Query         gi|254781007|ref|YP_003065420.1| hypothetical protein CLIBASIA_04540 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 411
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 30 03:00:40 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781007.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 cd01473 vWA_CTRP CTRP for  CS   52.9      17 0.00044   16.6   9.6  155  212-393    22-190 (192)
  2 cd01480 vWA_collagen_alpha_1-V  52.7      15 0.00037   17.1   2.9   63  302-378   109-171 (186)
  3 KOG0099 consensus               51.7      18 0.00046   16.5   3.3   46  271-338   325-370 (379)
  4 cd01475 vWA_Matrilin VWA_Matri  50.2      19 0.00048   16.3   3.7   46  344-391   134-181 (224)
  5 KOG2531 consensus               47.2      21 0.00053   16.0   3.1   47   73-119   114-166 (545)
  6 pfam07888 CALCOCO1 Calcium bin  46.7       6 0.00015   19.9   0.2   20  146-165   294-313 (546)
  7 COG4854 Predicted membrane pro  40.1      27 0.00068   15.3   3.4   39  317-355    44-82  (126)
  8 cd01481 vWA_collagen_alpha3-VI  38.8      28 0.00071   15.2   3.0   32  344-377   132-163 (165)
  9 cd01474 vWA_ATR ATR (Anthrax T  37.9      29 0.00073   15.1   6.7   50  344-395   133-183 (185)
 10 TIGR01271 CFTR_protein cystic   37.4      29 0.00074   15.0   6.7   36   56-93   1099-1134(1534)
 11 PRK03958 tRNA 2'-O-methylase;   32.1      35 0.00089   14.4   4.0   61  346-410     3-67  (175)
 12 KOG0829 consensus               30.7      37 0.00094   14.3   2.6   47  315-361    78-132 (169)
 13 TIGR02599 TIGR02599 Verrucomic  30.5      18 0.00047   16.4   0.6  151   32-195    12-185 (396)
 14 cd01469 vWA_integrins_alpha_su  30.0      38 0.00097   14.2   7.2   36  343-378   130-170 (177)
 15 cd01482 vWA_collagen_alphaI-XI  29.4      39 0.00099   14.1   2.6   27  344-372   129-155 (164)
 16 cd00049 MH1 MH1 is a small DNA  28.8      22 0.00057   15.8   0.8   14  222-235   107-120 (121)
 17 pfam07727 RVT_2 Reverse transc  27.5     5.5 0.00014   20.1  -2.5   49   30-80     68-132 (246)
 18 KOG0090 consensus               27.3      28 0.00072   15.1   1.1   27  302-329   152-178 (238)
 19 TIGR00955 3a01204 Pigment prec  27.1      17 0.00044   16.6  -0.1   28  212-241   463-490 (671)
 20 smart00523 DWA Domain A in dwa  25.7      24 0.00061   15.6   0.4   15  221-235    92-106 (109)
 21 pfam03165 MH1 MH1 domain. The   24.8      28 0.00072   15.1   0.7   14  221-234    93-106 (107)
 22 TIGR00708 cobA cob(I)alamin ad  23.9      21 0.00054   16.0  -0.1   35   39-73    118-165 (191)
 23 pfam03542 Tuberin Tuberin. Tub  23.5      42  0.0011   13.9   1.4   25  368-401   328-352 (356)
 24 pfam01727 consensus             22.2      45  0.0012   13.6   1.3   25  277-303    13-37  (81)
 25 TIGR01405 polC_Gram_pos DNA po  20.9      34 0.00086   14.5   0.5   16  175-190   687-702 (1264)
 26 TIGR01524 ATPase-IIIB_Mg magne  20.8     7.9  0.0002   19.0  -2.8   65  129-199   312-383 (892)
 27 pfam09702 Cas_Csa5 CRISPR-asso  20.6      54  0.0014   13.1   1.4   29  310-346    13-41  (105)
 28 PRK12703 tRNA 2'-O-methylase;   20.6      56  0.0014   13.0   3.7   38  285-328   215-252 (339)

No 1  
>cd01473 vWA_CTRP CTRP for  CS protein-TRAP-related protein: Adhesion of Plasmodium to host cells is an important phenomenon in parasite invasion and in malaria associated pathology.CTRP encodes a protein containing a putative signal sequence followed by a long extracellular region of 1990 amino acids, a transmembrane domain, and a short cytoplasmic segment. The extracellular region of CTRP contains two separated adhesive domains. The first domain contains six 210-amino acid-long homologous VWA domain repeats. The second domain contains seven repeats of 87-60  amino acids in length, which share similarities with the thrombospondin type 1 domain found in a variety of adhesive molecules. Finally, CTRP also contains consensus motifs found in the superfamily of haematopoietin receptors. The VWA domains in these proteins likely mediate protein-protein interactions.
Probab=52.91  E-value=17  Score=16.63  Aligned_cols=155  Identities=19%  Similarity=0.268  Sum_probs=82.7

