Query 007425
Match_columns 604
No_of_seqs 181 out of 397
Neff 4.1
Searched_HMMs 46136
Date Thu Mar 28 23:25:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007425.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007425hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10250 O-FucT: GDP-fucose pr 100.0 5.1E-57 1.1E-61 460.1 1.9 308 182-544 6-349 (351)
2 KOG3849 GDP-fucose protein O-f 95.8 0.068 1.5E-06 56.3 10.4 61 171-231 25-89 (386)
3 PF05830 NodZ: Nodulation prot 90.5 12 0.00025 40.6 15.9 251 175-521 2-283 (321)
4 PF00799 Gemini_AL1: Geminivir 43.1 27 0.00059 32.5 3.5 28 434-462 14-41 (114)
5 PF14771 DUF4476: Domain of un 41.6 7.4 0.00016 34.0 -0.4 39 436-489 39-77 (95)
6 PF10892 DUF2688: Protein of u 31.7 34 0.00074 28.7 1.9 17 432-449 41-57 (60)
7 PF06422 PDR_CDR: CDR ABC tran 30.5 64 0.0014 29.1 3.7 40 51-96 41-80 (103)
8 smart00874 B5 tRNA synthetase 25.7 65 0.0014 26.3 2.7 25 428-453 11-35 (71)
9 PRK10556 hypothetical protein; 24.2 50 0.0011 30.6 1.8 20 437-456 3-22 (111)
10 PF09400 DUF2002: Protein of u 22.7 46 0.001 31.0 1.3 19 437-455 3-21 (111)
11 COG4878 Uncharacterized protei 20.8 95 0.0021 33.5 3.3 121 442-577 93-221 (309)
No 1
>PF10250 O-FucT: GDP-fucose protein O-fucosyltransferase; InterPro: IPR019378 This is a family of conserved proteins representing the enzyme responsible for adding O-fucose to EGF (epidermal growth factor-like) repeats. Six highly conserved cysteines are present as well as a DXD-like motif (ERD), conserved in mammals, Drosophila, and Caenorhabditis elegans. Both features are characteristic of several glycosyltransferase families. The enzyme is a membrane-bound protein released by proteolysis and, as for most glycosyltransferases, is strongly activated by manganese []. ; PDB: 3ZY6_A 3ZY3_A 3ZY5_A 3ZY2_A 3ZY4_A.
Probab=100.00 E-value=5.1e-57 Score=460.08 Aligned_cols=308 Identities=39% Similarity=0.602 Sum_probs=210.6
Q ss_pred ecCchhhHHHHHHHHHHHHHHhcCeEEeccccCCCcccCCCC-----CCcccchHHHHHhcCCCeEEeccCchhhhchhh
Q 007425 182 ANGGMNQQRVAICNAVVLARLLNATLVVPKFMYSSVWRDVSQ-----FSDIYQEEHFINYLTPDIRMVKELPNKLQSLDL 256 (604)
Q Consensus 182 ~nGGLNQqR~~IcDaVaVARiLNATLViP~l~~ss~W~D~S~-----F~DIFD~dhFI~~Lk~DVrIVk~LP~~~~~~~~ 256 (604)
+.||+|+||.++++||++|++||+|||||.+...+.|+|.++ |+|+||+++|+++++++|.+.+.+|..+.....
