RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780620|ref|YP_003065033.1| iron-responsive
transcriptional regulator [Candidatus Liberibacter asiaticus str.
psy62]
(144 letters)
>gnl|CDD|171344 PRK11920, rirA, iron-responsive transcriptional regulator;
Reviewed.
Length = 153
Score = 261 bits (669), Expect = 4e-71
Identities = 87/144 (60%), Positives = 110/144 (76%)
Query: 1 MHLTKRTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGR 60
M LTK+T+Y IR+LMYCA ++ +RI +IA A +SELFLFKILQPLV+AG+VETVRGR
Sbjct: 1 MRLTKQTNYAIRMLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGR 60
Query: 61 RGGVRLCRPADQITILDVVKATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNAFFD 120
GGVRL RPA I++ DVV+ TE+SF +AECF + +CPLV SCGL S LRKALNAFF
Sbjct: 61 NGGVRLGRPAADISLFDVVRVTEDSFSMAECFENDASECPLVDSCGLNSALRKALNAFFA 120
Query: 121 VLTQYSIECLVRNRSSIKKIFNAG 144
VL++YSI LV+ R +I+ +
Sbjct: 121 VLSKYSIADLVKARPNIRFLLGLD 144
>gnl|CDD|129821 TIGR00738, rrf2_super, rrf2 family protein (putative
transcriptional regulator). This model represents a
superfamily of probable transcriptional regulators. One
member, RRF2 of Desulfovibrio vulgaris is an apparent
regulatory protein experimentally (MEDLINE:97293189).
The N-terminal region appears related to the DNA-binding
biotin repressor region of the BirA bifunctional
according to results after three rounds of PSI-BLAST
with a fairly high stringency.
Length = 132
Score = 118 bits (297), Expect = 7e-28
Identities = 52/133 (39%), Positives = 78/133 (58%), Gaps = 2/133 (1%)
Query: 1 MHLTKRTDYGIRVLMYCAIHNDY-PNRISQIAEACCISELFLFKILQPLVKAGIVETVRG 59
M LTK+T+Y +R L+ A++ D P + +IAE IS +L KIL+ L +AG+VE+VRG
Sbjct: 1 MKLTKKTEYALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESVRG 60
Query: 60 RRGGVRLCRPADQITILDVVKATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNAFF 119
GG RL RP ++IT+ DVV+A E +C + P C L +V R+ +A
Sbjct: 61 PGGGYRLARPPEEITVGDVVRAVEGPLAPVQCIGLNG-CHPGEEVCLLHAVWRELEDAIE 119
Query: 120 DVLTQYSIECLVR 132
D L + ++ LV+
Sbjct: 120 DFLREITLADLVK 132
>gnl|CDD|182900 PRK11014, PRK11014, transcriptional repressor NsrR; Provisional.
Length = 141
Score = 89.3 bits (222), Expect = 3e-19
Identities = 50/141 (35%), Positives = 72/141 (51%), Gaps = 5/141 (3%)
Query: 1 MHLTKRTDYGIRVLMYCA-IHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRG 59
M LT TDYG+R L+Y A + IS++ E +S + KI+ L +AG V VRG
Sbjct: 1 MQLTSFTDYGLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRG 60
Query: 60 RRGGVRLCRPADQITILDVVKATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNAFF 119
+ GG+RL +PA I I DVV+ E V C + C + +C L L KA+ +F
Sbjct: 61 KNGGIRLGKPASTIRIGDVVRELEPLSLV-NCSSEF---CHITPACRLKQALSKAVQSFL 116
Query: 120 DVLTQYSIECLVRNRSSIKKI 140
L Y++ LV + K+
Sbjct: 117 KELDNYTLADLVEENQPLYKL 137
>gnl|CDD|131989 TIGR02944, suf_reg_Xantho, FeS assembly SUF system regulator,
gammaproteobacterial. The SUF system is an
oxygen-resistant iron-sulfur cluster assembly system
found in both aerobes and facultative anaerobes. Its
presence appears to be a marker of oxygen tolerance;
strict anaerobes and microaerophiles tend to have
different FeS cluster biosynthesis systems. Members of
this protein family belong to the rrf2 family of
transcriptional regulators and are found, typically, as
the first gene of a SUF operon. It is found only in a
subset of genomes that encode the SUF system, including
the genus Xanthomonas. The conserved location suggests
an autoregulatory role.
