RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16225
(290 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 37.0 bits (86), Expect = 3e-04
Identities = 15/27 (55%), Positives = 18/27 (66%), Gaps = 2/27 (7%)
Query: 250 LVNHIRVHTGEKPFPCPFPTCGKVFAR 276
L H+R HTGEKP+ CP CGK F+
Sbjct: 2 LRRHMRTHTGEKPYKCPV--CGKSFSS 26
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 36.2 bits (83), Expect = 0.017
Identities = 24/55 (43%), Positives = 26/55 (47%)
Query: 235 DGCPRNGRPFKAKYKLVNHIRVHTGEKPFPCPFPTCGKVFARSENLKIHKRTHTE 289
D CP F L HIR HTGEKP C + C K F+R L H RTH
Sbjct: 34 DSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHN 88
Score = 28.1 bits (62), Expect = 6.0
Identities = 20/48 (41%), Positives = 23/48 (47%)
Query: 242 RPFKAKYKLVNHIRVHTGEKPFPCPFPTCGKVFARSENLKIHKRTHTE 289
R FK L HI H +P+ C P C K F R NL HK+ HT
Sbjct: 396 RNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTN 443
>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 = 30.4 bits (69), Expect = 0.061
Identities = 13/20 (65%), Positives = 14/20 (70%)
Query: 268 PTCGKVFARSENLKIHKRTH 287
P CGK F+R NLK H RTH
Sbjct: 3 PDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 31.7 bits (72), Expect = 0.52
Identities = 22/145 (15%), Positives = 34/145 (23%), Gaps = 22/145 (15%)
Query: 19 PHNHMMPLPGNNIKMI-NTFMETPTLASMGIKMSPPPPTSPHQLQSG----------GNH 67
P + P G+ ++ F+ P+ A + P P P LQ
Sbjct: 200 PPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQMPPPP 259
Query: 68 MMPLGGNNENHHNNHYNSYPMPHMQTGYSRDYLLRRDDYANNIHHPPPVPPPPVQPPGND 127
P + P L + N PP P P
Sbjct: 260 PQPPQQQQQPPQPQAQ----PPPQNQPTPHPGLPQG---QNAPLPPPQQPQ---LLPLVQ 309
Query: 128 MFFHHPVDPLSQHSML-YHHHHREP 151
P + ++ RE
Sbjct: 310 QPQGQQRGPQFREQLVQLSQQQREA 334
Score = 29.0 bits (65), Expect = 3.3
Identities = 11/117 (9%), Positives = 19/117 (16%), Gaps = 8/117 (6%)
Query: 48 IKMSPPPPTSPHQLQSGGNHMMPLGGNNENHHNNHYNSYPMPHMQTGYSRDYLLRRDDYA 107
++ QL ++P G P + + +
Sbjct: 159 VEAQLQQRQQAPQLPQPPQQVLPQGMPPRQAAFPQQGPPEQPPGYPQPPQGHPEQVQPQQ 218
Query: 108 NNIH--------HPPPVPPPPVQPPGNDMFFHHPVDPLSQHSMLYHHHHREPVYSNM 156
PP P P F + P
Sbjct: 219 FLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQMPPPPPQPPQQQQQPPQPQAQ 275
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 27.4 bits (61), Expect = 0.71
Identities = 12/25 (48%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 263 FPCPFPTCGKVFARSENLKIHKRTH 287
+ CP CGKVF L+ H RTH
Sbjct: 1 YRCPE--CGKVFKSKSALREHMRTH 23
>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit.
Transcription initiation factor IIA (TFIIA) is a
heterotrimer, the three subunits being known as alpha,
beta, and gamma, in order of molecular weight. The N and
C-terminal domains of the gamma subunit are represented
in pfam02268 and pfam02751, respectively. This family
represents the precursor that yields both the alpha and
beta subunits. The TFIIA heterotrimer is an essential
general transcription initiation factor for the
expression of genes transcribed by RNA polymerase II.
Together with TFIID, TFIIA binds to the promoter region;
this is the first step in the formation of a
pre-initiation complex (PIC). Binding of the rest of the
transcription machinery follows this step. After
initiation, the PIC does not completely dissociate from
the promoter. Some components, including TFIIA, remain
attached and re-initiate a subsequent round of
transcription.
