RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781218|ref|YP_003065631.1| hypothetical protein
CLIBASIA_05625 [Candidatus Liberibacter asiaticus str. psy62]
(205 letters)
>gnl|CDD|28977 cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins.
Prokaryotic DNA binding proteins belonging to the
xenobiotic response element family of transcriptional
regulators..
Length = 58
Score = 54.4 bits (131), Expect = 2e-08
Identities = 21/58 (36%), Positives = 34/58 (58%)
Query: 115 GARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWI 172
G RLK +RK+KG++Q E + LG+ ST+S E G+ P ++ K+ + LD +
Sbjct: 1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
Score = 38.2 bits (89), Expect = 0.002
Identities = 17/58 (29%), Positives = 28/58 (48%)
Query: 33 GTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWI 90
G R+K++RK TQ+E+A S ++ ENG + S+ L +S D +
Sbjct: 1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
>gnl|CDD|144828 pfam01381, HTH_3, Helix-turn-helix. This large family of DNA
binding helix-turn helix proteins includes Cro and CI.
Length = 55
Score = 52.1 bits (126), Expect = 1e-07
Identities = 18/55 (32%), Positives = 32/55 (58%)
Query: 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWI 172
LK +R++ G+SQ E + LG+ ST+S E G+ P ++ +K+ + LD +
Sbjct: 1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
Score = 29.4 bits (67), Expect = 0.69
Identities = 13/55 (23%), Positives = 25/55 (45%)
Query: 36 IKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWI 90
+K++R+ +Q+E+A S ++ ENG S+ L +S D +
Sbjct: 1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
>gnl|CDD|32767 COG2944, COG2944, Predicted transcriptional regulator
[Transcription].
Length = 104
Score = 46.5 bits (110), Expect = 6e-06
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 115 GARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKH 168
+K+IR+ G+SQ F + LG+ ST+ +EQGR P A K+ ++ + H
Sbjct: 46 PTEIKAIREKLGLSQPVFARYLGVSVSTVRKWEQGRKKPS-GAALKLLRIVQNH 98
>gnl|CDD|31665 COG1476, COG1476, Predicted transcriptional regulators
[Transcription].
Length = 68
Score = 39.8 bits (93), Expect = 5e-04
Identities = 20/61 (32%), Positives = 37/61 (60%)
Query: 117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFGD 176
+LK +R + G++Q E KL+G+ T+ E+G+ P ++ A KI +V K ++ I+ +
Sbjct: 5 KLKELRAELGLTQEELAKLVGVSRQTIIAIEKGKYNPSLELALKIARVFGKTIEDIFQLE 64
Query: 177 E 177
E
Sbjct: 65 E 65
Score = 27.5 bits (61), Expect = 2.8
Identities = 13/61 (21%), Positives = 27/61 (44%)
Query: 34 TRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDG 93
++K++R TQ+E+A + E G + S+ AL + + + + I+
Sbjct: 4 NKLKELRAELGLTQEELAKLVGVSRQTIIAIEKGKYNPSLELALKIARVFGKTIEDIFQL 63
Query: 94 E 94
E
Sbjct: 64 E 64
>gnl|CDD|31586 COG1396, HipB, Predicted transcriptional regulators
[Transcription].
Length = 120
Score = 39.6 bits (90), Expect = 7e-04
Identities = 24/85 (28%), Positives = 43/85 (50%), Gaps = 1/85 (1%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRT-IPEIKPARKIKQVTKKHLDWI 172
IG RLK +RK KG+SQ E + LG+ ST+S E+GR+ P ++ ++ LD +
Sbjct: 2 IGERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSESPSLELLARLAAALGVSLDEL 61
Query: 173 YFGDEVIVPKSIKRAKGNQSSKKSK 197
+E + + + ++ +
Sbjct: 62 LEEEEELEIEELNELAKLLLLEEEE 86
Score = 31.9 bits (70), Expect = 0.12
Identities = 19/85 (22%), Positives = 33/85 (38%), Gaps = 1/85 (1%)
Query: 31 DVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCST-SIRYALYLRNEYEISFDW 89
+G R+K++RK +Q+E+A S ++ E G + S+ L +S D
Sbjct: 1 SIGERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSESPSLELLARLAAALGVSLDE 60
Query: 90 IYDGEVIDRRYEDVTNKKRLDPYAI 114
+ + E E K L
Sbjct: 61 LLEEEEELEIEELNELAKLLLLEEE 85
>gnl|CDD|31998 COG1813, COG1813, Predicted transcription factor, homolog of
eukaryotic MBF1 [Transcription].
Length = 165
Score = 37.3 bits (86), Expect = 0.003
Identities = 16/57 (28%), Positives = 29/57 (50%)
Query: 115 GARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDW 171
G R++ R+ +G+SQ + L S + E+G P IK A+K++++ L
Sbjct: 81 GERIREAREKRGLSQEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLLGIKLVE 137
>gnl|CDD|31585 COG1395, COG1395, Predicted transcriptional regulator
[Transcription].