Length = 130
Score = 76.0 bits (187), Expect = 4e-15
Identities = 44/127 (34%), Positives = 65/127 (51%), Gaps = 1/127 (0%)
Query: 1 MHLTKRTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGR 60
+ ++K TDY VL A ++ P ++IAE ++ + KIL+ L AGIV + RG
Sbjct: 2 LKISKLTDYATLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSKRGV 61
Query: 61 RGGVRLCRPADQITILDVVKATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNAFFD 120
GG L R IT+ D+VKA E + EC K C L SCG+ S + + D
Sbjct: 62 EGGYTLARAPRDITVADIVKAVEGPVALTECSDDQKK-CSLGNSCGVRSNWKVINSQVLD 120
Query: 121 VLTQYSI 127
+L+ S+
Sbjct: 121 LLSSVSL 127
>gnl|CDD|131065 TIGR02010, IscR, iron-sulfur cluster assembly transcription factor
IscR. This model describes IscR, an iron-sulfur binding
transcription factor of the ISC iron-sulfur cluster
assembly system.
Length = 135
Score = 62.4 bits (152), Expect = 4e-11
Identities = 43/137 (31%), Positives = 71/137 (51%), Gaps = 5/137 (3%)
Query: 1 MHLTKRTDYGIRVLMYCAIHNDY-PNRISQIAEACCISELFLFKILQPLVKAGIVETVRG 59
M LT + Y + ++ A++ + P ++ I+E IS +L ++ L KAG+V++VRG
Sbjct: 1 MRLTTKGRYAVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRG 60
Query: 60 RRGGVRLCRPADQITILDVVKATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNA-F 118
GG +L RPA+ I++ D++ A +ES C K +C C LT L L+
Sbjct: 61 PGGGYQLGRPAEDISVADIIDAVDESVDATRCQG--KGNCRHGTRC-LTHDLWADLSKHI 117
Query: 119 FDVLTQYSIECLVRNRS 135
D L S+ LV ++
Sbjct: 118 RDYLESISLADLVNQQN 134
>gnl|CDD|182783 PRK10857, PRK10857, DNA-binding transcriptional regulator IscR;
Provisional.
Length = 164
Score = 49.9 bits (119), Expect = 2e-07
Identities = 39/136 (28%), Positives = 65/136 (47%), Gaps = 5/136 (3%)
Query: 1 MHLTKRTDYGIRVLMYCAIHNDY-PNRISQIAEACCISELFLFKILQPLVKAGIVETVRG 59
M LT + Y + ++ A++++ P ++ I+E IS +L ++ L K G+V +VRG
Sbjct: 1 MRLTSKGRYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRG 60
Query: 60 RRGGVRLCRPADQITILDVVKATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNA-F 118
GG L + A I + +V+ A +ES C K C C LT L + L+
Sbjct: 61 PGGGYLLGKDASSIAVGEVISAVDESVDATRC--QGKGGCQGGDKC-LTHALWRDLSDRL 117
Query: 119 FDVLTQYSIECLVRNR 134
L ++ LV N+
Sbjct: 118 TGFLNNITLGELVNNQ 133
>gnl|CDD|182885 PRK10991, fucI, L-fucose isomerase; Provisional.
Length = 588
Score = 29.2 bits (66), Expect = 0.38
Identities = 11/18 (61%), Positives = 12/18 (66%)
Query: 48 LVKAGIVETVRGRRGGVR 65
L K GI T+ GRR GVR
Sbjct: 4 LPKIGIRPTIDGRRMGVR 21
>gnl|CDD|184474 PRK14046, PRK14046, malate--CoA ligase subunit beta; Provisional.
