RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8537
(102 letters)
>gnl|CDD|201444 pfam00788, RA, Ras association (RalGDS/AF-6) domain. RasGTP
effectors (in cases of AF6, canoe and RalGDS); putative
RasGTP effectors in other cases. Recent evidence (not
yet in MEDLINE) shows that some RA domains do NOT bind
RasGTP. Predicted structure similar to that determined,
and that of the RasGTP-binding domain of Raf kinase.
Length = 87
Score = 30.4 bits (69), Expect = 0.045
Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 9/69 (13%)
Query: 2 ELKVWVE----GMQKIVSGVTESTTCQDIVFALA---HATGKTGRYTLI-ERFRNNERLL 53
L+V+ E G K + V+ +TT Q+++ A Y L+ ER+L
Sbjct: 1 VLRVYTEDGTPGTYKTIL-VSSTTTAQEVIRAALKKFGLADDPEDYVLVVLERGGEERVL 59
Query: 54 TPQDHPIKL 62
+ P+++
Sbjct: 60 PDDEKPLQI 68
>gnl|CDD|176363 cd01768, RA, RA (Ras-associating) ubiquitin domain. The RA
(Ras-associating) domain is structurally similar to
ubiquitin and is present in one or two copies in a
number of signalling molecules that bind and regulate a
small GTPase called Ras or the Ras-related GTPases, Ral
and Rap. RA-containing proteins include RalGDS, AF6,
RIN1, RASSF1, SNX27, CYR1, STE50, and phospholipase C
epsilon.
Length = 87
Score = 27.3 bits (61), Expect = 0.71
Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 5/63 (7%)
Query: 17 VTESTTCQDIVFALA---HATGKTGRYTLIERF--RNNERLLTPQDHPIKLIKFSHKFTD 71
V++ TT QD++ L Y L+E ERLL P + P+++ + + +
Sbjct: 19 VSKDTTAQDVIQQLLKKFGLDDDPEDYALVEVLGDGGLERLLLPDECPLQIQLNAPRQRE 78
Query: 72 NTS 74
+
Sbjct: 79 DLR 81
>gnl|CDD|213244 cd03277, ABC_SMC5_euk, ATP-binding cassette domain of eukaryotic
SMC5 proteins. The structural maintenance of
chromosomes (SMC) proteins are large (approximately 110
to 170 kDa), and each is arranged into five recognizable
domains. Amino-acid sequence homology of SMC proteins
between species is largely confined to the amino- and
carboxy-terminal globular domains. The amino-terminal
domain contains a 'Walker A' nucleotide-binding domain
(GxxGxGKS/T, in the single-letter amino-acid code),
which by mutational studies has been shown to be
essential in several proteins. The carboxy-terminal
domain contains a sequence (the DA-box) that resembles a
'Walker B' motif, and a motif with homology to the
signature sequence of the ATP-binding cassette (ABC)
family of ATPases. The sequence homology within the
carboxy-terminal domain is relatively high within the
SMC1-SMC4 group, whereas SMC5 and SMC6 show some
divergence in both of these sequences. In eukaryotic
cells, the proteins are found as heterodimers of SMC1
paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6
(formerly known as Rad18).
Length = 213
Score = 26.4 bits (59), Expect = 2.7
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 17/46 (36%)
Query: 41 TLIERFRNNERL--LTPQDHPIKLIKFSHKFTDNTSGGEKSVKTIF 84
L+ +FR E+L L P H+ SGGE+SV T+
Sbjct: 108 ELLVKFREGEQLQELDPH----------HQ-----SGGERSVSTML 138
>gnl|CDD|215418 PLN02782, PLN02782, Branched-chain amino acid aminotransferase.
