRAVVEAVMQAEQALQTAVAIRDKVVEAYQEILR   96 (99)
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             78988899999977999999999999999999999999987389979999999999999999999999999999999981


Q ss_pred             CCC
Q ss_conf             889
Q gi|254780379|r  106 MQI  108 (108)
Q Consensus       106 MqV  108 (108)
                      |||
T Consensus        97 M~i   99 (99)
T PRK00790         97 MPI   99 (99)
T ss_pred             CCC
T ss_conf             889


No 8  
>TIGR00205 fliE flagellar hook-basal body complex protein (FliE); InterPro: IPR001624   Four genes from the major Bacillus subtilis chemotaxis locus have been shown to encode proteins that are similar to the Salmonella typhimurium FlgB, FlgC, FlgG and FliF proteins; a further gene product is similar to the Escherichia coli FliE protein . All of these proteins are thought to form part of the hook-basal body complex of the bacterial flagella . The FlgB, FlgC and FlgG proteins are components of the proximal and distal rods; FliF forms the M-ring that anchors the rod assembly to the membrane; but the role of FliE has not yet been determined . The similarity between the proteins in these two organisms suggests that the structures of the M-ring and the rod may be similar . Nevertheless, some differences in size and amino acid composition between some of the homologues suggest the basal body proteins may be organised slightly differently within B. subtilis .   From gel electrophoresis and autoradiography of 35S-labelled S. typhimurium hook-basal body complexes and the deduced number of sulphur-containing residues in FliE, the stoichiometry of the protein in the hook-basal body complex has been estimated to be about nine subunits . FliE does not undergo cleavage of a signal peptide, nor does it show any similarity to the axial components like the rod or hook proteins, which are thought to be exported by the flagellum-specific export pathway . On this evidence, it has been suggested that FliE may be in the vicinity of the MS ring, perhaps acting as an adaptor protein between ring and rod substructures .; GO: 0003774 motor activity, 0005198 structural molecule activity, 0001539 ciliary or flagellar motility, 0009288 flagellin-based flagellum.
Probab=99.87  E-value=9.7e-22  Score=148.62  Aligned_cols=79  Identities=22%  Similarity=0.305  Sum_probs=72.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             7778888665999999999999999999999999998148--98999999999999999999999999999999996188
Q gi|254780379|r   30 NEEGGSSPISFSALLQDMAKGAIGDMEKAENVSLAALQGK--TSMREAVDHIMQAERTLNLSIALRDKILSAVSEVSKMQ  107 (108)
Q Consensus        30 ~~~~~~~~~sF~~~L~~~i~~vn~~q~~a~~~~~~~~~G~--~dl~~vmia~~kA~lsl~~~vqVRnK~v~AYqeImrMq  107 (108)
                      ..+.+.+..+|+++|+++|+++|++|..++....++++|+  +||||||||++||+++|+++.+||||+|+|||||||||
T Consensus        34 ~~~~~~~~~~F~~~L~~Si~~~n~sQ~~~~~~~~~~~~g~~~~~l~~v~ia~~KA~~sl~~~~~vrnk~v~AYqei~~~q  113 (114)
T TIGR00205        34 SKAQDSDIKSFSDLLKNSIDELNESQLASDKVTEKLALGEKSVDLHDVMIAMQKASVSLKLLLEVRNKAVKAYQEIMRMQ  113 (114)
T ss_pred             HCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             04677752028999999999886889999999999861998867889999999886999999999999999999996205


Q ss_pred             C
Q ss_conf             9
Q gi|254780379|r  108 I  108 (108)
Q Consensus       108 V  108 (108)
                      |
T Consensus       114 ~  114 (114)
T TIGR00205       114 V  114 (114)
T ss_pred             C
T ss_conf             9


No 9  
>PRK12729 fliE flagellar hook-basal body protein FliE; Provisional
Probab=99.79  E-value=3.6e-19  Score=133.40  Aligned_cols=71  Identities=13%  Similarity=0.183  Sum_probs=67.5

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             665999999999999999999999999998148--98999999999999999999999999999999996188
Q gi|254780379|r   37 PISFSALLQDMAKGAIGDMEKAENVSLAALQGK--TSMREAVDHIMQAERTLNLSIALRDKILSAVSEVSKMQ  107 (108)
Q Consensus        37 ~~sF~~~L~~~i~~vn~~q~~a~~~~~~~~~G~--~dl~~vmia~~kA~lsl~~~vqVRnK~v~AYqeImrMq  107 (108)
                      .++|++.|++++++||++|.+|+.+.++++.|.  +|+||||||++||+++|+++++||||+|+|||||++|-
T Consensus        55 a~sFa~~Lk~Al~~VNd~Qv~ADeLtqqmV~dpnSVDlHDVmIA~eKAsmsL~~T~~IrnKvVeAYqEIt~~R  127 (127)
T PRK12729         55 AESFSEAMKNALTSVNDLQVEADELTQKMVFDPNSVDAHDVMIASEKARVALTFTKTIADGVVRAYRELTSLR  127 (127)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             9999999999999865887224888777733987452999999998603059999999999999999987229


