RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1643
(962 letters)
>gnl|CDD|204614 pfam11221, Med21, Subunit 21 of Mediator complex. Med21 has been
known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in
Drosophila. The heterodimer of the two subunits Med7 and
Med21 appears to act as a hinge between the middle and
the tail regions of Mediator.
Length = 132
Score = 115 bits (290), Expect = 4e-30
Identities = 35/119 (29%), Positives = 61/119 (51%), Gaps = 3/119 (2%)
Query: 840 EQADNFCNSVGILQQTAIPSKFSGFD-RGGSQTPQQQ--TQQEDYAHLFATLISRCARDI 896
+ A+ FC ++G LQQ PS S + + E+ A I A+ I
Sbjct: 14 QLAEQFCATIGYLQQNHDPSPLSPDEPAVSDPKANAPPPEEFEEGQRELARDIILKAQQI 73
Query: 897 DALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAALTDIAQS 955
+ LI+SLP +S+ E QL +++LE++ + E+ V+ E LL++++A L +IA+
Sbjct: 74 EYLIDSLPGIESSEEEQLRRIKELEEELREVEAEREEAVKEKEKLLKKVEALLREIARG 132
>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit.
Transcription initiation factor IIA (TFIIA) is a
heterotrimer, the three subunits being known as alpha,
beta, and gamma, in order of molecular weight. The N and
C-terminal domains of the gamma subunit are represented
in pfam02268 and pfam02751, respectively. This family
represents the precursor that yields both the alpha and
beta subunits. The TFIIA heterotrimer is an essential
general transcription initiation factor for the
expression of genes transcribed by RNA polymerase II.
Together with TFIID, TFIIA binds to the promoter region;
this is the first step in the formation of a
pre-initiation complex (PIC). Binding of the rest of the
transcription machinery follows this step. After
initiation, the PIC does not completely dissociate from
the promoter. Some components, including TFIIA, remain
attached and re-initiate a subsequent round of
transcription.
Length = 332
Score = 37.0 bits (86), Expect = 0.035
Identities = 24/131 (18%), Positives = 37/131 (28%), Gaps = 19/131 (14%)
Query: 8 GGKNTNNSAPGAASTSQCSGGSAKPANQAGP---------SKQNVPANQAGPSKQNV--P 56
G ++ P + + A PA AGP VP +
Sbjct: 80 AGDQQQHNTPTGSPAANPPATFALPAGPAGPTIQTEPGQLYPVQVPVMVTQNPANSPLDQ 139
Query: 57 VNQGGAAKQNIQGS--------SSKQNVSANQAGPSKQNGPVKQTGASKQNGPVKQTSKE 108
Q A +Q Q S+Q + Q P +T + +G S+
Sbjct: 140 PAQQRALQQLQQRYGAPASGQLPSQQQSAQKNDESQLQQQPNGETPPQQTDGAGDDESEA 199
Query: 109 TPRSRRKPSSL 119
R R +L
Sbjct: 200 LVRLREADGTL 210
Score = 35.5 bits (82), Expect = 0.13
Identities = 24/91 (26%), Positives = 33/91 (36%), Gaps = 3/91 (3%)
Query: 21 STSQCSGGSAKPANQAGPSKQNVPAN--QAGPSKQNVPVNQGGAAKQNIQGSSSKQNVSA 78
S S + P+ QA P +P Q P++ + G + N S N A
Sbjct: 40 SQSGVAEFPWDPSPQAPPPVAQLPQPLPQPPPTQALQALPAGDQQQHNTPTGSPAANPPA 99
Query: 79 NQAGPSKQNGPVKQTGASKQNGPVKQTSKET 109
A P+ GP QT Q PV+ T
Sbjct: 100 TFALPAGPAGPTIQT-EPGQLYPVQVPVMVT 129
>gnl|CDD|185628 PTZ00449, PTZ00449, 104 kDa microneme/rhoptry antigen; Provisional.
