Query         gi|254780944|ref|YP_003065357.1| hypothetical protein CLIBASIA_04215 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 228
No_of_seqs    121 out of 807
Neff          6.4 
Searched_HMMs 39220
Date          Mon May 30 03:22:07 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780944.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 COG2928 Uncharacterized conser 100.0       0       0  427.2  22.7  206    9-218     1-206 (222)
  2 pfam04367 DUF502 Protein of un 100.0 4.9E-34 1.2E-38  228.9  11.9  107   70-180     2-108 (108)
  3 PRK10573 type IV pilin biogene  91.7     1.1 2.7E-05   24.2  10.7   29   91-119   240-270 (397)
  4 COG1459 PulF Type II secretory  82.7     3.8 9.6E-05   20.8   8.8   23   89-111   238-260 (397)
  5 PRK09824 beta-glucoside-specif  82.1       4  0.0001   20.7  10.2   19   26-44    218-236 (625)
  6 PRK09796 cellobiose/arbutin/sa  79.5     4.9 0.00012   20.1  10.2   81   24-117   220-305 (472)
  7 pfam01230 HIT HIT domain.       78.2     4.1  0.0001   20.6   4.3   42  162-204    10-52  (98)
  8 PRK09586 murP N-acetylmuramic   67.7     9.5 0.00024   18.3   9.5   83   24-117   228-311 (474)
  9 PRK11007 trehalose(maltose)-sp  67.6     9.6 0.00024   18.3   8.7   27   24-50    231-257 (473)
 10 cd01277 HINT_subgroup HINT (hi  60.9      13 0.00033   17.5   4.0   42  162-204    18-60  (103)
 11 PRK05700 fliQ flagellar biosyn  58.6      14 0.00036   17.3  11.0   82   10-105     6-87  (89)
 12 pfam06160 EzrA Septation ring   52.2      18 0.00046   16.6   3.3   59   67-128     3-63  (559)
 13 TIGR02120 GspF general secreti  50.5      19 0.00048   16.5   6.6   93    9-112   172-279 (414)
 14 TIGR02518 EutH_ACDH acetaldehy  49.0     9.5 0.00024   18.3   1.5   93   81-181    18-121 (528)
 15 PRK04778 septation ring format  48.4      20 0.00052   16.3   4.8   61   65-128     5-67  (569)
 16 PRK12781 fliQ flagellar biosyn  47.7      21 0.00054   16.2  11.2   81   10-104     6-86  (88)
 17 cd00468 HIT_like HIT family: H  47.4      21 0.00054   16.2   4.1   44  163-207     3-47  (86)
 18 pfam02674 Colicin_V Colicin V   47.3      21 0.00054   16.2  12.5   96   10-115    13-108 (145)
 19 COG0537 Hit Diadenosine tetrap  45.2      23 0.00059   16.0   4.0   43  163-206    20-63  (138)
 20 PRK12772 bifunctional flagella  43.6      24 0.00062   15.8  10.4   40    7-46    165-204 (609)
 21 PRK04949 putative sulfate tran  42.5      25 0.00064   15.7   9.1   28   23-50     29-60  (251)
 22 KOG0125 consensus               40.6      26 0.00066   15.7   2.7   48  127-174   120-173 (376)
 23 cd01276 PKCI_related Protein K  40.4      27  0.0007   15.5   3.4   38  162-200    18-56  (104)
 24 COG4956 Integral membrane prot  38.9      29 0.00073   15.4   9.4   30   91-120    65-94  (356)
 25 COG4794 EscS Type III secretor  38.5      29 0.00075   15.3   9.5   77   16-106    12-88  (89)
 26 COG1684 FliR Flagellar biosynt  36.0      32 0.00082   15.1  11.9   44    3-46    164-207 (258)
 27 pfam10173 DUF2343 Uncharacteri  35.7      32 0.00083   15.0   4.5   54   84-137     8-61  (106)
 28 cd01275 FHIT FHIT (fragile his  35.3      33 0.00084   15.0   4.1   41  163-204    19-60  (126)
 29 TIGR01995 PTS-II-ABC-beta PTS   35.1      33 0.00084   15.0   4.9   86   24-119   236-323 (660)
 30 COG1987 FliQ Flagellar biosynt  34.1      34 0.00088   14.9  11.3   82   10-105     6-87  (89)
 31 PRK11513 cytochrome b561; Prov  33.8      35 0.00089   14.9   6.5   15   67-81     48-62  (176)
 32 PRK11365 ssuC alkanesulfonate   33.2      36 0.00091   14.8   6.5   40   66-105    70-110 (263)
 33 pfam05552 TM_helix Conserved T  32.9      36 0.00092   14.8   4.3   28   70-97     18-45  (53)
 34 pfam11969 DcpS_C Scavenger mRN  32.7      36 0.00092   14.8   3.3   37  163-200    19-56  (113)
 35 TIGR01078 arcA arginine deimin  32.3      37 0.00094   14.7   2.9   33  109-141   244-276 (421)
 36 pfam03596 Cad Cadmium resistan  32.0      37 0.00095   14.7   6.8   85   67-173    34-120 (192)
 37 COG4756 Predicted cation trans  30.6      28 0.00071   15.5   1.5   18  200-217   306-323 (367)
 38 PRK06010 fliQ flagellar biosyn  29.8      40   0.001   14.5  11.1   81   10-104     6-86  (88)
 39 KOG2927 consensus               29.6      41   0.001   14.4   5.2   26   48-75    208-234 (372)
 40 TIGR02119 panF sodium/pantothe  29.1      42  0.0011   14.4   6.2   27   65-91     73-99  (474)
 41 COG3180 AbrB Putative ammonia   28.8      40   0.001   14.5   2.1   59   69-137    94-152 (352)
 42 pfam07854 DUF1646 Protein of u  28.3      32 0.00081   15.1   1.5   25  194-218   284-312 (347)
 43 PRK09765 2-O-a-mannosyl-D-glyc  27.9      44  0.0011   14.2   6.8  106    4-110   276-425 (638)
 44 pfam06711 DUF1198 Protein of u  27.8      39   0.001   14.5   1.9   36   69-104     5-40  (148)
 45 pfam02762 Cbl_N3 CBL proto-onc  27.3      38 0.00096   14.6   1.7   39  109-150    11-49  (86)
 46 PRK03776 phosphoglycerol trans  27.2      45  0.0012   14.2   6.9   66   17-83     26-98  (762)
 47 PRK11901 hypothetical protein;  27.1      45  0.0012   14.2   2.3   21   64-84     39-59  (329)
 48 TIGR02823 oxido_YhdH putative   26.6      40   0.001   14.5   1.7   62  133-203    56-125 (330)
 49 TIGR00630 uvra excinuclease AB  26.4      34 0.00087   14.9   1.3   16  188-203   814-830 (956)
 50 pfam06695 Sm_multidrug_ex Puta  24.1      51  0.0013   13.8   2.9   53   89-142    35-92  (121)
 51 TIGR00757 RNaseEG ribonuclease  24.0      52  0.0013   13.8   2.2   11  165-175   153-163 (464)
 52 PRK10892 D-arabinose 5-phospha  23.9      52  0.0013   13.8   5.1  101   86-209   195-300 (326)
 53 TIGR01937 nqrB NADH:ubiquinone  22.6      55  0.0014   13.6   5.6   32   14-45    115-146 (508)
 54 TIGR02188 Ac_CoA_lig_AcsA acet  21.6      51  0.0013   13.9   1.5   60   67-134   131-211 (643)
 55 PRK00042 tpiA triosephosphate   20.8      53  0.0013   13.7   1.4   37  111-152   143-179 (251)
 56 cd02435 CCC1 CCC1. CCC1: This   20.2      62  0.0016   13.3   5.8   41   47-90    170-210 (241)
 57 PRK11026 ftsX cell division pr  20.1      62  0.0016   13.3   9.8   11  140-150    94-104 (309)
 58 COG0841 AcrB Cation/multidrug   20.0      62  0.0016   13.3   5.2   35  164-199   589-625 (1009)

No 1  
>COG2928 Uncharacterized conserved protein [Function unknown]
Probab=100.00  E-value=0  Score=427.24  Aligned_cols=206  Identities=39%  Similarity=0.806  Sum_probs=197.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             69999999999999999999999999999999998764210512115011011023589999999999998777433788
Q gi|254780944|r    9 SISAKVRNNFFAGFIICAPIAITIWLSLSLIHWFDGFIVPYIPMQYNPEYYCDFSIPGFGLLVVIVGINIVGFFGRNLLG   88 (228)
Q Consensus         9 ~l~~~l~~~Fl~GLlvllPi~iTi~i~~~l~~~~~~~~~p~i~~~~~~~~~~~~~i~glg~~~~i~~i~liG~l~~~~~g   88 (228)
                      +.++|+||||+|||++++|+++|+|+++|+++|+|++++|.++..+.+..+.+..++|+|+++.+++++++|++++|.+|
T Consensus         1 k~~~~lk~~fltGLlvllPlaiT~~vv~~i~~~l~~~~~~~lp~~~~~~~~~~~~i~~lg~il~iili~l~G~l~~~~ig   80 (222)
T COG2928           1 KGAKRLKKYFLTGLLVLLPLAITLWVVSWIFGLLDQFVGPLLPDRLRPAVYFPFNIPGLGVILAIILIFLLGFLARNMIG   80 (222)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             91788999999889999999999999999999998764430421212221476034788999999999999999998755


Q ss_pred             HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCEEEEEEEECCCHHHHHHHHCCCCCCCEEE
Q ss_conf             99999999999533238899999999999973177553310399984887579999970687156555302467773899
Q gi|254780944|r   89 RFVFFLSESILNNTPIVRHLYKSTKQIIRTLLKEDSTSFKNACLVEYPSAGFWSLCFLTTEVKGEIKEKFSNIGCEDMVT  168 (228)
Q Consensus        89 ~~~~~~~e~~l~rIP~v~~IY~sikqi~~~~~~~~~~~f~~vVlVe~P~~g~~~iGFvT~~~~~~~~~~~~~~~~~~~v~  168 (228)
                      |++++++|++|.|||++|+||+++||+++++.++++++||+||+|||||+|+|++||+|++..+++++    ..+++|++
T Consensus        81 ~~l~~~~d~~L~RiPlv~~IY~s~kqi~etll~~~~~sfk~vvlVefP~~G~~~i~fvtg~~~~e~~~----~~~~~~v~  156 (222)
T COG2928          81 RSLLSLGDSLLRRIPLVKSIYKSAKQVVETLLSDQSGSFKQVVLVEFPRRGIWAIAFVTGEKAGELKE----KEGRPMVA  156 (222)
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCEEEEEECCCCCCCHHC----CCCCCEEE
T ss_conf             48999999997007528889999999999997268845000489877999817999851677750001----35885079


Q ss_pred             EEEECCCCCCCCEEEEEEHHHEEECCCCHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             99707985326889998777624779999999999870143378878876
Q gi|254780944|r  169 VFIPPTPLPTAGMLVFVPRNKVIMLKMSAEDSAKMLISGGLLIPDNISYD  218 (228)
Q Consensus       169 VfiPtsPnPtsG~~~~vp~~~v~~~dmsveeA~k~iiS~Gv~~P~~~~~~  218 (228)
                      ||+||||||||||+.+||+||++++||++|||+|+++|||+++|+.....
T Consensus       157 VfvPTTPNPTsGfl~~Vpkedi~~ldmtvEda~k~iIS~G~v~p~~~~~~  206 (222)
T COG2928         157 VFVPTTPNPTSGFLLLVPKEDIVPLDMTVEDALKYIISGGVVAPDSLPAK  206 (222)
T ss_pred             EECCCCCCCCCCEEEEEEHHHCEECCCCHHHHHHEEEECCCCCCCCCCCC
T ss_conf             98379998876459998889822353649877451666664489852311


