RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8717
(69 letters)
>gnl|CDD|214662 smart00436, TOP1Bc, Bacterial DNA topoisomeraes I ATP-binding
domain. Extension of TOPRIM in Bacterial DNA
topoisomeraes I and III, Eukaryotic DNA topoisomeraes
III, reverse gyrase beta subunit.
Length = 89
Score = 61.4 bits (150), Expect = 1e-14
Identities = 18/35 (51%), Positives = 23/35 (65%)
Query: 21 LDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYW 55
L ++S G QTPTLG VER +I+ F P+PYW
Sbjct: 54 LRNGVLSAGRVQTPTLGLIVEREREIKNFVPKPYW 88
>gnl|CDD|238110 cd00186, TOP1Ac, DNA Topoisomerase, subtype IA; DNA-binding,
ATP-binding and catalytic domain of bacterial DNA
topoisomerases I and III, and eukaryotic DNA
topoisomerase III and eubacterial and archael reverse
gyrases. Topoisomerases clevage single or double
stranded DNA and then rejoin the broken phosphodiester
backbone. Proposed catalytic mechanism of single
stranded DNA cleavage is by phosphoryl transfer through
a tyrosine nucleophile using acid/base catalysis. Tyr
is activated by a nearby group (not yet identified)
acting as a general base for nucleophilic attack on the
5' phosphate of the scissile bond. Arg and Lys
stabilize the pentavalent transition state. Glu then
acts as a proton donor for the leaving 3'-oxygen, upon
cleavage of the scissile strand.
Length = 381
Score = 63.8 bits (156), Expect = 6e-14
Identities = 16/34 (47%), Positives = 22/34 (64%)
Query: 24 SLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLL 57
++S G Q+PTLG VER +I+ F PE YW +
Sbjct: 33 GVLSAGRVQSPTLGLIVEREREIKAFVPEDYWEI 66
>gnl|CDD|216317 pfam01131, Topoisom_bac, DNA topoisomerase. This subfamily of
topoisomerase is divided on the basis that these
enzymes preferentially relax negatively supercoiled
DNA, from a 5' phospho- tyrosine linkage in the
enzyme-DNA covalent intermediate and has high affinity
for single stranded DNA.
Length = 365
Score = 59.5 bits (145), Expect = 2e-12
Identities = 18/30 (60%), Positives = 20/30 (66%)
Query: 26 ISYGPCQTPTLGFCVERHDKIRTFKPEPYW 55
+S G QTPTLG VER +I F PEPYW
Sbjct: 37 LSAGRVQTPTLGLIVEREKEIENFVPEPYW 66
>gnl|CDD|235971 PRK07219, PRK07219, DNA topoisomerase I; Validated.
Length = 822
Score = 57.3 bits (139), Expect = 1e-11
Identities = 18/37 (48%), Positives = 24/37 (64%)
Query: 26 ISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLN 62
+S G QTPTL F V+R +IR F PE YW ++ L+
Sbjct: 192 LSVGRVQTPTLAFIVDREREIRAFDPEDYWKIEALLD 228
>gnl|CDD|223624 COG0550, TopA, Topoisomerase IA [DNA replication, recombination,
and repair].
Length = 570
Score = 55.7 bits (135), Expect = 4e-11
Identities = 15/42 (35%), Positives = 20/42 (47%)
Query: 21 LDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLN 62
L ++S G Q+P L VER +I F PE YW +
Sbjct: 162 LKRGVLSAGRVQSPALRLVVEREREIEAFVPEEYWEIKAIFE 203
>gnl|CDD|184936 PRK14973, PRK14973, DNA topoisomerase I; Provisional.
Length = 936
Score = 49.1 bits (117), Expect = 1e-08
Identities = 18/45 (40%), Positives = 27/45 (60%)
Query: 24 SLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGEWV 68
+++S G Q+PTL V+R +I F PE YW+L L +GE +
Sbjct: 189 NILSVGRVQSPTLAMIVDREKEIEAFVPEKYWMLSLATEKDGEGI 233
>gnl|CDD|233253 TIGR01057, topA_arch, DNA topoisomerase I, archaeal. This model
describes topoisomerase I from archaea. These enzymes
are involved in the control of DNA topology. DNA
topoisomerase I belongs to the type I topoisomerases,
which are ATP-independent [DNA metabolism, DNA
replication, recombination, and repair].
