RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780351|ref|YP_003064764.1| MarR family transcriptional
regulator [Candidatus Liberibacter asiaticus str. psy62]
(171 letters)
>gnl|CDD|128641 smart00347, HTH_MARR, helix_turn_helix multiple antibiotic
resistance protein.
Length = 101
Score = 55.7 bits (135), Expect = 6e-09
Identities = 25/89 (28%), Positives = 45/89 (50%), Gaps = 4/89 (4%)
Query: 54 DVNAVQALLLFNIGDLE-LTAGELRSRGYYLGSNVSYNLKKLIDLGFIKHQRSRIDKRSI 112
+ Q L+L + + L+ EL R S V+ L +L G I+ S D+RS+
Sbjct: 7 GLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSV 66
Query: 113 RISLTQSGKEIAETISQLYQRHIESIDKV 141
+SLT+ G+E+ I +L + E++ ++
Sbjct: 67 LVSLTEEGREL---IEELLEARHETLAEL 92
>gnl|CDD|184319 PRK13777, PRK13777, transcriptional regulator Hpr; Provisional.
Length = 185
Score = 29.6 bits (67), Expect = 0.45
Identities = 12/32 (37%), Positives = 20/32 (62%)
Query: 92 KKLIDLGFIKHQRSRIDKRSIRISLTQSGKEI 123
KKL + G++ + DKR+ I LT+ G+E+
Sbjct: 81 KKLEERGYLTFSKKEDDKRNTYIELTEKGEEL 112
>gnl|CDD|168293 PRK05910, PRK05910, type III secretion system protein; Validated.
Length = 584
Score = 28.6 bits (64), Expect = 0.76
Identities = 19/99 (19%), Positives = 40/99 (40%), Gaps = 23/99 (23%)
Query: 96 DLGFIKHQRSRIDKRSIRISLTQSGKEIA------------------ETISQLY-QRHIE 136
+LG + + + L SG+E+ E IS+ + +R +E
Sbjct: 347 ELGVVFPEEIVVRHVESSPRLIFSGQEVYLRELSCPAILPSLRNLAPEAISERFVKRLVE 406
Query: 137 SIDKVGGLSVDDF----IAMNKLLQRLNRFWGDQIAYRL 171
+V G+S+++ I+ N L+ L ++++ L
Sbjct: 407 EFQEVAGISIEEIIPKKISENSLVFLLRALVRERVSLHL 445
>gnl|CDD|130944 TIGR01889, Staph_reg_Sar, staphylococcal accessory regulator
family. This model represents a family of
transcriptional regulatory proteins in Staphylococcus
aureus and Staphylococcus epidermidis. Some members
contain two tandem copies of this region. This family is
related to the MarR transcriptional regulator family
described by pfam model pfam01047.
Length = 109
Score = 28.4 bits (64), Expect = 0.94
Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 85 SNVSYNLKKLIDLGFIKHQRSRIDKRSIRISLT-QSGKEIAETISQLYQR 133
S + +KKL G++ +RS D+R + IS+ + +I IS++ Q
Sbjct: 58 SALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIESLISEIEQI 107
>gnl|CDD|183170 PRK11512, PRK11512, DNA-binding transcriptional repressor MarR;
Provisional.
Length = 144
Score = 28.3 bits (63), Expect = 1.0
Identities = 18/69 (26%), Positives = 35/69 (50%), Gaps = 1/69 (1%)
Query: 91 LKKLIDLGFIKHQRSRIDKRSIRISLTQSGKEIAETISQLYQRHIESIDKVGGLSVDDFI 150
L +L+ G+++ + DKR + + LT SG I E QL + + + L+ D+
Sbjct: 75 LDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQCHQLVGQDLHQ-ELTKNLTADEVA 133
Query: 151 AMNKLLQRL 159
+ LL+++
Sbjct: 134 TLEHLLKKV 142
>gnl|CDD|132396 TIGR03353, VI_chp_4, type VI secretion protein, VC_A0114 family.
Work by Mougous, et al. (2006), describes IAHP-related
loci as a type VI secretion system (PubMed:16763151).
This protein family is associated with type VI secretion
loci, although not treated explicitly by Mougous, et al.
Length = 439
Score = 28.4 bits (64), Expect = 1.1
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 8/52 (15%)
Query: 116 LTQSGKEIAETI----SQLYQRHIESIDKVGGLSVDDFIAMNKLLQRLNRFW 163
L Q +E+ + L R ES + G + DF+ LLQ LNR+
Sbjct: 194 LGQRLRELLGLLRARAEALAGRRRESDQQAGSADIADFL----LLQLLNRYE 241
>gnl|CDD|179596 PRK03573, PRK03573, transcriptional regulator SlyA; Provisional.
