RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14809
(90 letters)
>gnl|CDD|223581 COG0507, RecD, ATP-dependent exoDNAse (exonuclease V), alpha
subunit - helicase superfamily I member [DNA
replication, recombination, and repair].
Length = 696
Score = 41.7 bits (98), Expect = 8e-06
Identities = 24/94 (25%), Positives = 37/94 (39%), Gaps = 17/94 (18%)
Query: 1 MLRRNIDVSMGLVNGSIVYDLECVTTKFEVLPRAYV-----------HREQFSLCLEYAI 49
M RN D ++G+ NG I ++ V E L L YA+
Sbjct: 570 MQLRN-DRALGVFNGDIGV---ILSIVKRRQGDVLVVDFDGREVVVARSELPELELAYAM 625
Query: 50 TIHKCQGLSMNNALMDI--GSSVFSCGQAYVALS 81
TIHK QG + ++ + S + S Y A++
Sbjct: 626 TIHKSQGSEFDRVIVLLPSHSPMLSRELLYTAIT 659
>gnl|CDD|191413 pfam05970, PIF1, PIF1-like helicase. This family includes
homologues of the PIF1 helicase, which inhibits
telomerase activity and is cell cycle regulated. This
family includes a large number of largely
uncharacterized plant proteins. This family includes a
P-loop motif that is involved in nucleotide binding.
Length = 364
Score = 34.6 bits (80), Expect = 0.003
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 1 MLRRNIDVSMGLVNGS 16
ML RN+D S GL NG+
Sbjct: 342 MLLRNLDQSAGLCNGT 357
>gnl|CDD|237546 PRK13889, PRK13889, conjugal transfer relaxase TraA; Provisional.
Length = 988
Score = 33.1 bits (76), Expect = 0.009
Identities = 17/41 (41%), Positives = 21/41 (51%), Gaps = 13/41 (31%)
Query: 47 YAITIHKCQGLSMNNA------LMDIGSSVFSCGQAYVALS 81
YA TIHK QG++++ MD SS YVALS
Sbjct: 658 YAATIHKAQGMTVDRTHVLATPGMDAHSS-------YVALS 691
>gnl|CDD|233418 TIGR01448, recD_rel, helicase, putative, RecD/TraA family. This
model describes a family similar to RecD, the
exodeoxyribonuclease V alpha chain of TIGR01447. Members
of this family, however, are not found in a context of
RecB and RecC and are longer by about 200 amino acids at
the amino end. Chlamydia muridarum has both a member of
this family and a RecD [Unknown function, Enzymes of
unknown specificity].
Length = 720
Score = 31.3 bits (71), Expect = 0.043
Identities = 14/48 (29%), Positives = 21/48 (43%)
Query: 24 VTTKFEVLPRAYVHREQFSLCLEYAITIHKCQGLSMNNALMDIGSSVF 71
V F+ E F+L L YA +IHK QG ++ I ++
Sbjct: 626 VVVDFDGNEVELTRAELFNLTLAYATSIHKSQGSEFPTVILPIHTAHM 673
>gnl|CDD|214706 smart00516, SEC14, Domain in homologues of a S. cerevisiae
phosphatidylinositol transfer protein (Sec14p). Domain
in homologues of a S. cerevisiae phosphatidylinositol
transfer protein (Sec14p) and in RhoGAPs, RhoGEFs and
the RasGAP, neurofibromin (NF1). Lipid-binding domain.
The SEC14 domain of Dbl is known to associate with G
protein beta/gamma subunits.
Length = 158
Score = 28.8 bits (65), Expect = 0.25
Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 11/61 (18%)
Query: 17 IVYDLECVTTKFEVLPRAYVHREQFSLCLEYAITIHKCQGLSMNNALMDIGSSVFSCGQA 76
+VY LE + + E+ + +E I +GLSM+N + + + Q
Sbjct: 44 LVYVLEKI-----------LQEEKKTGGIEGFTVIFDLKGLSMSNPDLSVLRKILKILQD 92
Query: 77 Y 77
+
Sbjct: 93 H 93
>gnl|CDD|234003 TIGR02768, TraA_Ti, Ti-type conjugative transfer relaxase TraA.
This protein contains domains distinctive of a single
strand exonuclease (N-terminus, MobA/MobL, pfam03389) as
well as a helicase domain (central region, homologous to
the corresponding region of the F-type relaxase TraI,
TIGR02760). This protein likely fills the same role as
TraI(F), nicking (at the oriT site) and unwinding the
coiled plasmid prior to conjugative transfer.
