RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy639
(114 letters)
>gnl|CDD|197842 smart00717, SANT, SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding
domains.
Length = 49
Score = 39.1 bits (92), Expect = 1e-05
Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 51 WTQQEREVFRDKYIHH-QKNFGLIASFLERRTPSDCVEYYYLSKKR 95
WT++E E+ + + + N+ IA L RT C E + K
Sbjct: 4 WTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWRNLLKP 49
>gnl|CDD|238096 cd00167, SANT, 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding
domains. Tandem copies of the domain bind telomeric DNA
tandem repeatsas part of the capping complex. Binding
is sequence dependent for repeats which contain the G/C
rich motif [C2-3 A (CA)1-6]. The domain is also found
in regulatory transcriptional repressor complexes where
it also binds DNA.
Length = 45
Score = 38.3 bits (90), Expect = 2e-05
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 51 WTQQEREVFRDKYIHH-QKNFGLIASFLERRTPSDCVEYYY 90
WT++E E+ + + + N+ IA L RTP C E +
Sbjct: 2 WTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWR 42
>gnl|CDD|215818 pfam00249, Myb_DNA-binding, Myb-like DNA-binding domain. This
family contains the DNA binding domains from Myb
proteins, as well as the SANT domain family.
Length = 47
Score = 37.5 bits (88), Expect = 6e-05
Identities = 12/41 (29%), Positives = 18/41 (43%), Gaps = 1/41 (2%)
Query: 51 WTQQEREVFRDKYIHH-QKNFGLIASFLERRTPSDCVEYYY 90
WT +E E+ + H N+ IA L RT + C +
Sbjct: 4 WTPEEDELLIEAVKKHGNGNWSKIAKHLPGRTDNQCKNRWN 44
>gnl|CDD|212559 cd11661, SANT_MTA3_like, Myb-Like Dna-Binding Domain of MTA3 and
related proteins. Members in this SANT/myb family
include domains found in mouse metastasis-associated
protein 3 (MTA3) proteins and arginine-glutamic
dipeptide (RERE) repeats proteins. SANT (SWI3, ADA2,
N-CoR and TFIIIB) DNA-binding domains are a diverse set
of proteins that share a common 3 alpha-helix bundle.
MTA3 has been shown to interact with nucleosome
remodeling and deacetylase (NuRD) proteins CHD4 and
HDAC1, and the core cohesin complex protein RAD21 in
the ovary, and regulate G2/M progression in
proliferating granulosa cells. RERE belongs to the
atrophin family and has been identified as a nuclear
receptor corepressor; altered expression levels of RERE
are associated with cancer in humans while mutations of
Rere in mice cause failure in closing the anterior
neural tube and fusion of the telencephalic and optic
vesicles during embryogenesis.
Length = 46
Score = 35.7 bits (83), Expect = 2e-04
Identities = 14/45 (31%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 51 WTQQEREVFRDKYIHHQKNFGLI-ASFLERRTPSDCVEYYYLSKK 94
W++ E ++F + + K+F I FL ++ + VE+YY+ KK
Sbjct: 2 WSESEAKLFEEGLRKYGKDFHDIRQDFLPWKSVGELVEFYYMWKK 46
>gnl|CDD|206092 pfam13921, Myb_DNA-bind_6, Myb-like DNA-binding domain. This
family contains the DNA binding domains from Myb
proteins, as well as the SANT domain family.
Length = 59
Score = 31.1 bits (71), Expect = 0.021
Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 2/51 (3%)
Query: 51 WTQQEREVFRDKYIHHQKNFGLIASFLERRTPSDCVEYYYLSKKRENYKRA 101
WT++E E + ++ IA L RTPS C + + K R R
Sbjct: 1 WTEEEDEKLLKLVEKYGNDWKQIAEEL-GRTPSACRDRWR-RKLRPKRSRG 49
>gnl|CDD|238323 cd00578, L-fuc_L-ara-isomerases, L-fucose isomerase (FucIase) and
L-arabinose isomerase (AI) family; composed of FucIase,
AI and similar proteins. FucIase converts L-fucose, an
aldohexose, to its ketose form, which prepares it for
aldol cleavage (similar to the isomerization of glucose
in glycolysis). L-fucose (or 6-deoxy-L-galactose) is
found in various oligo- and polysaccharides in mammals,
bacteria and plants. AI catalyzes the isomerization of
L-arabinose to L-ribulose, the first reaction in its
conversion to D-xylulose-5-phosphate, an intermediate in
the pentose phosphate pathway, which allows L-arabinose
to be used as a carbon source. AI can also convert
D-galactose to D-tagatose at elevated temperatures in
the presence of divalent metal ions. D-tagatose, rarely
found in nature, is of commercial interest as a
low-calorie sugar substitute.