Length = 144
Score = 27.3 bits (61), Expect = 2.3
Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 10/75 (13%)
Query: 91 LKKLIDLGFIKHQRSRIDKRSIRISLTQSG----KEIAETISQLYQRHIESIDKVGGLSV 146
L +L + G I Q D+R+ RI LT+ E+ I++ + + G+S
Sbjct: 67 LDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEVEAVINK------TRAEILHGISA 120
Query: 147 DDFIAMNKLLQRLNR 161
++ + L+ +L +
Sbjct: 121 EEIEQLITLIAKLEK 135
>gnl|CDD|179411 PRK02304, PRK02304, adenine phosphoribosyltransferase; Provisional.
Length = 175
Score = 26.6 bits (60), Expect = 3.2
Identities = 29/102 (28%), Positives = 45/102 (44%), Gaps = 39/102 (38%)
Query: 78 SRGYYLGSNVSYNLKKLIDLGFIKHQRSRIDKRSIRISLTQSGKEIAETISQLYQR---- 133
+RG+ G+ ++Y L +GF+ + K GK ETIS+ Y+
Sbjct: 60 ARGFIFGAALAYKL----GIGFVP-----VRKP---------GKLPRETISESYELEYGT 101
Query: 134 -----HIESI---DKVGGLSVDDFIA----MN---KLLQRLN 160
H ++I D+V L VDD +A + KLL+RL
Sbjct: 102 DTLEIHKDAIKPGDRV--LIVDDLLATGGTLEAAIKLLERLG 141
>gnl|CDD|182412 PRK10365, PRK10365, transcriptional regulatory protein ZraR;
Provisional.
Length = 441
Score = 26.5 bits (58), Expect = 3.4
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 139 DKVGGLSVDDFIAMNKLLQRLNRFWGDQIA 168
D + L VDD I+ +LQ L R WG +A
Sbjct: 4 DNIDILVVDDDISHCTILQALLRGWGYNVA 33
>gnl|CDD|129416 TIGR00316, cdhC, CO dehydrogenase/CO-methylating acetyl-CoA
synthase complex, beta subunit. Nomenclature follows
the description for Methanosarcina thermophila. The
CO-methylating acetyl-CoA synthase is considered the
defining enzyme of the Wood-Ljungdahl pathway, used for
acetate catabolism by sulfate reducing bacteria but for
acetate biosynthesis by acetogenic bacteria such as
oorella thermoacetica (f. Clostridium thermoaceticum).
Length = 458
Score = 26.4 bits (58), Expect = 3.5
Identities = 20/90 (22%), Positives = 41/90 (45%), Gaps = 17/90 (18%)
Query: 84 GSNVSYNLKKLID------LGFIK-----HQRS----RIDKRSIRISLTQSGKEIAETIS 128
GSN+ +L+ +I+ L +I+ +QR RI+K + L K I + +
Sbjct: 75 GSNLEEDLEGVIERRIHEFLNYIEGVMHLNQRDQIWIRINKNAFNKGLRL--KHIGKAVM 132
Query: 129 QLYQRHIESIDKVGGLSVDDFIAMNKLLQR 158
L++ I+K+ + D + + L++
Sbjct: 133 MLFKEEFPFIEKIEVTIITDPDKVKEELEK 162
>gnl|CDD|162809 TIGR02337, HpaR, homoprotocatechuate degradation operon regulator,
HpaR. This Helix-Turn-Helix transcriptional regulator
is a member of the MarR family (pfam01047) and is found
in association with operons for the degradation of
4-hydroxyphenylacetic acid via homoprotocatechuate.
Length = 118
Score = 26.6 bits (59), Expect = 3.9
Identities = 20/80 (25%), Positives = 39/80 (48%), Gaps = 7/80 (8%)
Query: 62 LLFNIGDLELTAGELRSRGYYLGSNVSYNLKKLIDLGFIKHQRSRIDKRSIRISLTQSGK 121
+L G +E T +L ++ L +++ L +L G + ++ D+R + ISLT G+
Sbjct: 36 ILAEQGSMEFT--QLANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQ 93
Query: 122 ----EIAETISQLYQRHIES 137
++ I ++Y IE
Sbjct: 94 ALYASLSPQIEEIYAA-IEE 112
>gnl|CDD|130205 TIGR01135, glmS, glucosamine--fructose-6-phosphate aminotransferase
(isomerizing). The member from Methanococcus jannaschii
contains an intein.