Length = 943
Score = 34.3 bits (78), Expect = 0.41
Identities = 20/93 (21%), Positives = 34/93 (36%), Gaps = 7/93 (7%)
Query: 27 GGSAKPANQAGPSKQNVPANQAGPSKQNVPVNQGGAAKQNIQGSSSKQNVSANQAGPSKQ 86
G A P + + SK++ +GG + +G K + GP+K+
Sbjct: 513 GPEASGLPPKAPGDKEGEEGEHEDSKESDEPKEGGKPGETKEGEVGK------KPGPAKE 566
Query: 87 NGPVK-QTGASKQNGPVKQTSKETPRSRRKPSS 118
+ P K T + K P + P +KP
Sbjct: 567 HKPSKIPTLSKKPEFPKDPKHPKDPEEPKKPKR 599
>gnl|CDD|220819 pfam10599, Nup_retrotrp_bd, Retro-transposon transporting motif.
This is the highly conserved C-terminal motif
GRKIxxxxxRRKx of nucleoporins that plays a critical and
unique role in the nuclear import of retro-transposons
in both yeasts and higher organisms. It would appear
that the arginine residues at positions 2 and 9-10
constitute a bipartite nuclear localisation signal,
with two basic peptide motifs separated by an
interchangeable spacer sequence, that is crucial for
the retro-transposon activity.
Length = 101
Score = 31.6 bits (71), Expect = 0.42
Identities = 17/85 (20%), Positives = 29/85 (34%), Gaps = 2/85 (2%)
Query: 9 GKNTNNSAPGAASTSQCSGGSAKPANQAGPS-KQNVPANQAGPSKQNVPVNQGGAAKQNI 67
G +N+ A ++ S+ P+ + PAN A PS N P G+
Sbjct: 12 GMGNSNTNFNFAGSNNQPHTSSTPSTPFTFGASPSTPANAASPSGSNPP-AFSGSPASAP 70
Query: 68 QGSSSKQNVSANQAGPSKQNGPVKQ 92
+ N S + S + +
Sbjct: 71 NQFNVGSNNSNMFSSSSVSGRKIAR 95
>gnl|CDD|206155 pfam13985, YbgS, YbgS-like protein. This family of proteins is
functionally uncharacterized. The family includes the
YbgS protein from E. coli. This family of proteins is
found in bacteria. Proteins in this family are
approximately 130 amino acids in length. Some members
of this family are annotated as homeobox protein, but
this annotation cannot be verified.
Length = 122
Score = 32.2 bits (73), Expect = 0.46
Identities = 21/70 (30%), Positives = 31/70 (44%), Gaps = 7/70 (10%)
Query: 15 SAPGAASTSQCSGGSAKPANQAGP----SKQNVPANQAGPSKQNVPVNQGGAAKQNIQGS 70
+A A S +Q + G A A AG +KQNV N SK N G Q+ G+
Sbjct: 19 AALAADSGAQSNNGQANAAADAGQVAPDAKQNVAPNNVDNSKIN---TGSGGTMQHPNGT 75
Query: 71 SSKQNVSANQ 80
+ +S ++
Sbjct: 76 MNSDGMSKDE 85
>gnl|CDD|185641 PTZ00462, PTZ00462, Serine-repeat antigen protein; Provisional.
Length = 1004
Score = 33.1 bits (75), Expect = 1.0
Identities = 20/102 (19%), Positives = 35/102 (34%), Gaps = 7/102 (6%)
Query: 5 NKKGGKNTNNSAPGAAST---SQCSGGSAKPANQAGPSKQNVPANQAGPSKQNVPVNQGG 61
N GG+ A + + + A+ K++ AN G ++ +G
Sbjct: 32 NIGGGQAGGTGGDNAGNIDGSPIGNLDANIHASFGADPKESSGANLPGKKEKKKKEIRGH 91
Query: 62 AAKQN----IQGSSSKQNVSANQAGPSKQNGPVKQTGASKQN 99
N S KQ+ ++ K N +K TG +N
Sbjct: 92 DIMSNSDSQNSSSIEKQDNIQIKSALLKDNKGLKITGPCNEN 133
>gnl|CDD|240324 PTZ00234, PTZ00234, variable surface protein Vir12; Provisional.
