RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10682
(71 letters)
>gnl|CDD|187547 cd05236, FAR-N_SDR_e, fatty acyl CoA reductases (FARs), extended
(e) SDRs. SDRs are Rossmann-fold NAD(P)H-binding
proteins, many of which may function as fatty acyl CoA
reductases (FAR), acting on medium and long chain fatty
acids, and have been reported to be involved in diverse
processes such as biosynthesis of insect pheromones,
plant cuticular wax production, and mammalian wax
biosynthesis. In Arabidopsis thaliana, proteins with
this particular architecture have also been identified
as the MALE STERILITY 2 (MS2) gene product, which is
implicated in male gametogenesis. Mutations in MS2
inhibit the synthesis of exine (sporopollenin),
rendering plants unable to reduce pollen wall fatty
acids to corresponding alcohols. This N-terminal domain
shares the catalytic triad (but not the upstream Asn)
and characteristic NADP-binding motif of the extended
SDR family. 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 = 320
Score = 83.5 bits (207), Expect = 3e-21
Identities = 27/65 (41%), Positives = 39/65 (60%)
Query: 2 SQVTPAWREPLPGWVDNLNGPTGILVAGAKGVIRTMLCNGDYHAEVIPVDMAINGLIVIG 61
S V +EP PGW+DN NGP G+ +A KG++RTM + + A++IPVD+ N L+
Sbjct: 220 SIVGATLKEPFPGWIDNFNGPDGLFLAYGKGILRTMNADPNAVADIIPVDVVANALLAAA 279
Query: 62 YKIGS 66
G
Sbjct: 280 AYSGV 284
>gnl|CDD|219687 pfam07993, NAD_binding_4, Male sterility protein. This family
represents the C-terminal region of the male sterility
protein in a number of arabidopsis and drosophila. A
sequence-related jojoba acyl CoA reductase is also
included.
Length = 245
Score = 55.3 bits (134), Expect = 5e-11
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 10 EPLPGWVDNLN-GPTGILVAGAKGVIRTMLCNGDYHAEVIPVDMAINGL 57
E GW++ + GP G+L GV+ +L + D +++PVD N +
Sbjct: 197 ESRTGWINGDDFGPRGLLGGAGLGVLPDILGDPDARLDLVPVDYVANAI 245
>gnl|CDD|215538 PLN02996, PLN02996, fatty acyl-CoA reductase.
Length = 491
Score = 52.8 bits (127), Expect = 6e-10
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 12/80 (15%)
Query: 2 SQVTPAWREPLPGWVDNLNGPTGILVAGAKGVIRTMLCNGDYHAEVIPVDMAINGLIV-- 59
+ +T ++EP PGW++ L ++V KG + L + + +VIP DM +N +IV
Sbjct: 262 TMITSTYKEPFPGWIEGLRTIDSVIVGYGKGKLTCFLADPNSVLDVIPADMVVNAMIVAM 321
Query: 60 ----------IGYKIGSSQR 69
I Y +GSS +
Sbjct: 322 AAHAGGQGSEIIYHVGSSLK 341
>gnl|CDD|215279 PLN02503, PLN02503, fatty acyl-CoA reductase 2.
Length = 605
Score = 34.5 bits (79), Expect = 0.002
Identities = 17/68 (25%), Positives = 33/68 (48%)
Query: 2 SQVTPAWREPLPGWVDNLNGPTGILVAGAKGVIRTMLCNGDYHAEVIPVDMAINGLIVIG 61
S + W++P PGW++ I++ KG + L + + +V+P DM +N +
Sbjct: 376 SVIESTWKDPFPGWMEGNRMMDPIVLYYGKGQLTGFLADPNGVLDVVPADMVVNATLAAM 435
Query: 62 YKIGSSQR 69
K G + +
Sbjct: 436 AKHGGAAK 443
>gnl|CDD|181206 PRK08042, PRK08042, formate hydrogenlyase subunit 3; Reviewed.
