Query         gi|254780135|ref|YP_003064548.1| hypothetical protein CLIBASIA_00070 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 408
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Sun May 22 08:05:01 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780135.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 cd01474 vWA_ATR ATR (Anthrax T  60.1      12 0.00031   17.5   3.5   49  345-395   134-183 (185)
  2 cd01480 vWA_collagen_alpha_1-V  51.9      16  0.0004   16.7   3.0   32  345-378   140-171 (186)
  3 TIGR01947 rnfG electron transp  48.1      20  0.0005   16.0   4.8   59   17-75      2-60  (202)
  4 cd01469 vWA_integrins_alpha_su  44.9      22 0.00056   15.7   3.4   35  344-378   131-170 (177)
  5 cd01475 vWA_Matrilin VWA_Matri  41.6      25 0.00063   15.3   3.8   45  345-391   135-181 (224)
  6 PRK06132 hypothetical protein;  41.2      25 0.00063   15.3   3.8   38  266-306   146-183 (365)
  7 pfam01727 consensus             38.4      23  0.0006   15.5   2.2   35  277-316    13-47  (81)
  8 cd05727 Ig2_Contactin-2-like S  37.2      29 0.00073   14.9   2.6   38  223-260    23-63  (96)
  9 cd01481 vWA_collagen_alpha3-VI  36.5      29 0.00075   14.8   3.1   31  345-377   133-163 (165)
 10 KOG0090 consensus               33.9      20 0.00051   16.0   1.2   50   67-116   152-202 (238)
 11 TIGR01325 O_suc_HS_sulf O-succ  33.6      24 0.00061   15.4   1.6  200  107-332   173-382 (386)
 12 TIGR02599 TIGR02599 Verrucomic  32.2      17 0.00042   16.5   0.6  166   70-270    40-224 (396)
 13 cd01482 vWA_collagen_alphaI-XI  30.2      37 0.00093   14.1   2.6   26  345-372   130-155 (164)
 14 TIGR01271 CFTR_protein cystic   29.9      37 0.00094   14.1   6.7   70   22-95   1047-1136(1534)
 15 PRK04286 hypothetical protein;  29.0      38 0.00098   14.0   3.5   63  268-330   121-200 (294)
 16 TIGR01703 hybrid_clust hydroxy  27.2      24 0.00062   15.4   0.7   10  140-149   259-268 (567)
 17 TIGR01326 OAH_OAS_sulfhy O-ace  27.1      21 0.00054   15.8   0.4   23  310-332   407-429 (434)
 18 KOG0942 consensus               26.2      43  0.0011   13.6   2.4   66  182-261   525-594 (1001)
 19 pfam07299 FBP Fibronectin-bind  26.1      43  0.0011   13.6   2.3   35   77-111     6-41  (208)
 20 KOG0099 consensus               25.2      44  0.0011   13.5   3.1   44  271-336   325-368 (379)
 21 pfam03542 Tuberin Tuberin. Tub  24.0      40   0.001   13.8   1.3   24  368-400   328-351 (356)
 22 PHA01365 hypothetical protein   23.8      47  0.0012   13.3   1.7   15  320-334     3-17  (91)
 23 pfam07727 RVT_2 Reverse transc  23.0     7.5 0.00019   19.0  -2.5   48   31-80     69-132 (246)
 24 COG3955 Exopolysaccharide bios  22.6      50  0.0013   13.2   3.1   86  144-265   111-200 (211)
 25 TIGR01524 ATPase-IIIB_Mg magne  21.9     7.2 0.00018   19.1  -2.8   63  129-197   312-381 (892)
 26 COG3114 CcmD Heme exporter pro  21.8      51  0.0013   13.1   5.3   17   44-60     36-52  (67)
 27 pfam00522 VPR VPR/VPX protein.  21.1      53  0.0014   13.0   3.3   45  265-341    32-76  (83)
 28 KOG0333 consensus               20.8      54  0.0014   12.9   1.5   39  333-371   600-640 (673)
 29 cd03267 ABC_NatA_like Similar   20.8      54  0.0014   12.9   4.0  106  258-383     8-117 (236)
 30 pfam05482 Serendipity_A Serend  20.2      42  0.0011   13.7   0.8   15   32-46    137-151 (549)

No 1  
>cd01474 vWA_ATR ATR (Anthrax Toxin Receptor): Anthrax toxin is a key virulence factor for Bacillus anthracis, the causative agent of anthrax. ATR is the cellular receptor for the anthrax protective antigen and facilitates entry of the toxin into cells. The VWA domain in ATR contains the toxin binding site and mediates interaction with protective antigen. The binding is mediated by divalent cations that binds to the MIDAS motif. These proteins are a family of vertebrate ECM receptors expressed by endothelial cells.
Probab=60.07  E-value=12  Score=17.50  Aligned_cols=49  Identities=16%  Similarity=0.261  Sum_probs=36.6

Q ss_pred             EEEEEEEECCCCCCHHHHHHHHCCCCHHEEEECC-CCCHHHHHHHHHHHHHH
Q ss_conf             1899984148874302678762059032044258-76534478987777787
Q gi|254780135|r  345 AITIFSVGFSPDQDTRYTLRQCASDPSKYYEINS-DENVMPIAKSLARNVIT  395 (408)
Q Consensus       345 aitifsvgfspdqdtrytlrqcasdpskyyeins-denvmpiakslarnvit  395 (408)
                      .++||+||.+ +- .+-.|++-||+|++-|.++. =+..-.|...|...+-+
T Consensus       134 gV~i~aVGV~-~~-~~~eL~~IAs~p~~vf~v~~~F~~L~~i~~~l~~~iC~  183 (185)
T cd01474         134 GAIVYCVGVT-DF-LKSQLINIADSKEYVFPVTSGFQALSGIIESVVKKACI  183 (185)
T ss_pred             CCEEEEEECC-CC-CHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHHCC
T ss_conf             9489999716-25-99999987199864898347577789999999985287


No 2  
>cd01480 vWA_collagen_alpha_1-VI-type VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far.  Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=51.88  E-value=16  Score=16.70  Aligned_cols=32  Identities=22%  Similarity=0.226  Sum_probs=25.9

Q ss_pred             EEEEEEEECCCCCCHHHHHHHHCCCCHHEEEECC
Q ss_conf             1899984148874302678762059032044258
Q gi|254780135|r  345 AITIFSVGFSPDQDTRYTLRQCASDPSKYYEINS  378 (408)
Q Consensus       345 aitifsvgfspdqdtrytlrqcasdpskyyeins  378 (408)
                      .|+||.||.....  .-.|++.||+|++.+..++
T Consensus       140 GV~ifaVGVG~~~--~~eL~~IAs~p~~~~~~~~  171 (186)
T cd01480         140 GIKIFFVAVGSQN--EEPLSRIACDGKSALYREN  171 (186)
T ss_pred             CCEEEEEEECCCC--HHHHHHHHCCCCCEEEECC
T ss_conf             9899999947488--7999998589973897368


