RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254781218|ref|YP_003065631.1| hypothetical protein
CLIBASIA_05625 [Candidatus Liberibacter asiaticus str. psy62]
(205 letters)
>gnl|CDD|128803 smart00530, HTH_XRE, Helix-turn-helix XRE-family like proteins.
Length = 56
Score = 54.5 bits (132), Expect = 2e-08
Identities = 20/56 (35%), Positives = 34/56 (60%)
Query: 117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWI 172
RLK +R++KG++Q E + LG+ STLS E G+ P ++ +K+ + LD +
Sbjct: 1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
Score = 32.1 bits (74), Expect = 0.11
Identities = 15/56 (26%), Positives = 26/56 (46%)
Query: 35 RIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWI 90
R+K++R+ TQ+E+A S ++ ENG S+ L +S D +
Sbjct: 1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
>gnl|CDD|182039 PRK09706, PRK09706, transcriptional repressor DicA; Reviewed.
Length = 135
Score = 42.5 bits (100), Expect = 7e-05
Identities = 17/64 (26%), Positives = 32/64 (50%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY 173
+G R++ RK +SQ K + + + ++S +E+ T P K + + + W+
Sbjct: 6 LGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWLL 65
Query: 174 FGDE 177
FGDE
Sbjct: 66 FGDE 69
>gnl|CDD|163542 TIGR03830, CxxCG_CxxCG_HTH, putative zinc finger/helix-turn-helix
protein, YgiT family. This model describes a family of
predicted regulatory proteins with a conserved zinc
finger/HTH architecture. The amino-terminal region
contains a novel domain, featuring two CXXC motifs and
occuring in a number of small bacterial proteins as well
as in the present family. The carboxyl-terminal region
consists of a helix-turn-helix domain, modeled by
pfam01381. The predicted function is DNA binding and
transcriptional regulation.
Length = 127
Score = 41.8 bits (99), Expect = 1e-04
Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 2/83 (2%)
Query: 90 IYDGEVIDRRYEDVTN-KKRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQ 148
+ D E R + + +++D ++ IRK G+SQ E +LLG + S YE+
Sbjct: 41 LLDPEESKRNSAALADFYRKVDGLLTPPEIRRIRKKLGLSQREAAELLGGGVNAFSRYER 100
Query: 149 GRTIPEIKPARKIKQVTKKHLDW 171
G P K K+ ++ KH +
Sbjct: 101 GEVRPS-KALDKLLRLLDKHPEL 122
>gnl|CDD|182158 PRK09943, PRK09943, DNA-binding transcriptional repressor PuuR;
Provisional.
Length = 185
Score = 39.4 bits (92), Expect = 6e-04
Identities = 19/54 (35%), Positives = 30/54 (55%)
Query: 111 PYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQV 164
A G RL IR+ +G+SQ +L G+ +S +S EQ + P I +K+ +V
Sbjct: 5 GLAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKV 58
Score = 27.1 bits (60), Expect = 3.4
Identities = 14/54 (25%), Positives = 24/54 (44%)
Query: 33 GTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEIS 86
G R+ +IR+ +Q+ A + SA++ E S +I L Y +S
Sbjct: 9 GKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLS 62
>gnl|CDD|183994 PRK13355, PRK13355, bifunctional HTH-domain containing
protein/aminotransferase; Provisional.
Length = 517
Score = 36.6 bits (85), Expect = 0.005
Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 5/44 (11%)
Query: 115 GARLKSIRKDKGMSQIEFGKLLG-----MPNSTLSNYEQGRTIP 153
RLK K +G+ Q + + S +S Y G+T P
Sbjct: 5 AERLKQAMKARGLKQEDLVHAAEARGVKLGKSHISQYVSGKTGP 48
>gnl|CDD|182049 PRK09726, PRK09726, antitoxin HipB; Provisional.
Length = 88
Score = 30.7 bits (69), Expect = 0.25
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 110 DPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYE 147
P + +K +R+ G +Q E K +G+ +T+SN+E
Sbjct: 9 SPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFE 46
>gnl|CDD|102369 PRK06424, PRK06424, transcription factor; Provisional.
