RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780554|ref|YP_003064967.1| Holliday junction resolvase
[Candidatus Liberibacter asiaticus str. psy62]
(169 letters)
>gnl|CDD|178813 PRK00039, ruvC, Holliday junction resolvase; Reviewed.
Length = 164
Score = 232 bits (594), Expect = 4e-62
Identities = 78/157 (49%), Positives = 111/157 (70%), Gaps = 1/157 (0%)
Query: 5 IRIIGIDPGLRRTGWGIVDVAGDNLCFVSSGTIVSCVRQSLAFRLCQLYEGLTDVIKNWR 64
+RI+GIDPGLRRTG+G+++V G L +V+SG I + L RL Q+Y+GL+++I ++
Sbjct: 2 MRILGIDPGLRRTGYGVIEVEGRRLSYVASGVIRTPSDLDLPERLKQIYDGLSELIDEYQ 61
Query: 65 PEEAAVEQVFVNKDAVATLKLGQARAIAILSPALARIPVSEYAPNTIKKAVIGVGHGDKK 124
P+E A+E+VF NK+ + LKLGQAR +AIL+ A +PV+EY P +KKAV+G G DK+
Sbjct: 62 PDEVAIEEVFFNKNPQSALKLGQARGVAILAAAQRGLPVAEYTPLQVKKAVVGYGRADKE 121
Query: 125 QIHMMLKMLMP-ESFFKGKDAADALAIAVCHAYHANS 160
Q+ M+K L+ K DAADALAIA+CHA+ S
Sbjct: 122 QVQHMVKRLLNLPEIPKPDDAADALAIAICHAHRRQS 158
>gnl|CDD|129331 TIGR00228, ruvC, crossover junction endodeoxyribonuclease RuvC.
Endonuclease that resolves Holliday junction
intermediates in genetic recombination. The active form
of the protein is a dimer. Structure studies reveals
that the catalytic center, comprised of four acidic
residues, lies at the bottom of a cleft that fits a DNA
duplex. The model hits a single Synechocystis PCC6803
protein at a score of 30, below the trusted cutoff, that
appears orthologous and may act as authentic RuvC.
Length = 156
Score = 130 bits (327), Expect = 3e-31
Identities = 64/150 (42%), Positives = 96/150 (64%), Gaps = 1/150 (0%)
Query: 7 IIGIDPGLRRTGWGIVDVAGDNLCFVSSGTIVSCVRQSLAFRLCQLYEGLTDVIKNWRPE 66
I+GIDPG R TG+G++ G L ++ SG I + V L RL +Y G+T++I ++P
Sbjct: 1 ILGIDPGSRVTGYGVIRQVGRQLSYLGSGCIRTKV-DDLPSRLKLIYAGVTEIITQFQPN 59
Query: 67 EAAVEQVFVNKDAVATLKLGQARAIAILSPALARIPVSEYAPNTIKKAVIGVGHGDKKQI 126
A+EQVF+ K+A + LKLGQAR +AI++ +PV EYA +K+ V+G+G +K Q+
Sbjct: 60 YFAIEQVFMAKNADSALKLGQARGVAIVAAVNQELPVFEYAARQVKQTVVGIGSAEKSQV 119
Query: 127 HMMLKMLMPESFFKGKDAADALAIAVCHAY 156
M++ L+ DAADALAIA+ HA+
Sbjct: 120 QHMVRRLLKLPANPQADAADALAIAITHAH 149
>gnl|CDD|185216 PRK15316, PRK15316, RatA-like protein; Provisional.
Length = 2683
Score = 29.6 bits (66), Expect = 0.38
Identities = 13/37 (35%), Positives = 24/37 (64%), Gaps = 1/37 (2%)
Query: 80 VATLKLGQARAIAILSPALARIPVSEYAPNTIKKAVI 116
AT+++ Q++ + + +P L +PV+ Y PNT+ VI
Sbjct: 813 FATVEIKQSQGVGLSTP-LNIVPVNSYIPNTVNYNVI 848
>gnl|CDD|149657 pfam08672, APC2, Anaphase promoting complex (APC) subunit 2. The
anaphase promoting complex or cyclosome (APC2) is an E3
ubiquitin ligase which is part of the SCF family of
ubiquitin ligases. Ubiquitin ligases catalyse the
transfer of ubiquitin from the ubiquitin conjugating
enzyme (E2), to the substrate protein.
Length = 60
Score = 28.0 bits (63), Expect = 1.4
Identities = 6/11 (54%), Positives = 7/11 (63%)
Query: 125 QIHMMLKMLMP 135
+IH MLKM
Sbjct: 16 RIHSMLKMFPK 26
>gnl|CDD|128971 smart00732, YqgFc, Likely ribonuclease with RNase H fold. YqgF
proteins are likely to function as an alternative to
RuvC in most bacteria, and could be the principal
holliday junction resolvases in low-GC Gram-positive
bacteria. In Spt6p orthologues, the catalytic residues
are substituted indicating that they lack enzymatic
functions.
Length = 99
Score = 27.9 bits (63), Expect = 1.4
Identities = 13/66 (19%), Positives = 26/66 (39%), Gaps = 9/66 (13%)
Query: 5 IRIIGIDPGLRRTGWGIVDVAGDNLCFVSSGTIVSCVRQSLAFRLCQLYEGLTDVIKNWR 64
R++G+DPG + G +VD G ++ + L +IK ++
Sbjct: 1 KRVLGLDPGRKGIGVAVVDETGK---LADPLEVIPRTNKEADAAR------LKKLIKKYQ 51
Query: 65 PEEAAV 70
P+ +
Sbjct: 52 PDLIVI 57
>gnl|CDD|162338 TIGR01398, FlhA, flagellar biosynthesis protein FlhA. This model
describes flagellar biosynthesis protein FlhA, one of a
large number of genes associated with the biosynthesis
of functional bacterial flagella. Homologs of many such
proteins, including FlhA, function in type III protein
secretion systems. A separate model describes InvA
(Salmonella enterica), LcrD (Yersinia enterocolitica),
HrcV (Xanthomonas), etc., all of which score below the
noise cutoff for this model.