Length = 618
Score = 47.5 bits (113), Expect = 3e-08
Identities = 19/40 (47%), Positives = 24/40 (60%)
Query: 26 ISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNG 65
+S G Q PTL F VER +I F P+PYW++ TL G
Sbjct: 187 LSAGRVQGPTLAFLVEREREINLFVPKPYWVIKATLEKGG 226
>gnl|CDD|235602 PRK05776, PRK05776, DNA topoisomerase I; Provisional.
Length = 670
Score = 46.9 bits (112), Expect = 6e-08
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 27 SYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGE 66
S G Q+PTL + VER + F P PY+ + + + NG
Sbjct: 191 SAGRVQSPTLKYVVEREIERNLFVPLPYFSVSIIIEKNGY 230
>gnl|CDD|236078 PRK07726, PRK07726, DNA topoisomerase III; Provisional.
Length = 658
Score = 46.7 bits (112), Expect = 7e-08
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 8/58 (13%)
Query: 4 LLKLNLKEADYQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTL 61
L ++A Y G ++S G QTPTL V R ++I F P+PYW ++ L
Sbjct: 173 AYTLLGRKAGYNG--------VLSVGRVQTPTLALVVRRDEEIENFVPKPYWEVEAHL 222
>gnl|CDD|180892 PRK07220, PRK07220, DNA topoisomerase I; Validated.
Length = 740
Score = 46.7 bits (111), Expect = 8e-08
Identities = 20/48 (41%), Positives = 25/48 (52%)
Query: 19 GDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGE 66
G L +S G Q+PTL V+R + F P PYW + TL NGE
Sbjct: 185 GRLGKMFLSVGRVQSPTLALIVDREKEREAFVPTPYWEIYATLENNGE 232
>gnl|CDD|236172 PRK08173, PRK08173, DNA topoisomerase III; Validated.
Length = 862
Score = 43.9 bits (104), Expect = 6e-07
Identities = 16/27 (59%), Positives = 17/27 (62%)
Query: 29 GPCQTPTLGFCVERHDKIRTFKPEPYW 55
G QTPTL VER +KIR F P YW
Sbjct: 194 GRVQTPTLSIVVEREEKIRRFVPRDYW 220
>gnl|CDD|237803 PRK14724, PRK14724, DNA topoisomerase III; Provisional.
Length = 987
Score = 39.2 bits (91), Expect = 3e-05
Identities = 16/31 (51%), Positives = 18/31 (58%)
Query: 25 LISYGPCQTPTLGFCVERHDKIRTFKPEPYW 55
L + G QTPTL VER +KIR F YW
Sbjct: 198 LTTVGRVQTPTLSLVVEREEKIRKFVSRDYW 228
>gnl|CDD|233249 TIGR01051, topA_bact, DNA topoisomerase I, bacterial. This model
describes DNA topoisomerase I among the members of
bacteria. DNA topoisomerase I transiently cleaves one
DNA strand and thus relaxes negatively supercoiled DNA
during replication, transcription and recombination
events [DNA metabolism, DNA replication, recombination,
and repair].
Length = 610
Score = 38.5 bits (90), Expect = 6e-05
Identities = 15/40 (37%), Positives = 20/40 (50%)
Query: 27 SYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGE 66
S G Q+ L V+R +I+ F PE YW +D T E
Sbjct: 159 SAGRVQSVALRLIVDREREIKRFVPEEYWTIDATFQKGEE 198
>gnl|CDD|233252 TIGR01056, topB, DNA topoisomerase III, bacteria and conjugative
plasmid. This model describes topoisomerase III from
bacteria and its equivalents encoded on plasmids. The
gene is designated topB if found in the bacterial
chromosome, traE on conjugative plasmid RP4, etc. These
enzymes are involved in the control of DNA topology. DNA
topoisomerase III belongs to the type I topoisomerases,
which are ATP-independent [DNA metabolism, DNA
replication, recombination, and repair].