Q ss_pred             HHHHHHHCCCCCEECCCCHHHHHHHEEEEEEEEEECCCCCHHHHHCCCCCCCHHCCHHHHHHHHHHHHCCCCCCC-----
Q ss_conf             898876187432002720234434122112578625862125654186421100060899988874101346784-----
Q gi|254781007|r  212 VKNFLSQIPYKNFCMAPYHYSSILYWAVGTLTYSVDNKTTTREYYKDPYYATWDHFPYSFIKNVFDMTSNQFGDG-----  286 (411)
Q Consensus       212 vknflsqipyknfcmapyhyssilywavgtltysvdnktttreyykdpyyatwdhfpysfiknvfdmtsnqfgdg-----  286 (411)
                      +++|+..+- .+|-..|-.      --||-..||-.+++... .....+|   +  .-..++.+-.+...-+..|     
T Consensus        22 v~~F~~~lv-~~f~Ig~~~------~rvgvv~yS~~~~~~~~-f~~~~~~---~--k~~~l~~i~~l~~~~~~gg~T~tg   88 (192)
T cd01473          22 VIPFTEKII-NNLNISKDK------VHVGILLFAEKNRDVVP-FSDEERY---D--KNELLKKINDLKNSYRSGGETYIV   88 (192)
T ss_pred             HHHHHHHHH-HHCCCCCCC------EEEEEEEECCCCCEEEE-CCCCCCC---C--HHHHHHHHHHHHHCCCCCCCCHHH
T ss_conf             999999999-875659896------19999995588740132-3554434---8--999999999987314689824799


Q ss_pred             EEE--ECCCCCCCCCCCCC--CEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCHHHH
Q ss_conf             264--13674344676677--07999973451003330289999999985998875114764168997404887420267
Q gi|254781007|r  287 QVL--TNTNHCFPHGASQN--KYMLMLAIGNQLSRSSVEKEKIEKVLQDCHYMHKRHRTGRDAITIFSVGFSPDQDTRYT  362 (411)
Q Consensus       287 qvl--tntnhcfphgasqn--kymlmlaignqlsrssvekekiekvlqdchymhkrhrtgrdaitifsvgfspdqdtryt  362 (411)
                      +.|  ...+.-...|+.++  |.++++.=|+.-+++...-+...+.|.            ...|+||.||-.--  .+-.
T Consensus        89 ~AL~~~~~~~~~~~g~R~~vpkv~IvlTDG~s~~~~~~~~~~~a~~lr------------~~gV~i~avGVg~~--~~~e  154 (192)
T cd01473          89 EALKYGLKNYTKHGNRRKDAPKVTMLFTDGNDTSASKKELQDISLLYK------------EENVKLLVVGVGAA--SENK  154 (192)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCEEEEEEECCCCCCCCHHHHHHHHHHHH------------HCCCEEEEEEECCC--CHHH
T ss_conf             999999998634678888997499999569988731678999999999------------87978999980637--9999


Q ss_pred             HHHHCCCCHH-----EEEECCCCCHHHHHHHHHHHH
Q ss_conf             8763059032-----044258765344789877777
Q gi|254781007|r  363 LRQCASDPSK-----YYEINSDENVMPIAKSLARNV  393 (411)
Q Consensus       363 lrqcasdpsk-----yyeinsdenvmpiakslarnv  393 (411)
                      ||+-|+.|..     .|-..+=+++.+|.+.+.+++
T Consensus       155 L~~iag~~~~~~~c~~~~~~~fd~l~~i~~~l~~~v  190 (192)
T cd01473         155 LKLLAGCDINNDNCPNVIKTEWNNLNGISKFLTDKI  190 (192)
T ss_pred             HHHHHCCCCCCCCCCEEEECCHHHHHHHHHHHHHHH
T ss_conf             999869998899775799479789999999999972


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=52.72  E-value=15  Score=17.13  Aligned_cols=63  Identities=24%  Similarity=0.341  Sum_probs=37.7

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCHHHHHHHHCCCCHHEEEECC
Q ss_conf             77079999734510033302899999999859988751147641689974048874202678763059032044258
Q gi|254781007|r  302 QNKYMLMLAIGNQLSRSSVEKEKIEKVLQDCHYMHKRHRTGRDAITIFSVGFSPDQDTRYTLRQCASDPSKYYEINS  378 (411)
Q Consensus       302 qnkymlmlaignqlsrssvekekiekvlqdchymhkrhrtgrdaitifsvgfspdqdtrytlrqcasdpskyyeins  378 (411)
                      .+|-++.+.=|.  |.. -+...++...++..         +..|+||.||.....  .-.|++.||+|++.+-.++
T Consensus       109 ~~kvlvliTDG~--S~~-~~~~~~~~aa~~lr---------~~GV~ifaVGVG~~~--~~eL~~IAs~p~~~~~~~~  171 (186)
T cd01480         109 ENKFLLVITDGH--SDG-SPDGGIEKAVNEAD---------HLGIKIFFVAVGSQN--EEPLSRIACDGKSALYREN  171 (186)
T ss_pred             CCEEEEEEECCC--CCC-CCCHHHHHHHHHHH---------HCCCEEEEEEECCCC--HHHHHHHHCCCCCEEEECC
T ss_conf             853899984587--666-74066999999999---------879899999947488--7999998589973897368


No 3  
>KOG0099 consensus
Probab=51.72  E-value=18  Score=16.51  Aligned_cols=46  Identities=37%  Similarity=0.741  Sum_probs=38.4

