RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5804
(113 letters)
>gnl|CDD|227364 COG5031, COQ4, Uncharacterized protein involved in ubiquinone
biosynthesis [Coenzyme metabolism].
Length = 235
Score = 28.6 bits (64), Expect = 0.66
Identities = 9/36 (25%), Positives = 12/36 (33%), Gaps = 1/36 (2%)
Query: 37 EFLRQFHEGNFNYKYRDSLKRNYNLGQYFLEINIED 72
+ L Q E Y Y D +KR + D
Sbjct: 87 DQLAQLPENTLGYVYADWMKRE-GFDPDTRKPVPVD 121
>gnl|CDD|235552 PRK05670, PRK05670, anthranilate synthase component II;
Provisional.
Length = 189
Score = 27.8 bits (63), Expect = 0.99
Identities = 11/24 (45%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 77 FINNIDSLKRNYNLGQYFLEINIE 100
I+N DS YNL QY E+ E
Sbjct: 4 LIDNYDSF--TYNLVQYLGELGAE 25
>gnl|CDD|223586 COG0512, PabA, Anthranilate/para-aminobenzoate synthases component
II [Amino acid transport and metabolism / Coenzyme
metabolism].
Length = 191
Score = 27.1 bits (61), Expect = 1.6
Identities = 11/24 (45%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 77 FINNIDSLKRNYNLGQYFLEINIE 100
I+N DS YNL QY E+ E
Sbjct: 6 LIDNYDSF--TYNLVQYLRELGAE 27
>gnl|CDD|206643 cd00877, Ran, Ras-related nuclear proteins (Ran)/TC4 family of
small GTPases. Ran GTPase is involved in diverse
biological functions, such as nuclear transport, spindle
formation during mitosis, DNA replication, and cell
division. Among the Ras superfamily, Ran is a unique
small G protein. It does not have a lipid modification
motif at the C-terminus to bind to the membrane, which
is often observed within the Ras superfamily. Ran may
therefore interact with a wide range of proteins in
various intracellular locations. Like other GTPases, Ran
exists in GTP- and GDP-bound conformations that interact
differently with effectors. Conversion between these
forms and the assembly or disassembly of effector
complexes requires the interaction of regulator
proteins. The intrinsic GTPase activity of Ran is very
low, but it is greatly stimulated by a GTPase-activating
protein (RanGAP1) located in the cytoplasm. By contrast,
RCC1, a guanine nucleotide exchange factor that
generates RanGTP, is bound to chromatin and confined to
the nucleus. Ran itself is mobile and is actively
imported into the nucleus by a mechanism involving
NTF-2. Together with the compartmentalization of its
regulators, this is thought to produce a relatively high
concentration of RanGTP in the nucleus.
Length = 166
Score = 26.9 bits (60), Expect = 2.0
Identities = 14/36 (38%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 32 KRKFKEFLRQFHEGNFNYKYRD-SLKRNYNLGQYFL 66
RK K FH N +Y + S K NYN + FL
Sbjct: 118 DRKVKPKQITFH-RKKNLQYYEISAKSNYNFEKPFL 152
>gnl|CDD|173948 cd08189, Fe-ADH5, Iron-containing alcohol dehydrogenases-like.
Iron-containing alcohol dehydrogenase-like. Alcohol
dehydrogenase catalyzes the reduction of acetaldehyde to
alcohol with NADP as cofactor. Its activity requires
iron ions. The protein structure represents a
dehydroquinate synthase-like fold and belongs to the
alcohol dehydrogenase-like superfamily. They are
distinct from other alcohol dehydrogenases which
contains different protein domain. Proteins of this
family have not been characterized. Their specific
function is unknown.
Length = 374
Score = 26.8 bits (60), Expect = 2.5
Identities = 6/27 (22%), Positives = 10/27 (37%)
Query: 77 FINNIDSLKRNYNLGQYFLEINIEDLT 103
FI+ + L R + I D+
Sbjct: 319 FIDAVRELNRTLGIPTTLEAIKASDIP 345
>gnl|CDD|181566 PRK08857, PRK08857, para-aminobenzoate synthase component II;
Provisional.
