RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11637
(67 letters)
>gnl|CDD|233046 TIGR00603, rad25, DNA repair helicase rad25. All proteins in this
family for which functions are known are DNA-DNA
helicases used for the initiation of nucleotide excision
repair and transacription as part of the TFIIH
complex.This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 732
Score = 149 bits (378), Expect = 3e-44
Identities = 50/62 (80%), Positives = 54/62 (87%)
Query: 3 IDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNS 62
IDLKP+ +RPYQEKSL KMFGNGRARSG+IVLPCGAGKSLVGVTA CTV+K LVLC S
Sbjct: 248 IDLKPTTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTVKKSCLVLCTS 307
Query: 63 GV 64
V
Sbjct: 308 AV 309
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 71.3 bits (175), Expect = 1e-16
Identities = 25/52 (48%), Positives = 33/52 (63%), Gaps = 1/52 (1%)
Query: 10 VLRPYQEKSLRKMFGNGRA-RSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
LRPYQE++L + N R R GVIVLP GAGK++V A +++ LVL
Sbjct: 36 ELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAELKRSTLVLV 87
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 41.4 bits (98), Expect = 1e-06
Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 6/56 (10%)
Query: 10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVG---VTACCTVRKRALVLCNS 62
LRPYQE+++ ++ R G+IV+ G+GK+L + +K+ L +
Sbjct: 3 ELRPYQEEAIERLLEKKR---GLIVMATGSGKTLTAAALIARLAKGKKKVLFVVPR 55
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 40.2 bits (94), Expect = 1e-05
Identities = 16/63 (25%), Positives = 27/63 (42%), Gaps = 7/63 (11%)
Query: 3 IDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAC-----CTVRKRAL 57
I+ LRPYQ++++ + R ++ P G+GK+L + R L
Sbjct: 1 IEKFGFEPLRPYQKEAIEALLSGLR--DVILAAPTGSGKTLAALLPALEALKRGKGGRVL 58
Query: 58 VLC 60
VL
Sbjct: 59 VLV 61
>gnl|CDD|234468 TIGR04095, dnd_restrict_1, DNA phosphorothioation system
restriction enzyme. The DNA phosphorothioate
modification system dnd (DNA instability during
electrophoresis) recently has been shown to provide a
modification essential to a restriction system. This
protein family was detected by Partial Phylogenetic
Profiling as linked to dnd, and its members usually are
clustered with the dndABCDE genes.
Length = 451
Score = 31.5 bits (72), Expect = 0.013
Identities = 16/43 (37%), Positives = 26/43 (60%), Gaps = 4/43 (9%)
Query: 7 PSAVLRPYQEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTA 48
P+ LR YQ++++R F N GR G++ + G GK+L + A
Sbjct: 5 PTFELRDYQKEAIRAWFKNNGR---GILKMATGTGKTLTALAA 44
>gnl|CDD|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA
ligase-associated. Members of this protein family are
DEAD/DEAH box helicases found associated with a
bacterial ATP-dependent DNA ligase, part of a four-gene
system that occurs in about 12 % of prokaryotic
reference genomes. The actual motif in this family is
DE[VILW]H.
Length = 803
Score = 31.0 bits (71), Expect = 0.021
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 11 LRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVG 45
RP+Q + GR SG+++ P G+GK+L G
Sbjct: 14 PRPFQLEMWAA-ALEGR--SGLLIAPTGSGKTLAG 45
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 30.5 bits (69), Expect = 0.035
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 3/36 (8%)
Query: 11 LRPYQEKSLRKMFGNGRARSGVIVL--PCGAGKSLV 44
QEK+L + RS ++VL P G GK+
Sbjct: 196 GYELQEKALELIL-RLEKRSLLVVLEAPTGYGKTEA 230
>gnl|CDD|215193 PLN02337, PLN02337, lipoxygenase.
Length = 866
Score = 27.0 bits (60), Expect = 0.64
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 9 AVLRPYQEKSLRKMFGNGR 27
A LRPY+E+ L + G+G+
Sbjct: 172 APLRPYREEELVNLRGDGK 190
>gnl|CDD|222858 PHA02533, 17, large terminase protein; Provisional.
Length = 534
Score = 26.9 bits (60), Expect = 0.68
Identities = 11/35 (31%), Positives = 15/35 (42%), Gaps = 3/35 (8%)
Query: 10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLV 44
+R YQ+ L+ M N R L GK+ V
Sbjct: 59 QMRDYQKDMLKIMHKN---RFNACNLSRQLGKTTV 90
>gnl|CDD|222875 PHA02558, uvsW, UvsW helicase; Provisional.
Length = 501
Score = 25.7 bits (57), Expect = 1.5
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 3/33 (9%)
Query: 12 RPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLV 44
YQ ++ + N R ++ LP AGKSL+
Sbjct: 116 HWYQYDAVYEGLKNNR---RLLNLPTSAGKSLI 145
>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 = 25.8 bits (57), Expect = 1.6
Identities = 19/54 (35%), Positives = 26/54 (48%), Gaps = 10/54 (18%)
Query: 12 RPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVV 65
RP QE+ + + R ++V+P G GKSL C V AL+L VV
Sbjct: 15 RPGQEEIISHVL---DGRDVLVVMPTGGGKSL-----CYQV--PALLLKGLTVV 58
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 25.8 bits (57), Expect = 1.7
Identities = 9/37 (24%), Positives = 16/37 (43%), Gaps = 5/37 (13%)
Query: 29 RSGVIVLPCGAGKSLVGVTACCTV-----RKRALVLC 60
R ++ P G+GK+L + + + LVL
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLA 37
>gnl|CDD|238071 cd00124, MYSc, Myosin motor domain. This catalytic (head) domain
has ATPase activity and belongs to the larger group of
P-loop NTPases. Myosins are actin-dependent molecular
motors that play important roles in muscle contraction,
cell motility, and organelle transport. The head domain
is a molecular motor, which utilizes ATP hydrolysis to
generate directed movement toward the plus end along
actin filaments. A cyclical interaction between myosin
and actin provides the driving force. Rates of ATP
hydrolysis and consequently the speed of movement along
actin filaments vary widely, from about 0.04 micrometer
per second for myosin I to 4.5 micrometer per second for
myosin II in skeletal muscle. Myosin II moves in
discrete steps about 5-10 nm long and generates 1-5
piconewtons of force. Upon ATP binding, the myosin head
dissociates from an actin filament. ATP hydrolysis
causes the head to pivot and associate with a new actin
subunit. The release of Pi causes the head to pivot and
move the filament (power stroke). Release of ADP
completes the cycle.
