RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12583
(96 letters)
>gnl|CDD|168961 PRK07473, PRK07473, carboxypeptidase; Provisional.
Length = 376
Score = 34.0 bits (78), Expect = 0.006
Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 20/67 (29%)
Query: 31 FGP----INSSNFKSLQDIASTVRAGVNTDIPITVL----------------RNEGTRQR 70
+GP + N+ +L+ I RAG+ T +PITVL E R +
Sbjct: 106 YGPGILDMKGGNYLALEAIRQLARAGITTPLPITVLFTPDEEVGTPSTRDLIEAEAARNK 165
Query: 71 LVLRPQP 77
VL P+P
Sbjct: 166 YVLVPEP 172
>gnl|CDD|238489 cd00989, PDZ_metalloprotease, PDZ domain of bacterial and plant
zinc metalloprotases, presumably membrane-associated or
integral membrane proteases, which may be involved in
signalling and regulatory mechanisms. May be
responsible for substrate recognition and/or binding,
as most PDZ domains bind C-terminal polypeptides, and
binding to internal (non-C-terminal) polypeptides and
even to lipids has been demonstrated. In this subfamily
of protease-associated PDZ domains a C-terminal
beta-strand forms the peptide-binding groove base, a
circular permutation with respect to PDZ domains found
in Eumetazoan signaling proteins.
Length = 79
Score = 32.2 bits (74), Expect = 0.007
Identities = 19/55 (34%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 21 GLVKDDIILEFGPINSSNFKSLQDIASTVRAGVNTDIPITVLRNEGTRQRLVLRP 75
GL D IL IN KS +D+ V+ + +TV RN G L L P
Sbjct: 29 GLKAGDRILA---INGQKIKSWEDLVDAVQENPGKPLTLTVERN-GETITLTLTP 79
>gnl|CDD|238487 cd00987, PDZ_serine_protease, PDZ domain of tryspin-like serine
proteases, such as DegP/HtrA, which are oligomeric
proteins involved in heat-shock response, chaperone
function, and apoptosis. May be responsible for
substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, though binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal
beta-strand forms the peptide-binding groove base, a
circular permutation with respect to PDZ domains found
in Eumetazoan signaling proteins.
Length = 90
Score = 29.5 bits (67), Expect = 0.082
Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 3/53 (5%)
Query: 21 GLVKDDIILEFGPINSSNFKSLQDIASTVRAGVNTDIPITVLRNEGTRQRLVL 73
GL D+IL + L+ + ++ G + +TVLR G + +
Sbjct: 41 GLKPGDVILAVNGKPVKSVADLRRALAELKPG--DKVTLTVLRG-GKELTVTV 90
>gnl|CDD|215440 PLN02821, PLN02821, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate
reductase.
Length = 460
Score = 30.2 bits (68), Expect = 0.13
Identities = 17/36 (47%), Positives = 24/36 (66%), Gaps = 4/36 (11%)
Query: 13 RQDVDVYQGLVKD--DIILEFGPINSSNFKSLQDIA 46
RQD +Y+ LV++ D++L G NSSN LQ+IA
Sbjct: 351 RQDA-MYK-LVEEKLDLMLVVGGWNSSNTSHLQEIA 384
>gnl|CDD|198443 cd10475, EphR_LBD_B6, Ligand Binding Domain of Ephrin type-B
Receptor 6. Ephrin receptors (EphRs) comprise the
largest subfamily of receptor tyrosine kinases (RTKs).
Class EphB receptors bind to transmembrane ephrin-B
ligands. There are six vertebrate EhpB receptors
(EphB1-6), which display promiscuous interactions with
three ephrin-B ligands. EphB6, a kinase-defective member
of this family, is downregulated in MDA-MB-231-breast
cancer cells and myeloid cancers and upregulated in
neuroblasoma and glioblastoma. EphRs contain a ligand
binding domain and two fibronectin repeats
extracellularly, a transmembrane segment, and a
cytoplasmic tyrosine kinase domain. Binding of the
ephrin ligand to EphR requires cell-cell contact since
both are anchored to the plasma membrane. The resulting
downstream signals occur bidirectionally in both
EphR-expressing cells (forward signaling) and
ephrin-expressing cells (reverse signaling).
Length = 180
Score = 26.8 bits (59), Expect = 1.4
Identities = 9/31 (29%), Positives = 12/31 (38%)
Query: 9 EGYPRQDVDVYQGLVKDDIILEFGPINSSNF 39
E +P QGL + FGP+ F
Sbjct: 128 ESFPASLGKGGQGLQMNVKERSFGPLTQRGF 158
>gnl|CDD|215242 PLN02441, PLN02441, cytokinin dehydrogenase.
Length = 525
Score = 26.8 bits (60), Expect = 1.6
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 40 KSLQDIASTVRAGVNTDIPITV 61
S++DIAS VRA + P+TV
Sbjct: 72 SSVEDIASLVRAAYGSSSPLTV 93
>gnl|CDD|215559 PLN03074, PLN03074, auxin influx permease; Provisional.
Length = 473
Score = 26.2 bits (58), Expect = 2.7
Identities = 19/65 (29%), Positives = 26/65 (40%), Gaps = 12/65 (18%)
Query: 31 FGPINSSNFKSLQDIASTVRAGVNTDIP----ITVLRNEGTRQRLVLRPQPFEGQGLVGC 86
FGPINS+ L ++ TV IP + R+ RQ +P F G
Sbjct: 373 FGPINSAVGALL--VSFTVYI-----IPSLAHMLTYRSASARQNAAEKPPFFLP-SWTGM 424
Query: 87 YFLNV 91
Y +N
Sbjct: 425 YVVNA 429
>gnl|CDD|107337 cd06342, PBP1_ABC_LIVBP_like, Type I periplasmic ligand-binding
domain of ABC (Atpase Binding Cassette)-type active
transport systems that are involved in the transport of
all three branched chain aliphatic amino acids
(leucine, isoleucine and valine). This subgroup
includes the type I periplasmic ligand-binding domain
of ABC (Atpase Binding Cassette)-type active transport
systems that are involved in the transport of all three
branched chain aliphatic amino acids (leucine,
isoleucine and valine). This subgroup also includes a
leucine-specific binding protein (or LivK), which is
very similar in sequence and structure to
leucine-isoleucine-valine binding protein (LIVBP).
