RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13236
(280 letters)
>gnl|CDD|216401 pfam01267, F-actin_cap_A, F-actin capping protein alpha subunit.
Length = 269
Score = 353 bits (908), Expect = e-124
Identities = 138/272 (50%), Positives = 192/272 (70%), Gaps = 4/272 (1%)
Query: 6 EKVRVVSGFILHSPPGEFNEVFNDVRGLLNNDVLLKDDVSKAFVQYNKEQLTPVKLNNSD 65
EK+ ++S FI ++PPGE N+V D+R LL +D L+K +++A QYN+EQL PVKL S+
Sbjct: 1 EKIEIISSFIKNAPPGELNDVVADLRALLGDDPLIKSTIAEALEQYNEEQLVPVKLPGSE 60
Query: 66 LPVLISEHNDLGNGRFYDPRSKQSFKFDHLRIEASDLESWE-PDNSTETWRSLIELELDT 124
V+ISE+N LG R++DP SK+SF DHL+ +ASD+ES+E E +R ++ L
Sbjct: 61 -KVIISEYNKLGGNRYFDPVSKKSFTVDHLKQKASDVESYELESEELELYRKSLDKALSA 119
Query: 125 YTASHYKNGTSSVFAKKQGETLQINACIEDHQFQPKNYWNGRWRSYWTINIEGNNVEVKG 184
Y HY NG V+ K +G+ ++ I H++ PKN+WNGRWRS WT++ + +KG
Sbjct: 120 YVKDHYPNGACGVYPKSEGDK-ELAIIIVSHKYNPKNFWNGRWRSEWTLD-SSSTGSLKG 177
Query: 185 NLKVQVHYYEDGNVQLVSSKDIKETVVVTSEEQTAREIVKLIEESETAYQQAISENYMTM 244
+KV VHYYEDGNVQL SSKD +ETV V++++ TA IVK I E+E YQ A++EN+ T+
Sbjct: 178 KIKVDVHYYEDGNVQLKSSKDFEETVSVSNDDATASSIVKAIREAENEYQAALNENFNTL 237
Query: 245 SDTTFKALRRQLPVTRMKIDWNKIVSYSIGKE 276
+DTTFKALRRQLPVTR KI+W KI +Y +GK+
Sbjct: 238 NDTTFKALRRQLPVTRQKINWGKIGNYRLGKD 269
>gnl|CDD|119391 cd04508, TUDOR, Tudor domains are found in many eukaryotic
organisms and have been implicated in protein-protein
interactions in which methylated protein substrates bind
to these domains. For example, the Tudor domain of
Survival of Motor Neuron (SMN) binds to symmetrically
dimethylated arginines of arginine-glycine (RG) rich
sequences found in the C-terminal tails of Sm proteins.
The SMN protein is linked to spinal muscular atrophy.
Another example is the tandem tudor domains of 53BP1,
which bind to histone H4 specifically dimethylated at
Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA
damage checkpoint signal.
Length = 48
Score = 30.3 bits (69), Expect = 0.11
Identities = 7/29 (24%), Positives = 16/29 (55%)
Query: 180 VEVKGNLKVQVHYYEDGNVQLVSSKDIKE 208
+ + KV+V + + GN ++V D++
Sbjct: 20 TSILSDGKVEVFFVDYGNTEVVPLSDLRP 48
>gnl|CDD|238494 cd01012, YcaC_related, YcaC related amidohydrolases; E.coli YcaC is
an homooctameric hydrolase with unknown specificity.
Despite its weak sequence similarity, it is structurally
related to other amidohydrolases and shares conserved
active site residues with them. Multimerisation
interface seems not to be conserved in all members.
Length = 157
Score = 29.1 bits (66), Expect = 1.4
Identities = 11/45 (24%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 65 DLPVLISEHNDLGNGRFYDPRSKQSFKFDHLRIEASDLESWEPDN 109
D+PV+++E G G + D IE + WE +
Sbjct: 36 DVPVILTEQYPKGLGPTVPEL--REVFPDAPVIEKTSFSCWEDEA 78
>gnl|CDD|132851 cd07212, Pat_PNPLA9, Patatin-like phospholipase domain containing
protein 9. PNPLA9 is a Ca-independent phospholipase
that catalyzes the hydrolysis of glycerophospholipids at
the sn-2 position. PNPLA9 is also known as PLA2G6
(phospholipase A2 group VI) or iPLA2beta. PLA2G6 is
stimulated by ATP and inhibited by bromoenol lactone
(BEL). In humans, PNPLA9 in expressed ubiquitously and
is involved in signal transduction, cell proliferation,
and apoptotic cell death. Mutations in human PLA2G6
leads to infantile neuroaxonal dystrophy (INAD) and
idiopathic neurodegeneration with brain iron
accumulation (NBIA). This family includes PLA2G6 from
Homo sapiens and Rattus norvegicus.
