RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14410
(325 letters)
>gnl|CDD|227492 COG5163, NOP7, Protein required for biogenesis of the 60S ribosomal
subunit [Translation, ribosomal structure and
biogenesis].
Length = 591
Score = 98.6 bits (245), Expect = 8e-23
Identities = 51/169 (30%), Positives = 71/169 (42%), Gaps = 32/169 (18%)
Query: 14 MGQEEEDAAEFDYFPTNSEADAEKVEEFKREAEKVRKLKRLFEGLKVFLNREVPREPLTL 73
M + + D F N++ K + LK LF G K +++REVP + L
Sbjct: 314 MVECRLVEEKLDTFEDNNKNKDIMEMVSKPCSS----LKSLFSGFKFYISREVPGDSLEF 369
Query: 74 ALRSFGAQVSWDKTLFVGATFPEDDESITHQIVDRPSIGKQYISRVFDSINAKQLAPVEK 133
+ S G V + DE +THQIVDRP + + R
Sbjct: 370 IILSCGGSVVGSPCEADIHVSEKVDEKVTHQIVDRPVMKNKVEGRT-------------- 415
Query: 134 YFIGVTLPPHLSSYYVQPQWVFDSINAKQLAPVEKYFIGVTLPPHMSSY 182
Y+QPQW+FDSIN +LA VE Y +G LPPH+S +
Sbjct: 416 --------------YIQPQWLFDSINKGKLACVENYCVGKRLPPHLSPF 450
Score = 67.4 bits (164), Expect = 2e-12
Identities = 31/78 (39%), Positives = 39/78 (50%), Gaps = 12/78 (15%)
Query: 177 PHMSSY-----YVQPQWVFDSINAKQLAPVEKYFIGVTLPPHLSPFIDTTKTEHYVPPE- 230
P M + Y+QPQW+FDSIN +LA VE Y +G LPPHLSPF + Y P
Sbjct: 405 PVMKNKVEGRTYIQPQWLFDSINKGKLACVENYCVGKRLPPHLSPFAS---VDSYDPRAS 461
Query: 231 ---AEDPENERLRDPKNI 245
E+ + D N
Sbjct: 462 LMTMEETQRHSEEDLVNR 479
Score = 57.8 bits (139), Expect = 3e-09
Identities = 22/34 (64%), Positives = 26/34 (76%)
Query: 285 YVQPQWVFDSINAKQLAPVEKYFIGVTLPPHLFP 318
Y+QPQW+FDSIN +LA VE Y +G LPPHL P
Sbjct: 416 YIQPQWLFDSINKGKLACVENYCVGKRLPPHLSP 449
Score = 55.9 bits (134), Expect = 1e-08
Identities = 21/32 (65%), Positives = 25/32 (78%)
Query: 252 YVQPQWVFDSINAKQLAPVEKYFIGVTLPPHL 283
Y+QPQW+FDSIN +LA VE Y +G LPPHL
Sbjct: 416 YIQPQWLFDSINKGKLACVENYCVGKRLPPHL 447
>gnl|CDD|215978 pfam00533, BRCT, BRCA1 C Terminus (BRCT) domain. The BRCT domain
is found predominantly in proteins involved in cell
cycle checkpoint functions responsive to DNA damage. The
BRCT domain of XRCC1 forms a homodimer in the crystal
structure. This suggests that pairs of BRCT domains
associate as homo- or heterodimers. BRCT domains are
often found as tandem-repeat pairs. Structures of the
BRCA1 BRCT domains revealed a basis for a widely
utilised head-to-tail BRCT-BRCT oligomerisation mode.
This conserved tandem BRCT architecture facilitates
formation of the canonical BRCT phospho-peptide
interaction cleft at a groove between the BRCT domains.
Disease associated missense and nonsense mutations in
the BRCA1 BRCT domains disrupt peptide binding by
directly occluding this peptide binding groove, or by
disrupting key conserved BRCT core folding determinants.
Length = 77
Score = 38.9 bits (91), Expect = 2e-04
Identities = 18/107 (16%), Positives = 30/107 (28%), Gaps = 36/107 (33%)
Query: 54 LFEGLKVFLNR--EVPREPLTLALRSFGAQVSWDKTLFVGATFPEDDESITHQIVDRPSI 111
LF+G + + RE L + G +V+ + TH IV +
Sbjct: 5 LFKGKTFVITGLDSLEREELEELIEKLGGKVT-----------DSLSKKTTHVIVGENAG 53
Query: 112 GKQYISRVFDSINAKQLAPVEKYFIGVTLPPHLSSYYVQPQWVFDSI 158
+ + A I V +W+ D I
Sbjct: 54 TLKLL-----------KAIALGIPI------------VTEEWLLDCI 77
>gnl|CDD|214602 smart00292, BRCT, breast cancer carboxy-terminal domain.
