RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14488
(368 letters)
>gnl|CDD|236979 PRK11779, sbcB, exonuclease I; Provisional.
Length = 476
Score = 365 bits (940), Expect = e-124
Identities = 126/374 (33%), Positives = 203/374 (54%), Gaps = 15/374 (4%)
Query: 1 MFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNN 60
+F+RN +PY REW+N SRWDL++V++A Y L P GI WP +G PSFKLEHL+ N
Sbjct: 112 IFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSFKLEHLTKANG 171
Query: 61 LSHKKAHDALSDVRATLGLARLIRNNNPRLFNFILSLRKKKYVLAEIGWPIARPFFYITH 120
+ H+ AHDA+SDV AT+ +A+LI+ P+LF+++ LR K+ V A I P +P +++
Sbjct: 172 IEHENAHDAMSDVYATIAMAKLIKQKQPKLFDYLFQLRNKRKVAALIDVPAMKPLVHVSG 231
Query: 121 MFSSKHSYISLMWPICIHPMNKNILITWNLLHDPKKFLLNDINKIRDYLCFKKNSFKED- 179
MF ++ S + P+ HP NKN +I +L DP L D + +R+ L ++ E
Sbjct: 232 MFGAERGCTSWVAPLAWHPTNKNAVIVCDLAGDPSPLLELDADTLRERLYTRRADLAEGE 291
Query: 180 --IPISMIHLNRSPIVISNLKVLSSNLMFRYKFDLNCAFKNIKCASSILNNTYIWKKIF- 236
+P+ ++HLN+ P++ K L R D N+ + +F
Sbjct: 292 LPVPLKLVHLNKCPVLA-PAKTLRPEDAERLGIDRQQCLDNLALLRQNPDLREKVVAVFA 350
Query: 237 LDYKINNSDLELNIDEELYNNFISKKDNLKLAILRSMSPKKLSNVNFCFENKKLEELIFL 296
SD ++D +LY+ F S D + I+R P+ L+ ++ F++ +LEEL+F
Sbjct: 351 EAEPFAPSD---DVDAQLYDGFFSDADRRLMEIIRETEPENLAALDLTFDDPRLEELLFR 407
Query: 297 YRARNFIETLSYKELKRWKKYRISRFYNKKNNLYNINMFYLEIESLLKKANEHDTK--IL 354
YRARNF ETL +E +RW ++R R + + + E+E L ++ + + K +L
Sbjct: 408 YRARNFPETLDDEEQQRWLEHRRQRLTPE-----RLQQYAAELEQLAQEYEDDEEKQALL 462
Query: 355 NALLMYGKSITQKI 368
AL Y + + +
Sbjct: 463 KALYDYAEELVPTL 476
>gnl|CDD|225477 COG2925, SbcB, Exonuclease I [DNA replication, recombination, and
repair].
Length = 475
Score = 292 bits (749), Expect = 1e-95
Identities = 125/371 (33%), Positives = 200/371 (53%), Gaps = 20/371 (5%)
Query: 2 FWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNL 61
F+RN +PY W+N SRWDL++V++A Y L P GI WP ++G PSFKLEHL+ N +
Sbjct: 116 FYRNFYDPYAWSWQNGNSRWDLLDVVRACYALRPEGINWPENDDGLPSFKLEHLTKANGI 175
Query: 62 SHKKAHDALSDVRATLGLARLIRNNNPRLFNFILSLRKKKYVLAEIGWPIARPFFYITHM 121
H AHDA+SDV AT+ +A+L++ PRLF+++ LRKK +LA I P +P +++ M
Sbjct: 176 EHSNAHDAMSDVYATIAMAKLVKTAQPRLFDYLFQLRKKHKLLALIDIPNMQPLVHVSGM 235
Query: 122 FSSKHSYISLMWPICIHPMNKNILITWNLLHDPKKFLLNDINKIRDYLCFKKNSFKED-- 179
F ++ S + P+ HP N+N +I +L D L D + +R+ L +K E
Sbjct: 236 FGAERGNTSWVLPLAWHPTNRNAVIVCDLAGDISPLLELDADTLRERLYTRKADLGEGEL 295
Query: 180 -IPISMIHLNRSPIVISNLKVLSSNLMFRYKFDLNCAFKN---IKCASSILNNTYIWKKI 235
+P+ ++H+N+ PI+ K L R D N ++ + I
Sbjct: 296 AVPVKLVHINKCPILAP-AKTLRPEDADRLGIDRQHCLDNLELLRENPDVREK---VVAI 351
Query: 236 FLDYKINNSDLELNIDEELYNNFISKKDNLKLAILRSMSPKKLSNVNFCFENKKLEELIF 295
F + + ++D +LYN F S D + ILR P+ L+ ++ F +K+LEEL+F
Sbjct: 352 F--AEEEPFNPSDDVDAQLYNGFFSDADRAAMKILRETEPENLAALDITFVDKRLEELLF 409
Query: 296 LYRARNFIETLSYKELKRWKKYRISRFYNKKNNLYNINMFYLEIESLLKKANEHDTK--I 353
YRARNF ETL+ E +RW ++R R + + L +++L+++ ++ K +
Sbjct: 410 RYRARNFPETLTDAEQQRWLEHRRQRLTP------ELQGYELTLQALVQEHSDDKEKLAL 463
Query: 354 LNALLMYGKSI 364
L AL Y +
Sbjct: 464 LKALYEYAAEL 474
>gnl|CDD|219829 pfam08411, Exonuc_X-T_C, Exonuclease C-terminal. This bacterial
domain is found at the C-terminus of
Exodeoxyribonuclease I/Exonuclease I (pfam00929), which
is a single-strand specific DNA nuclease affecting
recombination and expression pathways. The exonuclease I
protein in E. coli is associated with DNA
deoxyribophosphodiesterase (dRPase).