Length = 660
Score = 38.3 bits (89), Expect = 6e-05
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 8/59 (13%)
Query: 10 KEADYQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGEWV 68
+EA G ++S G QTPTL V+R ++I+ F +P++ + T+N + +
Sbjct: 184 REAGNDG--------VLSVGRVQTPTLAMVVKRENEIKNFVGKPFYEVSATINKDEQEF 234
>gnl|CDD|181555 PRK08780, PRK08780, DNA topoisomerase I; Provisional.
Length = 780
Score = 34.4 bits (79), Expect = 0.002
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 26 ISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLD 58
+S G Q+P L VER ++I F YW ++
Sbjct: 166 LSAGRVQSPALRMIVEREEEIEAFIAREYWSIE 198
>gnl|CDD|235516 PRK05582, PRK05582, DNA topoisomerase I; Validated.
Length = 650
Score = 33.6 bits (78), Expect = 0.003
Identities = 13/40 (32%), Positives = 19/40 (47%)
Query: 27 SYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGE 66
S G Q+ L ++R +IR F PE YW +D +
Sbjct: 163 SAGRVQSVALKLIIDREKEIRAFVPEEYWTIDAEFKKGKK 202
>gnl|CDD|235840 PRK06599, PRK06599, DNA topoisomerase I; Validated.
Length = 675
Score = 32.1 bits (74), Expect = 0.008
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 26 ISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTL 61
+S G Q+ L ER D+I F P+ YW ++ L
Sbjct: 165 LSAGRVQSVALRLICEREDEIEAFIPQEYWTIEADL 200
>gnl|CDD|236048 PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated.
Length = 859
Score = 29.8 bits (68), Expect = 0.065
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 40 VERHDKIRTFKPEPYWLLDLTL 61
VER +I F PE YW + L
Sbjct: 189 VEREREIEAFVPEEYWDIHADL 210
>gnl|CDD|179468 PRK02749, PRK02749, photosystem I reaction center subunit IV;
Provisional.
Length = 71
Score = 27.8 bits (62), Expect = 0.18
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 40 VERHDKIRTFKPEPYW 55
+ R DK+R +PE YW
Sbjct: 3 ISRGDKVRILRPESYW 18
>gnl|CDD|235778 PRK06319, PRK06319, DNA topoisomerase I/SWI domain fusion protein;
Validated.
Length = 860
Score = 27.9 bits (62), Expect = 0.40
Identities = 12/32 (37%), Positives = 15/32 (46%)
Query: 24 SLISYGPCQTPTLGFCVERHDKIRTFKPEPYW 55
S +S G Q+ L V+R I F P YW
Sbjct: 161 SGVSAGRVQSVALKLVVDREKAIEAFVPVEYW 192
>gnl|CDD|215788 pfam00207, A2M, Alpha-2-macroglobulin family. This family
includes the C-terminal region of the
alpha-2-macroglobulin family.
Length = 92
Score = 26.8 bits (60), Expect = 0.51
Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 3/31 (9%)
Query: 31 CQTPTLGFCVERHDKIRTFKPEPYWLLDLTL 61
+P G V ++ FKP + +DL L
Sbjct: 35 ALSPDKGLGVAEPPEVTVFKP---FFVDLNL 62
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 26.6 bits (59), Expect = 0.97
Identities = 13/35 (37%), Positives = 19/35 (54%)
Query: 27 SYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTL 61
S G QTP LG+ V R+++ + + LDL L
Sbjct: 826 SAGRVQTPVLGWIVNRYEEYKEKRGYLVIQLDLDL 860
>gnl|CDD|173597 PTZ00407, PTZ00407, DNA topoisomerase IA; Provisional.
