Query         gi|254780894|ref|YP_003065307.1| hypothetical protein CLIBASIA_03955 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 103
No_of_seqs    46 out of 48
Neff          3.9 
Searched_HMMs 39220
Date          Mon May 30 00:36:08 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780894.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR02473 flagell_FliJ flagell  97.4  0.0065 1.6E-07   39.1  11.9   97    3-102     3-108 (141)
  2 pfam02050 FliJ Flagellar FliJ   90.2     1.7 4.2E-05   23.9  13.4  100    2-101     4-109 (143)
  3 COG4477 EzrA Negative regulato  88.7     2.1 5.4E-05   23.2   8.5   77   24-101   112-188 (570)
  4 PRK06231 F0F1 ATP synthase sub  63.2      13 0.00033   18.3   6.4   42   56-97     66-107 (201)
  5 PRK13453 F0F1 ATP synthase sub  61.0      14 0.00036   18.0   6.1   40   56-95     36-75  (173)
  6 PRK13460 F0F1 ATP synthase sub  60.6      14 0.00037   18.0   6.1   41   55-95     33-73  (173)
  7 PRK13461 F0F1 ATP synthase sub  59.9      15 0.00038   17.9   6.1   40   56-95     23-62  (159)
  8 pfam00430 ATP-synt_B ATP synth  56.8      17 0.00043   17.6   6.1   39   56-94     17-55  (132)
  9 pfam05983 Med7 MED7 protein. T  53.0      19 0.00049   17.2   5.0   34    3-36    127-160 (161)
 10 PRK05759 F0F1 ATP synthase sub  50.2      21 0.00055   16.9   6.2   37   57-93     23-59  (156)
 11 PRK07352 F0F1 ATP synthase sub  49.9      22 0.00055   16.9   6.2   40   56-95     37-76  (174)
 12 PRK08476 F0F1 ATP synthase sub  49.5      22 0.00056   16.8   6.0   25   57-81     26-50  (141)
 13 COG1071 AcoA Pyruvate/2-oxoglu  49.3     9.8 0.00025   19.1   1.6   69    1-74    284-356 (358)
 14 CHL00019 atpF ATP synthase CF0  43.9      27 0.00068   16.3   6.2   40   56-95     42-81  (184)
 15 TIGR01737 FGAM_synth_I phospho  37.2      34 0.00087   15.7   3.3   28   54-81     58-89  (264)
 16 TIGR02044 CueR Cu(I)-responsiv  35.9      36 0.00091   15.5   3.9   24   14-37     87-110 (127)
 17 PRK10636 putative ABC transpor  35.5      36 0.00092   15.5  11.4   74   19-94    555-630 (638)
 18 TIGR01120 rpiB ribose 5-phosph  35.3      23 0.00058   16.8   1.7   20   51-70     32-51  (143)
 19 pfam03962 Mnd1 Mnd1 family. Th  33.8      38 0.00098   15.3   9.4   66   13-93     62-127 (188)
 20 CHL00118 atpG ATP synthase CF0  32.7      40   0.001   15.2   6.0   33   57-89     41-73  (156)
 21 CHL00167 consensus              32.2      41   0.001   15.2   6.2   40   56-95     44-83  (182)
 22 TIGR00689 rpiB_lacA_lacB sugar  32.1      32 0.00081   15.8   2.0   20   51-70     31-51  (146)
 23 PRK10803 hypothetical protein;  30.4      44  0.0011   15.0   7.3   42    4-45     45-86  (262)
 24 KOG2509 consensus               27.1      50  0.0013   14.6   7.4   69   11-94     46-114 (455)
 25 COG0711 AtpF F0F1-type ATP syn  26.9      50  0.0013   14.6   6.2   30   57-86     25-54  (161)
 26 TIGR01144 ATP_synt_b ATP synth  25.5      54  0.0014   14.4   6.3   44   57-100    14-57  (147)
 27 pfam04652 DUF605 Vta1 like. Vt  25.4      54  0.0014   14.4   2.7   49   25-73     46-94  (312)
 28 pfam03285 Paralemmin Paralemmi  24.7      55  0.0014   14.3   3.6   29   19-47      2-30  (270)
 29 cd07624 BAR_SNX7_30 The Bin/Am  24.7      55  0.0014   14.3   9.3   74   28-101    75-159 (200)
 30 COG2882 FliJ Flagellar biosynt  24.6      56  0.0014   14.3  13.1   97    2-99      5-108 (148)
 31 pfam11180 DUF2968 Protein of u  24.5      56  0.0014   14.3   9.5   76   18-93     96-171 (192)
 32 PRK08475 F0F1 ATP synthase sub  24.5      56  0.0014   14.3   6.2   39   57-95     43-81  (170)
 33 COG4877 Uncharacterized protei  24.1      57  0.0014   14.3   2.7   38    8-45     19-56  (63)
 34 PRK06986 fliA flagellar biosyn  24.1      57  0.0014   14.3   4.2   18   53-70     56-74  (234)
 35 pfam12617 LdpA_C Iron-Sulfur b  23.5      42  0.0011   15.1   1.4   19   52-70    131-149 (182)
 36 PRK07353 F0F1 ATP synthase sub  23.1      59  0.0015   14.1   6.0   25   57-81     24-48  (140)
 37 pfam06160 EzrA Septation ring   21.0      65  0.0017   13.9   9.6   89   10-99     91-183 (559)
 38 TIGR03007 pepcterm_ChnLen poly  20.9      66  0.0017   13.9   7.0   35   14-48    268-302 (510)
 39 TIGR01256 modA molybdate ABC t  20.8      52  0.0013   14.5   1.4   24   47-70    105-128 (225)
 40 pfam07321 YscO Type III secret  20.7      66  0.0017   13.8  10.9   92    4-95      2-93  (152)
 41 TIGR00473 pssA CDP-diacylglyce  20.3      43  0.0011   15.0   0.9   12    6-17    104-115 (174)
 42 TIGR01020 rpsE_arch ribosomal   20.1      47  0.0012   14.8   1.0   22   48-69    172-199 (220)
 43 PRK04778 septation ring format  20.1      68  0.0017   13.7   9.7   89   10-99     95-187 (569)
 44 COG4970 FimT Tfp pilus assembl  20.0      69  0.0017   13.7   4.2   34   56-91     26-59  (181)

No 1  
>TIGR02473 flagell_FliJ flagellar export protein FliJ; InterPro: IPR012823    Members of this family are the FliJ protein found, in nearly every case, in the midst of other flagellar biosynthesis genes in bacterial genomes. Typically the fliJ gene is found adjacent to the gene for the flagellum-specific ATPase FliI. Closely related sequences include both probable FliJ proteins and components of bacterial type III secretion systems.; GO: 0006935 chemotaxis, 0016020 membrane, 0044461 flagellin-based flagellum part.
Probab=97.40  E-value=0.0065  Score=39.07  Aligned_cols=97  Identities=18%  Similarity=0.181  Sum_probs=73.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             6788899999889999999999999999999999999999999---------9999715770014318999999999999
Q gi|254780894|r    3 LQEQRTRLKEFRLNDERRQLQQLRATILEFRRIVADLEKQIAI---------EERQVGIYDKDHFAYPILAKSARQRIDN   73 (103)
Q Consensus         3 sretLIRLk~fqVdEkRR~laql~~m~~ef~~~~~~LE~qI~~---------Ee~~agi~d~~hFaY~tfAraa~~RRdn   73 (103)
                      ++..|..|..++.|   ....+|..++.+|..+...|..-+..         +...+|++.+.+..|+.|-...-.+++.
T Consensus         3 ~L~~ll~lr~~~e~---~~~~~l~~~~~~~~~~~~~L~~l~~~~~~~~~~~~~~~~~g~s~~~~~~~~~f~~~l~~~i~~   79 (141)
T TIGR02473         3 RLQKLLDLREKEEE---QAKLELAKAQAEFERLETQLQQLIKYREEYEQQANEKVQSGTSAAELSNYQRFIRQLDEAIQQ   79 (141)
T ss_pred             CHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             07899999999999---999999999888888888888888888889999887631699999999898888888888888


