RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16601
(177 letters)
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 32.5 bits (74), Expect = 0.041
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 3/53 (5%)
Query: 124 FICPKCSNRYVYKHNLKQHLKFECGVEPQFKCPYCDKRCKLKGNLMSHIALKH 176
++CP C + +LKQH+++ E CP C K + + + H+ KH
Sbjct: 74 YVCPLCLMPFSSSVSLKQHIRY---TEHSKVCPVCGKEFRNTDSTLDHVCKKH 123
Score = 27.5 bits (61), Expect = 2.4
Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 3/54 (5%)
Query: 50 FACPKCSKTYLRQYTLNAHLRYECGKRPKFKCPHCNKKCHQKCNLKSHIALKHD 103
+ CP C + +L H+RY CP C K+ + H+ KH+
Sbjct: 74 YVCPLCLMPFSSSVSLKQHIRY---TEHSKVCPVCGKEFRNTDSTLDHVCKKHN 124
>gnl|CDD|143477 cd07561, Peptidase_S41_CPP_like, C-terminal processing
peptidase-like; serine protease family S41. Bacterial
protease homologs of the S41 family related to
C-terminal processing peptidase (CPP). CPP-1 is
believed to be important for the degradation of
incorrectly synthesized proteins as well as protection
from thermal and osmotic stresses. CPP is synthesized
with an extension on its carboxyl-terminus and
specifically recognizes a C-terminal tripeptide, but
cleaves at variable distance from the C-terminus. The
CPP active site consists of a serine/lysine catalytic
dyad. Conservation of these residues is seen in the
CPP-like proteins of this group. CPP proteins contain a
PDZ domain that promotes protein-protein interactions
and is important for substrate recognition however, most
of CPP-like proteins only have an internal fragment or
lack the PDZ domain.
Length = 256
Score = 29.5 bits (67), Expect = 0.88
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 5/31 (16%)
Query: 16 LITNKRTASSDLLNL-----ITNKRTASSSE 41
L ++K A + LNL +T+ TAS+SE
Sbjct: 146 LFSSKTLAGGNSLNLSKVYVLTSGSTASASE 176
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 29.7 bits (68), Expect = 0.92
Identities = 14/69 (20%), Positives = 22/69 (31%), Gaps = 38/69 (55%)
Query: 72 ECGKRPKFKCPHCNK-----------KCHQKCNLKSHIALKHDQLLAPLAPRSYRRNSQL 120
+CG +CPHC+ +CH C + I P++
Sbjct: 386 DCGWV--AECPHCDASLTLHRFQRRLRCHH-CGYQEPI------------PKA------- 423
Query: 121 NGSFICPKC 129
CP+C
Sbjct: 424 -----CPEC 427
Score = 28.6 bits (65), Expect = 1.8
Identities = 13/36 (36%), Positives = 16/36 (44%), Gaps = 4/36 (11%)
Query: 126 CPKCSNRYVYKHNLKQHLK-FECG-VEPQFK-CPYC 158
CP C H ++ L+ CG EP K CP C
Sbjct: 393 CPHCDASLTL-HRFQRRLRCHHCGYQEPIPKACPEC 427
>gnl|CDD|226849 COG4425, COG4425, Predicted membrane protein [Function unknown].
Length = 588
Score = 29.4 bits (66), Expect = 0.98
Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 7/45 (15%)
Query: 7 QPPSTDLLNLITNKRTA-------SSDLLNLITNKRTASSSEDKP 44
+ PS DL +++ + A +S L N +T R A S E P
Sbjct: 412 EAPSMDLFDVLGDFDGALWSGPPFNSTLWNSLTADRDAGSPEWLP 456
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 26.3 bits (58), Expect = 1.1
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 79 FKCPHCNKKCHQKCNLKSHI 98
++CP C K K L+ H+
Sbjct: 1 YRCPECGKVFKSKSALREHM 20
Score = 24.3 bits (53), Expect = 5.6
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 153 FKCPYCDKRCKLKGNLMSHI 172
++CP C K K K L H+
Sbjct: 1 YRCPECGKVFKSKSALREHM 20
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 28.9 bits (64), Expect = 1.4
Identities = 19/86 (22%), Positives = 27/86 (31%), Gaps = 20/86 (23%)
Query: 38 SSSEDKPAGEDVFACP--KCSKTYLRQYTLNAHLRYE------------------CGKRP 77
S K + CP C+K Y Q L H+ + K
Sbjct: 338 PSRMLKVKDGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDK 397
Query: 78 KFKCPHCNKKCHQKCNLKSHIALKHD 103
++C C+K+ LK H HD
Sbjct: 398 PYRCEVCDKRYKNLNGLKYHRKHSHD 423
>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 = 25.7 bits (56), Expect = 2.2
Identities = 11/24 (45%), Positives = 12/24 (50%)
Query: 79 FKCPHCNKKCHQKCNLKSHIALKH 102
FKCP C K K LK H+ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
Score = 24.1 bits (52), Expect = 7.3
Identities = 10/24 (41%), Positives = 11/24 (45%)
Query: 153 FKCPYCDKRCKLKGNLMSHIALKH 176
FKCP C K K L H+ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
>gnl|CDD|214582 smart00245, TSPc, tail specific protease. tail specific protease.