Length = 392
Score = 28.5 bits (64), Expect = 0.71
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 49 VKAGIVETVRGRRGGVRLCRPADQI 73
VKA I RG+ GG++LCR +++
Sbjct: 45 VKAQIHSGARGKAGGIKLCRTYNEV 69
>gnl|CDD|162403 TIGR01531, glyc_debranch, glycogen debranching enzymye. glycogen
debranching enzyme possesses two different catalytic
activities; oligo-1,4-->1,4-glucantransferase (EC
2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33). Site
directed mutagenesis studies in S. cerevisiae indicate
that the transferase and glucosidase activities are
independent and located in different regions of the
polypeptide chain. Proteins in this model belong to the
larger alpha-amylase family. The model covers eukaryotic
proteins with a seed composed of human, nematode and
yeast sequences. Yeast seed sequence is well
characterized. The model is quite rigorous; either query
sequence yields large bit score or it fails to hit the
model altogether. There doesn't appear to be any middle
ground.
Length = 1464
Score = 28.3 bits (63), Expect = 0.77
Identities = 12/34 (35%), Positives = 22/34 (64%), Gaps = 1/34 (2%)
Query: 86 FFVAECFA-SHKIDCPLVGSCGLTSVLRKALNAF 118
+ VAE F S +D V G++S++R+A++A+
Sbjct: 537 YVVAELFTGSETLDNVFVNRLGISSLIREAMSAW 570
>gnl|CDD|181783 PRK09333, PRK09333, 30S ribosomal protein S19e; Provisional.
Length = 150
Score = 27.1 bits (61), Expect = 1.6
Identities = 12/20 (60%), Positives = 14/20 (70%), Gaps = 1/20 (5%)
Query: 43 KILQPLVKAGIVETV-RGRR 61
KILQ L KAG+VE +GR
Sbjct: 100 KILQQLEKAGLVEKTKKGRV 119
>gnl|CDD|177992 PLN02363, PLN02363, phosphoribosylanthranilate isomerase.
Length = 256
Score = 27.1 bits (60), Expect = 1.9
Identities = 13/30 (43%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 88 VAECFASHKIDCPLVGSCGLTSVLRKALNA 117
VA D PLV CG+TS R A A
Sbjct: 35 VAPKDDERGKDRPLVKMCGITSA-RDAAMA 63
>gnl|CDD|130161 TIGR01089, fucI, L-fucose isomerase. This enzyme catalyzes the
first step in fucose metabolism, and has been
characterized in Escherichia coli and Bacteroides
thetaiotaomicron.
Length = 587
Score = 26.4 bits (58), Expect = 3.0
Identities = 11/18 (61%), Positives = 12/18 (66%)
Query: 48 LVKAGIVETVRGRRGGVR 65
L K GI T+ GRR GVR
Sbjct: 3 LPKIGIRPTIDGRRMGVR 20
>gnl|CDD|162205 TIGR01108, oadA, oxaloacetate decarboxylase alpha subunit. This
model describes the bacterial oxaloacetate decarboxylase
alpha subunit and its equivalents in archaea. The
oxaloacetate decarboxylase Na+ pump is the paradigm of
the family of Na+ transport decarboxylases that present
in bacteria and archaea. It a multi subunit enzyme
consisting of a peripheral alpha-subunit and integral
membrane subunits beta and gamma. The energy released by
the decarboxylation reaction of oxaloacetate is coupled
to Na+ ion pumping across the membrane.
Length = 582
Score = 26.3 bits (58), Expect = 3.2
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 49 VKAGIVETVRGRRGGVRLCRPAD 71
+ A + + G + CRPAD
Sbjct: 375 INAELQRKILGDEKPIVDCRPAD 397
>gnl|CDD|172944 PRK14469, PRK14469, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 343
Score = 25.9 bits (57), Expect = 4.1
Identities = 6/21 (28%), Positives = 12/21 (57%)
Query: 112 RKALNAFFDVLTQYSIECLVR 132
R+ + F ++L + IE +R
Sbjct: 300 RERIERFKEILLKNGIEAEIR 320
>gnl|CDD|170049 PRK09692, PRK09692, integrase; Provisional.
