RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1560
(175 letters)
>gnl|CDD|200450 cd00069, GHB_like, Glycoprotein hormone beta chain homologues.
This family of cystine-knot hormones includes the beta
chains of gonadotropins, thyrotropins, follitropins,
choriogonadotropins and more. The members are
reproductive hormones that consist of two glycosylated
chains (alpha and beta), which form a tightly bound
dimer.
Length = 96
Score = 88.9 bits (221), Expect = 1e-23
Identities = 34/102 (33%), Positives = 42/102 (41%), Gaps = 6/102 (5%)
Query: 63 CHRRVYKYRVSQTDSLGRKCWDDIEVLSCWGRCDSNETSDWRFPYKRSHHPVCQHGARAL 122
CH R Y V + G I C GRCD+ + PYK SH PVC +
Sbjct: 1 CHPRNYTIAVEKE---GCGVCLAINTTICAGRCDTRDPVYKSPPYKPSHQPVCTYDEWRY 57
Query: 123 KVVILNNCEENVEQGTEVYRYLEALSCKCSVCKSSEASCEGL 164
+ V L C V Y Y ALSC+C +C + C L
Sbjct: 58 ETVRLPGCPPGV---DPTYTYPVALSCRCGLCNTDTTDCTRL 96
>gnl|CDD|234678 PRK00175, metX, homoserine O-acetyltransferase; Provisional.
Length = 379
Score = 30.5 bits (70), Expect = 0.38
Identities = 10/24 (41%), Positives = 11/24 (45%), Gaps = 5/24 (20%)
Query: 100 TSDWRFPYKRSHHPVCQHGARALK 123
TSDW FP RS + AL
Sbjct: 318 TSDWLFPPARS-----REIVDALL 336
>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein. This
family includes archaebacterial L12, eukaryotic P0, P1
and P2.
Length = 88
Score = 28.4 bits (64), Expect = 0.64
Identities = 10/10 (100%), Positives = 10/10 (100%)
Query: 17 KKEEEEEEEE 26
KKEEEEEEEE
Sbjct: 70 KKEEEEEEEE 79
>gnl|CDD|214502 smart00068, GHB, Glycoprotein hormone beta chain homologues. Also
called gonadotropins. Glycoprotein hormones consist of
two glycosylated chains (alpha and beta) of similar
topology.
Length = 107
Score = 28.8 bits (65), Expect = 0.73
Identities = 19/75 (25%), Positives = 26/75 (34%), Gaps = 4/75 (5%)
Query: 91 CWGRCDSNETSDWRFPYKRSHHPVCQHGARALKVVILNNCEENVEQGTEVYRYLEALSCK 150
C G C + ++ P VC + + V L C V+ V Y ALSC
Sbjct: 30 CAGYCYT-RDPVYKSPLPPLPQRVCTYRELRYETVRLPGCPPGVD---PVVTYPVALSCH 85
Query: 151 CSVCKSSEASCEGLR 165
C C + C
Sbjct: 86 CGKCNTDTTDCTVES 100
>gnl|CDD|233177 TIGR00901, 2A0125, AmpG-like permease. [Cellular processes,
Adaptations to atypical conditions].
Length = 356
Score = 29.3 bits (66), Expect = 1.0
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 48 LLFSYCAANQDITLDCHRR 66
L ++ +A QDI LD R
Sbjct: 91 FLIAFFSATQDIALDAWRL 109
>gnl|CDD|109076 pfam00007, Cys_knot, Cystine-knot domain. The family comprises
glycoprotein hormones and the C-terminal domain of
various extracellular proteins. It is believed to be
involved in disulfide-linked dimerisation.
Length = 105
Score = 27.8 bits (62), Expect = 1.6
Identities = 15/62 (24%), Positives = 21/62 (33%), Gaps = 3/62 (4%)
Query: 106 PYKRSHHPVCQHGARALKVVILNNCEENVEQGTEVYRYLEALSCKCSVCKSSEASCEGLR 165
+ VC + + V+L C V Y ALSC C C + + C L
Sbjct: 43 GRRAVSQRVCTYRDVTYETVVLPGCPPGV---DPTVTYPVALSCHCGNCPTDNSDCTRLS 99
Query: 166 YS 167
Sbjct: 100 LQ 101
>gnl|CDD|240635 cd12158, ErythrP_dh, D-Erythronate-4-Phosphate Dehydrogenase
NAD-binding and catalytic domains.
D-Erythronate-4-phosphate Dehydrogenase (E. coli gene
PdxB), a D-specific 2-hydroxyacid dehydrogenase family
member, catalyzes the NAD-dependent oxidation of
erythronate-4-phosphate, which is followed by
transamination to form 4-hydroxy-L-threonine-4-phosphate
within the de novo biosynthesis pathway of vitamin B6.