Length = 433
Score = 32.3 bits (73), Expect = 1.4
Identities = 22/107 (20%), Positives = 44/107 (41%), Gaps = 17/107 (15%)
Query: 63 AKQNIQGSSSKQN--------VSANQAGPSKQNGPVKQTGAS---KQNGPV-----KQTS 106
AK QGS+ Q+ S+ + PSK + ++ + K G + K+
Sbjct: 221 AKCKTQGSNGSQSSFLGWFWGSSSPKTAPSKGSPGAQEPAKTAVVKSPGGIPSAGGKRAG 280
Query: 107 KETPRSRRKPSSLPLQKEVEAI-RLRRRVKMKPLKNTQCSIHLKHLP 152
E + + +S+ + E + + V + PL ++Q +H+ H
Sbjct: 281 AEGAGANKGLASVAPSQSREVLNGTQNPVPVAPLGSSQAGVHMPHGS 327
>gnl|CDD|147458 pfam05268, GP38, Phage tail fibre adhesin Gp38. This family
contains several Gp38 proteins from T-even-like phages.
Gp38, together with a second phage protein, gp57,
catalyzes the organisation of gp37 but is absent from
the phage particle. Gp37 is responsible for receptor
recognition.
Length = 261
Score = 31.7 bits (72), Expect = 1.4
Identities = 23/72 (31%), Positives = 33/72 (45%), Gaps = 1/72 (1%)
Query: 8 GGKNTNNSAPGAASTSQCSGGSAKPANQAGPSKQNVPANQAGPSKQNVPVNQGGAAKQNI 67
GGK+ ++ + G AS + GGS + G + NV A N GGAA +
Sbjct: 184 GGKSGSHMSGGNASLTAPGGGSGTGSAYGGGNGGNVGAAGGRAWGGNGYEYGGGAAGYAV 243
Query: 68 QGSS-SKQNVSA 78
GS+ + QNV
Sbjct: 244 IGSAPTWQNVGT 255
>gnl|CDD|203679 pfam07544, Med9, RNA polymerase II transcription mediator complex
subunit 9. This family of Med9 proteins is conserved in
yeasts. It forms part of the middle region of Mediator.
Med9 has two functional domains. The species-specific
amino-terminal half (aa 1-63) plays a regulatory role in
transcriptional regulation, whereas this well-conserved
carboxy-terminal half (aa 64-149) has a more fundamental
function involved in direct binding to the
amino-terminal portions of Med4 and Med7 and the
assembly of Med9 into the Middle module. Also, some
unidentified factor(s) in med9 extracts may impact the
binding of TFIID to the promoter.
Length = 83
Score = 29.1 bits (66), Expect = 2.0
Identities = 12/42 (28%), Positives = 19/42 (45%)
Query: 898 ALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVRRGE 939
A +E LP + E Q A + +LE+ E L+ R +
Sbjct: 42 AAVEELPGISRSVEEQEAEIEELEEQIARKREVLQKFKERVD 83
>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau;
Validated.
Length = 824
Score = 31.9 bits (73), Expect = 2.0
Identities = 23/115 (20%), Positives = 37/115 (32%), Gaps = 1/115 (0%)
Query: 15 SAPGAASTSQCSGGSAKPANQAGPSKQNVPANQAGPSKQNVPVNQGGAAKQNIQGSSSKQ 74
SA AA + + +A PA A P+ P P+ P + G A S
Sbjct: 400 SAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPA 459
Query: 75 NVSANQAGPSKQNGPVKQTGASKQNGPVKQTSKETPRSRRKPSSLPLQKEVEAIR 129
+ Q P+ + T A P P + P++ + +R
Sbjct: 460 AAPSAQPAPAPA-AAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAGADDAATLR 513
>gnl|CDD|221576 pfam12439, GDE_N, Glycogen debranching enzyme N terminal. This
domain family is found in bacteria and archaea, and is
typically between 218 and 229 amino acids in length. The
family is found in association with pfam06202. Glycogen
debranching enzyme catalyzes the debranching of
amylopectin in glycogen. This is done by transferring
three glucose subunits of glycogen from one parallel
chain to another. This has the effect of enabling the
glucose residues to become more accessible for
glycolysis.
