RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9954
(196 letters)
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 42.4 bits (99), Expect = 7e-05
Identities = 27/58 (46%), Positives = 36/58 (62%)
Query: 5 FDFLCSQFPHCAKAFSRLENLKIHQRSHTGERPYSCTYEGCHKAFSNSSDRAKHQRTH 62
P+C +FSRLE+L H RSHTGE+P C+Y GC K+FS + ++H RTH
Sbjct: 29 NAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTH 86
Score = 41.6 bits (97), Expect = 1e-04
Identities = 29/118 (24%), Positives = 45/118 (38%), Gaps = 6/118 (5%)
Query: 15 CAKAFSRLENLKIHQRS--HTGE--RPYSCTYEGCHKAFSNSSDRAKHQRTHFDTRPYKC 70
C +FSR L H RS H+GE +P+SC Y C K FS + +H H P K
Sbjct: 295 CNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKE 354
Query: 71 MYKGCTKRYTDPSSLRKHAKNHNHDHLTPAKMRKLNYAKPGDIVPSVRNVNSSVPLNP 128
+ +++ + + L +K I R+ N S+ +
Sbjct: 355 KLLNSSSKFSPLLNNEPPQSLQQYKDLKN--DKKSETLSNSCIRNFKRDSNLSLHIIT 410
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 35.1 bits (81), Expect = 9e-04
Identities = 15/28 (53%), Positives = 20/28 (71%), Gaps = 2/28 (7%)
Query: 24 NLKIHQRSHTGERPYSCTYEGCHKAFSN 51
NL+ H R+HTGE+PY C C K+FS+
Sbjct: 1 NLRRHMRTHTGEKPYKCPV--CGKSFSS 26
Score = 25.4 bits (56), Expect = 2.7
Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 2/24 (8%)
Query: 57 KHQRTHFDTRPYKCMYKGCTKRYT 80
+H RTH +PYKC C K ++
Sbjct: 4 RHMRTHTGEKPYKCPV--CGKSFS 25
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 37.8 bits (87), Expect = 0.002
Identities = 22/81 (27%), Positives = 32/81 (39%), Gaps = 22/81 (27%)
Query: 34 GERPYSCTYEGCHKAFSNSS-------------------DRAKHQRTHFDTRPYKCMYKG 74
+PY C EGC+K + N + K +PY+C
Sbjct: 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEV-- 403
Query: 75 CTKRYTDPSSLRKHAKNHNHD 95
C KRY + + L+ H K H+HD
Sbjct: 404 CDKRYKNLNGLKYHRK-HSHD 423
Score = 31.6 bits (71), Expect = 0.26
Identities = 18/81 (22%), Positives = 31/81 (38%), Gaps = 7/81 (8%)
Query: 19 FSRLENLKIHQRSHTGERPYSCTYEGCHKAFSNSSDRAKHQRTHFDTRPYKCMYKGCTKR 78
S E + + + T + H N ++ + D +PYKC +GC K+
Sbjct: 305 ISTGEMIDVRKLPCTNSSS---NGKLAHGGERNIDTPSRMLKV-KDGKPYKCPVEGCNKK 360
Query: 79 YTDPSSLRKHAKNHNHDHLTP 99
Y + + L+ H H H
Sbjct: 361 YKNQNGLKYHML---HGHQNQ 378
>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 = 28.5 bits (64), Expect = 0.19
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 13 PHCAKAFSRLENLKIHQRSH 32
P C K+FSR NLK H R+H
Sbjct: 3 PDCGKSFSRKSNLKRHLRTH 22
Score = 26.5 bits (59), Expect = 1.1
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 43 EGCHKAFSNSSDRAKHQRTH 62
C K+FS S+ +H RTH
Sbjct: 3 PDCGKSFSRKSNLKRHLRTH 22
Score = 24.6 bits (54), Expect = 5.5
Identities = 6/20 (30%), Positives = 12/20 (60%)
Query: 73 KGCTKRYTDPSSLRKHAKNH 92
C K ++ S+L++H + H
Sbjct: 3 PDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|239270 cd02972, DsbA_family, DsbA family; consists of DsbA and DsbA-like
proteins, including DsbC, DsbG, glutathione (GSH)
S-transferase kappa (GSTK),
2-hydroxychromene-2-carboxylate (HCCA) isomerase, an
oxidoreductase (FrnE) presumed to be involved in
frenolicin biosynthesis, a 27-kDa outer membrane
protein, and similar proteins. Members of this family
contain a redox active CXXC motif (except GSTK and HCCA
isomerase) imbedded in a TRX fold, and an alpha helical
insert of about 75 residues (shorter in DsbC and DsbG)
relative to TRX. DsbA is involved in the oxidative
protein folding pathway in prokaryotes, catalyzing
disulfide bond formation of proteins secreted into the
bacterial periplasm. DsbC and DsbG function as protein
disulfide isomerases and chaperones to correct
non-native disulfide bonds formed by DsbA and prevent
aggregation of incorrectly folded proteins.
Length = 98
Score = 28.9 bits (65), Expect = 0.55
Identities = 9/27 (33%), Positives = 10/27 (37%), Gaps = 3/27 (11%)
Query: 4 IFDFLCSQFPHCAKAFSRLENLKIHQR 30
FD LC P+C LE L
Sbjct: 4 FFDPLC---PYCYLFEPELEKLLYADD 27
>gnl|CDD|224565 COG1651, DsbG, Protein-disulfide isomerase [Posttranslational
modification, protein turnover, chaperones].