No 3  
>TIGR01947 rnfG electron transport complex, RnfABCDGE type, G subunit; InterPro: IPR010209   The six-subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation . A closely related complex in Escherichia coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized . This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase (IPR003667 from INTERPRO), but is distinct. This entry describes the G subunit.; GO: 0006118 electron transport, 0009276 1-2nm peptidoglycan-based cell wall.
Probab=48.14  E-value=20  Score=16.02  Aligned_cols=59  Identities=19%  Similarity=0.254  Sum_probs=44.4

Q ss_pred             HCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHC
Q ss_conf             01048999999999878999999876777777888899998776410684323667741
Q gi|254780135|r   17 CTRGVFLVITAILLSSFVAIVDVVVDQVTVMQKTALLQEVLDHVIYRTSPKNLYDLREA   75 (408)
Q Consensus        17 ctrgvflvitaillssfvaivdvvvdqvtvmqktallqevldhviyrtspknlydlrea   75 (408)
                      |.-++|-.+.+.+|.-.-.+..-+..+...-|+.++|++||-+..|-.+|..-+.+..+
T Consensus         2 ~~L~~f~~~~~~~la~~n~~T~~~Ia~~~~~~~~~~l~~VLP~~~~dN~~~~~~~~~~d   60 (202)
T TIGR01947         2 LLLGLFAAVSAGLLALVNQFTKEQIAEAEAKQQLEALKQVLPDGLYDNDLEESFVLVKD   60 (202)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHCCCCCC
T ss_conf             66777899999999999986588999999999999998537831004772464122125


No 4  
>cd01469 vWA_integrins_alpha_subunit Integrins are a class of adhesion receptors that link the extracellular matrix to the cytoskeleton and cooperate with growth factor receptors to promote celll survival, cell cycle progression and cell migration. Integrins consist of an alpha and a beta sub-unit. Each sub-unit has a large extracellular portion, a single transmembrane segment and a short cytoplasmic domain. The N-terminal domains of the alpha and beta subunits associate to form the integrin headpiece, which contains the ligand binding site, whereas the C-terminal segments traverse the plasma membrane and mediate interaction with the cytoskeleton and with signalling proteins.The VWA domains present in the alpha subunits of integrins seem to be a chordate specific radiation of the gene family being found only in vertebrates. They mediate protein-protein interactions.
Probab=44.92  E-value=22  Score=15.69  Aligned_cols=35  Identities=20%  Similarity=0.487  Sum_probs=25.9

Q ss_pred             CEEEEEEEECCCCCCH---HHHHHHHCCCCHH--EEEECC
Q ss_conf             4189998414887430---2678762059032--044258
Q gi|254780135|r  344 GAITIFSVGFSPDQDT---RYTLRQCASDPSK--YYEINS  378 (408)
Q Consensus       344 gaitifsvgfspdqdt---rytlrqcasdpsk--yyeins  378 (408)
                      ..|.||+||..+.-+.   ...|+..||+|..  .|.+++
T Consensus       131 ~gv~vf~VGvG~~~~~~~~~~eL~~iAs~P~~~hvf~~~~  170 (177)
T cd01469         131 EGIIRYAIGVGGHFQRENSREELKTIASKPPEEHFFNVTD  170 (177)
T ss_pred             CCEEEEEEEECCCCCCCCCHHHHHHHHCCCCHHCEEEECC
T ss_conf             9908999995551467451999999967985871998379


No 5  
>cd01475 vWA_Matrilin VWA_Matrilin: In cartilaginous plate, extracellular matrix molecules mediate cell-matrix and matrix-matrix interactions thereby providing tissue integrity. Some members of the matrilin family are expressed specifically in developing cartilage rudiments. The matrilin family consists of at least four members. All the members of the matrilin family contain VWA domains, EGF-like domains and a heptad repeat coiled-coiled domain at the carboxy terminus which is responsible for the oligomerization of the matrilins. The VWA domains have been shown to be essential for matrilin network formation by interacting with matrix ligands.
Probab=41.58  E-value=25  Score=15.34  Aligned_cols=45  Identities=22%  Similarity=0.407  Sum_probs=31.5

Q ss_pred             EEEEEEEECCCCCCHHHHHHHHCCCCH--HEEEECCCCCHHHHHHHHHH
Q ss_conf             189998414887430267876205903--20442587653447898777
Q gi|254780135|r  345 AITIFSVGFSPDQDTRYTLRQCASDPS--KYYEINSDENVMPIAKSLAR  391 (408)
Q Consensus       345 aitifsvgfspdqdtrytlrqcasdps--kyyeinsdenvmpiakslar  391 (408)
                      .|.||.||..- - .+-.|++.||+|+  ..+.+++=+..-.+++.|..
T Consensus       135 GV~ifaVGVg~-~-~~~eL~~IAs~P~~~hvf~v~~F~~l~~l~~~l~~  181 (224)
T cd01475         135 GIEMFAVGVGR-A-DEEELREIASEPLADHVFYVEDFSTIEELTKKFQG  181 (224)
T ss_pred             CCEEEEEECCC-C-CHHHHHHHHCCCCHHCEEEECCHHHHHHHHHHHHH
T ss_conf             98899996374-7-98999998559737568994798899999999876


No 6  
>PRK06132 hypothetical protein; Provisional
Probab=41.23  E-value=25  Score=15.30  Aligned_cols=38  Identities=21%  Similarity=0.480  Sum_probs=26.7

Q ss_pred             CCCHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCCCEEE
Q ss_conf             07089998887410234678426513674354676653068
Q gi|254780135|r  266 HFPYSFIKNVFDMTSNQFGDGQVLTNTNHCFPHGASHSKYM  306 (408)
Q Consensus       266 hfpysfiknvfdmtsnqfgdgqvltntnhcfphgashskym  306 (408)
                      +.|+.|-+.+|++|..  |.--+.+. .+.-|...+|....
T Consensus       146 rlP~~fA~~lf~~t~~--g~~VIIs~-~~~aP~~~~HP~L~  183 (365)
T PRK06132        146 RLPMAFAKKLFGWTRM--GTRVIISD-GEVAPVEVAHPLLL  183 (365)
T ss_pred             CCCHHHHHHHHCCCCC--CCEEEECC-CCCCCCCCCCCCCC
T ss_conf             6978999998551458--97699728-98786214784124


No 7  
>pfam01727 consensus
Probab=38.36  E-value=23  Score=15.48  Aligned_cols=35  Identities=40%  Similarity=0.619  Sum_probs=25.6

Q ss_pred             HHHCCCCCCCEEEECCCCCCCCCCCCCEEEEEEEECCCCC
Q ss_conf             4102346784265136743546766530688676344100
Q gi|254780135|r  277 DMTSNQFGDGQVLTNTNHCFPHGASHSKYMLMFAIGNQLS  316 (408)
Q Consensus       277 dmtsnqfgdgqvltntnhcfphgashskymlmfaignqls  316 (408)
                      +-.-.|+|-|-.|++||  ||-|+|-|   |+|---+|++
T Consensus        13 ~k~YqqyG~Gl~l~dtn--l~gGSSGS---lv~Nq~kQI~   47 (81)
T pfam01727        13 GKEYQQYGYGLALNDTN--LPGGSSGS---LVFNQDKQIS   47 (81)
T ss_pred             CCCHHHHCCEEEEECCC--CCCCCCCC---EEECCCCEEE
T ss_conf             40255424205760366--69987666---5774777487