Q ss_pred             HHHHHHHHHCCCCCCCEEEECCCCCCCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99888741013467842641367434467667707999973451003330289999999985998875
Q gi|254781007|r  271 FIKNVFDMTSNQFGDGQVLTNTNHCFPHGASQNKYMLMLAIGNQLSRSSVEKEKIEKVLQDCHYMHKR  338 (411)
Q Consensus       271 fiknvfdmtsnqfgdgqvltntnhcfphgasqnkymlmlaignqlsrssvekekiekvlqdchymhkr  338 (411)
                      ||..-|--.|..-|||     ..+|+||=.                 ..|..|.|..|..||.-|-.|
T Consensus       325 fird~FlRiSta~~Dg-----~h~CYpHFT-----------------cAvDTenIrrVFnDcrdiIqr  370 (379)
T KOG0099         325 FIRDEFLRISTASGDG-----RHYCYPHFT-----------------CAVDTENIRRVFNDCRDIIQR  370 (379)
T ss_pred             HHHHHHHHHCCCCCCC-----CEECCCCEE-----------------EEECHHHHHHHHHHHHHHHHH
T ss_conf             4230677630346787-----530002346-----------------771538899998789999999


No 4  
>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=50.22  E-value=19  Score=16.35  Aligned_cols=46  Identities=22%  Similarity=0.369  Sum_probs=32.1

Q ss_pred             CEEEEEEEECCCCCCHHHHHHHHCCCCH--HEEEECCCCCHHHHHHHHHH
Q ss_conf             4168997404887420267876305903--20442587653447898777
Q gi|254781007|r  344 DAITIFSVGFSPDQDTRYTLRQCASDPS--KYYEINSDENVMPIAKSLAR  391 (411)
Q Consensus       344 daitifsvgfspdqdtrytlrqcasdps--kyyeinsdenvmpiakslar  391 (411)
                      +.|.||.||..- - .+-.|++.||+|+  ..+.+++=+..-.++..|..
T Consensus       134 ~GV~ifaVGVg~-~-~~~eL~~IAs~P~~~hvf~v~~F~~l~~l~~~l~~  181 (224)
T cd01475         134 LGIEMFAVGVGR-A-DEEELREIASEPLADHVFYVEDFSTIEELTKKFQG  181 (224)
T ss_pred             CCCEEEEEECCC-C-CHHHHHHHHCCCCHHCEEEECCHHHHHHHHHHHHH
T ss_conf             798899996374-7-98999998559737568994798899999999876


No 5  
>KOG2531 consensus
Probab=47.23  E-value=21  Score=16.04  Aligned_cols=47  Identities=26%  Similarity=0.196  Sum_probs=23.3

Q ss_pred             HHCCHHHHHHHHHHHHHHC---CCCCCCCCCC---CHHHHHHHHHEEECCCCC
Q ss_conf             7412235789999987400---3433334543---188874322113224673
Q gi|254781007|r   73 REAGRDNFIRHQIEKALNT---YNSRDLSNTG---SIESIVKDAVILTKNVNS  119 (411)
Q Consensus        73 reagrdnfirhqiekalnt---ynsrdlsntg---siesivkdaviltknvns  119 (411)
                      +.-.-+.+..+|+|.|+-.   -+-+|-|.|-   .+|.-|-.+--|.|-..|
T Consensus       114 ~~Ld~~~~L~eQle~aF~v~~sP~WmDsSTtkQC~ElE~~VGG~~~la~LTGS  166 (545)
T KOG2531         114 ESLDPEKSLHEQLESAFSVQTSPIWMDSSTTKQCQELEEAVGGAQELAKLTGS  166 (545)
T ss_pred             HCCCHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHCC
T ss_conf             63793367999998764146897622564088999999871648888776364


No 6  
>pfam07888 CALCOCO1 Calcium binding and coiled-coil domain (CALCOCO1) like. Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein coexpressed by Mus musculus (CoCoA/CALCOCO1). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1, and thus enhances transcriptional activation by a number of nuclear receptors. CALCOCO1 has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region.
Probab=46.68  E-value=6  Score=19.86  Aligned_cols=20  Identities=10%  Similarity=0.265  Sum_probs=10.2

Q ss_pred             HCCCCEEHHHHHHHHHHCCC
Q ss_conf             23582223554323332066
Q gi|254781007|r  146 QSKGKVDISRRKKVMYKQNI  165 (411)
Q Consensus       146 qskgkvdisrrkkvmykqni  165 (411)
                      ...+.+.-|+++-++....+
T Consensus       294 ~~qeql~AS~q~a~~L~~EL  313 (546)
T pfam07888       294 TLQERLESSQQKAGLLGEEL  313 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
T ss_conf             87888888899999999999


No 7  
>COG4854 Predicted membrane protein [Function unknown]
Probab=40.08  E-value=27  Score=15.29  Aligned_cols=39  Identities=23%  Similarity=0.405  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCC
Q ss_conf             333028999999998599887511476416899740488
Q gi|254781007|r  317 RSSVEKEKIEKVLQDCHYMHKRHRTGRDAITIFSVGFSP  355 (411)
Q Consensus       317 rssvekekiekvlqdchymhkrhrtgrdaitifsvgfsp  355 (411)
                      --|+-|+..++|+.|-.-..--.|..|..|.+||+|+.-
T Consensus        44 ~l~l~k~Rv~~vvEDER~lrvse~aSr~TiqV~~is~Al   82 (126)
T COG4854          44 LLSLVKRRVDEVVEDERTLRVSERASRRTIQVFSISAAL   82 (126)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEEEEEHHHH
T ss_conf             999999999988525889888875300257888846988


No 8  
>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=38.81  E-value=28  Score=15.16  Aligned_cols=32  Identities=28%  Similarity=0.405  Sum_probs=24.8

