RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12684
(163 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 = 118 bits (298), Expect = 1e-31
Identities = 51/156 (32%), Positives = 67/156 (42%), Gaps = 36/156 (23%)
Query: 6 STYLTYLNQLTDVQFEALRYLTGECNYGGRVTDDWDRRTLNTILYKFFCPAALEDENYLF 65
YL N V +E LRYL GE YGGR+TDDWDRR L T L +FF P + E
Sbjct: 304 DNYLD-ANAPDKVPWEDLRYLFGEIMYGGRITDDWDRRLLRTYLEEFFTPRLFDPE---- 358
Query: 66 DPSVTDDWDRRTLNTILYKFFCPAALEDENYLFDPSGFYYT-PNEPDYDGYLNYIKNLPL 124
P + P DY+GYL YI+ LP
Sbjct: 359 ------------------------------LELAPGDLGFAVPPGTDYEGYLQYIEELPP 388
Query: 125 VASPIIFGMNENADILKDQQETNLVLGNVLLTQERT 160
+SP +G++ NA+I Q+T ++ +L Q R
Sbjct: 389 ESSPEWYGLHPNAEIGFLTQQTEKLIRTLLELQPRE 424
>gnl|CDD|205520 pfam13340, DUF4096, Putative transposase of IS4/5 family
(DUF4096).
Length = 75
Score = 28.2 bits (64), Expect = 0.50
Identities = 16/38 (42%), Positives = 18/38 (47%), Gaps = 2/38 (5%)
Query: 15 LTDVQFEALR-YLTGECNYGGRVTDDWDRRTLNTILYK 51
LTD Q+ + L GGR D DR LN ILY
Sbjct: 1 LTDEQWALIEPLLPPPKRRGGRPRVD-DREVLNAILYV 37
>gnl|CDD|240245 PTZ00050, PTZ00050, 3-oxoacyl-acyl carrier protein synthase;
Provisional.
Length = 421
Score = 28.5 bits (64), Expect = 1.5
Identities = 15/96 (15%), Positives = 29/96 (30%), Gaps = 7/96 (7%)
Query: 57 ALEDENYLFDPSVTDDWDRRTLNTILYKFFCPAALEDENYLFDPSGFYYTPNEPDYDGYL 116
L + + + L C A E + FDPS F T E +
Sbjct: 25 KLTEFPKFLPDCIPEQKALENLVA---AMPCQIAAEVDQSEFDPSDFAPTKRESRATHFA 81
Query: 117 NYIKNLPLVASPIIFGMNENADILKDQQETNLVLGN 152
L + ++ ++ +++ N+ G
Sbjct: 82 MAAAREALADA----KLDILSEKDQERIGVNIGSGI 113
>gnl|CDD|107332 cd06337, PBP1_ABC_ligand_binding_like_4, Type I periplasmic
ligand-binding domain of uncharacterized ABC (ATPase
Binding Cassette)-type active transport systems that are
predicted to be involved in transport of amino acids,
peptides, or inorganic ions. This subgroup includes the
type I periplasmic ligand-binding domain of
uncharacterized ABC (ATPase Binding Cassette)-type
active transport systems that are predicted to be
involved in transport of amino acids, peptides, or
inorganic ions. Members of this group are
sequence-similar to members of the family of ABC-type
hydrophobic amino acid transporters, such as
leucine-isoleucine-valine-binding protein (LIVBP);
however their ligand specificity has not been determined
experimentally.
Length = 357
Score = 28.1 bits (63), Expect = 2.3
Identities = 11/34 (32%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 88 PAALEDENYLFDPSGFYYTPNEPDYDGYLNYIKN 121
PAAL D Y G + P D+ +N K
Sbjct: 169 PAALADAGYKLVDPG-RFEPGTDDFSSQINAFKR 201
>gnl|CDD|224816 COG1904, UxaC, Glucuronate isomerase [Carbohydrate transport and
metabolism].
Length = 463
Score = 27.3 bits (61), Expect = 4.3
Identities = 9/33 (27%), Positives = 15/33 (45%), Gaps = 8/33 (24%)
Query: 93 DENYLFDPSGFYYTPNEPDYDGYLNYIKNLPLV 125
E++L P EP Y+K+LP++
Sbjct: 4 TEDFLL--------PAEPATRRLHAYVKDLPII 28
>gnl|CDD|234053 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family.
Members of this protein family resemble the widely
distributed ATP-dependent protease La, also called Lon
and LonA. It resembles even more closely LonB, which is
a LonA paralog found in genomes if and only if the
species is capable of endospore formation (as in
Bacillus subtilis, Clostridium tetani, and select other
members of the Firmicutes) and expressed specifically in
the forespore compartment. Members of this family are
restricted to a subset of spore-forming species, and are
very likely to participate in the program of endospore
formation. We propose the designation LonC [Protein
fate, Degradation of proteins, peptides, and
glycopeptides, Cellular processes, Sporulation and
germination].
Length = 615
Score = 27.1 bits (60), Expect = 5.7
Identities = 10/29 (34%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 91 LEDENYLFDPSGFYYTPNEPDYDGYLNYI 119
LED+ F S YY P++P+ Y+ +
Sbjct: 289 LEDKRVEFSSS--YYDPDDPNVPKYIKKL 315
>gnl|CDD|233044 TIGR00600, rad2, DNA excision repair protein (rad2). All proteins
in this family for which functions are known are flap
endonucleases that generate the 3' incision next to DNA
damage as part of nucleotide excision repair. This
family is related to many other flap endonuclease
families including the fen1 family. This family is based
on the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 1034
Score = 26.4 bits (58), Expect = 8.3
Identities = 8/30 (26%), Positives = 15/30 (50%)
Query: 106 TPNEPDYDGYLNYIKNLPLVASPIIFGMNE 135
E D YL+ + +PL+A+ + +N
Sbjct: 433 IEVEDDDLDYLDQGEGIPLMAALQLSSVNS 462
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 0.140 0.433
Gapped
Lambda K H
0.267 0.0854 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,687,084
Number of extensions: 815077
Number of successful extensions: 583
Number of sequences better than 10.0: 1
Number of HSP's gapped: 582
Number of HSP's successfully gapped: 22
Length of query: 163
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 74
Effective length of database: 6,990,096
Effective search space: 517267104
Effective search space used: 517267104
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: 55 (24.7 bits)