Length = 805
Score = 26.4 bits (58), Expect = 0.99
Identities = 12/23 (52%), Positives = 13/23 (56%)
Query: 27 SYGPCQTPTLGFCVERHDKIRTF 49
S G QTP L ER DKI+ F
Sbjct: 220 SIGRVQTPALILINEREDKIKAF 242
>gnl|CDD|145527 pfam02427, PSI_PsaE, Photosystem I reaction centre subunit IV /
PsaE. PsaE is a 69 amino acid polypeptide from
photosystem I present on the stromal side of the
thylakoid membrane. The structure is comprised of a
well-defined five-stranded beta-sheet similar to SH3
domains.
Length = 61
Score = 25.4 bits (56), Expect = 1.2
Identities = 6/16 (37%), Positives = 10/16 (62%)
Query: 40 VERHDKIRTFKPEPYW 55
++R K+R + E YW
Sbjct: 1 IKRGSKVRILRKESYW 16
>gnl|CDD|233251 TIGR01054, rgy, reverse gyrase. This model describes reverse
gyrase, found in both archaeal and bacterial
thermophiles. This enzyme, a fusion of a type I
topoisomerase domain and a helicase domain, introduces
positive supercoiling to increase the melting
temperature of DNA double strands. Generally, these
gyrases are encoded as a single polypeptide. An
exception was found in Methanopyrus kandleri, where
enzyme is split within the topoisomerase domain,
yielding a heterodimer of gene products designated RgyB
and RgyA [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1171
Score = 25.9 bits (57), Expect = 1.7
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 26 ISYGPCQTPTLGFCVERHDKIRTFKPE 52
+S G QTP LG+ ++R+ + R +
Sbjct: 809 LSAGRVQTPVLGWIIDRYRESREKRGY 835
>gnl|CDD|180944 PRK07362, PRK07362, isocitrate dehydrogenase; Validated.
Length = 474
Score = 25.1 bits (55), Expect = 3.0
Identities = 12/25 (48%), Positives = 20/25 (80%), Gaps = 2/25 (8%)
Query: 45 KIRTFKPEPYWLLDLTLNLNGEWVS 69
+I+T +P+ Y +L TLNLNG+++S
Sbjct: 345 QIQT-RPQEYSIL-ATLNLNGDYIS 367
>gnl|CDD|212166 cd11652, SSH-N, N-terminal domain conserved in slingshot (SSH)
phosphatases. This domain or region conserved in
Bilateria is found N-terminal to the DEK_C-like and
catalytic domains of slingshot phosphatases. Slingshot
is a cofilin-specific phosphatase. Dephosphorylation
reactivates cofilin, which in turn depolymerizes actin
and is thus required for actin filament reorganization.
Slingshot is a member of the dual-specificity protein
phosphatase family. This N-terminal SSH region may be
involved in P-cofilin binding (the model C-terminus plus
the DEK_C-like domain, which are characterized as the
"B" domain in some of the literature), and may be
required for the F-actin mediated activation of
slingshot (the N-terminal region of this model,
sometimes referred to as the "A" domain).
Length = 233
Score = 25.0 bits (55), Expect = 3.8
Identities = 7/15 (46%), Positives = 7/15 (46%)
Query: 37 GFCVERHDKIRTFKP 51
GF V K FKP
Sbjct: 154 GFSVTSDGKTHIFKP 168
>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 24.5 bits (53), Expect = 6.0
Identities = 8/20 (40%), Positives = 14/20 (70%)
Query: 26 ISYGPCQTPTLGFCVERHDK 45
+S G QTP LG+ ++R+ +
Sbjct: 790 LSAGRVQTPVLGWIIQRYKE 809
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
0.320 0.142 0.456
Gapped
Lambda K H
0.267 0.0789 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,516,884
Number of extensions: 247408
Number of successful extensions: 200
Number of sequences better than 10.0: 1
Number of HSP's gapped: 200
Number of HSP's successfully gapped: 28
Length of query: 69
Length of database: 10,937,602
Length adjustment: 39
Effective length of query: 30
Effective length of database: 9,207,796
Effective search space: 276233880
Effective search space used: 276233880
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 (21.7 bits)
S2: 53 (24.1 bits)