RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12978
(210 letters)
>gnl|CDD|239088 cd02395, SF1_like-KH, Splicing factor 1 (SF1) K homology
RNA-binding domain (KH). Splicing factor 1 (SF1)
specifically recognizes the intron branch point sequence
(BPS) UACUAAC in the pre-mRNA transcripts during
spliceosome assembly. We show that the KH-QUA2 region of
SF1 defines an enlarged KH (hnRNP K) fold which is
necessary and sufficient for BPS binding. KH binds
single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional modifiers
of mRNA.
Length = 120
Score = 44.2 bits (105), Expect = 4e-06
Identities = 16/26 (61%), Positives = 19/26 (73%)
Query: 47 PQQAEGEDELKKRQLMELAIINGTYR 72
P G DELK+ QL ELA++NGTYR
Sbjct: 95 PAIEGGNDELKREQLRELALLNGTYR 120
>gnl|CDD|237350 PRK13322, PRK13322, pantothenate kinase; Reviewed.
Length = 246
Score = 28.8 bits (65), Expect = 1.9
Identities = 13/41 (31%), Positives = 15/41 (36%), Gaps = 11/41 (26%)
Query: 120 PGMPGMATQLRTPTATPLGAPLILSPRIPAIPTSAASLLNG 160
PG+ M LRT T RI +A SL G
Sbjct: 145 PGLYLMRDALRTHTR-----------RIRYDDGTADSLSPG 174
>gnl|CDD|215230 PLN02418, PLN02418, delta-1-pyrroline-5-carboxylate synthase.
Length = 718
Score = 28.2 bits (63), Expect = 3.4
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 66 IINGTYRDNNAKVLAAAVHILMLFPSSV-SFSAACDEEWRRMAVAAAQETQRL 117
I +G DN KVL + LF ++ + + R MAVAA + +++L
Sbjct: 259 ITSGYALDNIRKVLRGE-RVGTLFHQDAHLWAPSKEVGAREMAVAARESSRKL 310
>gnl|CDD|132707 TIGR03668, Rv0121_F420, PPOX class probable F420-dependent enzyme,
Rv0121 family. A Genome Properties metabolic
reconstruction for F420 biosynthesis shows that slightly
over 10 percent of all prokaryotes with fully sequenced
genomes, including about two thirds of the
Actinomycetales, make F420. A variant of the Partial
Phylogenetic Profiling algorithm, SIMBAL, shows that
this protein likely binds F420 in a cleft similar to
that in which the homologous enzyme pyridoxamine
phosphate oxidase (PPOX) binds FMN [Unknown function,
Enzymes of unknown specificity].
Length = 141
Score = 26.7 bits (59), Expect = 5.7
Identities = 14/50 (28%), Positives = 20/50 (40%), Gaps = 7/50 (14%)
Query: 100 DEEWRRMAVAAAQETQRLLSPGMPGMATQLRTPTA-------TPLGAPLI 142
D++W R+ A +L PG A +R A PL P+I
Sbjct: 81 DDDWTRLWWVRADGRAEILRPGEEEHAAAVRLLRAKYHQYQAVPLEGPVI 130
>gnl|CDD|227503 COG5176, MSL5, Splicing factor (branch point binding protein) [RNA
processing and modification].
Length = 269
Score = 27.2 bits (60), Expect = 6.1
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 4/49 (8%)
Query: 27 LDNVTESSMKILNVEFSSV-NPQQAEGEDELKKRQLMELAIINGTYRDN 74
D + LN + NP EG+++LK+ QL LA +NGT R +
Sbjct: 224 EDKICRLIKSQLNAIREARRNP---EGQNDLKRFQLRWLAHLNGTLRAD 269
>gnl|CDD|226067 COG3537, COG3537, Putative alpha-1,2-mannosidase [Carbohydrate
transport and metabolism].
Length = 768
Score = 27.5 bits (61), Expect = 7.3
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 119 SPGMPGMATQLRTPTATPLGAPL 141
G PG PT TP+G+PL
Sbjct: 99 QSGCPGFGDYSMLPTTTPVGSPL 121
>gnl|CDD|223445 COG0368, CobS, Cobalamin-5-phosphate synthase [Coenzyme
metabolism].
Length = 246
Score = 26.9 bits (60), Expect = 8.5
Identities = 16/84 (19%), Positives = 29/84 (34%), Gaps = 5/84 (5%)
Query: 78 VLAAAVHILMLFPSSVSFSAACDEEW---RRMAVAAAQETQRLLSPGMPGMATQLRTPTA 134
VL V L + + E RM + A + G+ G+ + P
Sbjct: 115 VLLLKVLALASLLDLGAAALLALAEVLAKSRMLLVAL--LSKPPYAGLGGLGKEFADPRK 172
Query: 135 TPLGAPLILSPRIPAIPTSAASLL 158
+GA L+L + A+ + +
Sbjct: 173 GLIGALLLLVLLLLALLFGLSGAI 196
>gnl|CDD|187553 cd05242, SDR_a8, atypical (a) SDRs, subgroup 8. This subgroup
contains atypical SDRs of unknown function. Proteins in
this subgroup have a glycine-rich NAD(P)-binding motif
consensus that resembles that of the extended SDRs,
(GXXGXXG or GGXGXXG), but lacks the characteristic
active site residues of the SDRs. A Cys often replaces
the usual Lys of the YXXXK active site motif, while the
upstream Ser is generally present and Arg replaces the
usual Asn. Atypical SDRs generally lack the catalytic
residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they 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 numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, 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. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, 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.
Length = 296
Score = 26.8 bits (60), Expect = 9.2
Identities = 16/60 (26%), Positives = 23/60 (38%), Gaps = 9/60 (15%)
Query: 90 PSSVSFSAACDEEWRRMAVAAAQETQRL--------LSPGMPGMATQLRTPTATPLGAPL 141
PS F A + W + A A++ R+ L P G ++ P LG PL
Sbjct: 129 PSGKDFLAEVCKAWEKAAQPASELGTRVVILRTGVVLGPD-GGALPKMLLPFRLGLGGPL 187
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
0.316 0.128 0.370
Gapped
Lambda K H
0.267 0.0808 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,615,414
Number of extensions: 979394
Number of successful extensions: 820
Number of sequences better than 10.0: 1
Number of HSP's gapped: 820
Number of HSP's successfully gapped: 16
Length of query: 210
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 117
Effective length of database: 6,812,680
Effective search space: 797083560
Effective search space used: 797083560
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (25.6 bits)