RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15079
(74 letters)
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 42.1 bits (100), Expect = 4e-07
Identities = 12/18 (66%), Positives = 15/18 (83%)
Query: 1 MTDAQVKTWFQNRRTKWR 18
+T+ QVK WFQNRR KW+
Sbjct: 39 LTERQVKVWFQNRRAKWK 56
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 37.6 bits (88), Expect = 2e-05
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 1 MTDAQVKTWFQNRRTKWR 18
+++ QVK WFQNRR KW+
Sbjct: 40 LSERQVKVWFQNRRAKWK 57
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved
in the transcriptional regulation of key eukaryotic
developmental processes; may bind to DNA as monomers or
as homo- and/or heterodimers, in a sequence-specific
manner.
Length = 59
Score = 36.8 bits (86), Expect = 5e-05
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 1 MTDAQVKTWFQNRRTKWR 18
+T+ QVK WFQNRR K +
Sbjct: 39 LTERQVKIWFQNRRAKLK 56
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 29.7 bits (67), Expect = 0.068
Identities = 13/69 (18%), Positives = 23/69 (33%), Gaps = 5/69 (7%)
Query: 1 MTDAQVKTWFQNRRTKWRPFSFEGVSKSKHIVVRPLIDKVNLYVIEA-VWTVLSALIDVN 59
M V+ WFQN+R K + V + L +L + + L +
Sbjct: 90 MPPKSVQIWFQNKRAKEKKKRSGKVEQRPGEEEADLAKIGSLSTGQISIIETLE----FS 145
Query: 60 RWPVDQDFS 68
R ++
Sbjct: 146 RTSYEEGGL 154
>gnl|CDD|237873 PRK14969, PRK14969, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 527
Score = 28.2 bits (63), Expect = 0.28
Identities = 11/22 (50%), Positives = 13/22 (59%), Gaps = 1/22 (4%)
Query: 16 KWRPFSFEGVSKSKHIVVRPLI 37
KWRP SF + +H VVR L
Sbjct: 9 KWRPKSFSELVGQEH-VVRALT 29
>gnl|CDD|181392 PRK08332, PRK08332, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 1740
Score = 25.9 bits (56), Expect = 2.6
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 43 YVIEAVWTVLSALIDVNRWPVDQDFSNNQIDR 74
YVI+ V L IDVN++P+ + N ++ R
Sbjct: 1336 YVIQKVAKYLDNAIDVNKFPLPEIDYNTKLTR 1367
>gnl|CDD|184925 PRK14961, PRK14961, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 363
Score = 25.5 bits (56), Expect = 2.7
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 16 KWRPFSFEGVSKSKHIV 32
KWRP F + KHIV
Sbjct: 9 KWRPQYFRDIIGQKHIV 25
>gnl|CDD|235505 PRK05563, PRK05563, DNA polymerase III subunits gamma and tau;
Validated.
Length = 559
Score = 24.4 bits (54), Expect = 5.9
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 16 KWRPFSFEGVSKSKHIV 32
KWRP +FE V +HI
Sbjct: 9 KWRPQTFEDVVGQEHIT 25
>gnl|CDD|233900 TIGR02504, NrdJ_Z, ribonucleoside-diphosphate reductase,
adenosylcobalamin-dependent. This model represents a
group of adenosylcobalamin(B12)-dependent ribonucleotide
reductases (Class II RNRs) related to the characterized
species from Pyrococcus , Thermoplasma , Corynebacterium
and Deinococcus. RNR's are responsible for the
conversion of the ribose sugar of RNA into the
deoxyribose sugar of DNA. This is the rate-limiting step
of DNA biosynthesis. This model identifies genes in a
wide range of deeply branching bacteria. All are
structurally related to the class I (non-heme iron
dependent) RNRs. In most species this gene is known as
NrdJ, while in mycobacteria it is called NrdZ [Purines,
pyrimidines, nucleosides, and nucleotides,
2'-Deoxyribonucleotide metabolism].
Length = 589
Score = 24.6 bits (54), Expect = 6.4
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 43 YVIEAVWTVLSALIDVNRWPVDQ 65
V+ L +ID+NR+P+ +
Sbjct: 314 EVVRLATRFLDNVIDLNRFPLPE 336
>gnl|CDD|176871 cd08862, SRPBCC_Smu440-like, Ligand-binding SRPBCC domain of
Streptococcus mutans Smu.440 and related proteins.
This family includes the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of
Streptococcus mutans Smu.440 and related proteins. This
domain belongs to the SRPBCC domain superfamily of
proteins that bind hydrophobic ligands. SRPBCC domains
have a deep hydrophobic ligand-binding pocket.
Streptococcus mutans is a dental pathogen, and the
leading cause of dental caries. In this pathogen, the
gene encoding Smu.440 is in the same operon as the gene
encoding SMU.441, a member of the MarR protein family
of transcriptional regulators involved in multiple
antibiotic resistance. It has been suggested that
SMU.440 is involved in polyketide-like antibiotic
resistance.
Length = 138
Score = 23.9 bits (52), Expect = 7.9
Identities = 9/18 (50%), Positives = 10/18 (55%), Gaps = 3/18 (16%)
Query: 46 EAVWTVLSALIDVNRWPV 63
E VW VL+ DV WP
Sbjct: 14 ERVWAVLT---DVENWPA 28
>gnl|CDD|177187 MTH00129, COX2, cytochrome c oxidase subunit II; Provisional.
Length = 230
Score = 23.9 bits (52), Expect = 8.1
Identities = 8/12 (66%), Positives = 10/12 (83%)
Query: 45 IEAVWTVLSALI 56
IE +WTVL A+I
Sbjct: 61 IEIIWTVLPAVI 72
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
0.323 0.134 0.432
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,711,614
Number of extensions: 272351
Number of successful extensions: 204
Number of sequences better than 10.0: 1
Number of HSP's gapped: 204
Number of HSP's successfully gapped: 16
Length of query: 74
Length of database: 10,937,602
Length adjustment: 44
Effective length of query: 30
Effective length of database: 8,986,026
Effective search space: 269580780
Effective search space used: 269580780
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 (22.0 bits)
S2: 53 (24.1 bits)