No 8  
>cd05727 Ig2_Contactin-2-like Second Ig domain of the neural cell adhesion molecule contactin-2 and similar proteins. Ig2_Contactin-2-like: second Ig domain of the neural cell adhesion molecule contactin-2. Contactins are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. Contactin-2 (aliases TAG-1, axonin-1) facilitates cell adhesion by homophilic binding between molecules in apposed membranes. The first four Ig domains form the intermolecular binding fragment which arranges as a compact U-shaped module by contacts between Ig domains 1 and 4, and domains 2 and 3. It has been proposed that a linear zipper-like array forms, from contactin-2 molecules alternatively provided by the two apposed membranes.
Probab=37.16  E-value=29  Score=14.88  Aligned_cols=38  Identities=26%  Similarity=0.591  Sum_probs=27.0

Q ss_pred             CEECCCCCCCE-EEEEEECCCEEECCCCEEEEEEC--CCEE
Q ss_conf             20027310000-34555425113035858999951--7368
Q gi|254780135|r  223 NFCMAPYHYKS-IFYWAFENFQYHQDNNMLIFYSH--RDFY  260 (408)
Q Consensus       223 nfcmapyhyks-ifywafenfqyhqdnnmlifysh--rdfy  260 (408)
                      -.|-.|-||-. .|||.+..|.-+...+--.|-|+  -+.|
T Consensus        23 L~C~PP~~~P~l~~~W~~n~~p~fv~~d~R~fVSq~~GnLY   63 (96)
T cd05727          23 LFCDPPPHYPDLSYRWLLNEFPNFIPEDGRRFVSQTNGNLY   63 (96)
T ss_pred             EECCCCCCCCCCEEEEEECCCCCCCCCCCCEEEECCCCCEE
T ss_conf             95689988998489998068875111576599965887489


No 9  
>cd01481 vWA_collagen_alpha3-VI-like VWA_collagen alpha 3(VI) like: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far.  Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=36.47  E-value=29  Score=14.80  Aligned_cols=31  Identities=29%  Similarity=0.421  Sum_probs=24.2

Q ss_pred             EEEEEEEECCCCCCHHHHHHHHCCCCHHEEEEC
Q ss_conf             189998414887430267876205903204425
Q gi|254780135|r  345 AITIFSVGFSPDQDTRYTLRQCASDPSKYYEIN  377 (408)
Q Consensus       345 aitifsvgfspdqdtrytlrqcasdpskyyein  377 (408)
                      .++||.||...  -.+-.|++-||+|+.-|.++
T Consensus       133 gV~i~aVGvg~--~~~~eL~~IAs~p~~vf~~~  163 (165)
T cd01481         133 GIVPFAIGARN--ADLAELQQIAFDPSFVFQVS  163 (165)
T ss_pred             CCEEEEEECCC--CCHHHHHHHHCCCCCEEECC
T ss_conf             97899996897--99999999858987769738


No 10 
>KOG0090 consensus
Probab=33.92  E-value=20  Score=15.97  Aligned_cols=50  Identities=32%  Similarity=0.255  Sum_probs=36.5

Q ss_pred             CHHHHHHHCCHHHHHHHHHHHHHHCCC-CCCHHHCCCHHHHHHHHHEEECC
Q ss_conf             323667741223578999998740034-22000000088774322023214
Q gi|254780135|r   67 KNLYDLREAGRDNFIRHQIEKALNTYN-SRDLSNIGSIESIVKDAVILTKN  116 (408)
Q Consensus        67 knlydlreagrdnfirhqiekalntyn-srdlsnigsiesivkdaviltkn  116 (408)
                      -|--|+--|--..+||.|.||.+++-+ +|.--.+++-|++.++...--..
T Consensus       152 CNKqDl~tAkt~~~Ir~~LEkEi~~lr~sRsa~~~~~~ed~~~~~tlg~~g  202 (238)
T KOG0090         152 CNKQDLFTAKTAEKIRQQLEKEIHKLRESRSALRSISDEDIAKDFTLGKEG  202 (238)
T ss_pred             ECCHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
T ss_conf             555223213859999999999999999877653025630013543136433


No 11 
>TIGR01325 O_suc_HS_sulf O-succinylhomoserine sulfhydrylase; InterPro: IPR006234    These sequences represent O-succinylhomoserine sulfhydrylase, one of several related pyridoxal phosphate-dependent enzymes of cysteine and methionine metabolism. This enzyme is part of an alternative pathway of homocysteine biosynthesis, a step in methionine biosynthesis..
Probab=33.56  E-value=24  Score=15.42  Aligned_cols=200  Identities=21%  Similarity=0.320  Sum_probs=95.7

Q ss_pred             HHHHHEEECCCCCCCEEEEEEEEEE-EEEEEHHHHHHHHHHCCCCEEHHHHHHHHHHCCCCEEEEEE-CCCCEEEECCCC
Q ss_conf             4322023214673303899988631-11221278999874236822235543223220666488630-004225312552
Q gi|254780135|r  107 VKDAVILTKNVNSLPLQFTVDIALS-TTVQLRGSLLQMFSQSKGKVDISRRKKVMYKQNIGLMIMPF-AWDGYWLASRGK  184 (408)
Q Consensus       107 vkdaviltknvnslplqftvdials-ttvqlrgsllqmfsqskgkvdisrrkkvmykqniglmimpf-awdgywlasrgk  184 (408)
                      |-|-+.+| -+-+-||..-+||..+ .|-..-|.=--|=.---|.-.+-..--.-|-..-|+-+-|| ||    +--.| 
T Consensus       173 vvDN~f~t-P~~qqPL~lGaDvvv~SATK~IDGqGRvlGGv~~G~~e~~~~~v~~~lr~~GpalSpFNAW----~lLkG-  246 (386)
T TIGR01325       173 VVDNVFAT-PVLQQPLKLGADVVVYSATKHIDGQGRVLGGVILGSEELMEEFVAKFLRHTGPALSPFNAW----VLLKG-  246 (386)
T ss_pred             EEHHHHHH-HHHCCCCCCCCEEEEECCCEEECCCCCEECCEEECCHHHHHHHHHHHHHCCCCCCCHHHHH----HHHHH-
T ss_conf             21145641-0013886456407986462011387540121453607775348999974257432367899----98503-


Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHCHHHH-HHHHHHHCCCCCEEC---CCCCCCEEEEEEECCCEEECCCC--EEEEEECCC
Q ss_conf             221123574200177899987052257-888876187432002---73100003455542511303585--899995173
Q gi|254780135|r  185 VADSQVHRPKYLEYSHYYQQYLNRNTL-VKNFLSQIPYKNFCM---APYHYKSIFYWAFENFQYHQDNN--MLIFYSHRD  258 (408)
Q Consensus       185 vadsqvhrpkyleyshyyqqylnrntl-vknflsqipyknfcm---apyhyksifywafenfqyhqdnn--mlifyshrd  258 (408)
                                 ||--.---|--+-+.+ .-+||..-|--.-..   -|-|-.       .|.--.|-+.  ..|-+.-.+
T Consensus       247 -----------lETL~lR~~~~~~sAl~lA~~L~~~p~v~~V~Y~~lP~HPq-------~~lar~Q~~GGG~Vv~f~l~~  308 (386)
T TIGR01325       247 -----------LETLSLRVQKQADSALALAEWLEEQPKVQAVYYPGLPDHPQ-------HELARRQQSGGGTVVAFDLKG  308 (386)
T ss_pred             -----------HHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCC-------HHHHHHHCCCCCEEEEEECCC
T ss_conf             -----------45789999861478999999997089557987587878852-------689998418996799973268


Q ss_pred             EEEEEECCCCHHHHHH--HHHHHCCCCCCCEEEECCCCCCCCCCCCCEEEEEEEECCCCCHHHCCHHHHHHHHHHH
Q ss_conf             6875500070899988--8741023467842651367435467665306886763441001111578899999988
Q gi|254780135|r  259 FYRITWDHFPYSFIKN--VFDMTSNQFGDGQVLTNTNHCFPHGASHSKYMLMFAIGNQLSRSSVGKETIDRILQDC  332 (408)
Q Consensus       259 fyritwdhfpysfikn--vfdmtsnqfgdgqvltntnhcfphgashskymlmfaignqlsrssvgketidrilqdc  332 (408)
                      =-.+. ..--+.||..  .+|. ||..||-.-+-.---.-.||+-...--+-..||.-+-|-|||-|.+|-...|.
T Consensus       309 ~edv~-~~aAf~~~d~~~lv~i-t~NLGD~ks~itHP~TTtHg~~~pe~r~~~gi~~g~vR~SVGLE~~~DL~~D~  382 (386)
T TIGR01325       309 GEDVA-REAAFKVLDALRLVDI-TNNLGDAKSTITHPATTTHGRMSPEERAAAGIGDGLVRLSVGLEDVDDLKADL  382 (386)
T ss_pred             CHHHH-HHHHHHHHCCEEEEEE-ECCCCCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCHHHHHHHH
T ss_conf             64579-9999998656146642-04520101020181888899988000231257887389985038657799999


No 12 
>TIGR02599 TIGR02599 Verrucomicrobium spinosum paralogous family TIGR02599.
Probab=32.17  E-value=17  Score=16.54  Aligned_cols=166  Identities=22%  Similarity=0.252  Sum_probs=72.8

Q ss_pred             HHHHHCCHHHH--HHHHHH-HHHHCCCCCCHHHCCCHHHHHHHH-HEEECCCCCCCEEEEEEEEE--EEE-EEE-HHHHH
Q ss_conf             66774122357--899999-874003422000000088774322-02321467330389998863--111-221-27899
Q gi|254780135|r   70 YDLREAGRDNF--IRHQIE-KALNTYNSRDLSNIGSIESIVKDA-VILTKNVNSLPLQFTVDIAL--STT-VQL-RGSLL  141 (408)
Q Consensus        70 ydlreagrdnf--irhqie-kalntynsrdlsnigsiesivkda-viltknvnslplqftvdial--stt-vql-rgsll  141 (408)
                      -..||| |.-|  |--+.+ -.||+|=.--.++-++ .++-.++ -+-++-.-.=-|+|-..-|-  -++ .+. .-+=-
T Consensus        40 ~qFREA-R~AFEaisr~LsQATLN~Yw~Y~~~~~~~-~~~~~~~~~~P~~Y~R~SELhFv~Gpa~~LL~~~~~ag~~~GH  117 (396)
T TIGR02599        40 EQFREA-RAAFEAISRRLSQATLNAYWDYKYNAGTS-RTVANAATEVPTGYERQSELHFVSGPASTLLGAVITAGAEPGH  117 (396)
T ss_pred             HHHHHH-HHHHHHHHHHHHHHHHCCHHHHHHCCCCC-CCCCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCC
T ss_conf             654999-99999985300023403135664326777-5566410115533126650167724562220123246887661


Q ss_pred             HHHHHCCCCEE-HHH-HHHH---HHHCCCCEEEEEECCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCHHHHHHHHH
Q ss_conf             98742368222-355-4322---322066648863000422531255222112357420017789998705225788887
Q gi|254780135|r  142 QMFSQSKGKVD-ISR-RKKV---MYKQNIGLMIMPFAWDGYWLASRGKVADSQVHRPKYLEYSHYYQQYLNRNTLVKNFL  216 (408)
Q Consensus       142 qmfsqskgkvd-isr-rkkv---mykqniglmimpfawdgywlasrgkvadsqvhrpkyleyshyyqqylnrntlvknfl  216 (408)
                      -+|=|.-=-++ ..- -.-+   --+.+-||--+--+| ||++.-+    +---+||-+|.-+                 
T Consensus       118 avFFQAPLG~~n~~p~a~~~GaP~~~~~~gL~~LLN~W-Gyyv~~~----~D~~~RP~FL~~~-----------------  175 (396)
T TIGR02599       118 AVFFQAPLGVTNLDPGADGSGAPEQAGTEGLDNLLNAW-GYYVEFG----SDLPRRPAFLAKS-----------------  175 (396)
T ss_pred             EEEECCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHC-CCEEEEC----CCCCCCCCCCCCC-----------------
T ss_conf             04540253556777778888887775144476545112-2437537----8888787423577-----------------


Q ss_pred             HHCCCCCEECCCCCCCEEEEEEECCCEEECCCCEEEEEECC------CEEEEEECCCCHH
Q ss_conf             61874320027310000345554251130358589999517------3687550007089
Q gi|254780135|r  217 SQIPYKNFCMAPYHYKSIFYWAFENFQYHQDNNMLIFYSHR------DFYRITWDHFPYS  270 (408)
Q Consensus       217 sqipyknfcmapyhyksifywafenfqyhqdnnmlifyshr------dfyritwdhfpys  270 (408)
                         +-|.  ..|-.|      -|-=.+|.|--.+++.|+..      |---+-|++-+-+
T Consensus       176 ---s~~~--~~p~R~------RFRLmEf~qPaE~~~lY~~~~~~aaA~a~~~f~l~~~a~  224 (396)
T TIGR02599       176 ---SAKP--TAPERY------RFRLMEFRQPAEKLRLYKLTLRIAAATAVPVFALETAAS  224 (396)
T ss_pred             ---CCCC--CCCCCC------CEEECCCCCCCCCCHHCCCCCCCCHHHCCCCCCCCHHHH
T ss_conf             ---7655--788862------031135477211200004414511011058875220889


No 13 
>cd01482 vWA_collagen_alphaI-XII-like Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=30.20  E-value=37  Score=14.11  Aligned_cols=26  Identities=38%  Similarity=0.681  Sum_probs=21.2

