Query gi|254780338|ref|YP_003064751.1| hypothetical protein CLIBASIA_01115 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 129
No_of_seqs 100 out of 102
Neff 5.1
Searched_HMMs 39220
Date Sun May 29 15:44:27 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780338.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1495 DsbB Disulfide bond fo 97.3 0.0037 9.4E-08 40.2 9.4 79 2-80 55-167 (170)
2 PRK04388 disulfide bond format 96.6 0.029 7.5E-07 34.6 9.5 76 2-78 51-163 (172)
3 pfam02600 DsbB Disulfide bond 96.3 0.03 7.8E-07 34.5 8.0 65 9-73 60-155 (159)
4 PRK01749 disulfide bond format 95.4 0.091 2.3E-06 31.5 7.2 61 18-78 73-163 (175)
5 PRK02110 disulfide bond format 95.3 0.25 6.5E-06 28.7 9.3 60 20-79 75-164 (169)
6 TIGR00957 MRP_assoc_pro multi 75.8 6.8 0.00017 19.8 5.7 64 62-125 133-203 (1542)
7 pfam11292 DUF3093 Protein of u 71.9 1.2 3.1E-05 24.4 0.4 12 118-129 120-131 (143)
8 TIGR00711 efflux_EmrB drug res 70.5 9 0.00023 19.0 4.7 85 35-121 112-221 (501)
9 PRK09824 beta-glucoside-specif 63.8 12 0.00031 18.2 5.1 66 9-77 376-446 (625)
10 TIGR02125 CytB-hydogenase Ni/F 57.8 9.4 0.00024 18.9 2.6 13 89-101 125-137 (229)
11 pfam05568 ASFV_J13L African sw 55.2 17 0.00044 17.3 3.6 33 48-80 22-54 (189)
12 TIGR02757 TIGR02757 conserved 44.6 8.4 0.00021 19.2 0.7 11 116-126 249-259 (269)
13 PRK10726 hypothetical protein; 40.1 30 0.00076 15.8 3.6 34 47-80 45-81 (107)
14 pfam03839 Sec62 Translocation 37.4 33 0.00083 15.5 5.0 33 52-84 98-130 (217)
15 pfam12084 DUF3561 Protein of u 33.3 38 0.00097 15.1 3.4 34 47-80 45-81 (107)
16 COG2991 Uncharacterized protei 32.9 39 0.00098 15.1 3.0 27 56-82 2-28 (77)
17 PRK09796 cellobiose/arbutin/sa 32.9 39 0.00098 15.1 7.4 57 9-67 382-442 (472)
18 TIGR00676 fadh2 5,10-methylene 30.3 43 0.0011 14.8 2.4 27 27-60 262-288 (302)
19 TIGR00800 ncs1 NCS1 nucleoside 29.4 44 0.0011 14.7 6.4 42 31-72 116-162 (465)
20 pfam07270 DUF1438 Protein of u 26.2 31 0.0008 15.7 1.1 16 111-126 130-146 (151)
21 TIGR00776 RhaT RhaT L-rhamnose 23.6 56 0.0014 14.1 5.3 49 59-108 285-333 (336)
22 pfam09674 DUF2400 Protein of u 22.7 32 0.00081 15.6 0.6 11 116-126 210-220 (230)
23 TIGR01473 cyoE_ctaB protoheme 20.2 66 0.0017 13.6 5.0 62 14-84 7-69 (297)
No 1
>COG1495 DsbB Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]
Probab=97.27 E-value=0.0037 Score=40.18 Aligned_cols=79 Identities=19% Similarity=0.426 Sum_probs=59.0
Q ss_pred HHHHHHHHHHCC----CCHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CC------------------------CCCC---
Q ss_conf 379999999508----867889999999999999999999986047-89------------------------9854---
Q gi|254780338|r 2 IGIGFLFNLISG----IKQRHYSIMILGAITTCIIATRQVLIHILP-GD------------------------LGYS--- 49 (129)
Q Consensus 2 vg~g~llNlr~G----~r~~hyg~~il~A~~G~~~s~RQi~lHi~p-g~------------------------~GyG--- 49 (129)
++++.+++.++| .|..++.++++++..|...|.+|+-++.-| ++ +.=+
T Consensus 55 ~~~i~~l~~~~~~~~~~r~~~~~l~l~g~~~giy~a~~~~~~~~~p~~~C~~~~~f~~~~~~~~~~~~~~~~~~~C~~~~ 134 (170)
T COG1495 55 LGVILLLALLIGPLNRLRLYGLALALIGAGLGIYHAGEHVVLQLGPFATCSFGLTFPEWLPLGKWAPLVFQGTGSCSEPV 134 (170)
T ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHCCCCCCHHCCHHHHHHHHHHCCCCCCCCCC
T ss_conf 99999999994852648999999999999999999999988615862333032122010327776676745888865644
Q ss_pred --HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf --5675225799999999999999999996076
Q gi|254780338|r 50 --IPVFGMHLYTWSLIFSLVIILFISVLMLFDT 80 (129)