Length = 222
Score = 31.0 bits (71), Expect = 2.0
Identities = 14/81 (17%), Positives = 27/81 (33%), Gaps = 20/81 (24%)
Query: 124 EVEAIRLRRRVKMKPLKNTQCSIHLKHLPAPKSTHAPAEFRLKCILLFKQEYPMF----Y 179
V + L +R+ M +NT + L + P RL+ P+ +
Sbjct: 91 RVGGVVLEKRIFMVQGENT-TVVRYTLLNGSE----PVTLRLR---------PLVNFRDH 136
Query: 180 HDNVKTPPVNFYYKFSTTKDR 200
H K N+ ++ +
Sbjct: 137 HALTKAN--NWSFEVEPVEGG 155
>gnl|CDD|223065 PHA03378, PHA03378, EBNA-3B; Provisional.
Length = 991
Score = 32.0 bits (72), Expect = 2.2
Identities = 29/110 (26%), Positives = 42/110 (38%), Gaps = 9/110 (8%)
Query: 15 SAPGAASTSQCSGGSAKPANQAGPSKQNVPANQAGPSKQNVPVNQGG-AAKQNIQGSSSK 73
+APG A + G A+P A + P QA P+ Q P +G + Q +
Sbjct: 749 AAPGRARPPAAAPGRARPPAAAPGAPTPQPPPQAPPAPQQRP--RGAPTPQPPPQAGPTS 806
Query: 74 QNVSANQAGPSKQNGPVKQTGASKQNGPVKQTSKETPRSRRKPSSLPLQK 123
+ Q GP KQ G VK+ S +KP++L Q
Sbjct: 807 MQLMPRA--APGQQGPTKQILRQLLTGGVKRGRP----SLKKPAALERQA 850
>gnl|CDD|192115 pfam08656, DASH_Dad3, DASH complex subunit Dad3. The DASH complex
is a ~10 subunit microtubule-binding complex that is
transferred to the kinetochore prior to mitosis. In
Saccharomyces cerevisiae DASH forms both rings and
spiral structures on microtubules in vitro.
Length = 78
Score = 28.8 bits (65), Expect = 2.4
Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 5/51 (9%)
Query: 871 TPQQQTQQEDYAHLFATLISRCARDIDALIESLPNEDSTTELQLASLRKLE 921
+P +Q ++Y L + L + + A ++ L + DS E L +LR+LE
Sbjct: 2 SPLEQEVLDEYQRLASNLKT-----LSAELKDLNSTDSPPEELLDNLRELE 47
>gnl|CDD|236792 PRK10905, PRK10905, cell division protein DamX; Validated.