Q ss_pred             CEEEEEEEECCCCCCHHHHHHHHCCCCHHEEEEC
Q ss_conf             4168997404887420267876305903204425
Q gi|254781007|r  344 DAITIFSVGFSPDQDTRYTLRQCASDPSKYYEIN  377 (411)
Q Consensus       344 daitifsvgfspdqdtrytlrqcasdpskyyein  377 (411)
                      ..+.||.||...  -.+-.|++-||+|+.-|.++
T Consensus       132 ~gV~i~aVGvg~--~~~~eL~~IAs~p~~vf~~~  163 (165)
T cd01481         132 AGIVPFAIGARN--ADLAELQQIAFDPSFVFQVS  163 (165)
T ss_pred             CCCEEEEEECCC--CCHHHHHHHHCCCCCEEECC
T ss_conf             897899996897--99999999858987769738


No 9  
>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=37.88  E-value=29  Score=15.06  Aligned_cols=50  Identities=16%  Similarity=0.229  Sum_probs=37.1

Q ss_pred             CEEEEEEEECCCCCCHHHHHHHHCCCCHHEEEECC-CCCHHHHHHHHHHHHHH
Q ss_conf             41689974048874202678763059032044258-76534478987777787
Q gi|254781007|r  344 DAITIFSVGFSPDQDTRYTLRQCASDPSKYYEINS-DENVMPIAKSLARNVIT  395 (411)
Q Consensus       344 daitifsvgfspdqdtrytlrqcasdpskyyeins-denvmpiakslarnvit  395 (411)
                      ..|+||+||.+ +- .+-.|++-||+|++-|.++. =+..-.|...|...+-+
T Consensus       133 ~gV~i~aVGV~-~~-~~~eL~~IAs~p~~vf~v~~~F~~L~~i~~~l~~~iC~  183 (185)
T cd01474         133 LGAIVYCVGVT-DF-LKSQLINIADSKEYVFPVTSGFQALSGIIESVVKKACI  183 (185)
T ss_pred             CCCEEEEEECC-CC-CHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHHCC
T ss_conf             89489999716-25-99999987199864898347577789999999985287


No 10 
>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=37.40  E-value=29  Score=15.01  Aligned_cols=36  Identities=36%  Similarity=0.613  Sum_probs=23.7

Q ss_pred             HHHHHHHCCCCCHHHHHHHCCHHHHHHHHHHHHHHCCC
Q ss_conf             98776520683323667741223578999998740034
Q gi|254781007|r   56 VLDHVIYRTSPKNLYDLREAGRDNFIRHQIEKALNTYN   93 (411)
Q Consensus        56 vldhviyrtspknlydlreagrdnfirhqiekalntyn   93 (411)
                      +..|.|  +|-|.|+.+|.-||..+..--..||||+..
T Consensus      1099 IFsHLi--~SLkGLWT~RAFGRQsYFETLFHKALN~HT 1134 (1534)
T TIGR01271      1099 IFSHLI--TSLKGLWTIRAFGRQSYFETLFHKALNLHT 1134 (1534)
T ss_pred             HHHHHH--HHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf             678899--875233443303787526789999887678


No 11 
>PRK03958 tRNA 2'-O-methylase; Reviewed
Probab=32.08  E-value=35  Score=14.44  Aligned_cols=61  Identities=28%  Similarity=0.555  Sum_probs=27.4

Q ss_pred             EEEEEEECCCCCCHHHHHHH----HCCCCHHEEEECCCCCHHHHHHHHHHHHHHHHHHHEEEEEEECCC
Q ss_conf             68997404887420267876----305903204425876534478987777787444332574130115
Q gi|254781007|r  346 ITIFSVGFSPDQDTRYTLRQ----CASDPSKYYEINSDENVMPIAKSLARNVITNWFSQFTITVVDSWR  410 (411)
Q Consensus       346 itifsvgfspdqdtrytlrq----casdpskyyeinsdenvmpiakslarnvitnwfsqftitvvdswr  410 (411)
                      |.+.-.|.-|+.|.|-|-.-    -|-..++.+--..|+.+    ..--+.|..+|=..|.+...++|+
T Consensus         3 I~VLRlGHR~~RD~RiTTHv~LtaRAfGA~~i~l~~~D~~~----~etv~~V~~rwGG~F~~e~~~~~~   67 (175)
T PRK03958          3 IVVLRLGHRPERDKRITTHVGLTARALGADKILFASEDEHV----KESVEDIVERWGGPFKVEVTKSWK   67 (175)
T ss_pred             EEEEECCCCCCCCCCHHHHHHHHHHHHCCCEEEECCCCHHH----HHHHHHHHHHCCCCEEEEECCCHH
T ss_conf             99995678876676313588898887268767876887668----999999998618966999768979


No 12 
>KOG0829 consensus
Probab=30.73  E-value=37  Score=14.28  Aligned_cols=47  Identities=32%  Similarity=0.357  Sum_probs=32.3

Q ss_pred             CCHHHHHH---H-----HHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCHHH
Q ss_conf             00333028---9-----99999998599887511476416899740488742026
Q gi|254781007|r  315 LSRSSVEK---E-----KIEKVLQDCHYMHKRHRTGRDAITIFSVGFSPDQDTRY  361 (411)
Q Consensus       315 lsrssvek---e-----kiekvlqdchymhkrhrtgrdaitifsvgfspdqdtry  361 (411)
                      -|||++..   |     +...|-|--.-|..|||.-+++|.|.+|.--|..|++-
T Consensus        78 dSRsG~HNmYkEyRd~t~~gAV~q~y~dMaaRhRar~~~I~Iikv~~v~a~~~kR  132 (169)
T KOG0829          78 DSRSGTHNMYKEYRDTTRVGAVEQCYRDMAARHRARFRSIQIIKVAEVPAEDCKR  132 (169)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEHHHHHH
T ss_conf             2577615789999876655589999999877765206612599887764887435


