RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16582
(109 letters)
>gnl|CDD|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain. The
Prosite family is restricted to DEAD/H helicases,
whereas this domain family is found in a wide variety
of helicases and helicase related proteins. It may be
that this is not an autonomously folding unit, but an
integral part of the helicase.
Length = 78
Score = 59.8 bits (146), Expect = 2e-13
Identities = 20/46 (43%), Positives = 28/46 (60%)
Query: 4 QTMLSFNRGITNILVATDVLEEGIDIQSCNLVIKFDPPQHTRSYVQ 49
+ + F G + +LVATDV GID+ NLVI +D P + SY+Q
Sbjct: 24 EILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLPWNPASYIQ 69
>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated
with DEXDc-, DEAD-, and DEAH-box proteins, yeast
initiation factor 4A, Ski2p, and Hepatitis C virus NS3
helicases; this domain is found in a wide variety of
helicases and helicase related proteins; may not be an
autonomously folding unit, but an integral part of the
helicase; 4 helicase superfamilies at present according
to the organization of their signature motifs; all
helicases share the ability to unwind nucleic acid
duplexes with a distinct directional polarity; they
utilize the free energy from nucleoside triphosphate
hydrolysis to fuel their translocation along DNA,
unwinding the duplex in the process.
Length = 131
Score = 56.1 bits (136), Expect = 2e-11
Identities = 18/46 (39%), Positives = 28/46 (60%)
Query: 4 QTMLSFNRGITNILVATDVLEEGIDIQSCNLVIKFDPPQHTRSYVQ 49
+ + F G +LVATDV+ GID+ + ++VI +D P SY+Q
Sbjct: 69 EVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQ 114
Score = 30.3 bits (69), Expect = 0.089
Identities = 9/38 (23%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 71 ERYLQYNSPKINRLLQLLRRY-NPDQRTIIFCQRRATI 107
+ L K+ LL+LL+ + + +IFC + +
Sbjct: 4 QYVLPVEDEKLEALLELLKEHLKKGGKVLIFCPSKKML 41
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 53.8 bits (130), Expect = 5e-11
Identities = 20/46 (43%), Positives = 28/46 (60%)
Query: 4 QTMLSFNRGITNILVATDVLEEGIDIQSCNLVIKFDPPQHTRSYVQ 49
+ + FN G +LVATDV E G+D+ +LVI +D P SY+Q
Sbjct: 28 EILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQ 73
>gnl|CDD|223587 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA
replication, recombination, and repair / Transcription /
Translation, ribosomal structure and biogenesis].
Length = 513
Score = 50.6 bits (121), Expect = 1e-08
Identities = 17/46 (36%), Positives = 23/46 (50%)
Query: 4 QTMLSFNRGITNILVATDVLEEGIDIQSCNLVIKFDPPQHTRSYVQ 49
+ + F G +LVATDV G+DI + VI +D P YV
Sbjct: 314 RALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVH 359
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 46.8 bits (112), Expect = 2e-07
Identities = 22/45 (48%), Positives = 29/45 (64%), Gaps = 2/45 (4%)
Query: 8 SFNRGITNILVATDVLEEGIDIQSCNLVIKFDP-PQHTRSYVQSK 51
F G N+LV+T V EEG+DI S +LVI ++P P RS +Q K
Sbjct: 418 KFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRS-IQRK 461
Score = 28.7 bits (65), Expect = 0.56
Identities = 12/31 (38%), Positives = 19/31 (61%), Gaps = 3/31 (9%)
Query: 79 PKINRLLQLLRR---YNPDQRTIIFCQRRAT 106