Length = 413
Score = 25.8 bits (56), Expect = 4.5
Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 6/35 (17%)
Query: 41 LFKILQPLVKAGIVETVRGRRGGVRLCRPADQITI 75
L + +QP+ G +ETVR RLC+ +++ I
Sbjct: 155 LVQAVQPVQARGALETVR------RLCQRINEVMI 183
>gnl|CDD|171489 PRK12423, PRK12423, LexA repressor; Provisional.
Length = 202
Score = 25.9 bits (57), Expect = 4.5
Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 7/50 (14%)
Query: 36 ISELFLF-------KILQPLVKAGIVETVRGRRGGVRLCRPADQITILDV 78
I++ F F K +Q L +AG++E V + G+RL A + +L++
Sbjct: 31 IAQAFGFASRSVARKHVQALAEAGLIEVVPNQARGIRLPGGAGRPELLEL 80
>gnl|CDD|184952 PRK14990, PRK14990, anaerobic dimethyl sulfoxide reductase subunit
A; Provisional.
Length = 814
Score = 25.4 bits (55), Expect = 5.2
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 3/61 (4%)
Query: 87 FVAECFASHKIDCPLVGSCGLTSVL---RKALNAFFDVLTQYSIECLVRNRSSIKKIFNA 143
+ +C AS ++D L SCG S + + + F+ T Y + + R +++ F
Sbjct: 526 LLPDCTASEQMDFALDASCGNMSYVIFNDQVIKPRFECKTIYEMTSELAKRLGVEQQFTE 585
Query: 144 G 144
G
Sbjct: 586 G 586
>gnl|CDD|184448 PRK14010, PRK14010, potassium-transporting ATPase subunit B;
Provisional.
Length = 673
Score = 25.4 bits (55), Expect = 5.4
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 45 LQPLVKAGIVETVRGRRG-GVR--LCRPADQITILDVVKATEESFFVAECFASHKID 98
L+ ++K G+VE R R G+ +C +++T + K FVAEC KI+
Sbjct: 438 LKDVIKDGLVERFRELREMGIETVMCTGDNELTAATIAKEAGVDRFVAECKPEDKIN 494
>gnl|CDD|116493 pfam07881, Fucose_iso_N1, L-fucose isomerase, first N-terminal
domain. The members of this family are similar to
L-fucose isomerase expressed by E. coli (EC:5.3.1.3).
This enzyme corresponds to glucose-6-phosphate
isomerase in glycolysis, and converts an aldo-hexose to
a ketose to prepare it for aldol cleavage. The enzyme
is a hexamer, with each subunit being wedge-shaped and
composed of three domains. Both domains 1 and 2 contain
central parallel beta-sheets with surrounding alpha
helices. Domain 1 demonstrates the
beta-alpha-beta-alpha- beta Rossman fold. The active
centre is shared between pairs of subunits related
along the molecular three-fold axis, with domains 2 and
3 from one subunit providing most of the
substrate-contacting residues, and domain 1 from the
adjacent subunit contributing some other residues.
Length = 171
Score = 25.0 bits (55), Expect = 6.9
Identities = 11/16 (68%), Positives = 12/16 (75%)
Query: 50 KAGIVETVRGRRGGVR 65
K GI T+ GRRGGVR
Sbjct: 5 KIGIRPTIDGRRGGVR 20
>gnl|CDD|182200 PRK10026, PRK10026, arsenate reductase; Provisional.
Length = 141
Score = 24.8 bits (54), Expect = 8.8
Identities = 9/28 (32%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 63 GVRLCRPADQITILDVVKATEESFFVAE 90
G RLCRP++ +L+++ ++ F E
Sbjct: 102 GTRLCRPSE--VVLEILPDAQKGAFTKE 127
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
0.329 0.141 0.428
Gapped
Lambda K H
0.267 0.0639 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,209,520
Number of extensions: 126646
Number of successful extensions: 313
Number of sequences better than 10.0: 1
Number of HSP's gapped: 309
Number of HSP's successfully gapped: 27
Length of query: 144
Length of database: 5,994,473
Length adjustment: 84
Effective length of query: 60
Effective length of database: 4,179,401
Effective search space: 250764060
Effective search space used: 250764060
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 52 (24.0 bits)