RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780687|ref|YP_003065100.1| flagellar C-ring protein [Candidatus Liberibacter asiaticus str. psy62] (318 letters) >gnl|CDD|180651 PRK06666, fliM, flagellar motor switch protein FliM; Validated. Length = 337 Score = 64.5 bits (158), Expect = 3e-11 Identities = 42/221 (19%), Positives = 85/221 (38%), Gaps = 35/221 (15%) Query: 102 NLVITLLENLLG---ASHETIPQLYNRSLSTVEKKLAKRTIAQISAVLNQCISTTQESSP 158 +LV +++NL G H + R + E+++ I +L +E+ Sbjct: 123 SLVFIMVDNLFGGDGRFHTKV----GREFTETEQRI-------IDRILKLAFENLKEA-- 169 Query: 159 NLEDFYDID--YLKKNTNR------LSNEFVTTINMNMTIENVASSFVLIIPQETL---- 206 I+ Y++ N NE V ++ ++ I + IP + Sbjct: 170 -WSSVVPIEPEYVRSEVNPQFANIVSPNEIVVVVSFHIEIGGGGGMMNICIPYSMIEPIR 228 Query: 207 --LKTTLISLSSQNKSENQSEDLIDPFARKTYQLNVNIDTRINLKKTTLKDVVTLKIGQV 264 L + S++K + ++L ++ Q V + + K TL +++ LK+G V Sbjct: 229 EKLSSPYWMSDSRDKDKRWRKEL----EQQVQQAEVELVAELGEIKLTLSEILNLKVGDV 284 Query: 265 IPFLHREKTCAILSANGKEIYSCELGRVGKNYTIRITDRIN 305 IP I+ +GK + C+ G+ ++I + I Sbjct: 285 IPLEKPADDPLIVYVDGKPKFLCQYGKSNGRKALQIEELIE 325 >gnl|CDD|130464 TIGR01397, fliM_switch, flagellar motor switch protein FliM. Members of this family are the flagellar motor switch protein FliM. The family excludes FliM homologs that lack an N-terminal region critical to interaction with phosphorylated CheY. One set lacking this N-terminal region is found in Rhizobium meliloti, in which the direction of flagellar rotation is not reversible (i.e. the FliM homolog does not act to reverse the motor direction), and in related species. Another is found in Buchnera, an obligate intracellular endosymbiont with genes for many of the components of the flagellar apparatus, but not, apparently, for flagellin iself. Length = 320 Score = 59.6 bits (145), Expect = 9e-10 Identities = 42/262 (16%), Positives = 98/262 (37%), Gaps = 14/262 (5%) Query: 50 FKEKMDLDVDISYTSCQSGKFSHIIHSFKENFVFSQASLSSWSSNFFIGCSNNLVITLLE 109 + V++S S + + S + + I +L+ T+++ Sbjct: 67 LSNMLRRFVEVSVASVDQLTYGEFLRSLPVPTSLNVFRMEPLRGTALIEIDPSLIYTMVD 126 Query: 110 NLLGASHETIPQLYNRSLSTVEKKLAKRTIAQISAVLNQCISTTQESSPNLEDFYDIDYL 169 L G ++P+ R + +E+++ R + ++ L + S P L+ Sbjct: 127 RLFGGQGRSVPE--GREFTEIERRVIDRILDRVLEDLKEAWSPVMPLEPELDR------S 178 Query: 170 KKNTNRLS----NEFVTTINMNMTIENVASSFVLIIPQETL--LKTTLISLSSQNKSENQ 223 + N NE V ++ ++ + + +P TL +++ L Q++ + Sbjct: 179 ETNPQFAQIVPPNEIVVLVSFSVEVGETEGMINICLPYSTLEPIRSKLSQRFMQSEKVER 238 Query: 224 SEDLIDPFARKTYQLNVNIDTRINLKKTTLKDVVTLKIGQVIPFLHREKTCAILSANGKE 283 D R+ + V++ + + +L+ ++ L++G VIP L G+ Sbjct: 239 DSSWRDALERELSTVPVDMRAVLGEVEVSLRQLLNLQVGDVIPLNTDMPEEVSLRVGGRP 298 Query: 284 IYSCELGRVGKNYTIRITDRIN 305 + + G G ++IT I Sbjct: 299 KFRAQPGVRGGKLAVQITRVIE 320 >gnl|CDD|183752 PRK12795, fliM, flagellar motor switch protein FliM; Reviewed. Length = 388 Score = 35.0 bits (81), Expect = 0.027 Identities = 17/75 (22%), Positives = 32/75 (42%) Query: 231 FARKTYQLNVNIDTRINLKKTTLKDVVTLKIGQVIPFLHREKTCAILSANGKEIYSCELG 290 A + +Q +V +D ++ + LK V+ LK+G + R L + +G Sbjct: 295 LATEIWQTDVEVDAVLDEQTLPLKRVLNLKVGDTLMLDARPDALVTLRCGDVPLTEGRMG 354 Query: 291 RVGKNYTIRITDRIN 305 RVG +R+ + Sbjct: 355 RVGDRVAVRVEKPLR 369 >gnl|CDD|181422 PRK08432, PRK08432, flagellar motor switch