RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3012
(272 letters)
>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 = 194 bits (495), Expect = 1e-61
Identities = 83/205 (40%), Positives = 138/205 (67%), Gaps = 6/205 (2%)
Query: 66 ILIAHPVEIARQLTLLEFDYFRSVKPSELVGSVWTKKNKAEY-SPNLIKIMKHTTNFTRW 124
L P E+A QLTLL+F+ FR ++P EL+GS+W+KK+K + SPNL + ++ N + W
Sbjct: 1 FLSLDPKELAEQLTLLDFELFRKIEPFELLGSLWSKKDKNIHLSPNLERFIERFNNLSNW 60
Query: 125 LEKIIVEAENFDERLAIMTRIIEMMIVLQKLNNFNGVLAVTSAMGSAAVYRLRFTFQALP 184
+ I+ N +R ++++ I++ ++LNNFN ++A+ SA+ S+ + RL+ T++ L
Sbjct: 61 VASEILLCTNPKKRARLLSKFIQVAKHCRELNNFNSLMAIVSALSSSPISRLKKTWEVLS 120
Query: 185 TRLQKVLEDAREL--NGDHFKKYQEKLRNI--NPPCIPFFGMYLTNILHIEEGNPDFLPD 240
++L+K+ E+ EL +FK Y++ L+++ NPPC+PF G+YL ++ + EGNPDFL
Sbjct: 121 SKLKKLFEELEELVDPSRNFKNYRKLLKSVGPNPPCVPFLGVYLKDLTFLHEGNPDFLEG 180
Query: 241 SKLINFTKRRKVAEIISEIQQYQTQ 265
L+NF KRRK+AEI+ EI+Q Q+
Sbjct: 181 -NLVNFEKRRKIAEILREIRQLQSN 204
>gnl|CDD|216025 pfam00617, RasGEF, RasGEF domain. Guanine nucleotide exchange
factor for Ras-like small GTPases.
Length = 185
Score = 192 bits (490), Expect = 1e-61
Identities = 74/184 (40%), Positives = 117/184 (63%), Gaps = 4/184 (2%)
Query: 70 HPVEIARQLTLLEFDYFRSVKPSELVGSVWTKKNKAEYSPNLIKIMKHTTNFTRWLEKII 129
P+E+ARQLTL+E + F ++ P EL+ S W KK+ SPN+ + +RW+ I
Sbjct: 4 DPLELARQLTLIESELFSAIDPRELLDSAWGKKDSKL-SPNIEAFISRFNQLSRWVATEI 62
Query: 130 VEAENFDERLAIMTRIIEMMIVLQKLNNFNGVLAVTSAMGSAAVYRLRFTFQALPTRLQK 189
+ E+ +R ++ + I++ ++LNNFN ++A+ S + S+ + RL+ T++ + + +K
Sbjct: 63 LSEEDLKKRAKVIKKFIKIAQHCRELNNFNSLMAIISGLNSSPISRLKKTWELVSKKYKK 122
Query: 190 VLEDAREL--NGDHFKKYQEKLRNINPPCIPFFGMYLTNILHIEEGNPDFLPDSKLINFT 247
+LE+ EL +FK Y+E L+ NPPCIPF G+YL ++ IEEGNPDFL + LINF
Sbjct: 123 LLEELEELMSPSKNFKNYREALKKANPPCIPFLGLYLKDLTFIEEGNPDFLDNG-LINFE 181
Query: 248 KRRK 251
KRRK
Sbjct: 182 KRRK 185
>gnl|CDD|214539 smart00147, RasGEF, Guanine nucleotide exchange factor for Ras-like
small GTPases.
Length = 242
Score = 192 bits (490), Expect = 6e-61
Identities = 83/204 (40%), Positives = 136/204 (66%), Gaps = 5/204 (2%)
Query: 66 ILIAHPVEIARQLTLLEFDYFRSVKPSELVGSVWTKKNKAEYSP-NLIKIMKHTTNFTRW 124
+L+ P E+A QLTLL+F+ FR + PSEL+GSVW K++K SP NL ++ + W
Sbjct: 1 LLLLDPKELAEQLTLLDFELFRKIDPSELLGSVWGKRSKKSPSPLNLEAFIRRFNEVSNW 60
Query: 125 LEKIIVEAENFDERLAIMTRIIEMMIVLQKLNNFNGVLAVTSAMGSAAVYRLRFTFQALP 184
+ I++ +R ++++ I++ ++LNNFN ++A+ SA+ S+ + RL+ T++ LP
Sbjct: 61 VATEILKQTTPKDRAELLSKFIQVAKHCRELNNFNSLMAIVSALSSSPISRLKKTWEKLP 120
Query: 185 TRLQKVLEDAREL--NGDHFKKYQEKLRNIN-PPCIPFFGMYLTNILHIEEGNPDFLPDS 241
++ +K+ E+ EL ++K Y+E L + N PPCIPF G+ L ++ I+EGNPDFL +
Sbjct: 121 SKYKKLFEELEELLSPERNYKNYREALSSCNLPPCIPFLGVLLKDLTFIDEGNPDFLEN- 179
Query: 242 KLINFTKRRKVAEIISEIQQYQTQ 265
L+NF KRR++AEI+ EI+Q Q+Q
Sbjct: 180 GLVNFEKRRQIAEILREIRQLQSQ 203
>gnl|CDD|179872 PRK04690, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 468
Score = 31.3 bits (71), Expect = 0.49
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 157 NFNGVLAVTSAMG--SAAVYRLRFTFQALPTRLQKV 190
N VLA A+G + A+ F+ LP RLQ++
Sbjct: 282 NLCAVLAALEALGLDAVALAPAAAGFRPLPNRLQEL 317
>gnl|CDD|225979 COG3448, COG3448, CBS-domain-containing membrane protein [Signal
transduction mechanisms].