No 2  
>pfam04367 DUF502 Protein of unknown function (DUF502). Predicted to be an integral membrane protein.
Probab=100.00  E-value=4.9e-34  Score=228.88  Aligned_cols=107  Identities=46%  Similarity=0.861  Sum_probs=99.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCEEEEEEEECC
Q ss_conf             99999999987774337889999999999953323889999999999997317755331039998488757999997068
Q gi|254780944|r   70 LVVIVGINIVGFFGRNLLGRFVFFLSESILNNTPIVRHLYKSTKQIIRTLLKEDSTSFKNACLVEYPSAGFWSLCFLTTE  149 (228)
Q Consensus        70 ~~~i~~i~liG~l~~~~~g~~~~~~~e~~l~rIP~v~~IY~sikqi~~~~~~~~~~~f~~vVlVe~P~~g~~~iGFvT~~  149 (228)
                      ++++++|+++|+++++++||++++++|+++.|||++|+||+++||++++++++++++|++||+||||++|+|++||+|+|
T Consensus         2 ~~~l~~i~~vG~l~~~~~g~~l~~~~e~~l~riP~v~~IY~~ikq~~~~~~~~~~~~f~~vVlV~~p~~g~~~iGFvT~~   81 (108)
T pfam04367         2 ILTLLLIFLVGLLARNFIGRWLLSLGERLLNRIPLVRSIYSSVKQIVETLLGDKKKSFRKVVLVEYPRPGLWAIGFVTGE   81 (108)
T ss_pred             EEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCEEEEEEECC
T ss_conf             52089999999999959899999999999997861989999999999998458875632589999459992899999257


Q ss_pred             CHHHHHHHHCCCCCCCEEEEEEECCCCCCCC
Q ss_conf             7156555302467773899997079853268
Q gi|254780944|r  150 VKGEIKEKFSNIGCEDMVTVFIPPTPLPTAG  180 (228)
Q Consensus       150 ~~~~~~~~~~~~~~~~~v~VfiPtsPnPtsG  180 (228)
                      ..+++.+    ..++|+++||+|||||||||
T Consensus        82 ~~~~~~~----~~~~~~v~VfvPtspnPtsG  108 (108)
T pfam04367        82 VGGELAE----RLGEDLVAVFVPTTPNPTSG  108 (108)
T ss_pred             CCCHHHC----CCCCCEEEEEECCCCCCCCC
T ss_conf             7304431----47996599992899999998


No 3  
>PRK10573 type IV pilin biogenesis protein; Provisional
Probab=91.68  E-value=1.1  Score=24.18  Aligned_cols=29  Identities=21%  Similarity=0.312  Sum_probs=19.8

Q ss_pred             HHHHHHHHHHHCCHHHHHHHHH--HHHHHHH
Q ss_conf             9999999995332388999999--9999997
Q gi|254780944|r   91 VFFLSESILNNTPIVRHLYKST--KQIIRTL  119 (228)
Q Consensus        91 ~~~~~e~~l~rIP~v~~IY~si--kqi~~~~  119 (228)
                      ...+.|+++.|+|+++.+|...  -++..++
T Consensus       240 ~~~~~~~~llkiP~~g~l~~~~~~~rf~~~L  270 (397)
T PRK10573        240 WQIREQRLLLRIPLMGSLIRGQKLSQIFTIL  270 (397)
T ss_pred             HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH
T ss_conf             7699999972124465999999999999999


No 4  
>COG1459 PulF Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=82.72  E-value=3.8  Score=20.79  Aligned_cols=23  Identities=13%  Similarity=0.059  Sum_probs=18.8

Q ss_pred             HHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             99999999999533238899999
Q gi|254780944|r   89 RFVFFLSESILNNTPIVRHLYKS  111 (228)
Q Consensus        89 ~~~~~~~e~~l~rIP~v~~IY~s  111 (228)
                      .+.-.+.|+++.|+|+++.+...
T Consensus       238 ~~~r~~~~~~llrlP~~g~l~~~  260 (397)
T COG1459         238 PAGRRRLDRLLLRLPLFGKLVRK  260 (397)
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHH
T ss_conf             47788888697607757799999


No 5  
>PRK09824 beta-glucoside-specific PTS system components IIABC; Provisional
Probab=82.15  E-value=4  Score=20.66  Aligned_cols=19  Identities=26%  Similarity=0.546  Sum_probs=6.7

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999987
Q gi|254780944|r   26 APIAITIWLSLSLIHWFDG   44 (228)
Q Consensus        26 lPi~iTi~i~~~l~~~~~~   44 (228)
                      +|+.++.|+..++-+|++.
T Consensus       218 iPiIl~v~~~s~vEk~l~K  236 (625)
T PRK09824        218 IPIIFSAWLCSILERRLNA  236 (625)
T ss_pred             HHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999987


No 6  
>PRK09796 cellobiose/arbutin/salicin-specific PTS system components IIBC; Provisional
Probab=79.54  E-value=4.9  Score=20.11  Aligned_cols=81  Identities=14%  Similarity=0.178  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999876421051211501101102358999999----999999877743378899999999999
Q gi|254780944|r   24 ICAPIAITIWLSLSLIHWFDGFIVPYIPMQYNPEYYCDFSIPGFGLLVV----IVGINIVGFFGRNLLGRFVFFLSESIL   99 (228)
Q Consensus        24 vllPi~iTi~i~~~l~~~~~~~~~p~i~~~~~~~~~~~~~i~glg~~~~----i~~i~liG~l~~~~~g~~~~~~~e~~l   99 (228)
                      -++|+.++.|+..|+-+|++.++-..+...+         .|.+.++++    ++++=-+|....+.++    .....+.
T Consensus       220 sViPiil~v~~~s~ier~l~K~iP~~l~~i~---------~P~ltlli~~~l~l~viGPig~~i~~~i~----~~v~~l~  286 (472)
T PRK09796        220 TVIPALVMTWCLSYIERWVDRITPAVTKNFL---------KPMLIVLIAAPLAILLIGPIGIWIGSAIS----ALVYTIH  286 (472)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHH
T ss_conf             0699999999999999999974819989989---------98999999999999999889999999999----9999998


Q ss_pred             HHCCHH-HHHHHHHHHHHH
Q ss_conf             533238-899999999999
Q gi|254780944|r  100 NNTPIV-RHLYKSTKQIIR  117 (228)
Q Consensus       100 ~rIP~v-~~IY~sikqi~~  117 (228)
                      .+.|.+ ..|++..-|.+=
T Consensus       287 ~~~~~i~g~i~g~~~~~lV  305 (472)
T PRK09796        287 GYLGWLSVAIMGALWPLLV  305 (472)
T ss_pred             HCCHHHHHHHHHHHHHHHH
T ss_conf             6053999999999999999


No 7  
>pfam01230 HIT HIT domain.
Probab=78.18  E-value=4.1  Score=20.57  Aligned_cols=42  Identities=19%  Similarity=0.487  Sum_probs=34.2

Q ss_pred             CCCCEEEEEEECCCCCCCCEEEEEEHHHEEEC-CCCHHHHHHHH
Q ss_conf             77738999970798532688999877762477-99999999998
Q gi|254780944|r  162 GCEDMVTVFIPPTPLPTAGMLVFVPRNKVIML-KMSAEDSAKML  204 (228)
Q Consensus       162 ~~~~~v~VfiPtsPnPtsG~~~~vp~~~v~~~-dmsveeA~k~i  204 (228)
                      -+++.+.+|+...|. +-|.++.+|+..+..+ |++.|+..++.
T Consensus        10 yed~~~~aflD~~P~-~~gH~LViPk~H~~~l~dl~~~~~~~l~   52 (98)
T pfam01230        10 YEDDLVLAFLDIDPQ-APGHVLVIPKKHIRELHDLTPEELGDLM   52 (98)
T ss_pred             EECCCEEEEECCCCC-CCCEEEEEEECCCCCCCCCCHHHHHHHH
T ss_conf             978979999878889-9971999961052851429999999999


No 8  
>PRK09586 murP N-acetylmuramic acid phosphotransfer permease; Reviewed
Probab=67.73  E-value=9.5  Score=18.31  Aligned_cols=83  Identities=16%  Similarity=0.109  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             9999999999999999999876421051211501101102358999999999-999877743378899999999999533
Q gi|254780944|r   24 ICAPIAITIWLSLSLIHWFDGFIVPYIPMQYNPEYYCDFSIPGFGLLVVIVG-INIVGFFGRNLLGRFVFFLSESILNNT  102 (228)
Q Consensus        24 vllPi~iTi~i~~~l~~~~~~~~~p~i~~~~~~~~~~~~~i~glg~~~~i~~-i~liG~l~~~~~g~~~~~~~e~~l~rI  102 (228)
                      .++|+.++.|+..++-+|++.++-..+...         ..|.+.+++++.+ ++++|=+. ++++.-+-..+..+ .--
T Consensus       228 sViPiIl~v~~~s~iek~l~K~iP~~l~~i---------~~P~ltllI~~pl~l~viGPig-~~l~~gi~~~~~~~-~~~  296 (474)
T PRK09586        228 NIIGVLIAAWAGARIERMVRRFMPDDLDML---------LTSLITLLITATLAYLIIMPLG-GWLFEGMSWLFMHL-NSN  296 (474)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHH-CCC
T ss_conf             409999999999999999997472999998---------9989999999999999999899-99999999999980-211


Q ss_pred             CHHHHHHHHHHHHHH
Q ss_conf             238899999999999
Q gi|254780944|r  103 PIVRHLYKSTKQIIR  117 (228)
Q Consensus       103 P~v~~IY~sikqi~~  117 (228)
                      |+...++...-|++=
T Consensus       297 ~~~~~ii~g~~~~lV  311 (474)
T PRK09586        297 PLGCAVLAGLFLIAV  311 (474)
T ss_pred             HHHHHHHHHHHHHHH
T ss_conf             899999999999996


No 9  
>PRK11007 trehalose(maltose)-specific PTS system components IIBC; Provisional
Probab=67.58  E-value=9.6  Score=18.30  Aligned_cols=27  Identities=7%  Similarity=0.033  Sum_probs=18.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             999999999999999999987642105
Q gi|254780944|r   24 ICAPIAITIWLSLSLIHWFDGFIVPYI   50 (228)
Q Consensus        24 vllPi~iTi~i~~~l~~~~~~~~~p~i   50 (228)
                      .++|+.++.|+..++-+|++.++-..+
T Consensus       231 sViPiIl~v~~~s~iEk~~~K~iP~~l  257 (473)
T PRK11007        231 QVIPALLAGLALGFIETRLKRIVPDYL  257 (473)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCHHHH
T ss_conf             089999999999999999986470998


No 10 
>cd01277 HINT_subgroup HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life. Although the biochemical function has not been characterised for many of the members of this subgroup, the proteins from Yeast have been shown to be involved in secretion, peroxisome formation and gene expression.
Probab=60.86  E-value=13  Score=17.52  Aligned_cols=42  Identities=21%  Similarity=0.414  Sum_probs=33.9

Q ss_pred             CCCCEEEEEEECCCCCCCCEEEEEEHHHEEEC-CCCHHHHHHHH
Q ss_conf             77738999970798532688999877762477-99999999998
Q gi|254780944|r  162 GCEDMVTVFIPPTPLPTAGMLVFVPRNKVIML-KMSAEDSAKML  204 (228)
Q Consensus       162 ~~~~~v~VfiPtsPnPtsG~~~~vp~~~v~~~-dmsveeA~k~i  204 (228)
                      -++|.+.+|.+..|. .-|-++.+||..+..+ |++-|+.-.+.
T Consensus        18 ~E~e~~~af~d~~P~-~pgH~LViPK~H~~~l~dl~~~~~~~l~   60 (103)
T cd01277          18 YEDDHVLAFLDINPA-SKGHTLVIPKKHYENLLDLDPEELAELI   60 (103)
T ss_pred             EECCCEEEEECCCCC-CCCEEEEEECCCCCCHHHCCHHHHHHHH
T ss_conf             979979999778889-9942999962577981139999999999


No 11 
>PRK05700 fliQ flagellar biosynthesis protein FliQ; Validated
Probab=58.56  E-value=14  Score=17.28  Aligned_cols=82  Identities=9%  Similarity=0.212  Sum_probs=54.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999999999987642105121150110110235899999999999987774337889
Q gi|254780944|r   10 ISAKVRNNFFAGFIICAPIAITIWLSLSLIHWFDGFIVPYIPMQYNPEYYCDFSIPGFGLLVVIVGINIVGFFGRNLLGR   89 (228)
Q Consensus        10 l~~~l~~~Fl~GLlvllPi~iTi~i~~~l~~~~~~~~~p~i~~~~~~~~~~~~~i~glg~~~~i~~i~liG~l~~~~~g~   89 (228)
                      ...-.|+.+...+.+..|+.+.-.++-.++..+.    .....+.          .-+.|+-=++.+++.=++.-.+.++
T Consensus         6 ~i~l~~~al~~~l~ls~P~L~~alvVGl~Isi~Q----A~TqIqE----------qTLsFvPKliav~~~l~~~g~Wm~~   71 (89)
T PRK05700          6 VMDLFREAMKVALMLAAPLLLVALIVGLVVSIFQ----AATQINE----------QTLSFIPKILAVLLTLIIAGPWMLN   71 (89)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999998889999999999999999----9999999----------8998799999999999998789999