T Consensus 6 ~~GGfnNQr~~~~~a~~~A~~LnRTLVLPp~~~~~~~~~~~~~~~ipf~~~fD~~~l~~~~~~vi~~~ef~~~~~~~~~~ 85 (351)
T PF10250_consen 6 CMGGFNNQRMGFENAVVFAKALNRTLVLPPFIKHYHWKDQSKQRHIPFSDFFDVEHLRKFLRPVITMEEFLPKHWDEVFR 85 (351)
T ss_dssp -SSSHHHHHHHHHHHHHHHHHHT-EEE--EEEEESSSS----EEEEEHHHHB-HHHHTTTS--EE-HHHHHHHHS-GGG-
T ss_pred CCCCHHHHHHHHHHHHHHHHHhCCEEEcCCccccccccccccccccChhhhccHHHHHHHhhCceehheeccchhccccc
Confidence 899999999999999999999999999999999999999988 999999999999999999999999987765422
Q ss_pred hhh------------------------cccccccCCCC-CCChHHHHHhhhhhhhhc------CeEEEeccCCcccCCCC
Q 007425 257 EAI------------------------GSVVTDVDIPK-ESKPSFYLKNIIPILLRN------GVVHLLGFGNRLAFDPI 305 (604)
Q Consensus 257 ~~~------------------------~~~~~~~~v~~-~s~~~~Y~~~VLP~L~k~------~VI~l~~f~~RLa~d~l 305 (604)
... +.......... ++.+.+|+++++|++.++ +|+.|.++..++..+..
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ 165 (351)
T PF10250_consen 86 LQYCWSPWESGSWDDNMKDGNPFGPFWDKFPIKFDPCEFWSSPSLYLEDVLPELREWNENSEHPVIAFTGFESRLPDNYL 165 (351)
T ss_dssp EEEESS-B--------TTSSTTHHHHHHHTT---SEEE-E-TTSTTTT-STTHHHHHHHHTT-SEEEESS-SS-SS--GG
T ss_pred hhhcccccccccchhhccccccccccccccceeeccccccCCchhhHHHhhhHHhhhccccccccceeccccccchhccc
Confidence 100 00011122233 778889999999999987 99999999999999888
Q ss_pred chhhhhhhhhhcccccccchhHHHHHHHHHHHHhccCCCCCCCCccccCCccchhhhhhhcccccCCceEEEeechhhhh
Q 007425 306 PFQLQRLRCRCNFHALQFAPKIQETGALLLRRLRKHEGHSGPLDHYLVGPYADSIMKEKRGQSAKASRYLAIHLRFEIDM 385 (604)
Q Consensus 306 P~diQrLRCrvnF~ALrF~p~I~~lg~~LV~RLR~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gkylALHLRfE~DM 385 (604)
+.++|| +|+|+++|+++|+++|++++..+ ++|||||||+|+||
T Consensus 166 ~~~~~r--------~l~~~~~i~~~a~~~i~~~~~~~-----------------------------~~yiavHlR~~~D~ 208 (351)
T PF10250_consen 166 DRDLQR--------YLRFSPEIRELADKFIKRLLAGG-----------------------------GPYIAVHLRRGKDW 208 (351)
T ss_dssp GGGGGG--------G--B-HHHHHHHHHHHHHH---------------------------------SSEEEEEE--SHHH
T ss_pred CccceE--------EEecCHHHHHHHHHHHHHhhccc-----------------------------CceEEEeecccCch
Confidence 999988 99999999999999999999332 34999999999999
Q ss_pred hhhccccCCCchhHHHHHHHHHHhhcchhhhccccCCCCChHhhhcCCCCCCCHHHHHHHHHHhCCCCCcEEEEEeceec
Q 007425 386 VAHSLCEFGGGEEERQELEKYREIHFPALAHLKKTTKLPSPAEIRSEGLCPLTPEEAVLMLAALGFNRKTHVFVAGAQIY 465 (604)
Q Consensus 386 lA~SgC~~ggg~~E~~EL~~~R~~~~~~~~~~~k~~~~i~~~~~R~~G~CPLTPeEvgl~L~ALGf~~~T~IYlA~geiY 465 (604)
+++|.+++ ++..|+.+|... .+.+.+...+..|.||++|++++.+++++|+.+.|.||||++++|
T Consensus 209 --~~~C~~~~---~~~~~~~~~~~~----------~~~~~~~~~~~~~~~p~~~~~~~~i~~~~~~~~~~~vYiAtd~~~ 273 (351)
T PF10250_consen 209 --FSACEFKG---ERHLLASPRCWG----------KKSINPEKKRRNGCCPSTPQEAKQILRALGKNNTTVVYIATDEIY 273 (351)
T ss_dssp --HHHHCT-T-------TTTHHHH-----------GGGTT-----HHHHS--HHHHHHHHHHHHHHHT-SEEEEEESS--