Length = 678
Score = 27.6 bits (62), Expect = 1.7
Identities = 14/64 (21%), Positives = 22/64 (34%), Gaps = 6/64 (9%)
Query: 37 IVSCVRQSLAFRLCQLYEGLTDVIKNWRPEEAAVEQVFVNKDAVATLKLGQARAIAILSP 96
+V VRQ L ++ Q Y V+ + +E L+ + L P
Sbjct: 558 LVEHVRQRLGRQITQQYLDEDGVLPVIT-LDPDLEAALAEA-----LQRDGEGELLDLEP 611
Query: 97 ALAR 100
AL
Sbjct: 612 ALLE 615
>gnl|CDD|168156 PRK05656, PRK05656, acetyl-CoA acetyltransferase; Provisional.
Length = 393
Score = 26.8 bits (59), Expect = 3.3
Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 2/45 (4%)
Query: 75 VNKDAVATLKLGQARAIAILSPALARIPVSEYAPNTIKKAVIGVG 119
+N A A L + A+A A+ P LA+I + YA + A++G+G
Sbjct: 250 LNDGAAAVLLMSAAKAKALGLPVLAKI--AAYANAGVDPAIMGIG 292
>gnl|CDD|181176 PRK07942, PRK07942, DNA polymerase III subunit epsilon;
Provisional.
Length = 232
Score = 26.5 bits (59), Expect = 3.4
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 78 DAVATLKLGQARAIAILSPALARIPVSE 105
DA+A ++ A A+A P LA + +E
Sbjct: 165 DALAAARV--AWALARRFPELAALSPAE 190
>gnl|CDD|180448 PRK06182, PRK06182, short chain dehydrogenase; Validated.
Length = 273
Score = 26.5 bits (59), Expect = 3.9
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 5 IRIIGIDPGLRRTGWGIVDVAGDNLCFVSSGT 36
I ++ I+PG +T WG D+A D+L S
Sbjct: 169 IDVVVIEPGGIKTEWG--DIAADHLLKTSGNG 198
>gnl|CDD|165505 PHA03246, PHA03246, large tegument protein UL36; Provisional.
Length = 3095
Score = 26.1 bits (57), Expect = 4.7
Identities = 13/29 (44%), Positives = 17/29 (58%)
Query: 32 VSSGTIVSCVRQSLAFRLCQLYEGLTDVI 60
+S G+ VSC+R SLAF GL V+
Sbjct: 89 LSPGSSVSCLRSSLAFLRIVFAYGLDTVL 117
>gnl|CDD|162567 TIGR01865, cas_Csn1, CRISPR-associated protein, Csn1 family.
CRISPR loci appear to be mobile elements with a wide
host range. This model represents a protein found only
in CRISPR-containing species, near other
CRISPR-associated proteins (cas), as part of the NMENI
subtype of CRISPR/Cas locus. The species range so far
for this protein is animal pathogens and commensals
only.
Length = 805
Score = 25.5 bits (56), Expect = 6.7
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 6 RIIGIDPGLRRTGWGIVD 23
I+G+D G+ GW IV+
Sbjct: 2 YILGLDIGIASVGWAIVE 19
>gnl|CDD|178870 PRK00109, PRK00109, Holliday junction resolvase-like protein;
Reviewed.
Length = 138
Score = 25.5 bits (57), Expect = 7.3
Identities = 17/66 (25%), Positives = 27/66 (40%), Gaps = 13/66 (19%)
Query: 4 SIRIIGIDPGLRRTGWGIVDVA-GDNLCFVSSG-TIVSCVRQSLAFRLCQLYEGLTDVIK 61
S RI+G+D G +R G VA D L + + + + L +IK
Sbjct: 3 SGRILGLDVGTKRIG-----VAVSDPLGGTAQPLETIKRNNGTPDWDR------LEKLIK 51
Query: 62 NWRPEE 67
W+P+
Sbjct: 52 EWQPDG 57
>gnl|CDD|132144 TIGR03100, hydr1_PEP, hydrolase, ortholog 1, exosortase system type
1 associated. This group of proteins are members of the
alpha/beta hydrolase superfamily. These proteins are
generally found in genomes containing the
exosortase/PEP-CTERM protein expoert system,
specifically the type 1 variant of this system described
by the Genome Property GenProp0652. When found in this
context they are invariably present in the vicinity of a
second, relatively unrelated enzyme (ortholog 2,
TIGR03101) of the same superfamily.
Length = 274
Score = 25.2 bits (55), Expect = 8.1
Identities = 12/49 (24%), Positives = 18/49 (36%)
Query: 47 FRLCQLYEGLTDVIKNWRPEEAAVEQVFVNKDAVATLKLGQARAIAILS 95
L GL D + R + V + + A L+ Q + ILS
Sbjct: 167 VNLGSSLRGLGDALLKARQKGDEVAHGGLAERMKAGLERFQGPVLFILS 215
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
0.323 0.136 0.406
Gapped
Lambda K H
0.267 0.0637 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,794,783
Number of extensions: 171822
Number of successful extensions: 316
Number of sequences better than 10.0: 1
Number of HSP's gapped: 313
Number of HSP's successfully gapped: 20
Length of query: 169
Length of database: 5,994,473
Length adjustment: 87
Effective length of query: 82
Effective length of database: 4,114,577
Effective search space: 337395314
Effective search space used: 337395314
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 (24.4 bits)