RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2882
(1428 letters)
>gnl|CDD|236979 PRK11779, sbcB, exonuclease I; Provisional.
Length = 476
Score = 565 bits (1459), Expect = 0.0
Identities = 189/478 (39%), Positives = 275/478 (57%), Gaps = 15/478 (3%)
Query: 307 HNGNSTFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRAC 366
TFLW+DYETFG N DRP QFA IRTD LN I P++ YCKPA D+LP P A
Sbjct: 2 KKMQPTFLWHDYETFGANPALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAV 61
Query: 367 LITKITPQFCLNNGIPEYKFASIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPY 426
LIT ITPQ L G+PE +FA+ I F +PGT +GYN I FDDE+TR++F+RN +PY
Sbjct: 62 LITGITPQEALEKGLPEAEFAARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPY 121
Query: 427 EREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNLSHKKAHDAL 486
REW+N SRWDL++V++A Y L P GI WP +G PSFKLEHL+ N + H+ AHDA+
Sbjct: 122 AREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSFKLEHLTKANGIEHENAHDAM 181
Query: 487 SDVRATLGLARLIRNNNPRLFNFILSLRKKKYVLAEIGWPIARPFFYITHMFSSKHSYIS 546
SDV AT+ +A+LI+ P+LF+++ LR K+ V A I P +P +++ MF ++ S
Sbjct: 182 SDVYATIAMAKLIKQKQPKLFDYLFQLRNKRKVAALIDVPAMKPLVHVSGMFGAERGCTS 241
Query: 547 LMWPICIHPMNKNILITWNLLHDPKKFLLNDINKIRDYLCFKKNSFKED---IPISMIHL 603
+ P+ HP NKN +I +L DP L D + +R+ L ++ E +P+ ++HL
Sbjct: 242 WVAPLAWHPTNKNAVIVCDLAGDPSPLLELDADTLRERLYTRRADLAEGELPVPLKLVHL 301
Query: 604 NRSPIVISNLKVLSSNLMFRYKFDLNCAFKNIKCASSILNNTYIWKKIF-LDYKINNSDL 662
N+ P++ K L R D N+ + +F SD
Sbjct: 302 NKCPVLA-PAKTLRPEDAERLGIDRQQCLDNLALLRQNPDLREKVVAVFAEAEPFAPSD- 359
Query: 663 ELNIDEELYNNFISKKDNLKLAILRSMSPKKLSNVNFCFENKKLEELIFLYRARNFIETL 722
++D +LY+ F S D + I+R P+ L+ ++ F++ +LEEL+F YRARNF ETL
Sbjct: 360 --DVDAQLYDGFFSDADRRLMEIIRETEPENLAALDLTFDDPRLEELLFRYRARNFPETL 417
Query: 723 SYKELKRWKKYRISRFYNKKNNLYNINMFYLEIESLLKKANEHDTK--ILNALLMYGK 778
+E +RW ++R R + + + E+E L ++ + + K +L AL Y +
Sbjct: 418 DDEEQQRWLEHRRQRLTPE-----RLQQYAAELEQLAQEYEDDEEKQALLKALYDYAE 470
>gnl|CDD|225477 COG2925, SbcB, Exonuclease I [DNA replication, recombination, and
repair].