Length = 328
Score = 31.1 bits (70), Expect = 2.7
Identities = 36/166 (21%), Positives = 67/166 (40%), Gaps = 20/166 (12%)
Query: 11 NTNNSAPGAASTSQCSGGSAKPANQAGPSKQNV--PANQAGPSKQNVPVNQGGAAKQNIQ 68
+ +A A+ Q + G+ AG ++Q+V P + P++ PV G + +Q
Sbjct: 39 DLAGNATDQANGVQPAPGTTSAEQTAGNTQQDVSLPPISSTPTQGQTPVATDGQQRVEVQ 98
Query: 69 GSSSK-----------QNVSANQAGPSKQNGPVKQTGASKQNGPVKQTSKETPRSRRKPS 117
G + NV+ N P++ T A +NG + + +T + R +
Sbjct: 99 GDLNNALTQPQNQQQLNNVAVNSTLPTE-----PATVAPVRNGNASRQTAKTQTAERPAT 153
Query: 118 SLPLQKE--VEAIRLRRRVKMKPLKNTQCSIHLKHLPAPKSTHAPA 161
+ P +K+ +E + + K +P Q + ST APA
Sbjct: 154 TRPARKQAVIEPKKPQATAKTEPKPVAQTPKRTEPAAPVASTKAPA 199
>gnl|CDD|133069 cd03857, M14-like_1, Peptidase M14-like domain; uncharacterized
subfamily. Peptidase M14-like domain of a functionally
uncharacterized subgroup of the M14 family of
metallocarboxypeptidases (MCPs). The M14 family are
zinc-binding carboxypeptidases (CPs) which hydrolyze
single, C-terminal amino acids from polypeptide chains,
and have a recognition site for the free C-terminal
carboxyl group, which is a key determinant of
specificity. Two major subfamilies of the M14 family,
defined based on sequence and structural homology, are
the A/B and N/E subfamilies. Enzymes belonging to the
A/B subfamily are normally synthesized as inactive
precursors containing preceding signal peptide, followed
by an N-terminal pro-region linked to the enzyme; these
proenzymes are called procarboxypeptidases. The A/B
enzymes can be further divided based on their substrate
specificity; Carboxypeptidase A-like (CPA-like) enzymes
favor hydrophobic residues while carboxypeptidase B-like
(CPB-like) enzymes only cleave the basic residues lysine
or arginine. The A forms have slightly different
specificities, with Carboxypeptidase A1 (CPA1)
preferring aliphatic and small aromatic residues, and
CPA2 preferring the bulky aromatic side chains. Enzymes
belonging to the N/E subfamily enzymes are not produced
as inactive precursors and instead rely on their
substrate specificity and subcellular
compartmentalization to prevent inappropriate cleavage.
They contain an extra C-terminal transthyretin-like
domain, thought to be involved in folding or formation
of oligomers. MCPs can also be classified based on
their involvement in specific physiological processes;
the pancreatic MCPs participate only in alimentary
digestion and include carboxypeptidase A and B (A/B
subfamily), while others, namely regulatory MCPs or the
N/E subfamily, are involved in more selective reactions,
mainly in non-digestive tissues and fluids, acting on
blood coagulation/fibrinolysis, inflammation and local
anaphylaxis, pro-hormone and neuropeptide processing,
cellular response and others. Another MCP subfamily,
is that of succinylglutamate desuccinylase
/aspartoacylase, which hydrolyzes N-acetyl-L-aspartate
(NAA), and deficiency in which is the established cause
of Canavan disease. Another subfamily (referred to as
subfamily C) includes an exceptional type of activity in
the MCP family, that of dipeptidyl-peptidase activity of
gamma-glutamyl-(L)-meso-diaminopimelate peptidase I
which is involved in bacterial cell wall metabolism.
Length = 226
Score = 30.5 bits (69), Expect = 3.6
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 904 PNEDSTTELQLASLRKLEQDNQGAAERLEDTV 935
NE + ++ L LR+L + A+ LE+ V
Sbjct: 42 GNESAGSDALLELLRQLASASDEEAKMLENIV 73
>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau;
Validated.
Length = 830
Score = 31.0 bits (70), Expect = 4.3
Identities = 18/116 (15%), Positives = 32/116 (27%), Gaps = 21/116 (18%)
Query: 12 TNNSAPGAASTSQCSGGSAKPANQAGPSKQNVPANQAGPSKQNVPVNQGGAAKQNIQGSS 71
T APG ++ +G P +A + A P+ V G A
Sbjct: 363 TGGGAPGGGVPARVAGAVPAPGARAAAA----VGASAVPAVTAVTGAAGAALAPK----- 413
Query: 72 SKQNVSANQAGPSKQNGPVKQTGASKQNGPVKQTSKETPRSRRKPSSLPLQKEVEA 127
+A A ++ P T+ + + +P + A
Sbjct: 414 -----AAAAAAATRAEAPPAAP-------APPATADRGDDAADGDAPVPAKANARA 457
>gnl|CDD|233727 TIGR02101, IpaC_SipC, type III secretion target, IpaC/SipC family.