T ss_pred --HhhcccCC---chHHHHHhHhhc----------cccccchhhhhcCCCCChHHHHHHHHHHhccCCCCEEEEecCccc
Confidence 88999955 778888888641 122456788899999999999999999999999999999999999
Q ss_pred cccccchhhHhhCCCccccccCCCccccccccccccccchheeeeeccCceeeeCCCCCchhhhhhcccccccCCCCcc
Q 007425 466 GGTRRLGALNSLYPYLVTKENLLSATELEPFKNFSSQLAALDFIGCTAANAFAMTDSGSQLSSLVSGYRIYYGGGKMPT 544 (604)
Q Consensus 466 GG~~~L~pL~~~FPnl~tKetLas~eEL~pF~~~sS~lAALDYiVcl~SDVFV~t~~G~nma~lV~GhR~y~G~~~~kT 544 (604)
||...|.+|++.||++++|+++.+.+|+++|.+ .++|+||++||++||+||+|. ||+|+..|+++|.|.|+.++||
T Consensus 274 ~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~--~~~a~vD~~i~~~s~~Figt~-~Stfs~~i~~~R~~~g~~~~~~ 349 (351)
T PF10250_consen 274 GGERRLDPLKNMFPNVVTKDDLLSHEELEPLND--DQLAMVDQEICSRSDVFIGTC-GSTFSSNIARERHYRGKPKRKS 349 (351)
T ss_dssp ---------HHHHHHHHGGGT--EE--S-------S--HHHHHHHHHHSSEEEE-T-T-HHHHHHHHHHHHSSSS---E
T ss_pred ccchhHHHHHHHhhhhEeccccCCHHHhhhccc--cchhHHHHHHHhcCCEEEecC-cchhHHHhhcccCcCCCCCCCC
Confidence 999999999999999999999999999999996 889999999999999999999 6789999999999999886554
No 2
>KOG3849 consensus GDP-fucose protein O-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=95.79 E-value=0.068 Score=56.32 Aligned_cols=61 Identities=26% Similarity=0.360 Sum_probs=46.6
Q ss_pred CCCCCceEEEE-ecCchhhHHHHHHHHHHHHHHhcCeEEecccc---CCCcccCCCCCCcccchH
Q 007425 171 SGGNNGYILVT-ANGGMNQQRVAICNAVVLARLLNATLVVPKFM---YSSVWRDVSQFSDIYQEE 231 (604)
Q Consensus 171 ~~~snGYL~V~-~nGGLNQqR~~IcDaVaVARiLNATLViP~l~---~ss~W~D~S~F~DIFD~d 231 (604)
....||||+.- |-|-+-+|--..--..|-|+.||.|||+|-+- +-.+-+---.|.-.|+++
T Consensus 25 ~~DP~GYl~yCPCMGRFGNQaDhFLGsLAFAKaLnRTL~lPpwiEy~~pe~~n~~vpf~~yF~ve 89 (386)
T KOG3849|consen 25 SWDPAGYLLYCPCMGRFGNQADHFLGSLAFAKALNRTLVLPPWIEYKHPETKNLMVPFEFYFQVE 89 (386)
T ss_pred CCCCCccEEEccccccccchHHHHHHHHHHHHHhcccccCCcchhccCCcccccccchhheeecc
Confidence 34689999876 99999999999999999999999999999642 222222234677888775
No 3
>PF05830 NodZ: Nodulation protein Z (NodZ); InterPro: IPR008716 The nodulation genes of Rhizobia are regulated by the nodD gene product in response to host-produced flavonoids and appear to encode enzymes involved in the production of a lipo-chitose signal molecule required for infection and nodule formation. NodZ is required for the addition of a 2-O-methylfucose residue to the terminal reducing N-acetylglucosamine of the nodulation signal. This substitution is essential for the biological activity of this molecule. Mutations in nodZ result in defective nodulation. nodZ represents a unique nodulation gene that is not under the control of NodD and yet is essential for the synthesis of an active nodulation signal [].; GO: 0016758 transferase activity, transferring hexosyl groups, 0009312 oligosaccharide biosynthetic process, 0009877 nodulation; PDB: 3SIX_A 2HLH_A 2HHC_A 3SIW_A 2OCX_A.