No 10 
>PRK01699 fliE flagellar hook-basal body protein FliE; Reviewed
Probab=99.64  E-value=1.8e-15  Score=111.49  Aligned_cols=69  Identities=14%  Similarity=0.186  Sum_probs=63.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             9999999999999999999999999981489-89999999999999999999999999999999961889
Q gi|254780379|r   40 FSALLQDMAKGAIGDMEKAENVSLAALQGKT-SMREAVDHIMQAERTLNLSIALRDKILSAVSEVSKMQI  108 (108)
Q Consensus        40 F~~~L~~~i~~vn~~q~~a~~~~~~~~~G~~-dl~~vmia~~kA~lsl~~~vqVRnK~v~AYqeImrMqV  108 (108)
                      -+..+-+.++++|+.|..++....++++|++ ++|||+|++.||+.+|.++.+||||++++|+|++||||
T Consensus        30 ~Gk~F~~ll~d~N~tQnna~~Av~~l~T~g~gn~hdvlIqmkKAes~mktaa~VRdn~IeaYKelinmQi   99 (99)
T PRK01699         30 EGKKFIDLLEDMNQTQNNAQTAVYDLLTKGVGETHDVLIQQKKAESQMKTAALVRDNLIENYKSLINMQI   99 (99)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             1026999999999988879999999884377729999999999999999999999999999999986129


No 11 
>PRK01482 fliE flagellar hook-basal body protein FliE; Reviewed
Probab=99.38  E-value=2.5e-12  Score=92.83  Aligned_cols=73  Identities=11%  Similarity=0.194  Sum_probs=67.7

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             88866599999999999999999999999999814--89899999999999999999999999999999999618
Q gi|254780379|r   34 GSSPISFSALLQDMAKGAIGDMEKAENVSLAALQG--KTSMREAVDHIMQAERTLNLSIALRDKILSAVSEVSKM  106 (108)
Q Consensus        34 ~~~~~sF~~~L~~~i~~vn~~q~~a~~~~~~~~~G--~~dl~~vmia~~kA~lsl~~~vqVRnK~v~AYqeImrM  106 (108)
                      .....+|.++|.+++++||+.|...+.+.++.+..  .+|+||+|||+.||+++|.++..|++|.|.|||||++.
T Consensus        33 n~~a~sF~~~lln~~~~vN~sQl~~~k~~eq~i~~P~SVDVHDv~IA~~kA~msLs~~k~v~dr~Vkayqdi~n~  107 (108)
T PRK01482         33 NKKAKTFKDTLLNAIDDVNNSQLNVSKVTEQAILDPESVDVHDVTIAMAKANMNLSIAKAVVERSIKAYQDIINI  107 (108)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             223656999999999887387604999988652695644299999999874003899999999999999998714


No 12 
>COG1166 SpeA Arginine decarboxylase (spermidine biosynthesis) [Amino acid transport and metabolism]
Probab=31.50  E-value=21  Score=16.30  Aligned_cols=26  Identities=12%  Similarity=-0.010  Sum_probs=10.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCHH
Q ss_conf             99999999999999999981489899
Q gi|254780379|r   48 AKGAIGDMEKAENVSLAALQGKTSMR   73 (108)
Q Consensus        48 i~~vn~~q~~a~~~~~~~~~G~~dl~   73 (108)
                      .+-.++.+..-+.....|..|-.||.
T Consensus       412 ~E~~hds~~~~~~~~~~f~~G~l~L~  437 (652)
T COG1166         412 REWYHDSQDDLEDAHSLFNLGYLSLQ  437 (652)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCHH
T ss_conf             99998767679999987503532288


No 13 
>KOG2280 consensus
Probab=28.97  E-value=43  Score=14.49  Aligned_cols=51  Identities=18%  Similarity=0.227  Sum_probs=41.2

Q ss_pred             HHHHHHHHHHHHHCCCC-HHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHC
Q ss_conf             99999999999814898-999999999999999999999999--9999999961
Q gi|254780379|r   55 MEKAENVSLAALQGKTS-MREAVDHIMQAERTLNLSIALRDK--ILSAVSEVSK  105 (108)
Q Consensus        55 q~~a~~~~~~~~~G~~d-l~~vmia~~kA~lsl~~~vqVRnK--~v~AYqeImr  105 (108)
                      -...-++..+-.+|+.| ++.|++.+.+-..-.++.+.+||-  .+.-|+++||
T Consensus       547 ~~~~~AL~kaies~d~~Li~~Vllhlk~~~~~s~l~~~l~~~p~a~~lY~~~~r  600 (829)
T KOG2280         547 KDSSLALKKAIESGDTDLIIQVLLHLKNKLNRSSLFMTLRNQPLALSLYRQFMR  600 (829)
T ss_pred             CHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHH
T ss_conf             547899999986289405999999999998888899998855113579999998


No 14 
>pfam07002 Copine Copine. This family represents a conserved region approximately 180 residues long within eukaryotic copines. Copines are Ca(2+)-dependent phospholipid-binding proteins that are thought to be involved in membrane-trafficking, and may also be involved in cell division and growth.
Probab=26.77  E-value=17  Score=16.86  Aligned_cols=50  Identities=20%  Similarity=0.375  Sum_probs=29.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-HH-CCC-CHHHHHHHHHHHH
Q ss_conf             888866599999999999999999999999999-81-489-8999999999999
Q gi|254780379|r   33 GGSSPISFSALLQDMAKGAIGDMEKAENVSLAA-LQ-GKT-SMREAVDHIMQAE   83 (108)
Q Consensus        33 ~~~~~~sF~~~L~~~i~~vn~~q~~a~~~~~~~-~~-G~~-dl~~vmia~~kA~   83 (108)
                      .-.++..|+.+++.+++-+...++... -..-+ ++ |++ |+.++.-+.-+|+
T Consensus        81 ~l~gPT~fapiI~~a~~~a~~~~~~~~-Y~VLlIiTDG~i~D~~~Ti~aIv~AS  133 (145)
T pfam07002        81 QLSGPTNFAPIIDAAARIAEATQKSGQ-YHVLLIITDGQVTDMKATIDAIVRAS  133 (145)
T ss_pred             EECCCCCHHHHHHHHHHHHHHHCCCCE-EEEEEEECCCCCCCHHHHHHHHHHHH
T ss_conf             654875279999999999997223771-89999963897356999999999982


Done!