RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13254
(132 letters)
>gnl|CDD|223327 COG0249, MutS, Mismatch repair ATPase (MutS family) [DNA
replication, recombination, and repair].
Length = 843
Score = 66.9 bits (164), Expect = 6e-14
Identities = 35/121 (28%), Positives = 53/121 (43%), Gaps = 18/121 (14%)
Query: 6 SGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCR 65
+G P + + L+E GYKVA EQ E + +R V R + T
Sbjct: 60 AGVPYHALDYYLAKLIELGYKVAICEQLEDPAEAKGVVERK--------VVRVVTPGT-- 109
Query: 66 GAQTFSIMDVDA-NYVDNKFLLGVTKEGD-RLGVCFIDTTIGEFHVGEFEDDKQFSRLST 123
+ D + +N +L + + D ++G+ FID + GEF V EFE +K S L
Sbjct: 110 ------LTDEALLSDRENNYLAALAIDRDGKVGLAFIDLSTGEFFVSEFEREKLLSELKR 163
Query: 124 L 124
L
Sbjct: 164 L 164
>gnl|CDD|216613 pfam01624, MutS_I, MutS domain I. This domain is found in proteins
of the MutS family (DNA mismatch repair proteins) and is
found associated with pfam00488, pfam05188, pfam05192
and pfam05190. The MutS family of proteins is named
after the Salmonella typhimurium MutS protein involved
in mismatch repair; other members of the family included
the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have
various roles in DNA repair and recombination. Human MSH
has been implicated in non-polyposis colorectal
carcinoma (HNPCC) and is a mismatch binding protein. The
aligned region corresponds with globular domain I, which
is involved in DNA binding, in Thermus aquaticus MutS as
characterized in.
Length = 113
Score = 55.3 bits (134), Expect = 6e-11
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 12/69 (17%)
Query: 1 NEYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREIC 60
+G PE ++ + + LV KGYKVA EQTE + + VV+RE+
Sbjct: 54 KRIPMAGVPEHAFETYLRRLVNKGYKVAICEQTEDPA------------EAKGVVKREVV 101
Query: 61 KITCRGAQT 69
++ G T
Sbjct: 102 RVITPGTLT 110
>gnl|CDD|235444 PRK05399, PRK05399, DNA mismatch repair protein MutS; Provisional.
Length = 854
Score = 51.6 bits (125), Expect = 1e-08
Identities = 29/105 (27%), Positives = 47/105 (44%), Gaps = 29/105 (27%)
Query: 19 TLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKI----TCRGAQTFSIMD 74
LV+KGYKVA EQ E K V+RE+ +I T + D
Sbjct: 80 KLVKKGYKVAICEQVEDPAT----AKG--------PVKREVVRIVTPGT--------VTD 119
Query: 75 ---VDANYVDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDK 116
+D N +L + ++G G+ ++D + GEF V E ++++
Sbjct: 120 EALLDEK--QNNYLAAIAQDGGGYGLAYLDLSTGEFRVTELDEEE 162
>gnl|CDD|233259 TIGR01070, mutS1, DNA mismatch repair protein MutS. [DNA
metabolism, DNA replication, recombination, and repair].
Length = 840
Score = 47.8 bits (114), Expect = 3e-07
Identities = 26/111 (23%), Positives = 45/111 (40%), Gaps = 19/111 (17%)
Query: 6 SGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCR 65
+G P + + + LV++G VA EQ E + + V RE+ ++
Sbjct: 60 AGIPYHAVEAYLEKLVKQGESVAICEQIEDPK------------TAKGPVEREVVQLITP 107
Query: 66 G--AQTFSIMDVDANYVDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFED 114
G + + + N L + +E + G+ +D T GEF V E D
Sbjct: 108 GTVSDEALLPERQDN-----LLAAIAQESNGFGLATLDLTTGEFKVTELAD 153
>gnl|CDD|218486 pfam05188, MutS_II, MutS domain II. This domain is found in
proteins of the MutS family (DNA mismatch repair
proteins) and is found associated with pfam00488,
pfam01624, pfam05192 and pfam05190. The MutS family of
proteins is named after the Salmonella typhimurium MutS
protein involved in mismatch repair; other members of
the family included the eukaryotic MSH 1,2,3, 4,5 and 6
proteins. These have various roles in DNA repair and
recombination. Human MSH has been implicated in
non-polyposis colorectal carcinoma (HNPCC) and is a
mismatch binding protein. This domain corresponds to
domain II in Thermus aquaticus MutS as characterized in,
and has similarity resembles RNAse-H-like domains (see
pfam00075).
Length = 133
Score = 45.4 bits (108), Expect = 5e-07
Identities = 17/42 (40%), Positives = 23/42 (54%), Gaps = 3/42 (7%)
Query: 90 KEGDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPC 131
+G+R G+ F+D + GEF V EFED F L +S P
Sbjct: 9 GDGNRYGLAFLDLSTGEFGVSEFED---FEELLAELSRLSPK 47
>gnl|CDD|107311 cd06316, PBP1_ABC_sugar_binding_like_7, Periplasmic sugar-binding
domain of uncharacterized ABC-type transport systems.