Q Consensus 50 --~~i~GlH~YTWA~i~f~~~i~~~av~l~~~~ 80 (129)
-.++|++|.-|+.++|.+.++...+.....+
T Consensus 135 ~~~~~Lglsm~~w~~~~~~~~~~~l~~~~~~~~ 167 (170)
T COG1495 135 AAWRLLGLSMPPWLLLIFFALLLLLLLLLFRKK 167 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 046760587999999999999999999998764
No 2
>PRK04388 disulfide bond formation protein B; Provisional
Probab=96.63 E-value=0.029 Score=34.56 Aligned_cols=76 Identities=21% Similarity=0.404 Sum_probs=49.1
Q ss_pred HHHHHHHHHHCCCCH-----HHHHHHHHHHHHHHHHHHHHHHHHHCCCCC--CCCH------------------------
Q ss_conf 379999999508867-----889999999999999999999986047899--8545------------------------
Q gi|254780338|r 2 IGIGFLFNLISGIKQ-----RHYSIMILGAITTCIIATRQVLIHILPGDL--GYSI------------------------ 50 (129)
Q Consensus 2 vg~g~llNlr~G~r~-----~hyg~~il~A~~G~~~s~RQi~lHi~pg~~--GyG~------------------------ 50 (129)
+|+..+....+++|. .+..+..+.|..|..+|.||+-+.-.|.|. .=|+
T Consensus 51 igl~~li~~l~~p~~~~~r~~~~~l~~l~a~~G~~~A~rhv~LQ~~p~~~~~~Cg~~l~~~~~~~p~~e~l~~~f~g~g~ 130 (172)
T PRK04388 51 LALLFLIGALHGPRNAGGRKAYGVLAFIAAGVGMGIAARHVWVQIRPKDMMSSCGPPLSFLSETMGPFEVFRTVLTGTGD 130 (172)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHCCCHHHHHHHHHCCCCC
T ss_conf 99999999995732025999999999999999999999999999388534787887166776213799999998568998
Q ss_pred ------HHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf ------6752257999999999999999999960
Q gi|254780338|r 51 ------PVFGMHLYTWSLIFSLVIILFISVLMLF 78 (129)
Q Consensus 51 ------~i~GlH~YTWA~i~f~~~i~~~av~l~~ 78 (129)
+++|+.+-.|+++.|.+..+. ++...+
T Consensus 131 Caev~W~flGlSmp~Wsli~F~~l~~~-~l~~~~ 163 (172)
T PRK04388 131 CGNIDWRFLGLSMPMWSMVWFVGLALW-ALYAGF 163 (172)
T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHH-HHHHHH
T ss_conf 685676516828899999999999999-999999
No 3
>pfam02600 DsbB Disulfide bond formation protein DsbB. This family consists of disulfide bond formation protein DsbB from bacteria. The DsbB protein oxidizes the periplasmic protein DsbA which in turn oxidizes cysteines in other periplasmic proteins in order to make disulfide bonds. DsbB acts as a redox potential transducer across the cytoplasmic membrane and is an integral membrane protein. DsbB posses six cysteines four of which are necessary for it proper function in vivo.
Probab=96.31 E-value=0.03 Score=34.46 Aligned_cols=65 Identities=20% Similarity=0.242 Sum_probs=47.2
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC--CCC-----------------------------HHHHHHHH
Q ss_conf 99508867889999999999999999999986047899--854-----------------------------56752257
Q gi|254780338|r 9 NLISGIKQRHYSIMILGAITTCIIATRQVLIHILPGDL--GYS-----------------------------IPVFGMHL 57 (129)
Q Consensus 9 Nlr~G~r~~hyg~~il~A~~G~~~s~RQi~lHi~pg~~--GyG-----------------------------~~i~GlH~ 57 (129)
.-|.+.|.......++.++.|...|.||+.++-.|.++ +=+ -.++|+.+
T Consensus 60 ~~~~~~~~~~~~~~~~~~~~G~~~a~~h~~le~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~lGlSm 139 (159)
T pfam02600 60 AGRRGRRRLALLLALLLALAGAGIALYHVGLQAGPWEGPPSCGALEGFPDWLPLDEWLPQVFAATGDCAEVAWTFLGLSM 139 (159)
T ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCHHHCCCCH
T ss_conf 33204899999999999999999999999998287578998888644455378999999866899985753457658489
Q ss_pred HHHHHHHHHHHHHHHH
Q ss_conf 9999999999999999
Q gi|254780338|r 58 YTWSLIFSLVIILFIS 73 (129)
Q Consensus 58 YTWA~i~f~~~i~~~a 73 (129)
-+|.++.|....+...