PK+ +L ++++ NPD R I+F Q R T
Sbjct: 347 PKLEKLREIVKEQLGKNPDSRIIVFTQYRDT 377
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 45.0 bits (107), Expect = 1e-06
Identities = 17/37 (45%), Positives = 25/37 (67%)
Query: 4 QTMLSFNRGITNILVATDVLEEGIDIQSCNLVIKFDP 40
+ + F +G N+LVAT V EEG+DI +LVI ++P
Sbjct: 416 EIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEP 452
Score = 30.0 bits (68), Expect = 0.17
Identities = 11/34 (32%), Positives = 18/34 (52%), Gaps = 3/34 (8%)
Query: 76 YNSPKINRLLQLLRRY---NPDQRTIIFCQRRAT 106
PK+ +L ++L+ N D R I+F + R T
Sbjct: 345 VEHPKLEKLREILKEQLEKNGDSRVIVFTEYRDT 378
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 43.8 bits (104), Expect = 3e-06
Identities = 18/45 (40%), Positives = 25/45 (55%)
Query: 4 QTMLSFNRGITNILVATDVLEEGIDIQSCNLVIKFDPPQHTRSYV 48
+ + G N+LVATDV GIDI + VI FD P+ +Y+
Sbjct: 286 EAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYL 330
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 41.7 bits (98), Expect = 1e-05
Identities = 18/43 (41%), Positives = 26/43 (60%)
Query: 6 MLSFNRGITNILVATDVLEEGIDIQSCNLVIKFDPPQHTRSYV 48
M F G T +L+ TD+L GID+Q +LVI +D P +Y+
Sbjct: 310 MREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYI 352
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 40.6 bits (96), Expect = 4e-05
Identities = 13/36 (36%), Positives = 22/36 (61%)
Query: 4 QTMLSFNRGITNILVATDVLEEGIDIQSCNLVIKFD 39
Q ++ F ++LVATDV G+DI++ VI ++
Sbjct: 283 QVLVRFANRSCSVLVATDVAARGLDIKALEAVINYE 318
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 39.8 bits (93), Expect = 6e-05
Identities = 18/45 (40%), Positives = 28/45 (62%)
Query: 4 QTMLSFNRGITNILVATDVLEEGIDIQSCNLVIKFDPPQHTRSYV 48
QT+ G +IL+ATDV G+D++ +LV+ +D P + SYV
Sbjct: 286 QTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYV 330
>gnl|CDD|233032 TIGR00580, mfd, transcription-repair coupling factor (mfd). All
proteins in this family for which functions are known
are DNA-dependent ATPases that function in the process
of transcription-coupled DNA repair in which the repair
of the transcribed strand of actively transcribed genes
is repaired at a higher rate than the repair of
non-transcribed regions of the genome and than the
non-transcribed strand of the same gene. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University). This family is
closely related to the RecG and UvrB families [DNA
metabolism, DNA replication, recombination, and repair].
Length = 926
Score = 38.9 bits (91), Expect = 2e-04
Identities = 14/35 (40%), Positives = 20/35 (57%)
Query: 5 TMLSFNRGITNILVATDVLEEGIDIQSCNLVIKFD 39
ML F +G +LV T ++E GIDI + N +I
Sbjct: 704 VMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIER 738
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 38.2 bits (89), Expect = 3e-04
Identities = 16/40 (40%), Positives = 22/40 (55%)
Query: 9 FNRGITNILVATDVLEEGIDIQSCNLVIKFDPPQHTRSYV 48
F G + I++ATDV G+D++ VI FD P YV
Sbjct: 423 FKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYV 462
>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II
helicase) [DNA replication, recombination, and repair /
Transcription].