Length = 193
Score = 26.8 bits (59), Expect = 2.8
Identities = 11/23 (47%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 78 INNIDSLKRNYNLGQYFLEINIE 100
I+N DS YNL QYF E+ +
Sbjct: 5 IDNYDSF--TYNLYQYFCELGAQ 25
>gnl|CDD|225918 COG3383, COG3383, Uncharacterized anaerobic dehydrogenase [General
function prediction only].
Length = 978
Score = 26.6 bits (59), Expect = 3.1
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 39 LRQFHEGNFNYKYRDSLKRNYNLGQYFLEINIED 72
L FHEGN + S + + + F+EI+ E
Sbjct: 833 LEHFHEGNMTRR---SEGLDSKVPEDFVEISPEL 863
>gnl|CDD|172776 PRK14288, PRK14288, chaperone protein DnaJ; Provisional.
Length = 369
Score = 26.6 bits (58), Expect = 3.3
Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 6/40 (15%)
Query: 4 FDDAGIFFSDNF-----GAEDQQSGIQVN-LQSVKRKFKE 37
F+D G FF D F G++ Q+S I + LQ+++ FKE
Sbjct: 87 FEDLGSFFEDAFGFGARGSKRQKSSIAPDYLQTIELSFKE 126
>gnl|CDD|225324 COG2604, COG2604, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 594
Score = 26.2 bits (58), Expect = 4.6
Identities = 15/61 (24%), Positives = 23/61 (37%)
Query: 41 QFHEGNFNYKYRDSLKRNYNLGQYFLEINIEDLTSFFINNIDSLKRNYNLGQYFLEINIE 100
Q F ++LK NY L + NI + F+ + L+RN L + N
Sbjct: 9 QALVNEFLKSKLENLKENYVLEKDTDNKNILKKETLFMGSKYELERNLELFLNLEKYNNY 68
Query: 101 D 101
Sbjct: 69 P 69
>gnl|CDD|180689 PRK06774, PRK06774, para-aminobenzoate synthase component II;
Provisional.
Length = 191
Score = 25.2 bits (55), Expect = 7.2
Identities = 12/23 (52%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 78 INNIDSLKRNYNLGQYFLEINIE 100
I+N DS YNL QYF E+ E
Sbjct: 5 IDNYDSF--TYNLYQYFCELGTE 25
>gnl|CDD|226146 COG3619, COG3619, Predicted membrane protein [Function unknown].
Length = 226
Score = 25.4 bits (56), Expect = 7.3
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 2/35 (5%)
Query: 74 TSFFINNIDSLKRNYNLGQYFLEINIEDLTSWRIF 108
T++ N+ S R LG+Y + E L W I+
Sbjct: 142 TTYVTGNLKSAGRG--LGRYLSGKDKEKLRDWLIY 174
>gnl|CDD|212671 cd10229, HSPA12_like_NBD, Nucleotide-binding domain of HSPA12A,
HSPA12B and similar proteins. Human HSPA12A (also known
as 70-kDa heat shock protein-12A) and HSPA12B (also
known as 70-kDa heat shock protein-12B, chromosome 20
open reading frame 60/C20orf60, dJ1009E24.2) belong 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). No co-chaperones
have yet been identified for HSPA12A or HSPA12B. The
gene encoding HSPA12A maps to 10q26.12, a cytogenetic
region that might represent a common susceptibility
locus for both schizophrenia and bipolar affective
disorder; reduced expression of HSPA12A has been shown
in the prefrontal cortex of subjects with schizophrenia.