Length = 403
Score = 26.3 bits (58), Expect = 2.7
Identities = 16/39 (41%), Positives = 18/39 (46%), Gaps = 9/39 (23%)
Query: 59 PIKLIKFSHKFTDNTSGGEKSVKTIFISPGWEWKNYAHV 97
PI LI ++F T GG VKTI NYA V
Sbjct: 228 PINLI-VENEFHRATPGGTGGVKTI--------GNYAAV 257
>gnl|CDD|198358 cd07781, FGGY_RBK, Ribulokinases; belongs to the FGGY family of
carbohydrate kinases. This subgroup is predominantly
composed of bacterial ribulokinases (RBK) which catalyze
the MgATP-dependent phosphorylation of L(or D)-ribulose
to produce L(or D)-ribulose 5-phosphate and ADP. RBK
also phosphorylates a variety of other sugar substrates
including ribitol and arabitol. The reason why L-RBK can
phosphorylate so many different substrates is not yet
clear. The presence of Mg2+ is required for catalytic
activity. This group belongs to the FGGY family of
carbohydrate kinases, the monomers of which contain two
large domains, which are separated by a deep cleft that
forms the active site. This model includes both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
Length = 498
Score = 26.4 bits (59), Expect = 2.9
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 13 IVSGVTESTTCQDIVFALAHATGKTGRYTLIERFRNN 49
++ G+T T ++I AL AT G +IERF
Sbjct: 397 LILGLTLQTKAEEIYRALIEATA-FGARAIIERFEEQ 432
>gnl|CDD|163640 cd07397, MPP_DevT, Myxococcus xanthus DevT and related proteins,
metallophosphatase domain. DevT is a component in the
C-signal response pathway in Myxococcus xanthus that
stimulates the developmentally regulated expression of
the FruA response regulator protein and is required for
methylation of FrzCD during fruiting body formation.
DevT mutants having an in-frame deletion in the devT
gene, display delayed aggregation and a cell autonomous
sporulation defect. DevT belongs to the
metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but all share a conserved domain
with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 238
Score = 25.4 bits (56), Expect = 6.6
Identities = 8/31 (25%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 8 EGMQKIVSGVTESTTCQDIVFALAHATGKTG 38
E Q+I++ ++ ++ LAH G +G
Sbjct: 131 ESAQRIIAAAKKAPPDLPLIL-LAHN-GPSG 159
>gnl|CDD|220155 pfam09258, Glyco_transf_64, Glycosyl transferase family 64 domain.
Members of this family catalyze the transfer reaction of
N-acetylglucosamine and N-acetylgalactosamine from the
respective UDP-sugars to the non-reducing end of
[glucuronic acid]beta 1-3[galactose]beta
1-O-naphthalenemethanol, an acceptor substrate analog of
the natural common linker of various
glycosylaminoglycans. They are also required for the
biosynthesis of heparan-sulphate.
Length = 244
Score = 25.3 bits (56), Expect = 7.0
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 10 MQKIVSGVTESTTCQDIV--FALAHATGK 36
+ I V E+ C+DI+ F +A+ TGK
Sbjct: 157 PKSIRDLVDETRNCEDILMNFLVANVTGK 185
>gnl|CDD|235239 PRK04172, pheS, phenylalanyl-tRNA synthetase subunit alpha;
Provisional.
Length = 489
Score = 25.2 bits (56), Expect = 7.0
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 46 FRNNERLLTPQDHP 59
F N + L PQDHP
Sbjct: 263 FWNFDALFQPQDHP 276
>gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit.
Length = 1070
Score = 25.2 bits (56), Expect = 7.1
Identities = 9/38 (23%), Positives = 14/38 (36%), Gaps = 10/38 (26%)
Query: 35 GKTGRYTLIERFR----NNERLLTPQD------HPIKL 62
G+ GR + + N L PQD + I +
Sbjct: 259 GRIGRRNMNRKLNLDIPENNTFLLPQDVLAAADYLIGM 296
>gnl|CDD|176370 cd01775, CYR1_RA, Ubiquitin domain of CYR1 adenylate cyclase.
CYR1 is a fungal adenylate cyclase with at least four
domains, an N-terminal RA (Ras association) domain, a
middle leucine-rich repeat domain, a catalytic domain.
The N-terminal RA domain of CYR1 post-translationally
modifies a small GTPase called Ras. The Ras-CYR1
pathway has been implicated in the transduction of a
glucose-triggered signal to an intracellular
environment where a protein phosphorylation cascade is
initiated by cyclic AMP.
