RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16846
(253 letters)
>gnl|CDD|204097 pfam08926, DUF1908, Domain of unknown function (DUF1908). This
domain is found in a set of hypothetical/structural
eukaryotic proteins.
Length = 282
Score = 69.1 bits (169), Expect = 7e-14
Identities = 33/61 (54%), Positives = 37/61 (60%), Gaps = 9/61 (14%)
Query: 187 PLESPRVASNQ---HFPFIPMKRPFNHLNTDCRSDGTRRWSVASLPSSGYGTTPGSSNVS 243
PL+SPR S +FPF + R+DG RRWSVASLPSSGYGT P SS VS
Sbjct: 1 PLDSPRNFSASASINFPFAR-----RIASRRGRADG-RRWSVASLPSSGYGTNPPSSTVS 54
Query: 244 S 244
S
Sbjct: 55 S 55
>gnl|CDD|99802 cd06206, bifunctional_CYPOR, These bifunctional proteins fuse
N-terminal cytochrome p450 with a cytochrome p450
reductase (CYPOR). NADPH cytochrome p450 reductase
serves as an electron donor in several oxygenase systems
and is a component of nitric oxide synthases and
methionine synthase reductases. CYPOR transfers two
electrons from NADPH to the heme of cytochrome p450 via
FAD and FMN. Ferredoxin-NADP+ (oxido)reductase is an
FAD-containing enzyme that catalyzes the reversible
electron transfer between NADP(H) and electron carrier
proteins such as ferredoxin and flavodoxin. Isoforms of
these flavoproteins (i.e. having a non-covalently bound
FAD as a prosthetic group) are present in chloroplasts,
mitochondria, and bacteria in which they participate in
a wide variety of redox metabolic pathways. The
C-terminal domain contains most of the NADP(H) binding
residues and the N-terminal domain interacts
non-covalently with the isoalloxazine rings of the
flavin molecule which lies largely in a large gap
betweed the two domains. Ferredoxin-NADP+ reductase
first accepts one electron from reduced ferredoxin to
form a flavin semiquinone intermediate. The enzyme then
accepts a second electron to form FADH2 which then
transfers two electrons and a proton to NADP+ to form
NADPH.
Length = 384
Score = 29.9 bits (68), Expect = 1.3
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 167 SFIANTSPTLPRCYSPMPSSPLESPRVAS 195
+F+A P PR YS + SSPL P A+
Sbjct: 151 TFLAMLPPMRPRQYS-ISSSPLVDPGHAT 178
>gnl|CDD|176479 cd08642, DNA_pol_A_pol_I_A, Polymerase I functions primarily to
fill DNA gaps that arise during DNA repair,
recombination and replication. Family A polymerase
(polymerase I) functions primarily to fill DNA gaps that
arise during DNA repair, recombination and replication.
DNA-dependent DNA polymerases can be classified in six
main groups based upon phylogenetic relationships with
E. coli polymerase I (classA), E. coli polymerase II
(class B), E.coli polymerase III (class C),
euryarchaaeota polymerase II (class D), human polymerase
beta (class x), E. coli UmuC/DinB and eukaryotic RAP
30/Xeroderma pigmentosum variant (class Y). Family A
polymerase are found primarily in organisms related to
prokaryotes and include prokaryotic DNA polymerase I
,mitochondrial polymerase delta, and several
bacteriphage polymerases including those from
odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is
have two functional domains located on the same
polypeptide; a 5'-3' polymerase and 5'-3' exonuclease.
Pol I uses its 5' nuclease activity to remove the
ribonucleotide portion of newly synthesized Okazaki
fragments and DNA polymerase activity to fill in the
resulting gap. A combination of phylogenomic and
signature sequence-based (or phonetic) approaches is
used to understand the evolutionary relationships among
bacteria. DNA polymerase I is one of the conserved
proteins that is used to search for protein signatures.
The structure of these polymerases resembles in overall
morphology a cupped human right hand, with fingers
(which bind an incoming nucleotide and interact with the
single-stranded template), palm (which harbors the
catalytic amino acid residues and also binds an incoming
dNTP) and thumb (which binds double-stranded DNA)
subdomains.
Length = 378
Score = 27.6 bits (62), Expect = 6.6
Identities = 16/68 (23%), Positives = 27/68 (39%), Gaps = 5/68 (7%)
Query: 89 KLWVEDDGGRRYSDSDKNDKKSKMKELDKNNEGSISNLVLMRKSNLGQSAPSLSNSMKDL 148
K W+ + GG D KK + L K G + VL + L +++ +M+
Sbjct: 36 KDWLNEQGGE----VDSLLKKDVVALLLKTAPGDVKR-VLELRQELSKTSVKKYEAMERA 90
Query: 149 TVPSGCLR 156
G +R
Sbjct: 91 VCSDGRVR 98
>gnl|CDD|235537 PRK05632, PRK05632, phosphate acetyltransferase; Reviewed.
Length = 684
Score = 27.8 bits (63), Expect = 6.8
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 235 TTPGSSNVSSIF 246
T PGSS VSS+F
Sbjct: 503 TAPGSSLVSSVF 514
>gnl|CDD|235223 PRK04132, PRK04132, replication factor C small subunit;
Provisional.
Length = 846
Score = 27.5 bits (61), Expect = 9.7
Identities = 10/36 (27%), Positives = 20/36 (55%)
Query: 22 SWSYKKPIRAPWEMVLEVFFLTEPLAKGDSTLNTPV 57
+WSY+K WE++ E+++ E L + L+ +
Sbjct: 374 NWSYRKAREISWELMKEIYYRLEELERLKKALSESI 409
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
0.312 0.127 0.374
Gapped
Lambda K H
0.267 0.0611 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,015,677
Number of extensions: 1050616
Number of successful extensions: 537
Number of sequences better than 10.0: 1
Number of HSP's gapped: 537
Number of HSP's successfully gapped: 10
Length of query: 253
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 158
Effective length of database: 6,723,972
Effective search space: 1062387576
Effective search space used: 1062387576
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 58 (26.4 bits)