RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8798
(114 letters)
>gnl|CDD|191218 pfam05182, Fip1, Fip1 motif. This short motif is about 40 amino
acids in length. In the Fip1 protein that is a component
of a yeast pre-mRNA polyadenylation factor that directly
interacts with poly(A) polymerase. This region of Fip1
is needed for the interaction with the Th1 subunit of
the complex and for specific polyadenylation of the
cleaved mRNA precursor.
Length = 45
Score = 71.1 bits (175), Expect = 4e-18
Identities = 23/35 (65%), Positives = 30/35 (85%)
Query: 74 HEFNLDQLEDKPWRKPGADITDYFNYGFTEETWRA 108
+++L+ E+KPWRKPGADI+DYFNYGF EETW+
Sbjct: 1 FDYDLESFEEKPWRKPGADISDYFNYGFNEETWKL 35
>gnl|CDD|227538 COG5213, FIP1, Polyadenylation factor I complex, subunit FIP1 [RNA
processing and modification].
Length = 266
Score = 57.7 bits (139), Expect = 3e-11
Identities = 24/66 (36%), Positives = 39/66 (59%), Gaps = 5/66 (7%)
Query: 49 QNPDPQGKFTVE-----EFEQIGTINSTAPHEFNLDQLEDKPWRKPGADITDYFNYGFTE 103
+ + G+ E + ++ T + + +++ +DKPWRKPGADI+DYFNYGF E
Sbjct: 89 KATESDGELIKEKTPEIDEDKEETEDGQNILDIDIESFKDKPWRKPGADISDYFNYGFNE 148
Query: 104 ETWRAH 109
TW+ +
Sbjct: 149 FTWKEY 154
>gnl|CDD|239052 cd02137, Nitroreductase_1, Nitroreductase-like family 1. A
subfamily of the nitroreductase family containing
uncharacterized proteins that are similar to
nitroreductase. Nitroreductase catalyzes the reduction
of nitroaromatic compounds such as nitrotoluenes,
nitrofurans and nitroimidazoles. This process requires
NAD(P)H as electron donor in an obligatory two-electron
transfer and uses FMN as cofactor. The enzyme is
typically a homodimer. Members of this family are also
called NADH dehydrogenase, oxygen-insensitive NAD(P)H
nitrogenase or dihydropteridine reductase.
Length = 148
Score = 26.8 bits (60), Expect = 2.2
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 5/36 (13%)
Query: 52 DPQGKFTVEEFEQIGTINSTAPHEFNLDQLEDKPWR 87
DP K EE ++I + + AP FNL +PWR
Sbjct: 14 DPDAKIPREELKEILELATLAPSSFNL-----QPWR 44
>gnl|CDD|235459 PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional.
Length = 308
Score = 26.7 bits (60), Expect = 3.1
Identities = 13/58 (22%), Positives = 24/58 (41%), Gaps = 20/58 (34%)
Query: 75 EFNLDQL--EDKPWR--------KPGADITDYFNY---------GFTEETWRAHHMSS 113
+ L+ + E+ R +PG ++ YFNY G TE ++ + +S
Sbjct: 12 DLKLEVVAGEEGLDREITTSDISRPGLELAGYFNYYHPERVQVLGKTEISY-LNQLSE 68
>gnl|CDD|184144 PRK13562, PRK13562, acetolactate synthase 1 regulatory subunit;
Provisional.
Length = 84
Score = 25.7 bits (56), Expect = 3.2
Identities = 13/51 (25%), Positives = 20/51 (39%), Gaps = 13/51 (25%)
Query: 56 KFTVEEFEQIGTINSTAPH----EFNLDQLEDKPWRKPG-------ADITD 95
K V + Q+ T+N ++N+D L +PG DI D
Sbjct: 6 KLQVAD--QVSTLNRITSAFVRLQYNIDTLHVTHSEQPGISNMEIQVDIQD 54
>gnl|CDD|183147 PRK11465, PRK11465, putative mechanosensitive channel protein;
Provisional.
Length = 741
Score = 25.9 bits (57), Expect = 6.8
Identities = 11/57 (19%), Positives = 25/57 (43%), Gaps = 5/57 (8%)
Query: 18 NTGDPNTTEPPQPDPKEQ-SSFSELPAFSDIAQNPDPQGKFTVEEFEQIGTINSTAP 73
+ D T P+PD +++ ++++ A +D+ N D K +++ P
Sbjct: 28 TSTDSTTEPAPEPDIEQKKAAYA---ALADVLDN-DTSRKELIDQLRTAAATPPAEP 80
>gnl|CDD|187590 cd05329, TR_SDR_c, tropinone reductase-I and II (TR-1, and
TR-II)-like, classical (c) SDRs. This subgroup includes
TR-I and TR-II; these proteins are members of the SDR
family. TRs catalyze the NADPH-dependent reductions of
the 3-carbonyl group of tropinone, to a beta-hydroxyl
group. TR-I and TR-II produce different stereoisomers
from tropinone, TR-I produces tropine
(3alpha-hydroxytropane), and TR-II, produces
pseudotropine (sigma-tropine, 3beta-hydroxytropane).
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 251
Score = 25.1 bits (55), Expect = 9.4
Identities = 7/25 (28%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 57 FTVEEFEQIGTINSTAPHEFNLDQL 81
+T E++ I + N A ++L +L
Sbjct: 103 YTEEDYSLIMSTNFEAA--YHLSRL 125
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
0.309 0.130 0.403
Gapped
Lambda K H
0.267 0.0604 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,050,403
Number of extensions: 505660
Number of successful extensions: 387
Number of sequences better than 10.0: 1
Number of HSP's gapped: 387
Number of HSP's successfully gapped: 15
Length of query: 114
Length of database: 10,937,602
Length adjustment: 78
Effective length of query: 36
Effective length of database: 7,477,990
Effective search space: 269207640
Effective search space used: 269207640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 53 (24.5 bits)