RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10818
(274 letters)
>gnl|CDD|216025 pfam00617, RasGEF, RasGEF domain. Guanine nucleotide exchange
factor for Ras-like small GTPases.
Length = 185
Score = 151 bits (385), Expect = 7e-46
Identities = 51/117 (43%), Positives = 74/117 (63%), Gaps = 1/117 (0%)
Query: 129 LSALEIAEQMTYIDYHIFKSIRSEEFFGQAWLKSEKLTKAPHIVLFTQRFNTMSKLVANE 188
L LE+A Q+T I+ +F +I E AW K + +P+I F RFN +S+ VA E
Sbjct: 3 LDPLELARQLTLIESELFSAIDPRELLDSAWGKKDS-KLSPNIEAFISRFNQLSRWVATE 61
Query: 189 ILNRSNMSQRVHVIEKWIAVANILRFLNNFNGVLTIISAMNNSSVFRLKKTWDKVSK 245
IL+ ++ +R VI+K+I +A R LNNFN ++ IIS +N+S + RLKKTW+ VSK
Sbjct: 62 ILSEEDLKKRAKVIKKFIKIAQHCRELNNFNSLMAIISGLNSSPISRLKKTWELVSK 118
>gnl|CDD|238087 cd00155, RasGEF, Guanine nucleotide exchange factor for Ras-like
small GTPases. Small GTP-binding proteins of the Ras
superfamily function as molecular switches in
fundamental events such as signal transduction,
cytoskeleton dynamics and intracellular trafficking.
Guanine-nucleotide-exchange factors (GEFs) positively
regulate these GTP-binding proteins in response to a
variety of signals. GEFs catalyze the dissociation of
GDP from the inactive GTP-binding proteins. GTP can then
bind and induce structural changes that allow
interaction with effectors.
Length = 237
Score = 126 bits (318), Expect = 2e-35
Identities = 47/124 (37%), Positives = 78/124 (62%), Gaps = 1/124 (0%)
Query: 126 IETLSALEIAEQMTYIDYHIFKSIRSEEFFGQAW-LKSEKLTKAPHIVLFTQRFNTMSKL 184
+L E+AEQ+T +D+ +F+ I E G W K + + +P++ F +RFN +S
Sbjct: 1 FLSLDPKELAEQLTLLDFELFRKIEPFELLGSLWSKKDKNIHLSPNLERFIERFNNLSNW 60
Query: 185 VANEILNRSNMSQRVHVIEKWIAVANILRFLNNFNGVLTIISAMNNSSVFRLKKTWDKVS 244
VA+EIL +N +R ++ K+I VA R LNNFN ++ I+SA+++S + RLKKTW+ +S
Sbjct: 61 VASEILLCTNPKKRARLLSKFIQVAKHCRELNNFNSLMAIVSALSSSPISRLKKTWEVLS 120
Query: 245 KTVR 248
++
Sbjct: 121 SKLK 124
>gnl|CDD|214539 smart00147, RasGEF, Guanine nucleotide exchange factor for Ras-like
small GTPases.
Length = 242
Score = 123 bits (312), Expect = 2e-34
Identities = 47/121 (38%), Positives = 73/121 (60%), Gaps = 1/121 (0%)
Query: 126 IETLSALEIAEQMTYIDYHIFKSIRSEEFFGQAWLKSEKLTKAPH-IVLFTQRFNTMSKL 184
+ L E+AEQ+T +D+ +F+ I E G W K K + +P + F +RFN +S
Sbjct: 1 LLLLDPKELAEQLTLLDFELFRKIDPSELLGSVWGKRSKKSPSPLNLEAFIRRFNEVSNW 60
Query: 185 VANEILNRSNMSQRVHVIEKWIAVANILRFLNNFNGVLTIISAMNNSSVFRLKKTWDKVS 244
VA EIL ++ R ++ K+I VA R LNNFN ++ I+SA+++S + RLKKTW+K+
Sbjct: 61 VATEILKQTTPKDRAELLSKFIQVAKHCRELNNFNSLMAIVSALSSSPISRLKKTWEKLP 120
Query: 245 K 245
Sbjct: 121 S 121
>gnl|CDD|100121 cd06224, REM, Guanine nucleotide exchange factor for Ras-like
GTPases; N-terminal domain (RasGef_N), also called REM
domain (Ras exchanger motif). This domain is common in
nucleotide exchange factors for Ras-like small GTPases
and is typically found immediately N-terminal to the
RasGef (Cdc25-like) domain. REM contacts the GTPase and
is assumed to participate in the catalytic activity of
the exchange factor. Proteins with the REM domain
include Sos1 and Sos2, which relay signals from
tyrosine-kinase mediated signalling to Ras, RasGRP1-4,
RasGRF1,2, CNrasGEF, and RAP-specific nucleotide
exchange factors, to name a few.