Length = 452
Score = 28.4 bits (64), Expect = 0.81
Identities = 11/62 (17%), Positives = 20/62 (32%), Gaps = 8/62 (12%)
Query: 25 GPRFINNNGRVTDYEAEMRDRAQAKMWTQQE--REVFRDKYI------HHQKNFGLIASF 76
R + G + E + W + + F + +I H ++G A
Sbjct: 380 RYRLVVGEGESVEPPEERPKLPVTRAWWKPPPDLDEFMEAWILAGGAHHTALSYGHTAEE 439
Query: 77 LE 78
LE
Sbjct: 440 LE 441
>gnl|CDD|238996 cd02040, NifH, NifH gene encodes component II (iron protein) of
nitrogenase. Nitrogenase is responsible for the
biological nitrogen fixation, i.e. reduction of
molecular nitrogen to ammonia. NifH consists of two
oxygen-sensitive metallosulfur proteins: the
mollybdenum-iron (alternatively, vanadium-iron or
iron-iron) protein (commonly referred to as component
1), and the iron protein (commonly referred to as
component 2). The iron protein is a homodimer, with an
Fe4S4 cluster bound between the subunits and two
ATP-binding domains. It supplies energy by ATP
hydrolysis, and transfers electrons from reduced
ferredoxin or flavodoxin to component 1 for the
reduction of molecular nitrogen to ammonia.
Length = 270
Score = 28.0 bits (63), Expect = 0.90
Identities = 25/89 (28%), Positives = 37/89 (41%), Gaps = 16/89 (17%)
Query: 25 GPRF--INNNGRVTDYEAEMRDRAQAKMWTQQEREVFRDKYIHHQKNFGLIASFLERRTP 82
G R + N R TD E E+ D ++ TQ V RD + + L +T
Sbjct: 174 GVRLGGLICNSRNTDREDELIDAFAKRLGTQMIHFVPRDNVVQR--------AELRGKT- 224
Query: 83 SDCVEYYYLSKKRENYK---RAIPTNNML 108
+EY SK+ + Y+ R I N +L
Sbjct: 225 --VIEYDPESKQADEYRELARKIVENKLL 251
>gnl|CDD|204337 pfam09916, DUF2145, Uncharacterized protein conserved in bacteria
(DUF2145). This domain, found in various hypothetical
prokaryotic proteins, has no known function.
Length = 200
Score = 27.3 bits (61), Expect = 1.7
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 6/38 (15%)
Query: 22 PFTGPRFINNNGRVTD-----YEAEMRDRAQAKMWTQQ 54
PF R+ N+N V + E DR QA+ W +
Sbjct: 112 PF-STRYQNSNEWVLEVLAAALYPETDDREQAQAWLRL 148
>gnl|CDD|131758 TIGR02711, symport_actP, cation/acetate symporter ActP. Members of
this family belong to the Sodium:solute symporter
family. Both members of this family and other close
homologs tend to be encoded next to a member of Pfam
family pfam04341, a set of uncharacterized membrane
proteins. The characterized member from E. coli is
encoded near and cotranscribed with the acetyl coenzyme
A synthetase (acs) gene. Proximity to an acs gene was
used as one criterion for determining the trusted cutoff
for this model. Closely related proteins may differ in
function and are excluded by the high cutoffs of this
model; members of the family of phenylacetic acid
transporter PhaJ can score as high as 1011 bits
[Transport and binding proteins, Carbohydrates, organic
alcohols, and acids].
Length = 549
Score = 27.2 bits (60), Expect = 2.0
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 53 QQEREVFRDKYIHHQKNFG 71
QERE+FR ++I Q G
Sbjct: 524 AQERELFRAQFIRSQTGLG 542
>gnl|CDD|165473 PHA03207, PHA03207, serine/threonine kinase US3; Provisional.
