RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10736
(104 letters)
>gnl|CDD|205602 pfam13424, TPR_12, Tetratricopeptide repeat.
Length = 78
Score = 38.1 bits (89), Expect = 4e-05
Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 23 RANSNLGNSHIFLGEYQAASEHYKRTLVLAQDLGDRAVE-AQACYSLGNTYTLLRDYPTA 81
A +NL LG+Y A E ++ L LA++LG+ E A+A +L Y L DY A
Sbjct: 6 AALNNLALVLRRLGDYDEALELLEKALELARELGEDHPETARALNNLARLYLALGDYDEA 65
Query: 82 IDYHLRHLIIAQQ 94
++Y + L + +
Sbjct: 66 LEYLEKALALREA 78
>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 = 34.7 bits (80), Expect = 0.002
Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 6/58 (10%)
Query: 27 NLGNSHIFLGEYQAASEHYKRTLVLAQDLGDRAVEAQACYSLGNTYTLLRDYPTAIDY 84
NLGN + LG+Y A E+Y++ L L D A A Y+L Y L Y A++
Sbjct: 5 NLGNLYYKLGDYDEALEYYEKALELDPD------NADAYYNLAAAYYKLGKYEEALED 56
Score = 34.3 bits (79), Expect = 0.002
Identities = 27/85 (31%), Positives = 42/85 (49%), Gaps = 11/85 (12%)
Query: 12 AREFGDKAAER-----RANSNLGNSHIFLGEYQAASEHYKRTLVLAQDLGDRAVEAQACY 66
A E+ +KA E A NL ++ LG+Y+ A E Y++ L L D A+A Y
Sbjct: 19 ALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEALEDYEKALELDPD------NAKAYY 72
Query: 67 SLGNTYTLLRDYPTAIDYHLRHLII 91
+LG Y L Y A++ + + L +
Sbjct: 73 NLGLAYYKLGKYEEALEAYEKALEL 97
>gnl|CDD|197478 smart00028, TPR, Tetratricopeptide repeats. Repeats present in 4
or more copies in proteins. Contain a minimum of 34
amino acids each and self-associate via a "knobs and
holes" mechanism.
Length = 34
Score = 30.1 bits (69), Expect = 0.019
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 62 AQACYSLGNTYTLLRDYPTAIDYHLRHLIIAQQ 94
A+A Y+LGN Y L DY A++Y+ + L +
Sbjct: 1 AEALYNLGNAYLKLGDYDEALEYYEKALELDPN 33
Score = 27.8 bits (63), Expect = 0.17
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 23 RANSNLGNSHIFLGEYQAASEHYKRTLVLAQD 54
A NLGN+++ LG+Y A E+Y++ L L +
Sbjct: 2 EALYNLGNAYLKLGDYDEALEYYEKALELDPN 33
>gnl|CDD|221958 pfam13176, TPR_7, Tetratricopeptide repeat.
Length = 36
Score = 29.1 bits (66), Expect = 0.068
Identities = 17/36 (47%), Positives = 22/36 (61%)
Query: 24 ANSNLGNSHIFLGEYQAASEHYKRTLVLAQDLGDRA 59
A SNLG + LG+Y+ A Y+R L LA+D DR
Sbjct: 1 ALSNLGRLYRKLGDYEKAISLYERALALAKDPEDRE 36
Score = 28.7 bits (65), Expect = 0.069
Identities = 12/32 (37%), Positives = 16/32 (50%)
Query: 64 ACYSLGNTYTLLRDYPTAIDYHLRHLIIAQQL 95
A +LG Y L DY AI + R L +A+
Sbjct: 1 ALSNLGRLYRKLGDYEKAISLYERALALAKDP 32
>gnl|CDD|201277 pfam00515, TPR_1, Tetratricopeptide repeat.
