RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16775
(306 letters)
>gnl|CDD|177300 PHA00732, PHA00732, hypothetical protein.
Length = 79
Score = 29.4 bits (66), Expect = 0.52
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 13/55 (23%)
Query: 187 RCPVCG--RVYQWKLLNHVARDHNMSLKPAHLSYKCTVCTATFGMYRQFENHVYS 239
+CP+CG V + L H R+H ++ KC VC + YR+ H YS
Sbjct: 3 KCPICGFTTVTLFALKQHARRNHTLT--------KCPVCNKS---YRRLNQHFYS 46
>gnl|CDD|187768 cd09637, Cas4_I-A_I-B_I-C_I-D_II-B, CRISPR/Cas system-associated
protein Cas4. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas4 is RecB-like nuclease with three-cysteine
C-terminal cluster.
Length = 178
Score = 30.1 bits (68), Expect = 0.93
Identities = 8/45 (17%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 112 KVKITPDLEQ-LRNHMQWIHKVKIHPKMIYNRPPLNCQKCQFRFF 155
+V+I+ +L + ++ I K+ + C+ C +R
Sbjct: 132 EVEISEELRKKAEKLLEEIRKLLEGELPPPVKSSPKCKFCPYREI 176
>gnl|CDD|234700 PRK00249, flgH, flagellar basal body L-ring protein; Reviewed.
Length = 222
Score = 30.2 bits (69), Expect = 1.1
Identities = 9/38 (23%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 80 KPLKINDEITIIPQPPRPTASSSSSTSSSNNNKVKITP 117
+ + D +T++ Q +AS S+ST+ S ++
Sbjct: 62 RARNVGDILTVVLQE-NTSASKSNSTNRSRDSSTNFGL 98
Score = 30.2 bits (69), Expect = 1.1
Identities = 9/38 (23%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 264 KPLKINDEITIIPQPPRPTASSSSSTSSSNNNKVKITP 301
+ + D +T++ Q +AS S+ST+ S ++
Sbjct: 62 RARNVGDILTVVLQE-NTSASKSNSTNRSRDSSTNFGL 98
>gnl|CDD|165133 PHA02768, PHA02768, hypothetical protein; Provisional.
Length = 55
Score = 27.3 bits (60), Expect = 1.5
Identities = 12/30 (40%), Positives = 19/30 (63%), Gaps = 3/30 (10%)
Query: 185 GGRCPVCGRVY--QWKLLNHVARDHNMSLK 212
G CP+CG +Y + ++ H+ R HN +LK
Sbjct: 5 GYECPICGEIYIKRKSMITHL-RKHNTNLK 33
>gnl|CDD|216792 pfam01927, DUF82, Protein of unknown function DUF82. This
prokaryotic protein family has no known function. The
protein contains four conserved cysteines that may be
involved in metal binding or disulphide bridges.
Length = 146
Score = 28.8 bits (65), Expect = 2.0
Identities = 10/12 (83%), Positives = 10/12 (83%), Gaps = 1/12 (8%)
Query: 187 RCPVCGRVYQWK 198
RCP CGRVY WK
Sbjct: 125 RCPKCGRVY-WK 135
>gnl|CDD|224974 COG2063, FlgH, Flagellar basal body L-ring protein [Cell motility
and secretion].
Length = 230
Score = 29.2 bits (66), Expect = 2.3
Identities = 15/76 (19%), Positives = 25/76 (32%), Gaps = 15/76 (19%)
Query: 40 TATFGMYRQFENHVYSAHSVAPRRPATDKKPQGQSTDPML---KPLKINDEITIIPQPPR 96
G ++ +S P+ + + D +TI+ Q
Sbjct: 38 PPQPGPAPIQPGSIFQGYS-----------LWNYGYQPLFEDRRASNVGDILTIVIQ-EN 85
Query: 97 PTASSSSSTSSSNNNK 112
+AS SSST+ S N
Sbjct: 86 TSASKSSSTNRSRKNS 101
Score = 29.2 bits (66), Expect = 2.3
Identities = 15/76 (19%), Positives = 25/76 (32%), Gaps = 15/76 (19%)
Query: 224 TATFGMYRQFENHVYSAHSVAPRRPATDKKPQGQSTDPML---KPLKINDEITIIPQPPR 280
G ++ +S P+ + + D +TI+ Q
Sbjct: 38 PPQPGPAPIQPGSIFQGYS-----------LWNYGYQPLFEDRRASNVGDILTIVIQ-EN 85
Query: 281 PTASSSSSTSSSNNNK 296
+AS SSST+ S N
Sbjct: 86 TSASKSSSTNRSRKNS 101
>gnl|CDD|144386 pfam00765, Autoind_synth, Autoinducer synthetase.