Length = 192
Score = 27.2 bits (61), Expect = 3.8
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 18 TNKRTASSDLLNLITNKRTASSSED 42
N S L ++ NK TAS+SE
Sbjct: 105 ANLGRKYSKPLVVLVNKGTASASEI 129
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 24.7 bits (54), Expect = 4.3
Identities = 10/26 (38%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 138 NLKQHLKFECGVEPQFKCPYCDKRCK 163
NL++H++ G +P +KCP C K
Sbjct: 1 NLRRHMRTHTGEKP-YKCPVCGKSFS 25
>gnl|CDD|232883 TIGR00225, prc, C-terminal peptidase (prc). A C-terminal peptidase
with different substrates in different species including
processing of D1 protein of the photosystem II reaction
center in higher plants and cleavage of a peptide of 11
residues from the precursor form of penicillin-binding
protein in E.coli E.coli and H influenza have the most
distal branch of the tree and their proteins have an
N-terminal 200 amino acids that show no homology to
other proteins in the database [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Protein fate, Protein modification and repair].
Length = 334
Score = 27.3 bits (61), Expect = 4.8
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 18 TNKRTASSDLLNLITNKRTASSSE 41
N R + L ++ N+ +AS+SE
Sbjct: 227 ANGRQPYNLPLVVLVNRGSASASE 250
>gnl|CDD|237799 PRK14715, PRK14715, DNA polymerase II large subunit; Provisional.
Length = 1627
Score = 27.5 bits (61), Expect = 5.4
Identities = 12/44 (27%), Positives = 14/44 (31%), Gaps = 17/44 (38%)
Query: 123 SFICPKCSNRYVYKHNLKQHLKFECGVEPQFKCPYCDKRCKLKG 166
F CPKC V CP+C R +LK
Sbjct: 674 FFKCPKCGK-----------------VGLYHVCPFCGTRVELKP 700
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 27.3 bits (61), Expect = 6.1
Identities = 9/41 (21%), Positives = 15/41 (36%), Gaps = 14/41 (34%)
Query: 72 ECGKRPKFKCPHCNK-----------KCHQKCNLKSHIALK 101
+CG +CP+C+ +CH C + I
Sbjct: 440 DCGYI--AECPNCDSPLTLHKATGQLRCHY-CGYQEPIPQS 477
>gnl|CDD|234471 TIGR04104, cxxc_20_cxxc, cxxc_20_cxxc protein. This small,
uncommon, poorly conserved protein is found primarily
in the Firmicutes. It features are pair of CxxC motifs
separated by about 20 amino acids, followed by a highly
hydrophobic region of about 45 amino acids. It has no
conserved gene neighborhood, and its function is
unknown.
Length = 94
Score = 25.8 bits (57), Expect = 7.0
Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 6/46 (13%)
Query: 52 CPKCSKTYLRQYTLNAHLRYECGKRPKFKCPHCNKKCHQKCNLKSH 97
C C++ + + L + KCP+C K Q KS
Sbjct: 3 CKNCNEKFSYKELLKSLFS----LYRPIKCPNCGTK--QYLTAKSR 42
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys. The
C2H2 zinc finger is composed of two short beta strands
followed by an alpha helix. The amino terminal part of
the helix binds the major groove in DNA binding zinc
fingers. The accepted consensus binding sequence for Sp1
is usually defined by the asymmetric hexanucleotide core
GGGCGG but this sequence does not include, among others,
the GAG (=CTC) repeat that constitutes a high-affinity
site for Sp1 binding to the wt1 promoter.
