RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9276
(583 letters)
>gnl|CDD|148285 pfam06584, DIRP, DIRP. DIRP (Domain in Rb-related Pathway) is
postulated to be involved in the Rb-related pathway,
which is encoded by multiple eukaryotic genomes and is
present in proteins including lin-9 of Caenorhabditis
elegans, aly of fruit fly and mustard weed. Studies of
lin-9 and aly of fruit fly proteins containing DIRP
suggest that this domain might be involved in
development. Aly, lin-9, act in parallel to, or
downstream of, activation of MAPK by the RTK-Ras
signalling pathway.
Length = 109
Score = 129 bits (325), Expect = 1e-35
Identities = 51/109 (46%), Positives = 69/109 (63%), Gaps = 4/109 (3%)
Query: 175 FYSNIDRPLFNDNDFITCMKESFPQLKKYVFSRTEWSMVRRMVGKPRRCSSSFFTEERIN 234
FYS ID+P F DNDF+ ++E FP L +R EW ++RR +GKPRR S++F EER
Sbjct: 1 FYSAIDKPWFEDNDFVRYLREHFPLLHTRRLTRAEWRLIRRSMGKPRRFSAAFLKEEREK 60
Query: 235 LERRRNVIRYLQQGKCGDQTT----VKDIPSEIPIQLVVGTKVTARVRS 279
LER+R IR LQQ K + ++D+P ++P+ L VG KVTAR
Sbjct: 61 LERKREKIRQLQQLKLHYKELNVGLLEDLPKDVPLPLAVGQKVTARHPR 109
>gnl|CDD|227318 COG4985, COG4985, ABC-type phosphate transport system, auxiliary
component [Inorganic ion transport and metabolism].
Length = 289
Score = 31.8 bits (72), Expect = 0.79
Identities = 22/89 (24%), Positives = 40/89 (44%), Gaps = 8/89 (8%)
Query: 388 KFKKTEVYQIRDMNSEAE-------RRQLYGEPYDRAFQKKYAGHILRLEKINKDVNTVL 440
+ K Q+R +NS+ E R QL G+ D FQ+ Y L+K + T L
Sbjct: 179 QVDKMVEQQVRVINSQLERLRLEKRRLQLNGQ-LDDEFQQHYVAEKSELQKRLAQLQTEL 237
Query: 441 ASLSVNLKKLSVTSENMSSQLYALSPSDL 469
+L L++ + +M + ++ S++
Sbjct: 238 DALRAELERQFLYLVDMQGETVSVPLSEI 266
>gnl|CDD|149738 pfam08771, Rapamycin_bind, Rapamycin binding domain. This domain
forms an alpha helical structure and binds to rapamycin.
Length = 100
Score = 29.9 bits (68), Expect = 0.90
Identities = 11/23 (47%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 314 PDYEVLSNDTPETLNRQSFLQMF 336
P +E+L PETL SF+Q F
Sbjct: 39 PLHEMLEK-GPETLREISFVQQF 60
>gnl|CDD|223755 COG0683, LivK, ABC-type branched-chain amino acid transport
systems, periplasmic component [Amino acid transport and
metabolism].
Length = 366
Score = 31.3 bits (71), Expect = 1.4
Identities = 10/35 (28%), Positives = 17/35 (48%)
Query: 479 EIVDTVNKKNGNKIVDDQPVVSLITDLTALVLQIK 513
+ K G ++V ++ TD +ALV +IK
Sbjct: 166 DAFKAALKALGGEVVVEEVYAPGDTDFSALVAKIK 200
>gnl|CDD|184900 PRK14907, rplD, 50S ribosomal protein L4; Provisional.
Length = 295
Score = 29.9 bits (67), Expect = 3.3
Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 2/67 (2%)
Query: 80 PRVNKTPNKTPTKKATPNSKKKKTPTSLVKFSSSSKLQSTLTETPEKFNDSKLKGSKKSR 139
KT K T++ P KK TS + ++T T+ +K K S K+
Sbjct: 2 AETKKTTKKKTTEEKKP--AAKKATTSKETAKTKKTAKTTSTKAAKKAAKVKKTKSVKTT 59
Query: 140 VRCSSPD 146
+ +
Sbjct: 60 TKKVTVK 66
>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC. All proteins in this family for
which functions are known are part of an exonuclease
complex with sbcD homologs. This complex is involved in
the initiation of recombination to regulate the levels
of palindromic sequences in DNA. This family is based on
the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 1042
Score = 30.3 bits (68), Expect = 4.0
Identities = 18/99 (18%), Positives = 41/99 (41%), Gaps = 6/99 (6%)
Query: 375 ELLEQVVRFKKLLKFKKTEVYQIRDMNSEAERRQLYGEPYDRAFQK-KYAGHILRLEKIN 433
E E+ ++ ++LLK + + ++R + E Q E +RA + A HI + +I
Sbjct: 250 EAQEEQLKKQQLLKQLRARIEELRAQEAVLEETQ---ERINRARKAAPLAAHIKAVTQIE 306
Query: 434 KDVNTVLASLSVNLKKLSVTSENMSSQLYALSPSDLQQE 472
+ + L ++ M + S ++++
Sbjct: 307 QQAQRIHTELQSKMRSR--AKLLMKRAAHVKQQSSIEEQ 343
>gnl|CDD|171490 PRK12425, PRK12425, fumarate hydratase; Provisional.