Length = 744
Score = 29.0 bits (65), Expect = 0.30
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 5/45 (11%)
Query: 47 YAITIHKCQGLSMNNALMDIGSSVFSCGQAYVALS----SQNTYW 87
YA TIHK QG++++ A + + S AYVA++ S Y
Sbjct: 665 YATTIHKSQGVTVDRAFV-LASKSMDRHLAYVAMTRHRESVQLYA 708
>gnl|CDD|225447 COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell
division and chromosome partitioning].
Length = 272
Score = 28.4 bits (64), Expect = 0.39
Identities = 12/18 (66%), Positives = 14/18 (77%), Gaps = 1/18 (5%)
Query: 4 RNIDVSMGLVNGSIVYDL 21
RN+D+ MGL N IVYDL
Sbjct: 44 RNLDLIMGLEN-RIVYDL 60
>gnl|CDD|237524 PRK13826, PRK13826, Dtr system oriT relaxase; Provisional.
Length = 1102
Score = 27.4 bits (61), Expect = 0.95
Identities = 19/56 (33%), Positives = 24/56 (42%), Gaps = 8/56 (14%)
Query: 9 SMGLVNGSIVYDLECVTTKFEVLPRAYVHREQ------FSLCLE--YAITIHKCQG 56
S+G+ NG I +E + HR Q F L+ YA TIHK QG
Sbjct: 648 SLGVKNGMIGKVVEAAPNRIVAEIGEGEHRRQVTVEQRFYNNLDHGYATTIHKSQG 703
>gnl|CDD|178584 PLN03007, PLN03007, UDP-glucosyltransferase family protein.
Length = 482
Score = 27.1 bits (60), Expect = 1.0
Identities = 15/30 (50%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 27 KFEVLPRAYVH-REQFSLCLEYAITIHKCQ 55
KF V PR H FSLC Y I +HK Q
Sbjct: 141 KFGV-PRLVFHGTGYFSLCASYCIRVHKPQ 169
>gnl|CDD|131231 TIGR02176, pyruv_ox_red, pyruvate:ferredoxin (flavodoxin)
oxidoreductase, homodimeric. This model represents a
single chain form of pyruvate:ferredoxin (or flavodoxin)
oxidoreductase. This enzyme may transfer electrons to
nitrogenase in nitrogen-fixing species. Portions of this
protein are homologous to gamma subunit of the four
subunit pyruvate:ferredoxin (flavodoxin) oxidoreductase.
Length = 1165
Score = 27.4 bits (61), Expect = 1.1
Identities = 14/57 (24%), Positives = 20/57 (35%), Gaps = 10/57 (17%)
Query: 37 HREQFSLCLEYAITI---------HKCQGLSMNNALMDIGSSVFSCGQA-YVALSSQ 83
RE E+AI I +G L + + CG+ YV L +Q
Sbjct: 766 QREAQVANWEFAINIPEKDNKLNIDTVKGSQFQRPLFEFSGACSGCGETPYVKLLTQ 822
>gnl|CDD|222209 pfam13538, UvrD_C_2, Family description. This domain is found at
the C-terminus of a wide variety of helicase enzymes.
This domain has a AAA-like structural fold.
Length = 105
Score = 26.6 bits (59), Expect = 1.3
Identities = 7/11 (63%), Positives = 9/11 (81%)
Query: 47 YAITIHKCQGL 57
YA+TIHK +G
Sbjct: 58 YALTIHKAKGS 68
>gnl|CDD|220440 pfam09848, DUF2075, Uncharacterized conserved protein (DUF2075).
This domain, found in various prokaryotic proteins
(including putative ATP/GTP binding proteins), has no
known function.
Length = 348
Score = 26.8 bits (60), Expect = 1.4
Identities = 7/27 (25%), Positives = 14/27 (51%)
Query: 44 CLEYAITIHKCQGLSMNNALMDIGSSV 70
+E +I+ CQGL ++ + G +
Sbjct: 262 TIEEVGSIYTCQGLELDYVGVIWGPDL 288
>gnl|CDD|217188 pfam02689, Herpes_Helicase, Helicase. This family consists of
Helicases from the Herpes viruses. Helicases are
responsible for the unwinding of DNA and are essential
for replication and completion of the viral life cycle.
Length = 801
Score = 26.5 bits (59), Expect = 1.7
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 48 AITIHKCQGLSMNNALMDIGSSVF-SCGQAYVALS 81
A+TI K QGLS++ + G+ YVA+S
Sbjct: 725 AMTIAKSQGLSLDKVAICFGNHKNLKLSHVYVAMS 759
>gnl|CDD|223040 PHA03311, PHA03311, helicase-primase subunit BBLF4; Provisional.
