RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14273
(115 letters)
>gnl|CDD|214693 smart00488, DEXDc2, DEAD-like helicases superfamily.
Length = 289
Score = 85.5 bits (212), Expect = 2e-21
Identities = 28/55 (50%), Positives = 33/55 (60%)
Query: 24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK 78
F FP++ Y IQ FM+ L LD K GI ESPTGTGK+LSL+C L W
Sbjct: 2 LFYFPYEPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFP 56
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 50.2 bits (120), Expect = 2e-08
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW 73
FP F+ Q + + L + + E+PTGTGK+L+ + L +
Sbjct: 10 AFP-GFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAY 58
>gnl|CDD|233047 TIGR00604, rad3, DNA repair helicase (rad3). All proteins in
this family for which funcitons are known are DNA-DNA
helicases that funciton in the initiation of
transcription and nucleotide excision repair 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 = 705
Score = 49.7 bits (119), Expect = 3e-08
Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 12/78 (15%)
Query: 27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW-----------Y 74
FP++ Y Q ++M++L +LD I E P+GTGK++SL+ IL + Y
Sbjct: 6 FPYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIY 65
Query: 75 SDHKIAGLEKIEAEIKDL 92
+ + LE+ E++ L
Sbjct: 66 ASRTHSQLEQATEELRKL 83
>gnl|CDD|236148 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 928
Score = 36.5 bits (85), Expect = 0.001
Identities = 18/72 (25%), Positives = 28/72 (38%), Gaps = 9/72 (12%)
Query: 2 ASKTPNEDKEFKEQR--PLAEVPSE----FPFPFDAYDI---QSNFMKNLYYTLDNSKFG 52
A + +K +E + Y+ Q MK +Y L +S+
Sbjct: 220 ALRKREVEKNLEETCRSDFDAFLEKTEEKLSLAMPKYEKREGQQEMMKEVYTALRDSEHA 279
Query: 53 IFESPTGTGKSL 64
+ E+ TGTGKSL
Sbjct: 280 LIEAGTGTGKSL 291
>gnl|CDD|187839 cd09708, Csf4_U, CRISPR/Cas system-associated DinG family
helicase Csf4. 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;
DinG family DNA helicase.
Length = 632
Score = 33.0 bits (75), Expect = 0.024
Identities = 13/44 (29%), Positives = 23/44 (52%)
Query: 35 QSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK 78
Q+ F +N +L + G+ E+ TG GK+L++I L +
Sbjct: 2 QALFYRNCLTSLRQKRIGMLEASTGVGKTLAMIMAALTMLKERP 45
>gnl|CDD|234113 TIGR03117, cas_csf4, CRISPR type AFERR-associated DEAD/DEAH-box
helicase Csf4. Members of this family show up near
CRISPR repeats in Acidithiobacillus ferrooxidans ATCC
23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens
DSM 15236. In the latter two species, the CRISPR/cas
locus is found on a plasmid. This family is one of
several characteristic of a type of CRISPR-associated
(cas) gene cluster we designate Aferr after A.
ferrooxidans, where it is both chromosomal and the only
type of cas gene cluster found. The gene is designated
csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein
1), as it lies farthest (fourth closest) from the
repeats in the A. ferrooxidans genome [Mobile and
extrachromosomal element functions, Other].
Length = 636
Score = 32.6 bits (74), Expect = 0.029
Identities = 13/44 (29%), Positives = 22/44 (50%)
Query: 35 QSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK 78
Q+ F N +L + G+ E+ TG GK+L++I L +
Sbjct: 2 QALFYLNCLTSLRQKRIGMLEASTGVGKTLAMIMAALTMLKERP 45
>gnl|CDD|236966 PRK11747, dinG, ATP-dependent DNA helicase DinG; Provisional.
Length = 697
Score = 30.6 bits (70), Expect = 0.15
Identities = 10/17 (58%), Positives = 13/17 (76%), Gaps = 1/17 (5%)
Query: 55 ESPTGTGKSLS-LICGI 70
E+ TG GK+LS L+ GI
Sbjct: 55 EAGTGVGKTLSYLLAGI 71
>gnl|CDD|182893 PRK11000, PRK11000, maltose/maltodextrin transporter ATP-binding
protein; Provisional.
