RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15588
(461 letters)
>gnl|CDD|214539 smart00147, RasGEF, Guanine nucleotide exchange factor for Ras-like
small GTPases.
Length = 242
Score = 234 bits (600), Expect = 5e-75
Identities = 87/204 (42%), Positives = 126/204 (61%), Gaps = 3/204 (1%)
Query: 239 LETFSAKELAFHMTLFDWDLFWSIHEYELVYHTVGRHRFQ-QITANLDVFLRRFNEIQYW 297
L KELA +TL D++LF I EL+ G+ + NL+ F+RRFNE+ W
Sbjct: 1 LLLLDPKELAEQLTLLDFELFRKIDPSELLGSVWGKRSKKSPSPLNLEAFIRRFNEVSNW 60
Query: 298 VITEILLVTSLNKRVQILRKMIKLAAYCKEYRNINALFAVLMGLSNVAVSRLSLTWDKLP 357
V TEIL T+ R ++L K I++A +C+E N N+L A++ LS+ +SRL TW+KLP
Sbjct: 61 VATEILKQTTPKDRAELLSKFIQVAKHCRELNNFNSLMAIVSALSSSPISRLKKTWEKLP 120
Query: 358 SKSKKTYTELEALIDPSKNHRAYRQAVSKL-QSPVIPFMPLLLKDLAFTHDGNKTVV-DG 415
SK KK + ELE L+ P +N++ YR+A+S P IPF+ +LLKDL F +GN + +G
Sbjct: 121 SKYKKLFEELEELLSPERNYKNYREALSSCNLPPCIPFLGVLLKDLTFIDEGNPDFLENG 180
Query: 416 LVNFEKMHMFAQTLRTLRYCRTRH 439
LVNFEK A+ LR +R +++
Sbjct: 181 LVNFEKRRQIAEILREIRQLQSQP 204
>gnl|CDD|216025 pfam00617, RasGEF, RasGEF domain. Guanine nucleotide exchange
factor for Ras-like small GTPases.
Length = 185
Score = 231 bits (591), Expect = 2e-74
Identities = 76/184 (41%), Positives = 112/184 (60%), Gaps = 2/184 (1%)
Query: 242 FSAKELAFHMTLFDWDLFWSIHEYELVYHTVGRHRFQQITANLDVFLRRFNEIQYWVITE 301
ELA +TL + +LF +I EL+ G+ + + N++ F+ RFN++ WV TE
Sbjct: 3 LDPLELARQLTLIESELFSAIDPRELLDSAWGKKDSKL-SPNIEAFISRFNQLSRWVATE 61
Query: 302 ILLVTSLNKRVQILRKMIKLAAYCKEYRNINALFAVLMGLSNVAVSRLSLTWDKLPSKSK 361
IL L KR ++++K IK+A +C+E N N+L A++ GL++ +SRL TW+ + K K
Sbjct: 62 ILSEEDLKKRAKVIKKFIKIAQHCRELNNFNSLMAIISGLNSSPISRLKKTWELVSKKYK 121
Query: 362 KTYTELEALIDPSKNHRAYRQAVSKLQSPVIPFMPLLLKDLAFTHDGNKTVVD-GLVNFE 420
K ELE L+ PSKN + YR+A+ K P IPF+ L LKDL F +GN +D GL+NFE
Sbjct: 122 KLLEELEELMSPSKNFKNYREALKKANPPCIPFLGLYLKDLTFIEEGNPDFLDNGLINFE 181
Query: 421 KMHM 424
K
Sbjct: 182 KRRK 185
>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 = 217 bits (554), Expect = 4e-68
Identities = 80/205 (39%), Positives = 124/205 (60%), Gaps = 4/205 (1%)
Query: 239 LETFSAKELAFHMTLFDWDLFWSIHEYELVYHTVG-RHRFQQITANLDVFLRRFNEIQYW 297
+ KELA +TL D++LF I +EL+ + + ++ NL+ F+ RFN + W
Sbjct: 1 FLSLDPKELAEQLTLLDFELFRKIEPFELLGSLWSKKDKNIHLSPNLERFIERFNNLSNW 60
Query: 298 VITEILLVTSLNKRVQILRKMIKLAAYCKEYRNINALFAVLMGLSNVAVSRLSLTWDKLP 357
V +EILL T+ KR ++L K I++A +C+E N N+L A++ LS+ +SRL TW+ L
Sbjct: 61 VASEILLCTNPKKRARLLSKFIQVAKHCRELNNFNSLMAIVSALSSSPISRLKKTWEVLS 120
Query: 358 SKSKKTYTELEALIDPSKNHRAYRQAVSKL--QSPVIPFMPLLLKDLAFTHDGNKTVVD- 414
SK KK + ELE L+DPS+N + YR+ + + P +PF+ + LKDL F H+GN ++
Sbjct: 121 SKLKKLFEELEELVDPSRNFKNYRKLLKSVGPNPPCVPFLGVYLKDLTFLHEGNPDFLEG 180
Query: 415 GLVNFEKMHMFAQTLRTLRYCRTRH 439
LVNFEK A+ LR +R ++
Sbjct: 181 NLVNFEKRRKIAEILREIRQLQSNS 205
>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 = 31.1 bits (71), Expect = 0.20
Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 14/69 (20%)
Query: 127 IFRVYCADHTFCTLRFPVNATAEQIKTSAAEKLAEQIKTSAAEKLGLLVSPSDLLLVEVK 186
++ + T+ TLR + TA+ + I+ +K GL P D LVEV
Sbjct: 4 VYPEDPSGGTYKTLRVSKDTTAQDV-----------IQQ-LLKKFGLDDDPEDYALVEVL 51