Length = 122
Score = 43.2 bits (102), Expect = 1e-05
Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 3/80 (3%)
Query: 22 DISPVEEVRNKRKESVLSTARTMQVLNVLQHWISKHTQDFIQDKELRYMTLEFLEEIVCT 81
+I+P E + + S ++VLNVL+ W+ + DF D+EL + EFL +V
Sbjct: 46 EIAPPENLEYNDWDKKKSKPIRLRVLNVLRTWVENYPYDFFDDEELLELLEEFLNRLVQE 105
Query: 82 PNLLPAEYKAATQLTQMLTK 101
LL + L ++L
Sbjct: 106 GALLQ---ELKKLLRKLLKL 122
>gnl|CDD|214571 smart00229, RasGEFN, Guanine nucleotide exchange factor for
Ras-like GTPases; N-terminal motif. A subset of guanine
nucleotide exchange factor for Ras-like small GTPases
appear to possess this domain N-terminal to the RasGef
(Cdc25-like) domain. The recent crystal structureof Sos
shows that this domain is alpha-helical and plays a
"purely structural role" (Nature 394, 337-343).
Length = 127
Score = 39.2 bits (92), Expect = 4e-04
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 3/54 (5%)
Query: 25 PVEEVRNKRKESVLSTARTMQVLNVLQHWISKHTQDFIQDKELRYMTLEFLEEI 78
P E ++ R VLN+L+ W+ + +DF D +L LEFLE +
Sbjct: 57 PPESWVEEKVNPRRVKNR---VLNILRTWVENYWEDFEDDPKLISFLLEFLELV 107
>gnl|CDD|216026 pfam00618, RasGEF_N, RasGEF N-terminal motif. A subset of
guanine nucleotide exchange factor for Ras-like small
GTPases appear to possess this motif/domain N-terminal
to the RasGef (Cdc25-like) domain.
Length = 94
Score = 30.8 bits (70), Expect = 0.19
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 4/40 (10%)
Query: 39 STARTMQVLNVLQHWISKHTQDFIQDKELRYMTLEFLEEI 78
++VLNVL+ WI + DF+ D EL L LEE
Sbjct: 59 YQEIRIRVLNVLRKWIENYNSDFVDDPEL----LSLLEEF 94
>gnl|CDD|219782 pfam08292, RNA_pol_Rbc25, RNA polymerase III subunit Rpc25.
Rpc25 is a strongly conserved subunit of RNA polymerase
III and has homology to Rpa43 in RNA polymerase I, Rpb7
in RNA polymerase II and the archaeal RpoE subunit.
Rpc25 is required for transcription initiation and is
not essential for the elongating properties of RNA
polymerase III.
Length = 121
Score = 28.8 bits (65), Expect = 1.1
Identities = 11/48 (22%), Positives = 22/48 (45%), Gaps = 8/48 (16%)
Query: 49 VLQHWISKHTQDFIQDKELRYMTLEFLEEIVCTPNLL--PAEYKAATQ 94
+L I + + I+ ++L F ++I P+ L P+E+ Q
Sbjct: 6 ILTGKIKSSSAEGIK------VSLGFFDDIFIPPDNLPEPSEFDEEEQ 47
>gnl|CDD|226759 COG4309, COG4309, Uncharacterized conserved protein [Function
unknown].