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99999999999999999999999997422
Q gi|254780894|r   74 LLLSIRDLLLRQESLESHLESESNSDKSV  102 (103)
Q Consensus        74 L~~Si~~l~~Q~e~a~~~L~~a~~~~k~~  102 (103)
                      +...+..+..+.+.++..|.+++...|++
T Consensus        80 q~~~~~~~~~~~e~~r~~l~~~~~e~k~~  108 (141)
T TIGR02473        80 QQQELALLEKELEAKRERLLEAAKERKAL  108 (141)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             88888888888888888889999999999


No 2  
>pfam02050 FliJ Flagellar FliJ protein.
Probab=90.19  E-value=1.7  Score=23.90  Aligned_cols=100  Identities=15%  Similarity=0.098  Sum_probs=80.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             86788899999889999999999999999999999999999999999------971577001431899999999999999
Q gi|254780894|r    2 RLQEQRTRLKEFRLNDERRQLQQLRATILEFRRIVADLEKQIAIEER------QVGIYDKDHFAYPILAKSARQRIDNLL   75 (103)
Q Consensus         2 KsretLIRLk~fqVdEkRR~laql~~m~~ef~~~~~~LE~qI~~Ee~------~agi~d~~hFaY~tfAraa~~RRdnL~   75 (103)
                      .++++|..|+....|+....|+...............|......=..      ..|++...--.|..|-...-.......
T Consensus         4 frL~~vl~l~~~~ee~a~~~la~a~~~~~~~~~~L~~L~~~~~~y~~~~~~~~~~g~~~~~l~~~~~fi~~L~~~i~~q~   83 (143)
T pfam02050         4 FRLQTLLDLAEKAEEEAARQLGEAQRELEQAEQQLEQLEQYRQEYRQQLQSKGQQGISAAQLRNYQAFIAQLDQAIAQQQ   83 (143)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             32599999999999999999999999999999999999999999999999764289999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999742
Q gi|254780894|r   76 LSIRDLLLRQESLESHLESESNSDKS  101 (103)
Q Consensus        76 ~Si~~l~~Q~e~a~~~L~~a~~~~k~  101 (103)
                      ..+..+..+++.++..|-++.-..|+
T Consensus        84 ~~l~~~~~~~e~~r~~~~~a~~~~k~  109 (143)
T pfam02050        84 QQVAQAEQQVEQAREAWQEAQQKRKA  109 (143)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999999


No 3  
>COG4477 EzrA Negative regulator of septation ring formation [Cell division and chromosome partitioning]
Probab=88.74  E-value=2.1  Score=23.22  Aligned_cols=77  Identities=19%  Similarity=0.157  Sum_probs=65.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999997157700143189999999999999999999999999999999999999742
Q gi|254780894|r   24 QLRATILEFRRIVADLEKQIAIEERQVGIYDKDHFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLESESNSDKS  101 (103)
Q Consensus        24 ql~~m~~ef~~~~~~LE~qI~~Ee~~agi~d~~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~~a~~~~k~  101 (103)
                      +|..+..+...+..++-.=+..|++-++-.+..-=-|.-.-+-+..+++++..++..++.+++.....|+ .|++++.
T Consensus       112 ~l~~iE~~i~~il~~l~~Lv~sEekN~~~i~~~~ely~elr~~vl~n~~~~Ge~~~~lEk~Le~i~~~l~-qf~~lt~  188 (570)
T COG4477         112 QLTLIEEDIEQILEDLNELVESEEKNSEEIDHVLELYEELRRDVLANRHQYGEAAPELEKKLENIEEELS-QFVELTS  188 (570)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHCC
T ss_conf             9999999999999999999998873478899999999999999987245532125899999999999999-9998615


No 4  
>PRK06231 F0F1 ATP synthase subunit B; Validated
Probab=63.24  E-value=13  Score=18.28  Aligned_cols=42  Identities=10%  Similarity=0.038  Sum_probs=33.7

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             014318999999999999999999999999999999999999
Q gi|254780894|r   56 DHFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLESESN   97 (103)
Q Consensus        56 ~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~~a~~   97 (103)
                      ..|+|+++.+.--.|++.+..++.+-....++|+.-+++.-.
T Consensus        66 ~k~awKPI~k~Ld~R~~kI~~~L~~Aekar~EAe~ll~e~e~  107 (201)
T PRK06231         66 IFLFWKPTQRFLNKRKELIEAEINQANELKQQAQQLLENAKQ  107 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999787899999999999999999999999999999999999


No 5  
>PRK13453 F0F1 ATP synthase subunit B; Provisional
Probab=60.99  E-value=14  Score=18.03  Aligned_cols=40  Identities=18%  Similarity=0.155  Sum_probs=29.5

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0143189999999999999999999999999999999999
Q gi|254780894|r   56 DHFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLESE   95 (103)
Q Consensus        56 ~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~~a   95 (103)
                      ..|+||++-+.--.|++.+...+.+.......|...+++.
T Consensus        36 ~kf~~~pi~~~L~~R~~~I~~~l~~Ae~~k~eA~~~~~e~   75 (173)
T PRK13453         36 KKFAWGPLKDVMDKRERDINRDIDDAEQAKLNAQKLEEEN   75 (173)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9998989999999999999988999999999999999999


No 6  
>PRK13460 F0F1 ATP synthase subunit B; Provisional
Probab=60.62  E-value=14  Score=17.99  Aligned_cols=41  Identities=17%  Similarity=0.193  Sum_probs=32.9

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             00143189999999999999999999999999999999999
Q gi|254780894|r   55 KDHFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLESE   95 (103)
Q Consensus        55 ~~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~~a   95 (103)
                      ..+|+||.+.+.--.|++.+..++.+-+....+|...+.+.
T Consensus        33 l~kf~~~pi~~~Ld~R~~~I~~~l~~Ae~~k~eA~~~~~e~   73 (173)
T PRK13460         33 LKKFAWDVILKALDERASGVQNDINKASELRLEAEALLKDY   73 (173)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99996888999999999999988999999999999999999


No 7  
>PRK13461 F0F1 ATP synthase subunit B; Provisional
Probab=59.89  E-value=15  Score=17.91  Aligned_cols=40  Identities=13%  Similarity=0.066  Sum_probs=30.9

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0143189999999999999999999999999999999999
Q gi|254780894|r   56 DHFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLESE   95 (103)
Q Consensus        56 ~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~~a   95 (103)
                      .+|.||++.+.--.|++.+..++.+.....+.|...+++.
T Consensus        23 ~kf~~~pi~~~l~~R~~~I~~~l~~Ae~~~~ea~~~~~e~   62 (159)
T PRK13461         23 KHFFFDKIKAVIDSRQSEIDEKIEKADEDAEKARELKLKN   62 (159)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9997888999999999999999999999999999999999