Length = 332
Score = 30.5 bits (69), Expect = 0.97
Identities = 14/122 (11%), Positives = 21/122 (17%), Gaps = 21/122 (17%)
Query: 13 PPPTTSPHNHMMPLPGNNIKMINTFMETPTLASMGIKMSPPPPTSPHQLQSGGNHMMPLG 72
P P + +P T + PP T G +
Sbjct: 67 PQPPPTQALQALPAGDQQQHNTPTGSPA----------ANPPATFALPAGPAGPTIQT-- 114
Query: 73 GNNENHHNNHYNSYPMPHMQTGYSRDYLLRRDDYANNIHHP------PPVPPPPVQPPGN 126
E M S + + +P N
Sbjct: 115 ---EPGQLYPVQVPVMVTQNPANSPLDQPAQQRALQQLQQRYGAPASGQLPSQQQSAQKN 171
Query: 127 DM 128
D
Sbjct: 172 DE 173
>gnl|CDD|235709 PRK06132, PRK06132, hypothetical protein; Provisional.
Length = 359
Score = 29.6 bits (67), Expect = 1.9
Identities = 8/15 (53%), Positives = 12/15 (80%)
Query: 78 HHNNHYNSYPMPHMQ 92
H +N Y++ PMP+MQ
Sbjct: 109 HRSNIYSNAPMPYMQ 123
>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 = 26.4 bits (58), Expect = 2.0
Identities = 12/25 (48%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 263 FPCPFPTCGKVFARSENLKIHKRTH 287
F CP CGK F+ + LK H R H
Sbjct: 1 FKCPL--CGKSFSSKDALKRHLRKH 23
>gnl|CDD|197463 smart00004, NL, Domain found in Notch and Lin-12. The Notch
protein is essential for the proper differentiation of
the Drosophila ectoderm. This protein contains 3 NL
domains.
Length = 38
Score = 26.5 bits (59), Expect = 2.2
Identities = 6/12 (50%), Positives = 6/12 (50%)
Query: 225 PECTTHACFWDG 236
EC C WDG
Sbjct: 24 EECNNAECLWDG 35
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 29.3 bits (65), Expect = 2.3
Identities = 9/26 (34%), Positives = 11/26 (42%)
Query: 259 GEKPFPCPFPTCGKVFARSENLKIHK 284
KP+ CP C K + LK H
Sbjct: 346 DGKPYKCPVEGCNKKYKNQNGLKYHM 371
>gnl|CDD|226100 COG3570, StrB, Streptomycin 6-kinase [Defense mechanisms].
Length = 274
Score = 29.0 bits (65), Expect = 2.7
Identities = 15/46 (32%), Positives = 18/46 (39%), Gaps = 10/46 (21%)
Query: 88 MPHMQTGYSRDYLLRR--DDYANNI--------HHPPPVPPPPVQP 123
+ S D L+R DD A I H P P PPP + P
Sbjct: 80 LERAGGERSLDVLVRDGNDDAATRIACEALARLHAPRPSPPPELLP 125
>gnl|CDD|236630 PRK09853, PRK09853, putative selenate reductase subunit YgfK;
Provisional.
Length = 1019
Score = 29.2 bits (66), Expect = 2.8
Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 11/48 (22%)
Query: 207 FNNMHEIVTHLTVEHVGG--PECTTHACFWDGCPRNGRPFKAKYKLVN 252
F N +IV H+ EC A F CP NG+P+K K L +
Sbjct: 915 FQNRFQIV------HLDAMCNECGNCAQF---CPWNGKPYKDKITLFS 953
>gnl|CDD|132358 TIGR03315, Se_ygfK, putative selenate reductase, YgfK subunit.
Members of this protein family are YgfK, predicted to be
one subunit of a three-subunit, molybdopterin-containing
selenate reductase. This enzyme is found, typically, in
genomic regions associated with xanthine dehydrogenase
homologs predicted to belong to the selenium-dependent
molybdenum hydroxylases (SDMH). Therefore, the selenate
reductase is suggested to play a role in furnishing
selenide for SelD, the selenophosphate synthase.
Length = 1012
Score = 29.0 bits (65), Expect = 3.2
Identities = 16/48 (33%), Positives = 21/48 (43%), Gaps = 11/48 (22%)
Query: 207 FNNMHEIVTHLTVEHVGG--PECTTHACFWDGCPRNGRPFKAKYKLVN 252
F + +IV H+ G EC A F CP +G P+K K L
Sbjct: 910 FRDQFQIV------HLDGMCNECGNCATF---CPYDGAPYKDKLTLFW 948
>gnl|CDD|215328 PLN02609, PLN02609, catalase.