Length = 268
Score = 188 bits (479), Expect = 1e-57
Identities = 79/274 (28%), Positives = 134/274 (48%), Gaps = 13/274 (4%)
Query: 98 RKKKYVLAEIGWPIARPFFYITHMFSSKHSYISLMWPICIHPMNKNILITWNLLHDPKKF 157
R KK V I +P +++ MF ++ S + P+ HP NKN +I +L DP
Sbjct: 1 RSKKAVAKLIDLVAMKPLVHVSGMFGAERGCTSWVLPLAWHPTNKNAVIVCDLAQDPSPL 60
Query: 158 LLNDINKIRDYLCFKKNSFKED---IPISMIHLNRSPIVISNLKVLSSNLMFRYKFDLNC 214
L ++R L K+ E +P+ ++HLN+ PI+ K L R D
Sbjct: 61 LDLSAEELRQRLYTKREDLAEGELRVPLKLVHLNKCPILA-PAKTLRPEDAERLGIDREQ 119
Query: 215 AFKNIK--CASSILNNTYIWKKIF-LDYKINNSDLELNIDEELYNNFISKKDNLKLAILR 271
KN+ + L K++F + + S ++D++LY+ F S D + I+R
Sbjct: 120 CLKNLALLRQNPELRE--KLKEVFEEEREFPPST---DVDQQLYDGFFSDADKRLMEIIR 174
Query: 272 SMSPKKLSNVNFCFENKKLEELIFLYRARNFIETLSYKELKRWKKYRISRFYNKKNNLYN 331
SP++L+ + F++K+L EL+F YRARNF ETLS +E +RW++Y R +
Sbjct: 175 ETSPEQLAELELNFDDKRLPELLFRYRARNFPETLSEEEQQRWQEYCQQRLLDPAGGALT 234
Query: 332 INMFYLEIESLLKKA-NEHDTKILNALLMYGKSI 364
+ + ++E L + ++ +L AL Y +S+
Sbjct: 235 LEDYEQKLEQLAAEYSDDEKQALLQALYDYAQSL 268
>gnl|CDD|99841 cd06138, ExoI_N, N-terminal DEDDh 3'-5' exonuclease domain of
Escherichia coli exonuclease I and similar proteins.
This subfamily is composed of the N-terminal domain of
Escherichia coli exonuclease I (ExoI) and similar
proteins. ExoI is a monomeric enzyme that hydrolyzes
single stranded DNA in the 3' to 5' direction. It plays
a role in DNA recombination and repair. It primarily
functions in repairing frameshift mutations. The
N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5
exonuclease containing three conserved sequence motifs
termed ExoI, ExoII and ExoIII, with a specific Hx(4)D
conserved pattern at ExoIII. These motifs are clustered
around the active site and contain four conserved acidic
residues that serve as ligands for the two metal ions
required for catalysis. The ExoI structure is unique
among DnaQ family enzymes in that there is a large
distance between the two metal ions required for
catalysis and the catalytic histidine is oriented away
from the active site.
