RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8083
(303 letters)
>gnl|CDD|112128 pfam03299, TF_AP-2, Transcription factor AP-2.
Length = 207
Score = 325 bits (834), Expect = e-113
Identities = 147/206 (71%), Positives = 176/206 (85%)
Query: 56 VFCSVPGRLSLLSSTSKYKVTVGEVQRRLSPPECLNASLLGGVLRRAKSKNGGRLLREKL 115
VFC VPGRLSLLSSTSKYKVTV EVQRRLSPPECLNASLLGGVLRRAKSKNGGRLLREKL
Sbjct: 2 VFCVVPGRLSLLSSTSKYKVTVAEVQRRLSPPECLNASLLGGVLRRAKSKNGGRLLREKL 61
Query: 116 EKIGLNLPAGRRKAANVTLLTSLVEGEAIHLARDFGYVCETEFPARQVAEYLSRQHTSDP 175
+KIGL LPAGRRKAANVTLLT+LVE EA+HLARDFGYVCETEFP+R +AE L+R+H +
Sbjct: 62 DKIGLTLPAGRRKAANVTLLTALVEEEAVHLARDFGYVCETEFPSRAIAEELTRKHLAPN 121
Query: 176 TESYRRKELIHATKQVTKELMDLLNQDRSPLCNTRPQHILDPSIQRHLTHFSLISHGFGS 235
+ RK ++ AT+++ KEL +LL+QDR P+ +RP+ L+PS+Q HL+HFSLI+HGFGS
Sbjct: 122 NDLDIRKNMLLATQKICKELTELLSQDRPPITGSRPKPKLEPSLQNHLSHFSLITHGFGS 181
Query: 236 PAIVAALTAIQNFLTESLKHLDKMYP 261
PAI A L ++QN + E+ K+LDK+Y
Sbjct: 182 PAICAVLRSLQNIINEAAKYLDKLYK 207
>gnl|CDD|192714 pfam11155, DUF2935, Domain of unknown function (DUF2935). This
family of proteins with unknown function appears to be
restricted to Firmicutes. The structure of this protein
has been solved and each domain is composed of four
alpha helices. A metal cluster composed of iron and
magnesium lies between the two domains.
Length = 124
Score = 30.7 bits (70), Expect = 0.32
Identities = 24/108 (22%), Positives = 35/108 (32%), Gaps = 27/108 (25%)
Query: 155 ETEFPARQVAEYLSRQHTS------DPTESYRRKELIHATKQVTKELMDLLNQDRSPLCN 208
E F R + E H DP E K+LI + KE LL +
Sbjct: 8 EHLFWLRIMKE-----HALFIRGLLDPKE----KKLIEEADEFKKEFEKLLLKAVELSGG 58
Query: 209 TRPQHILDPSIQRHLTHFSLISHGFGSPAIVAALTAIQNFLTESLKHL 256
R +L P++ L +L +NF E L+ +
Sbjct: 59 LRTSLVLFPAL-SRLNKEAL-----------ELTKEFRNFKKELLELI 94
>gnl|CDD|179443 PRK02551, PRK02551, flavoprotein NrdI; Provisional.
Length = 154
Score = 30.0 bits (68), Expect = 0.88
Identities = 10/35 (28%), Positives = 17/35 (48%)
Query: 160 ARQVAEYLSRQHTSDPTESYRRKELIHATKQVTKE 194
+++++YL+ QH K+LIH T E
Sbjct: 19 VKRLSDYLATQHKDIEVNPINIKDLIHETTDFFPE 53
>gnl|CDD|234667 PRK00149, dnaA, chromosomal replication initiation protein;
Reviewed.
