RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16498
(102 letters)
>gnl|CDD|201590 pfam01085, HH_signal, Hedgehog amino-terminal signalling domain.
For the carboxyl Hint module, see pfam01079. Hedgehog is
a family of secreted signal molecules required for
embryonic cell differentiation.
Length = 160
Score = 150 bits (380), Expect = 3e-48
Identities = 59/71 (83%), Positives = 67/71 (94%)
Query: 1 MNEWPGVRLRVIEGWDEEGHHASDSLHYEGRAVDITTSDRDSSKYGLLARMAVEAGFDWV 60
MN+WPGV+LRV EGWDE+GHH+ +SLHYEGRAVDITTSDRD SKYG+LAR+AVEAGFDWV
Sbjct: 90 MNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRSKYGMLARLAVEAGFDWV 149
Query: 61 YYESRNHIHCS 71
YYES+ HIHCS
Sbjct: 150 YYESKAHIHCS 160
>gnl|CDD|116875 pfam08291, Peptidase_M15_3, Peptidase M15.
Length = 110
Score = 38.9 bits (91), Expect = 4e-05
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 4/51 (7%)
Query: 22 ASDSLHYEGRAVDITTSDRDSSKYGLLARMAVEAG-FDWVYYESRNHIHCS 71
A DS H G A DIT S ++ + LA++A G F + +H
Sbjct: 63 ARDSQHLTGLAADITVSGKNPEE---LAQIARAHGPFGIGIGGHNSFVHVD 110
>gnl|CDD|236203 PRK08255, PRK08255, salicylyl-CoA 5-hydroxylase; Reviewed.
Length = 765
Score = 28.8 bits (65), Expect = 0.44
Identities = 11/22 (50%), Positives = 13/22 (59%), Gaps = 6/22 (27%)
Query: 49 ARMAVEAGFDWVYYESRNHIHC 70
AR A EAGFDW+ +HC
Sbjct: 557 ARRAAEAGFDWL------ELHC 572
>gnl|CDD|178754 PLN03215, PLN03215, ascorbic acid mannose pathway regulator 1;
Provisional.
Length = 373
Score = 28.0 bits (62), Expect = 0.71
Identities = 16/70 (22%), Positives = 29/70 (41%), Gaps = 12/70 (17%)
Query: 1 MNEWPGVRLRVIEGWDEEGHHASDSLHYEGRA--------VDITTSDRDSSKYGLLARMA 52
+N W G V++ + G+H SD + ++G+ V SD + S++G
Sbjct: 184 INYWDG---NVLKALKQMGYHFSDIIVHKGQTYALDSIGIVYWINSDLEFSRFGTSLDEN 240
Query: 53 VEAGFDWVYY 62
+ G W
Sbjct: 241 ITDG-CWTGD 249
>gnl|CDD|216083 pfam00724, Oxidored_FMN, NADH:flavin oxidoreductase / NADH oxidase
family.
Length = 336
Score = 27.7 bits (62), Expect = 0.90
Identities = 11/28 (39%), Positives = 15/28 (53%), Gaps = 6/28 (21%)
Query: 44 KYGLLARMAVEAGFDWVYYESRNHIHCS 71
++ A+ AVEAGFD V IH +
Sbjct: 144 EFVQAAKRAVEAGFDGVE------IHGA 165
>gnl|CDD|239184 cd02783, MopB_CT_2, The MopB_CT_2 CD includes a group of related
uncharacterized bacterial and archaeal
molybdopterin-binding oxidoreductase-like domains with a
putative N-terminal iron-sulfur [4Fe-4S] cluster binding
site and molybdopterin cofactor binding site. This CD is
of the conserved molybdopterin_binding C-terminal
(MopB_CT) region present in many, but not all, MopB
homologs.
Length = 156
Score = 27.4 bits (61), Expect = 0.99
Identities = 17/67 (25%), Positives = 24/67 (35%), Gaps = 15/67 (22%)
Query: 50 RMAVEAGF---DWVYYESRN-HIHCSVKT----------VLDMVGIASALWALGRGFPPG 95
+ A E G DWV+ ES N + + + +G W L P
Sbjct: 39 KTAKELGIKDGDWVWVESVNGRVKGQARFTETVEPGTVWTWNAIGKRPGAWGLKPDAPES 98
Query: 96 VD-FILN 101
V F+LN
Sbjct: 99 VKGFLLN 105
>gnl|CDD|224814 COG1902, NemA, NADH:flavin oxidoreductases, Old Yellow Enzyme
family [Energy production and conversion].