Length = 369
Score = 29.2 bits (66), Expect = 0.42
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 10/46 (21%)
Query: 40 KNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLEKI 85
K++ + +F +F P+G GKS L IAGLE I
Sbjct: 20 KDINLDIHEGEFVVFVGPSGCGKSTLLRM----------IAGLEDI 55
>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 = 29.0 bits (65), Expect = 0.50
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 35 QSNFMKNLYYTLDNSKFGIFESPTGTGKSL 64
Q + + L +S+ + E+PTGTGK+L
Sbjct: 250 QLKLAELVLDQLTHSEKSLIEAPTGTGKTL 279
>gnl|CDD|222875 PHA02558, uvsW, UvsW helicase; Provisional.
Length = 501
Score = 28.8 bits (65), Expect = 0.66
Identities = 7/27 (25%), Positives = 13/27 (48%), Gaps = 1/27 (3%)
Query: 48 NSKFGIFESPTGTGKSLSLICGILKWY 74
+ + PT GKSL + + ++Y
Sbjct: 128 KNNRRLLNLPTSAGKSL-IQYLLSRYY 153
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 28.3 bits (64), Expect = 0.81
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 56 SPTGTGKSLSLICGIL 71
SPTG+GK+L+ I+
Sbjct: 54 SPTGSGKTLAAFLAII 69
>gnl|CDD|213268 cd03301, ABC_MalK_N, The N-terminal ATPase domain of the maltose
transporter, MalK. ATP binding cassette (ABC) proteins
function from bacteria to human, mediating the
translocation of substances into and out of cells or
organelles. ABC transporters contain two
transmembrane-spanning domains (TMDs) or subunits and
two nucleotide binding domains (NBDs) or subunits that
couple transport to the hydrolysis of ATP. In the
maltose transport system, the periplasmic maltose
binding protein (MBP) stimulates the ATPase activity of
the membrane-associated transporter, which consists of
two transmembrane subunits, MalF and MalG, and two
copies of the ATP binding subunit, MalK, and becomes
tightly bound to the transporter in the catalytic
transition state, ensuring that maltose is passed to
the transporter as ATP is hydrolyzed.
Length = 213
Score = 28.0 bits (63), Expect = 0.91
Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 10/46 (21%)
Query: 40 KNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLEKI 85
+L + + +F + P+G GK+ +L IAGLE+
Sbjct: 17 DDLNLDIADGEFVVLLGPSGCGKTTTLRM----------IAGLEEP 52
>gnl|CDD|219986 pfam08715, Viral_protease, Papain like viral protease. This family
of viral proteases are similar to the papain protease
and are required for proteolytic processing of the
replicase polyprotein. The structure of this protein has
shown it adopts a fold similar that of de-ubiquitinating
enzymes.
Length = 320
Score = 27.5 bits (61), Expect = 1.4
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 42 LYYTLDNSKFGIFESPTGTGKSLSLICGI--LKW 73
Y TLD SK+GI+ S + G LKW
Sbjct: 74 YYATLDASKYGIYLSALTQKWKFPQVGGFRVLKW 107
>gnl|CDD|213266 cd03299, ABC_ModC_like, ATP-binding cassette domain similar to
the molybdate transporter. Archaeal protein closely
related to ModC. ModC is an ABC-type transporter and
the ATPase component of a molybdate transport system
that also includes the periplasmic binding protein ModA
and the membrane protein ModB. ABC transporters are a
large family of proteins involved in the transport of a
wide variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins.
Length = 235
Score = 27.3 bits (61), Expect = 1.9
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 38 FMKNLYYTLDNSKFGIFESPTGTGKS--LSLICGILK 72
+KN+ ++ + + PTG+GKS L I G +K
Sbjct: 14 KLKNVSLEVERGDYFVILGPTGSGKSVLLETIAGFIK 50
>gnl|CDD|226298 COG3775, GatC, Phosphotransferase system, galactitol-specific IIC
component [Carbohydrate transport and metabolism].