D-Erythronate-4-phosphate dehydrogenase has the common
architecture shared with D-isomer specific 2-hydroxyacid
dehydrogenases but contains an additional C-terminal
dimerization domain in addition to an NAD-binding domain
and the "lid" domain. The lid domain corresponds to the
catalytic domain of phosphoglycerate dehydrogenase and
other proteins of the D-isomer specific 2-hydroxyacid
dehydrogenase family, which include groups such as
formate dehydrogenase, glycerate dehydrogenase,
L-alanine dehydrogenase, and S-adenosylhomocysteine
hydrolase. Despite often low sequence identity, these
proteins typically have a characteristic arrangement of
2 similar subdomains of the alpha/beta Rossmann fold
NAD+ binding form. The NAD+ binding domain is inserted
within the linear sequence of the mostly N-terminal
catalytic domain, which has a similar domain structure
to the internal NAD binding domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD is bound, primarily to the
C-terminal portion of the 2nd (internal) domain. Some
related proteins have similar structural subdomain but
with a tandem arrangement of the catalytic and
NAD-binding subdomains in the linear sequence.
Length = 343
Score = 28.3 bits (64), Expect = 2.3
Identities = 9/22 (40%), Positives = 12/22 (54%), Gaps = 2/22 (9%)
Query: 133 NVEQGTEVYRYLEALSCKCSVC 154
NV G+ + R LEAL +C
Sbjct: 125 NV--GSRLARRLEALGMNVLLC 144
>gnl|CDD|130608 TIGR01545, YfhB_g-proteo, haloacid dehalogenase superfamily,
subfamily IF hydrolase, YfhB. This model describes a
clade of sequences limited to the gamma proteobacteria.
This group is a member of the haloacid dehalogenase
(HAD) superfamily of aspartate-dependent hydrolases and
all of the conserved catalytic motifs are present.
Although structurally similar to subfamily IA in that
the variable domain is predicted to consist of five
consecutive alpha helices (by PSI-PRED), it is
sufficiently divergent to warrant being regarded as a
separate sub-family (IF). The gene name comes from the
E. coli gene. There is currently no information
regarding the function of this gene.
Length = 210
Score = 27.2 bits (60), Expect = 3.7
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 6/50 (12%)
Query: 32 GHKRLIMLQSTIGFTLLLFS-YCAANQDITL--DCHRRVYKYRVSQTDSL 78
GH+++ L+ IG L L+S Y + QD L C R +RVS+ L
Sbjct: 160 GHEKVAQLEQKIGSPLKLYSGYSDSKQDNPLLAFCEHR---WRVSKRGEL 206
>gnl|CDD|218870 pfam06045, Rhamnogal_lyase, Rhamnogalacturonate lyase family.
Rhamnogalacturonate lyase (EC:4.2.2.-) degrades the
rhamnogalacturonan I (RG-I) backbone of pectin. This
family contains mainly members from plants, but also
contains the plant pathogen Erwinia chrysanthemi.
Length = 220
Score = 26.8 bits (59), Expect = 5.2
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 34 KRLIMLQSTIGF-TLLLFSYCAANQDITLDCHRRVYKYR 71
KRLIML+ GF + +F + + + L R V+K
Sbjct: 131 KRLIMLRGVSGFYSYAIFEHLSGWPAVNLSETRLVFKLN 169
>gnl|CDD|234062 TIGR02924, ICDH_alpha, isocitrate dehydrogenase. This family of
mainly alphaproteobacterial enzymes is a member of the
isocitrate/isopropylmalate dehydrogenase superfamily
described by pfam00180. Every member of the seed of this
model appears to have a TCA cycle lacking only a
determined isocitrate dehydrogenase. The precise
identity of the cofactor (NADH -- 1.1.1.41 vs. NADPH --
1.1.1.42) is unclear [Energy metabolism, TCA cycle].
Length = 473
Score = 27.0 bits (60), Expect = 6.0
Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 110 SHHPVCQHGARALKVVILNNCEENVEQGTEVYR 142
S+HP + + L +VI+ EE++ G E YR
Sbjct: 99 SYHPFIETKSPNLNIVIVRENEEDLYTGIE-YR 130
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
0.321 0.134 0.432
Gapped
Lambda K H
0.267 0.0742 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,267,730
Number of extensions: 699241
Number of successful extensions: 785
Number of sequences better than 10.0: 1
Number of HSP's gapped: 783
Number of HSP's successfully gapped: 16
Length of query: 175
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 85
Effective length of database: 6,945,742
Effective search space: 590388070
Effective search space used: 590388070
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 (21.9 bits)
S2: 56 (25.3 bits)