No 8  
>pfam00430 ATP-synt_B ATP synthase B/B' CF(0). Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in pfam00006
Probab=56.79  E-value=17  Score=17.58  Aligned_cols=39  Identities=21%  Similarity=0.233  Sum_probs=28.6

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             014318999999999999999999999999999999999
Q gi|254780894|r   56 DHFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLES   94 (103)
Q Consensus        56 ~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~~   94 (103)
                      ..|.||++.+.--.|++.+..++.+.......+...+++
T Consensus        17 ~~~~~~pi~~~l~~R~~~I~~~l~~a~~~~~ea~~~~~~   55 (132)
T pfam00430        17 IYFGYKPLGKILDERKEKIANNIKEAEERLKQAAALLAE   55 (132)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999798899999999999999999999999999999999


No 9  
>pfam05983 Med7 MED7 protein. This family consists of several eukaryotic proteins which are homologues of the yeast MED7 protein. Activation of gene transcription in metazoans is a multi-step process that is triggered by factors that recognize transcriptional enhancer sites in DNA. These factors work with co-activators such as MED7 to direct transcriptional initiation by the RNA polymerase II apparatus.
Probab=52.98  E-value=19  Score=17.20  Aligned_cols=34  Identities=24%  Similarity=0.446  Sum_probs=24.7

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             6788899999889999999999999999999999
Q gi|254780894|r    3 LQEQRTRLKEFRLNDERRQLQQLRATILEFRRIV   36 (103)
Q Consensus         3 sretLIRLk~fqVdEkRR~laql~~m~~ef~~~~   36 (103)
                      +|+|||-+=+-|+++||-.+.++..+.++...++
T Consensus       127 AResLi~~me~Ql~~kr~~i~~i~~~~~~v~~~l  160 (161)
T pfam05983       127 ARESLIMLMEEQLDEKREEIEAIRKVLEEVREVL  160 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999999999999862


No 10 
>PRK05759 F0F1 ATP synthase subunit B; Validated
Probab=50.19  E-value=21  Score=16.92  Aligned_cols=37  Identities=16%  Similarity=0.276  Sum_probs=18.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1431899999999999999999999999999999999
Q gi|254780894|r   57 HFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLE   93 (103)
Q Consensus        57 hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~   93 (103)
                      .|.||.+.+.--.|++.+...+.+.+.....|...++
T Consensus        23 ~~~~~pi~~~l~~R~~~I~~~l~~Ae~~~~~a~~~~~   59 (156)
T PRK05759         23 KFVWPPIMKALEERQKKIADGLAAAERAKKELEAAQA   59 (156)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9978789999999999999899999999999999999


No 11 
>PRK07352 F0F1 ATP synthase subunit B; Validated
Probab=49.85  E-value=22  Score=16.89  Aligned_cols=40  Identities=18%  Similarity=0.197  Sum_probs=31.0

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0143189999999999999999999999999999999999
Q gi|254780894|r   56 DHFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLESE   95 (103)
Q Consensus        56 ~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~~a   95 (103)
                      .+|.||+..+.--.|++.+..++.+-..-..+|...|.+.
T Consensus        37 ~~f~~~pi~~~L~~R~~~I~~~l~~Ae~~k~eA~~~l~e~   76 (174)
T PRK07352         37 YYFLRGFLGKILERRREAILQALKEAEERLRKAAQALAEA   76 (174)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9995989999999999999999999999999999999999


No 12 
>PRK08476 F0F1 ATP synthase subunit B'; Validated
Probab=49.47  E-value=22  Score=16.85  Aligned_cols=25  Identities=16%  Similarity=0.214  Sum_probs=11.1

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1431899999999999999999999
Q gi|254780894|r   57 HFAYPILAKSARQRIDNLLLSIRDL   81 (103)
Q Consensus        57 hFaY~tfAraa~~RRdnL~~Si~~l   81 (103)
                      +|.||+.-+..-.|.+.+..++...
T Consensus        26 kflykPi~k~ld~R~~~I~~~l~~A   50 (141)
T PRK08476         26 SWLYKPLLKFMDNRNASIKNDLEKV   50 (141)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9958789999999999999889999


No 13 
>COG1071 AcoA Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]
Probab=49.30  E-value=9.8  Score=19.06  Aligned_cols=69  Identities=13%  Similarity=0.142  Sum_probs=34.7

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----CCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             986788899999889999999999999999999999999999999999971----57700143189999999999999
Q gi|254780894|r    1 MRLQEQRTRLKEFRLNDERRQLQQLRATILEFRRIVADLEKQIAIEERQVG----IYDKDHFAYPILAKSARQRIDNL   74 (103)
Q Consensus         1 MKsretLIRLk~fqVdEkRR~laql~~m~~ef~~~~~~LE~qI~~Ee~~ag----i~d~~hFaY~tfAraa~~RRdnL   74 (103)
                      ++++++|+||++|=++.--=-=.+++.+.++...++.+-     .|...+.    .++..+.-|..+....+.++..+
T Consensus       284 ~~~~DPi~r~~~~L~~~g~~see~~~~i~~e~~~~V~ea-----~e~a~~~p~P~~~~~~~~Vy~~~~~~l~~q~~~~  356 (358)
T COG1071         284 WKKRDPIVRLRKYLIEAGILSEEELEAIEAEAKAEVDEA-----VEFAEASPYPDVSELFEDVYAEGPPHLEEQREEL  356 (358)
T ss_pred             HHCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHH-----HHHHHHCCCCCHHHHHHCCCCCCCHHHHHHHHHH
T ss_conf             750694999999999768989999999999999999999-----9999708999846765132147885089988763


No 14 
>CHL00019 atpF ATP synthase CF0 B subunit
Probab=43.87  E-value=27  Score=16.31  Aligned_cols=40  Identities=25%  Similarity=0.256  Sum_probs=30.2

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0143189999999999999999999999999999999999
Q gi|254780894|r   56 DHFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLESE   95 (103)
Q Consensus        56 ~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~~a   95 (103)
                      .+|.|+.+...--.|+++...+|.+-+....+|...|+++
T Consensus        42 ~~f~~~~L~~~L~~R~~~I~~~I~eAE~~~~eA~~~L~e~   81 (184)
T CHL00019         42 IYFGKGVLSDLLDNRKQRILNTIRNSEERREEAIEKLEKA   81 (184)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9995999999999999999999999999999999999999


No 15 
>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=37.21  E-value=34  Score=15.66  Aligned_cols=28  Identities=14%  Similarity=0.305  Sum_probs=19.6

Q ss_pred             CCCCCCHHHHHHH-HHHHH---HHHHHHHHHH
Q ss_conf             7001431899999-99999---9999999999
Q gi|254780894|r   54 DKDHFAYPILAKS-ARQRI---DNLLLSIRDL   81 (103)
Q Consensus        54 d~~hFaY~tfAra-a~~RR---dnL~~Si~~l   81 (103)
                      -||+|.|+.|=|| ||..+   --+..-|.++
T Consensus        58 lPGGFSyGDYLRaGAIAa~rvk~p~~~~V~~~   89 (264)
T TIGR01737        58 LPGGFSYGDYLRAGAIAALRVKSPIMQEVREF   89 (264)
T ss_pred             ECCCCCHHHHHHHHHHHHHHCCHHHHHHHHHH
T ss_conf             66877723577799999875030889999999