Length = 1139
Score = 38.0 bits (89), Expect = 3e-04
Identities = 14/33 (42%), Positives = 21/33 (63%)
Query: 4 QTMLSFNRGITNILVATDVLEEGIDIQSCNLVI 36
+ ML F G ++LV T ++E GIDI + N +I
Sbjct: 846 EVMLDFYNGEYDVLVCTTIIETGIDIPNANTII 878
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 36.0 bits (83), Expect = 0.002
Identities = 18/46 (39%), Positives = 24/46 (52%)
Query: 3 VQTMLSFNRGITNILVATDVLEEGIDIQSCNLVIKFDPPQHTRSYV 48
++T+ F G +LVATDV GI I + VI F P+ YV
Sbjct: 375 IKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYV 420
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 34.3 bits (79), Expect = 0.005
Identities = 14/41 (34%), Positives = 22/41 (53%)
Query: 9 FNRGITNILVATDVLEEGIDIQSCNLVIKFDPPQHTRSYVQ 49
F G +LV VL+EG+DI +++I P R ++Q
Sbjct: 328 FRTGGIKVLVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQ 368
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 34.1 bits (79), Expect = 0.007
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 4 QTMLSFNRGITNILVATDVLEEGIDI 29
M +F G +ILVAT V+E G+D+
Sbjct: 524 AVMEAFKEGEIDILVATTVIEVGVDV 549
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 34.0 bits (78), Expect = 0.009
Identities = 17/45 (37%), Positives = 24/45 (53%)
Query: 4 QTMLSFNRGITNILVATDVLEEGIDIQSCNLVIKFDPPQHTRSYV 48
+ M SF G ++VAT VL G+D+ VI FD P + Y+
Sbjct: 409 EVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYI 453
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 33.0 bits (75), Expect = 0.018
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 4 QTMLS-FNRGITNILVATDVLEEGIDIQSCNLVIKFDPPQHTRSYVQ 49
+++L+ F +G ILVATDV G+ I V +D P YV
Sbjct: 297 ESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVH 343
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 31.9 bits (73), Expect = 0.045
Identities = 17/40 (42%), Positives = 21/40 (52%)
Query: 9 FNRGITNILVATDVLEEGIDIQSCNLVIKFDPPQHTRSYV 48
F RG +ILVATDV G+ I + V +D P YV
Sbjct: 301 FTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYV 340
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 31.7 bits (73), Expect = 0.045
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 4 QTMLSFNRGITNILVATDVLEEGIDI 29
M +F G +ILVAT V+E G+D+
Sbjct: 522 AVMAAFKAGEIDILVATTVIEVGVDV 547
>gnl|CDD|233398 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase,
putative. This model represents a family of proteins in
Gram-positive bacteria. The N-terminal region of about
200 amino acids resembles the epsilon subunit of E. coli
DNA polymerase III and the homologous region of the
Gram-positive type DNA polymerase III alpha subunit. The
epsilon subunit contains an exonuclease domain. The
remainder of this protein family resembles a predicted
ATP-dependent helicase, the DNA damage-inducible protein
DinG of E. coli [DNA metabolism, DNA replication,
recombination, and repair].
Length = 850
Score = 30.9 bits (70), Expect = 0.085
Identities = 31/114 (27%), Positives = 40/114 (35%), Gaps = 23/114 (20%)
Query: 4 QTMLSFNRGITNILVATDVLEEGIDIQSCNLVI------KFDPPQHTRSYVQSKAFTVVR 57
+ FN G IL+ T EG+D LV F P+H +
Sbjct: 716 KIKKRFNNGEKAILLGTSSFWEGVDFPGNGLVCLVIPRLPFANPKH--PLTKKYW----- 768
Query: 58 HKAEQILSQYPKSERYLQYNSPK-INRLLQ----LLRRYNPDQRTIIFCQRRAT 106
Q L Q K+ Y Y P I RL Q L+RR N +I +R
Sbjct: 769 ----QKLEQEGKNPFY-DYVLPMAIIRLRQALGRLIRRENDRGSIVILDRRLVG 817
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 30.9 bits (70), Expect = 0.091
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 9 FNRGITNILVATDVLEEGIDIQSCNLVIKFDPPQHTRSYV 48
F G +LVATD+ G+DI+ V+ ++ P YV
Sbjct: 291 FKSGDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYV 330
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 30.7 bits (70), Expect = 0.10
Identities = 14/33 (42%), Positives = 17/33 (51%)
Query: 9 FNRGITNILVATDVLEEGIDIQSCNLVIKFDPP 41
G +VAT LE GIDI +LVI+ P
Sbjct: 300 LKEGELKAVVATSSLELGIDIGDIDLVIQLGSP 332
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 30.8 bits (70), Expect = 0.12
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 4 QTMLSFNRGITNILVATDVLEEGIDIQSCNLVIKFDP 40
M F G +ILVAT V+E G+D+ + +++ D
Sbjct: 499 AVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDA 535
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 30.7 bits (70), Expect = 0.13
Identities = 14/41 (34%), Positives = 18/41 (43%)
Query: 9 FNRGITNILVATDVLEEGIDIQSCNLVIKFDPPQHTRSYVQ 49
F ++VAT+ GID VI +D P SY Q
Sbjct: 276 FLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQ 316
>gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor;
Provisional.