Length = 78
Score = 33.5 bits (77), Expect = 0.020
Identities = 19/108 (17%), Positives = 35/108 (32%), Gaps = 35/108 (32%)
Query: 54 LFEGLKVFLNR---EVPREPLTLALRSFGAQVSWDKTLFVGATFPEDDESITHQIVDRPS 110
LF+G ++ + R+ L + + G +V+ + ++ TH IV P
Sbjct: 3 LFKGKTFYITGSFDKEERDELKELIEALGGKVTSSLS----------SKTTTHVIVGSPE 52
Query: 111 IGKQYISRVFDSINAKQLAPVEKYFIGVTLPPHLSSYYVQPQWVFDSI 158
GK A I V+ +W+ D +
Sbjct: 53 GGKLE----------LLKAIALGIPI------------VKEEWLLDCL 78
>gnl|CDD|237994 cd00027, BRCT, Breast Cancer Suppressor Protein (BRCA1),
carboxy-terminal domain. The BRCT domain is found within
many DNA damage repair and cell cycle checkpoint
proteins. The unique diversity of this domain
superfamily allows BRCT modules to interact forming
homo/hetero BRCT multimers, BRCT-non-BRCT interactions,
and interactions within DNA strand breaks.
Length = 72
Score = 30.4 bits (69), Expect = 0.23
Identities = 18/105 (17%), Positives = 33/105 (31%), Gaps = 37/105 (35%)
Query: 57 GLKVFLNREVP---REPLTLALRSFGAQVSWDKTLFVGATFPEDDESITHQIVDRPSIGK 113
GL + ++P R+ L + G +V+ + + TH IV + K
Sbjct: 1 GLTFVITGDLPSEERDELKELIEKLGGKVTSSVS-----------KKTTHVIVGSDAGPK 49
Query: 114 QYISRVFDSINAKQLAPVEKYFIGVTLPPHLSSYYVQPQWVFDSI 158
K + L + V P+W+ D +
Sbjct: 50 -------------------KLLKAIKLGIPI----VTPEWLLDCL 71
>gnl|CDD|192507 pfam10273, WGG, Pre-rRNA-processing protein TSR2. This entry
represents the central conserved section of a family of
proteins described as pre-rRNA-processing protein TSR2.
The region has a distinctive WGG motif but the function
is unknown.
Length = 82
Score = 29.5 bits (67), Expect = 0.44
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 4/48 (8%)
Query: 1 MSIAVTASGMSVPMGQEEED---AAEFDYFPTNSEADAEKVEEFKREA 45
+ +AV + P E+ D A D F +N + DA+ +E+ E
Sbjct: 16 LQLAVE-NNWGGPDSAEKADWLAGAIVDLFTSNKDVDADDLEDVLLEV 62
>gnl|CDD|235561 PRK05686, fliG, flagellar motor switch protein G; Validated.
Length = 339
Score = 30.5 bits (70), Expect = 1.0
Identities = 20/50 (40%), Positives = 27/50 (54%), Gaps = 10/50 (20%)
Query: 36 EKVEEFKRE-AEKVRKLKRLFEGLKVFLN--------REVPREPLTLALR 76
E +EE E AEK++ L +FE L V L+ REV + L LAL+
Sbjct: 224 ESLEEEDPELAEKIKDLMFVFEDL-VDLDDRSIQRLLREVDNDVLALALK 272
>gnl|CDD|213874 TIGR03857, F420_MSMEG_2249, probable F420-dependent oxidoreductase,
MSMEG_2249 family. Coenzyme F420 has a limited
phylogenetic distribution, including methanogenic
archaea, Mycobacterium tuberculosis and related species,
Colwellia psychrerythraea 34H, Rhodopseudomonas
palustris HaA2, and others. Partial phylogenetic
profiling identifies protein subfamilies, within the
larger family called luciferase-like monooxygenanases
(pfam00296), that appear only in F420-positive genomes
and are likely to be F420-dependent. This model
describes a distinctive subfamily, found only in
F420-biosynthesizing members of the Actinobacteria of
the bacterial luciferase-like monooxygenase (LLM)
superfamily [Unknown function, Enzymes of unknown
specificity].