No 13 
>TIGR02599 TIGR02599 Verrucomicrobium spinosum paralogous family TIGR02599.
Probab=30.50  E-value=18  Score=16.42  Aligned_cols=151  Identities=23%  Similarity=0.329  Sum_probs=63.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCHHHH--HHHHHH-HHHHCCCCCCCCCCCCHHHHHH
Q ss_conf             7899999987667777666789999877652068332366774122357--899999-8740034333345431888743
Q gi|254781007|r   32 SFVAIVDVVVDQVTVMQKTAWLQEVLDHVIYRTSPKNLYDLREAGRDNF--IRHQIE-KALNTYNSRDLSNTGSIESIVK  108 (411)
Q Consensus        32 sfvaivdvvvdqvtvmqktawlqevldhviyrtspknlydlreagrdnf--irhqie-kalntynsrdlsntgsiesivk  108 (411)
                      +.++|+=+|+-||+++-...|-+         ++-+ .-..||| |.-|  |--+.+ -.||+|=.--.++.++ .++-.
T Consensus        12 tvLsilm~v~~~v~~~tq~tw~~---------a~ar-~~qFREA-R~AFEaisr~LsQATLN~Yw~Y~~~~~~~-~~~~~   79 (396)
T TIGR02599        12 TVLSILMLVLAQVLSQTQRTWRR---------ATAR-AEQFREA-RAAFEAISRRLSQATLNAYWDYKYNAGTS-RTVAN   79 (396)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH---------HHHH-HHHHHHH-HHHHHHHHHHHHHHHHCCHHHHHHCCCCC-CCCCC
T ss_conf             99999999998877558888886---------4545-4654999-99999985300023403135664326777-55664


Q ss_pred             HH-HEEECCCCCCCEEEEEEEE---EEEEEEE-HHHHHHHHHHCCCCEE-HHH-HHHH---HHHCCCCEEEEEECCCCEE
Q ss_conf             22-1132246733138999886---3101110-3789998742358222-355-4323---3320666388630004225
Q gi|254781007|r  109 DA-VILTKNVNSLPLQFTVDIA---LSTTVQL-RGSLLQMFSQSKGKVD-ISR-RKKV---MYKQNIGLMIMPFAWDGYW  178 (411)
Q Consensus       109 da-viltknvnslplqftvdia---lsttvql-rgsllqmfsqskgkvd-isr-rkkv---mykqniglmimpfawdgyw  178 (411)
                      ++ -|-++-.-.=-|+|-..-|   |.+..+. .-+=--+|=|.-=-++ ..- -.-+   --+.+-||--+--+| ||+
T Consensus        80 ~~~~~P~~Y~R~SELhFv~Gpa~~LL~~~~~ag~~~GHavFFQAPLG~~n~~p~a~~~GaP~~~~~~gL~~LLN~W-Gyy  158 (396)
T TIGR02599        80 AATEVPTGYERQSELHFVSGPASTLLGAVITAGAEPGHAVFFQAPLGVTNLDPGADGSGAPEQAGTEGLDNLLNAW-GYY  158 (396)
T ss_pred             CCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHC-CCE
T ss_conf             1011553312665016772456222012324688766104540253556777778888887775144476545112-243


Q ss_pred             EECC-------CCCC-CC--CCCCCHH
Q ss_conf             3125-------5224-35--4387101
Q gi|254781007|r  179 LASR-------GKVA-DS--KVHPPKY  195 (411)
Q Consensus       179 lasr-------gkva-ds--kvhppky  195 (411)
                      +.-+       |-++ .|  +++|++|
T Consensus       159 v~~~~D~~~RP~FL~~~s~~~~~p~R~  185 (396)
T TIGR02599       159 VEFGSDLPRRPAFLAKSSAKPTAPERY  185 (396)
T ss_pred             EEECCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             753788887874235777655788862


No 14 
>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=29.99  E-value=38  Score=14.20  Aligned_cols=36  Identities=22%  Similarity=0.549  Sum_probs=26.7

Q ss_pred             CCEEEEEEEECCCCCCH---HHHHHHHCCCCHH--EEEECC
Q ss_conf             64168997404887420---2678763059032--044258
Q gi|254781007|r  343 RDAITIFSVGFSPDQDT---RYTLRQCASDPSK--YYEINS  378 (411)
Q Consensus       343 rdaitifsvgfspdqdt---rytlrqcasdpsk--yyeins  378 (411)
                      ++.|.||+||..+.-+.   ...|+..||+|..  .|.+++
T Consensus       130 ~~gv~vf~VGvG~~~~~~~~~~eL~~iAs~P~~~hvf~~~~  170 (177)
T cd01469         130 REGIIRYAIGVGGHFQRENSREELKTIASKPPEEHFFNVTD  170 (177)
T ss_pred             HCCEEEEEEEECCCCCCCCCHHHHHHHHCCCCHHCEEEECC
T ss_conf             79908999995551467451999999967985871998379


No 15 
>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=29.36  E-value=39  Score=14.13  Aligned_cols=27  Identities=37%  Similarity=0.607  Sum_probs=21.7