Query: 187 STG--ERVV 193
G ER++
Sbjct: 52 GDGGLERLL 60
>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 = 29.2 bits (66), Expect = 1.0
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 15/75 (20%)
Query: 127 IFRVYCADHT---FCTLRFPVNATAEQIKTSAAEKLAEQIKTSAAEKLGLLVSPSDLLLV 183
+ RVY D T + T+ TA+++ I+ A +K GL P D +LV
Sbjct: 1 VLRVYTEDGTPGTYKTILVSSTTTAQEV-----------IRA-ALKKFGLADDPEDYVLV 48
Query: 184 EVKSTGERVVFRDND 198
++ GE V D++
Sbjct: 49 VLERGGEERVLPDDE 63
>gnl|CDD|214612 smart00314, RA, Ras association (RalGDS/AF-6) domain. RasGTP
effectors (in cases of AF6, canoe and RalGDS); putative
RasGTP effectors in other cases. Kalhammer et al. have
shown that not all RA domains bind RasGTP. Predicted
structure similar to that determined, and that of the
RasGTP-binding domain of Raf kinase. Predicted RA
domains in PLC210 and nore1 found to bind RasGTP.
Included outliers (Grb7, Grb14, adenylyl cyclases etc.).
Length = 90
Score = 28.8 bits (65), Expect = 1.6
Identities = 19/67 (28%), Positives = 26/67 (38%), Gaps = 13/67 (19%)
Query: 127 IFRVYCADHTFCTLRFPVNATAEQIKTSAAEKLAEQIKTSAAEKLGLLVSPSDLLLVEVK 186
++ T+ TLR TA + I+ EK L P + +LVEV
Sbjct: 7 VYVDDLPGGTYKTLRVSSRTTARDV-----------IQQ-LLEKFHLTDDPEEYVLVEVL 54
Query: 187 STG-ERV 192
G ERV
Sbjct: 55 PDGKERV 61
>gnl|CDD|220129 pfam09159, Ydc2-catalyt, Mitochondrial resolvase Ydc2 / RNA
splicing MRS1. Members of this family adopt a secondary
structure consisting of two beta sheets and one alpha
helix, arranged as a beta-alpha-beta motif. Each beta
sheet has five strands, arranged in a 32145 order, with
the second strand being antiparallel to the rest.
Mitochondrial resolvase Ydc2 is capable of resolving
Holliday junctions and cleaves DNA after 5'-CT-3' and
5'-TT-3' sequences. This family also contains the
mitochondrial RNA-splicing protein MRS1 which is
involved in the excision of group I introns.
Length = 254
Score = 30.4 bits (69), Expect = 1.9
Identities = 15/67 (22%), Positives = 21/67 (31%), Gaps = 2/67 (2%)
Query: 339 MGLSNVAVSRLSLTWDKLPSKSKKTYTELEALIDPSKNHRAYRQAVSKLQSPVIPFMPLL 398
MG+ N A +L K P++S T L K A + P
Sbjct: 6 MGIKNFAFCKLKGPSMKAPTRSLPTLNAWLKLNLDEKIGADDAPATDEKSKIS--LSPRY 63
Query: 399 LKDLAFT 405
LA+
Sbjct: 64 YAFLAYK 70
>gnl|CDD|189005 cd09598, M4_uncharacterized, Peptidase M4 family containing mostly
uncharacterized proteins. This family of
uncharacterized bacterial proteins are homologs of the
M4 peptidase family that is also known as the
thermolysin-like peptidase (TLP) family. Typically, the
M4 peptidases consist of a presequence (signal
sequence), a propeptide sequence and a peptidase unit.
The presequence is cleaved off during export while the
propeptide has inhibitory and chaperone functions and
facilitates folding. The propeptide remains attached
until the peptidase is secreted and can be safely
activated. All peptidases in this family bind a single
catalytic zinc ion which is tetrahedrally co-ordinated
by three amino acid ligands and a water molecule that
forms the nucleophile on activation during catalysis.