Length = 1147
Score = 30.5 bits (69), Expect = 0.14
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 6 MLSFNRGITNILVATDVLEEGIDIQSCNLVI 36
M F+ N+LV T ++E GIDI + N +I
Sbjct: 854 MNDFHHQRFNVLVCTTIIETGIDIPTANTII 884
>gnl|CDD|129815 TIGR00732, dprA, DNA protecting protein DprA. Disruption of this
gene in both Haemophilus influenzae and Helicobacter
pylori drastically reduces the efficiency of
transformation with exogenous DNA, but with different
levels of effect on chromosomal (linear) and plasmid
(circular) DNA. This difference suggests the DprA is not
active in recombination, and it has been shown not to
affect DNA binding, leaving the intermediate step in
natural transformation, DNA processing. In Strep.
pneumoniae, inactivation of dprA had no effect on the
uptake of DNA. All of these data indicated that DprA is
required at a later stage in transformation.
Subsequently DprA and RecA were both shown in S.
pneumoniae to be required to protect incoming ssDNA from
immediate degradation. Role of DprA in non-transformable
species is not known. The gene symbol smf was assigned
in E. coli, but without assignment of function [Cellular
processes, DNA transformation].
Length = 220
Score = 28.8 bits (65), Expect = 0.44
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 12/54 (22%)
Query: 40 PPQHTRSYVQSKAFTVVRHKAEQ---ILSQYPKSERYLQYNSPKINRLLQLLRR 90
P Q+++ + AE +LS+YP + ++YN PK NR++ L R
Sbjct: 113 PRQNSK---------LAAKIAENGGLLLSEYPPDTKPIKYNFPKRNRIISGLSR 157
>gnl|CDD|130456 TIGR01389, recQ, ATP-dependent DNA helicase RecQ. The
ATP-dependent DNA helicase RecQ of E. coli is about 600
residues long. This model represents bacterial proteins
with a high degree of similarity in domain architecture
and in primary sequence to E. coli RecQ. The model
excludes eukaryotic and archaeal proteins with RecQ-like
regions, as well as more distantly related bacterial
helicases related to RecQ [DNA metabolism, DNA
replication, recombination, and repair].
Length = 591
Score = 28.5 bits (64), Expect = 0.67
Identities = 14/41 (34%), Positives = 20/41 (48%)
Query: 9 FNRGITNILVATDVLEEGIDIQSCNLVIKFDPPQHTRSYVQ 49
F ++VAT+ GID + VI +D P + SY Q
Sbjct: 270 FLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQ 310
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 28.6 bits (64), Expect = 0.72
Identities = 11/28 (39%), Positives = 18/28 (64%), Gaps = 1/28 (3%)
Query: 9 FNRGITNILVATDVLEEGIDIQSCNLVI 36
F + I+VAT V+E G+DI +++I
Sbjct: 490 FKQNEGFIVVATQVIEAGVDI-DFDVLI 516
>gnl|CDD|219230 pfam06925, MGDG_synth, Monogalactosyldiacylglycerol (MGDG)
synthase. This family represents a conserved region of
approximately 180 residues within plant and bacterial
monogalactosyldiacylglycerol (MGDG) synthase
(EC:2.4.1.46). In Arabidopsis, there are two types of
MGDG synthase which differ in their N-terminal portion:
type A and type B.
Length = 169
Score = 27.7 bits (62), Expect = 0.85
Identities = 8/37 (21%), Positives = 13/37 (35%), Gaps = 3/37 (8%)
Query: 65 SQYPKSERYLQYNSPKINRLLQLLRRYNPDQRTIIFC 101
+ P + + L LL+ + PD II
Sbjct: 62 PKIPHKSILAKLATFFARELAALLKEFQPD---IIIS 95
>gnl|CDD|132756 cd07071, NR_LBD_Nurr1, The ligand binding domain of Nurr1, a
member of conserved family of nuclear receptors. The
ligand binding domain of nuclear receptor Nurr1: Nurr1
belongs to the conserved family of nuclear receptors. It
is a transcription factor that is expressed in the
embryonic ventral midbrain and is critical for the
development of dopamine (DA) neurons. Structural studies
have shown that the ligand binding pocket of Nurr1 is
filled by bulky hydrophobic residues, making it unable
to bind to ligands. Therefore, it belongs to the class
of orphan receptors. However, Nurr1 forms heterodimers
with RXR and can promote signaling via its partner, RXR.
