RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12647
(410 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 33.1 bits (76), Expect = 0.010
Identities = 13/26 (50%), Positives = 19/26 (73%)
Query: 238 ELRQHVRQHTDERPFPCPVCQRTFRR 263
LR+H+R HT E+P+ CPVC ++F
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 33.1 bits (76), Expect = 0.010
Identities = 13/26 (50%), Positives = 19/26 (73%)
Query: 369 ELRQHVRQHTDERPFPCPVCQRTFRR 394
LR+H+R HT E+P+ CPVC ++F
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 25.0 bits (55), Expect = 6.6
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 29 QVHLRLHSGERRFPCEYCS 47
+ H+R H+GE+ + C C
Sbjct: 3 RRHMRTHTGEKPYKCPVCG 21
>gnl|CDD|129694 TIGR00606, rad50, rad50. All proteins in this family for which
functions are known are involvedin recombination,
recombinational repair, and/or non-homologous end
joining.They are components of an exonuclease complex
with MRE11 homologs. This family is distantly related to
the SbcC family of bacterial proteins.This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University).
Length = 1311
Score = 36.6 bits (84), Expect = 0.025
Identities = 21/58 (36%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 241 QHVRQHTDERPFPCPVCQRTFR-RKGLESFTFSLRLFCLYFPQELISHSSYHGGEERR 297
Q + Q TDE CPVCQR F+ L+ F L+ P +L S S +E+R
Sbjct: 667 QFITQLTDENQSCCPVCQRVFQTEAELQEFISDLQSKLRLAPDKLKSTESELKKKEKR 724
Score = 30.0 bits (67), Expect = 2.6
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 372 QHVRQHTDERPFPCPVCQRTFRRK 395
Q + Q TDE CPVCQR F+ +
Sbjct: 667 QFITQLTDENQSCCPVCQRVFQTE 690
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 32.3 bits (73), Expect = 0.48
Identities = 40/191 (20%), Positives = 56/191 (29%), Gaps = 29/191 (15%)
Query: 219 TGSLSYPC-TQCPGKFYSAYELRQHVRQHTDERPFPCPVCQRTFRR----KGLESFTFSL 273
GS +Y C + A +R CP+C+ +
Sbjct: 68 AGSTTYSARYPCGHQICHACAVRLRALYMQKG----CPLCRTETEAVVFTASSPADITDR 123
Query: 274 RLFCLYFPQELISHSSYHGGEER----RYVCNHMQCTRRFHSASLLARHVSTHAIQYTCH 329
R + + I + +E + C +C RR S L +H C
Sbjct: 124 RQWKGREEKVGIFYEGEDVRDEMEDLLSFKCPKSKCHRRCGSLKELKKHYKAQHGFVLCS 183
Query: 330 MCG---HMFTCKRRL-TQHLARLH-TGSLSYP-------CTQCPGKFYSAYELRQHVRQH 377
C F + RL R H G L C C FY ELR+H R
Sbjct: 184 ECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIYFYDDDELRRHCR-- 241
Query: 378 TDERPFPCPVC 388
R C +C
Sbjct: 242 --LRHEACHIC 250
Score = 31.1 bits (70), Expect = 1.0
Identities = 37/170 (21%), Positives = 51/170 (30%), Gaps = 23/170 (13%)
Query: 107 HVAACREK---RRKETFPCKRCDERFSTRDGLESFTFSLRLFCLYFPQELISHSSYHGGE 163
H A R + +K C+ E + R + + I + +
Sbjct: 85 HACAVRLRALYMQKGCPLCRTETEAVVFTASSPADITDRRQWKGREEKVGIFYEGEDVRD 144
Query: 164 ER----RYVCNHMQCTRRFHSASLLARHVSTHAIQYTCHMCG---HMFTCKRRL-TQHLA 215
E + C +C RR S L +H C C F + RL
Sbjct: 145 EMEDLLSFKCPKSKCHRRCGSLKELKKHYKAQHGFVLCSECIGNKKDFWNEIRLFRSSTL 204
Query: 216 RLH-TGSLSYP-------CTQCPGKFYSAYELRQHVRQHTDERPFPCPVC 257
R H G L C C FY ELR+H R R C +C
Sbjct: 205 RDHKNGGLEEEGFKGHPLCIFCKIYFYDDDELRRHCR----LRHEACHIC 250
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 30.2 bits (68), Expect = 0.92
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 224 YPCTQCPGKFYSAYELRQHVRQHTDERPFPCPVCQRTFR 262
Y C C F S+ L+QH+R E CPVC + FR
Sbjct: 74 YVCPLCLMPFSSSVSLKQHIRY--TEHSKVCPVCGKEFR 110
Score = 30.2 bits (68), Expect = 0.92
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 355 YPCTQCPGKFYSAYELRQHVRQHTDERPFPCPVCQRTFR 393
Y C C F S+ L+QH+R E CPVC + FR
Sbjct: 74 YVCPLCLMPFSSSVSLKQHIRY--TEHSKVCPVCGKEFR 110
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 31.3 bits (72), Expect = 0.97
Identities = 13/42 (30%), Positives = 14/42 (33%), Gaps = 8/42 (19%)
Query: 197 CHMCGHMFTCKR---RLTQHLA--RL---HTGSLSYPCTQCP 230
C CG + C LT H RL H G CP
Sbjct: 384 CRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACP 425
Score = 31.3 bits (72), Expect = 0.97
Identities = 13/42 (30%), Positives = 14/42 (33%), Gaps = 8/42 (19%)
Query: 328 CHMCGHMFTCKR---RLTQHLA--RL---HTGSLSYPCTQCP 361
C CG + C LT H RL H G CP
Sbjct: 384 CRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACP 425
>gnl|CDD|237665 PRK14295, PRK14295, chaperone protein DnaJ; Provisional.
