RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4339
(303 letters)
>gnl|CDD|205553 pfam13374, TPR_10, Tetratricopeptide repeat.
Length = 42
Score = 41.4 bits (98), Expect = 1e-05
Identities = 14/39 (35%), Positives = 25/39 (64%)
Query: 131 TAKHYGNIGRLYQSMQKFDEAERMQLKAIAIKEKVLGKD 169
TA N+ R ++ +++EAE + +A+AI+ +VLG D
Sbjct: 1 TAASLNNLARALRAQGRYEEAEELLEEALAIRRRVLGPD 39
>gnl|CDD|205602 pfam13424, TPR_12, Tetratricopeptide repeat.
Length = 78
Score = 40.8 bits (96), Expect = 5e-05
Identities = 22/59 (37%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 106 YKEAELLHQNALVLSLKHFGENNVQTAKHYGNIGRLYQSMQKFDEAERMQLKAIAIKEK 164
Y EA L + AL L + GE++ +TA+ N+ RLY ++ +DEA KA+A++E
Sbjct: 21 YDEALELLEKALEL-ARELGEDHPETARALNNLARLYLALGDYDEALEYLEKALALREA 78
Score = 40.0 bits (94), Expect = 7e-05
Identities = 17/78 (21%), Positives = 38/78 (48%), Gaps = 2/78 (2%)
Query: 130 QTAKHYGNIGRLYQSMQKFDEAERMQLKAIAIKEKVLGKDDYEVGLSVGHLASLYNYHML 189
A N+ + + + +DEA + KA+ + LG+D E ++ +LA LY +
Sbjct: 3 DLAAALNNLALVLRRLGDYDEALELLEKALELAR-ELGEDHPETARALNNLARLY-LALG 60
Query: 190 EYHKAEKLYFRSIEINDN 207
+Y +A + +++ + +
Sbjct: 61 DYDEALEYLEKALALREA 78
>gnl|CDD|232952 TIGR00391, hydA, hydrogenase (NiFe) small subunit (hydA). Called
(hupA/hydA/hupS/hoxK/vhtG) Involved in hydrogenase
reactions performing different specific functions in
different species eg (EC 1.12.2.1) in Desulfovibrio
gigas,(EC 1.12.99.3) in Wolinella succinogenes and (EC
1.18.99.1) in E.coli and a number of other species and
(EC 1.12.99.-) in the archea [Energy metabolism,
Electron transport].
Length = 365
Score = 31.0 bits (70), Expect = 0.83
Identities = 17/41 (41%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 78 LLTSAH-RVKALILEEIALDSNELISVQFYKEAELLHQNAL 117
LL SAH V+ LILE I+L+ +E + F +AE +A+
Sbjct: 68 LLRSAHPTVENLILETISLEYHETLMAAFGHQAEENKHDAI 108
>gnl|CDD|238048 cd00100, IL1, Interleukin-1 homologes; Cytokines with various
biological functions. Interleukin 1 alpha and beta are
also known as hematopoietin and catabolin. This family
also contains interleukin-1 receptor antagonists
(inhibitors).
Length = 144
Score = 29.7 bits (67), Expect = 1.0
Identities = 17/86 (19%), Positives = 32/86 (37%), Gaps = 15/86 (17%)
Query: 77 LLLTSAHRVKALILEEIALDSNELISVQFYKEAELLHQNALVLSLKHFGENNVQTAKHYG 136
L+L++ +KA L+ L+ + FY+ E + + L +
Sbjct: 12 LVLSNPQYLKAAHLQGQNLNLEVKFDMSFYQGEESDSKIPVTLGISK------------- 58
Query: 137 NIGRLYQSMQKFDEAERMQLKAIAIK 162
LY S K + +QL+ + K
Sbjct: 59 --TNLYLSCVKEGDDPPLQLEEVPPK 82
>gnl|CDD|227590 COG5265, ATM1, ABC-type transport system involved in Fe-S cluster
assembly, permease and ATPase components
[Posttranslational modification, protein turnover,
chaperones].
Length = 497
Score = 30.4 bits (69), Expect = 1.3
Identities = 33/106 (31%), Positives = 45/106 (42%), Gaps = 12/106 (11%)
Query: 19 LKLKQVLFGSENLQVAIAEDELAYA--LYVNEYSSGRFTESRRHAEKAIQTFKNLLPENH 76
LKL G E +VAIA L L ++E +S T H E+AIQ +
Sbjct: 398 LKLS----GGEKQRVAIARTILKNPPILILDEATSALDT----HTEQAIQAALREVSAGR 449
Query: 77 LLLTSAHRVKALI-LEEIALDSNELISVQFYKEAELLHQNALVLSL 121
L AHR+ +I +EI + N I V+ ELL L +
Sbjct: 450 TTLVIAHRLSTIIDADEIIVLDNGRI-VERGTHEELLAAGGLYAEM 494
>gnl|CDD|233032 TIGR00580, mfd, transcription-repair coupling factor (mfd). All
proteins in this family for which functions are known
are DNA-dependent ATPases that function in the process
of transcription-coupled DNA repair in which the repair
of the transcribed strand of actively transcribed genes
is repaired at a higher rate than the repair of
non-transcribed regions of the genome and than the
non-transcribed strand of the same gene. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University). This family is
closely related to the RecG and UvrB families [DNA
metabolism, DNA replication, recombination, and repair].