Length = 144
Score = 30.3 bits (68), Expect = 0.33
Identities = 13/47 (27%), Positives = 29/47 (61%)
Query: 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQV 164
+K+ R+ MSQ + + + +++ E+G +P+IK ARK++++
Sbjct: 89 VKNARERLSMSQADLAAKIFERKNVIASIERGDLLPDIKTARKLEKI 135
>gnl|CDD|163124 TIGR03070, couple_hipB, transcriptional regulator, y4mF family.
Members of this family belong to a clade of
helix-turn-helix DNA-binding proteins, among the larger
family pfam01381 (HTH_3; Helix-turn-helix). Members are
similar in sequence to the HipB protein of E. coli.
Genes for members of the seed alignment for this protein
family were found to be closely linked to genes encoding
proteins related to HipA. The HibBA operon appears to
have some features in common with toxin-antitoxin
post-segregational killing systems.
Length = 58
Score = 29.9 bits (68), Expect = 0.43
Identities = 10/42 (23%), Positives = 21/42 (50%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEI 155
IG +++ RK G++Q + L G+ + + E G+ +
Sbjct: 3 IGMLVRARRKALGLTQADLADLAGVGLRFIRDVENGKPTVRL 44
>gnl|CDD|115662 pfam07022, Phage_CI_repr, Bacteriophage CI repressor
helix-turn-helix domain. This family consists of
several phage CI repressor proteins and related
bacterial sequences. The CI repressor is known to
function as a transcriptional switch, determining
whether transcription is lytic or lysogenic.
Length = 65
Score = 29.6 bits (67), Expect = 0.56
Identities = 18/67 (26%), Positives = 29/67 (43%), Gaps = 10/67 (14%)
Query: 116 ARLKSIRKDKGMS-QIEFGKLLGMPNSTLSN-YEQGRTIPEIKPARKIKQVTKKH---LD 170
A ++ + K G + E LG+ STLS Y++ PA + + + LD
Sbjct: 1 AVIERLMKAYGFKSRSELADHLGVSKSTLSTWYKRDSF-----PAEWVIRCALETGVSLD 55
Query: 171 WIYFGDE 177
W+ GD
Sbjct: 56 WLATGDG 62
>gnl|CDD|179747 PRK04140, PRK04140, hypothetical protein; Provisional.
Length = 317
Score = 28.7 bits (65), Expect = 1.2
Identities = 16/50 (32%), Positives = 27/50 (54%)
Query: 115 GARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQV 164
G L+ R++ G+S E LG+ T+S YE G I+ A K++++
Sbjct: 128 GDVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEI 177
>gnl|CDD|179140 PRK00844, glgC, glucose-1-phosphate adenylyltransferase;
Provisional.
Length = 407
Score = 28.3 bits (64), Expect = 1.4
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 21 ITPEIRQYWKDVGT 34
T R YW+DVGT
Sbjct: 251 ATERDRGYWRDVGT 264
>gnl|CDD|183133 PRK11432, fbpC, ferric transporter ATP-binding subunit;
Provisional.
Length = 351
Score = 27.8 bits (62), Expect = 2.1
Identities = 11/32 (34%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 60 AVNLFENGMCST--SIRYALYLRNEYEISFDW 89
A+ L E G S +I++ Y+ +YE++ DW
Sbjct: 282 AITLSEQGEESQRCTIKHVAYMGPQYEVTVDW 313
>gnl|CDD|129371 TIGR00270, TIGR00270, conserved hypothetical protein TIGR00270.
Length = 154
Score = 27.6 bits (61), Expect = 2.2
Identities = 13/48 (27%), Positives = 22/48 (45%)
Query: 122 RKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHL 169
R+ +G SQ + K + S + E PE K K++++ K L
Sbjct: 78 REKRGWSQEQLAKKIQEKESLIKKIENAEIEPEPKVVEKLEKLLKIKL 125
>gnl|CDD|183286 PRK11713, PRK11713, 16S ribosomal RNA methyltransferase RsmE;
Provisional.