Q ss_pred             HHHHHHHHHHHHCCHH
Q ss_conf             9999999999533238
Q gi|254780944|r   90 FVFFLSESILNNTPIV  105 (228)
Q Consensus        90 ~~~~~~e~~l~rIP~v  105 (228)
                      .+.++..+++++||-+
T Consensus        72 ~l~~f~~~if~~ip~l   87 (89)
T PRK05700         72 TLLDYTRTLFTNIPTL   87 (89)
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             9999999999987766


No 12 
>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=52.22  E-value=18  Score=16.64  Aligned_cols=59  Identities=27%  Similarity=0.464  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHCCHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             9999999999998777433788999999999--9953323889999999999997317755331
Q gi|254780944|r   67 FGLLVVIVGINIVGFFGRNLLGRFVFFLSES--ILNNTPIVRHLYKSTKQIIRTLLKEDSTSFK  128 (228)
Q Consensus        67 lg~~~~i~~i~liG~l~~~~~g~~~~~~~e~--~l~rIP~v~~IY~sikqi~~~~~~~~~~~f~  128 (228)
                      +|+++++++++++|++.++..-+.+-.+-++  -+...|+.--+-. +|++  .+.|+....|.
T Consensus         3 i~iivivii~~~~~~~~rk~~~k~I~~Le~rk~~l~~~pv~~el~k-vk~L--~l~Ges~~~f~   63 (559)
T pfam06160         3 IGIIVIVIVAYLAGYFLRKKIYKQIDELEERKEELMNLPVNEELSK-VKKL--NLTGESEETFE   63 (559)
T ss_pred             EEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH-HHCC--CCCHHHHHHHH
T ss_conf             4089999999999999988899999999999999874988999999-8829--89705699999


No 13 
>TIGR02120 GspF general secretion pathway protein F; InterPro: IPR011850   This membrane protein is a component of the terminal branch complex of the general secretion pathway (GSP), also known as the "Type II" secretion pathway. The GSP transports proteins (generally virulence-associated cell wall hydrolases) across the outer membrase of the bacterial cell. Transport across the inner membrane is often, but not exclusively handled by the Sec system. GspF nearly always clusters with other GSP subunits. However, some genes from Xylella and Xanthomonas strains are excluded from this entry due to excessive divergence.; GO: 0008565 protein transporter activity, 0015628 protein secretion by the type II secretion system, 0015627 type II protein secretion system complex.
Probab=50.55  E-value=19  Score=16.48  Aligned_cols=93  Identities=16%  Similarity=0.296  Sum_probs=46.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHH--------------HHHHHHHHH
Q ss_conf             699999999999999999999999999999999987642105121150110110235--------------899999999
Q gi|254780944|r    9 SISAKVRNNFFAGFIICAPIAITIWLSLSLIHWFDGFIVPYIPMQYNPEYYCDFSIP--------------GFGLLVVIV   74 (228)
Q Consensus         9 ~l~~~l~~~Fl~GLlvllPi~iTi~i~~~l~~~~~~~~~p~i~~~~~~~~~~~~~i~--------------glg~~~~i~   74 (228)
                      .+.+++.+.      .+=|+.+|+--+.-+...+ +++-|=+-.+|.   ...-.+|              -.|+++.+ 
T Consensus       172 ~lr~Ki~~A------liYPa~l~vVa~~vv~~Ll-~~VVPkvV~~F~---~~~q~LPl~Tr~li~lSdFl~~~G~~~~~-  240 (414)
T TIGR02120       172 ALRSKITTA------LIYPAVLTVVAIGVVIFLL-AYVVPKVVEQFA---HMKQTLPLLTRALIALSDFLRSWGWALLA-  240 (414)
T ss_pred             HHHHHHHHH------HHHHHHHHHHHHHHHHHHH-HHHCCCEECHHH---CCCCCCCHHHHHHHHHCHHHHHHHHHHHH-
T ss_conf             999999998------7658999999999999999-420444031023---19978748999999845168889999999-


Q ss_pred             HHHHHHHHHHHHHHHH-HHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             9999877743378899-9999999995332388999999
Q gi|254780944|r   75 GINIVGFFGRNLLGRF-VFFLSESILNNTPIVRHLYKST  112 (228)
Q Consensus        75 ~i~liG~l~~~~~g~~-~~~~~e~~l~rIP~v~~IY~si  112 (228)
                      .+..++++....+.+. .-..+|+++-|+|++|.+-..+
T Consensus       241 ~~~~~~~l~~~~Lr~p~~r~~~dr~LLr~PviG~L~r~l  279 (414)
T TIGR02120       241 ALAALVVLFRRLLRDPAFRLRFDRRLLRLPVIGRLVRGL  279 (414)
T ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHCCHHHHHHHHHH
T ss_conf             999999999998438987504548783202456899999


No 14 
>TIGR02518 EutH_ACDH acetaldehyde dehydrogenase (acetylating); InterPro: IPR013357   Aldehyde dehydrogenases (1.2.1.3 from EC and 1.2.1.5 from EC) are enzymes which oxidize a wide variety of aliphatic and aromatic aldehydes using NAD(P) as a cofactor. In eukaryotes, at least twenty distinct aldehyde dehydrogenase families have been classified . Many aldehyde dehydrogenases have also been found in prokaryotic species. A glutamic acid and a cysteine residue have been implicated in the catalytic activity of mammalian aldehyde dehydrogenase, though these residues are not necessarily conserved in all the enzymes of this family.   The acetaldehyde dehydrogenase family (1.2.1.10 from EC) of bacterial enzymes catalyse the formation of acetyl-CoA from acetaldehyde in the degradation of phenols, cresols and catechol . Proteins in this entry occur in bacterial species and are annotated as probable acetaldehyde dehydrogenases, though this function has not been experimentally verified..
Probab=49.01  E-value=9.5  Score=18.33  Aligned_cols=93  Identities=16%  Similarity=0.175  Sum_probs=53.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCEE-----------EEEECCCCCEEEEEEEECC
Q ss_conf             77433788999999999995332388999999999999731775533103-----------9998488757999997068
Q gi|254780944|r   81 FFGRNLLGRFVFFLSESILNNTPIVRHLYKSTKQIIRTLLKEDSTSFKNA-----------CLVEYPSAGFWSLCFLTTE  149 (228)
Q Consensus        81 ~l~~~~~g~~~~~~~e~~l~rIP~v~~IY~sikqi~~~~~~~~~~~f~~v-----------VlVe~P~~g~~~iGFvT~~  149 (228)
                      =-+++-+.+.-.+.+|+++..|  +..-|...-++..+-  ..+++|.++           -.|---=+++.++|.+.-+
T Consensus        18 k~Aq~~~a~~~q~qID~iv~ai--~~~~~~~~~~LAkmA--~EETGFGk~eDKv~KN~fA~~~vY~~IKDmKTvG~~~E~   93 (528)
T TIGR02518        18 KVAQKKLANMTQEQIDKIVKAI--VDAAYENAVKLAKMA--NEETGFGKWEDKVIKNVFAAKIVYDSIKDMKTVGILEED   93 (528)
T ss_pred             HHHHHHHHHHCHHHHHHHHHHH--HHHHHHHHHHHHHHC--CCCCCCCCEECHHHHHHHHHHHHHHHCCCCCEEEEEEEC
T ss_conf             9999998740577787999999--998752278888741--542577411020244678777765410554135556415


Q ss_pred             CHHHHHHHHCCCCCCCEEEEEEECCCCCCCCE
Q ss_conf             71565553024677738999970798532688
Q gi|254780944|r  150 VKGEIKEKFSNIGCEDMVTVFIPPTPLPTAGM  181 (228)
Q Consensus       150 ~~~~~~~~~~~~~~~~~v~VfiPtsPnPtsG~  181 (228)
                      ....+-+.   .-+-+.|+=.+|.| ||||-.
T Consensus        94 ~~~~~~ev---~vP~G~vagl~PST-NPTSTa  121 (528)
T TIGR02518        94 KEKKVIEV---AVPVGVVAGLIPST-NPTSTA  121 (528)
T ss_pred             CCCCEEEE---ECCCEEEEECCCCC-CCHHHH
T ss_conf             54505885---05502344435878-854799


No 15 
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=48.45  E-value=20  Score=16.27  Aligned_cols=61  Identities=25%  Similarity=0.321  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHCCHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             589999999999998777433788999999999--9953323889999999999997317755331
Q gi|254780944|r   65 PGFGLLVVIVGINIVGFFGRNLLGRFVFFLSES--ILNNTPIVRHLYKSTKQIIRTLLKEDSTSFK  128 (228)
Q Consensus        65 ~glg~~~~i~~i~liG~l~~~~~g~~~~~~~e~--~l~rIP~v~~IY~sikqi~~~~~~~~~~~f~  128 (228)
                      ..+++++++++++++|++.++..-+.+-++-++  -+..+|+.-.+-. +|++  .+.|+....|.
T Consensus         5 iii~iivlvii~~~~~~~~rr~~~k~I~~Le~rK~~l~~~pv~~el~k-vk~L--~l~Get~~~fe   67 (569)
T PRK04778          5 LIIAIVVIIIIAYLVGYILRKRNYKRIDELEERKQELEDLPVNEELEK-VKKL--NLTGQSETKFE   67 (569)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH-HHCC--CCCCHHHHHHH
T ss_conf             789999999999999999999999899999999999876987999998-8808--67706599999


No 16 
>PRK12781 fliQ flagellar biosynthesis protein FliQ; Reviewed
Probab=47.73  E-value=21  Score=16.21  Aligned_cols=81  Identities=16%  Similarity=0.155  Sum_probs=55.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999999999987642105121150110110235899999999999987774337889
Q gi|254780944|r   10 ISAKVRNNFFAGFIICAPIAITIWLSLSLIHWFDGFIVPYIPMQYNPEYYCDFSIPGFGLLVVIVGINIVGFFGRNLLGR   89 (228)
Q Consensus        10 l~~~l~~~Fl~GLlvllPi~iTi~i~~~l~~~~~~~~~p~i~~~~~~~~~~~~~i~glg~~~~i~~i~liG~l~~~~~g~   89 (228)
                      ...-.|.-+..-+++-.|+.+.-.++-.++    ++++-....+.          .-+.|+-=++.+++.-++...+.++
T Consensus         6 vi~l~r~al~~~l~~s~PiL~~aL~VGl~I----sifQA~TQIQE----------~TLsFVPKi~av~~~l~l~g~wm~~   71 (88)
T PRK12781          6 ALELVRAAIWTIIVASGPAVGAAMLVGIAI----ALLQALTQIQE----------VTLTFVPKIVVILIVMAVTGSFVGA   71 (88)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999774999999999999----99999999999----------9998599899999999998779999


Q ss_pred             HHHHHHHHHHHHCCH
Q ss_conf             999999999953323
Q gi|254780944|r   90 FVFFLSESILNNTPI  104 (228)
Q Consensus        90 ~~~~~~e~~l~rIP~  104 (228)
                      .+.++.+++++|||-
T Consensus        72 ~l~~ft~~lf~~I~~   86 (88)
T PRK12781         72 QIYAFTEMVYGRIES   86 (88)
T ss_pred             HHHHHHHHHHHHHCC
T ss_conf             999999999986122


No 17 
>cd00468 HIT_like HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified in the literacture into three major branches: the Hint branch, which consists of adenosine 5' -monophosphoramide hydrolases, the Fhit branch, that consists of diadenosine polyphosphate hydrolases, and the GalT branch consisting of specific nucloside monophosphate transferases. Further sequence analysis reveals several new closely related, yet uncharacterized subgroups.
Probab=47.39  E-value=21  Score=16.17  Aligned_cols=44  Identities=18%  Similarity=0.362  Sum_probs=34.8