No 16 
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator; InterPro: IPR011789    This entry represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system . This protein is a member of the MerR family of transcriptional activators and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue .; GO: 0003677 DNA binding, 0005507 copper ion binding, 0016563 transcription activator activity, 0045941 positive regulation of transcription.
Probab=35.91  E-value=36  Score=15.53  Aligned_cols=24  Identities=8%  Similarity=0.302  Sum_probs=13.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             899999999999999999999999
Q gi|254780894|r   14 RLNDERRQLQQLRATILEFRRIVA   37 (103)
Q Consensus        14 qVdEkRR~laql~~m~~ef~~~~~   37 (103)
                      +|+|--|++++|+.|...+..+++
T Consensus        87 k~~E~~~kI~eL~~m~~qL~~la~  110 (127)
T TIGR02044        87 KVAELERKISELQEMKDQLEELAE  110 (127)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             899999999999889999999998


No 17 
>PRK10636 putative ABC transporter ATP-binding protein; Provisional
Probab=35.47  E-value=36  Score=15.48  Aligned_cols=74  Identities=20%  Similarity=0.230  Sum_probs=41.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999999999715770014318999--999999999999999999999999999999
Q gi|254780894|r   19 RRQLQQLRATILEFRRIVADLEKQIAIEERQVGIYDKDHFAYPILA--KSARQRIDNLLLSIRDLLLRQESLESHLES   94 (103)
Q Consensus        19 RR~laql~~m~~ef~~~~~~LE~qI~~Ee~~agi~d~~hFaY~tfA--raa~~RRdnL~~Si~~l~~Q~e~a~~~L~~   94 (103)
                      +.+...++..++.++..+..||.+|..=+..-  .||.-|..+..+  ..+.++.+.+...+.++..+-+++...|++
T Consensus       555 ~~~~~~~~~~~~~~e~~i~~le~~~~~l~~~l--~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~W~el~e~lE~  630 (638)
T PRK10636        555 RTQTQPLRKEIARLEKEMEKLNAQLAQAEEKL--GDSELYDQSRKAELTACLQQQASAKSGLEECEMAWLEAQEQLEQ  630 (638)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             87647999999999999999999999999984--39202356578999999999999999999999999999999999


No 18 
>TIGR01120 rpiB ribose 5-phosphate isomerase B; InterPro: IPR004785   Ribose 5-phosphate isomerase (5.3.1.6 from EC) forms a homodimer and catalyses the interconversion of D-ribose 5-phosphate and D-ribulose 5-phosphate in the non-oxidative branch of the pentose phosphate pathway. This reaction permits the synthesis of ribose from other sugars, as well as the recycling of sugars from nucleotide breakdown. Two unrelated enzymes can catalyse this reaction: RpiA (found in most organisms) and RpiB (found in some bacteria and eukaryotes). RpiB is also involved in metabolism of the rare sugar, allose, in addition to ribose sugars. The structures of RpiA and RpiB are distinct, RpiB having a Rossmann-type alpha/beta/alpha sandwich topology . This entry represents the RpiB enzyme.; GO: 0004751 ribose-5-phosphate isomerase activity, 0006098 pentose-phosphate shunt.
Probab=35.27  E-value=23  Score=16.75  Aligned_cols=20  Identities=25%  Similarity=0.385  Sum_probs=14.3

Q ss_pred             HCCCCCCCCHHHHHHHHHHH
Q ss_conf             15770014318999999999
Q gi|254780894|r   51 GIYDKDHFAYPILAKSARQR   70 (103)
Q Consensus        51 gi~d~~hFaY~tfAraa~~R   70 (103)
                      |.-+...-.||.||+-+.+.
T Consensus        32 GT~~~ertdYP~YAk~V~~a   51 (143)
T TIGR01120        32 GTLASERTDYPDYAKEVVRA   51 (143)
T ss_pred             CCCCCCCCCCCHHHHHHHHH
T ss_conf             37886763660689999999


No 19 
>pfam03962 Mnd1 Mnd1 family. This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair.
Probab=33.82  E-value=38  Score=15.32  Aligned_cols=66  Identities=24%  Similarity=0.362  Sum_probs=46.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             88999999999999999999999999999999999997157700143189999999999999999999999999999999
Q gi|254780894|r   13 FRLNDERRQLQQLRATILEFRRIVADLEKQIAIEERQVGIYDKDHFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHL   92 (103)
Q Consensus        13 fqVdEkRR~laql~~m~~ef~~~~~~LE~qI~~Ee~~agi~d~~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L   92 (103)
                      .....+++.+..|..-+.+....+..|+.+|..+  +.|-.+.             ..|..|..-+.+|..+....+.+|
T Consensus        62 ~~~~~~~~~~~~L~~~~~~~~~~i~~l~~~i~~~--k~~r~~~-------------~er~~ll~~l~~l~~~~~~L~~el  126 (188)
T pfam03962        62 QAKNKLKTRLEKLKKELEELKQRIAELQAQIEKL--KVGREET-------------EERTELLEELKQLEKELKKLKAEL  126 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHCCCCC-------------HHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999999999999999--8658551-------------669999999999999999999999


Q ss_pred             H
Q ss_conf             9
Q gi|254780894|r   93 E   93 (103)
Q Consensus        93 ~   93 (103)
                      +
T Consensus       127 ~  127 (188)
T pfam03962       127 E  127 (188)
T ss_pred             H
T ss_conf             9


No 20 
>CHL00118 atpG ATP synthase CF0 B' subunit; Validated
Probab=32.68  E-value=40  Score=15.20  Aligned_cols=33  Identities=9%  Similarity=0.086  Sum_probs=14.3

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             143189999999999999999999999999999
Q gi|254780894|r   57 HFAYPILAKSARQRIDNLLLSIRDLLLRQESLE   89 (103)
Q Consensus        57 hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~   89 (103)
                      .|.||++-+.--.|++.+..++.+.+.-.+.|.
T Consensus        41 kf~~~Pi~~~ld~R~~~I~~~l~~Ae~~~~ea~   73 (156)
T CHL00118         41 AIFYKPIGKILDEREEYIRSNLAKASSKLAKAN   73 (156)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             998989999999999999988999999999999


No 21 
>CHL00167 consensus
Probab=32.22  E-value=41  Score=15.15  Aligned_cols=40  Identities=23%  Similarity=0.213  Sum_probs=25.2

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0143189999999999999999999999999999999999
Q gi|254780894|r   56 DHFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLESE   95 (103)
Q Consensus        56 ~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~~a   95 (103)
                      ..|.++.+-..--.|+++...+|.+-+.....|...|.++
T Consensus        44 ~~fg~~~L~~~L~~Rke~I~~~I~eAE~r~~eA~~~L~ea   83 (182)
T CHL00167         44 IYLGKNFLGSSLEERQQKVLEAIQESEERLEQANSRLSES   83 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9984676898999999999999999999999999999999


