RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8227
(125 letters)
>gnl|CDD|153422 cd07973, Spt4, Transcription elongation factor Spt4. Spt4 is a
transcription elongation factor. Three
transcription-elongation factors Spt4, Spt5, and Spt6,
are conserved among eukaryotes and are essential for
transcription via the modulation of chromatin structure.
It is known that Spt4, Spt5, and Spt6 are general
transcription-elongation factors, controlling
transcription both positively and negatively in
important regulatory and developmental roles. Spt4
functions entirely in the context of the Spt4-Spt5
heterodimer and it has been found only as a complex to
Spt5 in Yeast and Human. Spt4 is a small protein that
has zinc finger at the N-terminus. Spt5 is a large
protein that has several interesting structural features
of an acidic N-terminus, a single NGN domain, five or
six KOW domains, and a set of simple C-termianl repeats.
Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not
essential for viability in yeast, however Spt4 is
critical for normal function of the Spt4-Spt5 complex.
Spt4 homolog is not found in bacteria.
Length = 98
Score = 87.3 bits (217), Expect = 9e-24
Identities = 29/48 (60%), Positives = 35/48 (72%)
Query: 78 RQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
R RACL CS IKT DQFE DGC NC+ +L MK + + VY+CTS NF+
Sbjct: 1 RGLRACLLCSLIKTEDQFERDGCPNCEGYLDMKGNHERVYDCTSPNFE 48
>gnl|CDD|203389 pfam06093, Spt4, Spt4/RpoE2 zinc finger. This family consists of
several eukaryotic transcription elongation Spt4
proteins as well as archaebacterial RpoE2. Three
transcription-elongation factors Spt4, Spt5, and Spt6
are conserved among eukaryotes and are essential for
transcription via the modulation of chromatin structure.
Spt4 and Spt5 are tightly associated in a complex, while
the physical association of the Spt4-Spt5 complex with
Spt6 is considerably weaker. It has been demonstrated
that Spt4, Spt5, and Spt6 play roles in transcription
elongation in both yeast and humans including a role in
activation by Tat. It is known that Spt4, Spt5, and Spt6
are general transcription-elongation factors,
controlling transcription both positively and negatively
in important regulatory and developmental roles. RpoE2
is one of 13 subunits in the archaeal RNA polymerase.
These proteins contain a C4-type zinc finger, and the
structure has been solved in. The structure reveals that
Spt4-Spt5 binding is governed by an acid-dipole
interaction between Spt5 and Spt4, and the complex binds
to and travels along the elongating RNA polymerase. The
Spt4-Spt5 complex is likely to be an ancient, core
component of the transcription elongation machinery.
Length = 77
Score = 72.7 bits (179), Expect = 3e-18
Identities = 30/45 (66%), Positives = 33/45 (73%), Gaps = 1/45 (2%)
Query: 81 RACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
RACL CS +KT DQFE DGC NC EFLHMK R+ V CTS NF+
Sbjct: 2 RACLLCSLVKTEDQFEDDGCPNC-EFLHMKGDRERVSECTSENFE 45
>gnl|CDD|227530 COG5204, SPT4, Transcription elongation factor SPT4
[Transcription].
Length = 112
Score = 51.5 bits (123), Expect = 1e-09
Identities = 23/46 (50%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 80 ARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125
+RACLGC +KT + F DGC NC L+MK NV CTS F+
Sbjct: 9 SRACLGCGIVKTLNGFRKDGCPNC-PMLNMKGGVTNVEECTSPKFE 53
>gnl|CDD|220597 pfam10139, Virul_Fac, Putative bacterial virulence factor. Members
of this family of prokaryotic proteins include various
putative virulence factor effector proteins. Their exact
function is, as yet, unknown.
Length = 852
Score = 28.5 bits (64), Expect = 0.84
Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 4/39 (10%)
Query: 2 IARDEVAQLWAYVRSHVHVQVGRMPESLAAKFTQHVGIL 40
++ D+V LW Y+ H G+ + LAA F L
Sbjct: 168 LSADDVVDLWDYLEHH----FGKRQQPLAAHFWPEAIEL 202
>gnl|CDD|212060 cd11491, SLC5sbd_SMIT, Na(+)/myo-inositol cotransporter SMIT and
related proteins; solute-binding domain. Human SMIT is
a high-affinity myo-inositol transporter, and is
expressed in brain, heart, kidney, and lung. Inhibition
of myo-inositol uptake, through down-regulation of SMIT,
may be a common mechanism of action of mood stabilizers,
including lithium, carbamazepine, and valproate. SMIT is
encoded by the SLC5A3 gene, which is a candidate gene
for pathogenesis of nervous system dysfunction in Down
syndrome (DS). The SNP, 21q22 near SLC5A3-MRPS6-KCNE2,
has been associated with coronary heart disease,
cardiovascular disease, and myocardial infarction. SMIT
may also be involved in the pathogeneisis of congenital
cataract. SMIT also plays roles in osteogenesis, bone
formation, and bone mineral density determination. This
subgroup belongs to the solute carrier 5 (SLC5)
transporter family.