protein FliY; Validated. Length = 283 Score = 33.1 bits (76), Expect = 0.10 Identities = 27/131 (20%), Positives = 53/131 (40%), Gaps = 17/131 (12%) Query: 150 ISTT---QESSPNLE-DFYDIDYLKKNTNRLSNEFVTTINMNMTIENVASSFVLIIPQE- 204 IST+ Q+ P L +++++ +N + LS+ + + IE++ S +L++ + Sbjct: 105 ISTSLGAQKLLPKLNFTIENVEFVDENPD-LSD-YAKLFLFSFKIEDIKSQIILLMDEAF 162 Query: 205 --TLLKTTLISLSSQNKSENQSEDLIDPFARKTYQLNV--------NIDTRINLKKTTLK 254 K S ++ N+ + RI KK LK Sbjct: 163 ENIFEKKPKEEGEETTDSASEEIKTHKASLSNEEIKNINMILDVKLPVRVRIGQKKMLLK 222 Query: 255 DVVTLKIGQVI 265 DV+++ IG V+ Sbjct: 223 DVLSMDIGSVV 233 >gnl|CDD|149080 pfam07814, WAPL, Wings apart-like protein regulation of heterochromatin. This family contains sequences expressed in eukaryotic organisms bearing high similarity to the WAPL conserved region of D. melanogaster wings apart-like protein. This protein is involved in the regulation of heterochromatin structure. hWAPL, the human homologue, is found to play a role in the development of cervical carcinogenesis, and is thought to have similar functions to Drosophila wapl protein. Malfunction of the hWAPL pathway is thought to activate an apoptotic pathway that consequently leads to cell death. Length = 362 Score = 27.8 bits (62), Expect = 3.8 Identities = 26/117 (22%), Positives = 42/117 (35%), Gaps = 18/117 (15%) Query: 48 KIFKEKMDLDVDISYTSCQSGKFSHIIHSFKENFVFSQASLSSWSSNFFIGCSNNLVITL 107 +IFK D D C + I + ++ + L S NL++ L Sbjct: 67 RIFKAISDALDDDLLALCAAT----IFYLLTQDGLNMDFLLDRD--------SLNLLLKL 114 Query: 108 LENLLGASHE--TIPQLYNRSLSTVEKKLAKRTIAQISAVLNQCISTTQESSPNLED 162 L LL + + ++ L + LS V +KL K S+ S + P L Sbjct: 115 LRVLLDVTSDLDSLGTLSAKGLSRVVEKLVKLCEEIKSSG----FSGGEPKHPELSS 167 >gnl|CDD|161781 TIGR00234, tyrS, tyrosyl-tRNA synthetase. This tyrosyl-tRNA synthetase model starts picking up tryptophanyl-tRNA synthetases at scores of 0 and below. The proteins found by this model have a deep split between two groups. One group contains bacterial and organellar eukaryotic examples. The other contains archaeal and cytosolic eukaryotic examples. Length = 377 Score = 27.4 bits (61), Expect = 4.7 Identities = 9/46 (19%), Positives = 16/46 (34%), Gaps = 8/46 (17%) Query: 16 ILLARLTGKLGD---KKTIEKISSSL-----GYLYKKFLPKIFKEK 53 +LL T +GD K K+ + KK + + + Sbjct: 67 VLLGDATALIGDPSGKSEERKLLTREEVQENAENIKKQIARFLDFE 112 >gnl|CDD|149389 pfam08314, Sec39, Secretory pathway protein Sec39. Mnaimneh et al identified Sec39p as a protein involved in ER-Golgi transport in a large scale promoter shut down analysis of essential yeast genes. Kraynack et al. (2005) showed that Sec39p (Dsl3p) is required for Golgi-ER retrograde transport and is part of a very stable protein complex that also includes Dsl1p (in mammals ZW10), Tip20p (Rint-1) and the ER localized Q-SNARE proteins Ufe1p (syntaxin-18), Sec20p and Use1p. This was confirmed in a genome-wide analysis of protein complexes by Gavin et al (2006). Length = 675 Score = 27.0 bits (60), Expect = 6.9 Identities = 20/109 (18%), Positives = 36/109 (33%), Gaps = 18/109 (16%) Query: 88 LSSWSSNFFIGCSNNLVITLLENLLGAS-HETIPQLYNRSLSTVEKKLAKRTIAQIS--- 143 L WS+ F + +LE LL AS E +Y S ++ + + + + Sbjct: 389 LQDWSALFTRLSKEEIEAEILEALLEASEFELAKSIYEESGLSLSSEQLEDLVLKAFWEF 