Length = 926
Score = 30.4 bits (69), Expect = 1.4
Identities = 27/162 (16%), Positives = 53/162 (32%), Gaps = 18/162 (11%)
Query: 50 SSGRFTESRRHAEKAIQTFKN-----LLPENHLLLTSAHRVKALILEEIALDSNELISVQ 104
S F E E+ + K + E+ + A R+K+L L E + + +
Sbjct: 215 SRLEFGEILAFKEELFRWLKAGFKITVAAES---ESQAERLKSL-LAEHDIAAQVIDESC 270
Query: 105 FYKEAELLHQNALVLSLKHFGENN---VQTAKHYGNIGRLYQSMQKFDEAERMQLKAIAI 161
A + S + ++ +G+ + L +
Sbjct: 271 IIIPAVRYVMIGALSSGFILPTAGLAVITESELFGSRVLRRPKKSRLKSKPIESLNELNP 330
Query: 162 KEKVLGKDDYEVGLSVG-----HLASLYNYHMLEYHKAEKLY 198
+ V+ D+ +G +G +Y +LEY +KLY
Sbjct: 331 GDYVV-HLDHGIGRFLGLETLEVGGIERDYLVLEYAGEDKLY 371
>gnl|CDD|131701 TIGR02653, Lon_rel_chp, conserved hypothetical protein. This
model describes a protein family of unknown function,
about 690 residues in length, in which some members
show C-terminal sequence similarity to pfam05362, which
is the Lon protease C-terminal proteolytic domain, from
MEROPS family S16. However, the annotated catalytic
sites of E. coli Lon protease are not conserved in
members of this family. Members have a motif
GP[RK][GS]TGKS, similar to the ATP-binding P-loop motif
GxxGxGK[ST] [Hypothetical proteins, Conserved].
Length = 675
Score = 29.8 bits (67), Expect = 2.1
Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 44 LYVNEYSSGRFTESRRHA--EKAIQTFKNLLPENHLLLTSAHRVKALILE 91
+YV EY G + S E+ +Q KN+L EN++ A +VK+LI E
Sbjct: 33 VYVLEYLLGMYCASDDEEVVEQGLQNVKNILAENYVRPDEAEKVKSLIRE 82
>gnl|CDD|192924 pfam12049, DUF3531, Protein of unknown function (DUF3531). This
family of proteins is functionally uncharacterized.
This protein is found in bacteria and eukaryotes.
Proteins in this family are typically between 149 to
199 amino acids in length.
Length = 147
Score = 28.4 bits (64), Expect = 2.8
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 26 FGSENLQVAIAEDELAYALYVNE 48
F +ENLQV A +L+Y Y NE
Sbjct: 47 FNAENLQVQEAGLDLSYMEYDNE 69
>gnl|CDD|205362 pfam13181, TPR_8, Tetratricopeptide repeat.
Length = 34
Score = 25.9 bits (58), Expect = 2.9
Identities = 7/30 (23%), Positives = 16/30 (53%)
Query: 135 YGNIGRLYQSMQKFDEAERMQLKAIAIKEK 164
Y +G++Y + ++EA+ KA+ +
Sbjct: 4 YYLLGQIYLQLGDYEEAKEYYEKALELDPN 33
>gnl|CDD|200562 cd10936, CE4_DAC2, Putative catalytic domain of family 2
polysaccharide deacetylases (DACs) from bacteria. This
family contains an uncharacterized protein BH1492 from
Bacillus halodurans, an uncharacterized protein ATU2773
from Agrobacterium tumefaciens C58, and other bacterial
hypothetical proteins. Although their functions are
still unknown, structural superposition and sequence
comparison suggest that BH1492 and ATU2773 might be
divergently related to the 7-stranded barrel catalytic
domain of polysaccharide deacetylases (DACs) from the
carbohydrate esterase 4 (CE4) superfamily, which remove
N-linked acetyl groups from cell wall polysaccharides.
This family is designated as DAC family 2, a divergent
DAC family.
Length = 215
Score = 28.7 bits (65), Expect = 3.3
Identities = 12/52 (23%), Positives = 21/52 (40%), Gaps = 5/52 (9%)
Query: 30 NLQVAIAEDELAYALYVNEYSSGRFTESRRHAEKAIQTFKNLLPENHLLLTS 81
L+ A+A + A+ VN + RFT R + ++ K + S
Sbjct: 83 RLEAALAR--VPGAVGVNNHMGSRFTADREAMRQVLEALKE---RGLFFVDS 129
>gnl|CDD|201277 pfam00515, TPR_1, Tetratricopeptide repeat.