Length = 244
Score = 28.3 bits (63), Expect = 2.4
Identities = 22/120 (18%), Positives = 39/120 (32%), Gaps = 20/120 (16%)
Query: 5 FDFLCSQFPHCAKAFSRLENLKIHQRSHTGE-----RPY-----SCTYEGCHKAFSNSSD 54
FD+ C P+C +AF L+ I G+ R + +C Y C +A +
Sbjct: 92 FDYTC---PYCKEAFPELKKKYI----DDGKVRLVLREFPFLDPACPY--CRRAAQAARC 142
Query: 55 RAKHQRTHFDTRPYKCMYKGCTKRYTDPSSLRKHAKNHNHDHLTPAKMRKLNYAKPGDIV 114
A + ++ + + K + L K KLN ++
Sbjct: 143 AADQGIVRYWAFHDA-LFGSQAEAWAASILCAKDLAKADLAALDEGKKAKLNQKACDALI 201
>gnl|CDD|236287 PRK08561, rps15p, 30S ribosomal protein S15P; Reviewed.
Length = 151
Score = 27.9 bits (63), Expect = 2.6
Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 8/40 (20%)
Query: 85 LRKHAKNHNHDH-------LTPAKMRKL-NYAKPGDIVPS 116
LRKH + + D L +K+R+L Y K ++P+
Sbjct: 98 LRKHLEENPKDLHNKRGLQLIESKIRRLVKYYKRTGVLPA 137
>gnl|CDD|151380 pfam10933, DUF2827, Protein of unknown function (DUF2827). This is
a family of uncharacterized proteins found in
Burkholderia.
Length = 364
Score = 27.4 bits (61), Expect = 5.6
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 170 ISRNLQDVPDLGLGFGYQEGEAA 192
I R +P+ GL FGY+ G A
Sbjct: 167 IERRTAALPEAGLRFGYRPGRPA 189
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 24.3 bits (53), Expect = 7.0
Identities = 9/25 (36%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 68 YKCMYKGCTKRYTDPSSLRKHAKNH 92
Y+C C K + S+LR+H + H
Sbjct: 1 YRCPE--CGKVFKSKSALREHMRTH 23
Score = 24.0 bits (52), Expect = 8.3
Identities = 10/25 (40%), Positives = 12/25 (48%), Gaps = 2/25 (8%)
Query: 38 YSCTYEGCHKAFSNSSDRAKHQRTH 62
Y C C K F + S +H RTH
Sbjct: 1 YRCPE--CGKVFKSKSALREHMRTH 23
Score = 24.0 bits (52), Expect = 9.1
Identities = 8/20 (40%), Positives = 10/20 (50%)
Query: 13 PHCAKAFSRLENLKIHQRSH 32
P C K F L+ H R+H
Sbjct: 4 PECGKVFKSKSALREHMRTH 23
>gnl|CDD|227662 COG5368, COG5368, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 451
Score = 26.8 bits (59), Expect = 8.1
Identities = 9/57 (15%), Positives = 16/57 (28%), Gaps = 12/57 (21%)
Query: 20 SRLENLKIHQRSHTGERPYSCTYEG--------CH--KAFSNSSDRAKHQRTHFDTR 66
SR + R + P G C K + +S + + + R
Sbjct: 268 SRRAQV--LHRDYANYNPCGFRGYGEDLWGLSACDGPKGYVVNSPGRRRRFFGYRAR 322
>gnl|CDD|173973 cd08208, RLP_Photo, Ribulose bisphosphate carboxylase like proteins
from phototrophic bacteria. Ribulose bisphosphate
carboxylase (Rubisco) plays an important role in the
Calvin reductive pentose phosphate pathway. It catalyzes
the primary CO2 fixation step. Rubisco is activated by
carbamylation of an active site lysine, stabilized by a
divalent cation, which then catalyzes the proton
abstraction from the substrate ribulose 1,5 bisphosphate
(RuBP) and leads to the formation of two molecules of
3-phosphoglycerate. Members of the Rubisco family can be
divided into 4 subgroups, Form I-IV, which differ in
their taxonomic distribution and subunit composition.
Form I-III have Rubisco activity, while Form IV, also
called Rubisco-like proteins (RLP), are missing critical
active site residues and therefore do not catalyze CO2
fixation. They are believed to utilize a related
enzymatic mechanism, but have divergent functions. The
specific function of this subgroup is unknown.
Length = 424
Score = 26.8 bits (59), Expect = 8.8
Identities = 13/26 (50%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 8 LCSQFPHCAKAFSRLENLKIHQRSHT 33
L + FP A +FSRLE IH R T
Sbjct: 280 LIAHFPFIA-SFSRLEKYGIHSRVMT 304
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 0.134 0.422
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: 9,691,759
Number of extensions: 835025
Number of successful extensions: 661
Number of sequences better than 10.0: 1
Number of HSP's gapped: 655
Number of HSP's successfully gapped: 35
Length of query: 196
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 104
Effective length of database: 6,857,034
Effective search space: 713131536
Effective search space used: 713131536
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: 56 (25.5 bits)