RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10490
(121 letters)
>gnl|CDD|235387 PRK05283, PRK05283, deoxyribose-phosphate aldolase; Provisional.
Length = 257
Score = 28.8 bits (65), Expect = 0.55
Identities = 20/53 (37%), Positives = 26/53 (49%), Gaps = 8/53 (15%)
Query: 13 IWSVFIAILRKSVRNLQACTDIGLIEHVLNRLPHA----DPVVAETHEG-SYG 60
I+ FI I RK++R Q +I I V N PH D +AET +YG
Sbjct: 47 IYPRFIPIARKTLRE-QGTPEIR-IATVTN-FPHGNDDIDIALAETRAAIAYG 96
>gnl|CDD|239821 cd04329, RNAP_II_Rpb7_N, RNAP_II_Rpb7_N: Rpb7, N-terminal
ribonucleoprotein (RNP) domain. Rpb7 is a subunit of
eukaryotic RNA polymerase (RNAP) II that is homologous
to Rpc25 of RNAP III, RpoE of archaeal RNAP, and Rpa43
of eukaryotic RNAP I. Rpb7 heterodimerizes with Rpb4
and this heterodimer binds the 10-subunit core of RNAP
II, forming part of the floor of the DNA-binding cleft.
Rpb7 has two domains, an N-terminal RNP domain and a
C-terminal oligonucleotide-binding (OB) domain, both of
which bind single-stranded RNA. Rpb7 is thought to
interact with the nascent RNA strand as it exits the
RNAP II complex during transcription elongation. The
Rpb7/Rpb4 heterodimer is also thought to serve as an
upstream interface between the C-terminal domain of
Rpb1 and the transcription factor IIB (TFIIB),
recruiting pol II to the pol II promoter.
Length = 80
Score = 26.4 bits (59), Expect = 1.8
Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 6/46 (13%)
Query: 36 LIEHVLNRLPHADPVVAETHEGSYGVWI---IFEDIREGRIQEGVG 78
L E++ +L V T G YG I +DI EG+I G G
Sbjct: 21 LKEYLEQKLLEE---VEGTCTGDYGYIIAVTDIDDIGEGKILPGTG 63
>gnl|CDD|132417 TIGR03374, ABALDH, 1-pyrroline dehydrogenase. Members of this
protein family are 1-pyrroline dehydrogenase (1.5.1.35),
also called gamma-aminobutyraldehyde dehydrogenase. This
enzyme can follow putrescine transaminase (EC 2.6.1.82)
for a two-step conversion of putrescine to
gamma-aminobutyric acid (GABA). The member from
Escherichia coli is characterized as a homotetramer that
binds one NADH per momomer. This enzyme belongs to the
medium-chain aldehyde dehydrogenases, and is quite
similar in sequence to the betaine aldehyde
dehydrogenase (EC 1.2.1.8) family.
Length = 472
Score = 26.9 bits (59), Expect = 3.6
Identities = 24/93 (25%), Positives = 39/93 (41%), Gaps = 9/93 (9%)
Query: 25 VRNLQACTDIGLIEHVLNRLPHADPVVAETHE--GSYGVWIIFEDIREGRIQEGVGAETH 82
VR + I EH+L+ H P + TH G I+F+D + EGV
Sbjct: 216 VRMVSLTGSIATGEHILS---HTAPSIKRTHMELGGKAPVIVFDDADIDAVVEGVRTFGF 272
Query: 83 LSAGQDNMLYCQGDIALVTNRWVFSSEQERMSN 115
+AGQD C+ + R ++ + E++
Sbjct: 273 YNAGQDCTAACR----IYAQRGIYDTLVEKLGA 301
>gnl|CDD|235750 PRK06228, PRK06228, F0F1 ATP synthase subunit epsilon; Validated.
Length = 131
Score = 25.7 bits (57), Expect = 4.9
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 39 HVLNRLPHADPVVAETHEGSYGV 61
V +VAET EGS+G+
Sbjct: 12 EVFAEKKGVTRIVAETREGSFGL 34
>gnl|CDD|200489 cd11352, AmyAc_5, Alpha amylase catalytic domain found in an
uncharacterized protein family. The Alpha-amylase
family comprises the largest family of glycoside
hydrolases (GH), with the majority of enzymes acting on
starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 443
Score = 25.7 bits (57), Expect = 7.1
Identities = 10/34 (29%), Positives = 10/34 (29%), Gaps = 2/34 (5%)
Query: 11 AEIWS--VFIAILRKSVRNLQACTDIGLIEHVLN 42
EI A V L A DI I L
Sbjct: 278 GEITGGREAAAYEDLDVTGLDAALDIPEIPFKLE 311
>gnl|CDD|182893 PRK11000, PRK11000, maltose/maltodextrin transporter ATP-binding
protein; Provisional.
Length = 369
Score = 25.8 bits (57), Expect = 7.4
Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 6/38 (15%)
Query: 70 EGRIQ--EGVGAET----HLSAGQDNMLYCQGDIALVT 101
EG +Q E +G ET + A + N++Y Q D+ LV
Sbjct: 299 EGEVQVVEQLGNETQIHIQIPAIRQNLVYRQNDVVLVE 336
>gnl|CDD|227623 COG5307, COG5307, SEC7 domain proteins [General function prediction
only].
Length = 1024
Score = 25.8 bits (57), Expect = 7.5
Identities = 5/35 (14%), Positives = 9/35 (25%)
Query: 21 LRKSVRNLQACTDIGLIEHVLNRLPHADPVVAETH 55
L + N T +IE + +
Sbjct: 153 LSRPSTNDPPETRSLIIEQLSILWISSPYFFLTLI 187
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 0.137 0.430
Gapped
Lambda K H
0.267 0.0727 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,158,451
Number of extensions: 525241
Number of successful extensions: 352
Number of sequences better than 10.0: 1
Number of HSP's gapped: 352
Number of HSP's successfully gapped: 10
Length of query: 121
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 37
Effective length of database: 7,211,866
Effective search space: 266839042
Effective search space used: 266839042
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 (24.2 bits)