Q ss_pred             CCCEEEEEEECCCCCCCCEEEEEEHHHEEEC-CCCHHHHHHHHHHC
Q ss_conf             7738999970798532688999877762477-99999999998701
Q gi|254780944|r  163 CEDMVTVFIPPTPLPTAGMLVFVPRNKVIML-KMSAEDSAKMLISG  207 (228)
Q Consensus       163 ~~~~v~VfiPtsPnPtsG~~~~vp~~~v~~~-dmsveeA~k~iiS~  207 (228)
                      ++|.+-+|+-..|. +-|=++.+||+.+..+ |++.|+.-++...+
T Consensus         3 Ede~~~af~Di~P~-~~gH~LViPk~h~~~l~dl~~~~~~~l~~~~   47 (86)
T cd00468           3 DDEHSFAFVNLKPA-APGHVLVCPKRHVETLPDLDEALLADLVITA   47 (86)
T ss_pred             CCCCEEEEECCCCC-CCCCEEEECCHHHCCHHHCCHHHHHHHHHHH
T ss_conf             27858999779889-9972999702241993469999999999999


No 18 
>pfam02674 Colicin_V Colicin V production protein. Colicin V production protein is required in E. Coli for colicin V production from plasmid pColV-K30. This protein is coded for in the purF operon.
Probab=47.28  E-value=21  Score=16.16  Aligned_cols=96  Identities=9%  Similarity=0.146  Sum_probs=53.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999999999987642105121150110110235899999999999987774337889
Q gi|254780944|r   10 ISAKVRNNFFAGFIICAPIAITIWLSLSLIHWFDGFIVPYIPMQYNPEYYCDFSIPGFGLLVVIVGINIVGFFGRNLLGR   89 (228)
Q Consensus        10 l~~~l~~~Fl~GLlvllPi~iTi~i~~~l~~~~~~~~~p~i~~~~~~~~~~~~~i~glg~~~~i~~i~liG~l~~~~~g~   89 (228)
                      ...-.+|=|+..++.++=..+.+++..+....+.+++.+.+..    +    .....+++++..+.+++++.+..+.+.+
T Consensus        13 ~~~G~~rG~i~e~~~l~~~i~~~~~a~~~~~~~~~~~~~~~~~----~----~~~~~~a~~iifi~~~~i~~~i~~~l~~   84 (145)
T pfam02674        13 ALLGFRRGFVREVLSLLGWVVAFFVASLFYPPLAPLLAEYVLS----P----ALAAIIAFLLIFLLVLLIGSLLGVLLRK   84 (145)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC----H----HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999999999999999998843797----8----9999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf             99999999995332388999999999
Q gi|254780944|r   90 FVFFLSESILNNTPIVRHLYKSTKQI  115 (228)
Q Consensus        90 ~~~~~~e~~l~rIP~v~~IY~sikqi  115 (228)
                      .+....-+.++|  +.+.+.+.+|-.
T Consensus        85 ~~~~~~l~~~dr--~lG~~~G~~k~~  108 (145)
T pfam02674        85 LVKLSGLGGLDR--LLGAVFGLLRGL  108 (145)
T ss_pred             HHHHHCCCHHHH--HHHHHHHHHHHH
T ss_conf             998805343899--999999999999


No 19 
>COG0537 Hit Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]
Probab=45.16  E-value=23  Score=15.96  Aligned_cols=43  Identities=21%  Similarity=0.430  Sum_probs=33.4

Q ss_pred             CCCEEEEEEECCCCCCCCEEEEEEHHHEEEC-CCCHHHHHHHHHH
Q ss_conf             7738999970798532688999877762477-9999999999870
Q gi|254780944|r  163 CEDMVTVFIPPTPLPTAGMLVFVPRNKVIML-KMSAEDSAKMLIS  206 (228)
Q Consensus       163 ~~~~v~VfiPtsPnPtsG~~~~vp~~~v~~~-dmsveeA~k~iiS  206 (228)
                      .++++.+|+=-.|. +-|.++.+|+..+..+ |++.++.-.+.-.
T Consensus        20 e~~~~~afld~~P~-~~gH~LviPk~h~~~l~~l~~~~~~~l~~~   63 (138)
T COG0537          20 EDEHVLAFLDIYPA-APGHTLVIPKRHVSDLEDLDPEELAELFLL   63 (138)
T ss_pred             ECCCEEEEECCCCC-CCCEEEEEECHHHHHHHHCCHHHHHHHHHH
T ss_conf             77988999777889-998699995554556760999999999999


No 20 
>PRK12772 bifunctional flagellar biosynthesis protein FliR/FlhB; Provisional
Probab=43.55  E-value=24  Score=15.81  Aligned_cols=40  Identities=15%  Similarity=0.210  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2169999999999999999999999999999999998764
Q gi|254780944|r    7 HTSISAKVRNNFFAGFIICAPIAITIWLSLSLIHWFDGFI   46 (228)
Q Consensus         7 ~~~l~~~l~~~Fl~GLlvllPi~iTi~i~~~l~~~~~~~~   46 (228)
                      ...+.+...+.|..|+-+-+|+.+++.+....++.+....
T Consensus       165 ~~~~~~~~~~~F~~a~~iA~Pii~~lll~dv~lGilaR~~  204 (609)
T PRK12772        165 IMHVINVFIQYFVIGIKIAIPIVLIILITDLTLGLISRTV  204 (609)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999999999999999999813


No 21 
>PRK04949 putative sulfate transport protein CysZ; Validated
Probab=42.54  E-value=25  Score=15.71  Aligned_cols=28  Identities=21%  Similarity=0.317  Sum_probs=16.5

Q ss_pred             HHHHHHHHHHHHH----HHHHHHHHHHHHHHC
Q ss_conf             9999999999999----999999987642105
Q gi|254780944|r   23 IICAPIAITIWLS----LSLIHWFDGFIVPYI   50 (228)
Q Consensus        23 lvllPi~iTi~i~----~~l~~~~~~~~~p~i   50 (228)
                      .+++|+.+++.++    +++++.+++++....
T Consensus        29 fv~iPlliNi~Lf~~~~~~l~~~~~~~~~~~~   60 (251)
T PRK04949         29 FVILPLLVNILLFGGAFWWLFTQLDAWIDWLM   60 (251)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99989999999999999999999999999998


No 22 
>KOG0125 consensus
Probab=40.64  E-value=26  Score=15.66  Aligned_cols=48  Identities=17%  Similarity=0.151  Sum_probs=30.5

Q ss_pred             CCEEEEEE--CCCCCEEEEEEEECCCHHHHHHHHC----CCCCCCEEEEEEECC
Q ss_conf             31039998--4887579999970687156555302----467773899997079
Q gi|254780944|r  127 FKNACLVE--YPSAGFWSLCFLTTEVKGEIKEKFS----NIGCEDMVTVFIPPT  174 (228)
Q Consensus       127 f~~vVlVe--~P~~g~~~iGFvT~~~~~~~~~~~~----~~~~~~~v~VfiPts  174 (228)
                      |.+|+=||  |-..|..-.||||=|++.+......    ..-+++.+-|=.-|+
T Consensus       120 fG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATa  173 (376)
T KOG0125         120 FGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATA  173 (376)
T ss_pred             HCCEEEEEEEECCCCCCCCCEEEECCHHHHHHHHHHHHCCEEECEEEEEECCCH
T ss_conf             175046899863677775234872282468999998504643012788741431


No 23 
>cd01276 PKCI_related Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a hydrophobic residue) that is a signature for this family. No enzymatic activity has been reported however, for PKCI and its related members.
Probab=40.41  E-value=27  Score=15.51  Aligned_cols=38  Identities=21%  Similarity=0.344  Sum_probs=31.1

Q ss_pred             CCCCEEEEEEECCCCCCCCEEEEEEHHHEEEC-CCCHHHH
Q ss_conf             77738999970798532688999877762477-9999999
Q gi|254780944|r  162 GCEDMVTVFIPPTPLPTAGMLVFVPRNKVIML-KMSAEDS  200 (228)
Q Consensus       162 ~~~~~v~VfiPtsPnPtsG~~~~vp~~~v~~~-dmsveeA  200 (228)
                      -++|.+.+|+...|. +-|-++.+||..+..+ |++-|++
T Consensus        18 yede~~~aflD~~P~-~~GH~LViPK~H~~~l~~l~~~~~   56 (104)
T cd01276          18 YEDDEVLAFHDINPQ-APVHILVIPKKHIASLSDATEEDE   56 (104)
T ss_pred             EECCCEEEEECCCCC-CCCEEEEEEEEEECCHHHCCHHHH
T ss_conf             979979999888999-983299985422298588998589


No 24 
>COG4956 Integral membrane protein (PIN domain superfamily) [General function prediction only]
Probab=38.95  E-value=29  Score=15.37  Aligned_cols=30  Identities=20%  Similarity=0.261  Sum_probs=20.4

Q ss_pred             HHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
Q ss_conf             999999999533238899999999999973
Q gi|254780944|r   91 VFFLSESILNNTPIVRHLYKSTKQIIRTLL  120 (228)
Q Consensus        91 ~~~~~e~~l~rIP~v~~IY~sikqi~~~~~  120 (228)
                      ..+++|+.+.|+|...-+|.++-=++..+.
T Consensus        65 ~~~~le~~i~k~~~~~ilf~tiGLiiGLli   94 (356)
T COG4956          65 WLKRLEEQIRKLPVTTILFGTIGLIIGLLI   94 (356)
T ss_pred             HHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
T ss_conf             999999999836899999987889999999


No 25 
>COG4794 EscS Type III secretory pathway, component EscS [Intracellular trafficking and secretion]
Probab=38.45  E-value=29  Score=15.32  Aligned_cols=77  Identities=17%  Similarity=0.304  Sum_probs=46.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999987642105121150110110235899999999999987774337889999999
Q gi|254780944|r   16 NNFFAGFIICAPIAITIWLSLSLIHWFDGFIVPYIPMQYNPEYYCDFSIPGFGLLVVIVGINIVGFFGRNLLGRFVFFLS   95 (228)
Q Consensus        16 ~~Fl~GLlvllPi~iTi~i~~~l~~~~~~~~~p~i~~~~~~~~~~~~~i~glg~~~~i~~i~liG~l~~~~~g~~~~~~~   95 (228)
                      +.+.-=|+.-+|-++    +..+++.+-++++.....+   |.       -++|.+-++.++..=++...+.|..++++.
T Consensus        12 qaL~liLilSlPpvi----vAsvvGllVslvQA~TQiQ---dQ-------Tl~f~iKLl~V~~tl~lt~~Wlg~~ll~fa   77 (89)
T COG4794          12 QALWLILILSLPPVI----VASVVGLLVSLVQALTQIQ---DQ-------TLPFGIKLLAVSATLFLTAGWLGATLLNFA   77 (89)
T ss_pred             HHHHHHHHHHCCHHH----HHHHHHHHHHHHHHHHHHH---HH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999611999----9999999999999999999---86-------788999999999999997077588999999


Q ss_pred             HHHHHHCCHHH
Q ss_conf             99995332388
Q gi|254780944|r   96 ESILNNTPIVR  106 (228)
Q Consensus        96 e~~l~rIP~v~  106 (228)
                      |..+.++|..|
T Consensus        78 ~~i~~~~~~~~   88 (89)
T COG4794          78 EQIFLNIPKAR   88 (89)
T ss_pred             HHHHHHHHHCC
T ss_conf             99999866405


No 26 
>COG1684 FliR Flagellar biosynthesis pathway, component FliR [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=35.95  E-value=32  Score=15.08  Aligned_cols=44  Identities=11%  Similarity=0.207  Sum_probs=35.6

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             76102169999999999999999999999999999999998764
Q gi|254780944|r    3 KKSFHTSISAKVRNNFFAGFIICAPIAITIWLSLSLIHWFDGFI   46 (228)
Q Consensus         3 ~~~~~~~l~~~l~~~Fl~GLlvllPi~iTi~i~~~l~~~~~~~~   46 (228)
                      ++.....+.+.+...|..|+..-+|+.....++...++.++...
T Consensus       164 ~~~~~~~l~~~l~~~F~~~l~iAlPii~~lLlvnlalGlv~R~~  207 (258)
T COG1684         164 NDNAFLLLAKALSAIFLIGLRLALPIIALLLLVNLALGLLNRLA  207 (258)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             74099999999999999999999899999999999999998425


