RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17374
(71 letters)
>gnl|CDD|200312 TIGR03689, pup_AAA, proteasome ATPase. In the Actinobacteria, as
shown for Mycobacterium tuberculosis, some proteins are
modified by ligation between an epsilon-amino group of a
lysine side chain and the C-terminal carboxylate of the
ubiquitin-like protein Pup. This modification leads to
protein degradation by the archaeal-like proteasome
found in the Actinobacteria. Members of this protein
family belong to the AAA family of ATPases and tend to
be clustered with the genes for Pup, the Pup ligase
PafA, and structural components of the proteasome. This
protein forms hexameric rings with ATPase activity
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 512
Score = 32.4 bits (74), Expect = 0.010
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 3 PNDYTPDDWQSIWSGSGNPLLYIRSVV 29
PN PDDW I G ++YIR++V
Sbjct: 486 PNTTNPDDWARISGRKGERIVYIRTLV 512
>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 = 32.3 bits (74), Expect = 0.010
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 5/30 (16%)
Query: 42 SSTYWRSPVDLSGLFHPHAFLSVLKQHTAR 71
T W LSG F+P +FL+ + Q AR
Sbjct: 561 PKTVW-----LSGFFNPQSFLTAIMQSVAR 585
>gnl|CDD|115758 pfam07125, DUF1378, Protein of unknown function (DUF1378). This
family consists of hypothetical bacterial and phage
proteins of around 59 residues in length. Bacterial
members of this family seem to be specific to
Enterobacteria. The function of this family is unknown.
Structural modelling suggests this domain may bind
nucleic acids.
Length = 59
Score = 25.3 bits (55), Expect = 1.4
Identities = 11/30 (36%), Positives = 15/30 (50%)
Query: 22 LLYIRSVVSRAVMVHKCYQVSSTYWRSPVD 51
LLY +VV +V Y+V Y R +D
Sbjct: 8 LLYFCTVVCALYLVSGGYKVIRNYIRRKID 37
>gnl|CDD|182714 PRK10769, folA, dihydrofolate reductase; Provisional.
Length = 159
Score = 25.9 bits (57), Expect = 1.7
Identities = 7/12 (58%), Positives = 11/12 (91%)
Query: 5 DYTPDDWQSIWS 16
DY PD+W+S++S
Sbjct: 127 DYEPDEWESVFS 138
>gnl|CDD|220311 pfam09609, Cas_GSU0054, CRISPR-associated protein, GSU0054 family
(Cas_GSU0054). This entry represents a rare
CRISPR-associated protein. So far, members are found in
Geobacter sulfurreducens and in two unpublished genomes:
Gemmata obscuriglobus and Actinomyces naeslundii.
CRISPR-associated proteins typically are found near
CRISPR repeats and other CRISPR-associated proteins,
have low levels of sequence identify, have sequence
relationships that suggest lateral transfer, and show
some sequence similarity to DNA-active proteins such as
helicases and repair proteins.
Length = 519
Score = 24.6 bits (53), Expect = 6.2
Identities = 9/44 (20%), Positives = 15/44 (34%), Gaps = 3/44 (6%)
Query: 3 PNDYTPDDW---QSIWSGSGNPLLYIRSVVSRAVMVHKCYQVSS 43
Y P W + W GS + + V+ R V ++
Sbjct: 79 TRHYVPRAWGRGKKNWHGSATLIRHRPVVLPRESPVIYVWRNVE 122
>gnl|CDD|226545 COG4059, MtrE, Tetrahydromethanopterin S-methyltransferase, subunit
E [Coenzyme metabolism].
Length = 304
Score = 24.1 bits (52), Expect = 7.0
Identities = 12/50 (24%), Positives = 19/50 (38%), Gaps = 2/50 (4%)
Query: 20 NPLLYIRSVVSRAVMVHKCYQVSSTYWRSPVDLSGLFHPHAFLSVLKQHT 69
PL + A VH + V+S R S P +L +++ H
Sbjct: 85 PPLFALALGAGIAACVHGTFAVTSHMGRI-ASQSRFGQP-VYLDMVRSHL 132
>gnl|CDD|187865 cd09734, Csb2_I-U, CRISPR/Cas system-associated protein Csb2.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Duplicated RAMP domains; also known as GSU0054 family.
Length = 495
Score = 24.2 bits (52), Expect = 7.8
Identities = 9/44 (20%), Positives = 14/44 (31%), Gaps = 3/44 (6%)
Query: 3 PNDYTPDDW---QSIWSGSGNPLLYIRSVVSRAVMVHKCYQVSS 43
Y P W + W GS + V+ R V ++
Sbjct: 67 TRHYVPRAWGRGKKNWHGSATLIFDRPVVLPRESPVIYLWRNVE 110
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 0.134 0.456
Gapped
Lambda K H
0.267 0.0560 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,535,175
Number of extensions: 240248
Number of successful extensions: 214
Number of sequences better than 10.0: 1
Number of HSP's gapped: 214
Number of HSP's successfully gapped: 7
Length of query: 71
Length of database: 10,937,602
Length adjustment: 41
Effective length of query: 30
Effective length of database: 9,119,088
Effective search space: 273572640
Effective search space used: 273572640
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 (22.0 bits)
S2: 53 (24.6 bits)