Like other members of the nuclear receptor (NR)
superfamily of ligand-activated transcription factors,
Nurr1 has a central well conserved DNA binding domain
(DBD), a variable N-terminal domain, a flexible hinge
and a C-terminal ligand binding domain (LBD).
Length = 238
Score = 27.3 bits (60), Expect = 1.4
Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 5/68 (7%)
Query: 39 DPPQHTRSY--VQSKAFTVVRHKAEQI--LSQYPKSERYLQYNSPKINR-LLQLLRRYNP 93
D QH + + + + + ++R AE+I + PK+++ L + S + +L+L R NP
Sbjct: 38 DDTQHIQQFYDLLTGSMEIIRGWAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNP 97
Query: 94 DQRTIIFC 101
+ +IFC
Sbjct: 98 VEGKLIFC 105
>gnl|CDD|218986 pfam06317, Arena_RNA_pol, Arenavirus RNA polymerase. This family
consists of several Arenavirus RNA polymerase proteins
(EC:2.7.7.48).
Length = 2206
Score = 26.9 bits (60), Expect = 2.6
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 3/43 (6%)
Query: 49 QSKAFTVVRHKAEQILSQYPKSER---YLQYNSPKINRLLQLL 88
QS F ++ E+ LS+ KS + N+ IN L +L
Sbjct: 901 QSDYFDEIKESVEKTLSKMRKSRKAKSGNLKNTKSINDLERLW 943
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 27.0 bits (60), Expect = 2.6
Identities = 15/42 (35%), Positives = 22/42 (52%)
Query: 8 SFNRGITNILVATDVLEEGIDIQSCNLVIKFDPPQHTRSYVQ 49
+F R I+VAT GI+ + V+ FD P++ SY Q
Sbjct: 281 AFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQ 322
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 26.8 bits (59), Expect = 2.9
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 17 LVATDVLEEGIDIQSCNLVIKFDPPQHTRSYVQ 49
+VAT LE GID+ + +LVI+ P S +Q
Sbjct: 331 VVATSSLELGIDMGAVDLVIQVATPLSVASGLQ 363
>gnl|CDD|220229 pfam09418, DUF2009, Protein of unknown function (DUF2009). This is
a eukaryotic family of proteins with unknown function.
Length = 458
Score = 26.6 bits (59), Expect = 3.1
Identities = 18/76 (23%), Positives = 29/76 (38%), Gaps = 19/76 (25%)
Query: 40 PPQHTRSYVQSKAFTVVRHKAEQILSQYPKSER-----------------YLQYNSPKIN 82
P TR+ +Q +A E + +Y S+ YL N +
Sbjct: 164 PEGKTRNQIQ-RAIKQKERAVETLAKKYSSSKLSKEDVRQCLYSLADYNAYLNANRDPVE 222
Query: 83 RLLQLLRRY-NPDQRT 97
R+L+LL + +PD T
Sbjct: 223 RMLELLEEFFSPDSAT 238
>gnl|CDD|236912 PRK11448, hsdR, type I restriction enzyme EcoKI subunit R;
Provisional.
Length = 1123
Score = 26.5 bits (59), Expect = 3.3
Identities = 13/22 (59%), Positives = 16/22 (72%), Gaps = 1/22 (4%)
Query: 15 NILVATDVLEEGIDIQS-CNLV 35
NI+V D+L GID+ S CNLV
Sbjct: 758 NIVVTVDLLTTGIDVPSICNLV 779
>gnl|CDD|216012 pfam00590, TP_methylase, Tetrapyrrole (Corrin/Porphyrin)
Methylases. This family uses S-AdoMet in the
methylation of diverse substrates. This family includes
a related group of bacterial proteins of unknown
function. This family includes the methylase Dipthine
synthase.