Probab=90.46 E-value=12 Score=40.56 Aligned_cols=251 Identities=16% Similarity=0.271 Sum_probs=119.2
Q ss_pred CceEEEEecCchhhHHHHHHHHHHHHHHhcCeEEeccccCCCcccCC----CCCCcccchHHHHHhcC--CCeEEecc--
Q 007425 175 NGYILVTANGGMNQQRVAICNAVVLARLLNATLVVPKFMYSSVWRDV----SQFSDIYQEEHFINYLT--PDIRMVKE-- 246 (604)
Q Consensus 175 nGYL~V~~nGGLNQqR~~IcDaVaVARiLNATLViP~l~~ss~W~D~----S~F~DIFD~dhFI~~Lk--~DVrIVk~-- 246 (604)
+.|++..--+||+.-=-+++-|-.+|+-.|.||||- |+++ -.|...|++ |-+-.. ..|+|.-.
T Consensus 2 ~r~~~~r~r~g~gd~l~~la~aw~~a~~~~r~l~id-------w~~s~~~~~~f~n~f~~--ffepv~~i~~~~~~~~d~ 72 (321)
T PF05830_consen 2 QRFVVSRRRTGLGDCLWSLAAAWRYAKRTGRTLVID-------WRGSCYLDQPFTNAFPV--FFEPVEDIAGVRVICDDR 72 (321)
T ss_dssp --EEEEE--S-HHHHHHHHHHHHHHHHHHT-EEEEE--------BT-TT-SSTTSBSHHH--HB---SEETTEEEE-SGG
T ss_pred CceEEEeccCCchhHHHHHHHHHHHHHHhCCeEEEE-------cCCceecCCcccccCCc--ccchhhhhcCceeEecch
Confidence 568999999999999999999999999999999984 6663 356555544 544444 25555522
Q ss_pred -----Cchhh--hchhhhhhcccccccCCCCCCChHHHH--Hhhhhhhh------hcCeEEEeccCCcccCCCCchhhhh
Q 007425 247 -----LPNKL--QSLDLEAIGSVVTDVDIPKESKPSFYL--KNIIPILL------RNGVVHLLGFGNRLAFDPIPFQLQR 311 (604)
Q Consensus 247 -----LP~~~--~~~~~~~~~~~~~~~~v~~~s~~~~Y~--~~VLP~L~------k~~VI~l~~f~~RLa~d~lP~diQr 311 (604)
+|-.+ +|-.+-+ ++........-+. +++--+++ .+.||+..=++-|- ..++.