Length = 363
Score = 27.6 bits (62), Expect = 1.1
Identities = 11/23 (47%), Positives = 12/23 (52%), Gaps = 6/23 (26%)
Query: 49 ARMAVEAGFDWVYYESRNHIHCS 71
AR A EAGFD V IH +
Sbjct: 155 ARRAKEAGFDGVE------IHGA 171
>gnl|CDD|237565 PRK13934, PRK13934, stationary phase survival protein SurE;
Provisional.
Length = 266
Score = 27.4 bits (61), Expect = 1.2
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 82 ASALWALGRGFPPGVDFI 99
A+A + L RG P GVD I
Sbjct: 151 ATAEYVLKRGMPKGVDVI 168
>gnl|CDD|236447 PRK09280, PRK09280, F0F1 ATP synthase subunit beta; Validated.
Length = 463
Score = 27.4 bits (62), Expect = 1.4
Identities = 9/11 (81%), Positives = 9/11 (81%)
Query: 1 MNEWPGVRLRV 11
MNE PG RLRV
Sbjct: 211 MNEPPGARLRV 221
>gnl|CDD|177345 PHA02101, PHA02101, hypothetical protein.
Length = 101
Score = 26.5 bits (58), Expect = 1.5
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 75 VLDMVGIASALWALGRGFPPGVD 97
V VG+AS W L R F PGV+
Sbjct: 57 VKTRVGLASYEWILARAFTPGVE 79
>gnl|CDD|178576 PLN02997, PLN02997, flavonol synthase.
Length = 325
Score = 27.3 bits (60), Expect = 1.5
Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 30 GRAVDITTSDRDSSKYGLLARMAVEAGFDWVYYESRNH-IHCSVKTVLDMVG 80
G AVD+ D S L R V+A +W ++ NH I + L MVG
Sbjct: 28 GSAVDVPVVDLSVSDEDFLVREVVKASEEWGVFQVVNHGIPTELMRQLQMVG 79
>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis
thaliana arginine/serine-rich-splicing factor RSp31 and
similar proteins from plants. This subfamily
corresponds to the RRM1in a family that represents a
novel group of arginine/serine (RS) or serine/arginine
(SR) splicing factors existing in plants, such as A.
thaliana RSp31, RSp35, RSp41 and similar proteins. Like
vertebrate RS splicing factors, these proteins function
as plant splicing factors and play crucial roles in
constitutive and alternative splicing in plants. They
all contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at their N-terminus, and
an RS domain at their C-terminus.
Length = 72
Score = 25.9 bits (57), Expect = 1.6
Identities = 13/36 (36%), Positives = 22/36 (61%), Gaps = 3/36 (8%)
Query: 28 YEGRAVDITTSDRDSSKYGLLARMAVEAGFDWVYYE 63
Y+ R +I +R KYG + R+ +++GF +VY E
Sbjct: 10 YDARQSEI---ERLFGKYGRVDRVDMKSGFAFVYME 42
>gnl|CDD|239242 cd02932, OYE_YqiM_FMN, Old yellow enzyme (OYE) YqjM-like FMN
binding domain. YqjM is involved in the oxidative stress
response of Bacillus subtilis. Like the other OYE
members, each monomer of YqjM contains FMN as a
non-covalently bound cofactor and uses NADPH as a
reducing agent. The YqjM enzyme exists as a
homotetramer that is assembled as a dimer of
catalytically dependent dimers, while other OYE members
exist only as monomers or dimers. Moreover, the protein
displays a shared active site architecture where an
arginine finger at the COOH terminus of one monomer
extends into the active site of the adjacent monomer and
is directly involved in substrate recognition. Another
remarkable difference in the binding of the ligand in
YqjM is represented by the contribution of the
NH2-terminal tyrosine instead of a COOH-terminal
tyrosine in OYE and its homologs.
Length = 336
Score = 26.7 bits (60), Expect = 1.9
Identities = 11/22 (50%), Positives = 12/22 (54%), Gaps = 6/22 (27%)
Query: 49 ARMAVEAGFDWVYYESRNHIHC 70
AR AVEAGFD + IH
Sbjct: 160 ARRAVEAGFDVI------EIHA 175
>gnl|CDD|223133 COG0055, AtpD, F0F1-type ATP synthase, beta subunit [Energy
production and conversion].