Length = 329
Score = 30.5 bits (69), Expect = 1.2
Identities = 14/31 (45%), Positives = 17/31 (54%)
Query: 186 PQWVFDSINAKQLAPVEKYFIGVTLPPHLSP 216
P VF +I K LA + F GV L P L+P
Sbjct: 152 PPLVFGAIGPKGLALAGRAFDGVILHPFLTP 182
>gnl|CDD|224667 COG1753, COG1753, Predicted antotoxin, copG family [Signal
transduction mechanisms].
Length = 74
Score = 28.3 bits (63), Expect = 1.4
Identities = 12/26 (46%), Positives = 19/26 (73%)
Query: 26 YFPTNSEADAEKVEEFKREAEKVRKL 51
F T SE + EK+++ ++EAEK+R L
Sbjct: 47 AFGTLSEEEVEKIKKEEKEAEKMRSL 72
>gnl|CDD|216141 pfam00833, Ribosomal_S17e, Ribosomal S17.
Length = 122
Score = 28.8 bits (65), Expect = 1.4
Identities = 12/37 (32%), Positives = 16/37 (43%)
Query: 16 QEEEDAAEFDYFPTNSEADAEKVEEFKREAEKVRKLK 52
QEEE +Y P SE D +E E ++ L
Sbjct: 74 QEEERERRDNYVPEVSELDVPLIEVDPDTKEMLKSLG 110
>gnl|CDD|172944 PRK14469, PRK14469, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 343
Score = 28.9 bits (65), Expect = 3.1
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 38 VEEFKREAEKVRKLKRLFEGLKVFLN 63
++ F E E +KL L +GLKVF+N
Sbjct: 259 IKGFNDEIEDAKKLAELLKGLKVFVN 284
>gnl|CDD|225347 COG2733, COG2733, Predicted membrane protein [Function unknown].
Length = 415
Score = 28.9 bits (65), Expect = 3.5
Identities = 19/109 (17%), Positives = 33/109 (30%), Gaps = 11/109 (10%)
Query: 30 NSEADAEKVEEFKREA---EKVRKLKR-LFEGLKVFLNREVPREPLTLALRSFGAQVSWD 85
+ A + E K E + ++ L +L + E L R A S
Sbjct: 270 HDPGMAARAEAIKSYLKEDEAIATAAGDMWTSLSEWLKEDYESEDSMLRKRLARAVQSVG 329
Query: 86 KTLFVGATFPED-DESITHQIVD-----RPSIGKQYISRVFDSINAKQL 128
+ L +E + I K +IS +A++L
Sbjct: 330 EELIADDALRAKLNEHLVQAAERLAEEKHAEITK-HISDTVKRWDAEEL 377
>gnl|CDD|183557 PRK12494, PRK12494, NADH dehydrogenase subunit J; Provisional.
Length = 172
Score = 28.0 bits (63), Expect = 4.4
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 8/34 (23%)
Query: 37 KVEEFKREAEKVRKLKRLFEGLKVFLNREVPREP 70
KV + + +VR LKVFL R+ PR P
Sbjct: 87 KVSDNADKPREVR--------LKVFLPRDDPRVP 112
>gnl|CDD|178717 PLN03173, PLN03173, chalcone synthase; Provisional.
Length = 391
Score = 27.7 bits (61), Expect = 8.5
Identities = 22/66 (33%), Positives = 29/66 (43%), Gaps = 6/66 (9%)
Query: 5 VTASGMSVPMGQEEEDAAEFDYFP-TNSEADAEKVEEFKREAEKVRKLKRLFEGLKVFLN 63
+ A G S P ++ YF TNSE E E+FKR EK KR + L
Sbjct: 19 IMAIGTSTPPNCVDQSTYPDYYFRITNSEHKVELKEKFKRMCEKSMIKKRY-----MHLT 73
Query: 64 REVPRE 69
E+ +E
Sbjct: 74 EEILKE 79
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
0.319 0.136 0.416
Gapped
Lambda K H
0.267 0.0697 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,564,000
Number of extensions: 1730758
Number of successful extensions: 1620
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1616
Number of HSP's successfully gapped: 27
Length of query: 325
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 228
Effective length of database: 6,635,264
Effective search space: 1512840192
Effective search space used: 1512840192
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 (21.7 bits)
S2: 59 (26.6 bits)