RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6459
(66 letters)
>gnl|CDD|178380 PLN02783, PLN02783, diacylglycerol O-acyltransferase.
Length = 315
Score = 26.9 bits (60), Expect = 0.58
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 8/40 (20%)
Query: 22 TVVKR--QAQNQSGVSSE--AEVL----KALKSLFEHHKA 53
VV + + + S E AEVL +AL+ LFE HKA
Sbjct: 264 VVVGKPIEVKKNPQPSQEEVAEVLEQFVEALQDLFEKHKA 303
>gnl|CDD|179262 PRK01250, PRK01250, inorganic pyrophosphatase; Provisional.
Length = 176
Score = 26.8 bits (60), Expect = 0.65
Identities = 10/19 (52%), Positives = 12/19 (63%), Gaps = 1/19 (5%)
Query: 41 LKALKSLFEHHKALDEKGK 59
+K FEH+K L EKGK
Sbjct: 132 KAQIKHFFEHYKDL-EKGK 149
>gnl|CDD|182103 PRK09837, PRK09837, copper/silver efflux system outer membrane
protein CusC; Provisional.
Length = 461
Score = 25.6 bits (56), Expect = 2.0
Identities = 16/41 (39%), Positives = 23/41 (56%)
Query: 14 RHERSLRSTVVKRQAQNQSGVSSEAEVLKALKSLFEHHKAL 54
R+ SL+ T+ + +A Q G S EVL A +SLF + L
Sbjct: 397 RYLASLQITLQRARALYQHGAVSYLEVLDAERSLFATRQTL 437
>gnl|CDD|223094 COG0015, PurB, Adenylosuccinate lyase [Nucleotide transport and
metabolism].
Length = 438
Score = 25.7 bits (57), Expect = 2.0
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 8 LEALVSRHERSLRSTVVKR 26
LE LV HER L + V+R
Sbjct: 299 LENLVLWHERDLTDSSVER 317
>gnl|CDD|212491 cd05233, SDR_c, classical (c) SDRs. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are
approximately 350 residues. Sequence identity between
different SDR enzymes are typically in the 15-30%
range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes 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 prostaglandin
dehydrogenase (PGDH) numbering). In addition to the Tyr
and Lys, there is often an upstream Ser (Ser-138, PGDH
numbering) and/or an Asn (Asn-107, PGDH numbering)
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. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. 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.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed
within the SDR family include isomerization,
decarboxylation, epimerization, C=N bond reduction,
dehydratase activity, dehalogenation, Enoyl-CoA
reduction, and carbonyl-alcohol oxidoreduction.
Length = 234
Score = 25.3 bits (56), Expect = 2.5
Identities = 12/51 (23%), Positives = 18/51 (35%), Gaps = 5/51 (9%)
Query: 10 ALVSRHERSLRSTVVKRQAQN-----QSGVSSEAEVLKALKSLFEHHKALD 55
L R+E +L Q+ VS E +V ++ E LD
Sbjct: 26 VLADRNEEALAELAAIEALGGNAVAVQADVSDEEDVEALVEEALEEFGRLD 76
>gnl|CDD|179933 PRK05093, argD, bifunctional
N-succinyldiaminopimelate-
aminotransferase/acetylornithine transaminase protein;
Reviewed.
Length = 403
Score = 24.9 bits (55), Expect = 2.9
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 8/56 (14%)
Query: 5 LEHLEALVSRHERSLRSTVVKRQAQNQSGV-SSEAEVLKALKSLFEHHKAL---DE 56
L ++A++ H VV Q + GV + E L+ L+ L + H AL DE
Sbjct: 174 LAAVKAVIDDHT----CAVVVEPIQGEGGVIPATPEFLQGLRELCDQHNALLIFDE 225
>gnl|CDD|235530 PRK05602, PRK05602, RNA polymerase sigma factor; Reviewed.
Length = 186
Score = 24.6 bits (54), Expect = 3.5
Identities = 8/27 (29%), Positives = 17/27 (62%)
Query: 1 MVLLLEHLEALVSRHERSLRSTVVKRQ 27
M + ++ LE+L++R R+LR+ +
Sbjct: 154 MDISVDALESLLARGRRALRAQLADLP 180
>gnl|CDD|237803 PRK14724, PRK14724, DNA topoisomerase III; Provisional.
Length = 987
Score = 24.5 bits (53), Expect = 4.3
Identities = 13/33 (39%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 22 TVVKRQAQNQSGVSSEAEVLKALKSLFEHHKAL 54
T ++R+A + G S++ L +SL+E HKAL
Sbjct: 302 TSLQREANGKFGFSAKT-TLALAQSLYERHKAL 333
>gnl|CDD|234819 PRK00711, PRK00711, D-amino acid dehydrogenase small subunit;
Validated.