Length = 464
Score = 29.9 bits (67), Expect = 4.5
Identities = 20/58 (34%), Positives = 27/58 (46%), Gaps = 6/58 (10%)
Query: 341 PNDHTNRTGKPE---PEAMD---ANHIDKELEGMLGEYPVELLEQVVRFKKLLKFKKT 392
PNDH NR+ P AM A + ++L + E L EQ R KL+K +T
Sbjct: 128 PNDHVNRSQSSNDCFPTAMHIAAAQAVHEQLLPAIAELSGGLAEQSARHAKLVKTGRT 185
>gnl|CDD|236355 PRK08943, PRK08943, lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA
acyltransferase; Validated.
Length = 314
Score = 29.5 bits (67), Expect = 4.6
Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 4/38 (10%)
Query: 354 EAMDANHIDKELEGMLGEYPVELLEQVVRFKKLLKFKK 391
+ A +++E+E +G +P EQ + KLLK +K
Sbjct: 274 DETIARRMNEEVEQFVGPHP----EQYMWILKLLKTRK 307
>gnl|CDD|236912 PRK11448, hsdR, type I restriction enzyme EcoKI subunit R;
Provisional.
Length = 1123
Score = 29.9 bits (68), Expect = 5.2
Identities = 20/56 (35%), Positives = 27/56 (48%), Gaps = 8/56 (14%)
Query: 4 DPPIQHQEIIEEGLREE----EVGLEPDLSKVKEEVIIKMEPEDDVDPEAESLNRR 55
+PPI+ IE L +E E G E ++ + I ED+VD E E NRR
Sbjct: 624 EPPIR----IETRLSQEGIHFEKGEEVEVINTQTGEIDLATLEDEVDFEVEDFNRR 675
>gnl|CDD|226889 COG4487, COG4487, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 438
Score = 29.4 bits (66), Expect = 5.3
Identities = 20/87 (22%), Positives = 31/87 (35%), Gaps = 5/87 (5%)
Query: 375 ELLEQVVRFKKLLKFKKTEVYQIRDMNSEAERRQLYGEPYDRAFQKKYAGHILRLEKINK 434
L + R + + T+V I +E E A +K L LEK K
Sbjct: 330 IALIGLFRNRAAQELALTKVQIIYYYLTEKEFEAF-----VEAIDEKLENTQLDLEKEKK 384
Query: 435 DVNTVLASLSVNLKKLSVTSENMSSQL 461
+ ++KL ++ENM L
Sbjct: 385 AIIRAWKKREKEIEKLIESTENMLGSL 411
>gnl|CDD|240667 cd11657, TIN2_N, N-terminal domain of TRF-interacting nuclear
factor 2; shelterin complex protein of telomeres. TIN2
is one of the six proteins of shelterin complex, which
acts to protect telomeres from DNA damage repair
machinery. TIN2 binds directly to TRF1 and TRF2 and
stabilizes TRF2 complex-telomere binding by tethering it
to the TRF1 complex. TIN2 binding to TRF2 is primarily
via the TRF binding motif (TBM) region and the
N-terminus, while the far C-terminal region has lower
affinity. The TIN2 TBM, but not the N-terminal region,
is involved in TIN2 binding to TRF1. Truncation of the
TIN2 N-terminus in mouse results in telomere elongation,
suggesting a negative regulatory function of this
region. Three shelterin components (TRF1, TRF2, POT1)
bind DNA and 3 components (TIN2, RAP1, TPP1) are
recruited by these DNA binding factors. TRF1 activity at
telomeres is regulated in part by selective
ubiquitination and degradation. Ubiquitination of TRF1
is mediated by Fbx4, which binds TRF1 in the TRFH
domain, via a small GTPase module. When bound to
telomeres, TIN2 acts to protect TRF1 from SCF-Fbx4
mediated ubiquitination. F-box proteins act in substrate
recognition as part of Skp1-Cul1-Rbx1-F- box (SCF)
protein complexes. Tankyrase-mediated ADP-ribosylation
releases TRF1 from telomeres, rendering them susceptible
to ubiquitination and degradation, promoting telomere
elongation. TIN2 also binds PIP1, which recruits POT1 to
telomeres.
Length = 188
Score = 28.8 bits (65), Expect = 5.5
Identities = 15/64 (23%), Positives = 28/64 (43%), Gaps = 11/64 (17%)
Query: 374 VELLEQVVRFKKLLK-----FKKTEVYQIRDMNSEAERRQLYGEPYDRAFQKKYAGHILR 428
+ E + F +L++ ++ E + E YGE +D+A +K + R
Sbjct: 93 ALMEEPQLNFLQLVQSLLKDPEEREHFFQEVFPVE------YGEEFDQALEKLLWEFLSR 146
Query: 429 LEKI 432
LEK+
Sbjct: 147 LEKL 150
>gnl|CDD|192217 pfam09150, Carot_N, Orange carotenoid protein, N-terminal. Members
of this family adopt an alpha-helical structure
consisting of two four-helix bundles. They are
predominantly found in prokaryotic orange carotenoid
protein, and carotenoid binding proteins.
Length = 159
Score = 28.2 bits (63), Expect = 8.1
Identities = 16/59 (27%), Positives = 25/59 (42%), Gaps = 3/59 (5%)
Query: 506 TALVLQIKTLSHSSRSAYEVEVLNKTMSDI---YKKLSPNNQSVFENCIGVHMEQIKAA 561
L+ QIK LS + ++ + + + Y LSPN + F + MEQ A
Sbjct: 59 EGLLGQIKALSFEEQLQVMRDLARREDTPLSREYGSLSPNTKLGFWYQLAELMEQGTVA 117
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
0.314 0.131 0.363
Gapped
Lambda K H
0.267 0.0538 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 29,363,698
Number of extensions: 2885092
Number of successful extensions: 2037
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2018
Number of HSP's successfully gapped: 38
Length of query: 583
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 481
Effective length of database: 6,413,494
Effective search space: 3084890614
Effective search space used: 3084890614
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 62 (28.1 bits)