RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7979
(186 letters)
>gnl|CDD|233295 TIGR01161, purK, phosphoribosylaminoimidazole carboxylase, PurK
protein. Phosphoribosylaminoimidazole carboxylase is a
fusion protein in plants and fungi, but consists of two
non-interacting proteins in bacteria, PurK and PurE.
This model represents PurK, N5-carboxyaminoimidazole
ribonucleotide synthetase, which hydrolyzes ATP and
converts AIR to N5-CAIR. PurE converts N5-CAIR to CAIR.
In the presence of high concentrations of bicarbonate,
PurE is reported able to convert AIR to CAIR directly
and without ATP [Purines, pyrimidines, nucleosides, and
nucleotides, Purine ribonucleotide biosynthesis].
Length = 352
Score = 29.6 bits (67), Expect = 0.91
Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 9/58 (15%)
Query: 41 YKLVPNLQANEMK----REREFYRIRGLPCPKDLLLEDEEEENTDQVNSDYHRLDEQV 94
KL P+ A + +++F + GLP P L+++DEEE +++ L V
Sbjct: 84 VKLFPSPDALAIIQDRLTQKQFLQKLGLPVPPFLVIKDEEE-----LDAALQELGFPV 136
>gnl|CDD|187597 cd05338, DHRS1_HSDL2-like_SDR_c, human dehydrogenase/reductase (SDR
family) member 1 (DHRS1) and human hydroxysteroid
dehydrogenase-like protein 2 (HSDL2), classical (c)
SDRs. This subgroup includes human DHRS1 and human
HSDL2 and related proteins. These are members of the
classical SDR family, with a canonical Gly-rich
NAD-binding motif and the typical YXXXK active site
motif. However, the rest of the catalytic tetrad is not
strongly conserved. DHRS1 mRNA has been detected in many
tissues, liver, heart, skeletal muscle, kidney and
pancreas; a longer transcript is predominantly expressed
in the liver , a shorter one in the heart. HSDL2 may
play a part in fatty acid metabolism, as it is found in
peroxisomes. 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 have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 246
Score = 28.9 bits (65), Expect = 1.3
Identities = 20/79 (25%), Positives = 28/79 (35%), Gaps = 14/79 (17%)
Query: 62 RGLPCPKDLLLEDEEEENTDQVNSDYHRLDEQVNVYLECSVA-TTSSLKTLKKRFIR--- 117
+ LP D+ ED+ + + RLD VN + T KRF
Sbjct: 65 QALPIVVDVRDEDQVRALVEATVDQFGRLDILVN---NAGAIWLSLVEDTPAKRFDLMQR 121
Query: 118 -------LSSQATITHLKK 129
L SQA + H+ K
Sbjct: 122 VNLRGTYLLSQAALPHMVK 140
>gnl|CDD|224798 COG1886, FliN, Flagellar motor switch/type III secretory pathway
protein [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 136
Score = 28.1 bits (63), Expect = 1.8
Identities = 20/86 (23%), Positives = 31/86 (36%), Gaps = 17/86 (19%)
Query: 72 LEDEEEENTDQVNSDYHRLDEQVNVYLECSVATTS-SLKTLKKRFIRLSSQATITHLKKF 130
+E E + +N L + V L + T L L + L + I
Sbjct: 50 VELTESTVLESLNESIDLL-LDIPVRLSVELGRTKMPLGEL----LALGKGSVIE----- 99
Query: 131 VALKLLDEKSKYKEIDILCNDELLGK 156
LD K + +DIL N L+G+
Sbjct: 100 -----LD-KLAGEPVDILVNGRLIGR 119
>gnl|CDD|240198 cd05693, S1_Rrp5_repeat_hs1_sc1, S1_Rrp5_repeat_hs1_sc1: Rrp5 is a
trans-acting factor important for biogenesis of both the
40S and 60S eukaryotic ribosomal subunits. Rrp5 has two
distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of A0-A2.
This CD includes H. sapiens S1 repeat 1 (hs1) and S.
cerevisiae S1 repeat 1 (sc1). Rrp5 is found in
eukaryotes but not in prokaryotes or archaea.
Length = 100
Score = 26.0 bits (58), Expect = 5.1
Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 70 LLLEDEEEENTDQVNSDYHRLDE--QVNVYLECSVATTSSLKTLKKRFIRLS 119
L E +EE + + L++ V + C V + K+ KKR I LS
Sbjct: 43 RLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSLDKSKSGKKR-IELS 93
>gnl|CDD|132423 TIGR03380, agmatine_aguA, agmatine deiminase. Members of this
family are agmatine deiminase (3.5.3.12), as
characterized in Pseudomonas aeruginosa and plants.
Related deiminases include the peptidyl-arginine
deiminase (3.5.3.15) as found in Porphyromonas
gingivalis [Central intermediary metabolism, Polyamine
biosynthesis].
Length = 357
Score = 27.3 bits (61), Expect = 5.5
Identities = 13/48 (27%), Positives = 19/48 (39%), Gaps = 7/48 (14%)
Query: 56 REFYRIRGLPCPKDLLLEDEEEENTDQVNSDYHRLDEQ------VNVY 97
R+ ++ LP P L + +EE D V R + VN Y
Sbjct: 255 RKL-KVHKLPIPGPLYITEEEAAGVDPVEGTLPREAGERLAASYVNFY 301
>gnl|CDD|179732 PRK04056, PRK04056, Maf-like protein; Reviewed.
Length = 180
Score = 26.1 bits (58), Expect = 9.8
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 99 ECSVATTSSLKTLKKRFIRLSSQATITHLKKF 130
E SV T LK+ +K ++ LS T KKF
Sbjct: 98 EISVLTCMILKSPEKEWLDLS--VTTYRFKKF 127
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 0.403
Gapped
Lambda K H
0.267 0.0699 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,414,612
Number of extensions: 867783
Number of successful extensions: 778
Number of sequences better than 10.0: 1
Number of HSP's gapped: 777
Number of HSP's successfully gapped: 16
Length of query: 186
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 95
Effective length of database: 6,901,388
Effective search space: 655631860
Effective search space used: 655631860
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: 56 (25.4 bits)