Length = 34
Score = 25.1 bits (56), Expect = 5.5
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 132 AKHYGNIGRLYQSMQKFDEAERMQLKAIAIKEK 164
AK N+G Y + K+DEA KA+ +
Sbjct: 1 AKALYNLGNAYLKLGKYDEALEYYEKALELNPN 33
>gnl|CDD|233374 TIGR01357, aroB, 3-dehydroquinate synthase. This model represents
3-dehydroquinate synthase, the enzyme catalyzing the
second of seven steps in the shikimate pathway of
chorismate biosynthesis. Chorismate is the last common
intermediate in the biosynthesis of all three aromatic
amino acids [Amino acid biosynthesis, Aromatic amino
acid family].
Length = 344
Score = 28.0 bits (63), Expect = 6.1
Identities = 19/109 (17%), Positives = 38/109 (34%), Gaps = 22/109 (20%)
Query: 151 AERMQLKAIAIKEKVLGKDDYEVGL--------SVGH-LASLYNYH------------ML 189
E + ++I +K ++ +D+ E GL ++GH + + Y +
Sbjct: 202 LEELIKRSIEVKASIVAEDEKESGLRAILNFGHTIGHAIEAEAGYGKIPHGEAVAIGMVC 261
Query: 190 EYHKAEKLYFRSIEINDNLKLFSASYSGLEYHYRDLKLFSASYSGLEYD 238
E +E+L E+ + L Y GL + + D
Sbjct: 262 EAKLSERLGLLPAELIERLVQLLKRY-GLPTDLPKDLDVDELLNAMLND 309
>gnl|CDD|182483 PRK10468, PRK10468, hydrogenase 2 small subunit; Provisional.
Length = 371
Score = 27.9 bits (62), Expect = 6.7
Identities = 16/41 (39%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 78 LLTSAH-RVKALILEEIALDSNELISVQFYKEAELLHQNAL 117
LL + H V+ L+LE I+L+ +E++S F + E NAL
Sbjct: 66 LLRATHPTVENLVLETISLEYHEVLSAAFGHQVEENKHNAL 106
>gnl|CDD|238112 cd00189, TPR, Tetratricopeptide repeat domain; typically contains
34 amino acids
[WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-
X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found
in a variety of organisms including bacteria,
cyanobacteria, yeast, fungi, plants, and humans in
various subcellular locations; involved in a variety of
functions including protein-protein interactions, but
common features in the interaction partners have not
been defined; involved in chaperone, cell-cycle,
transciption, and protein transport complexes; the
number of TPR motifs varies among proteins (1,3-11,13
15,16,19); 5-6 tandem repeats generate a right-handed
helical structure with an amphipathic channel that is
thought to accomodate an alpha-helix of a target
protein; it has been proposed that TPR proteins
preferably interact with WD-40 repeat proteins, but in
many instances several TPR-proteins seem to aggregate to
multi-protein complexes; examples of TPR-proteins
include, Cdc16p, Cdc23p and Cdc27p components of the
cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal
targeting signals, the Tom70p co-receptor for
mitochondrial targeting signals, Ser/Thr phosphatase 5C
and the p110 subunit of O-GlcNAc transferase; three
copies of the repeat are present here.
Length = 100
Score = 26.6 bits (59), Expect = 6.8
Identities = 17/71 (23%), Positives = 34/71 (47%), Gaps = 9/71 (12%)
Query: 135 YGNIGRLYQSMQKFDEAERMQLKAIAIKEKVLGKDDYEVGLSVGHLASLYNYHMLEYHKA 194
N+G LY + +DEA KA+ + + +LA+ Y Y + +Y +A
Sbjct: 3 LLNLGNLYYKLGDYDEALEYYEKALELDPD--------NADAYYNLAAAY-YKLGKYEEA 53
Query: 195 EKLYFRSIEIN 205
+ Y +++E++
Sbjct: 54 LEDYEKALELD 64
>gnl|CDD|225416 COG2861, COG2861, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 250
Score = 27.7 bits (62), Expect = 8.1
Identities = 22/104 (21%), Positives = 39/104 (37%), Gaps = 20/104 (19%)
Query: 42 YALYVNEYSSGRFTESRRHAEKAIQTFKNLLPENHLLL----TSAHRVKALILEEIAL-- 95
A+ +N + RFT + E A++ L E L T A+ + I +EI +
Sbjct: 121 DAVGLNNHMGSRFTSN----EDAMEKLMEALKERGLYFLDSGTIANSLAGKIAKEIGVPV 176
Query: 96 ----------DSNELISVQFYKEAELLHQNALVLSLKHFGENNV 129
D+ + Q +L +N + + H +N V
Sbjct: 177 IKRDVFLDDEDTEAAVLKQLDAAEKLARKNGSAIGIGHPHKNTV 220
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 0.133 0.373
Gapped
Lambda K H
0.267 0.0867 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,237,275
Number of extensions: 1461804
Number of successful extensions: 1141
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1129
Number of HSP's successfully gapped: 43
Length of query: 303
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 207
Effective length of database: 6,679,618
Effective search space: 1382680926
Effective search space used: 1382680926
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 (21.7 bits)
S2: 59 (26.3 bits)