Length = 202
Score = 25.8 bits (57), Expect = 4.4
Identities = 7/65 (10%), Positives = 19/65 (29%), Gaps = 3/65 (4%)
Query: 40 PPQHTRSYVQSKAFTVVRHKAEQILSQYPKSERYLQY-NSPKINRLLQLLRRYNPDQRTI 98
P V S + ++L + + + ++ + +LL D +
Sbjct: 123 PLTDGG--VVSLHGRGLETLRARLLEALLAGDTLVLLTDPHRLAEIAELLLELGDDDTPV 180
Query: 99 IFCQR 103
+
Sbjct: 181 AVVEN 185
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 26.0 bits (58), Expect = 4.4
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 11 RGITNILVATDVLEEGIDIQSCNLVIKFD 39
G ++LV ++L EG+D+ +LV D
Sbjct: 494 LGEFDVLVGINLLREGLDLPEVSLVAILD 522
>gnl|CDD|236914 PRK11466, PRK11466, hybrid sensory histidine kinase TorS;
Provisional.
Length = 914
Score = 26.0 bits (57), Expect = 4.7
Identities = 13/27 (48%), Positives = 13/27 (48%)
Query: 72 RYLQYNSPKINRLLQLLRRYNPDQRTI 98
R L S KIN LLQ LR D I
Sbjct: 83 RMLTAQSLKINALLQALREQGFDTTAI 109
>gnl|CDD|237011 PRK11892, PRK11892, pyruvate dehydrogenase subunit beta;
Provisional.
Length = 464
Score = 26.0 bits (58), Expect = 4.8
Identities = 15/34 (44%), Positives = 22/34 (64%), Gaps = 2/34 (5%)
Query: 2 DVQTMLSFNRGITNILVATDVLE-EGIDIQSCNL 34
DV T++SF+ G+T L A + L EGID + +L
Sbjct: 342 DV-TIVSFSIGMTYALKAAEELAKEGIDAEVIDL 374
>gnl|CDD|222037 pfam13307, Helicase_C_2, Helicase C-terminal domain. This domain
is the second of two tandem AAA domains found in a wide
variety of helicase enzymes.
Length = 165
Score = 25.6 bits (57), Expect = 4.9
Identities = 27/119 (22%), Positives = 37/119 (31%), Gaps = 23/119 (19%)
Query: 2 DVQTMLS-FNRGITNILVATDVLEEGIDIQ--SCNLVI----KFDPPQHTRSYVQSKAFT 54
+ +L F +G IL EGID + LVI F P
Sbjct: 47 SREKLLERFKKGKGAILFGVGSFWEGIDFPGDALRLVIIVGLPFPSPDDPL--------- 97
Query: 55 VVRHKAEQILSQYPKSERYLQYNSPKINRLLQ----LLRRYNPDQRTIIFCQRRATIPR 109
V + E + Q R Y I +L Q L+R + D +I R
Sbjct: 98 -VEARREYLDKQGKDGFREY-YLPQAIRKLNQAIGRLIRHED-DYGVVILLDERLLTRS 153
>gnl|CDD|183143 PRK11459, PRK11459, multidrug resistance outer membrane protein
MdtQ; Provisional.
Length = 478
Score = 26.1 bits (57), Expect = 4.9
Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 41 PQH-TRSYV--QSKAFTVVRHKAEQILSQYPKSERYLQYNSPKINRLLQLLRRYNPD 94
P H TR + Q+ A V + + +P S+ + Y+ +++ L+ + PD
Sbjct: 24 PMHETRQALSQQTPAAHVDTALPTALKNGWPDSQWWKAYHDNQLDSLINNALQNAPD 80
>gnl|CDD|190308 pfam02434, Fringe, Fringe-like. The drosophila protein fringe
(FNG) is a glucosaminyltransferase that controls the
response of the Notch receptor to specific ligands. FNG
is localised to the Golgi apparatus (not secreted as
previously thought). Modification of Notch occurs
through glycosylation by FNG. The xenopus homologue,
lunatic fringe, has been implicated in a variety of
functions.