Length = 782
Score = 26.8 bits (60), Expect = 1.7
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 48 AITIHKCQGLSMNNALMDIGSSVF-SCGQAYVALS 81
A+TI K QGLS++ + G+ YVA+S
Sbjct: 706 AMTIAKSQGLSLDKVAICFGNHKNLKLSHVYVAMS 740
>gnl|CDD|131023 TIGR01968, minD_bact, septum site-determining protein MinD. This
model describes the bacterial and chloroplast form of
MinD, a multifunctional cell division protein that
guides correct placement of the septum. The homologous
archaeal MinD proteins, with many archaeal genomes
having two or more forms, are described by a separate
model [Cellular processes, Cell division].
Length = 261
Score = 26.5 bits (59), Expect = 1.8
Identities = 10/18 (55%), Positives = 13/18 (72%), Gaps = 1/18 (5%)
Query: 4 RNIDVSMGLVNGSIVYDL 21
RN+D+ +GL N IVY L
Sbjct: 43 RNLDLLLGLEN-RIVYTL 59
>gnl|CDD|185330 PRK15432, PRK15432, autoinducer 2 ABC transporter permease LsrC;
Provisional.
Length = 344
Score = 25.8 bits (57), Expect = 3.7
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 1 MLRRNIDVSMGLVNG 15
ML RNIDVS+G + G
Sbjct: 58 MLTRNIDVSVGSITG 72
>gnl|CDD|237603 PRK14083, PRK14083, HSP90 family protein; Provisional.
Length = 601
Score = 25.3 bits (56), Expect = 4.6
Identities = 11/26 (42%), Positives = 14/26 (53%), Gaps = 4/26 (15%)
Query: 10 MGLVNGSIVYDLECVTTKFEVLPRAY 35
MG++NG YD E + E LPR
Sbjct: 411 MGVINGGYTYDSELL----ERLPRLR 432
>gnl|CDD|233417 TIGR01447, recD, exodeoxyribonuclease V, alpha subunit. This
family describes the exodeoxyribonuclease V alpha
subunit, RecD. RecD is part of a RecBCD complex. A
related family in the Gram-positive bacteria separates
in a phylogenetic tree, has an additional N-terminal
extension of about 200 residues, and is not supported as
a member of a RecBCD complex by neighboring genes. The
related family is consequently described by a different
model [DNA metabolism, DNA replication, recombination,
and repair].
Length = 586
Score = 25.1 bits (55), Expect = 6.2
Identities = 6/10 (60%), Positives = 9/10 (90%)
Query: 47 YAITIHKCQG 56
+A+T+HK QG
Sbjct: 522 FAMTVHKSQG 531
>gnl|CDD|176246 cd08286, FDH_like_ADH2, formaldehyde dehydrogenase (FDH)-like.
This group is related to formaldehyde dehydrogenase
(FDH), which is a member of the zinc-dependent/medium
chain alcohol dehydrogenase family. This family uses
NAD(H) as a cofactor in the interconversion of alcohols
and aldehydes, or ketones. Another member is identified
as a dihydroxyacetone reductase. Like the zinc-dependent
alcohol dehydrogenases (ADH) of the medium chain alcohol
dehydrogenase/reductase family (MDR), tetrameric FDHs
have a catalytic zinc that resides between the catalytic
and NAD(H)binding domains and a structural zinc in a
lobe of the catalytic domain. Unlike ADH, where
NAD(P)(H) acts as a cofactor, NADH in FDH is a tightly
bound redox cofactor (similar to nicotinamide proteins).
The medium chain alcohol dehydrogenase family (MDR) has
a NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit.
Length = 345
Score = 24.9 bits (55), Expect = 7.2
Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 4 RNIDVSMGLVN-GSIVYDLECVTTKFEVLPRAYV-HREQFSLCLEYAIT 50
+NI ++ GLV+ + L+ V++ ++ P V HR + S + T
Sbjct: 282 KNITITTGLVDTNTTPMLLKLVSSG-KLDPSKLVTHRFKLSEIEKAYDT 329
>gnl|CDD|173621 PTZ00431, PTZ00431, pyrroline carboxylate reductase; Provisional.
Length = 260
Score = 24.9 bits (54), Expect = 7.8
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 64 MDIGSSVFSCGQAYVAL 80
MDI +++ CG AYV L
Sbjct: 158 MDIATAISGCGPAYVFL 174
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
0.326 0.135 0.413
Gapped
Lambda K H
0.267 0.0735 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,247,146
Number of extensions: 316763
Number of successful extensions: 271
Number of sequences better than 10.0: 1
Number of HSP's gapped: 270
Number of HSP's successfully gapped: 22
Length of query: 90
Length of database: 10,937,602
Length adjustment: 58
Effective length of query: 32
Effective length of database: 8,365,070
Effective search space: 267682240
Effective search space used: 267682240
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 (21.7 bits)
S2: 53 (24.2 bits)