Length = 607
Score = 26.1 bits (58), Expect = 4.6
Identities = 10/27 (37%), Positives = 20/27 (74%), Gaps = 1/27 (3%)
Query: 104 RSRIDKRSIRISLTQSGKEIAETISQL 130
+ +DK ++ I+++QSG E A+T++ L
Sbjct: 333 KPVVDKDTLVIAISQSG-ETADTLAAL 358
>gnl|CDD|165086 PHA02713, PHA02713, hypothetical protein; Provisional.
Length = 557
Score = 26.1 bits (57), Expect = 4.7
Identities = 14/45 (31%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 113 RISLTQSGKEIAETISQ-LYQRHIESIDKVGGLSVDDFIAMNKLL 156
R++L K+ + I Q LY RHI S++ + L D++ ++ L+
Sbjct: 68 RVNLQMFDKDAVKNIVQYLYNRHISSMNVIDVLKCADYLLIDDLV 112
>gnl|CDD|128695 smart00418, HTH_ARSR, helix_turn_helix, Arsenical Resistance Operon
Repressor.
Length = 66
Score = 26.0 bits (58), Expect = 5.0
Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 11/64 (17%)
Query: 70 ELTAGELRSRGYYLG---SNVSYNLKKLIDLGFIKHQRSRIDKRSIRISLTQSGKEIAET 126
EL EL LG S VS++LKKL + G ++ SR + + + SLT +++A+
Sbjct: 10 ELCVCEL---AEILGLSQSTVSHHLKKLREAGLVE---SRREGKRVYYSLT--DEKVADL 61
Query: 127 ISQL 130
+ +L
Sbjct: 62 LEEL 65
>gnl|CDD|172813 PRK14337, PRK14337, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 446
Score = 25.8 bits (57), Expect = 5.6
Identities = 14/39 (35%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 30 RLVER--LHRSLLDVTRDEFERQGRSDVNAVQALLLFNI 66
RL E L SLLD + ER+ V A NI
Sbjct: 116 RLAEEPDLRLSLLDFSEHYPEREALWGNGTVPASAFVNI 154
>gnl|CDD|185441 PTZ00094, PTZ00094, serine hydroxymethyltransferase; Provisional.
Length = 452
Score = 25.7 bits (57), Expect = 6.6
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 113 RISLTQSGKEIAETISQLYQRHIESID 139
SL ++ E+ E I + +R IE ++
Sbjct: 12 NQSLKEADPELYELIEKEKERQIEGLE 38
>gnl|CDD|184692 PRK14466, PRK14466, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 345
Score = 25.5 bits (56), Expect = 7.0
Identities = 10/28 (35%), Positives = 18/28 (64%), Gaps = 3/28 (10%)
Query: 119 SGKEIAETISQLYQRHIESIDKVGGLSV 146
+ K+IA S LY + + SID++ +S+
Sbjct: 28 AAKQIA---SWLYDKKVTSIDEMTNISL 52
>gnl|CDD|182353 PRK10280, PRK10280, dipeptidyl carboxypeptidase II; Provisional.
Length = 681
Score = 25.6 bits (56), Expect = 7.1
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 122 EIAETISQLYQRHIESIDKVGGLSVDD 148
E A SQ QR + + +K GGL V+D
Sbjct: 164 EAATLTSQFNQRLLAA-NKSGGLVVND 189
>gnl|CDD|162025 TIGR00759, aceE, pyruvate dehydrogenase E1 component, homodimeric
type. WARNING: This family is classified as subfamily
rather than equivalog because it includes a
counterexample from Pseudomonas putida, MdeB, that is
active as an E1 component of an alpha-ketoglutarate
dehydrogenase complex rather than a pyruvate dehydrogase
complex. The second pyruvate dehydrogenase complex E1
protein from Alcaligenes eutrophus, PdhE, complements an
aceE mutant of E. coli but is not part of a pyruvate
dehydrogenase complex operon, is more similar to the
Pseudomonas putida MdeB than to E. coli AceE, and may
have also have a different primary specificity.
