RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4407
(130 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 28.5 bits (64), Expect = 0.12
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 82 HIKEHIRQHTGEKPFSCLLCEYK 104
+++ H+R HTGEKP+ C +C
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKS 23
>gnl|CDD|184955 PRK14993, PRK14993, tetrathionate reductase subunit B; Provisional.
Length = 244
Score = 30.2 bits (68), Expect = 0.21
Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 6/32 (18%)
Query: 35 CKYCYEFLPNDAEII------ADHCKFCSYKL 60
C YC + P DA I AD C FC ++L
Sbjct: 135 CAYCVQACPYDARFINHETQTADKCTFCVHRL 166
>gnl|CDD|234698 PRK00236, xerC, site-specific tyrosine recombinase XerC; Reviewed.
Length = 297
Score = 30.1 bits (69), Expect = 0.24
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 6 RSYYVLFLFYSSGLKVSE 23
R +L L Y SGL++SE
Sbjct: 137 RDRAILELLYGSGLRLSE 154
>gnl|CDD|132329 TIGR03286, methan_mark_15, putative methanogenesis marker protein
15. Members of this protein family, to date, are found
in a completed prokaryotic genome if and only if the
species is one of the archaeal methanogens. The exact
function is unknown, but likely is linked to
methanogenesis or a process closely connected to it.
Related proteins include the BadF/BadG/BcrA/BcrD ATPase
family (pfam01869), which includes an activator for
(R)-2-hydroxyglutaryl-CoA dehydratase [Energy
metabolism, Methanogenesis].
Length = 404
Score = 29.8 bits (67), Expect = 0.40
Identities = 9/29 (31%), Positives = 18/29 (62%)
Query: 63 DKTYIFTCFACEYHSAKRSHIKEHIRQHT 91
D +I TCF C + R+ ++ +I+++T
Sbjct: 74 DAVFIATCFRCAEGALVRNEVRRYIQENT 102
>gnl|CDD|238413 cd00798, INT_XerDC, XerD and XerC integrases, DNA
breaking-rejoining enzymes, N- and C-terminal domains.
XerD-like integrases are involved in the site-specific
integration and excision of lysogenic bacteriophage
genomes, transposition of conjugative transposons,
termination of chromosomal replication, and stable
plasmid inheritance. They share the same fold in their
catalytic domain containing six conserved active site
residues and the overall reaction mechanism with the DNA
breaking-rejoining enzyme superfamily. In Escherichia
coli, the Xer site-specific recombination system acts to
convert dimeric chromosomes, which are formed by
homologous recombination to monomers. Two related
recombinases, XerC and XerD, bind cooperatively to a
recombination site present in the E. coli chromosome.
Each recombinase catalyzes the exchange of one pair of
DNA strand in a reaction that proceeds through a
Holliday junction intermediate. These enzymes can bridge
two different and well-separated DNA sequences called
arm- and core-sites. The C-terminal domain binds,
cleaves and re-ligates DNA strands at the core-sites,
while the N-terminal domain is largely responsible for
high-affinity binding to the arm-type sites.
Length = 284
Score = 27.9 bits (63), Expect = 1.3
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 10 VLFLFYSSGLKVSEV 24
+L L YS+GL+VSE+
Sbjct: 132 LLELLYSTGLRVSEL 146
>gnl|CDD|227307 COG4973, XerC, Site-specific recombinase XerC [DNA replication,
recombination, and repair].
Length = 299
Score = 27.7 bits (62), Expect = 1.8
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 6 RSYYVLFLFYSSGLKVSEV 24
R +L L Y SGL++SE+
Sbjct: 136 RDRALLELMYGSGLRLSEL 154
>gnl|CDD|233788 TIGR02224, recomb_XerC, tyrosine recombinase XerC. The phage
integrase family describes a number of recombinases with
tyrosine active sites that transiently bind covalently
to DNA. Many are associated with mobile DNA elements,
including phage, transposons, and phase variation loci.
This model represents XerC, one of two closely related
chromosomal proteins along with XerD (TIGR02225). XerC
and XerD are site-specific recombinases which help
resolve chromosome dimers to monomers for cell division
after DNA replication. In species with a large
chromosome and homologs of XerC on other replicons, the
chomosomal copy was preferred for building this model.