Length = 98
Score = 27.1 bits (60), Expect = 4.0
Identities = 15/63 (23%), Positives = 25/63 (39%), Gaps = 5/63 (7%)
Query: 112 DLLAPPPQVANKENIETLSALEIAEQMTYIDYHIFKSIRSE---EFFGQAWLKSEKLTKA 168
D+ PP+ + L L+ E + I H + +R + EF G+ E L
Sbjct: 11 DVRPIPPRERHPLIFSMLGKLKEGESLEIISDHDPRPLRYQLSTEFPGK--FGWEYLENG 68
Query: 169 PHI 171
P +
Sbjct: 69 PEV 71
>gnl|CDD|173907 cd00814, MetRS_core, catalytic core domain of methioninyl-tRNA
synthetases. Methionine tRNA synthetase (MetRS)
catalytic core domain. This class I enzyme aminoacylates
the 2'-OH of the nucleotide at the 3' of the appropriate
tRNA. MetRS, which consists of the core domain and an
anti-codon binding domain, functions as a monomer.
However, in some species the anti-codon binding domain
is followed by an EMAP domain. In this case, MetRS
functions as a homodimer. The core domain is based on
the Rossman fold and is responsible for the
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in ATP
binding. As a result of a deletion event, MetRS has a
significantly shorter core domain insertion than IleRS,
ValRS, and LeuR. Consequently, the MetRS insertion
lacks the editing function.
Length = 319
Score = 27.9 bits (63), Expect = 6.2
Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 50 LQHWISKHTQDFIQDKELRYMTLEFLEE 77
L W+ K+ DFI + R L +L+E
Sbjct: 151 LLEWLEKN-PDFIWPENARNEVLSWLKE 177
>gnl|CDD|118081 pfam09545, RE_AccI, AccI restriction endonuclease. This family
includes the AccI (recognises and cleaves GT^MKAC)
restriction endonuclease.
Length = 366
Score = 28.1 bits (62), Expect = 6.3
Identities = 36/164 (21%), Positives = 71/164 (43%), Gaps = 28/164 (17%)
Query: 94 QLTQMLTKACTKHETNLQDLLAPPPQVANKENIETLSALEIAEQMTYIDYHIFKSIRSEE 153
+ T++ + K + D+L P A ++ IE L+++ AE + D+ +
Sbjct: 158 KFTEIAFETKDKILADFLDVLDHP---ARQKYIELLNSI-TAETINIADFKV-------- 205
Query: 154 FFGQAWLKSEKLTKAPHIVLFTQRFNTMSKLVANEILNRSNMSQRVHVIEKWIAVANILR 213
W +++L + + LF Q N + ++ + L+ + + + V+ KWI N+
Sbjct: 206 ---PGWRSNDRLIEVKN--LFKQLKNAIKEIQKRDYLSITPKVEDIKVVYKWIETFNVPH 260
Query: 214 FLN----------NFNGVLTIISAMNNSSV-FRLKKTWDKVSKT 246
F +F +L IIS +N V F ++K +KT
Sbjct: 261 FYFQVFFDKVYGISFEQILKIISDSDNDGVIFSVEKDTKNQNKT 304
>gnl|CDD|112169 pfam03342, Rhabdo_M1, Rhabdovirus M1 matrix protein (M1
polymerase-associated protein).
Length = 219
Score = 27.5 bits (61), Expect = 6.7
Identities = 24/75 (32%), Positives = 32/75 (42%), Gaps = 8/75 (10%)
Query: 65 KELRYMTLEFLEEIVCTPNL-----LPAEYKAATQ--LTQMLTKACTKHETNLQDLLAPP 117
L + L+F++E L L + K + Q LT L K T++ NLQ L
Sbjct: 56 TTLEQLILKFVDERRQLDALKRFGQLIRQIKMSHQEELTAHLEKVATENRANLQALTE-S 114
Query: 118 PQVANKENIETLSAL 132
Q K E LSAL
Sbjct: 115 QQEHEKVTKEILSAL 129
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
0.318 0.128 0.363
Gapped
Lambda K H
0.267 0.0717 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,354,785
Number of extensions: 1214784
Number of successful extensions: 1031
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1025
Number of HSP's successfully gapped: 24
Length of query: 274
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 179
Effective length of database: 6,723,972
Effective search space: 1203590988
Effective search space used: 1203590988
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.1 bits)