No 27 
>pfam10173 DUF2343 Uncharacterized conserved protein (DUF2343). This entry is of a family of proteins conserved from plants to humans. The function is not known.
Probab=35.65  E-value=32  Score=15.05  Aligned_cols=54  Identities=19%  Similarity=0.193  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCC
Q ss_conf             337889999999999953323889999999999997317755331039998488
Q gi|254780944|r   84 RNLLGRFVFFLSESILNNTPIVRHLYKSTKQIIRTLLKEDSTSFKNACLVEYPS  137 (228)
Q Consensus        84 ~~~~g~~~~~~~e~~l~rIP~v~~IY~sikqi~~~~~~~~~~~f~~vVlVe~P~  137 (228)
                      ....-++++++++++++|||-=----.|+--.....-.++...-++.+-+-||.
T Consensus         8 ~~gwk~kiv~~g~~ll~rIpyeE~~LKSiP~~~~~~~~~~~~~~~~~i~v~yP~   61 (106)
T pfam10173         8 EKGWKKKIVSLGNKLLDRIPYEEWGLKSIPSLSAILRRKELEGAKIPIEVYYPG   61 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHHHCCCCCEEEEECCC
T ss_conf             088999999999999976784888886158602888874310457615687797


No 28 
>cd01275 FHIT FHIT (fragile histidine family): FHIT proteins, related to the HIT family carry a motif HxHxH/Qxx (x, is a hydrophobic amino acid), On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified into three  branches: the Hint branch, which consists of adenosine 5' -monophosphoramide hydrolases, the Fhit branch, that consists of diadenosine polyphosphate hydrolases, and the GalT branch consisting of specific nucloside monophosphate transferases. Fhit plays a very important role in the development of tumours. Infact, Fhit deletions are among the earliest and most frequent genetic alterations in the development of tumours.
Probab=35.30  E-value=33  Score=15.01  Aligned_cols=41  Identities=20%  Similarity=0.325  Sum_probs=32.9

Q ss_pred             CCCEEEEEEECCCCCCCCEEEEEEHHHEEEC-CCCHHHHHHHH
Q ss_conf             7738999970798532688999877762477-99999999998
Q gi|254780944|r  163 CEDMVTVFIPPTPLPTAGMLVFVPRNKVIML-KMSAEDSAKML  204 (228)
Q Consensus       163 ~~~~v~VfiPtsPnPtsG~~~~vp~~~v~~~-dmsveeA~k~i  204 (228)
                      +++++.+|+...|. +-|-++.+||..+..+ |++.|+...+.
T Consensus        19 ede~~~aflD~~P~-~~GH~LViPK~H~~~l~dl~~~e~~~l~   60 (126)
T cd01275          19 RTKHSFAVVNLYPY-NPGHVLVVPYRHVPRLEDLTPEEIADLF   60 (126)
T ss_pred             ECCCEEEEECCCCC-CCCEEEEECCHHCCHHHCCCHHHHHHHH
T ss_conf             79969999768889-9960999755330515309999999999


No 29 
>TIGR01995 PTS-II-ABC-beta PTS system, beta-glucoside-specific IIABC component; InterPro: IPR011297   The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) ,  is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars.   The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC . These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII).    The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site.    An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose , , , .    This entry represents a family of PTS enzyme II proteins in which all three domains are found in the same polypeptide chain and which appear to have a broad specificity for beta-glucosides including salicin (beta-D-glucose-1-salicylate) and arbutin (hydroquinone-O-beta-D-glucopyranoside) . These are distinct from the closely related sucrose-specific and trehalose-specific PTS transporters.; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system.
Probab=35.08  E-value=33  Score=14.99  Aligned_cols=86  Identities=16%  Similarity=0.236  Sum_probs=45.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99999999999999999998764210512115011011023589999999999-99877743378899999999999533
Q gi|254780944|r   24 ICAPIAITIWLSLSLIHWFDGFIVPYIPMQYNPEYYCDFSIPGFGLLVVIVGI-NIVGFFGRNLLGRFVFFLSESILNNT  102 (228)
Q Consensus        24 vllPi~iTi~i~~~l~~~~~~~~~p~i~~~~~~~~~~~~~i~glg~~~~i~~i-~liG~l~~~~~g~~~~~~~e~~l~rI  102 (228)
                      .++|+.+.+|+..++=+|+    ..++|..+.-     +..|.+-+++++=+. +++|=+ .+++|.-+.+....+++..
T Consensus       236 sVIP~il~v~lm~y~eK~~----~K~~P~~~~~-----F~~Pll~~LI~~PltL~i~GP~-g~~~g~gi~~~~~~Ly~~~  305 (660)
T TIGR01995       236 SVIPVILAVWLMSYVEKFL----KKVIPKALKN-----FLTPLLVMLITVPLTLLILGPV-GVYLGEGIASGILFLYEVS  305 (660)
T ss_pred             HHHHHHHHHHHHHHHHEEE----ECCCCHHHHH-----HHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHH
T ss_conf             3689999999985340122----3036467898-----6414999999888888654358-9999999999999887430


Q ss_pred             CHH-HHHHHHHHHHHHHH
Q ss_conf             238-89999999999997
Q gi|254780944|r  103 PIV-RHLYKSTKQIIRTL  119 (228)
Q Consensus       103 P~v-~~IY~sikqi~~~~  119 (228)
                      |.+ ..+|+++-|++=+|
T Consensus       306 p~~A~~llaa~~p~~V~~  323 (660)
T TIGR01995       306 PWLAGALLAAVWPVLVMF  323 (660)
T ss_pred             HHHHHHHHHHHHHHHHHH
T ss_conf             389999999888999997


No 30 
>COG1987 FliQ Flagellar biosynthesis pathway, component FliQ [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=34.12  E-value=34  Score=14.89  Aligned_cols=82  Identities=12%  Similarity=0.202  Sum_probs=53.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999999999987642105121150110110235899999999999987774337889
Q gi|254780944|r   10 ISAKVRNNFFAGFIICAPIAITIWLSLSLIHWFDGFIVPYIPMQYNPEYYCDFSIPGFGLLVVIVGINIVGFFGRNLLGR   89 (228)
Q Consensus        10 l~~~l~~~Fl~GLlvllPi~iTi~i~~~l~~~~~~~~~p~i~~~~~~~~~~~~~i~glg~~~~i~~i~liG~l~~~~~g~   89 (228)
                      ...=.+.-+-.+|....|+.+.-.++.-++..+.+    ......          --+.|+=-++.++++-.+..-+.++
T Consensus         6 ~l~i~~~ai~~~L~l~~P~ll~alvvGLvIsifQA----~TQIqE----------qTLsFiPKIiai~~~l~~~gpWm~~   71 (89)
T COG1987           6 VLDIGQEAIWLVLMLSAPVLLVALVVGLVISIFQA----ATQIQE----------QTLSFIPKIIAVFLVLILLGPWMLN   71 (89)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999899999999999999999----999999----------9998599899999999997589999


Q ss_pred             HHHHHHHHHHHHCCHH
Q ss_conf             9999999999533238
Q gi|254780944|r   90 FVFFLSESILNNTPIV  105 (228)
Q Consensus        90 ~~~~~~e~~l~rIP~v  105 (228)
                      .+.++...+++|||..
T Consensus        72 ~l~dft~~if~~i~~~   87 (89)
T COG1987          72 QLLDFTVTIFSNIPQI   87 (89)
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             9999999999988766


No 31 
>PRK11513 cytochrome b561; Provisional
Probab=33.81  E-value=35  Score=14.86  Aligned_cols=15  Identities=7%  Similarity=0.217  Sum_probs=6.4

Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             999999999999877
Q gi|254780944|r   67 FGLLVVIVGINIVGF   81 (228)
Q Consensus        67 lg~~~~i~~i~liG~   81 (228)
                      +|+.+.++.+.-+.+
T Consensus        48 ~Gi~il~L~~~Rl~w   62 (176)
T PRK11513         48 CGISILVLMVVRLLI   62 (176)
T ss_pred             HHHHHHHHHHHHHHH
T ss_conf             999999999999999


No 32 
>PRK11365 ssuC alkanesulfonate transporter permease subunit; Provisional
Probab=33.18  E-value=36  Score=14.80  Aligned_cols=40  Identities=20%  Similarity=0.139  Sum_probs=17.3

Q ss_pred             HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHCCHH
Q ss_conf             899999999999987774-3378899999999999533238
Q gi|254780944|r   66 GFGLLVVIVGINIVGFFG-RNLLGRFVFFLSESILNNTPIV  105 (228)
Q Consensus        66 glg~~~~i~~i~liG~l~-~~~~g~~~~~~~e~~l~rIP~v  105 (228)
                      .+|+++..++=..+|.+. .+...+++++-.=..+.-+|.+
T Consensus        70 ~~Gf~l~~~~Gi~lGil~g~~~~~~~~~~P~~~~l~~iP~i  110 (263)
T PRK11365         70 LIGFSIGGSLGLILGLISGLSRWGERLLDTSIQMLRNVPHL  110 (263)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHCCHH
T ss_conf             99999999999999999998699998758599999765799


No 33 
>pfam05552 TM_helix Conserved TM helix. This alignment represents a conserved transmembrane helix as well as some flanking sequence. It is often found in association with pfam00924.
Probab=32.93  E-value=36  Score=14.77  Aligned_cols=28  Identities=29%  Similarity=0.406  Sum_probs=19.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999998777433788999999999
Q gi|254780944|r   70 LVVIVGINIVGFFGRNLLGRFVFFLSES   97 (228)
Q Consensus        70 ~~~i~~i~liG~l~~~~~g~~~~~~~e~   97 (228)
                      ++..++++++|++..+.+++.+-+.+++
T Consensus        18 ii~AivIL~vG~~va~~v~~~v~k~L~~   45 (53)
T pfam05552        18 LIAAILILLVGWLIAKIVRRLVTKLLEK   45 (53)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999999998


No 34 
>pfam11969 DcpS_C Scavenger mRNA decapping enzyme C-term binding. This family consists of several scavenger mRNA decapping enzymes (DcpS) and is the C-terminal region. DcpS is a scavenger pyrophosphatase that hydrolyses the residual cap structure following 3' to 5' decay of an mRNA. The association of DcpS with 3' to 5' exonuclease exosome components suggests that these two activities are linked and there is a coupled exonucleolytic decay-dependent decapping pathway. The C-terminal domain contains a histidine triad (HIT) sequence with three histidines separated by hydrophobic residues. The central histidine within the DcpS HIT motif is critical for decapping activity and defines the HIT motif as a new mRNA decapping domain, making DcpS the first member of the HIT family of proteins with a defined biological function.
Probab=32.72  E-value=36  Score=14.75  Aligned_cols=37  Identities=19%  Similarity=0.309  Sum_probs=30.0

Q ss_pred             CCCEEEEEEECCCCCCCCEEEEEEHHHEEEC-CCCHHHH
Q ss_conf             7738999970798532688999877762477-9999999
Q gi|254780944|r  163 CEDMVTVFIPPTPLPTAGMLVFVPRNKVIML-KMSAEDS  200 (228)
Q Consensus       163 ~~~~v~VfiPtsPnPtsG~~~~vp~~~v~~~-dmsveeA  200 (228)
                      ++|.+.+|....|. ..|-++.+|++.+..+ |++.|+.
T Consensus        19 edd~~vaf~D~~P~-~~gH~LVIPk~h~~~~~dl~~~~~   56 (113)
T pfam11969        19 EDDGFVAFKDIKPK-APLHLLVIPKKHIKSLRDLTKEHL   56 (113)
T ss_pred             ECCCEEEEECCCCC-CCCEEEEEEEECCCCCCCCCHHHH
T ss_conf             79999998689989-997599999974044354898799


No 35 
>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=32.26  E-value=37  Score=14.71  Aligned_cols=33  Identities=15%  Similarity=0.328  Sum_probs=27.3

Q ss_pred             HHHHHHHHHHHHCCCCCCCCEEEEEECCCCCEE
Q ss_conf             999999999973177553310399984887579
Q gi|254780944|r  109 YKSTKQIIRTLLKEDSTSFKNACLVEYPSAGFW  141 (228)
Q Consensus       109 Y~sikqi~~~~~~~~~~~f~~vVlVe~P~~g~~  141 (228)
                      -.|+-++..+++.+++..|++|+.++.|+.-.+
T Consensus       244 ~q~ve~LA~~LF~~k~~~f~~vlA~~~Pk~ra~  276 (421)
T TIGR01078       244 AQSVEKLAKSLFANKEGGFKKVLAIKIPKNRAL  276 (421)
T ss_pred             HHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCC
T ss_conf             889999999998403376555899717555678