Length = 416
Score = 24.4 bits (54), Expect = 4.9
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 41 LKALKSLFEHHKALDEKGKGTAFQ 64
LKA+K LF+ H L + G FQ
Sbjct: 62 LKAIKWLFQRHAPLAIRPDGDPFQ 85
>gnl|CDD|176467 cd01595, Adenylsuccinate_lyase_like, Adenylsuccinate lyase
(ASL)_like. This group contains ASL, prokaryotic-type
3-carboxy-cis,cis-muconate cycloisomerase (pCMLE), and
related proteins. These proteins are members of the
Lyase class I family. Members of this family for the
most part catalyze similar beta-elimination reactions in
which a C-N or C-O bond is cleaved with the release of
fumarate as one of the products. These proteins are
active as tetramers. The four active sites of the
homotetrameric enzyme are each formed by residues from
three different subunits. ASL catalyzes two steps in the
de novo purine biosynthesis: the conversion of
5-aminoimidazole-(N-succinylocarboxamide) ribotide
(SAICAR) into 5-aminoimidazole-4-carboxamide ribotide
(AICAR) and; the conversion of adenylsuccinate (SAMP)
into adenosine monophosphate (AMP). pCMLE catalyzes the
cyclization of 3-carboxy-cis,cis-muconate (3CM) to
4-carboxy-muconolactone, in the beta-ketoadipate
pathway. ASL deficiency has been linked to several
pathologies including psychomotor retardation with
autistic features, epilepsy and muscle wasting.
Length = 381
Score = 24.4 bits (54), Expect = 5.2
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 8 LEALVSRHERSLRSTVVKR 26
LE LV HER L + V+R
Sbjct: 290 LENLVQWHERDLSDSSVER 308
>gnl|CDD|212678 cd10236, HscA_like_NBD, Nucleotide-binding domain of HscA and
similar proteins. Escherichia coli HscA (heat shock
cognate protein A, also called Hsc66), belongs to the
heat shock protein 70 (HSP70) family of chaperones that
assist in protein folding and assembly and can direct
incompetent "client" proteins towards degradation.
Typically, HSP70s have a nucleotide-binding domain (NBD)
and a substrate-binding domain (SBD). The nucleotide
sits in a deep cleft formed between the two lobes of the
NBD. The two subdomains of each lobe change conformation
between ATP-bound, ADP-bound, and nucleotide-free
states. ATP binding opens up the substrate-binding site;
substrate-binding increases the rate of ATP hydrolysis.
HSP70 chaperone activity is regulated by various
co-chaperones: J-domain proteins and nucleotide exchange
factors (NEFs). HscA's partner J-domain protein is HscB;
it does not appear to require a NEF, and has been shown
to be induced by cold-shock. The HscA-HscB
chaperone/co-chaperone pair is involved in [Fe-S]
cluster assembly.
Length = 355
Score = 23.7 bits (52), Expect = 8.5
Identities = 12/52 (23%), Positives = 19/52 (36%), Gaps = 2/52 (3%)
Query: 7 HLEALVSRHERSLRSTVVKRQAQNQSGVSSEAEVLKALKSLFEHHKALDEKG 58
++ + ++ VS AE+LKALK E + KG
Sbjct: 82 PYLPILEGKNGGIILFHTQQGTVTPVEVS--AEILKALKERAEKSLGGEIKG 131
>gnl|CDD|224246 COG1327, COG1327, Predicted transcriptional regulator, consists of
a Zn-ribbon and ATP-cone domains [Transcription].
Length = 156
Score = 23.7 bits (52), Expect = 8.6
Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 10/45 (22%)
Query: 6 EHLEALVSRHERSLRSTVVKRQAQNQSGVSSEA---EVLKALKSL 47
E +E VS ER LRS + V S+ V++ LK L
Sbjct: 82 EQIEEAVSHIERQLRS-------SGEREVPSKEIGELVMEELKKL 119
>gnl|CDD|222792 PHA00435, PHA00435, capsid assembly protein.
Length = 306
Score = 23.6 bits (51), Expect = 9.4
Identities = 11/31 (35%), Positives = 19/31 (61%), Gaps = 2/31 (6%)
Query: 16 ERSL--RSTVVKRQAQNQSGVSSEAEVLKAL 44
+RS+ R+ K A G +S+AE++KA+
Sbjct: 252 KRSVTKRAKPAKPVAPKVEGFASQAEMIKAM 282
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
0.314 0.126 0.322
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,073,283
Number of extensions: 209389
Number of successful extensions: 212
Number of sequences better than 10.0: 1
Number of HSP's gapped: 212
Number of HSP's successfully gapped: 22
Length of query: 66
Length of database: 10,937,602
Length adjustment: 37
Effective length of query: 29
Effective length of database: 9,296,504
Effective search space: 269598616
Effective search space used: 269598616
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 53 (24.2 bits)