T Consensus 73 i~~~~~~g~~fp~~w~~p~-------~~~~~~pd~qi~re~d~l~~lf~~~~d~~a~~vv~d~c~~~~c-----~~~ae- 139 (321)
T PF05830_consen 73 INQFSFPGPFFPAWWNKPS-------IDCVYRPDEQIFRERDELRQLFQSQEDHEANTVVCDACLMWRC-----DEEAE- 139 (321)
T ss_dssp GGT----SSEESGGGGS-G-------GGGS---HHHHHHHHHHHHHHHHSSS--S-SEEEE-S--TTSS------HHHH-
T ss_pred hhhhcCCCCcChhHHhCCC-------cceecCChHHHhhhhHHHHHHhhcccccccchhhhHhhcCCcc-----hhHHH-
Confidence 11111 0101000 1111111111111 22333333 25577765554442 12333
Q ss_pred hhhhhcccccccchhHHHHHHHHHHHHhccCCCCCCCCccccCCccchhhhhhhcccccCCceEEEeech--hhhhhhhc
Q 007425 312 LRCRCNFHALQFAPKIQETGALLLRRLRKHEGHSGPLDHYLVGPYADSIMKEKRGQSAKASRYLAIHLRF--EIDMVAHS 389 (604)
Q Consensus 312 LRCrvnF~ALrF~p~I~~lg~~LV~RLR~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gkylALHLRf--E~DMlA~S 389 (604)
|.-|..|+-.|+|++..+.+.+.-=.. ..=|.||.|. .+|-+.+
T Consensus 140 ---R~if~slkpR~eIqarID~iy~ehf~g------------------------------~~~IGVHVRhGngeD~~~h- 185 (321)
T PF05830_consen 140 ---REIFSSLKPRPEIQARIDAIYREHFAG------------------------------YSVIGVHVRHGNGEDIMDH- 185 (321)
T ss_dssp ---HHHHHHS-B-HHHHHHHHHHHHHHTTT------------------------------SEEEEEEE------------
T ss_pred ---HHHHHhCCCCHHHHHHHHHHHHHHcCC------------------------------CceEEEEEeccCCcchhcc-
Confidence 247999999999999988877654321 1279999992 1233333
Q ss_pred cccCCCchhHHHHHHHHHHhhcchhhhccccCCCCChHhhhcCCCCCCCHHHHHHHHHHhCCCCCcEEEEEeceeccccc
Q 007425 390 LCEFGGGEEERQELEKYREIHFPALAHLKKTTKLPSPAEIRSEGLCPLTPEEAVLMLAALGFNRKTHVFVAGAQIYGGTR 469 (604)
Q Consensus 390 gC~~ggg~~E~~EL~~~R~~~~~~~~~~~k~~~~i~~~~~R~~G~CPLTPeEvgl~L~ALGf~~~T~IYlA~geiYGG~~ 469 (604)
+|++ .+++..|.+... ....++++=.+.++.|+||+-. ..
T Consensus 186 ~~~~---~D~e~~L~~V~~---------------------------------ai~~ak~~~~~k~~~IFLATDS----ae 225 (321)
T PF05830_consen 186 APYW---ADEERALRQVCT---------------------------------AIDKAKALAPPKPVRIFLATDS----AE 225 (321)
T ss_dssp -------HHHHHHHHHHHH---------------------------------HHHHHHTS--SS-EEEEEEES-----HH
T ss_pred Cccc---cCchHHHHHHHH---------------------------------HHHHHHhccCCCCeeEEEecCc----HH
Confidence 2332 222222221111 1122344556678999999986 57
Q ss_pred cchhhHhhCCCccccccCCCccccccccccc----c-ccchheeeeeccCceee-eCC
Q 007425 470 RLGALNSLYPYLVTKENLLSATELEPFKNFS----S-QLAALDFIGCTAANAFA-MTD 521 (604)
Q Consensus 470 ~L~pL~~~FPnl~tKetLas~eEL~pF~~~s----S-~lAALDYiVcl~SDVFV-~t~ 521 (604)
.++-+++.||.+++-+.=..+..-.+..+.. . ..|-+|-+.-..+|+.| ++-
T Consensus 226 Vid~fr~~FPdiiti~k~F~~~~~g~Lhs~~~g~~gg~~ALIDM~LLSrCD~LIr~~p 283 (321)
T PF05830_consen 226 VIDQFRKKFPDIITIPKQFPASQAGPLHSAAVGIEGGESALIDMYLLSRCDYLIRFPP 283 (321)
T ss_dssp HHHHHHHHSTTEE----------------HHHHHHHHHHHHHHHHHHTTSSEEEEEST
T ss_pred HHHHHHHHCCCeEEcccccCCCCCCcCcccccccchHHHHHHHHHHHHhCCeEEEcCC
Confidence 7899999999988875533332222332211 1 14778999999999998 443
No 4