Length = 679
Score = 25.7 bits (57), Expect = 2.0
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 16 EKSLRKMFGNGRARSGVIVLPCGAGKS 42
+++ R M + R +S +I GAGK+
Sbjct: 74 DRAYRNMLRDRRNQSIIISGESGAGKT 100
>gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family.
All proteins in this family for which functions are
known are 3'-5' DNA-DNA helicases. These proteins are
used for recombination, recombinational repair, and
possibly maintenance of chromosome stability. This
family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and
repair].
Length = 470
Score = 25.5 bits (56), Expect = 2.2
Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 3/49 (6%)
Query: 12 RPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
RP Q + + + R +V+P G GKSL LV+
Sbjct: 13 RPVQLEVINAVL---LGRDCFVVMPTGGGKSLCYQLPALCSDGITLVIS 58
>gnl|CDD|216835 pfam01994, Trm56, tRNA ribose 2'-O-methyltransferase, aTrm56. This
family is an aTrm56 that catalyzes the 2'-O-methylation
of the cytidine residue in archaeal tRNA, using
S-adenosyl-L-methionine. Biochemical assays showed that
aTrm56 forms a dimer and prefers the L-shaped tRNA to
the lambda form as its substrate. aTrm56 consists of the
SPOUT domain, which contains the characteristic deep
trefoil knot for AdoMet binding, and a unique C-terminal
beta-hairpin.
Length = 121
Score = 24.8 bits (55), Expect = 3.4
Identities = 9/33 (27%), Positives = 17/33 (51%), Gaps = 4/33 (12%)
Query: 12 RPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLV 44
R ++ K L + F + + + V+P GK +V
Sbjct: 91 RLFEGKELEREFEDAKLK----VIPSERGKRVV 119
>gnl|CDD|240399 PTZ00393, PTZ00393, protein tyrosine phosphatase; Provisional.
Length = 241
Score = 24.1 bits (52), Expect = 5.6
Identities = 7/40 (17%), Positives = 13/40 (32%)
Query: 13 PYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV 52
++ G+ R R GV + ++ C V
Sbjct: 13 ESHPPCNNRISGSSRGRDGVCSRSSASIPNIGRRRNCDQV 52
>gnl|CDD|184642 PRK14353, glmU, bifunctional N-acetylglucosamine-1-phosphate
uridyltransferase/glucosamine-1-phosphate
acetyltransferase; Provisional.
Length = 446
Score = 24.4 bits (54), Expect = 5.8
Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 14/64 (21%)
Query: 15 QEKSLRKMFGNGRARSGVIVL------PCGAGKSLV---GVTAC-----CTVRKRALVLC 60
++L ++ + V+VL P G G+ +V + A + +RA+ LC
Sbjct: 113 TAETLARLRERLADGADVVVLGFRAADPTGYGRLIVKGGRLVAIVEEKDASDEERAITLC 172
Query: 61 NSGV 64
NSGV
Sbjct: 173 NSGV 176
>gnl|CDD|234391 TIGR03906, quino_hemo_SAM, quinohemoprotein amine dehydrogenase
maturation protein. Members of this protein family are
radical SAM enzymes responsible for post-translational
modifications to the gamma subunit of quinohemoprotein
amine dehydrogenases. Ono, et al. (PMID:16546999)
suggest that this protein is responsible for
intrapeptidyl thioether cross-linking rather than
cysteine tryptophylquinone biogenesis in the gamma
subunit [Protein fate, Protein modification and repair].
Length = 467
Score = 24.3 bits (53), Expect = 6.4
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 34 VLPCGAGKSLVGV 46
VLPCGAG L+ V
Sbjct: 342 VLPCGAGLGLLAV 354
>gnl|CDD|152407 pfam11972, HTH_13, HTH DNA binding domain. This is a
helix-turn-helix DNA binding domain.
Length = 54
Score = 22.7 bits (49), Expect = 9.4
Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 2 TIDLKPSAVLRPYQEKSLRKMFGNGRARS-GVI 33
+ + P A LR +E LR+M G GR R+ G++
Sbjct: 22 ELKVTPRAALRLVKELGLREMTGRGRFRAWGIL 54
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
0.327 0.140 0.433
Gapped
Lambda K H
0.267 0.0643 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,307,190
Number of extensions: 244404
Number of successful extensions: 302
Number of sequences better than 10.0: 1
Number of HSP's gapped: 299
Number of HSP's successfully gapped: 19
Length of query: 67
Length of database: 10,937,602
Length adjustment: 38
Effective length of query: 29
Effective length of database: 9,252,150
Effective search space: 268312350
Effective search space used: 268312350
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.4 bits)