Length = 475
Score = 470 bits (1211), Expect = e-152
Identities = 185/477 (38%), Positives = 270/477 (56%), Gaps = 20/477 (4%)
Query: 310 NSTFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLIT 369
TFL+YDYETFG++ DRP QFA IRTDI N I PI+ YCKPA D+LP P A LIT
Sbjct: 8 QPTFLFYDYETFGVHPALDRPAQFAGIRTDIEFNIIGEPIVFYCKPADDYLPQPGAVLIT 67
Query: 370 KITPQFCLNNGIPEYKFASIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYERE 429
ITPQ GI E FA+ I +P T +GYN I FDDE+TR++F+RN +PY
Sbjct: 68 GITPQEAREKGINEAAFAARIHAELTQPNTCVLGYNNIRFDDEVTRYIFYRNFYDPYAWS 127
Query: 430 WKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNLSHKKAHDALSDV 489
W+N SRWDL++V++A Y L P GI WP ++G PSFKLEHL+ N + H AHDA+SDV
Sbjct: 128 WQNGNSRWDLLDVVRACYALRPEGINWPENDDGLPSFKLEHLTKANGIEHSNAHDAMSDV 187
Query: 490 RATLGLARLIRNNNPRLFNFILSLRKKKYVLAEIGWPIARPFFYITHMFSSKHSYISLMW 549
AT+ +A+L++ PRLF+++ LRKK +LA I P +P +++ MF ++ S +
Sbjct: 188 YATIAMAKLVKTAQPRLFDYLFQLRKKHKLLALIDIPNMQPLVHVSGMFGAERGNTSWVL 247
Query: 550 PICIHPMNKNILITWNLLHDPKKFLLNDINKIRDYLCFKKNSFKED---IPISMIHLNRS 606
P+ HP N+N +I +L D L D + +R+ L +K E +P+ ++H+N+
Sbjct: 248 PLAWHPTNRNAVIVCDLAGDISPLLELDADTLRERLYTRKADLGEGELAVPVKLVHINKC 307
Query: 607 PIVISNLKVLSSNLMFRYKFDLNCAFKN---IKCASSILNNTYIWKKIFLDYKINNSDLE 663
PI+ K L R D N ++ + IF + +
Sbjct: 308 PILAP-AKTLRPEDADRLGIDRQHCLDNLELLRENPDVREK---VVAIF--AEEEPFNPS 361
Query: 664 LNIDEELYNNFISKKDNLKLAILRSMSPKKLSNVNFCFENKKLEELIFLYRARNFIETLS 723
++D +LYN F S D + ILR P+ L+ ++ F +K+LEEL+F YRARNF ETL+
Sbjct: 362 DDVDAQLYNGFFSDADRAAMKILRETEPENLAALDITFVDKRLEELLFRYRARNFPETLT 421
Query: 724 YKELKRWKKYRISRFYNKKNNLYNINMFYLEIESLLKKANEHDTK--ILNALLMYGK 778
E +RW ++R R + + L +++L+++ ++ K +L AL Y
Sbjct: 422 DAEQQRWLEHRRQRLTP------ELQGYELTLQALVQEHSDDKEKLALLKALYEYAA 472
>gnl|CDD|235591 PRK05755, PRK05755, DNA polymerase I; Provisional.
Length = 880
Score = 343 bits (884), Expect = e-101
Identities = 129/273 (47%), Positives = 175/273 (64%), Gaps = 11/273 (4%)
Query: 779 IDGSSCIYRAFYAL-PDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFR 837
IDGSS ++RAFYAL P +RN D P GA+YG + ML KL K + T++A FDAKGK FR
Sbjct: 7 IDGSSLLFRAFYALLPTLRNSDGLPTGAVYGFLNMLLKLLKEEKPTHVAVAFDAKGKTFR 66
Query: 838 NILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHN 897
+ LYP YKA R MP +L QI LI ++++A+G P+L ++G EADDVIGTLAKQA
Sbjct: 67 HELYPEYKANRPPMPEDLREQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQA-EAAG 125
Query: 898 LKVIISTNDKDMAQLVSNKIALIN-----NNKIHDRTTIISRFGVSPEKIVDYFSLIGDM 952
+V+I T DKD+ QLV + + L++ N+ D ++ ++GV+PE+I+DY +L+GD
Sbjct: 126 YEVLIVTGDKDLLQLVDDNVTLLDTMGVSKNEELDPEEVVEKYGVTPEQIIDYLALMGDS 185
Query: 953 SDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKILTIK 1012
SDN+PGV IG KTA KLL +Y SLE + N + IKG + LR +K+ TIK
Sbjct: 186 SDNIPGVPGIGEKTAAKLLQEYGSLEGLYENLDEIKGKKKEKLRENKEQAFLSRKLATIK 245
Query: 1013 TDCDLTKNIVSIPESLILQPKDEKLLMQLFNKY 1045
TD L + E L LQP D + L+ LF +
Sbjct: 246 TDVPLEVD----LEDLELQPPDREKLIALFKEL 274
>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 = 285 bits (731), Expect = 9e-89
Identities = 102/184 (55%), Positives = 128/184 (69%), Gaps = 1/184 (0%)
Query: 314 LWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITP 373
L+YDYETFGLN D+ QFAAIRTD N I+ P ++C+ PD LP P A ++T ITP
Sbjct: 1 LFYDYETFGLNPSFDQILQFAAIRTDENFNEIE-PFNIFCRLPPDVLPSPEALIVTGITP 59
Query: 374 QFCLNNGIPEYKFASIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNN 433
Q L G+ EY+F + I ++F PGT VGYN I FDDE RF F+RNL +PY EWKN
Sbjct: 60 QQLLKEGLSEYEFIAKIHRLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNG 119
Query: 434 CSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNLSHKKAHDALSDVRATL 493
SRWDL++V++A+Y L P GI WP ++GKPSFKLE L+ N + H AHDALSDV AT+
Sbjct: 120 NSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKLEDLAQANGIEHSNAHDALSDVEATI 179
Query: 494 GLAR 497
LA+
Sbjct: 180 ALAK 183
>gnl|CDD|214682 smart00475, 53EXOc, 5'-3' exonuclease.