Length = 234
Score = 27.5 bits (62), Expect = 2.3
Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 147 EQ-GRT-IPEIKPARKIKQVTKKHLDWIYFGDEVIV 180
EQ GRT IPE++P +K+ ++ L +V
Sbjct: 136 EQSGRTRIPEVRPPISLKEFLEELLPADLKAGLKLV 171
>gnl|CDD|183884 PRK13189, PRK13189, peroxiredoxin; Provisional.
Length = 222
Score = 27.6 bits (62), Expect = 2.5
Identities = 17/62 (27%), Positives = 27/62 (43%), Gaps = 10/62 (16%)
Query: 147 EQGRTIPEIKPARKIKQVTKKH-----LDWI---YFGDEVIVP--KSIKRAKGNQSSKKS 196
E GR + EI K Q + + +W D+VIVP S++ AK +K+
Sbjct: 147 EVGRNMDEILRLVKALQTSDEKGVATPANWPPNDLIKDKVIVPPASSVEEAKKRLEAKEK 206
Query: 197 KK 198
+
Sbjct: 207 GE 208
>gnl|CDD|181699 PRK09206, PRK09206, pyruvate kinase; Provisional.
Length = 470
Score = 26.6 bits (59), Expect = 4.2
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 33 GTRIKDIRKANNKTQKEMAI 52
G RIK++R +KT K+ AI
Sbjct: 44 GQRIKNLRNVMSKTGKKAAI 63
>gnl|CDD|118954 pfam10433, MMS1, Mono-functional DNA-alkylating agent methyl
methanesulfonate. MMS1 is a protein that protects
against replication-dependent DNA damage in Saccharomyces
cerevisiae.
Length = 1134
Score = 26.1 bits (57), Expect = 6.4
Identities = 10/38 (26%), Positives = 17/38 (44%)
Query: 85 ISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIR 122
I F + I +ED + ++L P A K+I+
Sbjct: 1049 ILFYASLESHTITLYFEDPGSNEQLSPQGKWALDKAIK 1086
>gnl|CDD|162546 TIGR01820, TrpE-arch, anthranilate synthase component I, archaeal
clade. The Sulfolobus enzyme has been reported to be
part of a gene cluster for Trp biosynthesis.
Length = 421
Score = 26.2 bits (58), Expect = 7.0
Identities = 16/64 (25%), Positives = 28/64 (43%), Gaps = 11/64 (17%)
Query: 80 RNEYEISF----DWIYDGE----VIDRRYEDVTNKKRLDPYAIGARLKSIRKDKGMSQIE 131
R E+E + ++I+ G+ V+ R YE DP+ + L+ I M ++
Sbjct: 159 REEFEEAVEEAKEYIFAGDIFQVVLSREYEYRL---DGDPFELYYNLREINPSPYMFLLK 215
Query: 132 FGKL 135
FG
Sbjct: 216 FGDR 219
>gnl|CDD|179099 PRK00725, glgC, glucose-1-phosphate adenylyltransferase;
Provisional.
Length = 425
Score = 26.0 bits (58), Expect = 7.8
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 23 PEIRQYWKDVGT 34
PE YW+DVGT
Sbjct: 264 PEEEPYWRDVGT 275
>gnl|CDD|179997 PRK05293, glgC, glucose-1-phosphate adenylyltransferase;
Provisional.
Length = 380
Score = 25.6 bits (57), Expect = 9.8
Identities = 10/16 (62%), Positives = 13/16 (81%), Gaps = 1/16 (6%)
Query: 28 YWKDVGTRIKDIRKAN 43
YWKDVGT I+ + +AN
Sbjct: 240 YWKDVGT-IESLWEAN 254
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
0.315 0.133 0.379
Gapped
Lambda K H
0.267 0.0763 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,269,445
Number of extensions: 202307
Number of successful extensions: 376
Number of sequences better than 10.0: 1
Number of HSP's gapped: 375
Number of HSP's successfully gapped: 33
Length of query: 205
Length of database: 5,994,473
Length adjustment: 89
Effective length of query: 116
Effective length of database: 4,071,361
Effective search space: 472277876
Effective search space used: 472277876
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: 42 (22.0 bits)
S2: 55 (24.9 bits)