Length = 389
Score = 29.4 bits (66), Expect = 3.6
Identities = 17/56 (30%), Positives = 23/56 (41%), Gaps = 15/56 (26%)
Query: 211 TQHLARLHTG-SLSYPCTQCPGKFYSAYELRQHVRQHTDERPFPCPVCQRTFRRKG 265
T ++R G SLS PC C G+ A + PC VC+ + R K
Sbjct: 192 TGQVSRNSGGFSLSEPCPDCKGRGLIADD--------------PCLVCKGSGRAKS 233
>gnl|CDD|172776 PRK14288, PRK14288, chaperone protein DnaJ; Provisional.
Length = 369
Score = 28.9 bits (64), Expect = 5.3
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 91 CNSCGQTWL--GYTSWKQHVAACREKRRKETFPCKRC 125
CN GQ ++ G+ S+ Q AC+ K + PC+ C
Sbjct: 162 CNGQGQVFMRQGFMSFAQTCGACQGKGKIIKTPCQAC 198
>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 = 29.0 bits (65), Expect = 5.5
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 3/28 (10%)
Query: 167 YVCNHMQCTRRFHSASLLARHV-STHAI 193
YVC C F S LA H +TH+I
Sbjct: 74 YVC--NVCMAEFSSMDQLAEHQRTTHSI 99
Score = 29.0 bits (65), Expect = 5.5
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 3/28 (10%)
Query: 298 YVCNHMQCTRRFHSASLLARHV-STHAI 324
YVC C F S LA H +TH+I
Sbjct: 74 YVC--NVCMAEFSSMDQLAEHQRTTHSI 99
>gnl|CDD|200539 cd11278, Sema_MET, The Sema domain, a protein interacting module,
of MET (also called hepatocyte growth factor receptor,
HGFR). MET is encoded by the c-met protooncogene. MET
is a receptor tyrosine kinase that binds its ligand,
hepatocyte growth factor/scatter factor (HGF/SF). HGF/SF
and MET are essential for the development of several
tissues and organs, including the placenta, liver, and
several groups of skeletal muscles. It also plays a
major role in the abnormal migration of cancer cells as
a result of overexpression or MET mutations. MET is
composed of an alpha-beta heterodimer. The extracellular
alpha chain is disulfide linked to the beta chain, which
contains an extracellular ligand-binding region with a
Sema domain, a PSI domain and four IPT repeats, a
transmembrane segment, and an intracellular catalytic
tyrosine kinase domain. The cytoplasmic C-terminal
region acts as a docking site for multiple protein
substrates, including Grb2, Gab1, STAT3, Shc, SHIP-1 and
Src. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. The Sema domain of Met is necessary
for receptor dimerization and activation.
Length = 492
Score = 28.7 bits (64), Expect = 6.1
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 120 FPCKRCDERFSTRDGLESFTFSLRLFC-LYFPQELISHSSYHGGEERRYVCNH 171
FPC+ C ++ + +G+ ++ LF Y+ +LIS S + G +R+V H
Sbjct: 71 FPCQDCSDKANLSNGVWKDNVNMALFVETYYDDQLISCGSVNRGTCQRHVFPH 123
>gnl|CDD|165228 PHA02910, PHA02910, hypothetical protein; Provisional.
Length = 171
Score = 27.8 bits (61), Expect = 8.3
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 88 TFSCNSCGQTWLGYTSWKQHVAAC 111
+F+ NS G+ +GY SW H AC
Sbjct: 51 SFNSNSGGEKRIGYHSWFCHYGAC 74
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
0.331 0.139 0.476
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,403,490
Number of extensions: 1877213
Number of successful extensions: 2302
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2294
Number of HSP's successfully gapped: 60
Length of query: 410
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 311
Effective length of database: 6,546,556
Effective search space: 2035978916
Effective search space used: 2035978916
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 60 (26.9 bits)