Length = 468
Score = 26.8 bits (60), Expect = 2.0
Identities = 8/11 (72%), Positives = 9/11 (81%)
Query: 1 MNEWPGVRLRV 11
MNE PG R+RV
Sbjct: 214 MNEPPGARMRV 224
>gnl|CDD|185191 PRK15291, PRK15291, fimbrial protein StgD; Provisional.
Length = 355
Score = 26.6 bits (58), Expect = 2.4
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 7/64 (10%)
Query: 36 TTSDRDSSKYGLLARMAVEAGFDWVYYESRNHIHCSVK-------TVLDMVGIASALWAL 88
T + +S K G + F VYY +R+ + T+ D + IA+++ L
Sbjct: 61 TLTSSESYKVGCSCLTHFSSTFREVYYTARSPLSIDTTRNGYTYYTLNDNLSIATSIAVL 120
Query: 89 GRGF 92
GRGF
Sbjct: 121 GRGF 124
>gnl|CDD|129272 TIGR00168, infC, translation initiation factor IF-3. infC uses
abnormal initiation codons such as AUA, AUC, and CUG
which render its expression particularly sensitive to
excess of its gene product IF-3 thereby regulating its
own expression [Protein synthesis, Translation factors].
Length = 165
Score = 26.2 bits (58), Expect = 3.0
Identities = 5/26 (19%), Positives = 12/26 (46%)
Query: 7 VRLRVIEGWDEEGHHASDSLHYEGRA 32
+L+ + E+G ++ + GR
Sbjct: 95 FKLKQAIRFLEKGDKVKFTVRFRGRE 120
>gnl|CDD|237344 PRK13306, ulaD, 3-keto-L-gulonate-6-phosphate decarboxylase;
Provisional.
Length = 216
Score = 26.0 bits (58), Expect = 3.1
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 46 GLLARMAVEAGFDWV 60
+LA+MA EAG DWV
Sbjct: 70 KILAKMAFEAGADWV 84
>gnl|CDD|183615 PRK12597, PRK12597, F0F1 ATP synthase subunit beta; Provisional.
Length = 461
Score = 26.4 bits (59), Expect = 3.4
Identities = 8/11 (72%), Positives = 9/11 (81%)
Query: 1 MNEWPGVRLRV 11
MNE PG R+RV
Sbjct: 210 MNEPPGARMRV 220
>gnl|CDD|238553 cd01133, F1-ATPase_beta, F1 ATP synthase beta subunit,
nucleotide-binding domain. The F-ATPase is found in
bacterial plasma membranes, mitochondrial inner
membranes and in chloroplast thylakoid membranes. It has
also been found in the archaea Methanosarcina barkeri.
It uses a proton gradient to drive ATP synthesis and
hydrolyzes ATP to build the proton gradient. The
extrinisic membrane domain, F1, is composed of alpha,
beta, gamma, delta and epsilon subunits with a
stoichiometry of 3:3:1:1:1. The beta subunit of ATP
synthase is catalytic.
Length = 274
Score = 25.7 bits (57), Expect = 4.3
Identities = 8/11 (72%), Positives = 8/11 (72%)
Query: 1 MNEWPGVRLRV 11
MNE PG R RV
Sbjct: 136 MNEPPGARARV 146
>gnl|CDD|212563 cd11673, hemoglobin_linker_C, Globular domain of extracellular
hemoglobin linker. This family of hemoglobin linker
chains is restricted to annelid worms, and participates
in the formation of the large erythrocruorin
respiratory complex. Via its N-terminal coiled-coil
segment (not included in this model), the molecule
forms trimers, which are part of a scaffold organizing
the overall complex architecture; the latter
encompasses 36 linkers and 144 hemoglobins in total.
This C-terminal globular domain is involved in
trimerization, and also interacts with globins and
other C-terminal globular linker domains of neighboring
trimers. The structure resembles that of nitrophorins
and lipocalins.
Length = 120
Score = 25.4 bits (56), Expect = 4.8
Identities = 7/27 (25%), Positives = 13/27 (48%)
Query: 5 PGVRLRVIEGWDEEGHHASDSLHYEGR 31
P V+ V+ ++G + SL +G
Sbjct: 41 PKVKATVVIESTKDGDEQTSSLQVKGF 67
>gnl|CDD|240077 cd04726, KGPDC_HPS, 3-Keto-L-gulonate 6-phosphate decarboxylase
(KGPDC) and D-arabino-3-hexulose-6-phosphate synthase
(HPS). KGPDC catalyzes the formation of L-xylulose
5-phosphate and carbon dioxide from 3-keto-L-gulonate
6-phosphate as part of the anaerobic pathway for
L-ascorbate utilization in some eubacteria. HPS
catalyzes the formation of
D-arabino-3-hexulose-6-phosphate from D-ribulose
5-phosphate and formaldehyde in microorganisms that can
use formaldehyde as a carbon source. Both catalyze
reactions that involve the Mg2+-assisted formation and
stabilization of 1,2-enediolate reaction intermediates.