>PF00799 Gemini_AL1: Geminivirus Rep catalytic domain; InterPro: IPR022690 Geminiviruses are characterised by a genome of circular single-stranded DNA encapsidated in twinned (geminate) quasi-isometric particles, from which the group derives its name []. Most geminiviruses can be divided into two subgroups on the basis of host range and/or insect vector: i.e. those that infect dicotyledenous plants and are transmitted by the same whitefly species, and those that infect monocotyledenous plants and are transmitted by different leafhopper vectors. The genomes of the whitefly-transmitted African cassava mosaic virus, Tomato golden mosaic virus (TGMV) and Bean golden mosaic virus (BGMV) possess a bipartite genome. By contrast, only a single DNA component has been identified for the leafhopper-transmitted Maize streak virus (MSV) and Wheat dwarf virus (WDV) [, ]. Beet curly top virus (BCTV), and Tobacco yellow dwarf virus belong to a third possible subgroup. Like MSV and WDV, BCTV is transmitted by a specific leafhopper species, yet like the whitefly-transmitted geminiviruses it has a host range confined to dicotyledenous plants. Sequence comparison of the whitefly-transmitted Squash leaf curl virus (SqLCV) and Tomato yellow leaf curl virus (TYLCV) with the genomic components of TGMV and BGMV reveals a close evolutionary relationship [, , ]. Amino acid sequence alignments of Potato yellow mosaic virus (PYMV) proteins with those encoded by other geminiviruses show that PYMV is closely related to geminiviruses isolated from the New World, especially in the putative coat protein gene regions []. Comparison of MSV DNA-encoded proteins with those of other geminiviruses infecting monocotyledonous plants, including Panicum streak virus [] and Miscanthus streak virus (MiSV) [], reveal high levels of similarity. The AL1 proteins encodes the replication initiator protein (Rep) of geminiviruses, which is a replicon-specific initiator enzyme and is an essential component of the replisome []. For geminivirus Rep protein, this N-terminal region is crucial for origin recognition and DNA cleavage and nucleotidyl transfer []. It is found in association with PF08283 from PFAM. ; GO: 0006260 DNA replication; PDB: 1L5I_A 1L2M_A.
Probab=43.08 E-value=27 Score=32.49 Aligned_cols=28 Identities=29% Similarity=0.333 Sum_probs=16.0
Q ss_pred CCCCCHHHHHHHHHHhCCCCCcEEEEEec
Q 007425 434 LCPLTPEEAVLMLAALGFNRKTHVFVAGA 462 (604)
Q Consensus 434 ~CPLTPeEvgl~L~ALGf~~~T~IYlA~g 462 (604)
+|||||||+...|++|--+ ....||..+
T Consensus 14 qC~l~ke~~l~~L~~l~~~-~~~~yI~v~ 41 (114)
T PF00799_consen 14 QCSLTKEEALEQLKNLLTP-SNKKYIRVC 41 (114)
T ss_dssp T----HHHHHHHHHH---S-S-EEEEEEE
T ss_pred CCCCCHHHHHHHHHHhCCc-cCceEEEee
Confidence 7999999999999999754 467777554
No 5
>PF14771 DUF4476: Domain of unknown function (DUF4476)
Probab=41.59 E-value=7.4 Score=34.00 Aligned_cols=39 Identities=31% Similarity=0.559 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHhCCCCCcEEEEEeceeccccccchhhHhhCCCccccccCCC
Q 007425 436 PLTPEEAVLMLAALGFNRKTHVFVAGAQIYGGTRRLGALNSLYPYLVTKENLLS 489 (604)
Q Consensus 436 PLTPeEvgl~L~ALGf~~~T~IYlA~geiYGG~~~L~pL~~~FPnl~tKetLas 489 (604)
++|-.+++-+|+-+.|++ .+|..|+-++|++++++.--+
T Consensus 39 ~~T~~Qv~~il~~f~fd~---------------~kl~~lk~l~p~i~D~~n~~~ 77 (95)
T PF14771_consen 39 CFTCAQVKQILSLFSFDN---------------DKLKALKLLYPYIVDPQNYYT 77 (95)
