RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2083
(248 letters)
>gnl|CDD|222727 pfam14388, DUF4419, Domain of unknown function (DUF4419). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria, eukaryotes and
viruses. Proteins in this family are typically between
348 and 454 amino acids in length.
Length = 297
Score = 33.4 bits (77), Expect = 0.082
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 129 FIANENKKILTYYIPSLGPAPKWCGFLDNLTEELEENI 166
F+ +E KK L P L W + TEE+++NI
Sbjct: 48 FVDHEGKKELVVEDPGLLYDNDWDELTEEFTEEIQKNI 85
>gnl|CDD|238121 cd00200, WD40, WD40 domain, found in a number of eukaryotic
proteins that cover a wide variety of functions
including adaptor/regulatory modules in signal
transduction, pre-mRNA processing and cytoskeleton
assembly; typically contains a GH dipeptide 11-24
residues from its N-terminus and the WD dipeptide at its
C-terminus and is 40 residues long, hence the name WD40;
between GH and WD lies a conserved core; serves as a
stable propeller-like platform to which proteins can
bind either stably or reversibly; forms a propeller-like
structure with several blades where each blade is
composed of a four-stranded anti-parallel b-sheet;
instances with few detectable copies are hypothesized to
form larger structures by dimerization; each WD40
sequence repeat forms the first three strands of one
blade and the last strand in the next blade; the last
C-terminal WD40 repeat completes the blade structure of
the first WD40 repeat to create the closed ring
propeller-structure; residues on the top and bottom
surface of the propeller are proposed to coordinate
interactions with other proteins and/or small ligands; 7
copies of the repeat are present in this alignment.
Length = 289
Score = 30.8 bits (70), Expect = 0.52
Identities = 18/95 (18%), Positives = 35/95 (36%), Gaps = 27/95 (28%)
Query: 20 GDQTQFNNLCHIPESGMMFIANENKKILTYYIPAFYLYDIRADKPLRVKDHMYGLPIRDI 79
G + N++ P+ ++ +E+ I ++D+R + ++ +
Sbjct: 217 GHENGVNSVAFSPDGYLLASGSEDGTI--------RVWDLRTGECVQT-----------L 257
Query: 80 KFHDNYVLSMDSSVVKIWSKDNGSLFTCIESGDQT 114
H N V S+ WS D L + S D T
Sbjct: 258 SGHTNSVTSLA------WSPDGKRLASG--SADGT 284
>gnl|CDD|212672 cd10230, HYOU1-like_NBD, Nucleotide-binding domain of human HYOU1
and similar proteins. This subgroup includes human
HYOU1 (also known as human hypoxia up-regulated 1,
GRP170; HSP12A; ORP150; GRP-170; ORP-150; the human
HYOU1 gene maps to11q23.1-q23.3) and Saccharomyces
cerevisiae Lhs1p (also known as Cer1p, SsI1). Mammalian
HYOU1 functions as a nucleotide exchange factor (NEF)
for HSPA5 (alos known as BiP, Grp78 or HspA5) and may
also function as a HSPA5-independent chaperone. S.
cerevisiae Lhs1p, does not have a detectable endogenous
ATPase activity like canonical HSP70s, but functions as
a NEF for Kar2p; it's interaction with Kar2p is
stimulated by nucleotide-binding. In addition, Lhs1p has
a nucleotide-independent holdase activity that prevents
heat-induced aggregation of proteins in vitro. This
subgroup belongs to the 105/110 kDa heat shock protein
(HSP105/110) subfamily of the HSP70-like family.
HSP105/110s are believed to function generally as
co-chaperones of HSP70 chaperones, acting as NEFs, to
remove ADP from their HSP70 chaperone partners during
the ATP hydrolysis cycle. HSP70 chaperones assist in
protein folding and assembly, and can direct incompetent
"client" proteins towards degradation. Like HSP70
chaperones, HSP105/110s have an N-terminal
nucleotide-binding domain (NBD) and a C-terminal
substrate-binding domain (SBD). For HSP70 chaperones,
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 also
regulated by J-domain proteins.