Length = 183
Score = 129 bits (326), Expect = 4e-36
Identities = 47/80 (58%), Positives = 60/80 (75%)
Query: 2 FWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNL 61
F+RNL +PY EWKN SRWDL++V++A+Y L P GI WP ++GKPSFKLE L+ N +
Sbjct: 104 FYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKLEDLAQANGI 163
Query: 62 SHKKAHDALSDVRATLGLAR 81
H AHDALSDV AT+ LA+
Sbjct: 164 EHSNAHDALSDVEATIALAK 183
>gnl|CDD|236148 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 928
Score = 35.3 bits (82), Expect = 0.060
Identities = 12/31 (38%), Positives = 14/31 (45%)
Query: 46 GKPSFKLEHLSFVNNLSHKKAHDALSDVRAT 76
S+KL LS L H + H A SD T
Sbjct: 128 TAESYKLRDLSEELGLEHDQPHRADSDAEVT 158
>gnl|CDD|184752 PRK14573, PRK14573, bifunctional D-alanyl-alanine synthetase
A/UDP-N-acetylmuramate--L-alanine ligase; Provisional.
Length = 809
Score = 33.3 bits (76), Expect = 0.26
Identities = 31/127 (24%), Positives = 54/127 (42%), Gaps = 23/127 (18%)
Query: 249 NIDEELYNNFISKKDNLKLAILRSMSPKKLSNVNFCFENKKLEEL-------IFLYRARN 301
NID E +NF ++ L LA ++ + +K+ +N CF N L + + +
Sbjct: 178 NIDNEHLSNFEGDRELL-LASIQDFA-RKVQQINKCFYNGDCPRLKGCLQGHSYGFSSSC 235
Query: 302 FIETLSYKELKRWKKYRISRFYNKKNNLYNINMFYLEIESLLKKANEHDTKILNALLMYG 361
+ LSY + + W+ Y ++F Y +IE L H+ + NA G
Sbjct: 236 DLHILSYYQ-EGWRSYFSAKFLGVV---------YQDIE--LNLVGMHN--VANAAAAMG 281
Query: 362 KSITQKI 368
++T I
Sbjct: 282 IALTLGI 288
>gnl|CDD|176648 cd06127, DEDDh, DEDDh 3'-5' exonuclease domain family. DEDDh
exonucleases, part of the DnaQ-like (or DEDD)
exonuclease superfamily, catalyze the excision of
nucleoside monophosphates at the DNA or RNA termini in
the 3'-5' direction. These proteins contain four
invariant acidic residues in three conserved sequence
motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases
are classified as such because of the presence of
specific Hx(4)D conserved pattern at the ExoIII motif.
The four conserved acidic residues are clustered around
the active site and serve as ligands for the two metal
ions required for catalysis. Most DEDDh exonucleases are
the proofreading subunits (epsilon) or domains of
bacterial DNA polymerase III, the main replicating
enzyme in bacteria, which functions as the chromosomal
replicase. Other members include other DNA and RNA
exonucleases such as RNase T, Oligoribonuclease, and RNA
exonuclease (REX), among others.
Length = 159
Score = 31.9 bits (73), Expect = 0.27
Identities = 10/42 (23%), Positives = 15/42 (35%), Gaps = 3/42 (7%)
Query: 40 WPYKNNGKPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLAR 81
P + + L + + AH AL+D AT L
Sbjct: 121 LPGLRSHRLGLLLAER---YGIPLEGAHRALADALATAELLL 159
>gnl|CDD|214685 smart00479, EXOIII, exonuclease domain in DNA-polymerase alpha and
epsilon chain, ribonuclease T and other exonucleases.
Length = 169
Score = 30.7 bits (70), Expect = 0.69
Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 41 PYKNNGKPSFKLEHLSFVNNLSH-KKAHDALSDVRATLGLARLIRNNNP 88
N G P + L+ L+ L ++AH AL D RAT L + +
Sbjct: 121 RATNPGLPKYSLKKLAKRLLLEVIQRAHRALDDARATAKLFKKLLERLE 169
>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 = 31.3 bits (71), Expect = 1.1
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 49 SFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIR 84
S++L LS L+H+ H A SD +AT L L+
Sbjct: 127 SYQLSELSEALGLTHENPHRADSDAQATAELLLLLF 162
>gnl|CDD|99817 cd06221, sulfite_reductase_like, Anaerobic sulfite reductase
contains an FAD and NADPH binding module with structural
similarity to ferredoxin reductase and sequence
similarity to dihydroorotate dehydrogenases. Clostridium
pasteurianum inducible dissimilatory type sulfite
reductase is linked to ferredoxin and reduces NH2OH and
SeO3 at a lesser rate than it's normal substate SO3(2-).
Dihydroorotate dehydrogenases (DHODs) catalyze the only
redox reaction in pyrimidine de novo biosynthesis. They
catalyze the oxidation of (S)-dihydroorotate to orotate
coupled with the reduction of NAD+.
