RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2469
(220 letters)
>gnl|CDD|223205 COG0127, COG0127, Xanthosine triphosphate pyrophosphatase
[Nucleotide transport and metabolism].
Length = 194
Score = 31.0 bits (71), Expect = 0.26
Identities = 10/52 (19%), Positives = 22/52 (42%), Gaps = 3/52 (5%)
Query: 132 VAVAKPKKIMVTKHTKNMGKFSSVTVSTIDEEEDEIEAREIADSYANNARII 183
+A K+ + K++ + + ++ E EIE E ++ NA +
Sbjct: 6 LATGNKGKL---RELKSILAPGGIEIESLKELGVEIEVEETGLTFEENALLK 54
>gnl|CDD|216665 pfam01725, Ham1p_like, Ham1 family. This family consists of the
HAM1 protein and hypothetical archaeal bacterial and C.
elegans proteins. HAM1 controls 6-N-hydroxylaminopurine
(HAP) sensitivity and mutagenesis in S. cerevisiae
inosine triphosphate pyrophosphatase. The HAM1 protein
protects the cell from HAP, either on the level of
deoxynucleoside triphosphate or the DNA level by a yet
unidentified set of reactions.
Length = 181
Score = 30.2 bits (69), Expect = 0.58
Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 7/44 (15%)
Query: 146 TKNMGK-------FSSVTVSTIDEEEDEIEAREIADSYANNARI 182
T N GK + + ID + IE E D++ NA +
Sbjct: 5 TGNKGKLKEIKAILGDLGIEVIDLKHFPIEVEETGDTFEENALL 48
>gnl|CDD|182349 PRK10271, thiK, thiamine kinase; Provisional.
Length = 188
Score = 30.1 bits (68), Expect = 0.62
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 164 EDEIEAREIADSYANNARIIEKQLERK 190
E+ + R++ + YA A+I QL R+
Sbjct: 119 ENTEQHRQLVNDYATRAKIDAAQLWRQ 145
>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 = 30.7 bits (70), Expect = 0.68
Identities = 11/54 (20%), Positives = 19/54 (35%), Gaps = 13/54 (24%)
Query: 80 PEGIERQHRFKCKKCGLFLYYKHDPSSNIIFIVQGAVVKSSGEMPKMDIYNQVA 133
PEG++R G+ S I ++ AV G + D+ +
Sbjct: 118 PEGVQRP--------GIS---VIKTSLGPIMVL--AVTSPDGSYTQTDLRDYAD 158
>gnl|CDD|226375 COG3857, AddB, ATP-dependent nuclease, subunit B [DNA replication,
recombination, and repair].
Length = 1108
Score = 30.5 bits (69), Expect = 0.73
Identities = 12/68 (17%), Positives = 28/68 (41%), Gaps = 4/68 (5%)
Query: 149 MGKFSSVTVSTIDEEEDEIEAREIADSYANNARIIEKQLERKGMNKRKS----DSTTLNT 204
+G + + + E + +++D + + R++ K +G+ S D+ TL
Sbjct: 678 IGNYKATLSLLVSILRQEKDEEQVSDFWWDVYRVLSKSDHNQGLENPLSALSFDNETLKL 737
Query: 205 GETEVKKP 212
GE +
Sbjct: 738 GEETALQL 745
>gnl|CDD|236520 PRK09444, pntB, pyridine nucleotide transhydrogenase; Provisional.
Length = 462
Score = 29.7 bits (67), Expect = 1.2
Identities = 28/91 (30%), Positives = 36/91 (39%), Gaps = 30/91 (32%)
Query: 106 SNIIFIVQGAVVKSSGEMPKMDIYNQVAVAKPKKIMVTKHTKNM---------GKFSSVT 156
SN + IV GA+V SSG A IM K M G F +
Sbjct: 237 SNDLLIVTGALVGSSG-------------AILSYIMC----KAMNRSFISVIAGGFGTDG 279
Query: 157 VSTIDEEE----DEIEAREIADSYANNARII 183
ST D+EE E A E+A+ N+ +I
Sbjct: 280 SSTGDDEEVGEHRETTAEEVAEMLKNSHSVI 310
>gnl|CDD|234022 TIGR02813, omega_3_PfaA, polyketide-type polyunsaturated fatty acid
synthase PfaA. Members of the seed for this alignment
are involved in omega-3 polyunsaturated fatty acid
biosynthesis, such as the protein PfaA from the
eicosapentaenoic acid biosynthesis operon in
Photobacterium profundum strain SS9. PfaA is encoded
together with PfaB, PfaC, and PfaD, and the functions of
the individual polypeptides have not yet been described.
