RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9556
(62 letters)
>gnl|CDD|217325 pfam03028, Dynein_heavy, Dynein heavy chain and region D6 of dynein
motor. This family represents the C-terminal region of
dynein heavy chain. The chain also contains ATPase
activity and microtubule binding ability and acts as a
motor for the movement of organelles and vesicles along
microtubules. Dynein is also involved in cilia and
flagella movement. The dynein subunit consists of at
least two heavy chains and a number of intermediate and
light chains. The 380 kDa motor unit of dynein belongs
to the AAA class of chaperone-like ATPases. The core of
the 380 kDa motor unit contains a concatenated chain of
six AAA modules, of which four correspond to the ATP
binding sites with P-loop signatures described
previously, and two are modules in which the P loop has
been lost in evolution. This C-terminal domain carries
the D6 region of the dynein motor where the P-loop has
been lost in evolution but the general structure of a
potential ATP binding site appears to be retained.
Length = 706
Score = 62.7 bits (153), Expect = 1e-13
Identities = 22/60 (36%), Positives = 32/60 (53%)
Query: 1 MPVIYIYAINTTAGKDPKLYECPIYRKPQRTDLKYVGSIDFETDNNPRHWTLRGVALLCD 60
MPVI++ A+ ++ +YECP+Y+ R YV + +T P W L GVALL
Sbjct: 647 MPVIWVKAVPADKQEEKSVYECPVYKTETRGGTTYVFTFLLKTKEPPSKWILAGVALLLQ 706
>gnl|CDD|166698 PLN03059, PLN03059, beta-galactosidase; Provisional.
Length = 840
Score = 25.7 bits (56), Expect = 1.3
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 33 LKYVGSIDFETDNNP 47
LKYV I+F TDN P
Sbjct: 135 LKYVPGIEFRTDNGP 149
>gnl|CDD|217077 pfam02514, CobN-Mg_chel, CobN/Magnesium Chelatase. This family
contains a domain common to the cobN protein and to
magnesium protoporphyrin chelatase. CobN is implicated
in the conversion of hydrogenobyrinic acid a,c-diamide
to cobyrinic acid. Magnesium protoporphyrin chelatase is
involved in chlorophyll biosynthesis.
Length = 1079
Score = 25.2 bits (56), Expect = 1.9
Identities = 5/10 (50%), Positives = 7/10 (70%)
Query: 1 MPVIYIYAIN 10
+P IY Y +N
Sbjct: 460 LPHIYPYIVN 469
>gnl|CDD|214350 CHL00062, psbB, photosystem II 47 kDa protein.
Length = 504
Score = 25.4 bits (56), Expect = 2.0
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 38 SIDFETDNNPRHWTLRGVAL 57
SI ET NP W+ GVA
Sbjct: 79 SITGETVTNPGIWSYEGVAG 98
>gnl|CDD|173935 cd08176, LPO, Lactadehyde:propanediol oxidoreductase (LPO)
catalyzes the interconversion between L-lactaldehyde and
L-1,2-propanediol in Escherichia coli and other
enterobacteria. Lactadehyde:propanediol oxidoreductase
(LPO) is a member of the group III iron-activated
dehydrogenases which catalyze the interconversion
between L-lactaldehyde and L-1,2-propanediol in
Escherichia coli and other enterobacteria. L-Fucose and
L-rhamnose is used by Escherichia coli through an
inducible pathway mediated by the fucose regulon
comprising four linked oeprons fucO, fucA, fucPIK, and
fucR. The fucA-encoded aldolase catalyzes the formation
of dihydroxyacetone phosphate and L-lactaldehyde. Under
anaerobic conditions, with NADH as a cofactor,
lactaldehyde is converted by a fucO-encoded
Lactadehyde:propanediol oxidoreductase (LPO) to
L-1,2-propanediol, which is excreted as a fermentation
product. In mutant strains, E. coli adapted to grow on
L-1,2-propanediol, FucO catalyzes the oxidation of the
polyol to L-lactaldehyde. FucO is induced regardless of
the respiratory conditions of the culture, remains fully
active in the absence of oxygen. In the presence of
oxygen, this enzyme becomes oxidatively inactivated by a
metal-catalyzed oxidation mechanism. FucO is an
iron-dependent metalloenzyme that is inactivated by
other metals, such as zinc, copper, or cadmium. This
enzyme can also reduces glycol aldehyde with similar
efficiency. Beside L-1,2-propanediol, the enzyme is
also able to oxidize methanol as alternative substrates.