Length = 253
Score = 30.3 bits (69), Expect = 1.3
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 8/51 (15%)
Query: 267 LAILRSMSPKKLSNVNFCFEN-KKLEELIFLYRARNFIETLSYKELKRWKK 316
LA LRS+ +N+ +N + ++ LY AR + L +ELK W K
Sbjct: 110 LAPLRSL-------INYILDNREDYGKVTLLYGARTPEDLLFKEELKEWAK 153
>gnl|CDD|188663 cd08708, RGS_FLBA, Regulator of G protein signaling (RGS) domain
found in the FLBA (Fluffy Low BrlA) protein. The RGS
(Regulator of G-protein Signaling) domain is an
essential part of the FLBA (Fluffy Low BrlA) protein.
FLBA is a member of the RGS protein family, a diverse
group of multifunctional proteins that regulate cellular
signaling events downstream of G-protein coupled
receptors (GPCRs). As a major G-protein regulator, RGS
domain containing proteins are involved in many crucial
cellular processes such as regulation of intracellular
trafficking, glial differentiation, embryonic axis
formation, skeletal and muscle development, and cell
migration during early embryogenesis. RGS proteins play
a critical regulatory role as GTPase activating proteins
(GAPs) of the heterotrimeric G-protein G-alpha-subunits.
Deactivation of the G-protein signaling controlled by
the RGS domain accelerates the GTPase activity of the
alpha subunit by hydrolysis of GTP to GDP which results
in reassociation of the alpha-subunit with the
beta-gamma-dimer and thereby inhibition of downstream
activity. As a major G-protein regulator, RGS domain
containing proteins are involved in many crucial
cellular processes. The RGS domain of the FLBA protein
antagonizes G protein signaling to block proliferation
and allow development. It is required for control of
mycelial proliferation and activation of asexual
sporulation in yeast.
Length = 148
Score = 29.7 bits (67), Expect = 1.3
Identities = 18/72 (25%), Positives = 23/72 (31%), Gaps = 4/72 (5%)
Query: 222 ASSILNNTYIWKKIFLDYKINNSDLELNIDEELYNNFISKKDNLKLAILRSMSPKKLSNV 281
L Y I+ Y S ELNID L N + + SM + L V
Sbjct: 61 DRESLAQAY---HIYNTYLAPGSPCELNIDHNLRNRITTIMTEKIVGEDDSM-AESLQGV 116
Query: 282 NFCFENKKLEEL 293
FE +
Sbjct: 117 EALFEEAQNAVF 128
>gnl|CDD|216200 pfam00929, RNase_T, Exonuclease. This family includes a variety of
exonuclease proteins, such as ribonuclease T and the
epsilon subunit of DNA polymerase III.;.
Length = 161
Score = 28.9 bits (65), Expect = 2.6
Identities = 16/69 (23%), Positives = 24/69 (34%), Gaps = 5/69 (7%)
Query: 16 NNCSRWDLINVIKAFY----VLSPYGITWPYKNNGKPSFKLEHLSFVNNLSH-KKAHDAL 70
+D + +K + I G L+ L+ L ++AH AL
Sbjct: 92 VGFLLYDDLRFLKLPMPKLNDVIDTLILDKATYKGFKRRSLDALAEKLGLEKIQRAHRAL 151
Query: 71 SDVRATLGL 79
D RAT L
Sbjct: 152 DDARATAEL 160
>gnl|CDD|239127 cd02662, Peptidase_C19F, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 240
Score = 29.3 bits (66), Expect = 2.9
Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 3/53 (5%)
Query: 139 PMNKNILITWNLLHDPKKFLLNDINKIRDYLCFKKNSFKEDIPIS-MIHLNRS 190
N++ L H FL +I I DY C + + +P IHL+RS
Sbjct: 87 VPNQSSGSGTTLEHCLDDFLSTEI--IDDYKCDRCQTVIVRLPQILCIHLSRS 137
>gnl|CDD|216035 pfam00632, HECT, HECT-domain (ubiquitin-transferase). The name
HECT comes from Homologous to the E6-AP Carboxyl
Terminus.