Length = 248
Score = 25.7 bits (57), Expect = 5.0
Identities = 7/13 (53%), Positives = 9/13 (69%)
Query: 83 RLLQLLRRYNPDQ 95
RL++LL YN Q
Sbjct: 101 RLVRLLSCYNHTQ 113
>gnl|CDD|176569 cd08632, PI-PLCc_eta1, Catalytic domain of metazoan
phosphoinositide-specific phospholipase C-eta1. This
subfamily corresponds to the catalytic domain present in
metazoan phosphoinositide-specific phospholipase C
(PI-PLC, EC 3.1.4.11)-eta isozyme 1. PI-PLC is a
signaling enzyme that hydrolyzes the membrane
phospholipids phosphatidylinositol-4,5-bisphosphate
(PIP2) to generate two important second messengers in
eukaryotic signal transduction cascades, Inositol
1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG).
InsP3 triggers inflow of calcium from intracellular
stores, while DAG, together with calcium, activates
protein kinase C, which then phosphorylates other
molecules, leading to altered cellular activity. Calcium
is required for the catalysis. PI-PLC-eta represents a
class of neuron-speific PI-PLC that has an N-terminal
pleckstrin homology (PH) domain, an array of EF hands, a
PLC catalytic core domain, a C2 domain, and a unique
C-terminal tail that terminates with a PDZ-binding
motif, a potential interaction site for other signaling
proteins. The PLC catalytic core domain is a TIM barrel
with two highly conserved regions (X and Y) split by a
highly degenerate linker sequence. PI-PLC-eta1 is a
neuron-specific enzyme and expressed in only nerve
tissues such as the brain and spinal cord. It may
perform a fundamental role in the brain.
Length = 253
Score = 25.8 bits (56), Expect = 5.0
Identities = 16/71 (22%), Positives = 35/71 (49%), Gaps = 23/71 (32%)
Query: 14 TNILVATDVLEEGIDIQSCNLVIKFDPPQHTRSYVQSKAFTVVRHKAEQILSQYPKSERY 73
TN + A D++++G + N++ S+ +++A +V+ KAEQ +
Sbjct: 160 TNSVAAQDIVDDG---STGNVL----------SFSETRAHQLVQQKAEQ----------F 196
Query: 74 LQYNSPKINRL 84
+ YN ++ R+
Sbjct: 197 MTYNQKQLTRI 207
>gnl|CDD|217060 pfam02481, DNA_processg_A, DNA recombination-mediator protein A.
The SMF family, of DNA processing chain A, dprA, are a
group of bacterial proteins. In H. pylori, dprA is
required for natural chromosomal and plasmid
transformation. It has now been shown that DprA is found
to bind cooperatively to single-stranded DNA (ssDNA) and
to interact with RecA. In the process, DprA-RecA-ssDNA
filaments are produced and these filaments catalyze the
homology-dependent formation of joint molecules. While
the E.coli SSB protein limits access of RecA to ssDNA,
DprA alleviates this barrier. It is proposed that DprA
is a new member of the recombination-mediator protein
family, dedicated to natural bacterial transformation.
Length = 210
Score = 25.2 bits (56), Expect = 6.7
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 63 ILSQYPKSERYLQYNSPKINRL 84
+LS+YP + +Y+ P NR+
Sbjct: 128 LLSEYPPGTKPSRYHFPARNRI 149
>gnl|CDD|187849 cd09718, Cas1_I-F, CRISPR/Cas system-associated protein Cas1.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas1 is the most universal CRISPR system protein thought
to be involved in spacer integration; Cas1 is
metal-dependent deoxyribonuclease, also binds RNA; Shown
to possess a unique fold consisting of a N-terminal
beta-strand domain and a C-terminal alpha-helical
domain.
Length = 306
Score = 25.1 bits (55), Expect = 8.3
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 2/45 (4%)
Query: 50 SKAFTVVRHKAEQILSQYPKSERYLQYNSPKINRLLQLLRRYNPD 94
+KAF ++R E + + KS ++ P N L LL RY D
Sbjct: 122 AKAFQLIR--IELLSQHWKKSLDLKEHFYPDENALEALLNRYEQD 164
>gnl|CDD|143344 cd07839, STKc_CDK5, Catalytic domain of the Serine/Threonine
Kinase, Cyclin-Dependent protein Kinase 5.