T ss_pred ceeHHHHHHHHHHcCCCH---------------HHHHHHHHHhhhccCHHHHHH
Confidence 499999999999998874 579999999999999975433
No 6
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=31.71 E-value=34 Score=28.68 Aligned_cols=17 Identities=47% Similarity=0.661 Sum_probs=14.2
Q ss_pred CCCCCCCHHHHHHHHHHh
Q 007425 432 EGLCPLTPEEAVLMLAAL 449 (604)
Q Consensus 432 ~G~CPLTPeEvgl~L~AL 449 (604)
-|-| +||||-+.+++++
T Consensus 41 C~~C-itpEE~~~I~e~~ 57 (60)
T PF10892_consen 41 CGDC-ITPEEDREILEAT 57 (60)
T ss_pred hhcc-CCHHHHHHHHHHH
Confidence 3567 9999999999875
No 7
>PF06422 PDR_CDR: CDR ABC transporter; InterPro: IPR010929 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These 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 hydrolyse 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 polarise 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 [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). In yeast, the PDR and CDR ABC transporters display extensive sequence homology, and confer resistance to several anti-fungal compounds by actively transporting their substrates out of the cell. These transporters have two homologous halves, each with an N-terminal intracellular hydrophilic region that contains an ATP-binding site, followed by a C-terminal membrane-associated region containing six transmembrane segments []. This entry represents a domain of the PDR/CDR ABC transporter comprising extracellular loop 3, transmembrane segment 6 and a linker region.; GO: 0005524 ATP binding, 0042626 ATPase activity, coupled to transmembrane movement of substances, 0006810 transport, 0016021 integral to membrane
Probab=30.52 E-value=64 Score=29.12 Aligned_cols=40 Identities=13% Similarity=0.267 Sum_probs=30.1
Q ss_pred hhhccceeeeeeccceeeehHHHHHHHHHHHHHHHHHHHhcccccc
Q 007425 51 MKRKGEKAWYKRKRVKSLVGVIGLICFFFVVNWFMLVRLQYHGRKT 96 (604)
Q Consensus 51 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 (604)
.--.-.|.| |-+..++|++.||++++.+++..+.......
T Consensus 41 y~y~~sh~W------RN~GIli~f~i~f~~~~~~~~e~~~~~~~~~ 80 (103)
T PF06422_consen 41 YGYSYSHRW------RNFGILIAFWIFFIVLTLLATEFIKFEKSGG 80 (103)
T ss_pred ccccccchh------hhHHHHHHHHHHHHHHHHHHHHHhcccCCCc
Confidence 445567888 5569999999999999988887776555443
No 8
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=25.72 E-value=65 Score=26.29 Aligned_cols=25 Identities=40% Similarity=0.450 Sum_probs=20.7
Q ss_pred hhhcCCCCCCCHHHHHHHHHHhCCCC
Q 007425 428 EIRSEGLCPLTPEEAVLMLAALGFNR 453 (604)
Q Consensus 428 ~~R~~G~CPLTPeEvgl~L~ALGf~~ 453 (604)
-.+..|. .++++|+.-+|+.|||+-
T Consensus 11 i~~llG~-~i~~~ei~~~L~~lg~~~ 35 (71)
T smart00874 11 INRLLGL-DLSAEEIEEILKRLGFEV 35 (71)
T ss_pred HHHHHCC-CCCHHHHHHHHHHCCCeE
Confidence 3456665 499999999999999975
No 9
>PRK10556 hypothetical protein; Provisional
Probab=24.21 E-value=50 Score=30.57 Aligned_cols=20 Identities=30% Similarity=0.506 Sum_probs=17.4
Q ss_pred CCHHHHHHHHHHhCCCCCcE
Q 007425 437 LTPEEAVLMLAALGFNRKTH 456 (604)
Q Consensus 437 LTPeEvgl~L~ALGf~~~T~ 456 (604)
|-|.||+.+|..-||..+..