Q ss_pred             CEEEEEEEECCCCCCHHHHHHHHCCCCHH
Q ss_conf             41689974048874202678763059032
Q gi|254781007|r  344 DAITIFSVGFSPDQDTRYTLRQCASDPSK  372 (411)
Q Consensus       344 daitifsvgfspdqdtrytlrqcasdpsk  372 (411)
                      ..|+||.||. .+.| +..|++-||+|+.
T Consensus       129 ~gv~i~~VGV-g~~~-~~eL~~IAs~P~~  155 (164)
T cd01482         129 LGVNVFAVGV-KDAD-ESELKMIASKPSE  155 (164)
T ss_pred             CCCEEEEEEC-CCCC-HHHHHHHHCCCCH
T ss_conf             8938999978-8378-9999999689856


No 16 
>cd00049 MH1 MH1 is a small DNA binding domain, binding in an unusal way involving a beta hairpin structure binding to the major groove. MH1 is present in Smad proteins, an important family of proteins involved in TGF-beta signalling and frequent targets of tumorigenic mutations. Also known as Domain A in dwarfin family proteins.
Probab=28.76  E-value=22  Score=15.80  Aligned_cols=14  Identities=43%  Similarity=1.220  Sum_probs=11.3

Q ss_pred             CCEECCCCHHHHHH
Q ss_conf             32002720234434
Q gi|254781007|r  222 KNFCMAPYHYSSIL  235 (411)
Q Consensus       222 knfcmapyhyssil  235 (411)
                      ...|.-|||||-+.
T Consensus       107 ~~VC~NPyHy~rv~  120 (121)
T cd00049         107 DEVCINPYHYSRVV  120 (121)
T ss_pred             CEEEECCHHHHHHC
T ss_conf             95883850686512


No 17 
>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=27.50  E-value=5.5  Score=20.10  Aligned_cols=49  Identities=33%  Similarity=0.493  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC----------------HHHHHHHCCHHHH
Q ss_conf             98789999998766777766678999987765206833----------------2366774122357
Q gi|254781007|r   30 LSSFVAIVDVVVDQVTVMQKTAWLQEVLDHVIYRTSPK----------------NLYDLREAGRDNF   80 (411)
Q Consensus        30 lssfvaivdvvvdqvtvmqktawlqevldhviyrtspk----------------nlydlreagrdnf   80 (411)
                      +-+.+|.-|..+.|.-|  ++|.|+.-||+.||-.-|.                .||.||.|+|.=+
T Consensus        68 llaiaa~~~~~~~q~Dv--~tAFLn~~l~e~IYm~~P~G~~~~~~~~~V~kL~kaLYGLkqapr~W~  132 (246)
T pfam07727        68 LLALAAQRGWELHQMDV--KTAFLNGELEEEVYMKQPPGFEDPGKPNKVCRLKKSLYGLKQAPRAWY  132 (246)
T ss_pred             HHHHHHHCCCEEEEEEE--CHHHHCCCCCCCCEEECCCCCCCCCCCCEEEEEEEECCCCCCCHHHHH
T ss_conf             99999875986555454--112305767878449588764668888889999410016563689999


No 18 
>KOG0090 consensus
Probab=27.27  E-value=28  Score=15.08  Aligned_cols=27  Identities=37%  Similarity=0.315  Sum_probs=14.8

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHH
Q ss_conf             7707999973451003330289999999
Q gi|254781007|r  302 QNKYMLMLAIGNQLSRSSVEKEKIEKVL  329 (411)
Q Consensus       302 qnkymlmlaignqlsrssvekekiekvl  329 (411)
                      -||.-+..|--.+.-|...||| |+++.
T Consensus       152 CNKqDl~tAkt~~~Ir~~LEkE-i~~lr  178 (238)
T KOG0090         152 CNKQDLFTAKTAEKIRQQLEKE-IHKLR  178 (238)
T ss_pred             ECCHHHHHCCCHHHHHHHHHHH-HHHHH
T ss_conf             5552232138599999999999-99999


No 19 
>TIGR00955 3a01204 Pigment precourser permease; InterPro: IPR005284   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).    This family includes different parts of a membrane-spanning permease system necessary for the transport of pigment precursor into pigment cells responsible for eye color. White protein dimerises with brown protein for the transport of guanine and with scarlet protein for the transport of tryptophan.; GO: 0006810 transport.
Probab=27.07  E-value=17  Score=16.62  Aligned_cols=28  Identities=32%  Similarity=0.859  Sum_probs=23.1

Q ss_pred             HHHHHHHCCCCCEECCCCHHHHHHHEEEEE
Q ss_conf             898876187432002720234434122112
Q gi|254781007|r  212 VKNFLSQIPYKNFCMAPYHYSSILYWAVGT  241 (411)
Q Consensus       212 vknflsqipyknfcmapyhyssilywavgt  241 (411)
                      +-+.|+.+|.  |-+.|+-|.+|.||.+|-
T Consensus       463 lak~la~lP~--~i~~p~~f~~I~Ywm~GL  490 (671)
T TIGR00955       463 LAKTLAELPL--FIILPALFTSIVYWMIGL  490 (671)
T ss_pred             HHHHHHHHHH--HHHHHHHHHHHHHHHHCC
T ss_conf             9999998489--997479999999875156


No 20 
>smart00523 DWA Domain A in dwarfin family proteins.
Probab=25.69  E-value=24  Score=15.62  Aligned_cols=15  Identities=40%  Similarity=0.919  Sum_probs=11.7

