Query gi|255764484|ref|YP_003065144.2| hypothetical protein CLIBASIA_03090 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 43
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Sun May 29 19:14:55 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 255764484.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01943 rnfA electron transp 48.0 9.5 0.00024 19.7 1.4 25 18-42 147-177 (193)
2 TIGR02789 nickel_nikB nickel A 46.7 3 7.7E-05 22.3 -1.3 32 9-40 246-278 (315)
3 pfam03207 OspD Borrelia outer 44.7 19 0.00049 18.2 2.5 21 1-21 1-21 (264)
4 PHA02357 hypothetical protein 43.6 11 0.00027 19.4 1.1 38 1-38 1-50 (77)
5 COG3115 ZipA Cell division pro 43.1 19 0.00048 18.2 2.3 38 1-40 1-41 (324)
6 PRK02830 Na(+)-translocating N 39.7 17 0.00044 18.4 1.6 29 14-42 153-185 (202)
7 TIGR01666 YCCS hypothetical me 35.0 35 0.0009 16.8 2.6 31 1-31 507-537 (713)
8 PRK03427 cell division protein 30.7 31 0.0008 17.0 1.8 38 1-40 2-42 (331)
9 PRK05151 Na(+)-translocating N 28.7 41 0.0011 16.4 2.1 26 17-42 146-175 (192)
10 pfam11812 DUF3333 Domain of un 26.7 63 0.0016 15.5 3.3 25 12-36 24-48 (155)
11 PRK12456 Na(+)-translocating N 26.6 38 0.00096 16.6 1.6 26 17-42 153-182 (199)
12 TIGR00160 MGSA methylglyoxal s 25.9 36 0.00092 16.7 1.4 31 11-41 70-109 (143)
13 PRK04335 cell division protein 24.1 38 0.00096 16.6 1.2 37 1-39 1-40 (319)
14 pfam05297 Herpes_LMP1 Herpesvi 23.5 61 0.0016 15.5 2.2 15 7-21 52-66 (382)
15 TIGR02599 TIGR02599 Verrucomic 23.5 46 0.0012 16.2 1.6 20 4-25 4-24 (396)
No 1
>TIGR01943 rnfA electron transport complex, RnfABCDGE type, A subunit; InterPro: IPR011293 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, but is distinct. This entry describes the A subunit.; GO: 0006118 electron transport, 0009276 1-2nm peptidoglycan-based cell wall.
Probab=47.99 E-value=9.5 Score=19.72 Aligned_cols=25 Identities=44% Similarity=0.790 Sum_probs=20.0
Q ss_pred HHHHHHHHHHH----H-HHHHH-HHCCHHHH
Q ss_conf 99998666577----6-99998-54325640
Q gi|255764484|r 18 IIFLWADIREK----S-ISAFF-RDIPIALV 42 (43)
Q Consensus 18 iiflwadirek----s-isaff-rdipialv 42 (43)
.+-+.|-|||| + +.+.| |-.||||.
T Consensus 147 amV~FAgiREr~d~~devP~~fG~G~piaLi 177 (193)
T TIGR01943 147 AMVLFAGIRERLDLSDEVPKAFGRGSPIALI 177 (193)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHCCCCHHHHH
T ss_conf 9999999886665520440221276468999
No 2
>TIGR02789 nickel_nikB nickel ABC transporter, permease subunit NikB; InterPro: IPR014156 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 the NikB family of nickel ABC transporter permeases. Operons that contain this protein also contain a homologous permease subunit NikC. Nickel is used in cells as part of urease or certain hydrogenases or superoxide dismutases..
Probab=46.68 E-value=3 Score=22.27 Aligned_cols=32 Identities=44% Similarity=0.731 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-HHCCHH
Q ss_conf 98658999999998666577699998-543256
Q gi|255764484|r 9 LLSSFAVIAIIFLWADIREKSISAFF-RDIPIA 40 (43)
Q Consensus 9 llssfaviaiiflwadireksisaff-rdipia 40 (43)
|+..--||..||-|-.+---.|||-| ||+|+-
T Consensus 246 Ll~GT~viE~iFswPG~GRy~i~AifNRDyPvi 278 (315)
T TIGR02789 246 LLGGTLVIENIFSWPGVGRYAISAIFNRDYPVI 278 (315)
T ss_pred HHHCCEEEEEECCCCCHHHHHHHHHHHCCCHHH
T ss_conf 840711454101266610457433562376389
No 3
>pfam03207 OspD Borrelia outer surface protein D (OspD).