Length = 22
Score = 23.8 bits (52), Expect = 7.6
Identities = 9/19 (47%), Positives = 10/19 (52%)
Query: 154 KCPYCDKRCKLKGNLMSHI 172
KCP C K K NL H+
Sbjct: 1 KCPDCGKSFSRKSNLKRHL 19
>gnl|CDD|236170 PRK08166, PRK08166, NADH dehydrogenase subunit G; Validated.
Length = 791
Score = 26.8 bits (60), Expect = 7.7
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 3/31 (9%)
Query: 115 RRNSQLNGSFICPKCSNRYVYKH-NLKQHLK 144
R N +NG F+C + R+ Y + NLK +
Sbjct: 252 RYNGAVNGYFLCDR--GRFGYGYVNLKDRPR 280
>gnl|CDD|237996 cd00029, C1, Protein kinase C conserved region 1 (C1) .
Cysteine-rich zinc binding domain. Some members of this
domain family bind phorbol esters and diacylglycerol,
some are reported to bind RasGTP. May occur in tandem
arrangement. Diacylglycerol (DAG) is a second
messenger, released by activation of Phospholipase D.
Phorbol Esters (PE) can act as analogues of DAG and
mimic its downstream effects in, for example, tumor
promotion. Protein Kinases C are activated by DAG/PE,
this activation is mediated by their N-terminal
conserved region (C1). DAG/PE binding may be
phospholipid dependent. C1 domains may also mediate
DAG/PE signals in chimaerins (a family of Rac GTPase
activating proteins), RasGRPs (exchange factors for
Ras/Rap1), and Munc13 isoforms (scaffolding proteins
involved in exocytosis).
Length = 50
Score = 24.4 bits (53), Expect = 8.2
Identities = 7/20 (35%), Positives = 10/20 (50%)
Query: 73 CGKRPKFKCPHCNKKCHQKC 92
+ +C C KCH+KC
Sbjct: 23 GLFKQGLRCSWCKVKCHKKC 42
>gnl|CDD|225995 COG3464, COG3464, Transposase and inactivated derivatives [DNA
replication, recombination, and repair].
Length = 402
Score = 26.7 bits (59), Expect = 8.2
Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 10/49 (20%)
Query: 123 SFICPKCSNRYVYKHNLK----QHLK-FECGV-----EPQFKCPYCDKR 161
CP+C R + +H + Q L FE V + ++KC C KR
Sbjct: 38 KHRCPECGQRTIRRHGWRIRKIQDLPLFEVPVYLFLRKRRYKCCRCGKR 86
>gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A'.
This family consists of the archaeal A' subunit of the
DNA-directed RNA polymerase. The example from
Methanocaldococcus jannaschii contains an intein.
Length = 867
Score = 26.6 bits (59), Expect = 9.2
Identities = 15/57 (26%), Positives = 20/57 (35%), Gaps = 23/57 (40%)
Query: 52 CPKCSK---------TYLRQY------------TLNAHLRYECGKRPKFKCPHCNKK 87
C KC + YL + TL + E KR KCPHC ++
Sbjct: 96 CRKCGRITLTEEEIEQYLEKINKLKEEGGDLASTLIEKIVKEAAKR--MKCPHCGEE 150
>gnl|CDD|197519 smart00109, C1, Protein kinase C conserved region 1 (C1) domains
(Cysteine-rich domains). Some bind phorbol esters and
diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Length = 50
Score = 24.4 bits (53), Expect = 9.3
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 79 FKCPHCNKKCHQKC 92
+C C KCH+KC
Sbjct: 29 LRCSECKVKCHKKC 42
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 0.134 0.426
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: 7,980,890
Number of extensions: 648417
Number of successful extensions: 916
Number of sequences better than 10.0: 1
Number of HSP's gapped: 907
Number of HSP's successfully gapped: 83
Length of query: 177
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 86
Effective length of database: 6,901,388
Effective search space: 593519368
Effective search space used: 593519368
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 (21.9 bits)
S2: 56 (25.4 bits)