Length = 34
Score = 28.2 bits (64), Expect = 0.15
Identities = 12/28 (42%), Positives = 20/28 (71%)
Query: 27 NLGNSHIFLGEYQAASEHYKRTLVLAQD 54
NLGN+++ LG+Y A E+Y++ L L +
Sbjct: 6 NLGNAYLKLGKYDEALEYYEKALELNPN 33
Score = 27.8 bits (63), Expect = 0.16
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 62 AQACYSLGNTYTLLRDYPTAIDYHLRHLIIAQQ 94
A+A Y+LGN Y L Y A++Y+ + L +
Sbjct: 1 AKALYNLGNAYLKLGKYDEALEYYEKALELNPN 33
>gnl|CDD|225504 COG2956, COG2956, Predicted N-acetylglucosaminyl transferase
[Carbohydrate transport and metabolism].
Length = 389
Score = 28.5 bits (64), Expect = 0.63
Identities = 21/70 (30%), Positives = 30/70 (42%), Gaps = 10/70 (14%)
Query: 5 PNDRLKIAREFGDKAAER-----RANSNLGNSHIFLGEYQAASEHYKRTLVLAQD---LG 56
+ + ARE KA + RA+ LG + G+YQ A E +R VL Q+ L
Sbjct: 192 ASSDVDRARELLKKALQADKKCVRASIILGRVELAKGDYQKAVEALER--VLEQNPEYLS 249
Query: 57 DRAVEAQACY 66
+ CY
Sbjct: 250 EVLEMLYECY 259
>gnl|CDD|220706 pfam10345, Cohesin_load, Cohesin loading factor. Cohesin_load is a
common cohesin loading factor protein that is conserved
in fungi. It is associated with the cohesin complex and
is required in G1 for cohesin binding to chromosomes but
dispensable in G2 when cohesion has been established. It
is referred to as both Ssl3, in pombe, and Scc4, in
S.cerevisiae. It complexes with Mis4.
Length = 592
Score = 28.5 bits (64), Expect = 0.64
Identities = 9/39 (23%), Positives = 14/39 (35%)
Query: 32 HIFLGEYQAASEHYKRTLVLAQDLGDRAVEAQACYSLGN 70
+ G+ AA E+ + LA GDR +
Sbjct: 150 LLQSGDLAAALENLQSLAELANRRGDRKLFVVLSLLEAL 188
>gnl|CDD|191825 pfam07719, TPR_2, Tetratricopeptide repeat. This Pfam entry
includes outlying Tetratricopeptide-like repeats (TPR)
that are not matched by pfam00515.
Length = 34
Score = 25.2 bits (56), Expect = 1.9
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 23 RANSNLGNSHIFLGEYQAASEHYKRTLVLAQD 54
A NLG ++ LG+Y+ A E Y++ L L +
Sbjct: 2 EALYNLGLAYYKLGDYEEALEAYEKALELDPN 33
>gnl|CDD|222950 PHA02952, PHA02952, EEV maturation protein; Provisional.
Length = 648
Score = 26.9 bits (60), Expect = 2.0
Identities = 12/56 (21%), Positives = 22/56 (39%), Gaps = 2/56 (3%)
Query: 51 LAQDLGDRAVEAQACYSLGNTYTLLRDYPTAIDYHLRHLIIAQQ--LMDRVGEGMI 104
A LG ++ ++ +L+D A +R L IA L+ R+ +
Sbjct: 522 TAVRLGGYKIKELGALEWEDSIPVLKDGLEATIDAIRELNIATTDNLLSRLANNPL 577
>gnl|CDD|235953 PRK07188, PRK07188, nicotinate phosphoribosyltransferase;
Provisional.
Length = 352
Score = 25.7 bits (57), Expect = 5.2
Identities = 10/13 (76%), Positives = 11/13 (84%)
Query: 6 NDRLKIAREFGDK 18
D LK+AREFGDK
Sbjct: 217 TDSLKVAREFGDK 229
>gnl|CDD|176247 cd08287, FDH_like_ADH3, formaldehyde dehydrogenase (FDH)-like.
This group contains proteins identified as alcohol
dehydrogenases and glutathione-dependant formaldehyde
dehydrogenases (FDH) of the zinc-dependent/medium chain
alcohol dehydrogenase family. The MDR family uses
NAD(H) as a cofactor in the interconversion of alcohols
and aldehydes, or ketones. FDH converts formaldehyde
and NAD to formate and NADH. The initial step in this
process the spontaneous formation of a
S-(hydroxymethyl)glutathione adduct from formaldehyde
and glutathione, followed by FDH-mediated oxidation (and
detoxification) of the adduct to S-formylglutathione.