Length = 593
Score = 30.2 bits (68), Expect = 0.058
Identities = 10/44 (22%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 7 AWREPLPGWVDNLNGPTGILVAGAKGVIRTMLCNGDYHAEVIPV 50
++++ L GW+ + G G L A G T+L + + +
Sbjct: 10 SFQKALSGWIAGIGGAVGSLYTAAAGF--TVLTGAVGVSGALSL 51
>gnl|CDD|187780 cd09649, Cas5_I-A, CRISPR/Cas system-associated RAMP superfamily
protein Cas5. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas5 is a RAMP superfamily protein; Subunit of the
Cascade complex.
Length = 143
Score = 28.5 bits (64), Expect = 0.17
Identities = 15/67 (22%), Positives = 23/67 (34%), Gaps = 9/67 (13%)
Query: 2 SQVTPAWREPLPGWVDNLNGPTGILVAGAKGVIRTMLCNGDYHAEVIPVDMAINGLIVIG 61
S+V P+ P P + ++ A A G+ R G+ E N L +
Sbjct: 21 SKVRPSLPLPPP---------STLIGALAYGLARGGDGKGETSGEKRKALKGRNELFAVA 71
Query: 62 YKIGSSQ 68
K S
Sbjct: 72 TKKAESV 78
>gnl|CDD|172901 PRK14425, PRK14425, acylphosphatase; Provisional.
Length = 94
Score = 26.4 bits (58), Expect = 0.87
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 7 AWREPLPGWVDN-LNGPTGILVAGAKGVIRTML 38
A R L GWV N +G L+AG I M+
Sbjct: 29 AERLGLTGWVRNESDGSVTALIAGPDSAISAMI 61
>gnl|CDD|234887 PRK01001, PRK01001, putative inner membrane protein translocase
component YidC; Provisional.
Length = 795
Score = 25.1 bits (55), Expect = 3.3
Identities = 7/11 (63%), Positives = 9/11 (81%)
Query: 12 LPGWVDNLNGP 22
+PGW+DNL P
Sbjct: 674 IPGWIDNLTAP 684
>gnl|CDD|216542 pfam01512, Complex1_51K, Respiratory-chain NADH dehydrogenase 51
Kd subunit.
Length = 150
Score = 24.3 bits (54), Expect = 5.8
Identities = 12/62 (19%), Positives = 22/62 (35%), Gaps = 20/62 (32%)
Query: 22 PTGI-LVAGAKGVIRTMLCNGD--------------YHAEVIPVDMAINGLIVIGYKIGS 66
PT + L A I+ ++ NG I I G+++ Y +G+
Sbjct: 15 PTHVKLSPPADKKIKYLIVNGAECEPGLTKDRRLMRERPHEI-----IEGILIAAYALGA 69
Query: 67 SQ 68
+
Sbjct: 70 KK 71
>gnl|CDD|219070 pfam06516, NUP, Purine nucleoside permease (NUP). This family
consists of several purine nucleoside permease from
both bacteria and fungi.
Length = 315
Score = 24.1 bits (53), Expect = 6.3
Identities = 9/30 (30%), Positives = 13/30 (43%)
Query: 15 WVDNLNGPTGILVAGAKGVIRTMLCNGDYH 44
W++ L+ I V G + CN DY
Sbjct: 18 WLERLDLDHNITVPGLSPDYPDVHCNADYG 47
>gnl|CDD|185516 PTZ00215, PTZ00215, ribose 5-phosphate isomerase; Provisional.
Length = 151
Score = 24.2 bits (53), Expect = 7.0
Identities = 14/38 (36%), Positives = 16/38 (42%), Gaps = 12/38 (31%)
Query: 20 NGPTGILVAGA-----------KGVIRTMLCNGDYHAE 46
TGILV G+ KG IR LC+ Y A
Sbjct: 61 EADTGILVCGSGIGISIAANKVKG-IRCALCHDHYTAR 97
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 0.140 0.441
Gapped
Lambda K H
0.267 0.0778 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,686,286
Number of extensions: 278923
Number of successful extensions: 228
Number of sequences better than 10.0: 1
Number of HSP's gapped: 226
Number of HSP's successfully gapped: 14
Length of query: 71
Length of database: 10,937,602
Length adjustment: 41
Effective length of query: 30
Effective length of database: 9,119,088
Effective search space: 273572640
Effective search space used: 273572640
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 (24.1 bits)