RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9584
(466 letters)
>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 = 182 bits (464), Expect = 2e-51
Identities = 83/272 (30%), Positives = 123/272 (45%), Gaps = 23/272 (8%)
Query: 1 MCIQCLQAVFN-FKPPPRVEARTHLQLGNILLTHTKNIDLARNHLEQAWHLSQSINAFDD 59
IQCL+AV FK PPR EART L+L ILL T+NIDLA +L +A +++ N D
Sbjct: 40 TGIQCLEAVLKKFKLPPRQEARTRLRLARILLEETENIDLAETYLSKAILIAER-NGLID 98
Query: 60 VKFEAASVLAELYETQLLSNLSKPILRRAIELSQ----HSIYWHCRLI-FQLAQIHAGEK 114
+KF +LA L + + L + IE ++ ++ + RL+ QL
Sbjct: 99 LKFVCQFLLARLLF-KTNPKAALKSLNKLIEDAETYQHNAWVYAFRLLKIQLLLQSG--- 154
Query: 115 DYELASSLLGVGVDYANISNAQYTRVLFLLSRCMLLLIDKKVNDAVQLLTQAGYQ---VE 171
D A L + AN + V+ L +L L D ++LL +A ++
Sbjct: 155 DLAAALENLQSLAELANRRGDRKLFVVLSLLEALLHLYRGSPKDVLELLQEAIAAARSLQ 214
Query: 172 NWTGSQYQKEYLKVFFLVLQVCHYLMAGQVKSVKPCLKQLQQSILTIMQPT-WPS-DEVV 229
Q LK L+L + L VK+VK LKQLQ + + + W S D
Sbjct: 215 LD--DSEQIPQLKALRLLLDLLCSLQKDDVKNVKEKLKQLQSFLDELKNLSDWSSWDIDG 272
Query: 230 SGPNVGD-----MFIWMPKEHLYVVVYLVTVI 256
S +F W+PKE LY +VY ++ +
Sbjct: 273 SIKLKIVIRDPLVFSWLPKEDLYALVYFLSGL 304
Score = 126 bits (318), Expect = 3e-31
Identities = 52/171 (30%), Positives = 73/171 (42%), Gaps = 7/171 (4%)
Query: 270 TEVERLSQERELWTFANLNLAIVYLRGKR--EGDFAALLERINPETLTS-HSHSLRAAAY 326
R REL+ A LNL I+ + + LL+++ P S +S+ L A
Sbjct: 423 KVAARKGTFRELYILALLNLVIILQDEVSRLQSELNKLLDQLEPLCSNSPNSNILLWNAL 482
Query: 327 YVQGLQSFFQARYNEAKRYLRETLKMANAEDLNRLTSCSLVLLGHIFLSLGNHRESMNMV 386
+ + F N+ KR+L+E LK ANA +L S +L LL H G E
Sbjct: 483 LLATISLFPPISINQQKRHLQEALKQANAIGNTQLLSIALNLLSHRLFE-GVLGEQAKKS 541
Query: 387 TPAMQLASKIPDVHVQLW---ASAILKDLYKILNDPVRENEALQMHCNFSQ 434
A+QLA K PD LW A IL DL + L + + H S+
Sbjct: 542 ARALQLAKKSPDYSDGLWLLVAGGILMDLLEQLGTRDKAEQTRLQHDALSK 592
>gnl|CDD|205602 pfam13424, TPR_12, Tetratricopeptide repeat.