Length = 313
Score = 34.1 bits (78), Expect = 0.028
Identities = 18/86 (20%), Positives = 43/86 (50%), Gaps = 9/86 (10%)
Query: 115 GARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYF 174
G +L+ R++ G+S + +LG+ T+ YE+G + ++ A K++++ F
Sbjct: 127 GEKLREKREEMGLSLGDLATMLGVSRKTVYKYEKGLSDASLEVALKLEEI---------F 177
Query: 175 GDEVIVPKSIKRAKGNQSSKKSKKDK 200
G++++ P I + + + + D
Sbjct: 178 GEDIVKPIDILKIPEDDIKLEEEPDD 203
>gnl|CDD|31895 COG1709, COG1709, Predicted transcriptional regulator
[Transcription].
Length = 241
Score = 32.5 bits (74), Expect = 0.085
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGR-TIPEIKPARKI 161
G L+ R+ +SQ E + LG+ S +S+YE GR P I +K
Sbjct: 28 PGETLRKWREIFNVSQTELARELGVSPSVISDYESGRRKSPGIAFVKKF 76
>gnl|CDD|38608 KOG3398, KOG3398, KOG3398, Transcription factor MBF1
[Transcription].
Length = 135
Score = 32.0 bits (72), Expect = 0.11
Identities = 18/75 (24%), Positives = 33/75 (44%), Gaps = 2/75 (2%)
Query: 99 RYEDVTNKKRLD--PYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIK 156
+ + T + D P +G ++ R KGMSQ + + + + +YE GR IP +
Sbjct: 57 KLDRETEELGHDRVPLEVGKAIQQARAQKGMSQKDLAQKINEKPQVIQDYESGRAIPNQQ 116
Query: 157 PARKIKQVTKKHLDW 171
K+++ L
Sbjct: 117 ILSKMERALGVKLRG 131
>gnl|CDD|34409 COG4800, COG4800, Predicted transcriptional regulator with an HTH
domain [Transcription].
Length = 170
Score = 29.6 bits (66), Expect = 0.66
Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 115 GARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKI 161
G+ L+ + + G++ EF K +P STL +G P +I
Sbjct: 18 GSCLQKLLDELGLTPSEFAKRANIPLSTLYKILKGSD-PRYDTLTRI 63
>gnl|CDD|32592 COG2522, COG2522, Predicted transcriptional regulator [General
function prediction only].
Length = 119
Score = 29.1 bits (65), Expect = 0.95
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 113 AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGR 150
AI A L ++G+SQ KLLG+ + +S Y G+
Sbjct: 9 AIRALLAKELIEEGLSQYRIAKLLGLTQAAVSQYLSGK 46
>gnl|CDD|31615 COG1426, COG1426, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 284
Score = 28.5 bits (63), Expect = 1.2
Identities = 11/37 (29%), Positives = 19/37 (51%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGR 150
+G RL+ R++KG+S + + S L E+G
Sbjct: 4 LGERLRQAREEKGLSLEDVAARTKIRKSYLRALEEGN 40
>gnl|CDD|33419 COG3620, COG3620, Predicted transcriptional regulator with
C-terminal CBS domains [Transcription].
Length = 187
Score = 27.6 bits (61), Expect = 2.3
Identities = 10/44 (22%), Positives = 23/44 (52%)
Query: 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKI 161
L+ RK+ G++Q + + G+ ++ E G+ P + ++I
Sbjct: 10 LRKRRKELGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRI 53
>gnl|CDD|133048 cd06426, NTP_transferase_like_2, NTP_trnasferase_like_2 is a member
of the nucleotidyl transferase family. This is a
subfamily of nucleotidyl transferases. Nucleotidyl
transferases transfer nucleotides onto phosphosugars.
The activated sugars are precursors for synthesis of
lipopolysaccharide, glycolipids and polysaccharides.
Other subfamilies of nucleotidyl transferases include
Alpha-D-Glucose-1-Phosphate Cytidylyltransferase,
Mannose-1-phosphate guanyltransferase, and
Glucose-1-phosphate thymidylyltransferase.
Length = 220
Score = 26.7 bits (60), Expect = 4.1
Identities = 10/19 (52%), Positives = 13/19 (68%), Gaps = 1/19 (5%)
Query: 25 IRQYWKDVGTRIKDIRKAN 43
I +YW D+G R +D KAN
Sbjct: 203 IHEYWLDIG-RPEDYEKAN 220
>gnl|CDD|36179 KOG0961, KOG0961, KOG0961, Predicted Zn2+-dependent endopeptidase,
insulinase superfamily [Posttranslational modification,
protein turnover, chaperones].