Length = 885
Score = 25.5 bits (56), Expect = 7.9
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 66 IGDLELTAGELRSRGYYLG 84
IGDL A + R+RG+ LG
Sbjct: 604 IGDLCWAAADQRARGFLLG 622
>gnl|CDD|130874 TIGR01815, TrpE-clade3, anthranilate synthase, alpha
proteobacterial clade. This model represents a small
clade of anthranilate synthases from alpha
proteobacteria and Nostoc (a cyanobacterium). This
enzyme is the first step in the pathway for the
biosynthesis of tryprophan from chorismate.
Length = 717
Score = 25.2 bits (55), Expect = 8.0
Identities = 16/51 (31%), Positives = 22/51 (43%), Gaps = 2/51 (3%)
Query: 106 RIDKRSIRISLTQSGKEIAETISQLYQRHIESIDKVGGLSVDDFIAMNKLL 156
R DK R+ S K I +LY R I ++D V G A++ L
Sbjct: 355 RNDKS--RVCEPGSVKVIGRRQIELYSRLIHTVDHVEGRLRSGMDALDAFL 403
>gnl|CDD|185053 PRK15098, PRK15098, beta-D-glucoside glucohydrolase; Provisional.
Length = 765
Score = 25.4 bits (56), Expect = 8.1
Identities = 14/51 (27%), Positives = 23/51 (45%)
Query: 81 YYLGSNVSYNLKKLIDLGFIKHQRSRIDKRSIRISLTQSGKEIAETISQLY 131
Y G +SY + D+ R K + +++T +GK T+ QLY
Sbjct: 640 YPFGYGLSYTTFTVSDVKLSSPTMKRDGKVTASVTVTNTGKREGATVVQLY 690
>gnl|CDD|181860 PRK09440, avtA, valine--pyruvate transaminase; Provisional.
Length = 416
Score = 25.2 bits (56), Expect = 8.7
Identities = 8/30 (26%), Positives = 13/30 (43%), Gaps = 7/30 (23%)
Query: 111 SIRISLTQSGKEI-------AETISQLYQR 133
IR++ Q +EI AE + + Y
Sbjct: 386 CIRMNYVQDDEEIEKGIAILAEEVEKAYAE 415
>gnl|CDD|180548 PRK06380, PRK06380, metal-dependent hydrolase; Provisional.
Length = 418
Score = 25.2 bits (55), Expect = 8.9
Identities = 8/34 (23%), Positives = 23/34 (67%)
Query: 112 IRISLTQSGKEIAETISQLYQRHIESIDKVGGLS 145
+ + L+++ KE+ + + + +R +E ++K+G L+
Sbjct: 202 MHMHLSETRKEVYDHVKRTGERPVEHLEKIGFLN 235
>gnl|CDD|147844 pfam05913, DUF871, Bacterial protein of unknown function (DUF871).
This family consists of several conserved hypothetical
proteins from bacteria and archaea. The function of this
family is unknown.
Length = 357
Score = 25.2 bits (56), Expect = 9.3
Identities = 15/77 (19%), Positives = 34/77 (44%), Gaps = 13/77 (16%)
Query: 95 IDLGFIKHQRSRIDKRSIRISL---TQSGKEIAETISQLYQRHIESID--------KVGG 143
+D GF + + + K ++I L T + + + +S Y + E+++ G
Sbjct: 94 LDYGFTGEEIAELSKNPLKIELNASTITTEYLDNLLS--YGANFENLEACHNFYPRPYTG 151
Query: 144 LSVDDFIAMNKLLQRLN 160
LS + F+ N+ ++
Sbjct: 152 LSYEFFLEKNRWFKKYG 168
>gnl|CDD|128802 smart00529, HTH_DTXR, Helix-turn-helix diphteria tox regulatory
element. iron dependent repressor.
Length = 96
Score = 25.3 bits (56), Expect = 9.4
Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 9/51 (17%)
Query: 84 GSNVSYNLKKLIDLGFIKHQRSRIDKRSIRISLTQSGKEIAETISQLYQRH 134
V+ LKKL G ++++ R I+LT+ G+ +A +L ++H
Sbjct: 13 PPTVTQMLKKLEKDGLVEYEPYR------GITLTEKGRRLAR---RLLRKH 54
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
0.321 0.138 0.382
Gapped
Lambda K H
0.267 0.0836 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,716,834
Number of extensions: 166626
Number of successful extensions: 391
Number of sequences better than 10.0: 1
Number of HSP's gapped: 390
Number of HSP's successfully gapped: 39
Length of query: 171
Length of database: 5,994,473
Length adjustment: 87
Effective length of query: 84
Effective length of database: 4,114,577
Effective search space: 345624468
Effective search space used: 345624468
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (24.4 bits)