Q ss_pred             EEEEEEEECCCCCCHHHHHHHHCCCCHH
Q ss_conf             1899984148874302678762059032
Q gi|254780135|r  345 AITIFSVGFSPDQDTRYTLRQCASDPSK  372 (408)
Q Consensus       345 aitifsvgfspdqdtrytlrqcasdpsk  372 (408)
                      .|+||.||. .+.| +..|++-||+|+.
T Consensus       130 gv~i~~VGV-g~~~-~~eL~~IAs~P~~  155 (164)
T cd01482         130 GVNVFAVGV-KDAD-ESELKMIASKPSE  155 (164)
T ss_pred             CCEEEEEEC-CCCC-HHHHHHHHCCCCH
T ss_conf             938999978-8378-9999999689856


No 14 
>TIGR01271 CFTR_protein cystic fibrosis transmembrane conductor regulator (CFTR); InterPro: IPR005291   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).    These proteins are integral membrane proteins and they are involved in the transport of chloride ions. Many of these proteins are the cystis fibrosis transmembrane conductor regulators (CFTR) in eukaryotes. The principal role of this protein is chloride ion conductance. The protein is predicted to consist of 12 transmembrane domains. Mutations or lesions in the genetic loci have been linked to the aetiology of asthma, bronchiectasis, chronic obstructive pulmonary disease etc. Disease-causing mutations have been studied by 36Cl efflux assays in vitro cell cultures and electrophysiology, all of which point to the impairment of chloride channel stability and not the biosynthetic processing per se.; GO: 0005254 chloride channel activity, 0006811 ion transport, 0016020 membrane.
Probab=29.90  E-value=37  Score=14.08  Aligned_cols=70  Identities=33%  Similarity=0.546  Sum_probs=46.8

Q ss_pred             HHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHCCCCCHHHHHHHCCHHHHH
Q ss_conf             99999999987------8999999876777777888899--------------998776410684323667741223578
Q gi|254780135|r   22 FLVITAILLSS------FVAIVDVVVDQVTVMQKTALLQ--------------EVLDHVIYRTSPKNLYDLREAGRDNFI   81 (408)
Q Consensus        22 flvitaillss------fvaivdvvvdqvtvmqktallq--------------evldhviyrtspknlydlreagrdnfi   81 (408)
                      ..|+-||..-|      |+|-+.|.|--  ||-..-.|+              .+..|.|  +|-|.|+.+|.-||..+.
T Consensus      1047 LIV~GAI~~Vsvl~PY~~~AaiPv~ViF--i~LR~YFL~TsQQLKQLEsEaRSPIFsHLi--~SLkGLWT~RAFGRQsYF 1122 (1534)
T TIGR01271      1047 LIVVGAIAVVSVLQPYIFIAAIPVAVIF--IMLRAYFLRTSQQLKQLESEARSPIFSHLI--TSLKGLWTIRAFGRQSYF 1122 (1534)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHCCCCHHHHHHH--HHHHHHHHHHHCCCCCHH
T ss_conf             9999889988784258998998999999--999999862225667765215771678899--875233443303787526


Q ss_pred             HHHHHHHHHCCCCC
Q ss_conf             99999874003422
Q gi|254780135|r   82 RHQIEKALNTYNSR   95 (408)
Q Consensus        82 rhqiekalntynsr   95 (408)
                      ..-..||||+-...
T Consensus      1123 ETLFHKALN~HTA~ 1136 (1534)
T TIGR01271      1123 ETLFHKALNLHTAN 1136 (1534)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             78999988767899


No 15 
>PRK04286 hypothetical protein; Provisional
Probab=29.00  E-value=38  Score=13.97  Aligned_cols=63  Identities=29%  Similarity=0.487  Sum_probs=39.4

Q ss_pred             CHHHHHHHHHHH-CCCCCCCEEE--ECCCCC----CCCCCC--CCEEEEEEEECCCC----CHHH----CCHHHHHHHHH
Q ss_conf             089998887410-2346784265--136743----546766--53068867634410----0111----15788999999
Q gi|254780135|r  268 PYSFIKNVFDMT-SNQFGDGQVL--TNTNHC----FPHGAS--HSKYMLMFAIGNQL----SRSS----VGKETIDRILQ  330 (408)
Q Consensus       268 pysfiknvfdmt-snqfgdgqvl--tntnhc----fphgas--hskymlmfaignql----srss----vgketidrilq  330 (408)
                      .+-|.|++-+.. .-.+.||+..  ..|.-+    +|||+.  ..-|.+|+.|-..-    --|.    +-.|+++.|+.
T Consensus       121 a~~flk~~~~~~~~i~~aDg~~f~~g~~~i~fS~pvpHG~~gsklG~Vi~~~I~dg~~~~~~~SDvqG~~~~e~v~~il~  200 (294)
T PRK04286        121 AYGFLKAVKGIAKKIEYADGKEFRFGGTVIEFSPPVPHGAEGSKLGYVVMVRISDGDESFVFASDVQGPLNDEAVEFILE  200 (294)
T ss_pred             HHHHHHHHHHHCCEEEECCCCEEEECCEEEEECCCCCCCCCCCCCCEEEEEEEECCCEEEEECCCCCCCCCHHHHHHHHH
T ss_conf             99999976520434897588668878888996688778988885567999999749768998055667687899999986


No 16 
>TIGR01703 hybrid_clust hydroxylamine reductase; InterPro: IPR010048   Hybrid cluster proteins (HCP, or Prismane) have been identified in bacteria, archaea and eukaryotic protozoa. No specific function has yet been assigned to these proteins, but it may involve oxidoreductase enzymatic activity. These proteins contain one 4Fe-4S cluster, and one hybrid 4Fe-2O-2S cluster, the latter being similar to the Ni-Fe-S cluster found in carbon monoxide dehydrogenase enzymes (IPR010047 from INTERPRO) , .    This subfamily is heterogeneous with respect to the presence or absence of a region of about 100 amino acids not far from the N terminus of the protein. Members have been described as monomeric. ; GO: 0016661 oxidoreductase activity acting on other nitrogenous compounds as donors, 0051536 iron-sulfur cluster binding, 0006118 electron transport, 0005737 cytoplasm.
Probab=27.17  E-value=24  Score=15.35  Aligned_cols=10  Identities=30%  Similarity=0.664  Sum_probs=4.7

Q ss_pred             HHHHHHHCCC
Q ss_conf             9998742368
Q gi|254780135|r  140 LLQMFSQSKG  149 (408)
Q Consensus       140 llqmfsqskg  149 (408)
                      |-+...|.+|
T Consensus       259 L~~LL~QT~g  268 (567)
T TIGR01703       259 LEELLEQTEG  268 (567)
T ss_pred             HHHHHHHHHH
T ss_conf             9999998741