Probab=44.68 E-value=19 Score=18.16 Aligned_cols=21 Identities=48% Similarity=0.708 Sum_probs=16.8
Q ss_pred CHHHHHHHHHHHHHHHHHHHH
Q ss_conf 968999999865899999999
Q gi|255764484|r 1 MQRLIEILLLSSFAVIAIIFL 21 (43)
Q Consensus 1 mqrlieilllssfaviaiifl 21 (43)
|..||.|||||-|-...|-..
T Consensus 1 mkklikilllslflllsisc~ 21 (264)
T pfam03207 1 MKKLIKILLLSLFLLLSISCS 21 (264)
T ss_pred CHHHHHHHHHHHHHHHHHHHC
T ss_conf 915999999999999883222
No 4
>PHA02357 hypothetical protein
Probab=43.56 E-value=11 Score=19.44 Aligned_cols=38 Identities=24% Similarity=0.298 Sum_probs=24.8
Q ss_pred CHHHHHHHHHHHHHHHHHH------------HHHHHHHHHHHHHHHHHCC
Q ss_conf 9689999998658999999------------9986665776999985432
Q gi|255764484|r 1 MQRLIEILLLSSFAVIAII------------FLWADIREKSISAFFRDIP 38 (43)
Q Consensus 1 mqrlieilllssfaviaii------------flwadireksisaffrdip 38 (43)
||++|..+-+.||.|-+-+ -+-.+++||-..+.-..+.
T Consensus 1 MQKiINvlAi~S~~vS~~vVG~g~YvY~nkDaiIe~vK~kv~eavt~ai~ 50 (77)
T PHA02357 1 MQKIINIVAILSGLVSLAVVGGGAYVYVNMDTIRDSAKERATEAITESIG 50 (77)
T ss_pred CCHHHHHHHHHHCCCEEEEEEEEEEEEEECHHHHHHHHHHHHHHHHHHHH
T ss_conf 90478899998525046898025799984289999999999999999886
No 5
>COG3115 ZipA Cell division protein [Cell division and chromosome partitioning]
Probab=43.09 E-value=19 Score=18.17 Aligned_cols=38 Identities=42% Similarity=0.855 Sum_probs=26.8
Q ss_pred CHHHHHHHHH-HHHHHHHHHH--HHHHHHHHHHHHHHHHCCHH
Q ss_conf 9689999998-6589999999--98666577699998543256
Q gi|255764484|r 1 MQRLIEILLL-SSFAVIAIIF--LWADIREKSISAFFRDIPIA 40 (43)
Q Consensus 1 mqrlieilll-ssfaviaiif--lwadireksisaffrdipia 40 (43)
||.|-.||++ .-.|.||++| ||..-||+| .+|||-|.-
T Consensus 1 m~dLr~ILIIvG~IAIiaLLvhGlWtsRkE~s--~~F~~~p~~ 41 (324)
T COG3115 1 MQDLRLILIIVGAIAIIALLVHGLWTSRKERS--SYFRDRPLK 41 (324)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHC--CCCCCCCCC
T ss_conf 95334679999999999999863331101102--101247630
No 6
>PRK02830 Na(+)-translocating NADH-quinone reductase subunit E; Provisional
Probab=39.66 E-value=17 Score=18.39 Aligned_cols=29 Identities=31% Similarity=0.373 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHHHH----HHHHHHHCCHHHH
Q ss_conf 9999999986665776----9999854325640
Q gi|255764484|r 14 AVIAIIFLWADIREKS----ISAFFRDIPIALV 42 (43)
Q Consensus 14 aviaiiflwadireks----isaffrdipialv 42 (43)
.-.-.+++.|.+|||- +...||..||+++
T Consensus 153 Gf~lalvl~a~iRErl~~~~iP~~~~G~pi~li 185 (202)
T PRK02830 153 GWALAIVALAGIREKMKYSDVPAGLRGLGITFI 185 (202)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHH
T ss_conf 999999999999999735799800258669999
No 7
>TIGR01666 YCCS hypothetical membrane protein, TIGR01666; InterPro: IPR010019 This entry identifies a clade of sequences from gamma and beta proteobacteria. These proteins are more than 700 amino acids long and many have been annotated as putative membrane proteins. The gene from Salmonella has been annotated as a putative efflux transporter. The gene from Escherichia coli has been annotated as yccS..