This model represents a family of proteins associated
with bacterial type III secretion systems, which are
injection machines for virulence factors into host cell
cytoplasm. Characterized members of this protein family
are known to be secreted and are described as invasins,
including IpaC from Shigella flexneri and SipC from
Salmonella typhimurium (GB:AAA75170.1). Members may be
referred to as invasins, pathogenicity island effectors,
and cell invasion proteins [Cellular processes,
Pathogenesis].
Length = 317
Score = 30.3 bits (68), Expect = 5.2
Identities = 18/72 (25%), Positives = 29/72 (40%), Gaps = 1/72 (1%)
Query: 58 NQGGAAKQNIQGSSSKQNVSANQA-GPSKQNGPVKQTGASKQNGPVKQTSKETPRSRRKP 116
Q GA K+N++ S+ +A + QN P + + + ET R P
Sbjct: 134 KQSGALKKNLKPSNKLSAEAAQLKLQLNGQNAPKLVADSKRTGVAATKELGETTRHEIDP 193
Query: 117 SSLPLQKEVEAI 128
S+ L E +A
Sbjct: 194 SNKALSAEHKAQ 205
>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 30.5 bits (69), Expect = 5.4
Identities = 18/129 (13%), Positives = 31/129 (24%), Gaps = 15/129 (11%)
Query: 17 PGAASTSQCSGGSAKPANQA--GPSKQNVPANQAGPSKQNVPVNQGGAAKQNIQGSSSKQ 74
+ G + P+ P+ A S Q+ +
Sbjct: 363 TQKGDDASGGRGPKQHIKPVFTQPAAAPQPSAAAAASPSP---------SQSSAAAQPSA 413
Query: 75 NVSANQAGPSKQNGPVKQTGASKQNGPVKQTSKETPRSRRKPSSLPLQKEVEAIRLRRRV 134
SA Q + V A N P P ++ +P+ K R
Sbjct: 414 PQSATQPAGTPPTVSVDPPAAVPVNPPSTAPQAVRPAQFKEEKKIPVSKVSSLGPSTLR- 472
Query: 135 KMKPLKNTQ 143
P++
Sbjct: 473 ---PIQEKA 478
>gnl|CDD|233973 TIGR02680, TIGR02680, TIGR02680 family protein. Members of this
protein family belong to a conserved gene four-gene
neighborhood found sporadically in a phylogenetically
broad range of bacteria: Nocardia farcinica,
Symbiobacterium thermophilum, and Streptomyces
avermitilis (Actinobacteria), Geobacillus kaustophilus
(Firmicutes), Azoarcus sp. EbN1 and Ralstonia
solanacearum (Betaproteobacteria). Proteins in this
family average over 1400 amino acids in length
[Hypothetical proteins, Conserved].
Length = 1353
Score = 30.2 bits (68), Expect = 6.5
Identities = 19/76 (25%), Positives = 30/76 (39%), Gaps = 15/76 (19%)
Query: 894 RDIDALIESLPNEDSTTELQLASL---------RKLEQ------DNQGAAERLEDTVRRG 938
R++DA E+L E +L +L +LE+ Q AA +R
Sbjct: 300 RELDARTEALEREADALRTRLEALQGSPAYQDAEELERARADAEALQAAAADARQAIREA 359
Query: 939 ELLLEQIQAALTDIAQ 954
E LE+ + L + A
Sbjct: 360 ESRLEEERRRLDEEAG 375
>gnl|CDD|226682 COG4229, COG4229, Predicted enolase-phosphatase [Energy production
and conversion].
