RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7828
(503 letters)
>gnl|CDD|215997 pfam00566, RabGAP-TBC, Rab-GTPase-TBC domain. Identification of a
TBC domain in GYP6_YEAST and GYP7_YEAST, which are
GTPase activator proteins of yeast Ypt6 and Ypt7,
implies that these domains are GTPase activator proteins
of Rab-like small GTPases.
Length = 206
Score = 75.9 bits (187), Expect = 7e-16
Identities = 53/244 (21%), Positives = 93/244 (38%), Gaps = 46/244 (18%)
Query: 238 LRGKIWCQVLGSEATPDNSKYFEQLKSSVLTYDLLIDKLTIKDVQLTASNDDQYFVFE-- 295
LRG++W +LG+ + Q + D ++ KDV T + +F
Sbjct: 3 LRGEVWKLLLGNLSESKQRDSVSQYSKLLKLEDSPDEEQIEKDVPRTFPHHF-FFKNGEG 61
Query: 296 -DLLYQILLCFSRDTEILSIFEHSSASPLYGPLKNKNTNTENLVVYPPSGIIPFHGFTMY 354
L +IL +S N + V Y G
Sbjct: 62 QQQLRRILKAYS------------------------IYNPD--VGY-------CQGMNFI 88
Query: 355 ATPFCYLYDDVISLYFTFRA---FYLRYFYHLHQVSSNEQGILSLCILFHRLLQRYEPQL 411
A P + D ++ F + + LR F+ + G+ +F LL++++P+L
Sbjct: 89 AAPLLLVVLDEEEAFWCFVSLLEYLLRDFF-----LPSFPGLQRDLYVFEELLKKHDPEL 143
Query: 412 FLHFKTIHIHPIKIVFKWIMRCFSGHLPPDQILYLWDLILAYDSLEIISILAVAILSFRR 471
+ H + + + P KW + F+ LP + +L LWDL L + + A+AIL R
Sbjct: 144 YKHLQKLGLDPSLFASKWFLTLFARELPLETVLRLWDLFLEGGKFFLFRV-ALAILKRFR 202
Query: 472 ENLM 475
+ L+
Sbjct: 203 KELL 206
>gnl|CDD|214540 smart00164, TBC, Domain in Tre-2, BUB2p, and Cdc16p. Probable
Rab-GAPs. Widespread domain present in Gyp6 and Gyp7,
thereby giving rise to the notion that it performs a
GTP-activator activity on Rab-like GTPases.
Length = 216
Score = 65.8 bits (161), Expect = 3e-12
Identities = 51/251 (20%), Positives = 95/251 (37%), Gaps = 42/251 (16%)
Query: 231 KKGSPRCLRGKIWCQVLG--SEATPDNSKYFEQLKSSVLTYDLLIDKLTIKDVQLTASND 288
+KG P LRG +W +L T + + +L D I KD++ T
Sbjct: 2 RKGVPPSLRGVVWKLLLNAQPMDTSADKDLYSRLLKETAPDDKSIVHQIEKDLRRTFPEH 61
Query: 289 ----DQYFVFEDLLYQILLCFSRDTEILSIFEHSSASPLYGPLKNKNTNTENLVVYPPSG 344
D+ ++ L ++L ++ L N V Y
Sbjct: 62 SFFQDKEGPGQESLRRVLKAYA--------------------LYNPE------VGYCQ-- 93
Query: 345 IIPFHGFTMYATPFCYLYDDVISLYFTFRAFYLRYFYHLHQVSSNEQGILSLCILFHRLL 404
G A P + +D ++ RY + + + G+ + RL+
Sbjct: 94 -----GMNFLAAPLLLVMEDEEDAFWCLVKLMERYGPNFY--LPDMSGLQLDLLQLDRLV 146
Query: 405 QRYEPQLFLHFKTIHIHPIKIVFKWIMRCFSGHLPPDQILYLWDLILAYDSLEIISILAV 464
+ Y+P L+ H K + I P +W + F+ LP + +L +WD +L + + + +A+
Sbjct: 147 KEYDPDLYKHLKDLGITPSLYALRWFLTLFARELPLEIVLRIWD-VLFAEGSDFLFRVAL 205
Query: 465 AILSFRRENLM 475
A+L R+ L+
Sbjct: 206 ALLKLHRDVLL 216
>gnl|CDD|227535 COG5210, COG5210, GTPase-activating protein [General function
prediction only].
Length = 496
Score = 51.7 bits (124), Expect = 5e-07
Identities = 51/270 (18%), Positives = 101/270 (37%), Gaps = 53/270 (19%)
Query: 227 QEFLKKGSPRCLRGKIWCQVLGSEATPDNSKYFEQLKSSVLTYDLLIDKLTI-------K 279
+E ++KG P LRG +W +LG D + + L T K
Sbjct: 206 RELIRKGIPNELRGDVWEFLLGIGFDLDKNPGLYERL---LNLHREAKIPTQEIISQIEK 262
Query: 280 DVQLTASNDDQYFVFE----DLLYQILLCFS-RDTEILSIFEHSS-ASPLYGPLKNKNTN 333
D+ T ++ + + L ++L +S + E+ + + A+PL L+++
Sbjct: 263 DLSRTFPDNSLFQTEISIRAENLRRVLKAYSLYNPEVGYVQGMNFLAAPLLLVLESEEQA 322
Query: 334 TENLVVYPPSGIIPFHGFTMYATPFCYLYDDVISLYFTFRAFYLRYFYHLHQVSSNEQGI 393
LV + + L Y L +S G+
Sbjct: 323 FWCLV-------------------------------KLLKNYGLP-GYFLKNLS----GL 346
Query: 394 LSLCILFHRLLQRYEPQLFLHFKTIHIHPIKIVFKWIMRCFSGHLPPDQILYLWDLILAY 453
+ L++ +P+L+ H + + F+W + F P + L +WD +
Sbjct: 347 HRDLKVLDDLVEELDPELYEHLLREGVVLLMFAFRWFLTLFVREFPLEYALRIWDCLFLE 406
Query: 454 DSLEIISILAVAILSFRRENLMQVDTLQNV 483
S ++ LA+AIL R+ L+++D+ + +
Sbjct: 407 GS-SMLFQLALAILKLLRDKLLKLDSDELL 435
>gnl|CDD|236144 PRK08057, PRK08057, cobalt-precorrin-6x reductase; Reviewed.