TLPs are secreted eubacterial endopeptidases from
Gram-positive or Gram-negative sources that degrade
extracellular proteins and peptides for bacterial
nutrition. They contain HEXXH and EXXXD motifs as part
of their active site and belong to the Glu-zincins
family and are selectively inhibited by Steptomyces
metalloproteinase inhibitor (SMPI) as well as by
phosphoramidon from Streptomyces tanashiensis. A large
number of these enzymes are implicated as key factors in
the pathogenesis of various diseases, including
gastritis, peptic ulcer, gastric carcinoma, cholera and
several types of bacterial infections, and are therefore
important drug targets. Some enzymes of the family can
function at extremes of temperatures, while some
function in organic solvents, thus rendering them novel
targets for biotechnological applications.
Length = 261
Score = 30.4 bits (69), Expect = 1.9
Identities = 10/32 (31%), Positives = 14/32 (43%), Gaps = 1/32 (3%)
Query: 413 VDGLVNFEKMHMFAQTLRTLRYCRTRHLGRPL 444
V F H++A RTL +LGR +
Sbjct: 10 VVDPDPFHAQHVYAAARRTLDIWEG-YLGRRI 40
>gnl|CDD|216082 pfam00723, Glyco_hydro_15, Glycosyl hydrolases family 15. In
higher organisms this family is represented by
phosphorylase kinase subunits.
Length = 416
Score = 30.1 bits (68), Expect = 2.8
Identities = 16/79 (20%), Positives = 26/79 (32%), Gaps = 4/79 (5%)
Query: 259 FWSIHE-YELVYHTVGRHRFQQITANLDVFLRRFNEIQYWVITEILLVTSLNKRVQILRK 317
FW+ + Y+ +YH GR R+ F + S+ V+
Sbjct: 313 FWAAEQLYDELYHWAGRGRWTLTRYARG-FFEKLVSSTVGTPYSSSTFISIPLAVKEYAD 371
Query: 318 MIKLAAYCKEYRNINALFA 336
A +EY N L +
Sbjct: 372 GFVKA--VEEYANSLGLLS 388
>gnl|CDD|129310 TIGR00206, fliF, flagellar basal-body M-ring protein/flagellar
hook-basal body protein (fliF). Component of the M
(cytoplasmic associated) ring, one of four rings
(L,P,S,M) which make up the flagellar hook-basal body
which is a major portion of the flagellar organelle.
Although the basic structure of the flagella appears to
be similar for all bacteria, additional rings and
structures surrounding the basal body have been observed
for some bacteria (eg Vibrio cholerae and Treponema
pallidum) [Cellular processes, Chemotaxis and motility].
Length = 555
Score = 29.9 bits (67), Expect = 3.1
Identities = 32/134 (23%), Positives = 53/134 (39%), Gaps = 28/134 (20%)
Query: 145 NATAEQIKTSAAEKLAEQIKTSAAEKLGLLVSPSDLLLVEV-------KSTGERVVF--- 194
N T Q K SA E K S +K+ L+++ ++ V KS ++F
Sbjct: 2 NKTFTQFKVSAKEFF---KKLSKVQKIALILAGFAIIAALVFLILFATKSQSYALLFVEL 58
Query: 195 --RDNDL--------SIPTALSLNGRIFVSPKDHLDALTCI-SEQETYTEGMD----FDL 239
+D ++P LS +GRI + P+D + L I + + GM FD
Sbjct: 59 SDQDLGRISQRLDQENVPYFLSSDGRIILVPEDKVKELRAILAREGLPKTGMVGFELFDQ 118
Query: 240 ETFSAKELAFHMTL 253
+ F + + L
Sbjct: 119 DRFGITDFERSINL 132
>gnl|CDD|235329 PRK05007, PRK05007, PII uridylyl-transferase; Provisional.
Length = 884
Score = 29.9 bits (68), Expect = 3.3
Identities = 14/30 (46%), Positives = 19/30 (63%), Gaps = 6/30 (20%)
Query: 425 FAQTLRTLRYCRTRHLGRPL-----ARQRF 449
++ TLR LR+ R RHL +PL AR+ F
Sbjct: 387 YSTTLRQLRHAR-RHLNQPLCEIPEARKLF 415
>gnl|CDD|238663 cd01367, KISc_KIF2_like, Kinesin motor domain, KIF2-like group.