Length = 78
Score = 34.7 bits (80), Expect = 0.011
Identities = 18/68 (26%), Positives = 33/68 (48%), Gaps = 1/68 (1%)
Query: 319 HSLRAAAYYVQGLQSFFQARYNEAKRYLRETLKMAN-AEDLNRLTSCSLVLLGHIFLSLG 377
H AAA L Y+EA L + L++A + + T+ +L L ++L+LG
Sbjct: 1 HPDLAAALNNLALVLRRLGDYDEALELLEKALELARELGEDHPETARALNNLARLYLALG 60
Query: 378 NHRESMNM 385
++ E++
Sbjct: 61 DYDEALEY 68
>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 = 31.6 bits (72), Expect = 0.19
Identities = 21/97 (21%), Positives = 31/97 (31%), Gaps = 14/97 (14%)
Query: 24 LQLGNILLTHTKNIDLARNHLEQAWHLSQSINAFDDVKFEAA-SVLAELYETQLLSNLSK 82
L LGN+ + D A + E+A L D A LA Y +
Sbjct: 4 LNLGNLYYKL-GDYDEALEYYEKALEL--------DPDNADAYYNLAAAYYKLGKYEEAL 54
Query: 83 PILRRAIELSQHSIYWHCRLIFQLAQIHAGEKDYELA 119
+A+EL + + L + YE A
Sbjct: 55 EDYEKALELDPDNAKAYYN----LGLAYYKLGKYEEA 87
>gnl|CDD|234026 TIGR02823, oxido_YhdH, putative quinone oxidoreductase, YhdH/YhfP
family. This model represents a subfamily of pfam00107
as defined by Pfam, a superfamily in which some members
are zinc-binding medium-chain alcohol dehydrogenases
while others are quinone oxidoreductases with no bound
zinc. This subfamily includes proteins studied
crystallographically for insight into function: YhdH
from Escherichia coli and YhfP from Bacillus subtilis.
Members bind NADPH or NAD, but not zinc [Unknown
function, Enzymes of unknown specificity].
Length = 323
Score = 31.8 bits (73), Expect = 0.82
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 159 AVQLLTQAGYQVENWTGSQYQKEYLK 184
AV +L++ GY+V TG +++YLK
Sbjct: 162 AVAILSKLGYEVVASTGKAEEEDYLK 187
>gnl|CDD|176183 cd05280, MDR_yhdh_yhfp, Yhdh and yhfp-like putative quinone
oxidoreductases. Yhdh and yhfp-like putative quinone
oxidoreductases (QOR). QOR catalyzes the conversion of a
quinone + NAD(P)H to a hydroquinone + NAD(P)+. Quinones
are cyclic diones derived from aromatic compounds.
Membrane bound QOR actin the respiratory chains of
bacteria and mitochondria, while soluble QOR acts to
protect from toxic quinones (e.g. DT-diaphorase) or as a
soluble eye-lens protein in some vertebrates (e.g.
zeta-crystalin). QOR reduces quinones through a
semi-quinone intermediate via a NAD(P)H-dependent single
electron transfer. QOR is a member of the medium chain
dehydrogenase/reductase family, but lacks the
zinc-binding sites of the prototypical alcohol
dehydrogenases of this group. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG motif
after the first mononucleotide contact half allows the
close contact of the coenzyme with the ADH backbone.
The N-terminal catalytic domain has a distant homology
to GroES. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and have 2 tightly bound zinc atoms per
subunit, a catalytic zinc at the active site and a
structural zinc in a lobe of the catalytic domain.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine, the ribose of
NAD, a serine, then the alcohol, which allows the
transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 325
Score = 31.4 bits (72), Expect = 1.1
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 159 AVQLLTQAGYQVENWTGSQYQKEYLK 184
AV +L + GY V TG + Q +YLK
Sbjct: 163 AVAILAKLGYTVVALTGKEEQADYLK 188
>gnl|CDD|225461 COG2909, MalT, ATP-dependent transcriptional regulator
[Transcription].
Length = 894
Score = 30.4 bits (69), Expect = 2.2
Identities = 12/65 (18%), Positives = 25/65 (38%)
Query: 289 LAIVYLRGKREGDFAALLERINPETLTSHSHSLRAAAYYVQGLQSFFQARYNEAKRYLRE 348
L + + + A L R+ L ++ R A V G + + +A +++
Sbjct: 463 LRAQVALNRGDPEEAEDLARLALVQLPEAAYRSRIVALSVLGEAAHIRGELTQALALMQQ 522
Query: 349 TLKMA 353
+MA
Sbjct: 523 AEQMA 527
>gnl|CDD|100037 cd06061, PurM-like1, AIR synthase (PurM) related protein, subgroup
1 of unknown function. The family of PurM related
proteins includes Hydrogen expression/formation protein
HypE, AIR synthases, FGAM synthase and Selenophosphate
synthetase (SelD). They all contain two conserved
domains and seem to dimerize. The N-terminal domain
forms the dimer interface and is a putative ATP binding
domain.