Length = 382
Score = 30.2 bits (68), Expect = 1.2
Identities = 15/46 (32%), Positives = 26/46 (56%)
Query: 146 IEMMIVLQKLNNFNGVLAVTSAMGSAAVYRLRFTFQALPTRLQKVL 191
I M L+ L+ +G +A+T+ +G AV+RL + F P L ++
Sbjct: 117 IGAMFALRCLHPPSGAVALTAVLGGPAVHRLGYNFVLWPVALNSLI 162
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 29.5 bits (67), Expect = 2.4
Identities = 23/73 (31%), Positives = 33/73 (45%), Gaps = 20/73 (27%)
Query: 186 RLQKVLEDARELNGDHFKKYQEKLRNINPPCIPFFGMYLTNILHIEEGNPDFLPDSKLIN 245
R +K + A+EL+ +H K EKLR I + L PDS++I
Sbjct: 331 RFRKAVRKAKELDIEHPK--LEKLREI-----------VKEQLGKN-------PDSRIIV 370
Query: 246 FTKRRKVAEIISE 258
FT+ R AE I +
Sbjct: 371 FTQYRDTAEKIVD 383
>gnl|CDD|221466 pfam12220, U1snRNP70_N, U1 small nuclear ribonucleoprotein of 70kDa
MW N terminal. This domain is found in eukaryotes. This
domain is about 90 amino acids in length. This domain is
found associated with pfam00076. This domain is part of
U1 snRNP, which is the pre-mRNA binding protein of the
penta-snRNP spliceosome complex. It extends over a
distance of 180 A from its RNA binding domain, wraps
around the core domain of U1 snRNP consisting of the
seven Sm proteins and finally contacts U1-C, which is
crucial for 5'-splice-site recognition.
Length = 94
Score = 27.6 bits (62), Expect = 2.7
Identities = 17/66 (25%), Positives = 26/66 (39%), Gaps = 3/66 (4%)
Query: 153 QKLNNFNGVLAVTSAMGSAAVYRLRFTFQALPTRLQKVLEDARELNGDHFKKYQEKLRNI 212
+K N GV S Y+ + T L+K + RE KK +E+L+
Sbjct: 32 RKTNPITGVAQYLSEFKD---YKDEPPPEPTETWLEKREREKREKKEKLEKKLEEELKEW 88
Query: 213 NPPCIP 218
+P P
Sbjct: 89 DPNEDP 94
>gnl|CDD|164789 PHA00327, PHA00327, minor capsid protein.
Length = 187
Score = 27.7 bits (61), Expect = 5.0
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 164 VTSAMGSA-AVYRLRFTFQALPTRLQKVLEDARELNGD 200
V S + SA AV RL + + + LQ + E R +N +
Sbjct: 100 VESGLNSALAVQRLTYERKRMQAELQNLREQNRLINFN 137
>gnl|CDD|233625 TIGR01896, cas_AF1879, CRISPR-associated protein Cas4/Csa1, subtype
I-A/APERN. CRISPR is a term for Clustered, Regularly
Interspaced Short Palidromic Repeats. A number of
protein families appear only in association with these
repeats and are designated Cas (CRISPR-Associated)
proteins. This model describes a particularly strongly
conserved family found so only in the APERN subtype of
CRISPR/Cas loci and represented by AF1879 from
Archaeoglobus fulgidus. This family has four perfectly
preserved Cys residues. This subfamily is found in a
CRISPR/Cas locus we designate APERN, so the family is
designated Csa1, for CRISPR/Cas Subtype Protein 1
[Mobile and extrachromosomal element functions, Other].
Length = 271
Score = 27.4 bits (61), Expect = 7.1
Identities = 16/68 (23%), Positives = 21/68 (30%), Gaps = 7/68 (10%)
Query: 181 QALPTRLQKVLEDARELNGDHFKKYQEKLR--NINPPCIPFFGMYLTNILHIE-----EG 233
QA+ K LE+ R+L + + LR C Y I E
Sbjct: 71 QAIHEAFLKALEEVRKLIYSGYDMFSVLLRSFRAREFCAKELWKYGVEIYSAVMAYVFEK 130
Query: 234 NPDFLPDS 241
F DS
Sbjct: 131 ASFFSADS 138
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 0.138 0.397
Gapped
Lambda K H
0.267 0.0763 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,624,217
Number of extensions: 1457382
Number of successful extensions: 1400
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1389
Number of HSP's successfully gapped: 21
Length of query: 272
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 177
Effective length of database: 6,723,972
Effective search space: 1190143044
Effective search space used: 1190143044
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: 58 (26.1 bits)