Length = 446
Score = 26.9 bits (60), Expect = 2.5
Identities = 15/35 (42%), Positives = 17/35 (48%)
Query: 48 NSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGL 82
KFGIF P G L L+ GIL Y K+ L
Sbjct: 217 QKKFGIFGEPMFIGFILGLLIGILAGYDVKKVLQL 251
>gnl|CDD|213620 TIGR01433, CyoA, cytochrome o ubiquinol oxidase subunit II. This
enzyme catalyzes the oxidation of ubiquinol with the
concomitant reduction of molecular oxygen to water. This
acts as the terminal electron acceptor in the
respiratory chain. Subunit II is responsible for binding
and oxidation of the ubiquinone substrate. This sequence
is closely related to QoxA, which oxidizes quinol in
gram positive bacteria but which is in complex with
subunits which utilize cytochromes a in the reduction of
molecular oxygen. Slightly more distantly related is
subunit II of cytochrome c oxidase which uses cyt. c as
the oxidant [Energy metabolism, Electron transport].
Length = 226
Score = 26.7 bits (59), Expect = 2.5
Identities = 11/36 (30%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 69 GILKWYSDHKIAGLEKIEAEIKDLEISKNETVSEDW 104
G+L W + HK+ + +++K + I E V+ DW
Sbjct: 92 GVLTWITTHKLDPYRPLASDVKPITI---EVVALDW 124
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 27.0 bits (60), Expect = 2.6
Identities = 10/40 (25%), Positives = 16/40 (40%)
Query: 25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSL 64
F F+ Q + L + G+ PTG GK++
Sbjct: 31 VAFEFELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTV 70
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 26.0 bits (58), Expect = 2.9
Identities = 8/29 (27%), Positives = 14/29 (48%), Gaps = 1/29 (3%)
Query: 50 KFGIFESPTGTGKSLSLICGILKWYSDHK 78
K G+ TG+GK+L ++ + K
Sbjct: 19 KRGLIVMATGSGKTL-TAAALIARLAKGK 46
>gnl|CDD|190374 pfam02643, DUF192, Uncharacterized ACR, COG1430. Two structures
have been solved for members of this large (>500
members) family of bacterial proteins present mostly in
environmental bacteria and metagenomes (distant
homologues are also present in several Plasmodium
species). TOPSAN analysis for pdb:3pjy shows that there
is much similarity with the other solved structure,
pdb:3m7a, solved for UniProt:Q2GA55 (Saro_0823), a
homologue of Thermotoga maritima TM1668,
UniProt:Q9X1Z6., The homologue in Caulobacter
crescentus (CC1388), UniProt:Q9A8G6, is associated with
CspD, a cold shock protein (CC1387), UniProt:Q9A8G7.
However, the genomic context of UniProt:Q2GA55 is most
conserved with a putative xylose isomerase, suggesting
a possible role in extracellular sugar processing.
Saro_0821, UniProt:Q2GA57, is annotated as an
AMP-dependent synthetase and ligase. PDB:3m7a structure
corresponds to the C-terminal (27-165) fragment of the
YP_496102 (Saro_0823) protein and it is structurally
unique, as the best hits from Dali have a Z-score of
3.8 (1nt0, 2j1t, 3kq4) and it is thus a likely
candidate for a new fold. Interestingly, many of the
top Dali hits are involved in sugar metabolism. There
are no obvious active site-like cavities on the protein
surface of 3m7a (http://www.topsan.org/Proteins/JCSG/).
Length = 104
Score = 26.0 bits (58), Expect = 3.1
Identities = 7/21 (33%), Positives = 9/21 (42%)
Query: 27 FPFDAYDIQSNFMKNLYYTLD 47
F F + +MKN LD
Sbjct: 30 FVFPEPSPHTFWMKNTLIPLD 50
>gnl|CDD|152822 pfam12387, Peptidase_C74, Pestivirus NS2 peptidase. The pestivirus
NS2 peptidase is responsible for single cleavage between
NS2 and NS3 of the bovine viral diarrhea virus
polyprotein, a cleavage that is correlated with
cytopathogenicity. The peptidase is activated by its
interaction with 'J-domain protein interacting with
viral protein' - Jiv.
