RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1559
(138 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 = 4e-24
Identities = 34/102 (33%), Positives = 42/102 (41%), Gaps = 6/102 (5%)
Query: 26 CHRRVYKYRVSQTDSLGRKCWDDIEVLSCWGRCDSNETSDWRFPYKRSHHPVCQHGARAL 85
CH R Y V + G I C GRCD+ + PYK SH PVC +
Sbjct: 1 CHPRNYTIAVEKE---GCGVCLAINTTICAGRCDTRDPVYKSPPYKPSHQPVCTYDEWRY 57
Query: 86 KVVILNNCEENVEQGTEVYRYLEALSCKCSVCKSSEASCEGL 127
+ 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 = 30.2 bits (69), Expect = 0.28
Identities = 10/24 (41%), Positives = 11/24 (45%), Gaps = 5/24 (20%)
Query: 63 TSDWRFPYKRSHHPVCQHGARALK 86
TSDW FP RS + AL
Sbjct: 318 TSDWLFPPARS-----REIVDALL 336
>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 = 0.47
Identities = 19/75 (25%), Positives = 26/75 (34%), Gaps = 4/75 (5%)
Query: 54 CWGRCDSNETSDWRFPYKRSHHPVCQHGARALKVVILNNCEENVEQGTEVYRYLEALSCK 113
C G C + ++ P VC + + V L C V+ V Y ALSC
Sbjct: 30 CAGYCYT-RDPVYKSPLPPLPQRVCTYRELRYETVRLPGCPPGVD---PVVTYPVALSCH 85
Query: 114 CSVCKSSEASCEGLR 128
C C + C
Sbjct: 86 CGKCNTDTTDCTVES 100
>gnl|CDD|233177 TIGR00901, 2A0125, AmpG-like permease. [Cellular processes,
Adaptations to atypical conditions].
Length = 356
Score = 28.9 bits (65), Expect = 0.88
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 11 LLFSYCAANQDITLDCHRR 29
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 = 0.97
Identities = 15/62 (24%), Positives = 21/62 (33%), Gaps = 3/62 (4%)
Query: 69 PYKRSHHPVCQHGARALKVVILNNCEENVEQGTEVYRYLEALSCKCSVCKSSEASCEGLR 128
+ VC + + V+L C V Y ALSC C C + + C L
Sbjct: 43 GRRAVSQRVCTYRDVTYETVVLPGCPPGV---DPTVTYPVALSCHCGNCPTDNSDCTRLS 99
Query: 129 YS 130
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 = 27.9 bits (63), Expect = 1.6
Identities = 9/22 (40%), Positives = 12/22 (54%), Gaps = 2/22 (9%)
Query: 96 NVEQGTEVYRYLEALSCKCSVC 117
NV G+ + R LEAL +C
Sbjct: 125 NV--GSRLARRLEALGMNVLLC 144
>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 = 27.4 bits (61), Expect = 3.1
Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 73 SHHPVCQHGARALKVVILNNCEENVEQGTEVYR 105
S+HP + + L +VI+ EE++ G E YR
Sbjct: 99 SYHPFIETKSPNLNIVIVRENEEDLYTGIE-YR 130
>gnl|CDD|233309 TIGR01200, GLPGLI, GLPGLI family protein. This protein family
was first noted as a paralogous set in Porphyromonas
gingivalis, but it is more widely distributed among the
Bacteroidetes. The protein family is now renamed GLPGLI
after its best-conserved motif.
Length = 227
Score = 26.6 bits (59), Expect = 5.2
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 2/35 (5%)
Query: 6 IGFTLLLFSYCAANQDITLDCHRRVYKYRVSQTDS 40
+ LLLFS+ +A Q IT R Y+ + D
Sbjct: 5 LLLLLLLFSFSSAQQQITQL--RVTYELIYFKKDD 37
>gnl|CDD|218624 pfam05529, Bap31, B-cell receptor-associated protein 31-like.
Bap31 is a polytopic integral protein of the
endoplasmic reticulum membrane and a substrate of
caspase-8. Bap31 is cleaved within its cytosolic
domain, generating pro-apoptotic p20 Bap31.
Length = 149
Score = 25.6 bits (57), Expect = 8.2
Identities = 11/29 (37%), Positives = 14/29 (48%), Gaps = 10/29 (34%)
Query: 5 TIGFTLLLFSYCAANQDITLDCHRRVYKY 33
+ F L+LF +D RRVYKY
Sbjct: 54 LLIFLLVLF----------IDSVRRVYKY 72
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
0.322 0.133 0.436
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: 6,341,024
Number of extensions: 505846
Number of successful extensions: 384
Number of sequences better than 10.0: 1
Number of HSP's gapped: 383
Number of HSP's successfully gapped: 12
Length of query: 138
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 51
Effective length of database: 7,078,804
Effective search space: 361019004
Effective search space used: 361019004
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 (22.0 bits)
S2: 54 (24.6 bits)