Length = 298
Score = 29.5 bits (67), Expect = 3.2
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 63 EAASVLAELYETQLLSNLSKPILRRAIEL 91
E ++LA +E +L LS+ LR A +L
Sbjct: 164 EGTAILANDFEEELKKRLSEEELREAAKL 192
>gnl|CDD|222112 pfam13414, TPR_11, TPR repeat.
Length = 69
Score = 27.3 bits (61), Expect = 4.0
Identities = 16/63 (25%), Positives = 22/63 (34%), Gaps = 10/63 (15%)
Query: 322 RAAAYYVQGLQSFFQARYNEAKRYLRETLKMA--NAEDLNRLTSCSLVLLGHIFLSLGNH 379
A A G F Y+EA + L++ NAE + L +L LG
Sbjct: 2 NAEALKNLGNALFKLGDYDEAIEAYEKALELDPDNAE--------AYYNLALAYLKLGKD 53
Query: 380 RES 382
E
Sbjct: 54 YEE 56
>gnl|CDD|176249 cd08289, MDR_yhfp_like, Yhfp putative quinone oxidoreductases.
yhfp putative quinone oxidoreductases (QOR). QOR
catalyzes the conversion of a quinone + NAD(P)H to a
hydroquinone + NAD(P)+. Quinones are cyclic diones
derived from aromatic compounds. Membrane bound QOR
actin the respiratory chains of bacteria and
mitochondria, while soluble QOR acts to protect from
toxic quinones (e.g. DT-diaphorase) or as a soluble
eye-lens protein in some vertebrates (e.g.
zeta-crystalin). QOR reduces quinones through a
semi-quinone intermediate via a NAD(P)H-dependent single
electron transfer. QOR is a member of the medium chain
dehydrogenase/reductase family, but lacks the
zinc-binding sites of the prototypical alcohol
dehydrogenases of this group. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG motif
after the first mononucleotide contact half allows the
close contact of the coenzyme with the ADH backbone.
The N-terminal catalytic domain has a distant homology
to GroES. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and have 2 tightly bound zinc atoms per
subunit, a catalytic zinc at the active site, and a
structural zinc in a lobe of the catalytic domain.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine, the ribose of
NAD, a serine, then the alcohol, which allows the
transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 326
Score = 29.2 bits (66), Expect = 5.1
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 159 AVQLLTQAGYQVENWTGSQYQKEYLK 184
AV +L + GY+V TG +YLK
Sbjct: 163 AVSILAKLGYEVVASTGKADAADYLK 188
>gnl|CDD|221401 pfam12061, DUF3542, Protein of unknown function (DUF3542). This
family of proteins is functionally uncharacterized. This
protein is found in eukaryotes and viruses. Proteins in
this family are typically between 516 to 1283 amino
acids in length. This protein is found associated with
pfam00931.
Length = 403
Score = 29.1 bits (65), Expect = 5.6
Identities = 9/52 (17%), Positives = 24/52 (46%)
Query: 195 YLMAGQVKSVKPCLKQLQQSILTIMQPTWPSDEVVSGPNVGDMFIWMPKEHL 246
M ++KS++P ++++ +L ++ T P + + F+ +L
Sbjct: 138 DFMEMKIKSIQPDIRKIYIDVLQALKSTIPQAQKKHIADCEAGFVETLTHNL 189
>gnl|CDD|132870 cd07232, Pat_PLPL, Patain-like phospholipase. Patatin-like
phospholipase. This family consists of various patatin
glycoproteins from plants and fungi. The patatin protein
accounts for up to 40% of the total soluble protein in
potato tubers. Patatin is a storage protein, but it also
has the enzymatic activity of a lipid acyl hydrolase,
catalyzing the cleavage of fatty acids from membrane
lipids. Members of this family have been found also in
vertebrates.