Probab=34.97 E-value=35 Score=16.77 Aligned_cols=31 Identities=26% Similarity=0.580 Sum_probs=26.7
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9689999998658999999998666577699
Q gi|255764484|r 1 MQRLIEILLLSSFAVIAIIFLWADIREKSIS 31 (43)
Q Consensus 1 mqrlieilllssfaviaiiflwadireksis 31 (43)
|.|+++-|+=...|+.|+.++|.|-+-|...
T Consensus 507 lPRl~DTLiGcAiawaAVsyiwPDW~~~~L~ 537 (713)
T TIGR01666 507 LPRLLDTLIGCAIAWAAVSYIWPDWQYKRLD 537 (713)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH
T ss_conf 7889999998999999999861553430136
No 8
>PRK03427 cell division protein ZipA; Provisional
Probab=30.70 E-value=31 Score=17.04 Aligned_cols=38 Identities=39% Similarity=0.788 Sum_probs=23.1
Q ss_pred CHHHHHHHHHHH-HHHHHHHH--HHHHHHHHHHHHHHHHCCHH
Q ss_conf 968999999865-89999999--98666577699998543256
Q gi|255764484|r 1 MQRLIEILLLSS-FAVIAIIF--LWADIREKSISAFFRDIPIA 40 (43)
Q Consensus 1 mqrlieilllss-faviaiif--lwadireksisaffrdipia 40 (43)
||-|-.||..-. .|.+|+++ ||.--|||| +.|+|-|..
T Consensus 2 MqdLRliLIIvGaIAIiALL~HGlWtsRKErs--~~f~drp~k 42 (331)
T PRK03427 2 MQDLRLILIIVGAIAIIALLVHGFWTSRKERS--SMFRDRPLK 42 (331)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHCEECCCCCC--CCCCCCCCC
T ss_conf 35889999999999999999852022345544--100247433
No 9
>PRK05151 Na(+)-translocating NADH-quinone reductase subunit E; Provisional
Probab=28.75 E-value=41 Score=16.43 Aligned_cols=26 Identities=42% Similarity=0.671 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHH----HHHHHHHCCHHHH
Q ss_conf 9999986665776----9999854325640
Q gi|255764484|r 17 AIIFLWADIREKS----ISAFFRDIPIALV 42 (43)
Q Consensus 17 aiiflwadireks----isaffrdipialv 42 (43)
-.+.+.+++|||. +...||..||+++
T Consensus 146 Lalvl~a~iRErl~~~~vP~~~~G~pI~li 175 (192)
T PRK05151 146 LVLVLFAAIRERLAVADVPAPFRGNAIALI 175 (192)
T ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCHHHH
T ss_conf 999999999998725899801268859999
No 10
>pfam11812 DUF3333 Domain of unknown function (DUF3333). This family of proteins are functionally uncharacterized. This family is only found in bacteria. This presumed domain is typically between 116 to 159 amino acids in length.
Probab=26.67 E-value=63 Score=15.49 Aligned_cols=25 Identities=16% Similarity=0.278 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 5899999999866657769999854
Q gi|255764484|r 12 SFAVIAIIFLWADIREKSISAFFRD 36 (43)
Q Consensus 12 sfaviaiiflwadireksisaffrd 36 (43)
++++...++|..+|--+.++||++.
T Consensus 24 ~~al~fL~iLl~sI~s~G~~AF~qT 48 (155)
T pfam11812 24 LIGLAFLVILLGSIVSNGYGAFQQT 48 (155)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHE
T ss_conf 9999999999999998549988725
No 11
>PRK12456 Na(+)-translocating NADH-quinone reductase subunit E; Provisional
Probab=26.60 E-value=38 Score=16.65 Aligned_cols=26 Identities=27% Similarity=0.342 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHHH----HHHHHHHCCHHHH
Q ss_conf 9999986665776----9999854325640
Q gi|255764484|r 17 AIIFLWADIREKS----ISAFFRDIPIALV 42 (43)
Q Consensus 17 aiiflwadireks----isaffrdipialv 42 (43)
-.+.+-+.+|||- +...||..||+++
T Consensus 153 Lal~l~a~iRErl~~~~vP~~~~G~pI~~i 182 (199)
T PRK12456 153 LAIISMAGLREKMKYSNIPKGLQGLGIVFM 182 (199)
T ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCHHHH
T ss_conf 999999999999855899812478578999
No 12
>TIGR00160 MGSA methylglyoxal synthase; InterPro: IPR004363 Methylglyoxal synthase (MGS) catalyzes the conversion of dihydroxyacetone phosphate to methylglyoxal and phosphate: Glycerone phosphate = methylglyoxal + phosphate It provides bacteria with an alternative to triosephosphate isomerase for metabolizing dihydroxyacetone phosphate. MGS is a small protein of about 13 to 17 kDa. An aspartate residue is involved in the catalytic mechanism. Methylglyoxal synthase contains a domain shared by other enzymes. Other proteins containing this domain include purine biosynthesis protein PurH and carbamoyl phosphate synthetase.; GO: 0008929 methylglyoxal synthase activity, 0019242 methylglyoxal biosynthetic process, 0005737 cytoplasm.