No 17 
>TIGR01326 OAH_OAS_sulfhy O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase; InterPro: IPR006235   This family of sequences is a distinct clade of the Cys/Met metabolism pyridoxal phosphate-dependent enzyme superfamily. Members include examples of OAH/OAS sulfhydrylase, an enzyme with activity both as O-acetylhomoserine sulfhydrylase (OAH, 2.5.1.49 from EC) and O-acetylserine sulfhydrylase (OAS, 2.5.1.47 from EC). An alternate name for OAH sulfhydrylase is homocysteine synthase.; GO: 0016765 transferase activity transferring alkyl or aryl (other than methyl) groups, 0006520 amino acid metabolic process.
Probab=27.09  E-value=21  Score=15.78  Aligned_cols=23  Identities=43%  Similarity=0.548  Sum_probs=18.4

Q ss_pred             EECCCCCHHHCCHHHHHHHHHHH
Q ss_conf             63441001111578899999988
Q gi|254780135|r  310 AIGNQLSRSSVGKETIDRILQDC  332 (408)
Q Consensus       310 aignqlsrssvgketidrilqdc  332 (408)
                      -|-..+-|-|||-|-||-|++|-
T Consensus       407 GVt~~~iRlSvGIE~iDDIiaDL  429 (434)
T TIGR01326       407 GVTPGLIRLSVGIENIDDIIADL  429 (434)
T ss_pred             CCCCCEEEEEEECCCHHHHHHHH
T ss_conf             89757078987218767899999


No 18 
>KOG0942 consensus
Probab=26.16  E-value=43  Score=13.63  Aligned_cols=66  Identities=21%  Similarity=0.356  Sum_probs=34.1

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHCHHHHHHHHHHHC----CCCCEECCCCCCCEEEEEEECCCEEECCCCEEEEEECC
Q ss_conf             55222112357420017789998705225788887618----74320027310000345554251130358589999517
Q gi|254780135|r  182 RGKVADSQVHRPKYLEYSHYYQQYLNRNTLVKNFLSQI----PYKNFCMAPYHYKSIFYWAFENFQYHQDNNMLIFYSHR  257 (408)
Q Consensus       182 rgkvadsqvhrpkyleyshyyqqylnrntlvknflsqi----pyknfcmapyhyksifywafenfqyhqdnnmlifyshr  257 (408)
                      ++++-+-.-+|-.-   -+-++..-+|-.++.+.++|+    --++||-.         -.-+.++-+..|.|  |++-+
T Consensus       525 ~~~~~g~~~~r~~~---~~~~~~~n~~~~v~~e~l~~~~~rd~r~~f~~~---------~e~~dl~sd~~~e~--~~~l~  590 (1001)
T KOG0942         525 REKVVGITESRRMP---LRQRRRWNGRLQVVRELLTELSERDNRKEFCPS---------KERPDLKSDDENEL--FNPLP  590 (1001)
T ss_pred             CCCCCCCCHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC---------CCCCCCCCCCHHHH--HCCHH
T ss_conf             35314764554425---899999877877999999999878877414875---------45666443355776--40027


Q ss_pred             CEEE
Q ss_conf             3687
Q gi|254780135|r  258 DFYR  261 (408)
Q Consensus       258 dfyr  261 (408)
                      +|-|
T Consensus       591 ~~lr  594 (1001)
T KOG0942         591 SFLR  594 (1001)
T ss_pred             HHHH
T ss_conf             6653


No 19 
>pfam07299 FBP Fibronectin-binding protein (FBP). This family consists of several bacterial fibronectin-binding proteins which are thought to be involved in virulence in Listeria species.
Probab=26.08  E-value=43  Score=13.62  Aligned_cols=35  Identities=23%  Similarity=0.538  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHHHHHCCCC-CCHHHCCCHHHHHHHHH
Q ss_conf             235789999987400342-20000000887743220
Q gi|254780135|r   77 RDNFIRHQIEKALNTYNS-RDLSNIGSIESIVKDAV  111 (408)
Q Consensus        77 rdnfirhqiekalntyns-rdlsnigsiesivkdav  111 (408)
                      .=|||+.|++.-.|+|.+ -|.+-+-.+.+...+.+
T Consensus         6 qYN~IK~qv~~L~~~~~svnD~~vi~a~k~~~~~kI   41 (208)
T pfam07299         6 QYNFIKQQVAQLVNAYRTVNDRNVIKAVKALAIEKI   41 (208)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf             468999999999998641488899999999999999


No 20 
>KOG0099 consensus
Probab=25.23  E-value=44  Score=13.52  Aligned_cols=44  Identities=36%  Similarity=0.695  Sum_probs=36.7

Q ss_pred             HHHHHHHHHCCCCCCCEEEECCCCCCCCCCCCCEEEEEEEECCCCCHHHCCHHHHHHHHHHHHHHH
Q ss_conf             998887410234678426513674354676653068867634410011115788999999889887
Q gi|254780135|r  271 FIKNVFDMTSNQFGDGQVLTNTNHCFPHGASHSKYMLMFAIGNQLSRSSVGKETIDRILQDCYYMH  336 (408)
Q Consensus       271 fiknvfdmtsnqfgdgqvltntnhcfphgashskymlmfaignqlsrssvgketidrilqdcyymh  336 (408)
                      ||..-|--.|..-|||     ..+|+||=.                 ..|..|.|.|...||--|-
T Consensus       325 fird~FlRiSta~~Dg-----~h~CYpHFT-----------------cAvDTenIrrVFnDcrdiI  368 (379)
T KOG0099         325 FIRDEFLRISTASGDG-----RHYCYPHFT-----------------CAVDTENIRRVFNDCRDII  368 (379)
T ss_pred             HHHHHHHHHCCCCCCC-----CEECCCCEE-----------------EEECHHHHHHHHHHHHHHH
T ss_conf             4230677630346787-----530002346-----------------7715388999987899999


No 21 
>pfam03542 Tuberin Tuberin. Tuberous sclerosis complex (TSC) is an autosomal dominant disorder and is characterized by the presence of hamartomas in many organs, such as brain, skin, heart, lung, and kidney. It is caused by mutation either TSC1 or TSC2 tumour suppressor gene. The TSC2 gene codes for tuberin and interacts with hamartin pfam04388, containing two coiled-coil regions, which have been shown to mediate binding to tuberin. These two proteins function within the same pathway(s) regulating cell cycle, cell growth, adhesion, and vesicular trafficking.
Probab=24.00  E-value=40  Score=13.84  Aligned_cols=24  Identities=38%  Similarity=0.780  Sum_probs=18.1

Q ss_pred             CCCHHEEEECCCCCHHHHHHHHHHHHHHHHHHE
Q ss_conf             590320442587653447898777778733430
Q gi|254780135|r  368 SDPSKYYEINSDENVMPIAKSLARNVITNWFSQ  400 (408)
Q Consensus       368 sdpskyyeinsdenvmpiakslarnvitnwfsq  400 (408)
                      .+|+||-         --.-|||-+||..||-.
T Consensus       328 Tnp~ky~---------~YiVsLAhhVIa~WFlk  351 (356)
T pfam03542       328 TNPARYD---------HYTVSLAHHVIAAWFIK  351 (356)
T ss_pred             CCCCCCH---------HHHHHHHHHHHHHHHHH
T ss_conf             7864301---------68899999999999998