Length = 259
Score = 269 bits (690), Expect = 5e-82
Identities = 109/249 (43%), Positives = 162/249 (65%), Gaps = 7/249 (2%)
Query: 779 IDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRN 838
+DGSS +RA++ALP ++N P A+YG ++ML KL K + TY+A +FDAKGK FR+
Sbjct: 6 VDGSSLAFRAYFALPPLKNSKGEPTNAVYGFLRMLLKLIKEEKPTYVAVVFDAKGKTFRH 65
Query: 839 ILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNL 898
LYP YKA R K P L+ QI LI +++ A+G P+L ++G EADDVI TLAK+A
Sbjct: 66 ELYPEYKANRPKTPDELLEQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKA-EAEGY 124
Query: 899 KVIISTNDKDMAQLVSNKIALINNNKIHDRTT------IISRFGVSPEKIVDYFSLIGDM 952
+V I + DKD+ QLVS+K+++++ K +I ++G++PE+I+DY +L+GD
Sbjct: 125 EVRIVSGDKDLLQLVSDKVSVLDPTKGIKEFELYTPENVIEKYGLTPEQIIDYKALMGDS 184
Query: 953 SDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKILTIK 1012
SDN+PGV IG KTA KLL ++ SLENI+ N + +K + + L +K+ TI+
Sbjct: 185 SDNIPGVPGIGEKTAAKLLKEFGSLENILENLDKLKKKLREKLLAHKEDAKLSRKLATIE 244
Query: 1013 TDCDLTKNI 1021
TD L ++
Sbjct: 245 TDVPLEVDL 253
>gnl|CDD|233038 TIGR00593, pola, DNA polymerase I. All proteins in this family for
which functions are known are DNA polymerases Many also
have an exonuclease motif. 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 = 887
Score = 256 bits (655), Expect = 9e-71
Identities = 112/275 (40%), Positives = 155/275 (56%), Gaps = 13/275 (4%)
Query: 779 IDGSSCIYRAFYALP--DIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNF 836
IDG S +RA++AL + N P A+YG KML KL K + TY+A FD+ F
Sbjct: 4 IDGHSLAFRAYFALKNKPLTNSKGEPTNAVYGFTKMLLKLLKEEKPTYVAVAFDSGTPTF 63
Query: 837 RNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKH 896
R+ Y YKA R P LI QI LI +++ A+G PIL ++G EADDVI TLAKQA K
Sbjct: 64 RHEAYAEYKANRAPTPEELIEQIPLIKELLDALGIPILEVEGYEADDVIATLAKQA-EKE 122
Query: 897 NLKVIISTNDKDMAQLVSNKIALINNNKIHDRTTI-----ISRFGVSPEKIVDYFSLIGD 951
+V I + DKD+ QLVS+ + ++ T I + ++GV+P+++VD +L+GD
Sbjct: 123 GYEVRIISGDKDLLQLVSDNVKVLIPKGKTSFTEITPEYVVEKYGVTPDQLVDLKALVGD 182
Query: 952 MSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKG-VIGKNLRFALNWLPKLKKILT 1010
SDN+PGVK IG KTA KLL ++ SLENI N + IK + + L K++ T
Sbjct: 183 SSDNIPGVKGIGEKTAAKLLQEFGSLENIYENLDQIKSAKMREKLIAHKEDAFLSKELAT 242
Query: 1011 IKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKY 1045
I TD L ++ E L L D + L L +
Sbjct: 243 IVTDVPLEVDL----EDLRLSEPDRERLYALLQEL 273
>gnl|CDD|234694 PRK00228, PRK00228, hypothetical protein; Validated.