Length = 1022
Score = 26.2 bits (57), Expect = 6.0
Identities = 10/43 (23%), Positives = 14/43 (32%), Gaps = 6/43 (13%)
Query: 88 DWIYDGEVI-----DRR-YEDVTNKKRLDPYAIGARLKSIRKD 124
D DG + Y + K D + L+ I KD
Sbjct: 681 DRKRDGCTVLSSAVASMLYGKNSLKISFDELVLEKLLEEISKD 723
>gnl|CDD|144176 pfam00483, NTP_transferase, Nucleotidyl transferase. This family
includes a wide range of enzymes which transfer
nucleotides onto phosphosugars.
Length = 247
Score = 26.0 bits (58), Expect = 7.1
Identities = 9/22 (40%), Positives = 11/22 (50%), Gaps = 1/22 (4%)
Query: 28 YWKDVGTRIKDIRKANNKTQKE 49
YW DVGT + +AN K
Sbjct: 227 YWSDVGT-WDSLWEANLKLLTG 247
>gnl|CDD|145863 pfam02932, Neur_chan_memb, Neurotransmitter-gated ion-channel
transmembrane region. This family includes the four
transmembrane helices that form the ion channel.
Length = 228
Score = 26.1 bits (58), Expect = 7.1
Identities = 10/20 (50%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 80 RNEY-EISFDWIYDGEVIDR 98
R+E+ E+ DW Y VIDR
Sbjct: 191 RDEFDEVKEDWKYVAMVIDR 210
>gnl|CDD|58600 cd04234, AAK_AK, AAK_AK: Amino Acid Kinase Superfamily (AAK),
Aspartokinase (AK); this CD includes the N-terminal
catalytic domain of aspartokinase
(4-L-aspartate-4-phosphotransferase;). AK is the first
enzyme in the biosynthetic pathway of the aspartate
family of amino acids (lysine, threonine, methionine,
and isoleucine) and the bacterial cell wall component,
meso-diaminopimelate. It also catalyzes the conversion
of aspartate and ATP to aspartylphosphate and ADP. One
mechanism for the regulation of this pathway is by the
production of several isoenzymes of aspartokinase with
different repressors and allosteric inhibitors. Pairs of
ACT domains are proposed to specifically bind amino
acids leading to allosteric regulation of the enzyme. In
Escherichia coli, three different aspartokinase
isoenzymes are regulated specifically by lysine,
methionine, and threonine. AK-HSDHI (ThrA) and AK-HSDHII
(MetL) are bifunctional enzymes that consist of an
N-terminal AK and a C-terminal homoserine dehydrogenase
(HSDH). ThrA and MetL are involved in threonine and
methionine biosynthesis, respectively. The third
isoenzyme, AKIII (LysC), is monofunctional and is
involved in lysine synthesis. The three Bacillus
subtilis isoenzymes, AKI (DapG), AKII (LysC), and AKIII
(YclM), are feedback-inhibited by meso-diaminopimelate,
lysine, and lysine plus threonine, respectively. The E.
coli lysine-sensitive AK is described as a homodimer,
whereas, the B. subtilis lysine-sensitive AK is
described as a heterodimeric complex of alpha- and beta-
subunits that are formed from two in-frame overlapping
genes. A single AK enzyme type has been described in
Pseudomonas, Amycolatopsis, and Corynebacterium. The
fungal aspartate pathway is regulated at the AK step,
with L-Thr being an allosteric inhibitor of the
Saccharomyces cerevisiae AK (Hom3). At least two
distinct AK isoenzymes can occur in higher plants, one
is a monofunctional lysine-sensitive isoenzyme, which is
involved in the overall regulation of the pathway and
can be synergistically inhibited by
S-adenosylmethionine. The other isoenzyme is a
bifunctional, threonine-sensitive AK-HSDH protein. Also
included in this CD is the catalytic domain of the
Methylomicrobium alcaliphilum ectoine AK, the first
enzyme of the ectoine biosynthetic pathway, found in
this bacterium, and several other
halophilic/halotolerant bacteria..
Length = 227
Score = 25.5 bits (56), Expect = 9.7
Identities = 9/38 (23%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 155 IKPARKIKQVTKKHLDWI-YFGDEVIVPKSIKRAKGNQ 191
+ AR I +++ + YFG +V+ P++++ A+
Sbjct: 171 VPEARLIPEISYDEALELAYFGAKVLHPRAVEPARKAN 208
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.315 0.133 0.379
Gapped
Lambda K H
0.267 0.0718 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,410,994
Number of extensions: 120753
Number of successful extensions: 276
Number of sequences better than 10.0: 1
Number of HSP's gapped: 276
Number of HSP's successfully gapped: 34
Length of query: 205
Length of database: 6,263,737
Length adjustment: 89
Effective length of query: 116
Effective length of database: 4,340,536
Effective search space: 503502176
Effective search space used: 503502176
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 (25.0 bits)