Length = 182
Score = 28.8 bits (65), Expect = 2.6
Identities = 14/38 (36%), Positives = 18/38 (47%), Gaps = 5/38 (13%)
Query: 153 RFFTDQGLERHLLGSHGLVTS----SMQE-AANKGKDG 185
RFF D+ R LLG+ ++ SM A G DG
Sbjct: 95 RFFVDKARARGLLGNLAPISLMLFLSMINYARASGYDG 132
>gnl|CDD|212564 cd11674, lambda-1, inner capsid protein lambda-1 or VP3. The
reovirus inner capsid protein lambda-1 displays
nucleoside triphosphate phosphohydrolase (NTPase),
RNA-5'-triphosphatase (RTPase), and RNA helicase
activity and may play a role in the transcription of
the virus genome, the unwinding or reannealing of
double-stranded RNA during RNA synthesis. The RTPase
activity constitutes the first step in the capping of
RNA, resulting in a 5'-diphosphorylated RNA
plus-strand. lambda1 is an Orthoreovirus core protein,
VP3 is the homologous core protein in Aquareoviruses.
Length = 1166
Score = 29.7 bits (67), Expect = 2.6
Identities = 13/57 (22%), Positives = 20/57 (35%), Gaps = 1/57 (1%)
Query: 4 SAAIQDVYQWKLLNHVARDHNMSLKPAHLS-YKCTVCTATFGMYRQFENHVYSAHSV 59
+ K ++ + P + S Y C VC A F Q H + HS+
Sbjct: 43 DSIAAVANATKPAAVISPPQSKKATPINPSSYVCNVCMAEFSSMDQLAEHQRTTHSI 99
Score = 29.4 bits (66), Expect = 2.7
Identities = 12/37 (32%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 208 NMSLKPAHLS-YKCTVCTATFGMYRQFENHVYSAHSV 243
+ P + S Y C VC A F Q H + HS+
Sbjct: 63 SKKATPINPSSYVCNVCMAEFSSMDQLAEHQRTTHSI 99
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family
contains a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 26.1 bits (57), Expect = 2.9
Identities = 6/24 (25%), Positives = 11/24 (45%)
Query: 34 YKCTVCTATFGMYRQFENHVYSAH 57
+KC +C +F + H+ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
Score = 26.1 bits (57), Expect = 2.9
Identities = 6/24 (25%), Positives = 11/24 (45%)
Query: 218 YKCTVCTATFGMYRQFENHVYSAH 241
+KC +C +F + H+ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
Score = 24.9 bits (54), Expect = 6.9
Identities = 8/22 (36%), Positives = 10/22 (45%)
Query: 147 CQKCQFRFFTDQGLERHLLGSH 168
C C F + L+RHL H
Sbjct: 3 CPLCGKSFSSKDALKRHLRKHH 24
>gnl|CDD|152886 pfam12452, DUF3685, Protein of unknown function (DUF3685). This
domain family is found in bacteria and eukaryotes, and
is approximately 190 amino acids in length. There are
two completely conserved residues (L and D) that may be
functionally important.
Length = 193
Score = 28.7 bits (65), Expect = 2.9
Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 9/56 (16%)
Query: 110 NNKVKITPDLEQLRNHMQW---IHKVKIHPKMIYNRPPLNCQKCQFRFFTDQGLER 162
N+ + T +LE+ RN++ W + PK IY + + + G+E
Sbjct: 74 NSSLLSTRELERFRNNLSWQYRWQQYIEEPKAIYE------SRYRLFVIREGGIES 123
>gnl|CDD|224462 COG1545, COG1545, Predicted nucleic-acid-binding protein containing
a Zn-ribbon [General function prediction only].
Length = 140
Score = 28.1 bits (63), Expect = 3.1
Identities = 9/20 (45%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 177 EAANKGK-DGGRCPVCGRVY 195
+ +GK G +C CGRVY
Sbjct: 20 KGLKEGKLLGTKCKKCGRVY 39
>gnl|CDD|203007 pfam04423, Rad50_zn_hook, Rad50 zinc hook motif. The Mre11 complex
(Mre11 Rad50 Nbs1) is central to chromosomal maintenance
and functions in homologous recombination, telomere
maintenance and sister chromatid association. The Rad50
coiled-coil region contains a dimer interface at the
apex of the coiled coils in which pairs of conserved
Cys-X-X-Cys motifs form interlocking hooks that bind one
Zn ion. This alignment includes the zinc hook motif and
a short stretch of coiled-coil on either side.
Length = 54
Score = 26.5 bits (59), Expect = 3.7
Identities = 7/18 (38%), Positives = 9/18 (50%)
Query: 176 QEAANKGKDGGRCPVCGR 193
+ + G CPVCGR
Sbjct: 11 KAIEELKEAKGCCPVCGR 28
>gnl|CDD|224385 COG1468, COG1468, CRISPR-associated protein Cas4 (RecB family
exonuclease) [Defense mechanisms].