Length = 600
Score = 27.4 bits (61), Expect = 2.5
Identities = 10/27 (37%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 9 QLWAYVRSHVHVQVGR--MPESLAAKF 33
QL +V V++ G MPE L+ +F
Sbjct: 83 QLLGWVFIPVYIASGVVTMPEYLSKRF 109
>gnl|CDD|151903 pfam11464, Rbsn, Rabenosyn Rab binding domain. Rabenosyn-5
(Rbsn) is a multivalent effector with interacts with
the Rab family.Rsbn contains distinct Rab4 and Rab5
binding sites within residues 264-500 and 627-784
respectively. Rab proteins are GTPases involved in the
regulation of all stages of membrane trafficking.
Length = 42
Score = 25.1 bits (55), Expect = 3.0
Identities = 8/28 (28%), Positives = 15/28 (53%)
Query: 67 IDDFNNLAKYFRQARACLGCSQIKTFDQ 94
+ NN+ Y RQAR +++T ++
Sbjct: 2 LQQINNIKGYIRQARQAGRFDEVETLEE 29
>gnl|CDD|221587 pfam12458, DUF3686, ATPase involved in DNA repair. This domain
family is found in bacteria, and is approximately 450
amino acids in length. There are two conserved sequence
motifs: DVF and SPNGED.
Length = 448
Score = 26.4 bits (59), Expect = 4.2
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 67 IDDFNNLAKYFRQAR 81
+ DF L +Y+R R
Sbjct: 98 VRDFAELYRYYRNTR 112
>gnl|CDD|225395 COG2839, COG2839, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 160
Score = 25.8 bits (57), Expect = 6.3
Identities = 9/21 (42%), Positives = 9/21 (42%)
Query: 29 LAAKFTQHVGILCYCLWFLWT 49
L Q V IL LWFL
Sbjct: 137 LVGSIAQAVIILFMILWFLID 157
>gnl|CDD|177987 PLN02354, PLN02354, copper ion binding / oxidoreductase.
Length = 552
Score = 25.9 bits (57), Expect = 7.3
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 57 VHGTSNNNAKIDDFNNL 73
++ TSNNN I+ FNNL
Sbjct: 60 INSTSNNNIVINVFNNL 76
>gnl|CDD|235342 PRK05092, PRK05092, PII uridylyl-transferase; Provisional.
Length = 931
Score = 26.0 bits (58), Expect = 7.6
Identities = 11/20 (55%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 10 LWAYVRSHVHVQVGRMPESL 29
LWA VR H+H GR E L
Sbjct: 289 LWA-VRCHLHFLTGRAEERL 307
>gnl|CDD|233138 TIGR00813, sss, transporter, SSS family. The Solute:Sodium
Symporter (SSS) Family (TC 2.A.21) Members of the SSS
family catalyze solute:Na+ symport. The solutes
transported may be sugars, amino acids, nucleosides,
inositols, vitamins, urea or anions, depending on the
system. Members of the SSS family have been identified
in bacteria, archaea and animals, and all functionally
well characterized members catalyze solute uptake via
Na+ symport. Proteins of the SSS generally share a core
of 13 TMSs, but different members of the family may have
different numbers of TMSs. A 13 TMS topology with a
periplasmic N-terminus and a cytoplasmic C-terminus has
been experimentally determined for the proline:Na+
symporter, PutP, of E. coli [Transport and binding
proteins, Cations and iron carrying compounds].
Length = 407
Score = 25.7 bits (57), Expect = 9.2
Identities = 9/49 (18%), Positives = 18/49 (36%), Gaps = 6/49 (12%)
Query: 13 YVRSHVHVQVGRMPESLAAKFTQHVGILCYCLWFL--WTLVHSATMVHG 59
++ + + MPE L +F + + L + L S + G
Sbjct: 60 FINNGAYT----MPEYLEKRFGKRILRGLSVLSLILYIFLYMSVDLFSG 104
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
0.327 0.135 0.450
Gapped
Lambda K H
0.267 0.0764 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,981,117
Number of extensions: 471888
Number of successful extensions: 556
Number of sequences better than 10.0: 1
Number of HSP's gapped: 553
Number of HSP's successfully gapped: 16
Length of query: 125
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 40
Effective length of database: 7,167,512
Effective search space: 286700480
Effective search space used: 286700480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.1 bits)