Length = 392
Score = 26.0 bits (57), Expect = 4.7
Identities = 14/38 (36%), Positives = 15/38 (39%), Gaps = 6/38 (15%)
Query: 20 RHPFTGPRFINNNGRVTDYEAEMRDRAQAKMWT-QQER 56
R P+T P I G D E AKM T QE
Sbjct: 333 RPPYTIPPVIRKYGMHMDVE-----YLIAKMLTFDQEF 365
>gnl|CDD|234319 TIGR03705, poly_P_kin, polyphosphate kinase 1. Members of this
protein family are the enzyme polyphosphate kinase 1
(PPK1). This family is found in many prokaryotes and
also in Dictyostelium. Sequences in the seed alignment
were taken from prokaryotic consecutive two-gene pairs
in which the other gene encodes an exopolyphosphatase.
It synthesizes polyphosphate from the terminal phosphate
of ATP but not GTP, in contrast to PPK2 [Central
intermediary metabolism, Phosphorus compounds].
Length = 672
Score = 25.9 bits (58), Expect = 6.3
Identities = 10/26 (38%), Positives = 12/26 (46%), Gaps = 2/26 (7%)
Query: 5 RRHSLSVIPPIICDPRHPFTGPRFIN 30
R V+ P+ DP HPF P N
Sbjct: 124 REEVFPVLTPLALDPAHPF--PFLPN 147
>gnl|CDD|184951 PRK14989, PRK14989, nitrite reductase subunit NirD; Provisional.
Length = 847
Score = 25.8 bits (57), Expect = 6.5
Identities = 11/23 (47%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 80 RTPSDCVEYYYLSKKRENYKRAI 102
RTP Y YL + +E YKR I
Sbjct: 339 RTP-GARSYVYLDESKEIYKRLI 360
>gnl|CDD|233343 TIGR01287, nifH, nitrogenase iron protein. This model describes
nitrogenase (EC 1.18.6.1) iron protein, also called
nitrogenase reductase or nitrogenase component II. This
model includes molybdenum-iron nitrogenase reductase
(nifH), vanadium-iron nitrogenase reductase (vnfH), and
iron-iron nitrogenase reductase (anfH). The model
excludes the homologous protein from the
light-independent protochlorophyllide reductase [Central
intermediary metabolism, Nitrogen fixation].
Length = 275
Score = 25.4 bits (56), Expect = 6.9
Identities = 22/81 (27%), Positives = 31/81 (38%), Gaps = 16/81 (19%)
Query: 32 NGRVTDYEAEMRDRAQAKMWTQQEREVFRDKYIHHQKNFGLIASFLERRT----PSDCV- 86
N R D E E+ D K+ TQ V R + + + + T +
Sbjct: 182 NSRNVDDEKELIDEFAKKLGTQLIHFVPRSNIVQKAE--------IRKMTVIEYDPESEQ 233
Query: 87 --EYYYLSKK-RENYKRAIPT 104
EY L+KK EN + IPT
Sbjct: 234 ANEYRELAKKIYENTEFVIPT 254
>gnl|CDD|217072 pfam02503, PP_kinase, Polyphosphate kinase middle domain.
Polyphosphate kinase (Ppk) catalyzes the formation of
polyphosphate from ATP, with chain lengths of up to a
thousand or more orthophosphate molecules.
Length = 204
Score = 25.1 bits (56), Expect = 9.1
Identities = 10/29 (34%), Positives = 14/29 (48%), Gaps = 3/29 (10%)
Query: 5 RRHSLSVIPPIICDPRHPFTGPRFINNNG 33
R V+ P+ DP HPF F++N
Sbjct: 12 REEVFPVLTPLAVDPAHPFP---FLSNLS 37
>gnl|CDD|164775 PHA00009, F, capsid protein.
Length = 427
Score = 25.2 bits (55), Expect = 9.6
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 46 AQAKMWTQQEREVFRDKYIHHQKNFG 71
A A++ T+QER+ F +Y +FG
Sbjct: 199 AYAQLHTEQERDYFMTRYRDIISSFG 224
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
0.322 0.136 0.419
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,054,201
Number of extensions: 513129
Number of successful extensions: 490
Number of sequences better than 10.0: 1
Number of HSP's gapped: 489
Number of HSP's successfully gapped: 27
Length of query: 114
Length of database: 10,937,602
Length adjustment: 78
Effective length of query: 36
Effective length of database: 7,477,990
Effective search space: 269207640
Effective search space used: 269207640
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 (21.9 bits)
S2: 53 (24.1 bits)