Length = 229
Score = 29.4 bits (66), Expect = 6.9
Identities = 13/55 (23%), Positives = 25/55 (45%)
Query: 171 FKQEYPMFYHDNVKTPPVNFYYKFSTTKDRKAPAEMAIFNCVDQLVAQDKKDTIL 225
++ P F +N + V ++ A +E A+ + + +A+D KDT L
Sbjct: 29 AARKLPDFVRENTEDSEVKKIVDEVLSEFGIANSEEALVALLLEWIAEDSKDTPL 83
>gnl|CDD|234351 TIGR03773, anch_rpt_wall, putative ABC transporter-associated
repeat protein. Members of this protein family occur in
genomes that contain a three-gene ABC transporter operon
associated with the presence of domain TIGR03769. That
domain occurs as a single-copy insert in the
substrate-binding protein, and occurs in two or more
copies in members of this protein family. Members of
this family typically are encoded adjacent to the said
transporter operon and may serve as a substrate
receptor.
Length = 513
Score = 29.9 bits (67), Expect = 7.5
Identities = 13/80 (16%), Positives = 23/80 (28%), Gaps = 1/80 (1%)
Query: 40 KQNVPANQAGPSKQN-VPVNQGGAAKQNIQGSSSKQNVSANQAGPSKQNGPVKQTGASKQ 98
+ PA A + + N A K +S +++ S Q G S +
Sbjct: 171 DKIDPARCATGAGKPQNDANGPAADKPLFDDPASGVQALGDESAFSPGQQATVQIGKSVR 230
Query: 99 NGPVKQTSKETPRSRRKPSS 118
+ PS+
Sbjct: 231 LPADAPLGVAAVVVKAAPST 250
>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex
non-fungal. The approx. 70 residue Med15 domain of the
ARC-Mediator co-activator is a three-helix bundle with
marked similarity to the KIX domain. The sterol
regulatory element binding protein (SREBP) family of
transcription activators use the ARC105 subunit to
activate target genes in the regulation of cholesterol
and fatty acid homeostasis. In addition, Med15 is a
critical transducer of gene activation signals that
control early metazoan development.
Length = 768
Score = 30.0 bits (67), Expect = 8.1
Identities = 19/118 (16%), Positives = 27/118 (22%), Gaps = 19/118 (16%)
Query: 14 NSAPGAASTSQCSGGSAKPANQAGPSKQNVPA-----------NQAGPSKQN-------- 54
+ G P Q P + P Q P Q
Sbjct: 169 QQGQAQGQAGGMNQGQQGPVGQQQPPQMGQPGMPGGGGQGQMQQQGQPGGQQQQNPQMQQ 228
Query: 55 VPVNQGGAAKQNIQGSSSKQNVSANQAGPSKQNGPVKQTGASKQNGPVKQTSKETPRS 112
NQ QG + Q Q P + G Q +Q ++ P+
Sbjct: 229 QLQNQQQQQMDQQQGPADAQAQMGQQQQGQGGMQPQQMQGGQMQVPMQQQPPQQQPQQ 286
Score = 29.6 bits (66), Expect = 9.2
Identities = 14/99 (14%), Positives = 23/99 (23%), Gaps = 1/99 (1%)
Query: 1 MAKKNKKGGKNTNNSAPGAASTSQCSGGSAKPANQAGPSKQNVPANQAGPSKQNVPVNQG 60
M G + + Q G + + Q + N Q G ++
Sbjct: 123 MPMGAAGMGPHQMSRVGTMQPGGQAGGMMQQSSGQPQSQQPNQMGPQQGQAQGQAGGMNQ 182
Query: 61 GAAKQNIQGSSSKQNVSANQAGPSKQNGPVKQTGASKQN 99
G + Q G Q +Q Q
Sbjct: 183 GQQGP-VGQQQPPQMGQPGMPGGGGQGQMQQQGQPGGQQ 220
>gnl|CDD|184918 PRK14954, PRK14954, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 29.9 bits (67), Expect = 8.5
Identities = 17/88 (19%), Positives = 25/88 (28%), Gaps = 4/88 (4%)
Query: 15 SAPGAASTSQCSGGSAKPANQAGPSKQNVPANQAGPSKQNVPVNQGGAAKQNIQGSSSKQ 74
APGA S SA Q P ++ P P G + S +
Sbjct: 412 EAPGARPAELPSPASAPTPEQQPPVARSAPL-PPSPQASAPRNVASGKP--GVDLGSWQG 468
Query: 75 NVSANQAGPSKQNGPVKQTGASKQNGPV 102
S + PV+ + + V
Sbjct: 469 KFMNFTRNGS-RKQPVQASSSDAAQTGV 495
>gnl|CDD|220728 pfam10390, ELL, RNA polymerase II elongation factor ELL. ELL is a
family of RNA polymerase II elongation factors. It is
bound stably to elongation-associated factors 1 and 2,
EAFs, and together these act as a strong regulator of
transcription activity. by direct interaction with Pol
II. ELL binds to pol II on its own but the affinity is
greatly increased by the cooperation of EAF. Some
members carry an Occludin domain pfam07303 just
downstream. There is no S. cerevisiae member.