No 36 
>pfam03596 Cad Cadmium resistance transporter.
Probab=31.99  E-value=37  Score=14.68  Aligned_cols=85  Identities=16%  Similarity=0.217  Sum_probs=44.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCC--CCEEEEEECCCCCEEEEE
Q ss_conf             999999999999877743378899999999999533238899999999999973177553--310399984887579999
Q gi|254780944|r   67 FGLLVVIVGINIVGFFGRNLLGRFVFFLSESILNNTPIVRHLYKSTKQIIRTLLKEDSTS--FKNACLVEYPSAGFWSLC  144 (228)
Q Consensus        67 lg~~~~i~~i~liG~l~~~~~g~~~~~~~e~~l~rIP~v~~IY~sikqi~~~~~~~~~~~--f~~vVlVe~P~~g~~~iG  144 (228)
                      +|+...++.=++.++......-    +|+-.++.-+|+    |-.+|...+   +++++.  -++..--.-.++..|+++
T Consensus        34 lGf~~Lv~~Sl~~a~g~~~ip~----~wilGlLGliPi----~lGi~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~Va  102 (192)
T pfam03596        34 LGSVALVLVSLLFAFVLNLVPE----KWILGLLGLIPI----YLGIKVLIK---GDDDDEEEILELLNSGKNNSLFGTVA  102 (192)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCH----HHHHHHHHHHHH----HHHHHHHHH---CCCCCCHHHHHHHCCCCCCCCEEEEE
T ss_conf             7799999999999999874799----999998758999----999999972---76655134444420256677059999


Q ss_pred             EEECCCHHHHHHHHCCCCCCCEEEEEEEC
Q ss_conf             97068715655530246777389999707
Q gi|254780944|r  145 FLTTEVKGEIKEKFSNIGCEDMVTVFIPP  173 (228)
Q Consensus       145 FvT~~~~~~~~~~~~~~~~~~~v~VfiPt  173 (228)
                      .+|=-+           .+.|-..||+|-
T Consensus       103 ~vTiAn-----------cGgDNIgiYvPl  120 (192)
T pfam03596       103 IITFAS-----------CGADNIGIFVPY  120 (192)
T ss_pred             EEEEEC-----------CCCCEEEEEEEE
T ss_conf             999951-----------578516897521


No 37 
>COG4756 Predicted cation transporter [General function prediction only]
Probab=30.61  E-value=28  Score=15.46  Aligned_cols=18  Identities=50%  Similarity=0.863  Sum_probs=13.1

Q ss_pred             HHHHHHHCCCCCCCCCCC
Q ss_conf             999987014337887887
Q gi|254780944|r  200 SAKMLISGGLLIPDNISY  217 (228)
Q Consensus       200 A~k~iiS~Gv~~P~~~~~  217 (228)
                      -|.+++|||+..|.+++.
T Consensus       306 lmsLvIsGGmlIPGNiPN  323 (367)
T COG4756         306 LMSLVISGGMLIPGNIPN  323 (367)
T ss_pred             HHHHHHCCCEECCCCCCC
T ss_conf             999977287335788862


No 38 
>PRK06010 fliQ flagellar biosynthesis protein FliQ; Reviewed
Probab=29.84  E-value=40  Score=14.46  Aligned_cols=81  Identities=14%  Similarity=0.143  Sum_probs=53.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999999999987642105121150110110235899999999999987774337889
Q gi|254780944|r   10 ISAKVRNNFFAGFIICAPIAITIWLSLSLIHWFDGFIVPYIPMQYNPEYYCDFSIPGFGLLVVIVGINIVGFFGRNLLGR   89 (228)
Q Consensus        10 l~~~l~~~Fl~GLlvllPi~iTi~i~~~l~~~~~~~~~p~i~~~~~~~~~~~~~i~glg~~~~i~~i~liG~l~~~~~g~   89 (228)
                      ...-.|+-+..-+.+-.|+.++-.++-.++.    +++.....+.          .-+.|+-=++.+++.-.+...+.++
T Consensus         6 vi~l~~~al~~~l~ls~P~L~valvVGl~Is----lfQA~TQIqE----------qTLsFvPKliav~~~l~~~~pwm~~   71 (88)
T PRK06010          6 ALDVVRDAIWTVLIASGPAVLAAMVVGVAIA----LFQALTQIQE----------MTLTFVPKIVAIFVTLLLTLPFMGA   71 (88)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999998769999999999999----9999999999----------8998799999999999998889999


Q ss_pred             HHHHHHHHHHHHCCH
Q ss_conf             999999999953323
Q gi|254780944|r   90 FVFFLSESILNNTPI  104 (228)
Q Consensus        90 ~~~~~~e~~l~rIP~  104 (228)
                      .+.++.++++.+||.
T Consensus        72 ~l~~ft~~if~~I~g   86 (88)
T PRK06010         72 QISAFTLRIYSRIAG   86 (88)
T ss_pred             HHHHHHHHHHHHHCC
T ss_conf             999999999987134


No 39 
>KOG2927 consensus
Probab=29.57  E-value=41  Score=14.43  Aligned_cols=26  Identities=31%  Similarity=0.498  Sum_probs=10.2

Q ss_pred             HHCCCCCCH-HHHCCCHHHHHHHHHHHHH
Q ss_conf             105121150-1101102358999999999
Q gi|254780944|r   48 PYIPMQYNP-EYYCDFSIPGFGLLVVIVG   75 (228)
Q Consensus        48 p~i~~~~~~-~~~~~~~i~glg~~~~i~~   75 (228)
                      |+.|..... .+|+.  +++.||+..++.
T Consensus       208 PLWP~~mR~gvyY~s--ig~~gfl~~Ilv  234 (372)
T KOG2927         208 PLWPRRMRQGVYYLS--IGAGGFLAFILV  234 (372)
T ss_pred             CCCCHHHHCCEEEEE--CCHHHHHHHHHH
T ss_conf             358388742211344--031599999999


No 40 
>TIGR02119 panF sodium/pantothenate symporter; InterPro: IPR011849   Pantothenate (vitamin B5) is a precursor of coenzyme A and is made from aspartate and 2-oxoisovalerate in most bacteria with completed genome sequences. However, some pathogens must import pantothenate. This entry describes PanF, a sodium/pantothenate symporter. Several species that have this transporter appear to lack all enzymes of pantothenate biosynthesis, namely Haemophilus influenzae, Pasteurella multocida, Fusobacterium nucleatum, and Borrelia burgdorferi (Lyme disease spirochete) .; GO: 0015081 sodium ion transmembrane transporter activity, 0015233 pantothenate transporter activity, 0031402 sodium ion binding, 0006814 sodium ion transport, 0015887 pantothenate transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=29.05  E-value=42  Score=14.37  Aligned_cols=27  Identities=15%  Similarity=0.212  Sum_probs=20.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             589999999999998777433788999
Q gi|254780944|r   65 PGFGLLVVIVGINIVGFFGRNLLGRFV   91 (228)
Q Consensus        65 ~glg~~~~i~~i~liG~l~~~~~g~~~   91 (228)
                      .|+|+++.-..=...||++=..+||++
T Consensus        73 ~GLGWVLLa~iQvpt~~~~LgVLGKKf   99 (474)
T TIGR02119        73 YGLGWVLLAMIQVPTVYLVLGVLGKKF   99 (474)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             152699999999999999997899999


No 41 
>COG3180 AbrB Putative ammonia monooxygenase [General function prediction only]
Probab=28.82  E-value=40  Score=14.49  Aligned_cols=59  Identities=12%  Similarity=0.345  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCC
Q ss_conf             999999999987774337889999999999953323889999999999997317755331039998488
Q gi|254780944|r   69 LLVVIVGINIVGFFGRNLLGRFVFFLSESILNNTPIVRHLYKSTKQIIRTLLKEDSTSFKNACLVEYPS  137 (228)
Q Consensus        69 ~~~~i~~i~liG~l~~~~~g~~~~~~~e~~l~rIP~v~~IY~sikqi~~~~~~~~~~~f~~vVlVe~P~  137 (228)
                      .+.+++.-.+.||+.+++-   ..+..+.++.-.|+      ...++.. +..|.+...+.|.+++|=|
T Consensus        94 ~~~tl~~s~l~g~ll~r~~---~~~~~Ta~~gs~PG------gas~m~~-iA~d~gAd~~~VAl~Q~lR  152 (352)
T COG3180          94 LLLTLLSSILLGWLLKRFS---ILPGNTAFLGSSPG------GASAMVS-IAQDYGADLRLVALMQYLR  152 (352)
T ss_pred             HHHHHHHHHHHHHHHHHHC---CCCCCHHHHHCCCC------HHHHHHH-HHHHHCCCHHHHHHHHHHH
T ss_conf             9999999999999999954---89962135752874------6899999-9998489735789999999


No 42 
>pfam07854 DUF1646 Protein of unknown function (DUF1646). Some of the members of this family are hypothetical bacterial and archaeal proteins, but others are annotated as being cation transporters expressed by the archaebacterium Methanosarcina mazei.
Probab=28.29  E-value=32  Score=15.09  Aligned_cols=25  Identities=48%  Similarity=0.737  Sum_probs=19.3

Q ss_pred             CCCHHH----HHHHHHHCCCCCCCCCCCC
Q ss_conf             999999----9999870143378878876
Q gi|254780944|r  194 KMSAED----SAKMLISGGLLIPDNISYD  218 (228)
Q Consensus       194 dmsvee----A~k~iiS~Gv~~P~~~~~~  218 (228)
                      .|+.|+    -|.+++|||+..|.+++.-
T Consensus       284 ~M~~~qI~aiLmgLliSGGMLIPGNIPNI  312 (347)
T pfam07854       284 EMTEEQIRSILMGLLISGGMLIPGNIPNI  312 (347)
T ss_pred             CCCHHHHHHHHHHHHHCCCEECCCCCCHH
T ss_conf             24899999999999992871047886402


No 43 
>PRK09765 2-O-a-mannosyl-D-glycerate specific PTS transporten components IIABC; Provisional
Probab=27.85  E-value=44  Score=14.24  Aligned_cols=106  Identities=16%  Similarity=0.182  Sum_probs=54.9

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------------------------HHCCCCCC
Q ss_conf             61021699999999999999999999999999999999987642----------------------------10512115
Q gi|254780944|r    4 KSFHTSISAKVRNNFFAGFIICAPIAITIWLSLSLIHWFDGFIV----------------------------PYIPMQYN   55 (228)
Q Consensus         4 ~~~~~~l~~~l~~~Fl~GLlvllPi~iTi~i~~~l~~~~~~~~~----------------------------p~i~~~~~   55 (228)
                      ...+++..+++++.+++|.=..+|+++.=-++.-+-..+++..+                            |++.....
T Consensus       276 ~~~~~~~~~~iyk~lmtGVS~MlPfVVaGGiliAi~~l~~~~~g~~~~~~~~~~~~~~~~~igg~~~~~lmvPvla~yIA  355 (638)
T PRK09765        276 TQPVKSVKTELKQALLSGISFAVPLIVAGGTVLAVAVLLSQIFGLQDLFNEENSWLWMYRKLGGGLLGILMVPVLAAYTA  355 (638)
T ss_pred             CCCCCCHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             44433056899999983521546299985899999998602457653345666499999998789999999999999999


Q ss_pred             HH-HHCCCHHH-----------HHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHH--HCCHHHHHHH
Q ss_conf             01-10110235-----------899999999999987774337889--99999999995--3323889999
Q gi|254780944|r   56 PE-YYCDFSIP-----------GFGLLVVIVGINIVGFFGRNLLGR--FVFFLSESILN--NTPIVRHLYK  110 (228)
Q Consensus        56 ~~-~~~~~~i~-----------glg~~~~i~~i~liG~l~~~~~g~--~~~~~~e~~l~--rIP~v~~IY~  110 (228)
                      .. ..-+-..|           +.||+-.++.=|+.||++... .+  ++-++++.+..  -+|++.++-.
T Consensus       356 ySIadrpglapGfi~G~~A~~~~aGFlGaii~GflaGy~v~~l-kk~iklp~~l~gl~piliiPl~~~li~  425 (638)
T PRK09765        356 YSLADKPALAPGFAAGLAANMIGSGFLGAVVGGLIAGYLMRWV-KNHLRLSSKFNGFLTFYLYPVLGTLGA  425 (638)
T ss_pred             HHHCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH-HHHCCCCHHHHCCCCEEEHHHHHHHHH
T ss_conf             9862874107899999997325640789999999999999999-985778776754477886168999999