No 22 
>TIGR00689 rpiB_lacA_lacB sugar-phosphate isomerases, RpiB/LacA/LacB family; InterPro: IPR003500   This entry represents the sugar isomerase enzymes ribose 5-phosphate isomerase B (rpiB), galactose isomerase subunit A (LacA) and galactose isomerase subunit B (LacB).    Galactose-6-phosphate isomerase (5.3.1.26 from EC) is a heteromultimeric protein consisting of subunits LacA and LacB, and catalyses the conversion of D-galactose 6-phosphate to D-tagatose and 6-phosphate in the tagatose 6-phosphate pathway of lactose catabolism . Galactose-6-phosphate isomerase is induced by galactose or lactose. This entry represents the LacB subunit.   Ribose 5-phosphate isomerase (5.3.1.6 from EC) forms a homodimer and catalyses the interconversion of D-ribose 5-phosphate and D-ribulose 5-phosphate in the non-oxidative branch of the pentose phosphate pathway. This reaction permits the synthesis of ribose from other sugars, as well as the recycling of sugars from nucleotide breakdown. Two unrelated enzymes can catalyse this reaction: RpiA (found in most organisms) and RpiB (found in some bacteria and eukaryotes). RpiB is also involved in metabolism of the rare sugar, allose, in addition to ribose sugars. The structures of RpiA and RpiB are distinct, RpiB having a Rossmann-type alpha/beta/alpha sandwich topology .; GO: 0005975 carbohydrate metabolic process.
Probab=32.13  E-value=32  Score=15.84  Aligned_cols=20  Identities=30%  Similarity=0.526  Sum_probs=15.0

Q ss_pred             HCCC-CCCCCHHHHHHHHHHH
Q ss_conf             1577-0014318999999999
Q gi|254780894|r   51 GIYD-KDHFAYPILAKSARQR   70 (103)
Q Consensus        51 gi~d-~~hFaY~tfAraa~~R   70 (103)
                      |..+ ...-.||.||..+.++
T Consensus        31 G~~~~~~~~DYPdYA~~Va~~   51 (146)
T TIGR00689        31 GTLEYDESVDYPDYAKLVAQK   51 (146)
T ss_pred             CCCCCCCCCCCHHHHHHHHHH
T ss_conf             676788998874789999999


No 23 
>PRK10803 hypothetical protein; Provisional
Probab=30.37  E-value=44  Score=14.96  Aligned_cols=42  Identities=17%  Similarity=0.162  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             788899999889999999999999999999999999999999
Q gi|254780894|r    4 QEQRTRLKEFRLNDERRQLQQLRATILEFRRIVADLEKQIAI   45 (103)
Q Consensus         4 retLIRLk~fqVdEkRR~laql~~m~~ef~~~~~~LE~qI~~   45 (103)
                      +|-++......+.+.++||.+++.-+.++.+.+.++..+|..
T Consensus        45 LEr~~~~~~~~~~qlq~Ql~~LQ~EV~~LRGqiEe~~~~l~q   86 (262)
T PRK10803         45 LERISNAHSQLLTQLQQQLSDNQSDIDSLRGQIQENQYQLNQ   86 (262)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999742799999999999999999998799999999999


No 24 
>KOG2509 consensus
Probab=27.14  E-value=50  Score=14.61  Aligned_cols=69  Identities=17%  Similarity=0.163  Sum_probs=47.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99889999999999999999999999999999999999971577001431899999999999999999999999999999
Q gi|254780894|r   11 KEFRLNDERRQLQQLRATILEFRRIVADLEKQIAIEERQVGIYDKDHFAYPILAKSARQRIDNLLLSIRDLLLRQESLES   90 (103)
Q Consensus        11 k~fqVdEkRR~laql~~m~~ef~~~~~~LE~qI~~Ee~~agi~d~~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~   90 (103)
                      -+|++|+.+++-+.+...|.. ..|.. =|.....++.++.++.-             .++-+|.....++......+++
T Consensus        46 ~~~~ldeln~~~n~l~k~i~~-~k~kk-ke~~~~l~~~~~~~~~~-------------~~~~~l~e~~~~~~~~~~~l~~  110 (455)
T KOG2509          46 TRFELDELNKEKNKLNKEIGD-LKLKK-KEDIGQLEESKAKNTEG-------------AERKLLKEEAVELEEDESKLED  110 (455)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH-HHHHH-CCHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             668788888888776667667-88764-02125777766676556-------------6655457887766789999999


Q ss_pred             HHHH
Q ss_conf             9999
Q gi|254780894|r   91 HLES   94 (103)
Q Consensus        91 ~L~~   94 (103)
                      +|-+
T Consensus       111 el~~  114 (455)
T KOG2509         111 ELYE  114 (455)
T ss_pred             HHHH
T ss_conf             9999


No 25 
>COG0711 AtpF F0F1-type ATP synthase, subunit b [Energy production and conversion]
Probab=26.95  E-value=50  Score=14.59  Aligned_cols=30  Identities=13%  Similarity=0.199  Sum_probs=11.3

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             143189999999999999999999999999
Q gi|254780894|r   57 HFAYPILAKSARQRIDNLLLSIRDLLLRQE   86 (103)
Q Consensus        57 hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e   86 (103)
                      .|.||++-++--.|.+++...+.+-+....
T Consensus        25 ~~~~~pi~~~l~~R~~~I~~~l~~A~~~~~   54 (161)
T COG0711          25 KFVWKPILKALDERQAKIADDLAEAERLKE   54 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             996867999999999999988999999899


No 26 
>TIGR01144 ATP_synt_b ATP synthase F0, B subunit; InterPro: IPR005864   ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (F-, V- and A-ATPases contain rotary motors) and in the type of ions they transport , .  F-ATPases (F1F0-ATPases) in mitochondria, chloroplasts and bacterial plasma membranes are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases) are primarily found in eukaryotic vacuoles, catalysing ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases) are found in Archaea and function like F-ATPases. P-ATPases (E1E2-ATPases) are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.   F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis . These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient.   This entry represents subunit B from the F0 complex in F-ATPases found in bacterial plasma membranes. The B subunits are part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In bacterial F-ATPases, the peripheral stalk is composed of one copy of the delta subunit (homologous to OSCP in mitochondria), and two copies of subunit B .   More information about this protein can be found at Protein of the Month: ATP Synthases .; GO: 0046933 hydrogen ion transporting ATP synthase activity rotational mechanism, 0046961 hydrogen ion transporting ATPase activity rotational mechanism, 0015986 ATP synthesis coupled proton transport, 0016469 proton-transporting two-sector ATPase complex.
Probab=25.46  E-value=54  Score=14.42  Aligned_cols=44  Identities=14%  Similarity=0.131  Sum_probs=31.0

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             14318999999999999999999999999999999999999974
Q gi|254780894|r   57 HFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLESESNSDK  100 (103)
Q Consensus        57 hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~~a~~~~k  100 (103)
                      =|.||+.+++-=+|++++-+++.......+++...=..+-..+|
T Consensus        14 KY~w~Pl~~~~~~R~~~IA~~L~~AE~~~~~~~~~~~~~~~~l~   57 (147)
T TIGR01144        14 KYVWPPLAKAIETRQKKIADDLASAERAKKEAALAQKEAQVLLK   57 (147)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             86237999999988998598899999988889999989889999