T Consensus 140 a~wn~i~f~~l~i~~~ 155 (159)
T pfam02600 140 PGWSLVAFLLLALLLL 155 (159)
T ss_pred HHHHHHHHHHHHHHHH
T ss_conf 9999999999999999
No 4
>PRK01749 disulfide bond formation protein B; Provisional
Probab=95.39 E-value=0.091 Score=31.51 Aligned_cols=61 Identities=10% Similarity=0.261 Sum_probs=43.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCC---CCCH---------------------------HHHHHHHHHHHHHHHHH
Q ss_conf 89999999999999999999986047899---8545---------------------------67522579999999999
Q gi|254780338|r 18 HYSIMILGAITTCIIATRQVLIHILPGDL---GYSI---------------------------PVFGMHLYTWSLIFSLV 67 (129)
Q Consensus 18 hyg~~il~A~~G~~~s~RQi~lHi~pg~~---GyG~---------------------------~i~GlH~YTWA~i~f~~ 67 (129)
+....+++|+.|...|.||+-++-.|.+. +.+. +++|+.+--|.++.|..
T Consensus 73 ~~~l~~~sa~~G~~~A~rhv~lQ~~P~~~~~C~~~~~fp~~~Pl~e~lp~~F~g~G~Caev~W~flGLSmp~W~li~F~~ 152 (175)
T PRK01749 73 ALAIWLYSAWKGLQLAYEHTDLQLNPSPFNTCDFFVRFPEWLPLDKWFPQVFVASGDCSERQWQFLGLEMPQWLVGIFAA 152 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999999999999998088878888964244120769999999975888857678577650399899999999
Q ss_pred HHHHHHHHHHC
Q ss_conf 99999999960
Q gi|254780338|r 68 IILFISVLMLF 78 (129)
Q Consensus 68 ~i~~~av~l~~ 78 (129)
..+...+.++-
T Consensus 153 ~~iv~vl~~~~ 163 (175)
T PRK01749 153 YLVVAVLVVIS 163 (175)
T ss_pred HHHHHHHHHHH
T ss_conf 99999999999
No 5
>PRK02110 disulfide bond formation protein B; Provisional
Probab=95.34 E-value=0.25 Score=28.71 Aligned_cols=60 Identities=28% Similarity=0.506 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCC-CCC-----------------------------HHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999999999999986047899-854-----------------------------56752257999999999999
Q gi|254780338|r 20 SIMILGAITTCIIATRQVLIHILPGDL-GYS-----------------------------IPVFGMHLYTWSLIFSLVII 69 (129)
Q Consensus 20 g~~il~A~~G~~~s~RQi~lHi~pg~~-GyG-----------------------------~~i~GlH~YTWA~i~f~~~i 69 (129)
....+.+..|...|.||+.+...|.|. |-- -.+||+.+-.|.++.|....
T Consensus 75 ~l~~l~a~~G~~~A~rhv~lq~~P~~~Cg~~~l~~~~~~~pl~~~l~~lf~~~g~Caev~w~flGLsmp~Wsli~F~~~~ 154 (169)
T PRK02110 75 GLIVLSALGGIGTAGRHVYIQLNPGFSCGIDALQPIVDSLPPAKWLPGVFKVDGLCETPYPPILGLSLPGWALIAFVLIA 154 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf 99999999999999999999829984226871554875076999999997689998987776216789999999999999
Q ss_pred HHHHHHHHCC
Q ss_conf 9999999607
Q gi|254780338|r 70 LFISVLMLFD 79 (129)
Q Consensus 70 ~~~av~l~~~ 79 (129)
+...+.+.=.
T Consensus 155 i~~l~~l~r~ 164 (169)
T PRK02110 155 VAVAVGLIRN 164 (169)
T ss_pred HHHHHHHHHH
T ss_conf 9999999986
No 6
>TIGR00957 MRP_assoc_pro multi drug resistance-associated protein (MRP); InterPro: IPR005292 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 consists of multi drug resistance-associated protein (MRP) in eukaryotes. The multidrug resistance-associated protein is an integral membrane protein that causes multidrug resistance when overexpressed in mammalian cells. It belongs to the ABC transporter superfamily. The protein topology and function was experimentally demonstrated by epitope tagging and immunofluorescence. Insertion of tags in the critical regions associated with drug efflux reduced its function. The C-terminal domain seems to be highly conserved. ; GO: 0005215 transporter activity, 0006810 transport, 0016021 integral to membrane.