No 44 
>pfam06711 DUF1198 Protein of unknown function (DUF1198). This family consists of several bacterial proteins of around 150 residues in length which are specific to Escherichia coli, Salmonella species and Yersinia pestis. The function of this family is unknown.
Probab=27.78  E-value=39  Score=14.53  Aligned_cols=36  Identities=22%  Similarity=0.184  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH
Q ss_conf             999999999987774337889999999999953323
Q gi|254780944|r   69 LLVVIVGINIVGFFGRNLLGRFVFFLSESILNNTPI  104 (228)
Q Consensus        69 ~~~~i~~i~liG~l~~~~~g~~~~~~~e~~l~rIP~  104 (228)
                      ++.+++.+|++|+=+-+.=.|+..+.+-..++--|+
T Consensus         5 ilAtLvVVFivGfRvLTSdtRrAi~rLs~rL~I~pv   40 (148)
T pfam06711         5 ILATLIVVFIVGFRVLTSDTRRAIDRLSERLKIKPV   40 (148)
T ss_pred             HHHHHHHHHHEEEEEECCCHHHHHHHHHHHHCCCCE
T ss_conf             886889974202344346528999999987299835


No 45 
>pfam02762 Cbl_N3 CBL proto-oncogene N-terminus, SH2-like domain. Cbl is an adaptor protein that binds EGF receptors (or other tyrosine kinases) and SH3 domains, functioning as a negative regulator of many signaling pathways. The N-terminal domain is evolutionarily conserved, and is known to bind to phosphorylated tyrosine residues. The so called N-terminal domain is actually 3 structural domains, of which this is the C-terminal SH2 domain.
Probab=27.34  E-value=38  Score=14.65  Aligned_cols=39  Identities=15%  Similarity=0.445  Sum_probs=23.4

Q ss_pred             HHHHHHHHHHHHCCCCCCCCEEEEEECCCCCEEEEEEEECCC
Q ss_conf             999999999973177553310399984887579999970687
Q gi|254780944|r  109 YKSTKQIIRTLLKEDSTSFKNACLVEYPSAGFWSLCFLTTEV  150 (228)
Q Consensus       109 Y~sikqi~~~~~~~~~~~f~~vVlVe~P~~g~~~iGFvT~~~  150 (228)
                      |.-+|.-.+.+.. +-.++  +--..--|-|-|+||+||.|.
T Consensus        11 YDevk~rL~~~~~-kpGSY--iFRlSCTrlGQWAIgyVt~dg   49 (86)
T pfam02762        11 YDEVKARLQKFIH-KPGSY--IFRLSCTRLGQWAIGYVTADG   49 (86)
T ss_pred             HHHHHHHHHHHHC-CCCCE--EEEEECCCCCCEEEEEECCCC
T ss_conf             9999999999745-99736--997523633525789985788


No 46 
>PRK03776 phosphoglycerol transferase I; Provisional
Probab=27.16  E-value=45  Score=14.17  Aligned_cols=66  Identities=14%  Similarity=0.339  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH--H----HHHHCCCCCCHHHHCCCHHHHHHHHHHHHHHHH-HHHHH
Q ss_conf             9999999999999999999999999987--6----421051211501101102358999999999999-87774
Q gi|254780944|r   17 NFFAGFIICAPIAITIWLSLSLIHWFDG--F----IVPYIPMQYNPEYYCDFSIPGFGLLVVIVGINI-VGFFG   83 (228)
Q Consensus        17 ~Fl~GLlvllPi~iTi~i~~~l~~~~~~--~----~~p~i~~~~~~~~~~~~~i~glg~~~~i~~i~l-iG~l~   83 (228)
                      +.+.-++++|-+.+-+.+++++-+.+.|  +    +-.+. ..+.-..+..+.+|++++++.+.++|. ..+..
T Consensus        26 ~w~~~~l~~lg~~iiln~~l~asnYfTGdGINDAVifhLt-~~l~Gagv~~YIlP~I~~i~~l~lvF~~l~~~L   98 (762)
T PRK03776         26 WWFAATLTVLGLFVVLNITLFASDYFTGDGINDAVLYTLT-NSLTGAGVSKYILPGIGIVLALTAVFGALGWIL   98 (762)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEE-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHE
T ss_conf             1699999999999999999999751267887712899996-267654501101688999999999999988740


No 47 
>PRK11901 hypothetical protein; Reviewed
Probab=27.07  E-value=45  Score=14.16  Aligned_cols=21  Identities=29%  Similarity=0.471  Sum_probs=15.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             358999999999999877743
Q gi|254780944|r   64 IPGFGLLVVIVGINIVGFFGR   84 (228)
Q Consensus        64 i~glg~~~~i~~i~liG~l~~   84 (228)
                      +-|+|+++++++|..||-..+
T Consensus        39 MiGiGILVLLLLIIgIgSALK   59 (329)
T PRK11901         39 MIGIGILVLLLLIIAIGSALK   59 (329)
T ss_pred             HHHHHHHHHHHHHHHHHHHHC
T ss_conf             999999999999998656432


No 48 
>TIGR02823 oxido_YhdH putative quinone oxidoreductase, YhdH/YhfP family; InterPro: IPR014188   This entry represents a subfamily of the alcohol dehydrogenase, a superfamily in which some members are zinc-binding medium-chain alcohol dehydrogenases while others are quinone oxidoreductases with no bound zinc. This entry includes YhdH from Escherichia coli and YhfP from Bacillus subtilis both of which bind NADPH or NAD, but not zinc. Both proteins have been studied crystallographically for insight into function. .
Probab=26.55  E-value=40  Score=14.50  Aligned_cols=62  Identities=18%  Similarity=0.191  Sum_probs=39.0

Q ss_pred             EECCC-CCEEEEEEEECCCHHHHHHHHCCCCCCCEEEEE---EECCCCCCCCE--EEEEEHHHEEEC--CCCHHHHHHH
Q ss_conf             98488-757999997068715655530246777389999---70798532688--999877762477--9999999999
Q gi|254780944|r  133 VEYPS-AGFWSLCFLTTEVKGEIKEKFSNIGCEDMVTVF---IPPTPLPTAGM--LVFVPRNKVIML--KMSAEDSAKM  203 (228)
Q Consensus       133 Ve~P~-~g~~~iGFvT~~~~~~~~~~~~~~~~~~~v~Vf---iPtsPnPtsG~--~~~vp~~~v~~~--dmsveeA~k~  203 (228)
                      =+||. +|+=.-|-|-....+       .+..+|.|-|.   +=.  +-++||  ..-||-|++.++  +||..|||-+
T Consensus        56 R~yP~~PGID~aG~Vv~S~dp-------~F~~GD~VivTGyglG~--~H~GGysqyaRVp~dWlVpLP~glsl~eAM~~  125 (330)
T TIGR02823        56 RSYPMIPGIDLAGTVVSSEDP-------RFRPGDEVIVTGYGLGV--SHDGGYSQYARVPADWLVPLPEGLSLREAMAL  125 (330)
T ss_pred             EECCCCCCCCCEEEEEECCCC-------CCCCCCEEEEEEECCCC--CCCCCCEEEEEECHHHEECCCCCCCHHHHHHH
T ss_conf             877876881754689844887-------75788718997402456--51576223567332310158898898899986


No 49 
>TIGR00630 uvra excinuclease ABC, A subunit; InterPro: IPR004602   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).  During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products . The UvrC protein contain 4 conserved regions: a central region which interact with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases.; GO: 0009381 excinuclease ABC activity, 0006289 nucleotide-excision repair, 0009380 excinuclease repair complex.
Probab=26.37  E-value=34  Score=14.92  Aligned_cols=16  Identities=19%  Similarity=0.437  Sum_probs=8.0

Q ss_pred             HHEEE-CCCCHHHHHHH
Q ss_conf             76247-79999999999
Q gi|254780944|r  188 NKVIM-LKMSAEDSAKM  203 (228)
Q Consensus       188 ~~v~~-~dmsveeA~k~  203 (228)
                      ..|.+ ||||||||-.|
T Consensus       814 K~IadVLdMtveEA~eF  830 (956)
T TIGR00630       814 KNIADVLDMTVEEAREF  830 (956)
T ss_pred             CEEHHHHCCCHHHHHHH
T ss_conf             71123315866899887


No 50 
>pfam06695 Sm_multidrug_ex Putative small multi-drug export protein. This family contains a small number of putative small multi-drug export proteins.
Probab=24.07  E-value=51  Score=13.81  Aligned_cols=53  Identities=13%  Similarity=0.236  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCE-----EEEEECCCCCEEE
Q ss_conf             99999999999533238899999999999973177553310-----3999848875799
Q gi|254780944|r   89 RFVFFLSESILNNTPIVRHLYKSTKQIIRTLLKEDSTSFKN-----ACLVEYPSAGFWS  142 (228)
Q Consensus        89 ~~~~~~~e~~l~rIP~v~~IY~sikqi~~~~~~~~~~~f~~-----vVlVe~P~~g~~~  142 (228)
                      -.++++..+++.|.|..+.+|.-..+=.+.- +++=+++.-     -|.+..|..|.|+
T Consensus        35 l~~~~~i~~~~~~~~~~~k~~~~~~~k~~k~-~~~iekyg~~gL~lFVaIPLPgTGawT   92 (121)
T pfam06695        35 LLFLRKVFKWLKRTKLFKKIYDWLEERARKG-SGKVEKYGFLGLILFVAIPLPGTGAWT   92 (121)
T ss_pred             HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHCCCCCCCHHH
T ss_conf             9999999999985715899999999999854-078999999999999957888750899


No 51 
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family; InterPro: IPR004659   The eubacterial degradosome is a large, multiprotein, multienzyme complex involved in RNA processing and degradation in Escherichia coli and other proteobacteria .    The components of the RNA degradosome in E. coli (EBI-1169250 from INTACT) are:  Ribonuclease E (Rne), P21513 from SWISSPROT, IPR004659 from INTERPRO ATP-dependent RNA helicase (RhlB), P0A8J8 from SWISSPROT, IPR000629 from INTERPRO Polynucleotide phosphorylase (Pnp), , IPR012162 from INTERPRO Enolase (Eno), P0A6P9 from SWISSPROT, IPR000941 from INTERPRO       Associated components:   The chaperone protein DnaK (,IPR012725 from INTERPRO) associates to abnormal complexes in which the canonical components RhlB and PNPase are not present or present in limiting amount and could be involved in repairing such incorrectly assembled degradosomes. Polyphosphate kinase (Ppk), P0A7B1 from SWISSPROT, IPR003414 from INTERPRO appears to maintain an appropriate microenvironment, removing inhibitory polyphosphate and NDPs and regenerating ATP.   Subunit composition of the E. coli degradosome(see: http://biocyc.org/ECOLI/NEW-IMAGE?type=POLYPEPTIDE&object=CPLX0-2381): [(Ppk)4][(Rne)4][(RhlB)2][(Pnp)3][(Eno)2]      In vitro a "minimal" degradosome composed of only RNase E, PNPase and RhlB degrades malEF REP RNA in an ATP-dependent manner in vitro, with activity equivalent to purified whole degradosomes. RNase E enzymatic function is dispensible, whereas PNPase must be catalytically active and incorporated into the degradosome for degradation to occur . RNase E provides the organizational structure for the degradosome . It is tethered to the cytoplasmic membrane via its amino-terminus and its carboxy-terminal half, which is largly unstructured and poorly conserved, cooridnates the binding of PNPase, RhlB and enolase. The loss of this portion of the protein prevents degradation of a number of degradosome substrates, including the ptsG and mukB mRNAs and RNA I , , .    Ribonuclease E 3.1.4 from EC is responsible for maturing 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of ColE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in Escherichia coli, and initiates decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly A tails by an endonucleolytic process. Ribonuclease G is smaller than RNase E lacking the C-terminal region. It is involved in processing of the 5' end of 16S rRNA, and may be involved in chromosome segregation and cell division too.   RNase E is a major subunit the eubacterial degradosome. It is a large, multiprotein, multienzyme complex involved in RNA processing and degradation in Escherichia coli and other proteobacteria . It consists of the RNA degradation enzymes RNase E (Rne) and PNPase (Pnp), as well as the ATP-dependent RNA helicase (RhlB) and the metabolic enzyme enolase (Eno) , , .; GO: 0004540 ribonuclease activity, 0006396 RNA processing, 0005737 cytoplasm.
Probab=24.00  E-value=52  Score=13.81  Aligned_cols=11  Identities=27%  Similarity=0.410  Sum_probs=5.3