Length = 200
Score = 26.3 bits (58), Expect = 3.4
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 7/42 (16%)
Query: 70 ILKWYSDHKIAGLEKIEAEIKDLEISKNE-----TVSE--DW 104
+ WY + +I G+ K+ IK +SKN+ TV E DW
Sbjct: 132 VAHWYGEEEIYGMPKLVTIIKAATLSKNKHCILCTVCENRDW 173
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 26.3 bits (58), Expect = 3.5
Identities = 11/41 (26%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 32 YDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK 72
Q ++ L L + I +PTG+GK+L+ + L+
Sbjct: 10 RPYQKEAIEAL---LSGLRDVILAAPTGSGKTLAALLPALE 47
>gnl|CDD|220471 pfam09923, DUF2155, Uncharacterized protein conserved in bacteria
(DUF2155). This domain, found in various hypothetical
prokaryotic proteins, has no known function.
Length = 91
Score = 25.6 bits (57), Expect = 4.1
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 79 IAGLEKIEAEIKDLEISKNETV 100
+ GL+KI DLE+ ET
Sbjct: 3 LRGLDKITGRTTDLELKVGETA 24
>gnl|CDD|129907 TIGR00827, EIIC-GAT, PTS system, galactitol-specific IIC component.
Bacterial PTS transporters transport and concomitantly
phosphorylate their sugar substrates, and typically
consist of multiple subunits or protein domains. The
only characterized member of this family of PTS
transporters is the E. coli galactitol transporter. Gat
family PTS systems typically have 3 components: IIA, IIB
and IIC. This family is specific for the IIC component
of the PTS Gat family [Transport and binding proteins,
Carbohydrates, organic alcohols, and acids, Signal
transduction, PTS].
Length = 407
Score = 26.3 bits (58), Expect = 4.6
Identities = 16/46 (34%), Positives = 18/46 (39%), Gaps = 13/46 (28%)
Query: 29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY 74
DA IQ +FGIF P G L LI G+L Y
Sbjct: 201 ADADTIQR-------------RFGIFGEPVFIGLVLGLIIGLLAGY 233
>gnl|CDD|236739 PRK10703, PRK10703, DNA-binding transcriptional repressor PurR;
Provisional.
Length = 341
Score = 25.8 bits (57), Expect = 5.4
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 6/51 (11%)
Query: 62 KSLSLICGILKWYSDHKIAGLEKIEAEIKDLEISKNETVSEDWIEQQSFEP 112
+ + +I G L+ + G ++ +K +E N V E+WI Q FEP
Sbjct: 179 RDIGVIPGPLE-----RNTGAGRLAGFMKAME-EANIKVPEEWIVQGDFEP 223
>gnl|CDD|182744 PRK10802, PRK10802, peptidoglycan-associated outer membrane
lipoprotein; Provisional.
Length = 173
Score = 25.6 bits (56), Expect = 7.0
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 27 FPFDAYDIQSNFMKNL 42
F D YDI+S+F + L
Sbjct: 73 FDLDKYDIRSDFAQML 88
>gnl|CDD|240227 PTZ00009, PTZ00009, heat shock 70 kDa protein; Provisional.
Length = 653
Score = 25.5 bits (56), Expect = 7.1
Identities = 19/92 (20%), Positives = 37/92 (40%), Gaps = 13/92 (14%)
Query: 2 ASKTPNEDKEFKEQRPLAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTG 61
A K ED+ +E+ +A + N+ ++ TL + K S +
Sbjct: 524 AEKYKAEDEANRER-------------VEAKNGLENYCYSMKNTLQDEKVKGKLSDSDKA 570
Query: 62 KSLSLICGILKWYSDHKIAGLEKIEAEIKDLE 93
I L+W +++A E+ E + K++E
Sbjct: 571 TIEKAIDEALEWLEKNQLAEKEEFEHKQKEVE 602
>gnl|CDD|215360 PLN02672, PLN02672, methionine S-methyltransferase.
Length = 1082
Score = 25.9 bits (57), Expect = 7.3
Identities = 12/42 (28%), Positives = 19/42 (45%), Gaps = 2/42 (4%)
Query: 38 FMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKI 79
F+ L L + E P G+ + +LI G ++ Y H I
Sbjct: 406 FLAYLASALKGLSYFPCEPPAGSKRFRNLIAGFMRIY--HHI 445
>gnl|CDD|213249 cd03282, ABC_MSH4_euk, ATP-binding cassette domain of eukaryotic
MutS4 homolog. The MutS protein initiates DNA mismatch
repair by recognizing mispaired and unpaired bases
embedded in duplex DNA and activating endo- and
exonucleases to remove the mismatch. Members of the
MutS family possess C-terminal domain with a conserved
ATPase activity that belongs to the ATP binding
cassette (ABC) superfamily. MutS homologs (MSH) have
been identified in most prokaryotic and all eukaryotic
organisms examined. Prokaryotes have two homologs
(MutS1 and MutS2), whereas seven MSH proteins (MSH1 to
MSH7) have been identified in eukaryotes. The homodimer
MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are
primarily involved in mitotic mismatch repair, whereas
MSH4-MSH5 is involved in resolution of Holliday
junctions during meiosis. All members of the MutS
family contain the highly conserved Walker A/B ATPase
domain, and many share a common mechanism of action.
MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to
form sliding clamps, and recognition of specific DNA
structures or lesions results in ADP/ATP exchange.
Length = 204
Score = 25.4 bits (56), Expect = 8.1
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 36 SNFMKNLYY-TLDNSKFGIFESPTGTGKSLSL 66
NF+ N Y T +S+F I P +GKS L
Sbjct: 15 KNFIPNDIYLTRGSSRFHIITGPNMSGKSTYL 46
>gnl|CDD|220299 pfam09586, YfhO, Bacterial membrane protein YfhO. This protein is
a conserved membrane protein. The yfhO gene is
transcribed in Difco sporulation medium and the
transcription is affected by the YvrGHb two-component
system. Some members of this family have been annotated
as glycosyl transferases of the PMT family.
Length = 835
Score = 25.7 bits (57), Expect = 8.4
Identities = 8/37 (21%), Positives = 14/37 (37%), Gaps = 3/37 (8%)
Query: 16 RPLAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFG 52
R EV F + D+ K L + + ++ G
Sbjct: 243 RAYTEVSILLTFDINPLDL---LAKLLIGSFNFTQMG 276
>gnl|CDD|238549 cd01129, PulE-GspE, PulE/GspE The type II secretory pathway is
the main terminal branch of the general secretory
pathway (GSP). It is responsible for the export the
majority of Gram-negative bacterial exoenzymes and
toxins. PulE is a cytoplasmic protein of the GSP, which
contains an ATP binding site and a tetracysteine motif.
This subgroup also includes PillB and HofB.
Length = 264
Score = 25.3 bits (56), Expect = 9.5
Identities = 9/33 (27%), Positives = 14/33 (42%), Gaps = 2/33 (6%)
Query: 36 SNFMKNLYYTLDNSKFGI--FESPTGTGKSLSL 66
++ L GI PTG+GK+ +L
Sbjct: 65 KPENLEIFRKLLEKPHGIILVTGPTGSGKTTTL 97
>gnl|CDD|240380 PTZ00362, PTZ00362, hypothetical protein; Provisional.
Length = 479
Score = 25.1 bits (55), Expect = 9.5
Identities = 9/35 (25%), Positives = 21/35 (60%)
Query: 9 DKEFKEQRPLAEVPSEFPFPFDAYDIQSNFMKNLY 43
++EF++Q L ++PS + F + +++N K +
Sbjct: 351 EREFEDQNELTDLPSPYFFEISSMFLENNIFKKVT 385
>gnl|CDD|217188 pfam02689, Herpes_Helicase, Helicase. This family consists of
Helicases from the Herpes viruses. Helicases are
responsible for the unwinding of DNA and are essential
for replication and completion of the viral life cycle.
Length = 801
Score = 25.4 bits (56), Expect = 9.9
Identities = 11/39 (28%), Positives = 14/39 (35%), Gaps = 7/39 (17%)
Query: 16 RPLAEVPSEFPFPFDAYDI-------QSNFMKNLYYTLD 47
P F PF AY I +S ++ L LD
Sbjct: 46 DPEDPEDPNFALPFSAYLITGTAGAGKSTSIQTLNENLD 84
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 0.133 0.387
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,815,878
Number of extensions: 490898
Number of successful extensions: 430
Number of sequences better than 10.0: 1
Number of HSP's gapped: 430
Number of HSP's successfully gapped: 43
Length of query: 115
Length of database: 10,937,602
Length adjustment: 79
Effective length of query: 36
Effective length of database: 7,433,636
Effective search space: 267610896
Effective search space used: 267610896
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: 53 (24.3 bits)