Probab=75.78 E-value=6.8 Score=19.81 Aligned_cols=64 Identities=13% Similarity=0.256 Sum_probs=44.5
Q ss_pred HHHHHHHHHHHHHHHHCCC----CCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHCCCCCC--CCCCCCC
Q ss_conf 9999999999999996076----633311334899999999999999999-99994187688--9998532
Q gi|254780338|r 62 LIFSLVIILFISVLMLFDT----AEIKVAKSPVREIAIYLFVFLIFANFI-STILECGLTQC--FDNPTFY 125 (129)
Q Consensus 62 ~i~f~~~i~~~av~l~~~~----~~~~~~~~~~~~~a~~l~~~vi~~N~v-stflecG~~~c--pddP~~Y 125 (129)
+++||.+-+.||+..+=.+ +.++....++|-..+++.+.+++..++ |.|-||-|.-- .-||-+|
T Consensus 133 ll~FWl~~~vCAl~~lRSKI~~A~~~~~~~D~FR~~TFY~yF~LvL~~LvL~CF~~~~PlFS~~~~DpNP~ 203 (1542)
T TIGR00957 133 LLIFWLVALVCALAILRSKILLALKEDAIVDLFRDTTFYIYFALVLVQLVLSCFSDKSPLFSETVHDPNPC 203 (1542)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
T ss_conf 99999999999999988899877634772252101689999999999999864047788654436688648
No 7
>pfam11292 DUF3093 Protein of unknown function (DUF3093). This family of proteins with unknown function appears to be restricted to Actinobacteria. Some members are annotated as alanine rich membrane proteins however this cannot be confirmed.
Probab=71.94 E-value=1.2 Score=24.43 Aligned_cols=12 Identities=33% Similarity=0.362 Sum_probs=9.9
Q ss_pred CCCCCCCCCCCC
Q ss_conf 899985322469
Q gi|254780338|r 118 CFDNPTFYQLLN 129 (129)
Q Consensus 118 cpddP~~Y~ll~ 129 (129)
=|+||++|||.+
T Consensus 120 Dp~DPtPYWlvS 131 (143)
T pfam11292 120 DPADPTPYWLVS 131 (143)
T ss_pred CCCCCCCEEEEE
T ss_conf 999998648997
No 8
>TIGR00711 efflux_EmrB drug resistance MFS transporter, drug:H+ antiporter-1 (14 Spanner) (DHA2) family; InterPro: IPR004638 This subfamily of drug efflux proteins, a part of the major facilitator family, is predicted to have 14 potential membrane-spanning regions. Members with known activities include EmrB (multiple drug resistance efflux pump) in Escherichia coli, FarB (antibacterial fatty acid resistance) in Neisseria gonorrhoeae, TcmA (tetracenomycin C resistance) in Streptomyces glaucescens, etc. In most cases, the efflux pump is described as having a second component encoded in the same operon, such as EmrA of E. coli.; GO: 0006810 transport, 0016021 integral to membrane.
Probab=70.48 E-value=9 Score=19.02 Aligned_cols=85 Identities=20% Similarity=0.342 Sum_probs=52.9
Q ss_pred HHHHHHHCCCCC-CCCHHHHHH-----------------HHHHHHHHHHHHHHHHHHHHHH----CCC-CCCCCHHHHHH
Q ss_conf 999986047899-854567522-----------------5799999999999999999996----076-63331133489
Q gi|254780338|r 35 RQVLIHILPGDL-GYSIPVFGM-----------------HLYTWSLIFSLVIILFISVLML----FDT-AEIKVAKSPVR 91 (129)
Q Consensus 35 RQi~lHi~pg~~-GyG~~i~Gl-----------------H~YTWA~i~f~~~i~~~av~l~----~~~-~~~~~~~~~~~ 91 (129)
.-+++.+.|... |-+-+++|+ ..|+|-++.|.-+.+++.+... +.+ ++++.+++++.