T Consensus 3 LRPDEVArVLe~aGF~~D~v 22 (111)
T PRK10556 3 LRPDEVARVLEKAGFTVDVV 22 (111)
T ss_pred cChHHHHHHHHhcCceEEEe
Confidence 67999999999999987753
No 10
>PF09400 DUF2002: Protein of unknown function (DUF2002); InterPro: IPR018994 This entry represents a group of putative cytoplasmic proteins. The structure of these proteins form an antiparallel beta sheet and contain some alpha helical regions. ; PDB: 2G7J_A.
Probab=22.69 E-value=46 Score=31.03 Aligned_cols=19 Identities=37% Similarity=0.658 Sum_probs=14.6
Q ss_pred CCHHHHHHHHHHhCCCCCc
Q 007425 437 LTPEEAVLMLAALGFNRKT 455 (604)
Q Consensus 437 LTPeEvgl~L~ALGf~~~T 455 (604)
|-|.||+.+|..-||..+.
T Consensus 3 lrpdeva~vle~~gf~~d~ 21 (111)
T PF09400_consen 3 LRPDEVARVLEKAGFERDY 21 (111)
T ss_dssp --HHHHHHHHHHTT-EEEE
T ss_pred cChHHHHHHHHhcCceEEE
Confidence 6799999999999998764
No 11
>COG4878 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.77 E-value=95 Score=33.49 Aligned_cols=121 Identities=16% Similarity=0.097 Sum_probs=73.8
Q ss_pred HHHHHHHhCCC-CCcEEEEEeceeccccccchhhHhhCCCccccccCCCcccccccccccccc-chheeeeeccCceeee
Q 007425 442 AVLMLAALGFN-RKTHVFVAGAQIYGGTRRLGALNSLYPYLVTKENLLSATELEPFKNFSSQL-AALDFIGCTAANAFAM 519 (604)
Q Consensus 442 vgl~L~ALGf~-~~T~IYlA~geiYGG~~~L~pL~~~FPnl~tKetLas~eEL~pF~~~sS~l-AALDYiVcl~SDVFV~ 519 (604)
++..+..|--. -+|.||++-+.| +-+..-..|.+-||++-|-.++.+.+|+.+|..-+-+. .+ |. |==
T Consensus 93 L~~y~~~ls~~~y~~~vfVppSni-l~q~gk~alvk~~p~lktissiy~~deykd~~se~g~~ktg-----~~----lPR 162 (309)
T COG4878 93 LADYGDILSITGYDTFVFVPPSNI-LLQKGKFALVKQAPSLKTISSIYNTDEYKDFNSESGIQKTG-----LI----LPR 162 (309)
T ss_pred HHHHHHHHhccccceEEEeCcccc-cchhHHHHHHHhCCCcceeeeEecccccCcccchheecccc-----cc----ccc
Confidence 34455555333 479999999999 55777899999999999999999999999997544332 22 11 111
Q ss_pred CCCCC-----chhhhhhcccccccCCCCccccccHHHHHHHHhcC-CCccHHHHHHHHHHHHHh
Q 007425 520 TDSGS-----QLSSLVSGYRIYYGGGKMPTIRPNKRRLAAIFVKN-STIEWKVFEQRVRKAVRQ 577 (604)
Q Consensus 520 t~~G~-----nma~lV~GhR~y~G~~~~kTI~Pdrk~la~Lf~~~-~~i~W~~F~~~Vr~~~~~ 577 (604)
+.+|. .|-.++.+--.+--..| -++||-..=+ +.+ .-..|++...+.+.++.+
T Consensus 163 ~tSg~y~d~~t~w~~~n~l~~~g~~~h--fvHPddvidl---Dr~~k~k~Wnel~k~~~sl~~e 221 (309)
T COG4878 163 VTSGSYEDHFTHWLFPNLLQHSGSLEH--FVHPDDVIDL---DRDCKVKAWNELSKQLTSLLWE 221 (309)
T ss_pred cccCccchHHHHHHhcchhhcccceee--ecCchhhhcc---ccCcccccHHHHHHHHHHHHHH
Confidence 12232 12222222212211222 5778754211 112 346899988888887765
Done!