Length = 191
Score = 230 bits (590), Expect = 2e-69
Identities = 76/186 (40%), Positives = 118/186 (63%), Gaps = 14/186 (7%)
Query: 1073 NLTNHFLIAMPGFSTPFFDGAVVYLCEHNSNGAFGIIINKPTDMTI-NILLDNDSNLKLK 1131
NL LIAMP P F +V+Y+CEHN NGA G++IN+P+++ + +L +L
Sbjct: 9 NLQGQLLIAMPDLQDPNFARSVIYICEHNENGAMGLVINRPSELDVAEVLP------QLD 62
Query: 1132 LVPNTKEFILEKTTKTIMFGGPIQIDRGFVLHNITNEKSPIFNSTLNIASDISLTTSRDI 1191
++ E L++ + GGP+Q DRGFVLH+ F+S++ ++ + LTTSRD+
Sbjct: 63 ILATPPEIRLDQP---VFLGGPVQTDRGFVLHSPR----DGFDSSIRVSDGLVLTTSRDV 115
Query: 1192 LESFSRGDGPSQLLISLGCSGWGAGQLEEEIMNNHWLIVDANSEVIFNVPCEQRFFAAVK 1251
LE+ + G GP +L++LG +GWGAGQLE+EI N WL A+ E++F+ P E R+ AA++
Sbjct: 116 LEALATGPGPEGVLVALGYAGWGAGQLEQEIEENAWLTAPADPEILFDTPPEDRWRAALR 175
Query: 1252 LLGVNP 1257
LG++
Sbjct: 176 RLGIDL 181
>gnl|CDD|223336 COG0258, Exo, 5'-3' exonuclease (including N-terminal domain of PolI)
[DNA replication, recombination, and repair].
Length = 310
Score = 227 bits (581), Expect = 1e-66
Identities = 107/277 (38%), Positives = 155/277 (55%), Gaps = 10/277 (3%)
Query: 779 IDGSSCIYRAFYALP-DIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFR 837
IDGSS +YRA +ALP + N P GA+ G + ML +L + T+ +FD K FR
Sbjct: 16 IDGSSLLYRALHALPQPLGNPLGDPTGAVSGFLGMLYRLIRLLEPTHPVVVFDGKPPTFR 75
Query: 838 NILYPSYKATRKK-MPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKH 896
+ L YKA R+K MP L QI ++ +++ A+G P+L + G+EADD I TLA Q K
Sbjct: 76 HELLEEYKANREKEMPDELAPQIPILTELLVALGIPLLELMGIEADDPIETLA-QKAYKK 134
Query: 897 NLKVIISTNDKDMAQLVSNKIALINNNKIH-----DRTTIISRF-GVSPEKIVDYFSLIG 950
V+I + DKD+ QLVS + +IN K D + +F G++PE+++D +L+G
Sbjct: 135 GDVVLIISGDKDLLQLVSPNVLVINGKKGEPEKFLDLEEVEEKFKGLTPEQLIDLKALVG 194
Query: 951 DMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKILT 1010
D SDN+PGVK IGPKTA+KLL +Y SLE + N + IK + L K + T
Sbjct: 195 DSSDNIPGVKGIGPKTALKLLQEYGSLEGLYENLDIIKKKTREKLLEDKEKAFLSKPLAT 254
Query: 1011 IKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYNI 1047
IKTD L ++ I L++ D L++ +
Sbjct: 255 IKTDVPLEFDLEDI-LELLVPEHDFSKLLEERVELGF 290
>gnl|CDD|217150 pfam02622, DUF179, Uncharacterized ACR, COG1678.