Q ss_pred             CEEEEEEECCC
Q ss_conf             38999970798
Q gi|254780944|r  165 DMVTVFIPPTP  175 (228)
Q Consensus       165 ~~v~VfiPtsP  175 (228)
                      +.|.||+|.+|
T Consensus       153 GrYlVlmP~~~  163 (464)
T TIGR00757       153 GRYLVLMPNTS  163 (464)
T ss_pred             CCEEEECCCCC
T ss_conf             21078557889


No 52 
>PRK10892 D-arabinose 5-phosphate isomerase; Provisional
Probab=23.86  E-value=52  Score=13.79  Aligned_cols=101  Identities=16%  Similarity=0.236  Sum_probs=59.2

Q ss_pred             HHHHHHHHHHHHHHH---HCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCEEEEEEEECCCHHHHHHHHCCCC
Q ss_conf             788999999999995---33238899999999999973177553310399984887579999970687156555302467
Q gi|254780944|r   86 LLGRFVFFLSESILN---NTPIVRHLYKSTKQIIRTLLKEDSTSFKNACLVEYPSAGFWSLCFLTTEVKGEIKEKFSNIG  162 (228)
Q Consensus        86 ~~g~~~~~~~e~~l~---rIP~v~~IY~sikqi~~~~~~~~~~~f~~vVlVe~P~~g~~~iGFvT~~~~~~~~~~~~~~~  162 (228)
                      .+||+++-..++++.   ++|+++. ..+++|.+..++.   +.+.-++.++   +.-...|.+|.   +++...+..  
T Consensus       195 ~LGk~Ll~~V~dlM~~~~~lP~v~~-~~~l~dai~~mt~---k~lG~v~Vvd---~~gkL~GIiTD---GDLRR~l~~--  262 (326)
T PRK10892        195 ALGRKLLLRVSDIMHTGDEIPHVKK-TASLRDALLEITR---KNLGMTVICD---DNMMIEGIFTD---GDLRRVFDM--  262 (326)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCC-CCHHHHHHHHHCC---CCCEEEEEEC---CCCCEEEEEEC---HHHHHHHHH--
T ss_conf             7778888789998513765885377-6029999998745---8934999985---89968999862---689999870--


Q ss_pred             CCCEEEEE--EECCCCCCCCEEEEEEHHHEEECCCCHHHHHHHHHHCCC
Q ss_conf             77389999--707985326889998777624779999999999870143
Q gi|254780944|r  163 CEDMVTVF--IPPTPLPTAGMLVFVPRNKVIMLKMSAEDSAKMLISGGL  209 (228)
Q Consensus       163 ~~~~v~Vf--iPtsPnPtsG~~~~vp~~~v~~~dmsveeA~k~iiS~Gv  209 (228)
                      +.+....-  ==+++||.+           ..-|+.+.||+++.=.--+
T Consensus       263 ~~~i~~~~~~diMT~nP~t-----------I~~d~la~eAL~iMe~~kI  300 (326)
T PRK10892        263 GVDLRQLSIADVMTPGGIR-----------VRPGILAVDALNLMQSRHI  300 (326)
T ss_pred             CCCCCCCCHHHHHCCCCCE-----------ECCCCCHHHHHHHHHHCCC
T ss_conf             6883128799971899967-----------8998869999999986398


No 53 
>TIGR01937 nqrB NADH:ubiquinone oxidoreductase, Na(+)-translocating, B subunit; InterPro: IPR010966   This entry represents the NqrB subunit of the six-protein (NqrA to NqrF), membrane-associated Na(+)-pumping NADH-quinone reductase of a number of marine and pathogenic Gram-negative bacteria . The Nqr complex catalyses the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of sodium ions from the cytoplasm to the periplasm. NqrA to NqrE are probably involved in the second step, the conversion of ubisemiquinone to ubiquinol. Both the NqrB and NqrC subunits contain a FMN cofactor that is covalently attached by a phosphate group to a threonine residue .; GO: 0010181 FMN binding, 0016655 oxidoreductase activity acting on NADH or NADPH quinone or similar compound as acceptor, 0006118 electron transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=22.61  E-value=55  Score=13.64  Aligned_cols=32  Identities=9%  Similarity=0.124  Sum_probs=25.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999999876
Q gi|254780944|r   14 VRNNFFAGFIICAPIAITIWLSLSLIHWFDGF   45 (228)
Q Consensus        14 l~~~Fl~GLlvllPi~iTi~i~~~l~~~~~~~   45 (228)
                      +...++.|+...||+.++.|++--..+.+-..
T Consensus       115 ~~~~l~~G~~~fLP~l~~~y~VG~~~Evlfa~  146 (508)
T TIGR01937       115 IGSKLLLGAKIFLPLLLVSYAVGGTWEVLFAV  146 (508)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             35689964899868999999898789888876


No 54 
>TIGR02188 Ac_CoA_lig_AcsA acetate--CoA ligase; InterPro: IPR011904   Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme) is a ubiquitous enzyme, found in both prokaryotes and eukaryotes, which catalyses the formation of acetyl-CoA from acetate, coenzyme A (CoA) and ATP as shown below : ATP + acetate + CoA = AMP + diphosphate + acetyl-CoA The activity of this enzyme is crucial for maintaining the required levels of acetyl-CoA, a key intermediate in many important biosynthetic and catabolic processes. It is especially important in eukayotic species as it is the only route for the activation of acetate to acetyl-CoA in these organisms (some prokaryotic species can also activate acetate by either acetate kinase/phosphotransacetylase or by ADP-forming acetyl-CoA synthase). Eukaryotes typically have two isoforms of acetyl-CoA synthase, a cytosolic form involved in biosynthetic processes and a mitochondrial form primarily involved in energy generation.   The crystal structures of a eukaryotic (Q01574 from SWISSPROT, from yeast) and bacterial (Q8ZKF6 from SWISSPROT, from Salmonella) form of this enzyme have been determined , . The yeast enzyme is trimeric, while the bacterial enzyme is monomeric. The trimeric state of the yeast protein may be unique to this organism however, as the residues involved in the trimer interface are poorly conserved in other sequences. Despite differences in the oligomeric state of the two enzyme, the structures of the monomers are almost identical. A large N-terminal domain (~500 residues) containing two parallel beta sheets is followed by a small (~110 residues) C-terminal domain containing a three-stranded beta sheet with helices. The active site occurs at the domain interface, with its contents determining the orientation of the C-terminal domain.; GO: 0003987 acetate-CoA ligase activity, 0016208 AMP binding.
Probab=21.58  E-value=51  Score=13.87  Aligned_cols=60  Identities=18%  Similarity=0.288  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHH-----------------HCCHHHHHHHHHHHHHHHHHCCCCC---
Q ss_conf             99999999999987774337889999-99999995-----------------3323889999999999997317755---
Q gi|254780944|r   67 FGLLVVIVGINIVGFFGRNLLGRFVF-FLSESILN-----------------NTPIVRHLYKSTKQIIRTLLKEDST---  125 (228)
Q Consensus        67 lg~~~~i~~i~liG~l~~~~~g~~~~-~~~e~~l~-----------------rIP~v~~IY~sikqi~~~~~~~~~~---  125 (228)
                      -..++++++|.-+|.+-+-+||-.-= .+-||+..                 .|||        |+.+|--.....+   
T Consensus       131 PEa~~AMLACaRIGA~HSVVFgGFSa~aL~~Ri~Da~ak~VITAD~g~RgGK~~~L--------K~~VD~AL~~~~~~~~  202 (643)
T TIGR02188       131 PEAAIAMLACARIGAIHSVVFGGFSAEALADRINDAGAKLVITADEGLRGGKVIPL--------KAIVDEALEKCPDTCP  202 (643)
T ss_pred             HHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHCCCCCEEEECCCCCCCCCCCCH--------HHHHHHHHHHCCCCCC
T ss_conf             89999998864368526787257747899887532777589943774058864303--------6899999960786745


Q ss_pred             CCCEEEEEE
Q ss_conf             331039998
Q gi|254780944|r  126 SFKNACLVE  134 (228)
Q Consensus       126 ~f~~vVlVe  134 (228)
                      +-++|-.++
T Consensus       203 ~V~~VlV~~  211 (643)
T TIGR02188       203 SVEKVLVVR  211 (643)
T ss_pred             CCCEEEEEE
T ss_conf             300678998


No 55 
>PRK00042 tpiA triosephosphate isomerase; Provisional
Probab=20.83  E-value=53  Score=13.74  Aligned_cols=37  Identities=19%  Similarity=0.372  Sum_probs=24.2

Q ss_pred             HHHHHHHHHHCCCCCCCCEEEEEECCCCCEEEEEEEECCCHH
Q ss_conf             999999997317755331039998488757999997068715
Q gi|254780944|r  111 STKQIIRTLLKEDSTSFKNACLVEYPSAGFWSLCFLTTEVKG  152 (228)
Q Consensus       111 sikqi~~~~~~~~~~~f~~vVlVe~P~~g~~~iGFvT~~~~~  152 (228)
                      -.+|+-+.+.+-++..++++++ -|  +-+|+||  |+..+.
T Consensus       143 l~~Ql~~~l~~~~~~~~~~iiI-AY--EPvWAIG--TG~~as  179 (251)
T PRK00042        143 VARQLEAALAGLGAEDFANLVI-AY--EPVWAIG--TGKTAT  179 (251)
T ss_pred             HHHHHHHHHHCCCHHHCCCEEE-EE--CCHHHCC--CCCCCC
T ss_conf             9999999996689877053599-96--7577507--999999


No 56 
>cd02435 CCC1 CCC1. CCC1: This domain is present in the CCC1, an iron and manganese transporter of Saccharomyces cerevisiae. CCC1 is a transmembrane protein that is located in the vacuole and transfers the iron and manganese ions from the cytosol to the vacuole. This domain may be unique to certain fungi and plants.
Probab=20.19  E-value=62  Score=13.33  Aligned_cols=41  Identities=15%  Similarity=0.374  Sum_probs=22.9

Q ss_pred             HHHCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             21051211501101102358999999999999877743378899
Q gi|254780944|r   47 VPYIPMQYNPEYYCDFSIPGFGLLVVIVGINIVGFFGRNLLGRF   90 (228)
Q Consensus        47 ~p~i~~~~~~~~~~~~~i~glg~~~~i~~i~liG~l~~~~~g~~   90 (228)
                      -|++|..+.+...   ......++++.+.++++|++...+.|++
T Consensus       170 iPLlpy~~~~~~~---~al~~S~~~t~~aL~~~G~~k~~~tg~~  210 (241)
T cd02435         170 IPLLPYFFVSTVG---EALLLSVIVTLVALFVFGYVKTWFTGGW  210 (241)
T ss_pred             HHHHHHHHCCCCH---HHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             8878999705503---8999999999999999999987201678


No 57 
>PRK11026 ftsX cell division protein FtsX; Provisional
Probab=20.06  E-value=62  Score=13.31  Aligned_cols=11  Identities=18%  Similarity=0.244  Sum_probs=4.4

Q ss_pred             EEEEEEEECCC
Q ss_conf             79999970687
Q gi|254780944|r  140 FWSLCFLTTEV  150 (228)
Q Consensus       140 ~~~iGFvT~~~  150 (228)
                      +..+-|+++|.
T Consensus        94 V~~v~~vskee  104 (309)
T PRK11026         94 VEKVNYLSREE  104 (309)
T ss_pred             CCEEEEECHHH
T ss_conf             43798867999


No 58 
>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]
Probab=20.00  E-value=62  Score=13.31  Aligned_cols=35  Identities=14%  Similarity=-0.060  Sum_probs=13.2

Q ss_pred             CCEEEEEEEC--CCCCCCCEEEEEEHHHEEECCCCHHH
Q ss_conf             7389999707--98532688999877762477999999
Q gi|254780944|r  164 EDMVTVFIPP--TPLPTAGMLVFVPRNKVIMLKMSAED  199 (228)
Q Consensus       164 ~~~v~VfiPt--sPnPtsG~~~~vp~~~v~~~dmsvee  199 (228)
                      -+.+.-++-.  ++| .+|..+..-+++-.+.+-+.++
T Consensus       589 v~~v~~~~G~g~~~~-~~~~~~~~Lk~~~er~~~~~~~  625 (1009)
T COG0841         589 VESVFTVVGFGSGQN-NAGRAFVSLKPWSERKENSAQA  625 (1009)
T ss_pred             EEEEEEEECCCCCCC-CCCEEEEECCCHHHCCCCCHHH
T ss_conf             169999845677777-7615999448735355655789


Done!