T Consensus 112 ~~~l~~~~PP~~Rg~~~~~~Gl~v~~AP~~GP~LGGwI~e~~~Wrw~F~~NvPiG~~v~~~a~~~l~~d~~~~~~~~~~D 191 (501)
T TIGR00711 112 FSLLLNIYPPEKRGLAMAIWGLTVLVAPALGPTLGGWIIENYEWRWIFYINVPIGIIVVVVALFILPEDREKEKASKNLD 191 (501)
T ss_pred HHHHHHHCCCCCCCCEEEEHHHHHHHHHCCCCCCHHHHHHCCCCHHEEEHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHH
T ss_conf 99999747912158356421066874202353104688732622220212578999999999998446666616663112
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCC--CCCCC
Q ss_conf 9999999999999999999941876--88999
Q gi|254780338|r 92 EIAIYLFVFLIFANFISTILECGLT--QCFDN 121 (129)
Q Consensus 92 ~~a~~l~~~vi~~N~vstflecG~~--~cpdd 121 (129)
+ +.+++..+..-..+-.+|.|.- +..||
T Consensus 192 ~--~G~~L~~~g~~~Ll~~ls~g~~~GW~~~~ 221 (501)
T TIGR00711 192 F--LGLLLLSVGLGSLLYVLSEGQEEGWFDSN 221 (501)
T ss_pred H--HHHHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf 7--88999999999999875215668899863
No 9
>PRK09824 beta-glucoside-specific PTS system components IIABC; Provisional
Probab=63.85 E-value=12 Score=18.20 Aligned_cols=66 Identities=20% Similarity=0.222 Sum_probs=40.5
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC-CCHHH----HHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 995088678899999999999999999999860478998-54567----5225799999999999999999996
Q gi|254780338|r 9 NLISGIKQRHYSIMILGAITTCIIATRQVLIHILPGDLG-YSIPV----FGMHLYTWSLIFSLVIILFISVLML 77 (129)
Q Consensus 9 Nlr~G~r~~hyg~~il~A~~G~~~s~RQi~lHi~pg~~G-yG~~i----~GlH~YTWA~i~f~~~i~~~av~l~ 77 (129)
|+||+ || .|+.+|=+|+.|+..+.-|+..... |.+| .+.+. -|.+.+-|+.++..++-+.++..+.
T Consensus 376 ~L~~k-kP-fi~a~IGgaiGG~~~g~~~v~~~a~-g~~gi~~~~~~i~~~~~~~~~~~~~i~~~ia~~~~fv~t 446 (625)
T PRK09824 376 NLPRK-YP-FVIACISGALGATIIGYAQTKVYSF-GLPSIFTFMQTIPSTGIDFTVWASVIGGVIAIGCAFVGT 446 (625)
T ss_pred ECCCC-CH-HHHHHHHHHHHHHHHHHHHHEEEEE-ECCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 21455-28-7999998999999999852012454-002465556655876644118999999999999999999
No 10
>TIGR02125 CytB-hydogenase Ni/Fe-hydrogenase, b-type cytochrome subunit; InterPro: IPR000516 Bacterial membrane-bound nickel-dependent hydrogenases , , seem to be associated with a b-type cytochrome involved in electron transfer from hydrogen to oxygen. This cytochrome is a protein of about 28 kDa that seems to have four transmembrane regions, which include several histidine residues that may be involved in coordination of the haem iron group. The gene coding for this cytochrome is adjacent to that coding for the large subunit of the hydrogenase. It has been assigned a variety of names in different species: hupC, hyaC, hydC or hoxZ. Every genome which contains a member of this family posesses a Ni/Fe hydrogenase according to Genome Properties (GenProp0177), and most are gene clustered with other hydrogenase components. Some Ni/Fe hydrogenase-containing species lack a member of this family but contain other CytB homologs, which may substitute for it.; GO: 0016491 oxidoreductase activity, 0006118 electron transport, 0016020 membrane.
Probab=57.78 E-value=9.4 Score=18.91 Aligned_cols=13 Identities=31% Similarity=0.685 Sum_probs=4.9
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 4899999999999
Q gi|254780338|r 89 PVREIAIYLFVFL 101 (129)
Q Consensus 89 ~~~~~a~~l~~~v 101 (129)
|+.+++...+.++
T Consensus 125 P~q~~ay~~~~~l 137 (229)
T TIGR02125 125 PLQFVAYFGFIVL 137 (229)
T ss_pred CHHHHHHHHHHHH
T ss_conf 2899999999999
No 11
>pfam05568 ASFV_J13L African swine fever virus J13L protein. This family consists of several African swine fever virus J13L proteins.
Probab=55.17 E-value=17 Score=17.28 Aligned_cols=33 Identities=27% Similarity=0.563 Sum_probs=21.5
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 545675225799999999999999999996076
Q gi|254780338|r 48 YSIPVFGMHLYTWSLIFSLVIILFISVLMLFDT 80 (129)
Q Consensus 48 yG~~i~GlH~YTWA~i~f~~~i~~~av~l~~~~ 80 (129)
--+.+|.-||||--.-+-+.+|+-+-++-+|..