No 22 
>PHA01365 hypothetical protein
Probab=23.79  E-value=47  Score=13.34  Aligned_cols=15  Identities=33%  Similarity=0.618  Sum_probs=11.4

Q ss_pred             CCHHHHHHHHHHHHH
Q ss_conf             157889999998898
Q gi|254780135|r  320 VGKETIDRILQDCYY  334 (408)
Q Consensus       320 vgketidrilqdcyy  334 (408)
                      -|||.|.|++|.|+-
T Consensus         3 ~~~~~i~~~~~k~fk   17 (91)
T PHA01365          3 DYKNGIKKLLQKCFK   17 (91)
T ss_pred             CHHHHHHHHHHHHHC
T ss_conf             278899999999847


No 23 
>pfam07727 RVT_2 Reverse transcriptase (RNA-dependent DNA polymerase). A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.
Probab=23.00  E-value=7.5  Score=18.99  Aligned_cols=48  Identities=31%  Similarity=0.465  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC----------------HHHHHHHCCHHHH
Q ss_conf             8789999998767777778888999987764106843----------------2366774122357
Q gi|254780135|r   31 SSFVAIVDVVVDQVTVMQKTALLQEVLDHVIYRTSPK----------------NLYDLREAGRDNF   80 (408)
Q Consensus        31 ssfvaivdvvvdqvtvmqktallqevldhviyrtspk----------------nlydlreagrdnf   80 (408)
                      -+.+|.-|..+.|.-|  +||.|+.-||+.||-.-|.                .||.||.|+|.=+
T Consensus        69 laiaa~~~~~~~q~Dv--~tAFLn~~l~e~IYm~~P~G~~~~~~~~~V~kL~kaLYGLkqapr~W~  132 (246)
T pfam07727        69 LALAAQRGWELHQMDV--KTAFLNGELEEEVYMKQPPGFEDPGKPNKVCRLKKSLYGLKQAPRAWY  132 (246)
T ss_pred             HHHHHHCCCEEEEEEE--CHHHHCCCCCCCCEEECCCCCCCCCCCCEEEEEEEECCCCCCCHHHHH
T ss_conf             9999875986555454--112305767878449588764668888889999410016563689999


No 24 
>COG3955 Exopolysaccharide biosynthesis protein [Cell envelope biogenesis, outer membrane]
Probab=22.62  E-value=50  Score=13.18  Aligned_cols=86  Identities=34%  Similarity=0.461  Sum_probs=49.0

Q ss_pred             HHHCCCCEEHHHHHHHHHHCCCCEEEEEECCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCHHHHHHHHHHHCCCCC
Q ss_conf             74236822235543223220666488630004225312552221123574200177899987052257888876187432
Q gi|254780135|r  144 FSQSKGKVDISRRKKVMYKQNIGLMIMPFAWDGYWLASRGKVADSQVHRPKYLEYSHYYQQYLNRNTLVKNFLSQIPYKN  223 (408)
Q Consensus       144 fsqskgkvdisrrkkvmykqniglmimpfawdgywlasrgkvadsqvhrpkyleyshyyqqylnrntlvknflsqipykn  223 (408)
                      -|-...+-+-.+|||-|-..|.=.|  --.-||        |                      ...+|+.| .+.||||
T Consensus       111 ~S~eEAk~kWe~RkkRin~~NLfik--m~~kd~--------v----------------------~Ek~v~~f-DnLPykN  157 (211)
T COG3955         111 ASFEEAKNKWELRKKRINLKNLFIK--MTDKDG--------V----------------------NEKLVKRF-DNLPYKN  157 (211)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEE--EECCCC--------C----------------------CHHHHHHH-HCCCCCC
T ss_conf             3088887579988763140034899--745777--------6----------------------69999986-3688666


Q ss_pred             ---EECCCCC-CCEEEEEEECCCEEECCCCEEEEEECCCEEEEEEC
Q ss_conf             ---0027310-00034555425113035858999951736875500
Q gi|254780135|r  224 ---FCMAPYH-YKSIFYWAFENFQYHQDNNMLIFYSHRDFYRITWD  265 (408)
Q Consensus       224 ---fcmapyh-yksifywafenfqyhqdnnmlifyshrdfyritwd  265 (408)
                         |.-.||. |||+.|-.  .++. |--|+-||-|..+.-.-+.|
T Consensus       158 Kvif~~kPyk~~KS~~~ip--~~~~-~~~~~ai~t~~~~l~~~~~d  200 (211)
T COG3955         158 KVIFTPKPYKAYKSAYFIP--RYIW-QCQNGAIFTSNGWLGKFYMD  200 (211)
T ss_pred             EEEECCCCCHHHCEEEEEC--CHHH-HCCCCCEECCCCCCCEEEEE
T ss_conf             3786068724434378853--1687-58565465136654316664


No 25 
>TIGR01524 ATPase-IIIB_Mg magnesium-translocating P-type ATPase; InterPro: IPR006415   This group describes the magnesium translocating P-type ATPase found in a limited number of bacterial species and best described in Salmonella typhimurium, which contains two isoforms . These transporters are active in low external Mg2+ concentrations and pump the ion into the cytoplasm. The magnesium ATPases have been classified as type IIIB by a phylogenetic analysis .; GO: 0015444 magnesium-importing ATPase activity, 0015693 magnesium ion transport, 0016021 integral to membrane.
Probab=21.93  E-value=7.2  Score=19.12  Aligned_cols=63  Identities=27%  Similarity=0.445  Sum_probs=37.7

Q ss_pred             EEEEEEEEHHHHHHHHHH---CCCCEEHHHHHHHHHH----CCCCEEEEEECCCCEEEECCCCCCCCCCCCCCCCC
Q ss_conf             631112212789998742---3682223554322322----06664886300042253125522211235742001
Q gi|254780135|r  129 ALSTTVQLRGSLLQMFSQ---SKGKVDISRRKKVMYK----QNIGLMIMPFAWDGYWLASRGKVADSQVHRPKYLE  197 (408)
Q Consensus       129 alsttvqlrgsllqmfsq---skgkvdisrrkkvmyk----qniglmimpfawdgywlasrgkvadsqvhrpkyle  197 (408)
                      ||+-.|-|.-..|.|.--   .||-+..||||-.|-+    ||+|-|=.-      ---..|........--+|+.
T Consensus       312 AlavAVGLTPEMLPMIVssnLAkGAi~mSk~KVIvK~L~AIQNfGAMDiL------CTDKTGTLT~Dki~L~~h~D  381 (892)
T TIGR01524       312 ALAVAVGLTPEMLPMIVSSNLAKGAIKMSKKKVIVKRLDAIQNFGAMDIL------CTDKTGTLTQDKIVLEKHLD  381 (892)
T ss_pred             HHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCC------CCCCCCCCCCHHHHHHHHHC
T ss_conf             99987447723122677435678999861274256303300143432221------13888874301332211102


No 26 
>COG3114 CcmD Heme exporter protein D [Intracellular trafficking and secretion]
Probab=21.84  E-value=51  Score=13.08  Aligned_cols=17  Identities=29%  Similarity=0.430  Sum_probs=14.3