Length = 492
Score = 28.9 bits (65), Expect = 3.9
Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 7/66 (10%)
Query: 56 TSPHQLQSGGNHMM-PLGGNNENHHNNHYNSYPMPHMQTGYSRDYLLRRDDYANNIHHPP 114
T H+L G N++ P+ HHNNH+ + M M +Y R D + H
Sbjct: 351 TQRHRL--GPNYLQLPVNAPKCAHHNNHHEGF-MNFMHRDEEVNYFPSRFD---PVRHAE 404
Query: 115 PVPPPP 120
VP P
Sbjct: 405 RVPIPH 410
>gnl|CDD|178520 PLN02932, PLN02932, 3-ketoacyl-CoA synthase.
Length = 478
Score = 28.5 bits (63), Expect = 4.6
Identities = 11/23 (47%), Positives = 18/23 (78%), Gaps = 2/23 (8%)
Query: 245 KAKYKLVNHIRVHTG--EKPFPC 265
+AKY+LV+ +RVHTG ++ + C
Sbjct: 277 RAKYELVHTVRVHTGADDRSYEC 299
>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 = 26.8 bits (60), Expect = 6.0
Identities = 10/42 (23%), Positives = 18/42 (42%), Gaps = 9/42 (21%)
Query: 177 FFRYMRQPIKQDMTCLWIDTPGPRKTCGKMFNNMHEIVTHLT 218
Y+R+ I + CL+ CGK F ++ + H+
Sbjct: 39 LLNYLREKIHEGNECLY---------CGKQFKSLEALRQHMR 71
>gnl|CDD|216368 pfam01213, CAP_N, Adenylate cyclase associated (CAP) N terminal.
Length = 313
Score = 27.9 bits (62), Expect = 7.3
Identities = 7/19 (36%), Positives = 8/19 (42%)
Query: 113 PPPVPPPPVQPPGNDMFFH 131
P PPPP PP +
Sbjct: 231 SAPPPPPPPPPPSVPTISN 249
>gnl|CDD|227505 COG5178, PRP8, U5 snRNP spliceosome subunit [RNA processing and
modification].
Length = 2365
Score = 28.0 bits (62), Expect = 8.0
Identities = 12/24 (50%), Positives = 12/24 (50%), Gaps = 4/24 (16%)
Query: 113 PPPVPPPPVQPPGNDMFFHHPVDP 136
PP PPPP PPG F P P
Sbjct: 5 PPGNPPPPPPPPG----FEPPSQP 24
Score = 28.0 bits (62), Expect = 8.3
Identities = 10/24 (41%), Positives = 11/24 (45%), Gaps = 3/24 (12%)
Query: 113 PPPVPPPPVQPPGNDMFFHHPVDP 136
PPP PPP +PP P P
Sbjct: 10 PPPPPPPGFEPPSQPPP---PPPP 30
>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein. This
protein is covalently attached to the terminii of
replicating DNA in vivo.
Length = 548
Score = 27.7 bits (62), Expect = 8.8
Identities = 11/40 (27%), Positives = 15/40 (37%), Gaps = 3/40 (7%)
Query: 68 MMPLGGNNENHHNNHYNSYPMPHMQTGYSRDYLLRR-DDY 106
+ L P PH+ GY YL+R +DY
Sbjct: 2 LEDLAPRGPATAQWPLYGLPPPHLLVGYQ--YLVRTLNDY 39
>gnl|CDD|218397 pfam05044, Prox1, Homeobox prospero-like protein (PROX1). The
homeobox gene Prox1 is expressed in a subpopulation of
endothelial cells that, after budding from veins, gives
rise to the mammalian lymphatic system. Prox1 has been
found to be an early specific marker for the developing
liver and pancreas in the mammalian foregut endoderm.
This family contains an atypical homeobox domain.
Length = 908
Score = 27.7 bits (61), Expect = 9.4
Identities = 12/42 (28%), Positives = 13/42 (30%), Gaps = 1/42 (2%)
Query: 111 HHPPPVPPPPVQPPGNDMFF-HHPVDPLSQHSMLYHHHHREP 151
P + P PPG D P S H L HH
Sbjct: 663 FQSPHLGAPSGSPPGKDRDSPDLPRPTTSLHPKLLSAHHHPG 704
>gnl|CDD|240386 PTZ00370, PTZ00370, STEVOR; Provisional.
Length = 296
Score = 27.3 bits (61), Expect = 9.7
Identities = 7/10 (70%), Positives = 8/10 (80%)
Query: 75 NENHHNNHYN 84
EN+ NNHYN
Sbjct: 16 YENYLNNHYN 25
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 0.136 0.456
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,955,515
Number of extensions: 1368955
Number of successful extensions: 1724
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1651
Number of HSP's successfully gapped: 70
Length of query: 290
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 194
Effective length of database: 6,679,618
Effective search space: 1295845892
Effective search space used: 1295845892
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: 58 (26.3 bits)