448 Query: 144 --------------AVLNQCISTTQESSPNLEDFYDIDYLKKNTNRLSN 178 + + + PN ++ L K T+ LS Sbjct: 449 FNNASNGNRSRGEMKKAEEILQLFPKHFPNSTVAQQLEALLKATDALSR 497 >gnl|CDD|181654 PRK09109, motC, flagellar motor protein; Reviewed. Length = 246 Score = 26.8 bits (60), Expect = 7.1 Identities = 10/20 (50%), Positives = 13/20 (65%) Query: 221 ENQSEDLIDPFARKTYQLNV 240 E+ ++ DPFARK QL V Sbjct: 97 EDVADREPDPFARKGLQLLV 116 >gnl|CDD|131533 TIGR02480, fliN, flagellar motor switch protein FliN. Proteins that consist largely of the domain described by this model can be designated flagellar motor switch protein FliN. Longer proteins in which this region is a C-terminal domain typically are designated FliY. More distantly related sequences, outside the scope of this family, are associated with type III secretion and include the surface presentation of antigens protein SpaO required or invasion of host cells by Salmonella enterica. Length = 77 Score = 26.8 bits (60), Expect = 7.5 Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 4/71 (5%) Query: 238 LNVNIDTRINLKKT--TLKDVVTLKIGQVIPFLHREKTCAI-LSANGKEIYSCELGRVGK 294 L++ ++ + L +T TL D++ L G VI L + + + NG+ I E+ V Sbjct: 6 LDIPVELTVELGRTRITLGDLLKLGEGSVIE-LDKLAGEPLDILVNGRLIARGEVVVVED 64 Query: 295 NYTIRITDRIN 305 + IRIT+ ++ Sbjct: 65 KFGIRITEIVD 75 >gnl|CDD|150058 pfam09258, Glyco_transf_64, Glycosyl transferase family 64 domain. Members of this family catalyse the transfer reaction of N-acetylglucosamine and N-acetylgalactosamine from the respective UDP-sugars to the non-reducing end of [glucuronic acid]beta 1-3[galactose]beta 1-O-naphthalenemethanol, an acceptor substrate analog of the natural common linker of various glycosylaminoglycans. They are also required for the biosynthesis of heparan-sulphate. Length = 244 Score = 26.8 bits (60), Expect = 7.7 Identities = 8/36 (22%), Positives = 15/36 (41%) Query: 163 FYDIDYLKKNTNRLSNEFVTTINMNMTIENVASSFV 198 FY YL T+ L ++ E++ +F+ Sbjct: 143 FYHRYYLYLYTHSLPKSIRDLVDETRNCEDILMNFL 178 >gnl|CDD|172317 PRK13779, PRK13779, bifunctional PTS system fructose-specific transporter subunit IIA/HPr protein; Provisional. Length = 503 Score = 26.4 bits (58), Expect = 9.6 Identities = 23/106 (21%), Positives = 39/106 (36%), Gaps = 22/106 (20%) Query: 14 HPILLARLTGKLGDKKTIEKISSSLGYLYKKF---------LPKIFKEKMDLDVD----I 60 H LL +LT L D+ T K+++ K+F + + LDVD + Sbjct: 106 HLSLLRQLTHVLSDEDTAAKLATLTD--VKEFRAILMGETEPFSVPAANISLDVDTQSLL 163 Query: 61 SYTSCQSGKFSHIIHSFKENFVFSQASLSSWSSNFFIGCSNNLVIT 106 + + +GK +E +S SN + L +T Sbjct: 164 TLVAINAGK-------LQEQSAVENRFISEVISNPALPLGKGLWVT 202 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.317 0.132 0.365 Gapped Lambda K H 0.267 0.0723 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 4,763,176 Number of extensions: 286559 Number of successful extensions: 567 Number of sequences better than 10.0: 1 Number of HSP's gapped: 564 Number of HSP's successfully gapped: 28 Length of query: 318 Length of database: 5,994,473 Length adjustment: 93 Effective length of query: 225 Effective length of database: 3,984,929 Effective search space: 896609025 Effective search space used: 896609025 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 57 (25.7 bits)