Length = 97
Score = 24.7 bits (54), Expect = 7.6
Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 2/46 (4%)
Query: 21 TTCQDIVFALAHAT--GKTGRYTLIERFRNNERLLTPQDHPIKLIK 64
TT +++ LA G Y L + + R+L P + P+ + K
Sbjct: 23 TTVSELIPQLAKKFYLPSGGNYQLSLKKHDLSRVLRPTEKPLLIQK 68
>gnl|CDD|238277 cd00496, PheRS_alpha_core, Phenylalanyl-tRNA synthetase (PheRS)
alpha chain catalytic core domain. PheRS belongs to
class II aminoacyl-tRNA synthetases (aaRS) based upon
its structure and the presence of three characteristic
sequence motifs. This domain is primarily responsible
for ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. While class II aaRSs generally
aminoacylate the 3'-OH ribose of the appropriate tRNA,
PheRS is an exception in that it attaches the amino
acid at the 2'-OH group, like class I aaRSs. PheRS is
an alpha-2/ beta-2 tetramer.
Length = 218
Score = 24.8 bits (55), Expect = 7.8
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 46 FRNNERLLTPQDHP 59
F N + L PQDHP
Sbjct: 31 FYNFDALNIPQDHP 44
>gnl|CDD|227411 COG5079, SAC3, Nuclear protein export factor [Intracellular
trafficking and secretion / Cell division and
chromosome partitioning].
Length = 646
Score = 25.3 bits (55), Expect = 8.2
Identities = 12/56 (21%), Positives = 20/56 (35%)
Query: 4 KVWVEGMQKIVSGVTESTTCQDIVFALAHATGKTGRYTLIERFRNNERLLTPQDHP 59
+ MQ VS + + L +T T + L+++ R ER L
Sbjct: 9 RSHKARMQAPVSKDRFDLGMRVFMVLLFSSTLDTNPFELLKKLRAKERELLEAKSA 64
>gnl|CDD|234153 TIGR03270, methan_mark_4, putative methanogen marker protein 4.
Members of this protein family, to date, are found in a
completed prokaryotic genome if and only if the species
is one of the archaeal methanogens. The exact function
is unknown, but likely is linked to methanogenesis or a
process closely linked to it. Some members have been
suggested to be a methyltransferase, based on the
proximity of its gene to genes of the multi-subunit
complex, N5-methyl-tetrahydromethanopterin--coenzyme M
methyltransferase. That context is not conserved,
however. The family shows similarity to various
phosphate acyltranferases [Energy metabolism,
Methanogenesis].
Length = 202
Score = 25.0 bits (55), Expect = 8.5
Identities = 15/71 (21%), Positives = 24/71 (33%), Gaps = 17/71 (23%)
Query: 26 IVFALAHATGKTGRYTLIERFRNNERLLTPQ--------DHPIKLIKFSHKFTDNT---- 73
+ L A GK R +++E LL P +K+I+ + +F
Sbjct: 32 TIRELKKALGKIYRASILETADGRIFLLAPVGIDEGWTISDKVKIIELASEFLRRLGREP 91
Query: 74 -----SGGEKS 79
SGG
Sbjct: 92 KVAVLSGGRLG 102
>gnl|CDD|213580 TIGR01060, eno, phosphopyruvate hydratase. Alternate name: enolase
[Energy metabolism, Glycolysis/gluconeogenesis].
Length = 425
Score = 25.0 bits (55), Expect = 9.1
Identities = 16/48 (33%), Positives = 21/48 (43%), Gaps = 3/48 (6%)
Query: 9 GMQKIVS---GVTESTTCQDIVFALAHATGKTGRYTLIERFRNNERLL 53
G ++S G TE TT D+ A KTG + ER +LL
Sbjct: 357 GYTAVISHRSGETEDTTIADLAVATNAGQIKTGSLSRSERIAKYNQLL 404
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
0.319 0.133 0.406
Gapped
Lambda K H
0.267 0.0746 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,123,972
Number of extensions: 411861
Number of successful extensions: 347
Number of sequences better than 10.0: 1
Number of HSP's gapped: 347
Number of HSP's successfully gapped: 19
Length of query: 102
Length of database: 10,937,602
Length adjustment: 68
Effective length of query: 34
Effective length of database: 7,921,530
Effective search space: 269332020
Effective search space used: 269332020
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 (21.8 bits)
S2: 53 (24.2 bits)