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             77777888899998776
Q gi|254780135|r   44 VTVMQKTALLQEVLDHV   60 (408)
Q Consensus        44 vtvmqktallqevldhv   60 (408)
                      .+|+|++++|++|.+.-
T Consensus        36 ~sv~qrr~iL~~v~r~~   52 (67)
T COG3114          36 HSVLQRRAILRGVARQR   52 (67)
T ss_pred             HHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999


No 27 
>pfam00522 VPR VPR/VPX protein.
Probab=21.08  E-value=53  Score=12.97  Aligned_cols=45  Identities=27%  Similarity=0.444  Sum_probs=32.0

Q ss_pred             CCCCHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCCCEEEEEEEECCCCCHHHCCHHHHHHHHHHHHHHHHHCCC
Q ss_conf             00708999888741023467842651367435467665306886763441001111578899999988988763135
Q gi|254780135|r  265 DHFPYSFIKNVFDMTSNQFGDGQVLTNTNHCFPHGASHSKYMLMFAIGNQLSRSSVGKETIDRILQDCYYMHKHHRT  341 (408)
Q Consensus       265 dhfpysfiknvfdmtsnqfgdgqvltntnhcfphgashskymlmfaignqlsrssvgketidrilqdcyymhkhhrt  341 (408)
                      .|||-.++-.+..-.-+..||-.                                -|++.+-||||.+.++|-....
T Consensus        32 rHFpr~~L~~lgq~iy~~~gDt~--------------------------------~g~~~~irilQ~aLFiHfr~GC   76 (83)
T pfam00522        32 KHFPRELLFAVWQYIYEYWGDEQ--------------------------------GGAYKYIRLLQRALFVHFRAGC   76 (83)
T ss_pred             HCCCHHHHHHHHHHHHHHCCCHH--------------------------------HHHHHHHHHHHHHHHHHHHCCC
T ss_conf             74999999999879999309779--------------------------------9999999999999999998278


No 28 
>KOG0333 consensus
Probab=20.84  E-value=54  Score=12.94  Aligned_cols=39  Identities=31%  Similarity=0.474  Sum_probs=26.7

Q ss_pred             HHHHHHCCCCCCEEEEEEEECCCCCCHH--HHHHHHCCCCH
Q ss_conf             9887631357741899984148874302--67876205903
Q gi|254780135|r  333 YYMHKHHRTGRGAITIFSVGFSPDQDTR--YTLRQCASDPS  371 (408)
Q Consensus       333 yymhkhhrtgrgaitifsvgfspdqdtr--ytlrqcasdps  371 (408)
                      -|.|.--||||.+-.--.+.|-...||.  |.|+||-+...
T Consensus       600 DYtHRIGRTgRAGk~GtaiSflt~~dt~v~ydLkq~l~es~  640 (673)
T KOG0333         600 DYTHRIGRTGRAGKSGTAISFLTPADTAVFYDLKQALRESV  640 (673)
T ss_pred             HHHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHH
T ss_conf             99887423444666753689864011177899999999864


No 29 
>cd03267 ABC_NatA_like Similar in sequence to NatA, this is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled to proton or K+ uptake.  NatB possess six putative membrane spanning regions at its C-terminus.  In B. subtilis, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane.  The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system.  Hence, the functional NatAB is presumably assembled with two copies of the single ATP-binding protein and the single intergral membrane protein.
Probab=20.77  E-value=54  Score=12.93  Aligned_cols=106  Identities=15%  Similarity=0.288  Sum_probs=68.7

Q ss_pred             CEEEEEECCCCHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCCCEEEEEEEECCCCCHHHCCHHHHHHHHHHHHHHHH
Q ss_conf             36875500070899988874102346784265136743546766530688676344100111157889999998898876
Q gi|254780135|r  258 DFYRITWDHFPYSFIKNVFDMTSNQFGDGQVLTNTNHCFPHGASHSKYMLMFAIGNQLSRSSVGKETIDRILQDCYYMHK  337 (408)
Q Consensus       258 dfyritwdhfpysfiknvfdmtsnqfgdgqvltntnhcfphgashskymlmfaignqlsrssvgketidrilqdcyymhk  337 (408)
                      .+||+.|.. |- +|.++...-...||+-++|.+-|-..+.|.-.       +   -+..+..||-|+=+++-.-.    
T Consensus         8 k~y~~~~~~-~~-~~~~~~~~l~K~yg~~~al~~vsf~i~~Gei~-------g---LlGpNGaGKSTllk~l~Gl~----   71 (236)
T cd03267           8 KSYRVYSKE-PG-LIGSLKSLFKRKYREVEALKGISFTIEKGEIV-------G---FIGPNGAGKTTTLKILSGLL----   71 (236)
T ss_pred             EEEECCCCC-HH-HHHHHHHHEECCCCCEEEECCCEEEECCCCEE-------E---EECCCCCHHHHHHHHHHCCC----
T ss_conf             898868786-02-88986645245549989866805788489599-------9---99999830999999996494----


Q ss_pred             HCCCCCCEEEEEEEECCCCCCHHHHHHHHCC---C-CHHEEEECCCCCHH
Q ss_conf             3135774189998414887430267876205---9-03204425876534
Q gi|254780135|r  338 HHRTGRGAITIFSVGFSPDQDTRYTLRQCAS---D-PSKYYEINSDENVM  383 (408)
Q Consensus       338 hhrtgrgaitifsvgfspdqdtrytlrqcas---d-pskyyeinsdenvm  383 (408)
                        +.-.|.|.++  |..|.....-..+++..   + +.-|.+....||+.
T Consensus        72 --~p~~G~I~v~--G~~~~~~~~~~~~~ig~v~~q~~~l~~~ltv~e~l~  117 (236)
T cd03267          72 --QPTSGEVRVA--GLVPWKRRKKFLRRIGVVFGQKTQLWWDLPVIDSFY  117 (236)
T ss_pred             --CCCCEEEEEC--CEECCCCHHHHHHHEEEEECCCCCCCCCCCHHHHHH
T ss_conf             --8871599999--998510409888437999577542467993999999


No 30 
>pfam05482 Serendipity_A Serendipity locus alpha protein (SRY-A). The Drosophila serendipity alpha (sry alpha) gene is specifically transcribed at the blastoderm stage, from nuclear cycle 11 to the onset of gastrulation, in all somatic nuclei. SRY-A is required for the cellularisation of the embryo and is involved in the localisation of the actin filaments just prior to and during plasma membrane invagination.
Probab=20.16  E-value=42  Score=13.72  Aligned_cols=15  Identities=33%  Similarity=0.736  Sum_probs=9.3

Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             789999998767777
Q gi|254780135|r   32 SFVAIVDVVVDQVTV   46 (408)
Q Consensus        32 sfvaivdvvvdqvtv   46 (408)
                      |||..+|...|.+.-
T Consensus       137 sFv~LlDlALD~L~~  151 (549)
T pfam05482       137 SFVELMDLALDHLEA  151 (549)
T ss_pred             CHHHHHHHHHHHHHH
T ss_conf             599999999998999


Done!