Length = 312
Score = 29.2 bits (66), Expect = 2.4
Identities = 21/100 (21%), Positives = 36/100 (36%), Gaps = 16/100 (16%)
Query: 32 GLL-NNDVLLKDDVSKAFVQYNK-EQLTPVKLNNSDLPVLISEHNDLGNGRFYDPRSKQS 89
GL+ NN L D +YNK + K + ++S LG G
Sbjct: 173 GLIANNPTL---DAMTEIHEYNKTLKSKGRKNKVKKIGCVVS----LGTGII------PQ 219
Query: 90 FKFDHLRIEASDLESWEPDNSTETWRSLIELELDTYTASH 129
+ + + WE + ++L ++ +D TAS
Sbjct: 220 TPVNTVDVFRPS-NPWELAKTVFGAKNLGKMVVDQCTASD 258
>gnl|CDD|197660 smart00333, TUDOR, Tudor domain. Domain of unknown function
present in several RNA-binding proteins. 10 copies in
the Drosophila Tudor protein. Initial proposal that the
survival motor neuron gene product contain a Tudor
domain are corroborated by more recent database search
techniques such as PSI-BLAST (unpublished).
Length = 57
Score = 26.5 bits (59), Expect = 2.7
Identities = 8/28 (28%), Positives = 16/28 (57%)
Query: 180 VEVKGNLKVQVHYYEDGNVQLVSSKDIK 207
V+V G +V + + GN ++V D++
Sbjct: 24 VKVDGEQLYEVFFIDYGNEEVVPPSDLR 51
>gnl|CDD|213843 TIGR03654, L6_bact, ribosomal protein L6, bacterial type. [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 175
Score = 27.8 bits (63), Expect = 5.0
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 8/46 (17%)
Query: 172 TINIEGNNVEVKG---NLKVQVHYY-----EDGNVQLVSSKDIKET 209
+ I+GN V VKG L +H EDG + + D KE
Sbjct: 15 EVTIDGNVVTVKGPKGELSRTLHPGVTVKVEDGQLTVSRPNDSKEA 60
>gnl|CDD|227211 COG4874, COG4874, Uncharacterized protein conserved in bacteria
containing a pentein-type domain [Function unknown].
Length = 318
Score = 28.0 bits (62), Expect = 5.8
Identities = 11/40 (27%), Positives = 19/40 (47%)
Query: 236 AISENYMTMSDTTFKALRRQLPVTRMKIDWNKIVSYSIGK 275
AI E++ + D R+ + + D +IVS SI +
Sbjct: 207 AIGEHFAVICDEAIPEYERRFVIRSLAKDGKEIVSISIEQ 246
>gnl|CDD|225768 COG3227, LasB, Zinc metalloprotease (elastase) [Amino acid
transport and metabolism].
Length = 507
Score = 27.8 bits (62), Expect = 7.3
Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 7/45 (15%)
Query: 12 SGFILHSPPGEFNEVFNDVRGLL-------NNDVLLKDDVSKAFV 49
+G I G NE F+DV G L D L+ DD+ +
Sbjct: 354 AGLIYRGQSGALNESFSDVFGTLIEQYVKNQVDWLIGDDIYTPGI 398
>gnl|CDD|181433 PRK08455, fliL, flagellar basal body-associated protein FliL;
Reviewed.
Length = 182
Score = 27.0 bits (60), Expect = 9.3
Identities = 15/57 (26%), Positives = 31/57 (54%)
Query: 172 TINIEGNNVEVKGNLKVQVHYYEDGNVQLVSSKDIKETVVVTSEEQTAREIVKLIEE 228
+I++E +N ++K L + D ++++SSK ++E +E+ EIV + E
Sbjct: 108 SISLELSNEKLKPELDKKDPVIRDIIIRILSSKTVEEVSTNKGKERLKDEIVGKLNE 164
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 27.5 bits (62), Expect = 9.7
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 6/51 (11%)
Query: 208 ETVVVTSEEQTAREIV----KLIEESETAYQQAIS-EN-YMTMSDTTFKAL 252
+ VV +E+ AREI + E + A QQ +S EN + M + K L
Sbjct: 497 DEFVVVEDEKKAREIAEYRQEKAREKKLARQQRVSLENLFEQMKEGEVKEL 547
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
0.313 0.130 0.375
Gapped
Lambda K H
0.267 0.0748 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,944,568
Number of extensions: 1287558
Number of successful extensions: 961
Number of sequences better than 10.0: 1
Number of HSP's gapped: 956
Number of HSP's successfully gapped: 23
Length of query: 280
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 184
Effective length of database: 6,679,618
Effective search space: 1229049712
Effective search space used: 1229049712
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 58 (26.1 bits)