Length = 158
Score = 210 bits (537), Expect = 8e-63
Identities = 76/173 (43%), Positives = 108/173 (62%), Gaps = 15/173 (8%)
Query: 1082 MPGFSTPFFDGAVVYLCEHNSNGAFGIIINKPTDMTINILLDNDSNLKLKLVPNTKEFIL 1141
MPG P F +VV LCEHN GA G+I+N+P D+T+ LL+ +L + P
Sbjct: 1 MPGLGDPNFARSVVLLCEHNEEGAMGLILNRPLDLTLADLLE-----QLDIEPGAFS--- 52
Query: 1142 EKTTKTIMFGGPIQIDRGFVLHNITNEKSPIFNSTLNIASDISLTTSRDILESFSRGDGP 1201
+ + FGGP++ DRGFVLH+ S+L ++ + LTTS DILE+ +RG+GP
Sbjct: 53 ---DQPVYFGGPVEPDRGFVLHSPD----DGEPSSLEVSDGLYLTTSLDILEAIARGEGP 105
Query: 1202 SQLLISLGCSGWGAGQLEEEIMNNHWLIVDANSEVIFNVPCEQRFFAAVKLLG 1254
+L+ LG +GWGAGQLE+EI N WL+ A+ E+IF+ P E R+ AA++ LG
Sbjct: 106 EDILVFLGYAGWGAGQLEQEIAENSWLVAPADPEIIFDTPPEDRWEAALRRLG 158
>gnl|CDD|224592 COG1678, COG1678, Putative transcriptional regulator [Transcription].
Length = 194
Score = 209 bits (534), Expect = 5e-62
Identities = 82/187 (43%), Positives = 120/187 (64%), Gaps = 14/187 (7%)
Query: 1073 NLTNHFLIAMPGFSTPFFDGAVVYLCEHNSNGAFGIIINKPTD-MTINILLDNDSNLKLK 1131
NL HFL+AMP P F +VVY+CEHN NGA G+IIN+P++ +T+ LL LKL+
Sbjct: 12 NLQGHFLVAMPDMQDPIFARSVVYICEHNENGAMGLIINRPSETLTLAELL---EKLKLE 68
Query: 1132 LVPNTKEFILEKTTKTIMFGGPIQIDRGFVLHNITNEKSPIFNSTLNIASDISLTTSRDI 1191
+ K + GGP+Q DRGFVLH +++ F S+L ++ ++LTTS D+
Sbjct: 69 IKILRLP-------KPVYLGGPVQRDRGFVLH--SSDYGA-FQSSLRVSDGLALTTSLDV 118
Query: 1192 LESFSRGDGPSQLLISLGCSGWGAGQLEEEIMNNHWLIVDANSEVIFNVPCEQRFFAAVK 1251
LE+ + G GP + L++LG +GW AGQLEEEI +N WL V A+ E++F+ P E R+ A++
Sbjct: 119 LEAIAAGKGPEKALVALGYAGWAAGQLEEEIEDNDWLTVPADPEILFDTPPEDRWARALR 178
Query: 1252 LLGVNPL 1258
LG++
Sbjct: 179 RLGIDLA 185
>gnl|CDD|189029 cd09859, PIN_53EXO, PIN domain of the 5'-3' exonuclease of Taq DNA
polymerase I and homologs. The 5'-3' exonuclease
(53EXO) PIN (PilT N terminus) domain of multi-domain DNA
polymerase I and single domain protein homologs are
included in this family. Taq contains a polymerase
domain for synthesizing a new DNA strand and a 53EXO PIN
domain for cleaving RNA primers or damaged DNA strands.
Taq's 53EXO PIN domain recognizes and
endonucleolytically cleaves a structure-specific DNA
substrate that has a bifurcated downstream duplex and an
upstream template-primer duplex that overlaps the
downstream duplex by 1 bp. The 53EXO PIN domain cleaves
the unpaired 5'-arm of the overlap flap DNA substrate.
5'-3' exonucleases are members of the
structure-specific, 5' nuclease family that catalyzes
hydrolysis of DNA duplex-containing nucleic acid
structures during DNA replication, repair, and
recombination. These nucleases contain a PIN domain with
a helical arch/clamp region (I domain) of variable
length (approximately 16 residues in 53EXO PIN domains)
and a H3TH (helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA/RNA binding. The active site
includes a set of conserved acidic residues that are
essential for binding divalent metal ions required for
nuclease activity.