Q ss_pred             CCCEECCCCHHHHHH
Q ss_conf             432002720234434
Q gi|254781007|r  221 YKNFCMAPYHYSSIL  235 (411)
Q Consensus       221 yknfcmapyhyssil  235 (411)
                      ....|.-||||+-|-
T Consensus        92 ~~~VC~NPYHy~Rv~  106 (109)
T smart00523       92 SDEVCCNPYHYSRVE  106 (109)
T ss_pred             CCEEEECCCCCCCCC
T ss_conf             997870883120011


No 21 
>pfam03165 MH1 MH1 domain. The MH1 (MAD homology 1) domain is found at the amino terminus of MAD related proteins such as Smads. This domain is separated from the MH2 domain by a non-conserved linker region. The crystal structure of the MH1 domain shows that a highly conserved 11 residue beta hairpin is used to bind the DNA consensus sequence GNCN in the major groove, shown to be vital for the transcriptional activation of target genes. Not all examples of MH1 can bind to DNA however. Smad2 cannot bind DNA and has a large insertion within the hairpin that presumably abolishes DNA binding. A basic helix (H2) in MH1 with the nuclear localisation signal KKLKK has been shown to be essential for Smad3 nuclear import. Smads also use the MH1 domain to interact with transcription factors such as Jun, TFE3, Sp1, and Runx.
Probab=24.84  E-value=28  Score=15.10  Aligned_cols=14  Identities=43%  Similarity=1.127  Sum_probs=10.9

Q ss_pred             CCCEECCCCHHHHH
Q ss_conf             43200272023443
Q gi|254781007|r  221 YKNFCMAPYHYSSI  234 (411)
Q Consensus       221 yknfcmapyhyssi  234 (411)
                      ....|.-||||+-+
T Consensus        93 ~~~VC~NPyHy~Rv  106 (107)
T pfam03165        93 KDEVCINPYHYSRV  106 (107)
T ss_pred             CCEEEECCCCHHHC
T ss_conf             99388487334324


No 22 
>TIGR00708 cobA cob(I)alamin adenosyltransferase; InterPro: IPR003724   ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2.5.1.17 from EC), catalyse the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12) . Adenosylcobalamin (AdoCbl) is required for the ativity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type , EutT-type  and PduO-type . Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution.    This entry represnts the ATP:cob(I)alamin adenosyltransferases CobA (Salmonella typhimurium), CobO (Pseudomonas denitrificans), and ButR (Escherichia coli). There is a high degree of sequence identity between these proteins . CobA is responsible for attaching the adenosyl moiety from ATP to the cobalt ion of the corrin ring, necessary for the convertion of cobalamin to adenosylcobalamin , . ; GO: 0005524 ATP binding, 0008817 cob(I)yrinic acid ac-diamide adenosyltransferase activity, 0009236 cobalamin biosynthetic process.
Probab=23.90  E-value=21  Score=15.96  Aligned_cols=35  Identities=37%  Similarity=0.627  Sum_probs=24.4

Q ss_pred             HHHHHHHHHHHHHHH--HHHHHH---------HH--HCCCCCHHHHHH
Q ss_conf             987667777666789--999877---------65--206833236677
Q gi|254781007|r   39 VVVDQVTVMQKTAWL--QEVLDH---------VI--YRTSPKNLYDLR   73 (411)
Q Consensus        39 vvvdqvtvmqktawl--qevldh---------vi--yrtspknlydlr   73 (411)
                      |..|.+|||-+-.||  .||++-         ||  =|-.|+.|+++-
T Consensus       118 vLLDE~~~~l~~GyL~veeV~~~L~~kp~~~~vvlTGR~aP~~L~~~A  165 (191)
T TIGR00708       118 VLLDELTVALKFGYLDVEEVVEVLQEKPKSQHVVLTGRGAPQELVELA  165 (191)
T ss_pred             EEHHHHHHHHHCCCCCHHHHHHHHHCCCCCCEEEEECCCCCHHHHHHC
T ss_conf             403423455534897889999998558456778886687868899751


No 23 
>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=23.53  E-value=42  Score=13.87  Aligned_cols=25  Identities=36%  Similarity=0.739  Sum_probs=18.7

Q ss_pred             CCCHHEEEECCCCCHHHHHHHHHHHHHHHHHHHE
Q ss_conf             5903204425876534478987777787444332
Q gi|254781007|r  368 SDPSKYYEINSDENVMPIAKSLARNVITNWFSQF  401 (411)
Q Consensus       368 sdpskyyeinsdenvmpiakslarnvitnwfsqf  401 (411)
                      .+|+||-         --.-|||-+||..||-.-
T Consensus       328 Tnp~ky~---------~YiVsLAhhVIa~WFlkc  352 (356)
T pfam03542       328 TNPARYD---------HYTVSLAHHVIAAWFIKC  352 (356)
T ss_pred             CCCCCCH---------HHHHHHHHHHHHHHHHHH
T ss_conf             7864301---------688999999999999981


No 24 
>pfam01727 consensus
Probab=22.24  E-value=45  Score=13.65  Aligned_cols=25  Identities=36%  Similarity=0.602  Sum_probs=19.6

Q ss_pred             HHHCCCCCCCEEEECCCCCCCCCCCCC
Q ss_conf             410134678426413674344676677
Q gi|254781007|r  277 DMTSNQFGDGQVLTNTNHCFPHGASQN  303 (411)
Q Consensus       277 dmtsnqfgdgqvltntnhcfphgasqn  303 (411)
                      +-.-.|+|-|-.|++||  ||-|+|--
T Consensus        13 ~k~YqqyG~Gl~l~dtn--l~gGSSGS   37 (81)
T pfam01727        13 GKEYQQYGYGLALNDTN--LPGGSSGS   37 (81)
T ss_pred             CCCHHHHCCEEEEECCC--CCCCCCCC
T ss_conf             40255424205760366--69987666