HSPA12A is also a candidate gene for forelimb-girdle
muscular anomaly, an autosomal recessive disorder of
Japanese black cattle. HSPA12A is predominantly
expressed in neuronal cells. It may also play a role in
the atherosclerotic process. The gene encoding HSPA12B
maps to 20p13. HSPA12B is predominantly expressed in
endothelial cells, is required for angiogenesis, and may
interact with known angiogenesis mediators. It may be
important for host defense in microglia-mediated immune
response. HSPA12B expression is up-regulated in
lipopolysaccharide (LPS)-induced inflammatory response
in the spinal cord, and mostly located in active
microglia; this induced expression may be regulated by
activation of MAPK-p38, ERK1/2 and SAPK/JNK signaling
pathways. Overexpression of HSPA12B also protects
against LPS-induced cardiac dysfunction and involves the
preserved activation of the PI3K/Akt signaling pathway.
Length = 404
Score = 25.7 bits (57), Expect = 7.3
Identities = 22/90 (24%), Positives = 35/90 (38%), Gaps = 16/90 (17%)
Query: 31 VKRKFKEFLRQFHEGNFNYKYRDSLKRNYNLGQYFLEI-----------NIEDLTSFFIN 79
V R F+E L++ F S L ++F I NI S ++
Sbjct: 248 VDRAFEELLKERLGELFYELPSKSPALWLILMRFFETIKRSFGGTDNDTNIVLPGSLALS 307
Query: 80 NIDSLKRNYNLGQYFLEINIEDLTSWRIFK 109
D +R G+ L+I+ ED+ S +F
Sbjct: 308 KKD-PERGIRNGE--LKISGEDMKS--LFD 332
>gnl|CDD|217144 pfam02615, Ldh_2, Malate/L-lactate dehydrogenase. This family
consists of bacterial and archaeal Malate/L-lactate
dehydrogenase. L-lactate dehydrogenase, EC:1.1.1.27,
catalyzes the reaction (S)-lactate + NAD(+) <=> pyruvate
+ NADH. Malate dehydrogenase, EC:1.1.1.37 and
EC:1.1.1.82, catalyzes the reactions: (S)-malate +
NAD(+) <=> oxaloacetate + NADH, and (S)-malate + NADP(+)
<=> oxaloacetate + NADPH respectively.
Length = 334
Score = 25.4 bits (56), Expect = 7.5
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 89 NLGQYFLEINIEDLTSWRIFK 109
NLGQ F+ IN E F+
Sbjct: 260 NLGQLFIAINPEFFIDGEEFR 280
>gnl|CDD|181070 PRK07658, PRK07658, enoyl-CoA hydratase; Provisional.
Length = 257
Score = 25.4 bits (56), Expect = 8.8
Identities = 11/35 (31%), Positives = 16/35 (45%)
Query: 2 EGFDDAGIFFSDNFGAEDQQSGIQVNLQSVKRKFK 36
EG F + F +ED + G+Q L+ K F
Sbjct: 221 EGVKREAKIFGEVFTSEDAKEGVQAFLEKRKPSFS 255
>gnl|CDD|215981 pfam00536, SAM_1, SAM domain (Sterile alpha motif). It has been
suggested that SAM is an evolutionarily conserved
protein binding domain that is involved in the
regulation of numerous developmental processes in
diverse eukaryotes. The SAM domain can potentially
function as a protein interaction module through its
ability to homo- and heterooligomerise with other SAM
domains.
Length = 62
Score = 24.1 bits (53), Expect = 9.2
Identities = 9/37 (24%), Positives = 15/37 (40%)
Query: 50 KYRDSLKRNYNLGQYFLEINIEDLTSFFINNIDSLKR 86
+Y D+ + Y G L + EDL + K+
Sbjct: 17 QYADNFRAGYIDGDALLLLTEEDLLKLGVTLPGHRKK 53
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 0.141 0.411
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,911,118
Number of extensions: 522982
Number of successful extensions: 600
Number of sequences better than 10.0: 1
Number of HSP's gapped: 598
Number of HSP's successfully gapped: 62
Length of query: 113
Length of database: 10,937,602
Length adjustment: 77
Effective length of query: 36
Effective length of database: 7,522,344
Effective search space: 270804384
Effective search space used: 270804384
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: 53 (24.2 bits)