T Consensus 22 ~tpsffsthmytiliaivvliiiiivliylfss 54 (189)
T pfam05568 22 PAPSFFSTHMYTILIAIVVLIIIIIVLIYLFSS 54 (189)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 882067788999999999999999999999722
No 12
>TIGR02757 TIGR02757 conserved hypothetical protein TIGR02757; InterPro: IPR014127 Members of this uncharacterised protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighbourhoods show little conservation..
Probab=44.64 E-value=8.4 Score=19.22 Aligned_cols=11 Identities=18% Similarity=0.311 Sum_probs=8.6
Q ss_pred CCCCCCCCCCC
Q ss_conf 68899985322
Q gi|254780338|r 116 TQCFDNPTFYQ 126 (129)
Q Consensus 116 ~~cpddP~~Y~ 126 (129)
-.|||||++|-
T Consensus 249 ~~~p~DP~kYD 259 (269)
T TIGR02757 249 KLNPEDPIKYD 259 (269)
T ss_pred HHCCCCCCCCC
T ss_conf 61788595244
No 13
>PRK10726 hypothetical protein; Provisional
Probab=40.12 E-value=30 Score=15.80 Aligned_cols=34 Identities=24% Similarity=0.502 Sum_probs=23.9
Q ss_pred CCCHHHHHHHHHHHHHHHH---HHHHHHHHHHHHCCC
Q ss_conf 8545675225799999999---999999999996076
Q gi|254780338|r 47 GYSIPVFGMHLYTWSLIFS---LVIILFISVLMLFDT 80 (129)
Q Consensus 47 GyG~~i~GlH~YTWA~i~f---~~~i~~~av~l~~~~ 80 (129)
=||+.-+=.-.|||.|... +.++++++.-.+...
T Consensus 45 ~YG~nTlfF~LYTWPFFLALmPvsVlvGi~~~~Ll~g 81 (107)
T PRK10726 45 IYGSNTLFFFLYTWPFFLALMPVSVVVGIALHSLLDG 81 (107)
T ss_pred HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 5077614789987699999969999999999998177
No 14
>pfam03839 Sec62 Translocation protein Sec62.
Probab=37.37 E-value=33 Score=15.53 Aligned_cols=33 Identities=15% Similarity=0.009 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 752257999999999999999999960766333
Q gi|254780338|r 52 VFGMHLYTWSLIFSLVIILFISVLMLFDTAEIK 84 (129)
Q Consensus 52 i~GlH~YTWA~i~f~~~i~~~av~l~~~~~~~~ 84 (129)
.=|.+.++|..-+.+++.+...+|.-.++.+-+
T Consensus 98 Ye~~~~~~~l~~~~~v~~v~a~~lFPlWP~~~r 130 (217)
T pfam03839 98 YDPVPLMTYLIGVIGVLGIIALVLFPLWPRFMR 130 (217)
T ss_pred ECCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHH
T ss_conf 658739999999999999999984126879998
No 15
>pfam12084 DUF3561 Protein of unknown function (DUF3561). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are about 110 amino acids in length.
Probab=33.30 E-value=38 Score=15.12 Aligned_cols=34 Identities=21% Similarity=0.472 Sum_probs=23.2
Q ss_pred CCCHHHHHHHHHHHHHHHH---HHHHHHHHHHHHCCC
Q ss_conf 8545675225799999999---999999999996076
Q gi|254780338|r 47 GYSIPVFGMHLYTWSLIFS---LVIILFISVLMLFDT 80 (129)
Q Consensus 47 GyG~~i~GlH~YTWA~i~f---~~~i~~~av~l~~~~ 80 (129)
-||+.-+=.-.|||.|... +.+++++++-.+...
T Consensus 45 ~YG~nTLfF~LYTWPFFLALmPvsVlvGi~~~~Ll~g 81 (107)
T pfam12084 45 VYGSNTLFFFLYTWPFFLALMPVAVLVGIALHSLLRG 81 (107)
T ss_pred EECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 0377610258886599999958999999999998177
No 16
>COG2991 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.90 E-value=39 Score=15.08 Aligned_cols=27 Identities=15% Similarity=0.228 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 579999999999999999999607663
Q gi|254780338|r 56 HLYTWSLIFSLVIILFISVLMLFDTAE 82 (129)
Q Consensus 56 H~YTWA~i~f~~~i~~~av~l~~~~~~ 82 (129)
.+|--.|++|..+|+++++--++.++.