Serine/Threonine Kinases (STKs), Cyclin-Dependent
protein Kinase 5 (CDK5) subfamily, catalytic (c) domain.
STKs catalyze the transfer of the gamma-phosphoryl group
from ATP to serine/threonine residues on protein
substrates. The CDK5 subfamily is part of a larger
superfamily that includes the catalytic domains of other
protein STKs, protein tyrosine kinases, RIO kinases,
aminoglycoside phosphotransferase, choline kinase, and
phosphoinositide 3-kinase. CDKs belong to a large family
of STKs that are regulated by their cognate cyclins.
Together, they are involved in the control of cell-cycle
progression, transcription, and neuronal function. CDK5
is unusual in that it is regulated by non-cyclin
proteins, p35 and p39. It is highly expressed in the
nervous system and is critical in normal neural
development and function. It plays a role in neuronal
migration and differentiation, and is also important in
synaptic plasticity and learning. CDK5 also participates
in protecting against cell death and promoting
angiogenesis. Impaired CDK5 activity is implicated in
Alzheimer's disease, amyotrophic lateral sclerosis,
Parkinson's disease, Huntington's disease and acute
neuronal injury.
Length = 284
Score = 25.1 bits (55), Expect = 8.8
Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 12/45 (26%)
Query: 64 LSQYPKSERYLQYNS--------PKINR----LLQLLRRYNPDQR 96
+S+ P + Y Y + PK+N LLQ L NP QR
Sbjct: 228 VSKLPDYKPYPMYPATTSLVNVVPKLNSTGRDLLQNLLVCNPVQR 272
>gnl|CDD|236909 PRK11424, PRK11424, DNA-binding transcriptional activator TdcR;
Provisional.
Length = 114
Score = 24.6 bits (53), Expect = 8.9
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 13/78 (16%)
Query: 33 NLVIKFDPPQHTRSYVQSKAFTVVRHKAEQILSQYPKSERYLQYNSPK-----INRLLQL 87
NL+ KF +++ +K F+ + + A I S+Y ++L Y K I+ L QL
Sbjct: 41 NLMSKFS------NFIINKPFSAINNAARHIFSRYLLENKHLFYQYFKISNTGIDHLEQL 94
Query: 88 LRR--YNPDQRTIIFCQR 103
+ ++ D+ + C R
Sbjct: 95 INVNFFSSDRTSFCECNR 112
>gnl|CDD|223829 COG0758, Smf, Predicted Rossmann fold nucleotide-binding protein
involved in DNA uptake [DNA replication, recombination,
and repair / Intracellular trafficking and secretion].
Length = 350
Score = 25.0 bits (55), Expect = 9.0
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 63 ILSQYPKSERYLQYNSPKINRLL 85
++S+YP + N P+ NRL+
Sbjct: 196 LISEYPPDTEPNKGNFPRRNRLI 218
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 25.2 bits (55), Expect = 9.2
Identities = 22/106 (20%), Positives = 37/106 (34%), Gaps = 22/106 (20%)
Query: 9 FNRGITNILVATDVLEEGIDIQ--SCNLVI----KFDPPQHTRSYVQSKAFTVVRHKAEQ 62
G ILV EG+D + LV+ F P +++ + E
Sbjct: 524 KASGEGLILVGGGSFWEGVDFPGDALRLVVIVGLPFPNPDD----------PLLKARLE- 572
Query: 63 ILSQYPKSERYLQYNSPKINRLLQ----LLRRYNPDQRTIIFCQRR 104
L + Y P + +L Q L+R + D+ I+ +R
Sbjct: 573 FLKRLGGDPFEEFYLPPAVIKLRQAVGRLIRSED-DRGVIVLLDKR 617
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 0.137 0.394
Gapped
Lambda K H
0.267 0.0781 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,465,744
Number of extensions: 453679
Number of successful extensions: 840
Number of sequences better than 10.0: 1
Number of HSP's gapped: 838
Number of HSP's successfully gapped: 78
Length of query: 109
Length of database: 10,937,602
Length adjustment: 74
Effective length of query: 35
Effective length of database: 7,655,406
Effective search space: 267939210
Effective search space used: 267939210
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: 53 (24.1 bits)