This model does not detect all XerC, as some apparent
XerC examples score in the gray zone between trusted
(450) and noise (410) cutoffs, along with some XerD
examples. XerC and XerD interact with cell division
protein FtsK [DNA metabolism, DNA replication,
recombination, and repair].
Length = 295
Score = 27.6 bits (62), Expect = 2.0
Identities = 10/14 (71%), Positives = 12/14 (85%)
Query: 10 VLFLFYSSGLKVSE 23
+L L YSSGL+VSE
Sbjct: 134 ILELLYSSGLRVSE 147
>gnl|CDD|171495 PRK12434, PRK12434, tRNA pseudouridine synthase A; Reviewed.
Length = 245
Score = 27.0 bits (60), Expect = 2.5
Identities = 14/58 (24%), Positives = 27/58 (46%), Gaps = 6/58 (10%)
Query: 24 VDFRF-ETEMLTCKYCYEFLPND---AEIIADHCKFCSYKLRPDKTYIFTCFACEYHS 77
D + E ++ KY E+LPND + +F + KTY++ + ++H+
Sbjct: 67 TDEKLSEDKIK--KYLNEYLPNDIVVTNVEEVDERFHARYNVKSKTYLYKIWNEKFHN 122
>gnl|CDD|130763 TIGR01702, CO_DH_cata, carbon-monoxide dehydrogenase, catalytic
subunit. This model represents the carbon-monoxide
dehydrogenase catalytic subunit. This protein is
related to prismane (also called hybrid cluster
protein), a complex whose activity is not yet fully
described; the two share similar sets of ligands to
unusual metal-containing clusters.
Length = 621
Score = 27.4 bits (61), Expect = 2.8
Identities = 10/42 (23%), Positives = 15/42 (35%), Gaps = 9/42 (21%)
Query: 16 SSGLKVSEVDFRFETEMLTCKYCYEFLPNDAEIIADHCKFCS 57
+ V RFE + CK+ E L C+ C+
Sbjct: 13 AKDDGVETAFDRFEAQQPQCKFGLEGL---------CCRLCA 45
>gnl|CDD|235696 PRK06092, PRK06092, 4-amino-4-deoxychorismate lyase; Reviewed.
Length = 268
Score = 26.7 bits (60), Expect = 3.9
Identities = 12/39 (30%), Positives = 14/39 (35%), Gaps = 5/39 (12%)
Query: 10 VLFLFYSSGLKVSEVDFRFET-----EMLTCKYCYEFLP 43
+L L SG V EVD E E+ C P
Sbjct: 205 ILELLAQSGYPVVEVDASLEELLQADEVFICNSLMPVWP 243
>gnl|CDD|221755 pfam12756, zf-C2H2_2, C2H2 type zinc-finger (2 copies). This
family contains two copies of a C2H2-like zinc finger
domain.
Length = 100
Score = 25.3 bits (56), Expect = 7.4
Identities = 7/23 (30%), Positives = 10/23 (43%)
Query: 97 SCLLCEYKAAKKSNLTKHMSKKH 119
CL C + + +HM K H
Sbjct: 1 DCLFCNHTSDTVEENLEHMFKSH 23
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 25.8 bits (56), Expect = 9.6
Identities = 14/58 (24%), Positives = 19/58 (32%), Gaps = 3/58 (5%)
Query: 60 LRPDKTYIFTCFACEYHSAKRS---HIKEHIRQHTGEKPFSCLLCEYKAAKKSNLTKH 114
+ +C + S H+ HIR HTGEKP C + L
Sbjct: 23 TLKSLSNAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELS 80
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
0.325 0.136 0.433
Gapped
Lambda K H
0.267 0.0672 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,253,039
Number of extensions: 505365
Number of successful extensions: 683
Number of sequences better than 10.0: 1
Number of HSP's gapped: 681
Number of HSP's successfully gapped: 39
Length of query: 130
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 44
Effective length of database: 7,123,158
Effective search space: 313418952
Effective search space used: 313418952
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.3 bits)