No 27 
>pfam04652 DUF605 Vta1 like. Vta1 (VPS20-associated protein 1) is a positive regulator of Vps4. Vps4 is an ATPase that is required in the multivesicular body (MVB) sorting pathway to dissociate the endosomal sorting complex required for transport (ESCRT). Vta1 promotes correct assembly of Vps4 and stimulates its ATPase activity through its conserved Vta1/SBP1/LIP5 region.
Probab=25.40  E-value=54  Score=14.41  Aligned_cols=49  Identities=14%  Similarity=0.206  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999715770014318999999999999
Q gi|254780894|r   25 LRATILEFRRIVADLEKQIAIEERQVGIYDKDHFAYPILAKSARQRIDN   73 (103)
Q Consensus        25 l~~m~~ef~~~~~~LE~qI~~Ee~~agi~d~~hFaY~tfAraa~~RRdn   73 (103)
                      +-.+++.++.+...+...-+...+.+|..-+-.||+-.|.+|-.+-|.+
T Consensus        46 l~~Lmd~LE~~K~~~~d~~ai~d~~~~~a~ve~FAl~lF~~AD~~dRag   94 (312)
T pfam04652        46 LTKLLDQLEAFKKELGDNDAITDEVAAQAYVENFALKLFNRADKQDRAG   94 (312)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             9999999999987567336564089999999999999999999998606


No 28 
>pfam03285 Paralemmin Paralemmin.
Probab=24.69  E-value=55  Score=14.32  Aligned_cols=29  Identities=24%  Similarity=0.377  Sum_probs=18.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999999
Q gi|254780894|r   19 RRQLQQLRATILEFRRIVADLEKQIAIEE   47 (103)
Q Consensus        19 RR~laql~~m~~ef~~~~~~LE~qI~~Ee   47 (103)
                      |||+.+=+...-.|+.-|.+||++|..=+
T Consensus         2 rrQ~qEDE~k~k~LEe~I~RLE~Eie~LE   30 (270)
T pfam03285         2 KKQMQEDEAKTRELEETIQRLERELEELE   30 (270)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             11677789999889999999999999885


No 29 
>cd07624 BAR_SNX7_30 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins 7 and 30. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. This subfamily consists of SNX7, SNX30, and similar proteins. The specific functions of SNX7 and SNX30 have not been elucidated. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=24.67  E-value=55  Score=14.32  Aligned_cols=74  Identities=22%  Similarity=0.142  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999971577001431899999999999999-----------999999999999999999999
Q gi|254780894|r   28 TILEFRRIVADLEKQIAIEERQVGIYDKDHFAYPILAKSARQRIDNLL-----------LSIRDLLLRQESLESHLESES   96 (103)
Q Consensus        28 m~~ef~~~~~~LE~qI~~Ee~~agi~d~~hFaY~tfAraa~~RRdnL~-----------~Si~~l~~Q~e~a~~~L~~a~   96 (103)
                      +-.-++.-+.-++..+..+...-...---...|+.--+++..+||+.+           ....+|..+++.+++.++.+-
T Consensus        75 ~~~~~d~~s~~l~~l~~~~~~~~~~~Lkeyv~y~~slk~vlk~Rdq~Q~~~E~~~e~L~~k~~eL~~~ve~~~~~~E~~~  154 (200)
T cd07624          75 VSSAVERCTAALEVLLSDHEFVFLPPLREYLLYSDAVKDVLKRRDQFQIEYELSVEELNKKRLELLKEVEKLQDKLECAN  154 (200)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99889999999999998537776788999999999999999989999987999999999879999988999888999988


Q ss_pred             HHHHH
Q ss_conf             99742
Q gi|254780894|r   97 NSDKS  101 (103)
Q Consensus        97 ~~~k~  101 (103)
                      +..|+
T Consensus       155 ~~~k~  159 (200)
T cd07624         155 ADLKA  159 (200)
T ss_pred             HHHHH
T ss_conf             99999


No 30 
>COG2882 FliJ Flagellar biosynthesis chaperone [Cell motility and secretion / Intracellular trafficking and secretion / Posttranslational modification, protein turnover, chaperones]
Probab=24.60  E-value=56  Score=14.32  Aligned_cols=97  Identities=11%  Similarity=0.076  Sum_probs=64.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             867888999998899999999999999999999999999-------9999999997157700143189999999999999
Q gi|254780894|r    2 RLQEQRTRLKEFRLNDERRQLQQLRATILEFRRIVADLE-------KQIAIEERQVGIYDKDHFAYPILAKSARQRIDNL   74 (103)
Q Consensus         2 KsretLIRLk~fqVdEkRR~laql~~m~~ef~~~~~~LE-------~qI~~Ee~~agi~d~~hFaY~tfAraa~~RRdnL   74 (103)
                      +++++|..|+++++++.-..|..+..-.......+..|.       +++ ++.-.+|++...--+|-.|--..=...+..
T Consensus         5 ~~L~~l~dl~~k~~e~a~~el~k~~~~~~~~~~qL~~l~~y~~ey~q~~-~~k~~~G~s~~q~~nyq~fI~~Le~~I~q~   83 (148)
T COG2882           5 FALQKLLDLAKKEEEEAAIELSKIRSEKENAEEQLKMLSGYRNEYEQNL-NEKLKSGVSAAQWQNYQQFISQLEVAIDQQ   83 (148)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             4789999999977889999999999999999999999999999999888-998863450999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999997
Q gi|254780894|r   75 LLSIRDLLLRQESLESHLESESNSD   99 (103)
Q Consensus        75 ~~Si~~l~~Q~e~a~~~L~~a~~~~   99 (103)
                      ...+..++-+++.++..+.+.--..
T Consensus        84 ~~~~~~~~~~ve~~r~~w~ek~~~~  108 (148)
T COG2882          84 QSQLSKLRKQVEQKREIWQEKQIEL  108 (148)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9889999999999999999999999


No 31 
>pfam11180 DUF2968 Protein of unknown function (DUF2968). This family of proteins has no known function.
Probab=24.52  E-value=56  Score=14.30  Aligned_cols=76  Identities=17%  Similarity=0.153  Sum_probs=39.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999999999971577001431899999999999999999999999999999999
Q gi|254780894|r   18 ERRQLQQLRATILEFRRIVADLEKQIAIEERQVGIYDKDHFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLE   93 (103)
Q Consensus        18 kRR~laql~~m~~ef~~~~~~LE~qI~~Ee~~agi~d~~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~   93 (103)
                      --.+|++.+.....++.....+|++|..-+.++.---..-=.-.+=-.++..|....+.-...|..|..++...|.
T Consensus        96 Qt~~LA~~eirr~~LeAQka~~eR~ia~~q~ra~~Lqadl~~a~~Q~~~va~rQ~q~r~ea~aL~aqr~~aq~QL~  171 (192)
T pfam11180        96 QTAQLADVEIRRAQLEAQKAQLERQIAASEARAERLQADLQLAQAQEQQVAARQQQARQEAVALEAQRQAAQAQLR  171 (192)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999878999999999899999999999999999999779999999999999999999999999999999999999


No 32 
>PRK08475 F0F1 ATP synthase subunit B; Validated
Probab=24.46  E-value=56  Score=14.30  Aligned_cols=39  Identities=10%  Similarity=0.181  Sum_probs=27.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             143189999999999999999999999999999999999
Q gi|254780894|r   57 HFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLESE   95 (103)
Q Consensus        57 hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~~a   95 (103)
                      +|..+.....-..|++++..++.+.+....+|...|.++
T Consensus        43 yf~~kpi~~~l~~R~~~I~~~L~eae~~~~eA~~~l~~~   81 (170)
T PRK08475         43 YFAAKPIKNFYKSRINSISKRLEEIQAKLKESKEKKKDA   81 (170)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             992878999999899999999999999999999999999