Length = 388
Score = 28.7 bits (65), Expect = 2.8
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 3/22 (13%)
Query: 167 IENVYDDYKF---VTRQELEDL 185
IE++YDD F +TR E E+L
Sbjct: 294 IESLYDDIDFKTKITRAEFEEL 315
>gnl|CDD|218873 pfam06050, HGD-D, 2-hydroxyglutaryl-CoA dehydratase, D-component.
Degradation of glutamate via the hydroxyglutarate
pathway involves the syn-elimination of water from
2-hydroxyglutaryl-CoA. This anaerobic process is
catalyzed by 2-hydroxyglutaryl-CoA dehydratase, an
enzyme with two components (A and D) that reversibly
associate during reaction cycles. This component
contains one non-reducible [4Fe-4S]2+ cluster and a
reduced riboflavin 5'-monophosphate.
Length = 347
Score = 28.5 bits (64), Expect = 3.6
Identities = 18/76 (23%), Positives = 28/76 (36%), Gaps = 7/76 (9%)
Query: 126 GMMFIANENKKILTYYIPSLGPAPKWCGFLDNLTEELEENIIENVYDDYKFVTRQELEDL 185
G + E K++L IP P+ K L E +EE V DD +R + +
Sbjct: 196 GNYVVRKELKRLLLTGIPVWYPSLK-------LIELIEEAGAVVVGDDLCLGSRAFADLV 248
Query: 186 GLGHLIGTSLLRAYMH 201
+L Y+
Sbjct: 249 DEDGDPLEALAERYLR 264
>gnl|CDD|131316 TIGR02263, benz_CoA_red_C, benzoyl-CoA reductase, subunit C. This
model describes C subunit of benzoyl-CoA reductase, a
4-subunit enzyme. Many aromatic compounds are
metabolized by way of benzoyl-CoA. This enzyme acts
under anaerobic conditions.
Length = 380
Score = 28.4 bits (63), Expect = 3.7
Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 11/87 (12%)
Query: 157 NLTEELEENIIENVYDDYKFVTRQELEDLGLGHLIGTSLLRAYMHGFFMDIRLYRKAKSV 216
NL + +E + V DD+ V R E D+ L +L A++H + S
Sbjct: 249 NLIKSIELSGCYIVDDDFIIVHRFENNDVALAGDPLQNLALAFLH----------DSIST 298
Query: 217 SAPFEFEEFKKKK-IRERIEQERTRGV 242
+A ++ +E K K + +++ + GV
Sbjct: 299 AAKYDDDEADKGKYLLDQVRKNAAEGV 325
>gnl|CDD|235824 PRK06545, PRK06545, prephenate dehydrogenase; Validated.
Length = 359
Score = 28.3 bits (64), Expect = 3.7
Identities = 9/14 (64%), Positives = 10/14 (71%), Gaps = 1/14 (7%)
Query: 185 LGLGHLIGTSLLRA 198
+GLG LIG SL A
Sbjct: 6 VGLG-LIGGSLALA 18
>gnl|CDD|113868 pfam05113, DUF693, Protein of unknown function (DUF693). This
family consists of several uncharacterized proteins from
Borrelia burgdorferi (Lyme disease spirochete).
Length = 311
Score = 28.3 bits (63), Expect = 4.3
Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 4/64 (6%)
Query: 175 KFVTRQELEDLGLGHLIGTSLLRAYMHGFF---MDIRLYRKAKSVSAPFEFEEFKKKKIR 231
KF ++ + + G+L GT + Y G F +D+RL ++ + E++ FK K ++
Sbjct: 90 KFAHEKDFDFIMAGYL-GTPMSTDYPGGDFSVELDVRLLSRSNFFNRKLEYKNFKGKTVQ 148
Query: 232 ERIE 235
E IE
Sbjct: 149 EAIE 152
>gnl|CDD|222018 pfam13274, DUF4065, Protein of unknown function (DUF4065). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria, archaea and
viruses. Proteins in this family are typically between
155 and 202 amino acids in length.