Length = 202
Score = 25.2 bits (56), Expect = 5.5
Identities = 8/15 (53%), Positives = 9/15 (60%)
Query: 46 GLLARMAVEAGFDWV 60
L A MA +AG D V
Sbjct: 67 ALEAEMAFKAGADIV 81
>gnl|CDD|214349 CHL00060, atpB, ATP synthase CF1 beta subunit.
Length = 494
Score = 25.4 bits (56), Expect = 7.6
Identities = 8/11 (72%), Positives = 9/11 (81%)
Query: 1 MNEWPGVRLRV 11
MNE PG R+RV
Sbjct: 235 MNEPPGARMRV 245
>gnl|CDD|211621 TIGR01039, atpD, ATP synthase, F1 beta subunit. The sequences of
ATP synthase F1 alpha and beta subunits are related and
both contain a nucleotide-binding site for ATP and ADP.
They have a common amino terminal domain but vary at the
C-terminus. The beta chain has catalytic activity, while
the alpha chain is a regulatory subunit. Proton
translocating ATP synthase, F1 beta subunit is
homologous to proton translocating ATP synthase
archaeal/vacuolar(V1), A subunit [Energy metabolism,
ATP-proton motive force interconversion].
Length = 461
Score = 25.1 bits (55), Expect = 8.0
Identities = 8/11 (72%), Positives = 9/11 (81%)
Query: 1 MNEWPGVRLRV 11
MNE PG R+RV
Sbjct: 210 MNEPPGARMRV 220
>gnl|CDD|239471 cd03376, TPP_PFOR_porB_like, Thiamine pyrophosphate (TPP family),
PFOR porB-like subfamily, TPP-binding module; composed
of proteins similar to the beta subunit (porB) of the
Helicobacter pylori four-subunit pyruvate ferredoxin
oxidoreductase (PFOR), which are also found in archaea
and some hyperthermophilic bacteria. PFOR catalyzes the
oxidative decarboxylation of pyruvate to form
acetyl-CoA, a crucial step in many metabolic pathways.
Archaea, anaerobic bacteria and eukaryotes that lack
mitochondria (and therefore pyruvate dehydrogenase) use
PFOR to oxidatively decarboxylate pyruvate, with
ferredoxin or flavodoxin as the electron acceptor. The
36-kDa porB subunit contains the binding sites for the
cofactors, TPP and a divalent metal cation, which are
required for activity.
Length = 235
Score = 24.9 bits (55), Expect = 8.6
Identities = 13/23 (56%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 41 DSSKYGLLARMAVEAGFDWVYYE 63
D SK +AR+AVE GF W YE
Sbjct: 208 DPSKTIEIARLAVETGF-WPLYE 229
>gnl|CDD|181619 PRK09039, PRK09039, hypothetical protein; Validated.
Length = 343
Score = 24.9 bits (55), Expect = 9.5
Identities = 7/24 (29%), Positives = 16/24 (66%)
Query: 77 DMVGIASALWALGRGFPPGVDFIL 100
++ +A+AL L + PP ++++L
Sbjct: 242 EIAKLAAALIELAKEIPPEINWVL 265
>gnl|CDD|223347 COG0269, SgbH, 3-hexulose-6-phosphate synthase and related
proteins [Carbohydrate transport and metabolism].
Length = 217
Score = 24.9 bits (55), Expect = 9.6
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 46 GLLARMAVEAGFDWV 60
+ ARMA EAG DWV
Sbjct: 70 AIEARMAFEAGADWV 84
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 0.138 0.448
Gapped
Lambda K H
0.267 0.0644 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,347,545
Number of extensions: 436695
Number of successful extensions: 537
Number of sequences better than 10.0: 1
Number of HSP's gapped: 536
Number of HSP's successfully gapped: 44
Length of query: 102
Length of database: 10,937,602
Length adjustment: 68
Effective length of query: 34
Effective length of database: 7,921,530
Effective search space: 269332020
Effective search space used: 269332020
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: 53 (24.4 bits)