No 33 
>COG4877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.10  E-value=57  Score=14.26  Aligned_cols=38  Identities=13%  Similarity=0.058  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999889999999999999999999999999999999
Q gi|254780894|r    8 TRLKEFRLNDERRQLQQLRATILEFRRIVADLEKQIAI   45 (103)
Q Consensus         8 IRLk~fqVdEkRR~laql~~m~~ef~~~~~~LE~qI~~   45 (103)
                      --|.+|--||.|-.-+||+.|..|-.+...++-.++..
T Consensus        19 ~Aia~wA~de~RSiNaQIE~lL~E~lrq~gr~~~~~~d   56 (63)
T COG4877          19 AAIAQWAEDEFRSINAQIEILLKEALRQRGRATADAAD   56 (63)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHCC
T ss_conf             99999977777656689999999999982665033325


No 34 
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=24.06  E-value=57  Score=14.25  Aligned_cols=18  Identities=17%  Similarity=0.270  Sum_probs=14.1

Q ss_pred             CCCC-CCCHHHHHHHHHHH
Q ss_conf             7700-14318999999999
Q gi|254780894|r   53 YDKD-HFAYPILAKSARQR   70 (103)
Q Consensus        53 ~d~~-hFaY~tfAraa~~R   70 (103)
                      .||. +|..+|||.-|+..
T Consensus        56 FDp~~G~rFsTYA~~~Ir~   74 (234)
T PRK06986         56 YDGEQGASFETYAGQRIRG   74 (234)
T ss_pred             HCCCCCCCHHHHHHHHHHH
T ss_conf             1886699969999999999


No 35 
>pfam12617 LdpA_C Iron-Sulfur binding protein C terminal. This domain family is found in bacteria and eukaryotes, and is typically between 179 and 201 amino acids in length. The family is found in association with pfam00037. LdpA (light-dependent period) plays a role in controlling the redox state in cyanobacteria to modulate its. circadian clock. LdpA is a protein with Iron-Sulfur cluster-binding motifs.
Probab=23.50  E-value=42  Score=15.09  Aligned_cols=19  Identities=21%  Similarity=-0.010  Sum_probs=15.1

Q ss_pred             CCCCCCCCHHHHHHHHHHH
Q ss_conf             5770014318999999999
Q gi|254780894|r   52 IYDKDHFAYPILAKSARQR   70 (103)
Q Consensus        52 i~d~~hFaY~tfAraa~~R   70 (103)
                      ...+.+.||++|||.-.+.
T Consensus       131 ~~~~aGVAfGs~ARkll~p  149 (182)
T pfam12617       131 SVFIAGVAYGSYARKLLQP  149 (182)
T ss_pred             CCCCCEEEECHHHHHHHHH
T ss_conf             7788767761999999899


No 36 
>PRK07353 F0F1 ATP synthase subunit B'; Validated
Probab=23.06  E-value=59  Score=14.13  Aligned_cols=25  Identities=16%  Similarity=0.191  Sum_probs=9.8

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1431899999999999999999999
Q gi|254780894|r   57 HFAYPILAKSARQRIDNLLLSIRDL   81 (103)
Q Consensus        57 hFaY~tfAraa~~RRdnL~~Si~~l   81 (103)
                      .|.||++-+.--.|++.+..++.+.
T Consensus        24 k~l~~Pi~~~ld~R~~~I~~~l~~A   48 (140)
T PRK07353         24 ALFYKPVGKVVEEREDYIRTNRAEA   48 (140)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9988889999999999998889999


No 37 
>pfam06160 EzrA Septation ring formation regulator, EzrA. During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.
Probab=21.02  E-value=65  Score=13.87  Aligned_cols=89  Identities=12%  Similarity=0.156  Sum_probs=66.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9998899999999999999999999999999999----999999715770014318999999999999999999999999
Q gi|254780894|r   10 LKEFRLNDERRQLQQLRATILEFRRIVADLEKQI----AIEERQVGIYDKDHFAYPILAKSARQRIDNLLLSIRDLLLRQ   85 (103)
Q Consensus        10 Lk~fqVdEkRR~laql~~m~~ef~~~~~~LE~qI----~~Ee~~agi~d~~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~   85 (103)
                      +.+|.+-.-++.+.+++.++...+..+..+-.++    ..|++-...-+...=-|-.+-+.....+..+..++..|..|+
T Consensus        91 ~~~~rf~ka~~~i~~~~~~i~~~e~~i~~i~~~l~~L~~~e~~nr~~v~~lk~~y~~lrk~ll~~~~~yG~a~~~LE~~L  170 (559)
T pfam06160        91 NDKFRFLKAKKAIKEIEELLDTIEEDIEQILEELNELKESEEKNRKEVEELKDKYRELRKTLLAKSFSYGPALDELEKQL  170 (559)
T ss_pred             HHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
T ss_conf             86062899999999999999999999999999999999878988999999999999999999985222013689999999


Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             99999999999997
Q gi|254780894|r   86 ESLESHLESESNSD   99 (103)
Q Consensus        86 e~a~~~L~~a~~~~   99 (103)
                      +..+..+. .|+++
T Consensus       171 ~~ie~~F~-~f~~l  183 (559)
T pfam06160       171 DELEEEFE-QFVEL  183 (559)
T ss_pred             HHHHHHHH-HHHHH
T ss_conf             99999899-99999


No 38 
>TIGR03007 pepcterm_ChnLen polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; InterPro: IPR014345   Members of this entry belong to the family of polysaccharide chain length determinant proteins. They are found in species that encode the PEP-CTERM/exosortase system and are predicted to act in protein sorting in a number of Gram-negative bacteria, they are also found near the epsH homologue that is the putative exosortase gene..
Probab=20.87  E-value=66  Score=13.85  Aligned_cols=35  Identities=23%  Similarity=0.297  Sum_probs=16.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             89999999999999999999999999999999999
Q gi|254780894|r   14 RLNDERRQLQQLRATILEFRRIVADLEKQIAIEER   48 (103)
Q Consensus        14 qVdEkRR~laql~~m~~ef~~~~~~LE~qI~~Ee~   48 (103)
                      ++|+.+=+-++-+--+-+.-+.+..|+.+-..|-+
T Consensus       268 ~Ld~L~l~YTd~HPdv~~~k~~Ia~L~~~~~~e~~  302 (510)
T TIGR03007       268 QLDALRLRYTDKHPDVIATKREIAQLEEQKEEELE  302 (510)
T ss_pred             HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99986336301155899999999999999889998


No 39 
>TIGR01256 modA molybdate ABC transporter, periplasmic molybdate-binding protein; InterPro: IPR005950   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).     This entry describes the molybdate ABC transporter periplasmic binding protein in bacteria and archae. Several of the periplasmic receptors constitute a diverse class of binding proteins that differ widely in size, sequence and ligand specificity. It has been shown experimentally by radioactive labeling that ModA represents a hydrophylioc periplasmic-binding protein in Gram-negative organisms and its counterpart in Gram-positive organisms is a lipoprotein. The other components of the system include ModB, an integral membrane protein and ModC, the ATP-binding subunit. Almost all of them display a common beta/alpha folding motif and have similar tertiary structures consisting of two globular domains.; GO: 0015412 molybdate transmembrane-transporting ATPase activity, 0015689 molybdate ion transport, 0030288 outer membrane-bounded periplasmic space.
Probab=20.79  E-value=52  Score=14.50  Aligned_cols=24  Identities=33%  Similarity=0.434  Sum_probs=20.7

