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)