The medium chain alcohol dehydrogenase family (MDR) has
a NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit.
Length = 345
Score = 25.3 bits (56), Expect = 6.0
Identities = 11/18 (61%), Positives = 12/18 (66%), Gaps = 2/18 (11%)
Query: 7 DRLKIAREFG--DKAAER 22
DR +AREFG D AER
Sbjct: 204 DRQALAREFGATDIVAER 221
>gnl|CDD|162434 TIGR01580, narG, respiratory nitrate reductase, alpha subunit. The
Nitrate reductase enzyme complex allows bacteria to use
nitrate as an electron acceptor during anaerobic growth.
The enzyme complex consists of a tetramer that has an
alpha, beta and 2 gamma subunits. The alpha and beta
subunits have catalytic activity and the gamma subunits
attach the enzyme to the membrane and is a b-type
cytochrome that receives electrons from the quinone pool
and transfers them to the beta subunit. This model is
specific for the alpha subunit for nitrate reductase I
(narG) and nitrate reductase II (narZ) for gram positive
and gram negative bacteria.A few thermophiles and
archaea also match the model The seed members used to
make the model include Nitrate reductases from
Pseudomonas fluorescens (GP:11344601), E.coli and
B.subtilis. All seed members are experimentally
characterized. Some unpublished nitrate reductases, that
are shorter sequences, and probably fragments fall in
between the noise and trusted cutoffs. Pfam models
pfam00384 (Molybdopterin oxidoreductase) and
pfam01568(Molydopterin dinucleotide binding domain) will
also match the nitrate reductase, alpha subunit [Energy
metabolism, Anaerobic].
Length = 1235
Score = 25.3 bits (55), Expect = 8.1
Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 8/44 (18%)
Query: 2 GVQPNDRLKIAREFGDKAAERRANSNLGNSHIFLGEYQAASEHY 45
GV ++IAREF D A + G S I +G A H+
Sbjct: 512 GVSREQIIRIAREFADNADKTH-----GRSMIIVG---AGLNHW 547
>gnl|CDD|227346 COG5013, NarG, Nitrate reductase alpha subunit [Energy production
and conversion].
Length = 1227
Score = 25.0 bits (55), Expect = 9.5
Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 8/44 (18%)
Query: 2 GVQPNDRLKIAREFGDKAAERRANSNLGNSHIFLGEYQAASEHY 45
GV ++IAREF D A + G S I +G A H+
Sbjct: 510 GVPRAQAIRIAREFADNADKTH-----GRSMIIVG---AGINHW 545
>gnl|CDD|173902 cd00805, TyrRS_core, catalytic core domain of tyrosinyl-tRNA
synthetase. Tyrosinyl-tRNA synthetase (TyrRS)
catalytic core domain. TyrRS is a homodimer which
attaches Tyr to the appropriate tRNA. TyrRS is a class
I tRNA synthetases, so it aminoacylates the 2'-OH of
the nucleotide at the 3' end of the tRNA. The core
domain is based on the Rossman fold and is responsible
for the ATP-dependent formationof the enzyme bound
aminoacyl-adenylate. It contains the class I
characteristic HIGH and KMSKS motifs, which are
involved in ATP binding.
Length = 269
Score = 24.9 bits (55), Expect = 9.8
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 79 PTAIDYHLRHLIIAQQLMD 97
PTA HL HL+ +L D
Sbjct: 9 PTAPSLHLGHLVPLMKLRD 27
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 0.136 0.391
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: 5,315,433
Number of extensions: 442820
Number of successful extensions: 441
Number of sequences better than 10.0: 1
Number of HSP's gapped: 437
Number of HSP's successfully gapped: 48
Length of query: 104
Length of database: 10,937,602
Length adjustment: 69
Effective length of query: 35
Effective length of database: 7,877,176
Effective search space: 275701160
Effective search space used: 275701160
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: 53 (23.9 bits)