ABC-type active transport systems are transmembrane
proteins that function in the transport of diverse sets
of substrates across extra- and intracellular
membranes, including carbohydrates, amino acids,
inorganic ions, dipeptides and oligopeptides, metabolic
products, lipids and sterols, and heme, to name a few.
Length = 334
Score = 26.0 bits (58), Expect = 3.0
Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 7 DSEGYPRQDVDVYQGLVKDDIILEFGPINSSNFKSLQDIASTVRAGV 53
D + P+Q V V Q LV D ++ G +NS I + AG+
Sbjct: 47 DDQADPKQAVAVAQKLVDDGVVGVVGHLNSGVTIPASPIYA--DAGI 91
>gnl|CDD|223811 COG0740, ClpP, Protease subunit of ATP-dependent Clp proteases
[Posttranslational modification, protein turnover,
chaperones / Intracellular trafficking and secretion].
Length = 200
Score = 25.7 bits (57), Expect = 3.8
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 17 DVYQGLVKDDIILEFGPINSS 37
D+Y L+K+ II G I
Sbjct: 19 DIYSRLLKERIIFLGGEIEDH 39
>gnl|CDD|237367 PRK13371, PRK13371, 4-hydroxy-3-methylbut-2-enyl diphosphate
reductase; Provisional.
Length = 387
Score = 25.3 bits (56), Expect = 6.4
Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 4/36 (11%)
Query: 13 RQDVDVYQGLVKD--DIILEFGPINSSNFKSLQDIA 46
RQD LV++ D+++ G NSSN LQ+IA
Sbjct: 277 RQDA--MFSLVEEPLDLMVVIGGYNSSNTTHLQEIA 310
>gnl|CDD|172788 PRK14300, PRK14300, chaperone protein DnaJ; Provisional.
Length = 372
Score = 25.0 bits (54), Expect = 9.0
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 40 KSLQDIASTVRAGVNTDIPITVLRNEGTRQRLVL 73
K + + ST+R + T I + V +N RQR +L
Sbjct: 313 KGMSKMRSTIRGDMLTHIHVEVPKNLSKRQRELL 346
>gnl|CDD|238488 cd00988, PDZ_CTP_protease, PDZ domain of C-terminal processing-,
tail-specific-, and tricorn proteases, which function
in posttranslational protein processing, maturation,
and disassembly or degradation, in Bacteria, Archaea,
and plant chloroplasts. May be responsible for
substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, and binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal
beta-strand forms the peptide-binding groove base, a
circular permutation with respect to PDZ domains found
in Eumetazoan signaling proteins.
Length = 85
Score = 24.1 bits (53), Expect = 9.9
Identities = 13/53 (24%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 26 DIILEFGPIN--SSNFKSLQDIASTVRAGVNTDIPITVLRNEGTRQRLVLRPQ 76
DII+ I+ + SL+D+ +R T + +T+ R +G + + L
Sbjct: 35 DIIVA---IDGEPVDGLSLEDVVKLLRGKAGTKVRLTLKRGDGEPREVTLTRL 84
>gnl|CDD|235880 PRK06860, PRK06860, lipid A biosynthesis lauroyl acyltransferase;
Provisional.
Length = 309
Score = 24.5 bits (54), Expect = 9.9
Identities = 9/22 (40%), Positives = 14/22 (63%), Gaps = 2/22 (9%)
Query: 73 LRPQPFEGQG--LVGCYFLNVE 92
+R +G+G LVG +FL +E
Sbjct: 118 IREVQAQGRGVLLVGVHFLTLE 139
>gnl|CDD|187574 cd05264, UDP_G4E_5_SDR_e, UDP-glucose 4-epimerase (G4E), subgroup
5, extended (e) SDRs. This subgroup partially conserves
the characteristic active site tetrad and NAD-binding
motif of the extended SDRs, and has been identified as
possible UDP-glucose 4-epimerase (aka UDP-galactose
4-epimerase), a homodimeric member of the extended SDR
family. UDP-glucose 4-epimerase catalyzes the
NAD-dependent conversion of UDP-galactose to
UDP-glucose, the final step in Leloir galactose
synthesis. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. 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. 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. 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 = 300
Score = 24.6 bits (54), Expect = 10.0
Identities = 11/35 (31%), Positives = 14/35 (40%), Gaps = 9/35 (25%)
Query: 57 IPITVLR--NE-GTRQRLVLRPQPFEGQGLVGCYF 88
+ TVLR N G QR P QG++
Sbjct: 158 LDYTVLRISNPYGPGQR------PDGKQGVIPIAL 186
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
0.318 0.140 0.403
Gapped
Lambda K H
0.267 0.0755 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,849,567
Number of extensions: 397073
Number of successful extensions: 349
Number of sequences better than 10.0: 1
Number of HSP's gapped: 349
Number of HSP's successfully gapped: 24
Length of query: 96
Length of database: 10,937,602
Length adjustment: 63
Effective length of query: 33
Effective length of database: 8,143,300
Effective search space: 268728900
Effective search space used: 268728900
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: 53 (24.1 bits)