T Consensus 2 ~t~lltFg~Fllvi~gMsiG~I~krk~ 28 (77)
T COG2991 2 TTFLLTFGIFLLVIAGMSIGYIFKRKS 28 (77)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHEECCC
T ss_conf 157999999999999976764302450
No 17
>PRK09796 cellobiose/arbutin/salicin-specific PTS system components IIBC; Provisional
Probab=32.85 E-value=39 Score=15.08 Aligned_cols=57 Identities=11% Similarity=0.125 Sum_probs=30.7
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHH----HHHHHHHHHHHHHH
Q ss_conf 995088678899999999999999999999860478998545675----22579999999999
Q gi|254780338|r 9 NLISGIKQRHYSIMILGAITTCIIATRQVLIHILPGDLGYSIPVF----GMHLYTWSLIFSLV 67 (129)
Q Consensus 9 Nlr~G~r~~hyg~~il~A~~G~~~s~RQi~lHi~pg~~GyG~~i~----GlH~YTWA~i~f~~ 67 (129)
|+||+ | --++..|=+++.|+.++.-++..+.....+-++.+-+ +-+.+.|.++...+
T Consensus 382 ~L~~k-k-pfi~a~iggaigG~~~g~~~v~~~~~~~~gl~~~~~~~~~~~~~~~~~~~~~~~i 442 (472)
T PRK09796 382 AIRLK-R-PLIASLISGFICGAVAGMAGLASHSMAAPGLFTSVQFFDPANPMSIVWVFAVMAL 442 (472)
T ss_pred CCCCC-H-HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHHHHHHHH
T ss_conf 45654-1-9999999999999999998644523003357756788277784059999999999
No 18
>TIGR00676 fadh2 5,10-methylenetetrahydrofolate reductase; InterPro: IPR004620 The enzyme activities methylenetetrahydrofolate reductase (1.5.1.20 from EC) and 5,10-methylenetetrahydrofolate reductase (FADH) (1.7.99.5 from EC) differ in that the former (assigned in many eukaryotes) is defined to use NADP+ as an acceptor, while the latter (assigned in many bacteria) is flexible with respect to the acceptor. Both convert 5-methyltetrahydrofolate to 5,10-methylenetetrahydrofolate. From a larger set of proteins assigned as one or the other, this family describes the subset of proteins found in bacteria, and currently designated 5,10-methylenetetrahydrofolate reductase. This protein is an FAD-containing flavoprotein.; GO: 0009086 methionine biosynthetic process.
Probab=30.34 E-value=43 Score=14.82 Aligned_cols=27 Identities=33% Similarity=0.283 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH
Q ss_conf 9999999999998604789985456752257999
Q gi|254780338|r 27 ITTCIIATRQVLIHILPGDLGYSIPVFGMHLYTW 60 (129)
Q Consensus 27 ~~G~~~s~RQi~lHi~pg~~GyG~~i~GlH~YTW 60 (129)
-+|...|..|+--=+.-|-+ |+|+||=
T Consensus 262 ~~G~e~A~~q~~~L~~~GV~-------g~HfYTl 288 (302)
T TIGR00676 262 AVGIEYATDQCEDLIAEGVP-------GIHFYTL 288 (302)
T ss_pred HHHHHHHHHHHHHHHHCCCC-------EECHHHC
T ss_conf 99999999999999976897-------2112104
No 19
>TIGR00800 ncs1 NCS1 nucleoside transporter family; InterPro: IPR012681 The Nucleobase Cation Symporter-1 (NCS1) family consists of bacterial and yeast transporters for nucleobases including purines and pyrimidines. Members of this family possess twelve putative transmembrane a-helical spanners (TMSs). At least some of them have been shown to function in uptake by substrate:H+ symport mechanism. ; GO: 0015205 nucleobase transmembrane transporter activity, 0015931 nucleobase nucleoside nucleotide and nucleic acid transport, 0016020 membrane.
Probab=29.37 E-value=44 Score=14.71 Aligned_cols=42 Identities=24% Similarity=0.333 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHCCCCCCCCH----HHHHHHHHHHH-HHHHHHHHHHH
Q ss_conf 99999999860478998545----67522579999-99999999999
Q gi|254780338|r 31 IIATRQVLIHILPGDLGYSI----PVFGMHLYTWS-LIFSLVIILFI 72 (129)
Q Consensus 31 ~~s~RQi~lHi~pg~~GyG~----~i~GlH~YTWA-~i~f~~~i~~~ 72 (129)
..+..+.+..|.|+..+.+. +..|+|++-|. |++|+++...+
T Consensus 116 ~~~v~~~L~~i~~~~~~~~~~~~~~~~g~~~~~~~~f~if~~~~~~~ 162 (465)
T TIGR00800 116 GLAVALLLDSIFPGFLHLGNPDTFTKLGLTTLELICFIIFWVLVLVV 162 (465)
T ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999732554467888542122224689999999998888652
No 20
>pfam07270 DUF1438 Protein of unknown function (DUF1438). This family consists of several hypothetical proteins of around 170 residues in length which appear to be mouse specific. The function of this family is unknown.