Periplasmic sugar-binding domain of uncharacterized
ABC-type transport systems that share homology with a
family of pentose/hexose sugar-binding proteins of the
type I periplasmic binding protein superfamily, which
consists of two domains connected by a three-stranded
hinge. The substrate specificity of this group is not
known, but it is predicted to be involved in the
transport of sugar-containing molecules and chemotaxis.
Length = 294
Score = 30.5 bits (69), Expect = 0.18
Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 5/43 (11%)
Query: 87 GVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYP 129
G E +LG+ + TT +F KQ + + T +S P
Sbjct: 20 GAKDEFAKLGIEVVATTDAQFDP-----AKQVADIETTISQKP 57
>gnl|CDD|182835 PRK10916, PRK10916, ADP-heptose:LPS heptosyltransferase II;
Provisional.
Length = 348
Score = 27.3 bits (61), Expect = 2.2
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 9 PEISYGKFAQTLVEKGYKVA 28
P Y + AQ L+++GY+V
Sbjct: 198 PHYHYAELAQQLIDEGYQVV 217
>gnl|CDD|181502 PRK08611, PRK08611, pyruvate oxidase; Provisional.
Length = 576
Score = 26.5 bits (59), Expect = 4.4
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 2 EYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESA 36
EYA ++ Y KFA+ KGY+V + E+ + A
Sbjct: 479 EYA-IDLSDMDYAKFAEACGGKGYRVEKAEELDPA 512
>gnl|CDD|235259 PRK04219, rpl5p, 50S ribosomal protein L5P; Reviewed.
Length = 177
Score = 26.0 bits (58), Expect = 6.7
Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 11/40 (27%)
Query: 19 TLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRRE 58
TL GY+VAR R KR K+P + RV + E
Sbjct: 134 TLERPGYRVARR-----------RRKRRKIPSRHRVTKEE 162
>gnl|CDD|236905 PRK11396, PRK11396, hypothetical protein; Provisional.
Length = 191
Score = 26.0 bits (57), Expect = 7.0
Identities = 14/51 (27%), Positives = 19/51 (37%), Gaps = 2/51 (3%)
Query: 24 GYKVARVEQTESAEQMD--IRTKRDKVPQKQRVVRREICKITCRGAQTFSI 72
+V + + T MD I T+ D K R+ R RG F I
Sbjct: 89 ADQVVKAKLTAGQMSMDFNIMTRLDVCKAKVRIAERTFTTFGSRGGVVFVI 139
>gnl|CDD|234086 TIGR03012, sulf_tusD_dsrE, sulfur relay protein TusD/DsrE. The
three proteins TusB, TusC, and TusD form a
heterohexamer responsible for a sulfur relay reaction.
In large numbers of proteobacterial species, this
complex acts on a Cys-derived persulfide moiety,
delivered by the cysteine desulfurase IscS to TusA,
then to TusBCD. The activated sulfur group is then
transferred to TusE (DsrC), then by MnmA (TrmU) for
modification of an anticodon nucleotide in tRNAs for
Glu, Lys, and Gln. The sulfur relay complex TusBCD is
also found, under the designation DsrEFH, in
phototrophic and chemotrophic sulfur bacteria, such as
Chromatium vinosum. In these organisms, it seems the
primary purpose is related to sulfur flux, such as
oxidation from sulfide to molecular sulfur to sulfate
[Protein synthesis, tRNA and rRNA base modification].
Length = 127
Score = 25.3 bits (56), Expect = 9.1
Identities = 8/16 (50%), Positives = 14/16 (87%)
Query: 15 KFAQTLVEKGYKVARV 30
+FAQ L+ KG++++RV
Sbjct: 21 QFAQALLAKGHEISRV 36
>gnl|CDD|217984 pfam04244, DPRP, Deoxyribodipyrimidine photo-lyase-related
protein. This family appears to be related to
pfam00875.
Length = 223
Score = 25.6 bits (57), Expect = 9.5
Identities = 5/27 (18%), Positives = 10/27 (37%)
Query: 15 KFAQTLVEKGYKVARVEQTESAEQMDI 41
FA+ L G+ V + + +
Sbjct: 53 HFAEELRAAGHTVIYLTLDDPDNTGSL 79
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
0.321 0.136 0.402
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,455,131
Number of extensions: 543700
Number of successful extensions: 442
Number of sequences better than 10.0: 1
Number of HSP's gapped: 437
Number of HSP's successfully gapped: 20
Length of query: 132
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 46
Effective length of database: 7,123,158
Effective search space: 327665268
Effective search space used: 327665268
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 (21.8 bits)
S2: 53 (24.2 bits)