Q ss_pred             HHHHHCCCCCCCCHHHHHHHHHHH
Q ss_conf             999715770014318999999999
Q gi|254780894|r   47 ERQVGIYDKDHFAYPILAKSARQR   70 (103)
Q Consensus        47 e~~agi~d~~hFaY~tfAraa~~R   70 (103)
                      -++.+|-||.|--||.||..|.+-
T Consensus       105 ~~~vaigdP~~~P~G~~A~E~L~~  128 (225)
T TIGR01256       105 DKTVAIGDPKHAPYGAAAKEVLQK  128 (225)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             370234682444357999999970


No 40 
>pfam07321 YscO Type III secretion protein YscO. This family contains the bacterial type III secretion protein YscO, which is approximately 150 residues long. YscO has been shown to be required for high-level expression and secretion of the anti-host proteins V antigen and Yops in Yersinia pestis.
Probab=20.74  E-value=66  Score=13.83  Aligned_cols=92  Identities=12%  Similarity=0.107  Sum_probs=71.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             78889999988999999999999999999999999999999999997157700143189999999999999999999999
Q gi|254780894|r    4 QEQRTRLKEFRLNDERRQLQQLRATILEFRRIVADLEKQIAIEERQVGIYDKDHFAYPILAKSARQRIDNLLLSIRDLLL   83 (103)
Q Consensus         4 retLIRLk~fqVdEkRR~laql~~m~~ef~~~~~~LE~qI~~Ee~~agi~d~~hFaY~tfAraa~~RRdnL~~Si~~l~~   83 (103)
                      ..+|.+++.|.+|.-.+.|.--+.....-......-..++..-..|-..-...-|+-+.-+--....-|.++..|+-|+.
T Consensus         2 i~~Ll~Ik~~R~~~A~~a~~~qe~~l~~a~~~~~~a~~~~~dyr~Wr~~EE~Rl~~~~~~~~~~~kele~~q~~ia~Lr~   81 (152)
T pfam07321         2 IARLLEIKKLRAERAEKAVKRQEQALVQARARHREAQQSLQDYRQWRQQEENRLFAELQGATVLLKELEKWQQQVGLLRE   81 (152)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH
T ss_conf             37789989998889999999999999999999999999898899988888998999985135107769999999899998


Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999999999999
Q gi|254780894|r   84 RQESLESHLESE   95 (103)
Q Consensus        84 Q~e~a~~~L~~a   95 (103)
                      .-......+.++
T Consensus        82 ~e~~le~~~~ea   93 (152)
T pfam07321        82 NEASLEQQLAEA   93 (152)
T ss_pred             HHHHHHHHHHHH
T ss_conf             787899999999


No 41 
>TIGR00473 pssA CDP-diacylglycerol--serine O-phosphatidyltransferase; InterPro: IPR004533 This enzyme, CDP-diacylglycerol--serine O-phosphatidyltransferase, is involved in phospholipid biosynthesis catalyzing the reaction CDP-diacylglycerol + L-serine = CMP + L-1-phosphatidylserine. Members of this family do not bear any significant sequence similarity to the corresponding Escherichia coli protein.; GO: 0003882 CDP-diacylglycerol-serine O-phosphatidyltransferase activity, 0008654 phospholipid biosynthetic process, 0046341 CDP-diacylglycerol metabolic process, 0016020 membrane.
Probab=20.29  E-value=43  Score=15.03  Aligned_cols=12  Identities=25%  Similarity=0.282  Sum_probs=8.7

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             889999988999
Q gi|254780894|r    6 QRTRLKEFRLND   17 (103)
Q Consensus         6 tLIRLk~fqVdE   17 (103)
                      .++||+||+|..
T Consensus       104 G~lRLaRFNv~~  115 (174)
T TIGR00473       104 GILRLARFNVLT  115 (174)
T ss_pred             HHHHHHHHCCCC
T ss_conf             999888733335


No 42 
>TIGR01020 rpsE_arch ribosomal protein S5; InterPro: IPR005711   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .   This model finds eukaryotic ribosomal protein S2 as well as archaeal ribosomal protein S5.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=20.11  E-value=47  Score=14.78  Aligned_cols=22  Identities=27%  Similarity=0.133  Sum_probs=15.6

Q ss_pred             HHHHCCCCCCCCH------HHHHHHHHH
Q ss_conf             9971577001431------899999999
Q gi|254780894|r   48 RQVGIYDKDHFAY------PILAKSARQ   69 (103)
Q Consensus        48 ~~agi~d~~hFaY------~tfAraa~~   69 (103)
                      +-|||+|+=.|+-      .+||||.=.
T Consensus       172 ~LAGI~DVWt~T~G~T~Tt~NFAkAtF~  199 (220)
T TIGR01020       172 RLAGIKDVWTQTRGETRTTVNFAKATFE  199 (220)
T ss_pred             HHCCCCEEEECCCCCCCCCCHHHHHHHH
T ss_conf             7459623540455602233038899999


No 43 
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=20.10  E-value=68  Score=13.75  Aligned_cols=89  Identities=15%  Similarity=0.166  Sum_probs=66.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9998899999999999999999999999999999----999999715770014318999999999999999999999999
Q gi|254780894|r   10 LKEFRLNDERRQLQQLRATILEFRRIVADLEKQI----AIEERQVGIYDKDHFAYPILAKSARQRIDNLLLSIRDLLLRQ   85 (103)
Q Consensus        10 Lk~fqVdEkRR~laql~~m~~ef~~~~~~LE~qI----~~Ee~~agi~d~~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~   85 (103)
                      +.+|.+-.-++.+.+++.++...+..+..+-..+    ..|++-...-+...=-|-.+-+.....+..+..++..|..++
T Consensus        95 ~~~~rf~kak~~l~~~~~~l~~~e~~i~~i~~~l~~L~~~e~~nr~~v~~lk~~y~~lrk~ll~~~~~yG~a~~~LE~~L  174 (569)
T PRK04778         95 NDKFRFFKAKHEINEIESLLDEIEEDIEQILEELQELLESEEKNREEVEQLKDKYRELRKSLLANSFSFGPALDELEKQL  174 (569)
T ss_pred             HHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
T ss_conf             87252899999999999999999999999999999999868998999999999999999999985221033699999999


Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             99999999999997
Q gi|254780894|r   86 ESLESHLESESNSD   99 (103)
Q Consensus        86 e~a~~~L~~a~~~~   99 (103)
                      ...+..++ .|+++
T Consensus       175 ~~le~~f~-~f~~l  187 (569)
T PRK04778        175 ENLEEEFS-QFVEL  187 (569)
T ss_pred             HHHHHHHH-HHHHH
T ss_conf             99999899-99999


No 44 
>COG4970 FimT Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=20.03  E-value=69  Score=13.74  Aligned_cols=34  Identities=15%  Similarity=0.108  Sum_probs=27.4

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             014318999999999999999999999999999999
Q gi|254780894|r   56 DHFAYPILAKSARQRIDNLLLSIRDLLLRQESLESH   91 (103)
Q Consensus        56 ~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~   91 (103)
                      ..||+|.|..-..  +..|.++..+|-..+--||.+
T Consensus        26 a~~A~P~fs~~i~--~~rl~s~a~eL~a~l~lARte   59 (181)
T COG4970          26 AVIAAPNFSQWIR--SQRLRSAADELAAALQLARTE   59 (181)
T ss_pred             HHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHH
T ss_conf             9985100888877--878988999999999999999


Done!