More distant homologs of PfaA, also included with the
reach of this model, appear to be involved in
polyketide-like biosynthetic mechanisms of
polyunsaturated fatty acid biosynthesis, an alternative
to the more familiar iterated mechanism of chain
extension and desaturation, and in most cases are encoded
near genes for homologs of PfaB, PfaC, and/or PfaD.
Length = 2582
Score = 28.8 bits (64), Expect = 2.6
Identities = 15/56 (26%), Positives = 25/56 (44%)
Query: 131 QVAVAKPKKIMVTKHTKNMGKFSSVTVSTIDEEEDEIEAREIADSYANNARIIEKQ 186
QVAV + ++ + +SVT+ TID+ E ++I + A I Q
Sbjct: 1781 QVAVVRSPWVVSHSASPLASAIASVTLGTIDDTSIEAVIKDIEEKTAQIDGFIHLQ 1836
>gnl|CDD|181053 PRK07590, PRK07590, L,L-diaminopimelate aminotransferase;
Validated.
Length = 409
Score = 28.7 bits (65), Expect = 2.7
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 163 EEDEIEAREIADSYANNARIIEKQLERKGM 192
E + + +E+ D Y NA+II + LE G
Sbjct: 308 PEGKAQIKELIDYYMENAKIIREGLESAGF 337
>gnl|CDD|165430 PHA03159, PHA03159, hypothetical protein; Provisional.
Length = 160
Score = 28.0 bits (62), Expect = 2.7
Identities = 19/85 (22%), Positives = 35/85 (41%), Gaps = 18/85 (21%)
Query: 90 KCKKCGLFLYYKHDPSSNIIFIVQGAVV---KSSGEMPKMDI--YNQVAVAKPKKIMVTK 144
+C+ C H +I+ + + K MP I ++++ ++ T+
Sbjct: 16 ECQDC-------HHQQDSIVRAIHSVIHQYNKFEALMPDFSICAHDRIKFTGEAILLTTE 68
Query: 145 HTKNMGK------FSSVTVSTIDEE 163
H N GK FS+ + TIDE+
Sbjct: 69 HNTNWGKVVAMISFSAAALQTIDED 93
>gnl|CDD|184375 PRK13891, PRK13891, conjugal transfer protein TrbE; Provisional.
Length = 852
Score = 28.2 bits (63), Expect = 3.9
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 18/74 (24%)
Query: 131 QVAVAKPKKIMVTKHTKNMGKFSSVTVSTIDEEEDEIEAREIADSYANNARIIEKQLERK 190
+ A+A+ +V G ++SV V +DE+ + +EA +A ++EK + R
Sbjct: 359 EAAIAEVNSGLV-----AQGYYTSVVV-LMDEDRERLEA---------SALLVEKAINRL 403
Query: 191 GMNKRKSDSTTLNT 204
G R T+NT
Sbjct: 404 GFAAR---IETINT 414
>gnl|CDD|132302 TIGR03258, PhnT, 2-aminoethylphosphonate ABC transport system,
ATP-binding component PhnT. This ATP-binding component
of an ABC transport system is found in Salmonella and
Burkholderia lineages in the vicinity of enzymes for the
breakdown of 2-aminoethylphosphonate.
Length = 362
Score = 28.0 bits (62), Expect = 4.1
Identities = 11/45 (24%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 114 GAVVKSSGEMPKMDIYNQVAVAKPKKIMVTKHTKNMGKFSSVTVS 158
GAV+ + G+ + D +++A +P+ + +T G+F + S
Sbjct: 265 GAVIFAFGD-GRHDGRDKLACIRPEHLALTPRPAGEGRFHATIAS 308
>gnl|CDD|215108 PLN00222, PLN00222, tubulin gamma chain; Provisional.
Length = 454
Score = 27.9 bits (62), Expect = 4.9
Identities = 11/52 (21%), Positives = 26/52 (50%), Gaps = 3/52 (5%)
Query: 136 KPKKIMVTKHTKNMGKFSSVTVSTIDEEEDEIEAREIADSYANNARIIEKQL 187
+ K IMV+ + + + +S ++ + E++ ++ S RI E++L
Sbjct: 299 QTKNIMVSSYARTKEASQAKYISILNIIQGEVDPTQVHKSL---QRIRERKL 347
>gnl|CDD|143620 cd07374, CYTH-like_Pase, CYTH-like (also known as triphosphate
tunnel metalloenzyme (TTM)-like) Phosphatases.