Length = 407
Score = 29.2 bits (66), Expect = 5.6
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 400 HVQLWASAILKDLYKILNDPVRE 422
+ +W + L D +IL+DP E
Sbjct: 351 TITIWPRSTLSDFLRILSDPTPE 373
>gnl|CDD|176248 cd08288, MDR_yhdh, Yhdh putative quinone oxidoreductases. Yhdh
putative quinone oxidoreductases (QOR). QOR catalyzes
the conversion of a quinone + NAD(P)H to a hydroquinone
+ NAD(P)+. Quinones are cyclic diones derived from
aromatic compounds. Membrane bound QOR actin the
respiratory chains of bacteria and mitochondria, while
soluble QOR acts to protect from toxic quinones (e.g.
DT-diaphorase) or as a soluble eye-lens protein in some
vertebrates (e.g. zeta-crystalin). QOR reduces quinones
through a semi-quinone intermediate via a
NAD(P)H-dependent single electron transfer. QOR is a
member of the medium chain dehydrogenase/reductase
family, but lacks the zinc-binding sites of the
prototypical alcohol dehydrogenases of this group.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 324
Score = 28.7 bits (65), Expect = 6.3
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 159 AVQLLTQAGYQVENWTGSQYQKEYLK 184
AV LL + GY+V TG + +YL+
Sbjct: 163 AVALLARLGYEVVASTGRPEEADYLR 188
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 28.7 bits (65), Expect = 6.6
Identities = 8/31 (25%), Positives = 12/31 (38%)
Query: 19 EARTHLQLGNILLTHTKNIDLARNHLEQAWH 49
+A HL+ L + +DL L A
Sbjct: 398 QAAEHLEDALQQLELGQPLDLLAEDLRLAQE 428
>gnl|CDD|179448 PRK02603, PRK02603, photosystem I assembly protein Ycf3;
Provisional.
Length = 172
Score = 28.1 bits (63), Expect = 6.8
Identities = 22/77 (28%), Positives = 33/77 (42%), Gaps = 5/77 (6%)
Query: 322 RAAAYYVQGLQSFFQARYNEAKRYLRETLKMA-NAEDLNRLTSCSLVLLGHIFLSLGNHR 380
A YY G+ + Y EA E LK+ + D S L +G I+ S G H
Sbjct: 34 EAFVYYRDGMSAQADGEYAEALENYEEALKLEEDPND----RSYILYNMGIIYASNGEHD 89
Query: 381 ESMNMVTPAMQLASKIP 397
+++ A++L K P
Sbjct: 90 KALEYYHQALELNPKQP 106
>gnl|CDD|219193 pfam06824, DUF1237, Protein of unknown function (DUF1237). This
family contains a number of hypothetical proteins of
about 450 residues in length. Their function is unknown,
and most are bacterial. However, structurally this
family is part of the 6 hairpin glycosidase superfamily,
suggesting a glycosyl hydrolase function.
Length = 403
Score = 28.7 bits (65), Expect = 7.0
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 380 RESMNMVTPAMQLASKIPDVHVQLWASAILKDLYKILNDP 419
R+S + P + LA + P++ L I + IL DP
Sbjct: 44 RDSTAQLWPYLPLAKEDPELR-NLILGVINRQARYILIDP 82
>gnl|CDD|219384 pfam07350, DUF1479, Protein of unknown function (DUF1479). This
family consists of several hypothetical Enterobacterial
proteins, of around 420 residues in length. Members of
this family are often known as YbiU. The function of
this family is unknown.
Length = 408
Score = 28.4 bits (64), Expect = 8.6
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 7/52 (13%)
Query: 95 SIYWHCRLIFQLAQIHAGEKDYELASSLLGVGVDYANISNAQY---TRVLFL 143
++WHC LI + H G+ D SS++ + +NA Y R FL
Sbjct: 322 YVFWHCDLIHAVDPEHNGKGD----SSVMYIPAAPLCETNAAYLARQREAFL 369
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
0.323 0.135 0.404
Gapped
Lambda K H
0.267 0.0709 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,446,394
Number of extensions: 2267025
Number of successful extensions: 1941
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1929
Number of HSP's successfully gapped: 36
Length of query: 466
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 366
Effective length of database: 6,502,202
Effective search space: 2379805932
Effective search space used: 2379805932
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 61 (27.3 bits)