RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3195
(119 letters)
>gnl|CDD|201954 pfam01753, zf-MYND, MYND finger.
Length = 39
Score = 54.0 bits (130), Expect = 3e-11
Identities = 18/39 (46%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 69 CANCNREAFA--ECSMCRQTPYCSTFCQRKDWTTHQVEC 105
CA C +EA CS C+ YCS CQ+ DW H+ EC
Sbjct: 1 CAVCGKEALKLLRCSRCKSVYYCSKECQKADWPYHKKEC 39
>gnl|CDD|226116 COG3588, COG3588, Fructose-1,6-bisphosphate aldolase [Carbohydrate
transport and metabolism].
Length = 332
Score = 30.2 bits (68), Expect = 0.23
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 5 IQQNAPNAQSGDESNTSADQNSFIDQAYVES 35
+Q+ A A GDE N + Q + I++ Y S
Sbjct: 293 LQEGALKAWQGDEENFAKAQAASIERIYEAS 323
>gnl|CDD|133918 PHA00660, PHA00660, hypothetical protein.
Length = 215
Score = 27.5 bits (60), Expect = 1.5
Identities = 25/78 (32%), Positives = 33/78 (42%), Gaps = 7/78 (8%)
Query: 8 NAPNAQSGDESNTSADQNSFIDQAY-------VESASLPVLPIRLSIGNTAQVQGPLTIV 60
NA A+ G +S A Q Q + A+L I L G+ A+VQ IV
Sbjct: 58 NASIAELGAQSALEAGQQQIAAQTLKAGQLKGAQRAALAANGIDLGEGSAAEVQVSSDIV 117
Query: 61 ENIDLRTRCANCNREAFA 78
+ ID T AN R A+
Sbjct: 118 KQIDTDTLRANAARTAWG 135
>gnl|CDD|215607 PLN03158, PLN03158, methionine aminopeptidase; Provisional.
Length = 396
Score = 26.7 bits (59), Expect = 2.9
Identities = 11/41 (26%), Positives = 19/41 (46%), Gaps = 7/41 (17%)
Query: 69 CANCNREAFAECSMC-------RQTPYCSTFCQRKDWTTHQ 102
CA C++ A +C C +CS C + W++H+
Sbjct: 12 CARCSKPAHLQCPKCLELKLPREGASFCSQDCFKAAWSSHK 52
>gnl|CDD|180247 PRK05767, rpl44e, 50S ribosomal protein L44e; Validated.
Length = 92
Score = 25.3 bits (56), Expect = 5.0
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 3/34 (8%)
Query: 44 RLSIGNTAQ---VQGPLTIVENIDLRTRCANCNR 74
R +IG + V G + +DLR RC C +
Sbjct: 42 RKTIGYGGKFSPVPGGAKPTKKVDLRYRCTECGK 75
>gnl|CDD|226068 COG3538, COG3538, Uncharacterized conserved protein [Function
unknown].
Length = 434
Score = 25.8 bits (57), Expect = 6.2
Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 7/66 (10%)
Query: 38 LPVLPIRLSIGNTAQVQGPLTIV-ENIDLRTRCANCNREAFAECSMCRQTPYCSTFCQRK 96
+P + +R S TAQV+ L + E+ +LR A + PY + F +
Sbjct: 58 IPAMWLRDS---TAQVRPYLPLAKEDEELRRLIAGLVKRQAR---YILLDPYANAFNETA 111
Query: 97 DWTTHQ 102
+ HQ
Sbjct: 112 NGAGHQ 117
>gnl|CDD|197214 cd09115, PLDc_PPK1_C2, Catalytic C-terminal domain, second
repeat, of prokaryotic polyphosphate kinase 1 and
similar proteins. Catalytic C-terminal domain, second
repeat (C2 domain), of bacterial polyphosphate kinases
1 (Poly P kinase 1 or PPK1, EC 2.7.4.1) and similar
proteins. Inorganic polyphosphate (Poly P) plays an
important role in bacterial stress responses and
stationary-phase survival. PPK1 is the key enzyme
responsible for the synthesis of Poly P in bacteria. It
can catalyze the reversible conversion of the
terminal-phosphate of ATP to Poly P. Therefore, PPK1 is
essential for bacterial motility, quorum sensing,
biofilm formation, and the production of virulence
factors and may serve as an attractive antimicrobial
drug target. Dimerization is crucial for the enzymatic
activity of PPK1. Each PPK1 monomer includes four
structural domains, the N-terminal (N) domain, the head
(H) domain, and two closely related C-terminal (C1 and
C2) domains. The N domain provides the upper binding
interface for the adenine ring of the ATP. The H domain
is involved in dimerization, while both the C1 and C2
domains contain residues crucial for catalytic
activity. The intersection of the N, C1, and C2 domains
forms a structural tunnel in which the PPK catalytic
reactions are carried out. In spite of the lack of
sequence homology, the C1 and C2 domains of PPK1 are
structurally similar to the two repetitive catalytic
domains of phospholipase D (PLD). Moreover, some
residues in the HKD motif (H-x-K-x(4)-D, where x
represents any amino acid residue) of the PLD
superfamily are spatially conserved in the active site
of PPK1. It is possible that the bacterial PPK1 family
and the PLD family have a common ancestor and diverged
early in evolution. There is a second bacterial-type
enzyme, PPK2, which is involved in the synthesis of
poly P from GTP or ATP. PPK2 shows no sequence
similarity to PPK1 and belongs to different
superfamily.
Length = 162
Score = 25.2 bits (55), Expect = 8.8
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 4/71 (5%)
Query: 1 MYSVIQQNAPNAQSGDESNTSADQNSFIDQAYVE---SASLPVLPIRLSI-GNTAQVQGP 56
+Y +I + NAQ G + + NS D+ V+ AS +PI L + G + G
Sbjct: 14 LYEMIDREIANAQQGLPAGITLKLNSLTDKKLVDRLYKASSAGVPIDLVVRGMCCLIPGL 73
Query: 57 LTIVENIDLRT 67
I +NI +R+
Sbjct: 74 EGISDNIRVRS 84
>gnl|CDD|201483 pfam00873, ACR_tran, AcrB/AcrD/AcrF family. Members of this family
are integral membrane proteins. Some are involved in
drug resistance. AcrB cooperates with a membrane fusion
protein, AcrA, and an outer membrane channel TolC. The
structure shows the AcrB forms a homotrimer.
Length = 1021
Score = 25.3 bits (56), Expect = 9.7
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 35 SASLPVLPIRLSIGNTAQVQGPLTIV 60
+A L VLP+ +S G +++Q PL IV
Sbjct: 972 AAILGVLPLAISTGAGSELQQPLGIV 997
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
0.318 0.128 0.384
Gapped
Lambda K H
0.267 0.0703 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,270,510
Number of extensions: 397894
Number of successful extensions: 298
Number of sequences better than 10.0: 1
Number of HSP's gapped: 298
Number of HSP's successfully gapped: 15
Length of query: 119
Length of database: 10,937,602
Length adjustment: 82
Effective length of query: 37
Effective length of database: 7,300,574
Effective search space: 270121238
Effective search space used: 270121238
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.2 bits)