CYTH-like superfamily enzymes hydrolyze
triphosphate-containing substrates and require metal
cations as cofactors. They have a unique active site
located at the center of an eight-stranded antiparallel
beta barrel tunnel (the triphosphate tunnel). The name
CYTH originated from the gene designation for bacterial
class IV adenylyl cyclases (CyaB), and from thiamine
triphosphatase. Class IV adenylate cyclases catalyze
the conversion of ATP to 3',5'-cyclic AMP (cAMP) and
PPi. Thiamine triphosphatase is a soluble cytosolic
enzyme which converts thiamine triphosphate to thiamine
diphosphate. This domain superfamily also contains RNA
triphosphatases, membrane-associated polyphosphate
polymerases, tripolyphosphatases, nucleoside
triphosphatases, nucleoside tetraphosphatases and other
proteins with unknown functions.
Length = 174
Score = 27.4 bits (61), Expect = 5.0
Identities = 16/46 (34%), Positives = 17/46 (36%), Gaps = 15/46 (32%)
Query: 40 LDCAVEKLPLRRRDGARVIDGPKHAHKLTCEPDEVFHLKRPEGIER 85
L A L LRRR G D +HLK P GI R
Sbjct: 44 LRLARAGLRLRRRTGG---------------ADAGWHLKLPGGISR 74
>gnl|CDD|233830 TIGR02350, prok_dnaK, chaperone protein DnaK. Members of this
family are the chaperone DnaK, of the DnaK-DnaJ-GrpE
chaperone system. All members of the seed alignment were
taken from completely sequenced bacterial or archaeal
genomes and (except for Mycoplasma sequence) found
clustered with other genes of this systems. This model
excludes DnaK homologs that are not DnaK itself, such as
the heat shock cognate protein HscA (TIGR01991).
However, it is not designed to distinguish among DnaK
paralogs in eukaryotes. Note that a number of dnaK genes
have shadow ORFs in the same reverse (relative to dnaK)
reading frame, a few of which have been assigned
glutamate dehydrogenase activity. The significance of
this observation is unclear; lengths of such shadow ORFs
are highly variable as if the presumptive protein
product is not conserved [Protein fate, Protein folding
and stabilization].
Length = 595
Score = 27.7 bits (62), Expect = 5.1
Identities = 27/101 (26%), Positives = 42/101 (41%), Gaps = 25/101 (24%)
Query: 142 VTKHTKNMGKFSSVTV---STIDEEE-------------------DEIEAREIADSYANN 179
V+ K GK S+T+ S + EEE +EIEAR ADS A
Sbjct: 477 VSAKDKGTGKEQSITITASSGLSEEEIERMVKEAEANAEEDKKRKEEIEARNNADSLAYQ 536
Query: 180 ARIIEKQLERKGMNKRKSDSTTLNTGETEVKKPVRGTLIDK 220
A EK L+ G + + E+K+ ++G +++
Sbjct: 537 A---EKTLKEAGDKLPAEEKEKIEKAVAELKEALKGEDVEE 574
>gnl|CDD|226314 COG3791, COG3791, Uncharacterized conserved protein [Function
unknown].
Length = 133
Score = 26.2 bits (58), Expect = 9.2
Identities = 20/100 (20%), Positives = 29/100 (29%), Gaps = 25/100 (25%)
Query: 22 EEKPLHIYYCVCGQMTLILDCAVEKLPLRRRDGARVIDGPKHAHKLTCEPDEVFHLKRPE 81
E P H+ C C DC R+ GA A P + R
Sbjct: 18 EGDPGHVSACHCS------DC-------RKASGA-----AFAA--YAVVPRDALRGTRGL 57
Query: 82 GIERQ-----HRFKCKKCGLFLYYKHDPSSNIIFIVQGAV 116
R C CG L+++ + + GA+
Sbjct: 58 PTYYFSSGSAGRGFCPTCGSPLFWRGPDEDPFVGVNAGAL 97
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
0.317 0.134 0.387
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,967,622
Number of extensions: 1022954
Number of successful extensions: 900
Number of sequences better than 10.0: 1
Number of HSP's gapped: 900
Number of HSP's successfully gapped: 31
Length of query: 220
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 127
Effective length of database: 6,812,680
Effective search space: 865210360
Effective search space used: 865210360
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 (21.6 bits)
S2: 57 (25.6 bits)