Length = 298
Score = 29.2 bits (66), Expect = 3.6
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 231 IWKKIFLDYKINNSDLELNIDEELYNNFISKKDN 264
WKK+ L I DLE +D ELY + S +
Sbjct: 66 FWKKL-LGKPITLEDLEE-VDPELYRSLKSLLEL 97
>gnl|CDD|225587 COG3045, CreA, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 165
Score = 28.6 bits (64), Expect = 3.9
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 314 WKKYRISRFYNKKNN 328
+K ++ R Y+KK N
Sbjct: 113 FKSLQVVRIYDKKRN 127
>gnl|CDD|239864 cd04399, RhoGAP_fRGD2, RhoGAP_fRGD2: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain of
fungal RGD2-like proteins. Yeast Rgd2 is a GAP protein
for Cdc42 and Rho5. Small GTPases cluster into distinct
families, and all act as molecular switches, active in
their GTP-bound form but inactive when GDP-bound. The
Rho family of GTPases activates effectors involved in a
wide variety of developmental processes, including
regulation of cytoskeleton formation, cell proliferation
and the JNK signaling pathway. GTPases generally have a
low intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 212
Score = 28.5 bits (64), Expect = 4.2
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 339 IESLLKKANEHDTKILNALLMYGKSI 364
IESLL ++H K LL + I
Sbjct: 182 IESLLTIGDKHGYKFFRDLLTHKDQI 207
>gnl|CDD|219603 pfam07842, GCFC, GC-rich sequence DNA-binding factor-like protein.
Sequences found in this family are similar to a region
of a human GC-rich sequence DNA-binding factor homolog.
This is thought to be a protein involved in
transcriptional regulation due to partial homologies to
a transcription repressor and histone-interacting
protein. This family also contains tuftelin interacting
protein 11 which has been identified as both a nuclear
and cytoplasmic protein, and has been implicated in the
secretory pathway. Sip1, a septin interacting protein is
also a member of this family.
Length = 275
Score = 28.6 bits (64), Expect = 5.1
Identities = 11/52 (21%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 128 YISLMWPICIHPMNKNILITWNLLHDPKKFLLNDINKIRDYLCFKKNSFKED 179
Y+SL+ P + P+ + L+ W+ L DP + ++ + + + L +
Sbjct: 23 YLSLLAPALVAPLLRLELLEWDPLEDP-TYGVDILKRWKALLELDSSDDTGG 73
>gnl|CDD|221003 pfam11150, DUF2927, Protein of unknown function (DUF2927). This
family is conserved in Proteobacteria. Several members
are described as being putative lipoproteins, but
otherwise the function is not known.
Length = 212
Score = 28.3 bits (64), Expect = 5.9
Identities = 8/26 (30%), Positives = 12/26 (46%)
Query: 297 YRARNFIETLSYKELKRWKKYRISRF 322
AR+F+E E R R+ R+
Sbjct: 4 DLARDFLEIAFGDEYGRAGLPRLRRW 29
>gnl|CDD|222122 pfam13429, TPR_15, Tetratricopeptide repeat.
Length = 279
Score = 28.4 bits (64), Expect = 6.2
Identities = 15/57 (26%), Positives = 20/57 (35%), Gaps = 1/57 (1%)
Query: 290 LEELIFLYRARNFIETLSYKELKRWKKYRISRFYNKKNNLYNINMFYLEIESLLKKA 346
+ LI+LY + EL W++Y R LY Y I LL
Sbjct: 80 YDRLIYLYYDAEPKDAARLAEL-GWRRYHSPRHLQSALYLYTRAGDYKRIVDLLASL 135
>gnl|CDD|226229 COG3706, PleD, Response regulator containing a CheY-like receiver
domain and a GGDEF domain [Signal transduction
mechanisms].
Length = 435
Score = 28.4 bits (64), Expect = 7.0
Identities = 17/74 (22%), Positives = 26/74 (35%), Gaps = 4/74 (5%)
Query: 288 KKLEELIFLYRARNFIETLSYKELKRWKKYRISRFYNKK--NNLYNINMFYLEIESLLKK 345
K +EE R R + Y+ R R+ L+N F + L K+
Sbjct: 235 KPIEEGELRARLRRQLRRKRYERQLRESLERLQELALVDGLTGLFNRRYFDEHLADLWKR 294
Query: 346 ANEHDTKILNALLM 359
A + +LLM
Sbjct: 295 ALREGRPL--SLLM 306
>gnl|CDD|180905 PRK07246, PRK07246, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 820
Score = 28.5 bits (64), Expect = 8.0
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 50 FKLEHLSFVNNLSHKKAHDALSDVRAT 76
+ L HLS N+ AH A++D RAT
Sbjct: 133 YSLSHLSRELNIDLADAHTAIADARAT 159
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 0.139 0.429
Gapped
Lambda K H
0.267 0.0649 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,063,854
Number of extensions: 1904476
Number of successful extensions: 2421
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2390
Number of HSP's successfully gapped: 121
Length of query: 368
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 270
Effective length of database: 6,590,910
Effective search space: 1779545700
Effective search space used: 1779545700
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 (21.5 bits)
S2: 60 (27.1 bits)