Length = 248
Score = 32.1 bits (74), Expect = 0.50
Identities = 10/31 (32%), Positives = 13/31 (41%)
Query: 96 CNEIGIQLSRFRLPSDRDDMKDKWTELSTYE 126
C +GI R PS D+W E+ E
Sbjct: 88 CRALGIPYLRLERPSWLPQPGDRWIEVDDIE 118
>gnl|CDD|239755 cd04088, EFG_mtEFG_II, EFG_mtEFG_II: this subfamily represents the
domain II of elongation factor G (EF-G) in bacteria and,
the C-terminus of mitochondrial Elongation factor G1
(mtEFG1) and G2 (mtEFG2)_like proteins found in
eukaryotes. During the process of peptide synthesis and
tRNA site changes, the ribosome is moved along the mRNA
a distance equal to one codon with the addition of each
amino acid. In bacteria this translocation step is
catalyzed by EF-G_GTP, which is hydrolyzed to provide
the required energy. Thus, this action releases the
uncharged tRNA from the P site and transfers the newly
formed peptidyl-tRNA from the A site to the P site.
Eukaryotic cells harbor 2 protein synthesis systems: one
localized in the cytoplasm, the other in the
mitochondria. Most factors regulating mitochondrial
protein synthesis are encoded by nuclear genes,
translated in the cytoplasm, and then transported to the
mitochondria. The eukaryotic system of elongation factor
(EF) components is more complex than that in
prokaryotes, with both cytoplasmic and mitochondrial
elongation factors and multiple isoforms being expressed
in certain species. mtEFG1 and mtEFG2 show significant
homology to bacterial EF-Gs. Mutants in yeast mtEFG1
have impaired mitochondrial protein synthesis,
respiratory defects and a tendency to lose mitochondrial
DNA. No clear phenotype has been found for mutants in
the yeast homologue of mtEFG2, MEF2.
Length = 83
Score = 29.4 bits (67), Expect = 1.0
Identities = 14/33 (42%), Positives = 17/33 (51%), Gaps = 6/33 (18%)
Query: 415 FKTIHIHPI--KIVFKWIMRCFSGHLPPDQILY 445
FKTIH P K+ F +R +SG L LY
Sbjct: 6 FKTIH-DPFVGKLSF---VRVYSGTLKAGSTLY 34
>gnl|CDD|164902 PHA02115, PHA02115, hypothetical protein.
Length = 105
Score = 28.9 bits (64), Expect = 2.3
Identities = 13/46 (28%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 88 IQKSLNSMCNEIGIQLSRFRLPSD-RDDMKDKWTELSTYEVDLTQY 132
IQK + + +G++ S F++PS + K W+ + +E + T Y
Sbjct: 3 IQKEIQEIEKRLGVEASEFKMPSVWKVARKPGWSYGAVFEQEFTAY 48
>gnl|CDD|221856 pfam12922, Cnd1_N, non-SMC mitotic condensation complex subunit 1,
N-term. The three non-SMC (structural maintenance of
chromosomes) subunits of the mitotic condensation
complex are Cnd1-3. The whole complex is essential for
viability and the condensing of chromosomes in mitosis.
This is the conserved N-terminus of the subunit 1.
Length = 169
Score = 29.5 bits (67), Expect = 2.6
Identities = 9/34 (26%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 82 FQWEKRIQKSLNSMCNEIGIQLSR-FRLPSDRDD 114
++WE + +++L + + + LSR F +RD
Sbjct: 90 WKWEAQRERALELIAKVLQLDLSRLFGTTPERDT 123
>gnl|CDD|223652 COG0579, COG0579, Predicted dehydrogenase [General function
prediction only].
Length = 429
Score = 29.5 bits (67), Expect = 3.9
Identities = 9/43 (20%), Positives = 16/43 (37%)
Query: 197 NNPNPYFNALESERITLGEKVLNSKHAPVAQEFLKKGSPRCLR 239
P+P ++ + L EKV + + LK+ P
Sbjct: 381 LGPSPGASSAVPIMLRLLEKVFEERARSEWEPKLKEIVPSYGE 423
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
0.323 0.139 0.426
Gapped
Lambda K H
0.267 0.0731 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,803,245
Number of extensions: 2515929
Number of successful extensions: 2057
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2056
Number of HSP's successfully gapped: 22
Length of query: 503
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 402
Effective length of database: 6,457,848
Effective search space: 2596054896
Effective search space used: 2596054896
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 61 (27.3 bits)