Length = 190
Score = 28.1 bits (63), Expect = 4.1
Identities = 10/44 (22%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 113 VKITPDL-EQLRNHMQWIHKVKIHPKMIYNRPPLNCQKCQFRFF 155
V++T +L E++ ++ I ++ K + C+KC +R
Sbjct: 142 VELTEELREEVERVLKEIEEILEGGKPPPPKKKKKCKKCAYREI 185
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 25.5 bits (56), Expect = 4.2
Identities = 5/22 (22%), Positives = 8/22 (36%)
Query: 34 YKCTVCTATFGMYRQFENHVYS 55
Y+C C F H+ +
Sbjct: 1 YRCPECGKVFKSKSALREHMRT 22
Score = 25.5 bits (56), Expect = 4.2
Identities = 5/22 (22%), Positives = 8/22 (36%)
Query: 218 YKCTVCTATFGMYRQFENHVYS 239
Y+C C F H+ +
Sbjct: 1 YRCPECGKVFKSKSALREHMRT 22
>gnl|CDD|221624 pfam12532, DUF3732, Protein of unknown function (DUF3732). This
domain family is found in bacteria and eukaryotes, and
is typically between 180 and 198 amino acids in length.
There is a conserved DQP sequence motif.
Length = 190
Score = 27.7 bits (62), Expect = 5.5
Identities = 8/43 (18%), Positives = 15/43 (34%)
Query: 90 IIPQPPRPTASSSSSTSSSNNNKVKITPDLEQLRNHMQWIHKV 132
I+ QP + S + K++ DL +R +
Sbjct: 105 ILDQPSQVYFPKSDKDEDFDEEKLRRDEDLAAVRKAFSLLADF 147
>gnl|CDD|215036 PLN00034, PLN00034, mitogen-activated protein kinase kinase;
Provisional.
Length = 353
Score = 27.9 bits (62), Expect = 6.6
Identities = 12/32 (37%), Positives = 20/32 (62%)
Query: 91 IPQPPRPTASSSSSTSSSNNNKVKITPDLEQL 122
+P PP ++SSSSS+SS++ + L +L
Sbjct: 45 LPLPPPSSSSSSSSSSSASGSAPSAAKSLSEL 76
>gnl|CDD|224570 COG1656, COG1656, Uncharacterized conserved protein [Function
unknown].
Length = 165
Score = 27.4 bits (61), Expect = 6.9
Identities = 8/12 (66%), Positives = 10/12 (83%), Gaps = 1/12 (8%)
Query: 187 RCPVCGRVYQWK 198
RCP CG++Y WK
Sbjct: 132 RCPKCGKIY-WK 142
>gnl|CDD|188441 TIGR03926, T7_EssB, type VII secretion protein EssB. Members of
this family are associated with type VII secretion of
WXG100 family targets in the Firmicutes, but not in the
Actinobacteria. This protein is designated YukC in
Bacillus subtilis and EssB is Staphylococcus aureus
[Protein fate, Protein and peptide secretion and
trafficking].
Length = 377
Score = 27.7 bits (62), Expect = 8.0
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 3/53 (5%)
Query: 76 DPMLKPLKIN---DEITIIPQPPRPTASSSSSTSSSNNNKVKITPDLEQLRNH 125
P+ P +I+ DE I QPP S S + N K+++ +L L H
Sbjct: 41 SPLFVPAEIDEDEDEFVISYQPPPAAKSFESIKKKTRNEKLRLALNLADLEEH 93
>gnl|CDD|232944 TIGR00372, cas4, CRISPR-associated protein Cas4. This model
represents a family of proteins associated with CRISPR
repeats in a wide set of prokaryotic genomes. This scope
of this model has been broadened since it was first
built to describe an archaeal subset only. The function
of the protein is undefined. Distantly related proteins,
excluded from this model, include ORFs from
Mycobacteriophage D29 and Sulfolobus islandicus
filamentous virus and a region of the
Schizosaccharomyces pombe DNA replication helicase Dna2p
[Mobile and extrachromosomal element functions, Other].
Length = 178
Score = 27.4 bits (61), Expect = 8.1
Identities = 8/45 (17%), Positives = 20/45 (44%), Gaps = 2/45 (4%)
Query: 113 VKITPDL-EQLRNHMQWIHKVKIHPKMIY-NRPPLNCQKCQFRFF 155
V+I+ +L ++ ++ I ++ K + C+ C +R
Sbjct: 131 VEISEELRKKAEKLIEKIRELLEGGKPPSPPKSSRKCKFCPYREI 175
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 26.8 bits (59), Expect = 9.2
Identities = 10/24 (41%), Positives = 16/24 (66%), Gaps = 2/24 (8%)
Query: 188 CPVCGRVYQWK--LLNHVARDHNM 209
CPVCG+ ++ L+HV + HN+
Sbjct: 102 CPVCGKEFRNTDSTLDHVCKKHNI 125
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
0.316 0.129 0.397
Gapped
Lambda K H
0.267 0.0655 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,778,186
Number of extensions: 1295116
Number of successful extensions: 1607
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1598
Number of HSP's successfully gapped: 39
Length of query: 306
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 209
Effective length of database: 6,635,264
Effective search space: 1386770176
Effective search space used: 1386770176
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.7 bits)