Length = 377
Score = 24.9 bits (55), Expect = 2.5
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 2 PVIYIYAINTTAG 14
P + I AINTTAG
Sbjct: 126 PAVPIVAINTTAG 138
>gnl|CDD|200498 cd11237, Sema_1A, The Sema domain, a protein interacting module, of
semaphorin 1A (Sema1A). Sema1A is a transmembrane
protein. It has been shown to mediate the
defasciculation of motor axon bundles at specific choice
points. Sema1A binds to its receptor plexin A (PlexA),
which in turn triggers downstream signaling events
involving the receptor tyrosine kinase Otk, the
evolutionarily conserved flavoprotein monooxygenase
molecule interacting with CasL (MICAL), and the A kinase
anchoring protein Nervy, leading to repulsive
growth-cone response. Sema1A has also been shown to be
involved in synaptic formation. It is a member of the
semaphorin family of proteins. Semaphorins are
regulatory molecules in the development of the nervous
system and in axonal guidance. They also play important
roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems and
cancer. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as a receptor-recognition
and -binding module.
Length = 446
Score = 25.0 bits (55), Expect = 2.7
Identities = 14/39 (35%), Positives = 18/39 (46%), Gaps = 14/39 (35%)
Query: 13 AGKDPKLYECPIYRKPQRT---DLK------YVGSIDFE 42
+G DP IYR+P RT DLK +V S +
Sbjct: 136 SGADPL-----IYREPLRTERYDLKQLNAPNFVSSFAYG 169
>gnl|CDD|220644 pfam10238, Eapp_C, E2F-associated phosphoprotein. This entry
represents the conserved C-terminal portion of an E2F
binding protein. E2F transcription factors play an
essential role in cell proliferation and apoptosis and
their activity is frequently deregulated in human
cancers. E2F activity is regulated by a variety of
mechanisms, frequently mediated by proteins binding to
individual members or a subgroup of the family. EAPP
interacts with a subset of E2F factors and influences
E2F-dependent promoter activity. EAPP is present
throughout the cell cycle but disappears during
mitosis.
Length = 128
Score = 24.6 bits (54), Expect = 3.4
Identities = 12/41 (29%), Positives = 19/41 (46%)
Query: 6 IYAINTTAGKDPKLYECPIYRKPQRTDLKYVGSIDFETDNN 46
++AIN ++ LY PI RK +R + K T +
Sbjct: 56 MFAINCKVDEEKVLYSKPINRKKRRRNSKKNELNPNNTATS 96
>gnl|CDD|216405 pfam01274, Malate_synthase, Malate synthase.
Length = 517
Score = 24.2 bits (53), Expect = 4.9
Identities = 10/26 (38%), Positives = 13/26 (50%), Gaps = 4/26 (15%)
Query: 37 GSIDFETDNNPRHWTLR----GVALL 58
G IDF +N + + L G ALL
Sbjct: 133 GRIDFRDENAGKSYKLNDGLHGRALL 158
>gnl|CDD|199903 cd10150, CobN_like, CobN subunit of cobaltochelatase, bchH and chlH
subunits of magnesium chelatases, and similar proteins.
Cobaltochelatase is a complex enzyme that catalyzes the
insertion of cobalt into hydrogenobyrinic acid
a,c-diamide, resulting in cobyrinic acid, as
demonstrated for Pseudomonas denitrificans. This is an
essential step in the bacterial synthesis of cobalamine
(B12). The insertion of cobalt requires a complex
composed of three polypeptides, cobN, cobS, and cobT.
Also included in this family are protoporphyrin IX
magnesium chelatases involved in the synthesis of
chlorophyll and bacteriochlorophyll, specifically the
large (chlH or bchH) subunits.They are thought to bind
both the protoporphyrin and the magnesium ion.
Hydrolysis of ATP by the smaller subunits in the complex
may trigger a conformational change that results in the
insertion of the ion into the protoporphyrin scaffold.
Cryo electron microscopy studies have suggested that a
distinct bchH C-terminal domain may bind tightly to the
N-terminal domain upon substrate binding, requiring a
substantial conformational change of the bchH subunit.
It has also been suggested that chlH of higher plants
binds abscisic acid via a C-terminal domain and plays a
role in abscisic acid signaling, and that the protein
spans the chloroplast envelope, with the C-terminus
exposed to the cytosol.
Length = 910
Score = 24.1 bits (53), Expect = 6.2
Identities = 4/10 (40%), Positives = 7/10 (70%)
Query: 1 MPVIYIYAIN 10
+P IY Y ++
Sbjct: 528 LPNIYPYIVD 537
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 0.142 0.458
Gapped
Lambda K H
0.267 0.0702 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,133,380
Number of extensions: 207891
Number of successful extensions: 154
Number of sequences better than 10.0: 1
Number of HSP's gapped: 154
Number of HSP's successfully gapped: 9
Length of query: 62
Length of database: 10,937,602
Length adjustment: 33
Effective length of query: 29
Effective length of database: 9,473,920
Effective search space: 274743680
Effective search space used: 274743680
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)