Length = 285
Score = 29.3 bits (66), Expect = 9.5
Identities = 17/64 (26%), Positives = 27/64 (42%)
Query: 50 PSKQNVPVNQGGAAKQNIQGSSSKQNVSANQAGPSKQNGPVKQTGASKQNGPVKQTSKET 109
+KQ P G K I+ S+ +VS+ A KQ+ P + +S++ K
Sbjct: 139 GTKQIKPGGPEGGKKVQIKKPLSEISVSSPLASNRKQSLPGNGSSSSRKANGSSAVMKRP 198
Query: 110 PRSR 113
R R
Sbjct: 199 LRER 202
>gnl|CDD|111993 pfam03157, Glutenin_hmw, High molecular weight glutenin subunit.
Members of this family include high molecular weight
subunits of glutenin. This group of gluten proteins is
thought to be largely responsible for the elastic
properties of gluten, and hence, doughs. Indeed,
glutenin high molecular weight subunits are classified
as elastomeric proteins, because the glutenin network
can withstand significant deformations without breaking,
and return to the original conformation when the stress
is removed. Elastomeric proteins differ considerably in
amino acid sequence, but they are all polymers whose
subunits consist of elastomeric domains, composed of
repeated motifs, and non-elastic domains that mediate
cross-linking between the subunits. The elastomeric
domain motifs are all rich in glycine residues in
addition to other hydrophobic residues. High molecular
weight glutenin subunits have an extensive central
elastomeric domain, flanked by two terminal non-elastic
domains that form disulphide cross-links. The central
elastomeric domain is characterized by the following
three repeated motifs: PGQGQQ, GYYPTS[P/L]QQ, GQQ. It
possesses overlapping beta-turns within and between the
repeated motifs, and assumes a regular helical secondary
structure with a diameter of approx. 1.9 nm and a pitch
of approx. 1.5 nm.
Length = 779
Score = 29.7 bits (65), Expect = 9.9
Identities = 25/108 (23%), Positives = 41/108 (37%), Gaps = 9/108 (8%)
Query: 9 GKNTNNSAPGAASTSQCSGGSAKPANQAGPSKQNVPANQAGPSKQNVPVNQGGAAKQNIQ 68
G+ PG S G +P + S+Q + + G +Q V QG A+ Q
Sbjct: 291 GQQPGQGQPGHYPASPQQPGQGQPGHYPASSQQPTQSQEPGQGQQGQQVGQGQQAQIPAQ 350
Query: 69 GSSSKQNVSANQAGPSKQNGP---------VKQTGASKQNGPVKQTSK 107
G Q + Q GP ++Q G +Q G ++Q++
Sbjct: 351 GQQPGQGQPGHYPASPLQQGPGQPGHYLTSLQQLGQGQQIGQLQQSAP 398
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
0.315 0.130 0.368
Gapped
Lambda K H
0.267 0.0593 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 46,500,682
Number of extensions: 4481477
Number of successful extensions: 4185
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4170
Number of HSP's successfully gapped: 49
Length of query: 962
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 856
Effective length of database: 6,236,078
Effective search space: 5338082768
Effective search space used: 5338082768
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: 64 (28.7 bits)