Probab=25.86 E-value=36 Score=16.75 Aligned_cols=31 Identities=29% Similarity=0.536 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHHH----HHHHHHHHHH-----HCCHHH
Q ss_conf 658999999998666----5776999985-----432564
Q gi|255764484|r 11 SSFAVIAIIFLWADI----REKSISAFFR-----DIPIAL 41 (43)
Q Consensus 11 ssfaviaiiflwadi----reksisaffr-----dipial 41 (43)
+.=..-++||+|.-. .|--+||..| .||+|.
T Consensus 70 aeg~Id~~IFf~~PL~AqPHEPDV~ALlRLc~V~nIPlAt 109 (143)
T TIGR00160 70 AEGKIDAVIFFRDPLNAQPHEPDVKALLRLCDVYNIPLAT 109 (143)
T ss_pred HHCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCHHHH
T ss_conf 6122654450330014788880078898786450250344
No 13
>PRK04335 cell division protein ZipA; Provisional
Probab=24.07 E-value=38 Score=16.64 Aligned_cols=37 Identities=35% Similarity=0.714 Sum_probs=22.2
Q ss_pred CHHHHHHHHH-HHHHHHHHHH--HHHHHHHHHHHHHHHHCCH
Q ss_conf 9689999998-6589999999--9866657769999854325
Q gi|255764484|r 1 MQRLIEILLL-SSFAVIAIIF--LWADIREKSISAFFRDIPI 39 (43)
Q Consensus 1 mqrlieilll-ssfaviaiif--lwadireksisaffrdipi 39 (43)
||-|--||.. ...|.+|+++ ||.--||+ |+-|+|-|.
T Consensus 1 MQdLrlILIIvGaIAIiALL~HGlWtsRKEr--s~~f~drp~ 40 (319)
T PRK04335 1 MQELRFVLIVVGALAIAALLFHGLWTSKKEG--KSKFGDKPL 40 (319)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCC--CCCCCCCCC
T ss_conf 9314029999999999999984011004455--543466865
No 14
>pfam05297 Herpes_LMP1 Herpesvirus latent membrane protein 1 (LMP1). This family consists of several latent membrane protein 1 or LMP1s mostly from Epstein-Barr virus. LMP1 of EBV is a 62-65 kDa plasma membrane protein possessing six membrane spanning regions, a short cytoplasmic N-terminus and a long cytoplasmic carboxy tail of 200 amino acids. EBV latent membrane protein 1 (LMP1) is essential for EBV-mediated transformation and has been associated with several cases of malignancies. EBV-like viruses in Cynomolgus monkeys (Macaca fascicularis) have been associated with high lymphoma rates in immunosuppressed monkeys.
Probab=23.50 E-value=61 Score=15.55 Aligned_cols=15 Identities=53% Similarity=0.859 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHHHH
Q ss_conf 999865899999999
Q gi|255764484|r 7 ILLLSSFAVIAIIFL 21 (43)
Q Consensus 7 illlssfaviaiifl 21 (43)
.+.|+||||+-||..
T Consensus 52 ~~VL~SFAvvLIIII 66 (382)
T pfam05297 52 LLVLYSFALILIIII 66 (382)
T ss_pred HHHHHHHHHHHHHHH
T ss_conf 999999999999999
No 15
>TIGR02599 TIGR02599 Verrucomicrobium spinosum paralogous family TIGR02599.
Probab=23.48 E-value=46 Score=16.17 Aligned_cols=20 Identities=45% Similarity=0.792 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHHHHHHHH-HHHH
Q ss_conf 999999865899999999-8666
Q gi|255764484|r 4 LIEILLLSSFAVIAIIFL-WADI 25 (43)
Q Consensus 4 lieilllssfaviaiifl-wadi 25 (43)
||| ||-|.+|++|+.+ -+++
T Consensus 4 LvE--LLVSmtvLsilm~v~~~v 24 (396)
T TIGR02599 4 LVE--LLVSMTVLSILMLVLAQV 24 (396)
T ss_pred EEH--HHHHHHHHHHHHHHHHHH
T ss_conf 202--488999999999999887
Done!