Length = 401
Score = 30.5 bits (70), Expect = 1.1
Identities = 13/55 (23%), Positives = 23/55 (41%), Gaps = 17/55 (30%)
Query: 160 ARQVAEYLSRQHTSDPTESYRR--KEL--------IHATKQVTKELMDLLNQDRS 204
RQ+A YL+++ T S + +HA +++ K LL +D
Sbjct: 340 PRQIAMYLAKELTD---LSLPEIGRAFGGRDHTTVLHAVRKIEK----LLEEDPE 387
>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 29.6 bits (67), Expect = 2.4
Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 16/54 (29%)
Query: 160 ARQVAEYLSRQHTSDPTESYRR--KEL-------IHATKQVTKELMDLLNQDRS 204
RQ+A YL+R+ T+ S K +HA +++ + L+ +D S
Sbjct: 352 PRQIAMYLARELTNL---SLPEIGKAFGRDHTTVLHAVRKIEQ----LIEEDDS 398
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 28.9 bits (66), Expect = 3.8
Identities = 10/34 (29%), Positives = 18/34 (52%), Gaps = 4/34 (11%)
Query: 176 TESYRRKELI----HATKQVTKELMDLLNQDRSP 205
T+ R ++I AT +V K +M L++D+
Sbjct: 652 TDGERYNKVIDIWSKATDEVAKAMMKNLSKDQES 685
>gnl|CDD|233085 TIGR00675, dcm, DNA-methyltransferase (dcm). All proteins in this
family for which functions are known are DNA-cytosine
methyltransferases. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 315
Score = 28.4 bits (64), Expect = 4.0
Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 2/51 (3%)
Query: 41 IGDLPLLKRVSAPSDVFCSVPGRLSLLSSTSKYKVTVGEVQRRLSPPECLN 91
+++ +SA + V G S+L K V RRL+P EC
Sbjct: 230 ESKSSIIRTLSA--RGYTFVKGGKSVLIVPHKSTVVHPGRIRRLTPRECAR 278
>gnl|CDD|232941 TIGR00362, DnaA, chromosomal replication initiator protein DnaA.
DnaA is involved in DNA biosynthesis; initiation of
chromosome replication and can also be transcription
regulator. The C-terminal of the family hits the pfam
bacterial DnaA (bac_dnaA) domain family. For a review,
see Kaguni (2006) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 405
Score = 28.6 bits (65), Expect = 4.8
Identities = 6/14 (42%), Positives = 10/14 (71%)
Query: 160 ARQVAEYLSRQHTS 173
RQ+A YL+++ T
Sbjct: 377 PRQIAMYLAKELTD 390
>gnl|CDD|234570 PRK00009, PRK00009, phosphoenolpyruvate carboxylase; Reviewed.
Length = 911
Score = 28.6 bits (65), Expect = 4.9
Identities = 14/65 (21%), Positives = 26/65 (40%), Gaps = 6/65 (9%)
Query: 146 LARDFGYVCETEFPARQVAEYLSRQH-----TSDPTESYRRKELIHATKQVTKELMDLLN 200
LA + ++A L T+ PTE +R+ L+ +++ L L +
Sbjct: 109 LAETLRRLKAAGVSPEELARALEELDIEPVLTAHPTEV-QRRTLLDKQREIAALLRQLDD 167
Query: 201 QDRSP 205
D +P
Sbjct: 168 VDLTP 172
>gnl|CDD|197863 smart00760, Bac_DnaA_C, Bacterial dnaA protein helix-turn-helix
domain. Could be involved in DNA-binding.
Length = 69
Score = 26.3 bits (59), Expect = 5.4
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 160 ARQVAEYLSRQHTSDPTE 177
ARQ+A YL+R+ T
Sbjct: 32 ARQIAMYLARELTDLSLP 49
>gnl|CDD|119330 cd06571, Bac_DnaA_C, C-terminal domain of bacterial DnaA proteins.
The DNA-binding C-terminal domain of DnaA contains a
helix-turn-helix motif that specifically interacts with
the DnaA box, a 9-mer motif that occurs repetitively in
the replication origin oriC. Multiple copies of DnaA,
which is an ATPase, bind to 9-mers at the origin and
form an initial complex in which the DNA strands are
being separated in an ATP-dependent step.
Length = 90
Score = 25.9 bits (58), Expect = 9.5
Identities = 11/43 (25%), Positives = 24/43 (55%), Gaps = 7/43 (16%)
Query: 160 ARQVAEYLSRQHTSDPT----ESYRRKE---LIHATKQVTKEL 195
ARQ+A YL+R+ T ++ ++ ++HA +++ + L
Sbjct: 31 ARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELL 73
>gnl|CDD|227061 COG4717, COG4717, Uncharacterized conserved protein [Function
unknown].
Length = 984
Score = 27.9 bits (62), Expect = 9.7
Identities = 6/27 (22%), Positives = 11/27 (40%)
Query: 177 ESYRRKELIHATKQVTKELMDLLNQDR 203
+ + + + TKEL D L +
Sbjct: 680 QKEEARLALEGNIERTKELNDELRAEL 706
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.317 0.132 0.382
Gapped
Lambda K H
0.267 0.0830 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,938,725
Number of extensions: 1409262
Number of successful extensions: 1253
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1253
Number of HSP's successfully gapped: 15
Length of query: 303
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 207
Effective length of database: 6,679,618
Effective search space: 1382680926
Effective search space used: 1382680926
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 (21.6 bits)
S2: 59 (26.3 bits)