No 25 
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha subunit, Gram-positive type; InterPro: IPR006308   These are the polypeptide chains of DNA polymerase III. Full-length homologs of this protein are restricted to the Gram-positive lineages, including the Mycoplasmas. This protein is designated alpha chain and given the gene symbol polC, but is not a full-length homolog of other polC genes. The N-terminal region of about 200 amino acids is rich in low-complexity sequence and poorly alignable. ; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0005737 cytoplasm.
Probab=20.91  E-value=34  Score=14.55  Aligned_cols=16  Identities=56%  Similarity=0.879  Sum_probs=8.4

Q ss_pred             CCEEEECCCCCCCCCC
Q ss_conf             4225312552243543
Q gi|254781007|r  175 DGYWLASRGKVADSKV  190 (411)
Q Consensus       175 dgywlasrgkvadskv  190 (411)
                      |||...|||-|.-|=|
T Consensus       687 DGYlVGSRGSVGSSlV  702 (1264)
T TIGR01405       687 DGYLVGSRGSVGSSLV  702 (1264)
T ss_pred             CCCEECCCCCCHHHHH
T ss_conf             8846637743114578


No 26 
>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=20.79  E-value=7.9  Score=19.00  Aligned_cols=65  Identities=29%  Similarity=0.457  Sum_probs=42.7

Q ss_pred             EEEEEEEEHHHHHHHHHH---CCCCEEHHHHHHHHHH----CCCCEEEEEECCCCEEEECCCCCCCCCCCCCHHCCHH
Q ss_conf             631011103789998742---3582223554323332----0666388630004225312552243543871010277
Q gi|254781007|r  129 ALSTTVQLRGSLLQMFSQ---SKGKVDISRRKKVMYK----QNIGLMIMPFAWDGYWLASRGKVADSKVHPPKYLEYS  199 (411)
Q Consensus       129 alsttvqlrgsllqmfsq---skgkvdisrrkkvmyk----qniglmimpfawdgywlasrgkvadskvhppkyleys  199 (411)
                      ||+-.|-|--..|-|.--   .||-+..||||-+|-+    ||+|-|=.      ----.-|.....|..--+|+.-|
T Consensus       312 AlavAVGLTPEMLPMIVssnLAkGAi~mSk~KVIvK~L~AIQNfGAMDi------LCTDKTGTLT~Dki~L~~h~D~s  383 (892)
T TIGR01524       312 ALAVAVGLTPEMLPMIVSSNLAKGAIKMSKKKVIVKRLDAIQNFGAMDI------LCTDKTGTLTQDKIVLEKHLDVS  383 (892)
T ss_pred             HHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCC------CCCCCCCCCCCHHHHHHHHHCCC
T ss_conf             9998744772312267743567899986127425630330014343222------11388887430133221110258


No 27 
>pfam09702 Cas_Csa5 CRISPR-associated protein (Cas_Csa5). CRISPR is a term for Clustered, Regularly Interspaced Short Palindromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This entry represents a minor family of Cas proteins found in various species of Sulfolobus and Pyrococcus (all archaeal). It is found with two different CRISPR loci in Sulfolobus solfataricus.
Probab=20.64  E-value=54  Score=13.13  Aligned_cols=29  Identities=45%  Similarity=0.608  Sum_probs=18.5

Q ss_pred             EECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEE
Q ss_conf             7345100333028999999998599887511476416
Q gi|254781007|r  310 AIGNQLSRSSVEKEKIEKVLQDCHYMHKRHRTGRDAI  346 (411)
Q Consensus       310 aignqlsrssvekekiekvlqdchymhkrhrtgrdai  346 (411)
                      -|||.||     ||..|+||-||.-.-   |+|++.-
T Consensus        13 Ri~NALs-----kEaV~~vl~e~~Ri~---~sg~~~~   41 (105)
T pfam09702        13 RIGNALS-----KEAVEKVLYEAQRIV---RSGIERG   41 (105)
T ss_pred             HHHHHCC-----HHHHHHHHHHHHHHH---HHHHCCC
T ss_conf             9853247-----788999999999999---9754002


No 28 
>PRK12703 tRNA 2'-O-methylase; Reviewed
Probab=20.60  E-value=56  Score=13.02  Aligned_cols=38  Identities=13%  Similarity=0.321  Sum_probs=16.0

Q ss_pred             CCEEEECCCCCCCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             84264136743446766770799997345100333028999999
Q gi|254781007|r  285 DGQVLTNTNHCFPHGASQNKYMLMLAIGNQLSRSSVEKEKIEKV  328 (411)
Q Consensus       285 dgqvltntnhcfphgasqnkymlmlaignqlsrssvekekiekv  328 (411)
                      -|..|..-..|-.||-..      -.+|..+-|+---.|++-+.
T Consensus       215 aGaLLHDiGRs~Th~i~H------~v~Ga~i~r~~g~~e~v~~I  252 (339)
T PRK12703        215 AGALLHDIGRTKTNGIDH------AVAGAEILRKENIDDRVVSI  252 (339)
T ss_pred             HHHHHHHHCCCCCCCCHH------HHHHHHHHHHCCCCHHHHHH
T ss_conf             415775303343268407------77689999975998899999


Done!