Length = 99
Score = 26.9 bits (60), Expect = 4.7
Identities = 13/33 (39%), Positives = 22/33 (66%), Gaps = 1/33 (3%)
Query: 153 GFLDNLTEELEENIIENVYDDYKFVTRQELEDL 185
G LD L+EE E+ I++ V + Y ++ +EL +L
Sbjct: 58 GDLDELSEE-EKEILDEVIEKYGNLSAKELSEL 89
>gnl|CDD|216465 pfam01379, Porphobil_deam, Porphobilinogen deaminase, dipyromethane
cofactor binding domain.
Length = 213
Score = 27.6 bits (62), Expect = 5.3
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 168 ENVYDDYKFVTRQELEDLGLGHLIGTSLLR 197
E+ D + LEDL G ++GTS LR
Sbjct: 98 EDPRDALVSSNGKSLEDLPAGSVVGTSSLR 127
>gnl|CDD|216225 pfam00977, His_biosynth, Histidine biosynthesis protein. Proteins
involved in steps 4 and 6 of the histidine biosynthesis
pathway are contained in this family. Histidine is
formed by several complex and distinct biochemical
reactions catalyzed by eight enzymes. The enzymes in
this Pfam entry are called His6 and His7 in eukaryotes
and HisA and HisF in prokaryotes. The structure of HisA
is known to be a TIM barrel fold. In some archaeal HisA
proteins the TIM barrel is composed of two tandem
repeats of a half barrel . This family belong to the
common phosphate binding site TIM barrel family.
Length = 230
Score = 27.1 bits (61), Expect = 7.7
Identities = 14/43 (32%), Positives = 26/43 (60%), Gaps = 4/43 (9%)
Query: 180 QELEDLGLGHLIGTSLLR-AYMHGFFMDIRLYRK-AKSVSAPF 220
++LE+LG G ++ T + R + G D+ L R+ A++V+ P
Sbjct: 155 KKLEELGAGEILLTDIDRDGTLSGP--DLELTRELAEAVNIPV 195
>gnl|CDD|227498 COG5170, CDC55, Serine/threonine protein phosphatase 2A, regulatory
subunit [Signal transduction mechanisms].
Length = 460
Score = 27.3 bits (60), Expect = 9.2
Identities = 15/35 (42%), Positives = 17/35 (48%), Gaps = 4/35 (11%)
Query: 76 IRDIKFHDN--YVLSMDSSVVKIWSK--DNGSLFT 106
I D KF DN Y+LS D VKIW + T
Sbjct: 283 ISDFKFSDNGRYILSRDYLTVKIWDVNMAKNPIKT 317
>gnl|CDD|232831 TIGR00115, tig, trigger factor. Trigger factor is a
ribosome-associated molecular chaperone and is the first
chaperone to interact with nascent polypeptide. Trigger
factor can bind at the same time as the signal
recognition particle (SRP), but is excluded by the SRP
receptor (FtsY). The central domain of trigger factor
has peptidyl-prolyl cis/trans isomerase activity. This
protein is found in a single copy in virtually every
bacterial genome [Protein fate, Protein folding and
stabilization].
Length = 408
Score = 27.1 bits (61), Expect = 9.9
Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 213 AKSVSAPFE-FEEFKKKKIRERIEQERTR 240
AKS+ FE EE K IR+ +E+E+
Sbjct: 242 AKSLGEEFETLEELKAD-IRKNLEREKKE 269
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 0.139 0.418
Gapped
Lambda K H
0.267 0.0709 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,847,287
Number of extensions: 1225391
Number of successful extensions: 1212
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1211
Number of HSP's successfully gapped: 25
Length of query: 248
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 154
Effective length of database: 6,768,326
Effective search space: 1042322204
Effective search space used: 1042322204
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 (21.9 bits)
S2: 58 (26.2 bits)