KIF2 is a protein expressed in neurons, which has been
associated with axonal transport and neuron development;
alternative splice forms have been implicated in
lysosomal translocation. This catalytic (head) domain
has ATPase activity and belongs to the larger group of
P-loop NTPases. Kinesins are microtubule-dependent
molecular motors that play important roles in
intracellular transport and in cell division. In this
subgroup the motor domain is found in the middle
(M-type) of the protein chain. M-type kinesins are (+)
end-directed motors, i.e. they transport cargo towards
the (+) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and move
along the microtubule at a speed of about 6400 Angstroms
per second (KIF2 may be slower). To achieve that,
kinesin head groups work in pairs. Upon replacing ADP
with ATP, a kinesin motor domain increases its affinity
for microtubule binding and locks in place. Also, the
neck linker binds to the motor domain, which repositions
the other head domain through the coiled-coil domain
close to a second tubulin dimer, about 80 Angstroms
along the microtubule. Meanwhile, ATP hydrolysis takes
place, and when the second head domain binds to the
microtubule, the first domain again replaces ADP with
ATP, triggering a conformational change that pulls the
first domain forward.
Length = 322
Score = 29.5 bits (67), Expect = 3.5
Identities = 21/69 (30%), Positives = 30/69 (43%), Gaps = 16/69 (23%)
Query: 372 DPSKNHRAYRQAVSKLQSPVIPFMPLLLKDLAFTHDGN-KTVVDGLVNFEKMHMFAQTLR 430
+K H +R SKL +L+D +F GN KTV+ ++ TL
Sbjct: 268 ASNKAHVPFRG--SKLT--------QVLRD-SF--IGNSKTVMIATIS-PSASSCEHTLN 313
Query: 431 TLRY-CRTR 438
TLRY R +
Sbjct: 314 TLRYADRVK 322
>gnl|CDD|236400 PRK09188, PRK09188, serine/threonine protein kinase; Provisional.
Length = 365
Score = 29.3 bits (66), Expect = 4.9
Identities = 9/31 (29%), Positives = 13/31 (41%)
Query: 268 VYHTVGRHRFQQITANLDVFLRRFNEIQYWV 298
V+ TV R F RR +E+ +W
Sbjct: 30 VFSTVERGYFAGDPGTARAVRRRVSEVPWWS 60
>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 = 27.8 bits (62), Expect = 6.6
Identities = 8/54 (14%), Positives = 22/54 (40%)
Query: 29 DSSNHDKDFILSCKRSVVQFVFRWVSVIRHVVFDDTGTMNFIQDLASEVESDST 82
+ ++ DK + V+ + WV + FDD + +++ + + +
Sbjct: 54 EYNDWDKKKSKPIRLRVLNVLRTWVENYPYDFFDDEELLELLEEFLNRLVQEGA 107
>gnl|CDD|224131 COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope
biogenesis, outer membrane].
Length = 291
Score = 28.7 bits (65), Expect = 6.7
Identities = 12/26 (46%), Positives = 13/26 (50%), Gaps = 7/26 (26%)
Query: 294 IQYWV-------ITEILLVTSLNKRV 312
IQY V I EIL+VT KR
Sbjct: 38 IQYIVEEAVAAGIEEILIVTGRGKRA 63
>gnl|CDD|223507 COG0430, RCL1, RNA 3'-terminal phosphate cyclase [RNA processing
and modification].
Length = 341
Score = 28.4 bits (64), Expect = 7.4
Identities = 24/98 (24%), Positives = 40/98 (40%), Gaps = 30/98 (30%)
Query: 147 TAEQIKTSAAEKLAEQIKTSAA--EKLGLLVSPSDLLLVEVKSTGERVVFRDNDLSIPTA 204
+AE + AA++L ++++ AA E L D L+ A
Sbjct: 260 SAEVVGEEAAKELLRELESGAAVDEHLA------DQLIP------------------YMA 295
Query: 205 LSLNGRIFVSPKD-HLDALTCISEQETYTEGMDFDLET 241
L+ G V+ HL LT I E + G++F++E
Sbjct: 296 LAGIGEFTVAEVTSHL--LTNIWVIERFL-GVEFEVEG 330
>gnl|CDD|223703 COG0630, VirB11, Type IV secretory pathway, VirB11 components, and
related ATPases involved in archaeal flagella
biosynthesis [Cell motility and secretion /
Intracellular trafficking and secretion].
Length = 312
Score = 28.1 bits (63), Expect = 9.9
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 164 KTSAAEKLGLLVSPSDLLLVEVKSTGERVVFRDNDLSIPTALSLNGRIFVSPKDHLDA 221
KT+ L + P + +V ++ T E + +N + + T +G VS +D L A
Sbjct: 156 KTTLLNALLDFI-PPEERIVTIEDTPELKLPHENWVQLVTREGESGSSEVSLEDLLRA 212
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
0.324 0.135 0.406
Gapped
Lambda K H
0.267 0.0735 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,365,864
Number of extensions: 2256985
Number of successful extensions: 2400
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2389
Number of HSP's successfully gapped: 23
Length of query: 461
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 361
Effective length of database: 6,502,202
Effective search space: 2347294922
Effective search space used: 2347294922
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 61 (27.3 bits)