Probab=26.25 E-value=31 Score=15.65 Aligned_cols=16 Identities=25% Similarity=0.449 Sum_probs=12.7
Q ss_pred HHCCCCCCCC-CCCCCC
Q ss_conf 9418768899-985322
Q gi|254780338|r 111 LECGLTQCFD-NPTFYQ 126 (129)
Q Consensus 111 lecG~~~cpd-dP~~Y~ 126 (129)
..|-.|-||| ||.++.
T Consensus 130 etcdGGDCpdqDpasds 146 (151)
T pfam07270 130 ETCDGGDCPDQDPASDS 146 (151)
T ss_pred EECCCCCCCCCCCCCCC
T ss_conf 53369888887855554
No 21
>TIGR00776 RhaT RhaT L-rhamnose-proton symporter family protein; InterPro: IPR004673 These proteins are members of the L-Rhamnose Symporter (RhaT) family. This family includes two characterised members, both of which function as L-rhamnose:H+ symporters and have 10 GES predicted transmembrane domains.; GO: 0015153 rhamnose transmembrane transporter activity, 0008645 hexose transport, 0016021 integral to membrane.
Probab=23.57 E-value=56 Score=14.05 Aligned_cols=49 Identities=16% Similarity=0.179 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999999960766333113348999999999999999999
Q gi|254780338|r 59 TWSLIFSLVIILFISVLMLFDTAEIKVAKSPVREIAIYLFVFLIFANFIS 108 (129)
Q Consensus 59 TWA~i~f~~~i~~~av~l~~~~~~~~~~~~~~~~~a~~l~~~vi~~N~vs 108 (129)
.|+|..+-..++...+=..+-.+|++ .++++.-+...+.+++|++|...
T Consensus 285 at~F~~SQ~~~i~stlGGI~~l~E~K-~Kr~~~~~~~GiiliiiAa~~~g 333 (336)
T TIGR00776 285 ATSFSLSQLGVIISTLGGILILGEKK-TKRELIAIVVGIILIIIAAVILG 333 (336)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999999987887630378-75200145457899887899987
No 22
>pfam09674 DUF2400 Protein of unknown function (DUF2400). Members of this uncharacterized protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighbourhoods show little conservation.
Probab=22.66 E-value=32 Score=15.62 Aligned_cols=11 Identities=27% Similarity=0.341 Sum_probs=8.8
Q ss_pred CCCCCCCCCCC
Q ss_conf 68899985322
Q gi|254780338|r 116 TQCFDNPTFYQ 126 (129)
Q Consensus 116 ~~cpddP~~Y~ 126 (129)
-.+|+||++|-
T Consensus 210 ~~dp~DPvKYD 220 (230)
T pfam09674 210 ELDPDDPVKYD 220 (230)
T ss_pred HCCCCCCCHHH
T ss_conf 60988981045
No 23
>TIGR01473 cyoE_ctaB protoheme IX farnesyltransferase; InterPro: IPR006369 This family describes protoheme IX farnesyltransferase, also called haeme O synthase, an enzyme that creates an intermediate in the biosynthesis of haeme A . Prior to the description of its enzymatic function, this protein was often called a cytochrome o ubiquinol oxidase assembly factor. ; GO: 0008495 protoheme IX farnesyltransferase activity, 0006783 heme biosynthetic process, 0016021 integral to membrane.
Probab=20.18 E-value=66 Score=13.62 Aligned_cols=62 Identities=18% Similarity=0.128 Sum_probs=39.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHH-HHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 8678899999999999999999999-8604789985456752257999999999999999999960766333
Q gi|254780338|r 14 IKQRHYSIMILGAITTCIIATRQVL-IHILPGDLGYSIPVFGMHLYTWSLIFSLVIILFISVLMLFDTAEIK 84 (129)
Q Consensus 14 ~r~~hyg~~il~A~~G~~~s~RQi~-lHi~pg~~GyG~~i~GlH~YTWA~i~f~~~i~~~av~l~~~~~~~~ 84 (129)
.|||=...+.+.+..|.+.+.|+.. +|-..+.+..--+..| ...++--+++..+.+|++-++
T Consensus 7 tKp~~~~L~~~t~~~G~~lA~~~~~~~~~~~~~~~~~~~~~G---------~~L~~~~A~a~N~~~DrdiD~ 69 (297)
T TIGR01473 7 TKPRVISLLLITAFAGMWLASGGADKLSFLVNLPLLLLTLLG---------TTLAAASANAFNMYIDRDIDK 69 (297)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHH---------HHHHHHHHHHHHHHHCCCCCC
T ss_conf 867899999999999987622566654311168999999999---------999999987972121466100
Done!