RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3949
(103 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 30.4 bits (69), Expect = 0.016
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 52 SMKSHLRKHSGEKPYKCLFCDYHCTQ 77
+++ H+R H+GEKPYKC C +
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
>gnl|CDD|219477 pfam07585, DUF1551, Protein of unknown function (DUF1551). A
family of proteins identified in Rhodopirellula baltica.
Length = 338
Score = 28.5 bits (64), Expect = 0.45
Identities = 8/46 (17%), Positives = 16/46 (34%), Gaps = 2/46 (4%)
Query: 44 PYHTTYSQSMKSHLRKHSGEKPYKCLFCDYHCTQSGPLR--RHMKI 87
P S S+ S +S E + + L R++++
Sbjct: 114 PNALAGSVSIDSSTELYSAEANARLFLSGGGGFRVDLLVGYRYLRL 159
>gnl|CDD|222863 PHA02540, 61, DNA primase; Provisional.
Length = 337
Score = 28.0 bits (63), Expect = 0.86
Identities = 12/55 (21%), Positives = 18/55 (32%), Gaps = 9/55 (16%)
Query: 2 RCQYCKHSLSVSNGFEIVLSHTKSCTYISRPDHNYRFVCYTCPYHTTYSQSMKSH 56
RC C S K+ +I F C+ C YH + +K +
Sbjct: 29 RCPICGDSQK---------DKNKARGWIYEKKDGGVFKCHNCGYHRPFGNFLKDY 74
>gnl|CDD|150045 pfam09237, GAGA, GAGA factor. Members of this family bind to a
5'-GAGAG-3' DNA consensus binding site, and contain a
Cys2-His2 zinc finger core as well as an N-terminal
extension containing two highly basic regions. The zinc
finger core binds in the DNA major groove and
recognises the first three GAG bases of the consensus
in a manner similar to that seen in other classical
zinc finger-DNA complexes. The second basic region
forms a helix that interacts in the major groove
recognising the last G of the consensus, while the
first basic region wraps around the DNA in the minor
groove and recognises the A in the fourth position of
the consensus sequence.
Length = 54
Score = 26.5 bits (58), Expect = 0.90
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 59 KHSGEKPYKCLFCDYHCTQSGPLRRHMKIKHL 90
K E+P C C QS LRRH++++H
Sbjct: 18 KSQSEQPATCPICQAVIRQSRNLRRHLELRHF 49
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 27.7 bits (61), Expect = 1.1
Identities = 16/53 (30%), Positives = 21/53 (39%), Gaps = 8/53 (15%)
Query: 45 YHTTYSQSMKSHLRKHSGEKPYKCLFCDY-HCTQSGPLRRHMKIKHLMESSNS 96
Y+ T + + L P FC+ H G L H IK+ ME NS
Sbjct: 1944 YYLTLQEPKEDDL-------PSFGAFCEVEHSLSDGTLHIHSSIKYRMEYINS 1989
>gnl|CDD|214407 MTH00032, ND5, NADH dehydrogenase subunit 5; Provisional.
Length = 669
Score = 26.8 bits (59), Expect = 2.6
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 20 LSHTKSCTYISRPDHNYRFVCY 41
L H S +Y+S H RF+CY
Sbjct: 95 LVHIYSTSYMSDDPHVPRFLCY 116
>gnl|CDD|183125 PRK11413, PRK11413, putative hydratase; Provisional.
Length = 751
Score = 26.1 bits (58), Expect = 3.6
Identities = 11/20 (55%), Positives = 13/20 (65%), Gaps = 2/20 (10%)
Query: 83 RHMKIKHLMESSNSHDITFV 102
+KIK +S SHDITFV
Sbjct: 52 DKLKIK--FDSLASHDITFV 69
>gnl|CDD|222450 pfam13909, zf-H2C2_5, C2H2-type zinc-finger domain.
Length = 24
Score = 23.7 bits (52), Expect = 4.7
Identities = 11/24 (45%), Positives = 13/24 (54%), Gaps = 1/24 (4%)
Query: 66 YKCLFCDYHCTQSGPLRRHMKIKH 89
YKC C Y T L RH+K+ H
Sbjct: 1 YKCSHCPYSSTPKK-LERHLKLHH 23
>gnl|CDD|164925 PHA02524, 43A, DNA polymerase subunit A; Provisional.
Length = 498
Score = 25.7 bits (56), Expect = 5.2
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 44 PYHTTYSQSMKSHLRKHSGEKPY 66
P + Y M SH+R H+G+K Y
Sbjct: 123 PKYAKYEIDMISHVRLHNGKKTY 145
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 25.4 bits (55), Expect = 6.3
Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 5/49 (10%)
Query: 46 HTTYSQS-MKSHLRKHSGEKPYK----CLFCDYHCTQSGPLRRHMKIKH 89
+ S ++ H E+ +K C+FC + LRRH +++H
Sbjct: 196 IRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIYFYDDDELRRHCRLRH 244
>gnl|CDD|222754 pfam14438, SM-ATX, SM domain found in Ataxin-2. SM domain found
in Ataxin-2.
Length = 113
Score = 24.9 bits (55), Expect = 6.4
Identities = 5/17 (29%), Positives = 9/17 (52%)
Query: 8 HSLSVSNGFEIVLSHTK 24
H+ S + F +VL +
Sbjct: 30 HTASPEDDFGVVLKMAR 46
>gnl|CDD|221755 pfam12756, zf-C2H2_2, C2H2 type zinc-finger (2 copies). This
family contains two copies of a C2H2-like zinc finger
domain.
Length = 100
Score = 24.5 bits (54), Expect = 7.9
Identities = 7/22 (31%), Positives = 9/22 (40%)
Query: 68 CLFCDYHCTQSGPLRRHMKIKH 89
CLFC++ HM H
Sbjct: 2 CLFCNHTSDTVEENLEHMFKSH 23
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
0.325 0.134 0.447
Gapped
Lambda K H
0.267 0.0672 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,614,244
Number of extensions: 332541
Number of successful extensions: 470
Number of sequences better than 10.0: 1
Number of HSP's gapped: 469
Number of HSP's successfully gapped: 36
Length of query: 103
Length of database: 10,937,602
Length adjustment: 69
Effective length of query: 34
Effective length of database: 7,877,176
Effective search space: 267823984
Effective search space used: 267823984
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.3 bits)