Length = 174
Score = 203 bits (520), Expect = 3e-60
Identities = 71/154 (46%), Positives = 101/154 (65%), Gaps = 2/154 (1%)
Query: 779 IDGSSCIYRAFYALPDIRNIDN-FPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFR 837
IDGSS ++RA+YALP + N D+ P A+YG + ML KL K + T++A FDAKG FR
Sbjct: 4 IDGSSLLFRAYYALPPLTNSDDGEPTNAVYGFLNMLLKLLKEEKPTHVAVAFDAKGPTFR 63
Query: 838 NILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHN 897
+ LYP YKA R MP L Q+ LI ++++A+G P+L ++G EADDVIGTLAK+A +
Sbjct: 64 HELYPEYKANRPPMPEELRPQLPLIKELLEALGIPVLEVEGYEADDVIGTLAKKAE-EEG 122
Query: 898 LKVIISTNDKDMAQLVSNKIALINNNKIHDRTTI 931
+V+I + DKD+ QLVS + +++ K
Sbjct: 123 YEVVIVSGDKDLLQLVSENVRVLDPKKGSKFELY 156
>gnl|CDD|237877 PRK14976, PRK14976, 5'-3' exonuclease; Provisional.
Length = 281
Score = 201 bits (514), Expect = 5e-58
Identities = 108/278 (38%), Positives = 159/278 (57%), Gaps = 14/278 (5%)
Query: 779 IDGSSCIYRAFYAL----PDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGK 834
IDG+S I+R++YA P ++N P A++ + M+ K+ K +YI FDA K
Sbjct: 8 IDGNSLIFRSYYATLKQGPKLKNNKGLPTNAIHTFLTMIFKILKKLNPSYILIAFDAGRK 67
Query: 835 NFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVT 894
FR+ LY YK RKK P +LI QI L+ +++K G G EADD+IG+LAK+ +
Sbjct: 68 TFRHQLYDEYKQGRKKTPESLISQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKL-S 126
Query: 895 KHNLKVIISTNDKDMAQLVSNKIALINNNK-----IHDRTTIISRFGVSPEKIVDYFSLI 949
K N+ V+I ++DKD+ QLV+ ++ K I + +G+ P++I+DY L+
Sbjct: 127 KQNITVLIYSSDKDLLQLVNENTDVLLKKKGTSHFILNTNNFFELYGIEPKQIIDYKGLV 186
Query: 950 GDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKIL 1009
GD SDN+ GVK IGPKTA+KLLN+Y ++ENI N + IK I L A KK+
Sbjct: 187 GDSSDNIKGVKGIGPKTAIKLLNKYGNIENIYENIDKIKKKIKNKLSEAKEKALLSKKLA 246
Query: 1010 TIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYNI 1047
TIKTD L I E + L+ D+ L ++F + +
Sbjct: 247 TIKTDVPLDFQI----EDIKLKKLDQPELKKIFEELEL 280
>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 = 191 bits (488), Expect = 1e-54
Identities = 78/272 (28%), Positives = 132/272 (48%), Gaps = 13/272 (4%)
Query: 514 RKKKYVLAEIGWPIARPFFYITHMFSSKHSYISLMWPICIHPMNKNILITWNLLHDPKKF 573
R KK V I +P +++ MF ++ S + P+ HP NKN +I +L DP
Sbjct: 1 RSKKAVAKLIDLVAMKPLVHVSGMFGAERGCTSWVLPLAWHPTNKNAVIVCDLAQDPSPL 60
Query: 574 LLNDINKIRDYLCFKKNSFKED---IPISMIHLNRSPIVISNLKVLSSNLMFRYKFDLNC 630
L ++R L K+ E +P+ ++HLN+ PI+ K L R D
Sbjct: 61 LDLSAEELRQRLYTKREDLAEGELRVPLKLVHLNKCPILA-PAKTLRPEDAERLGIDREQ 119
Query: 631 AFKNIK--CASSILNNTYIWKKIF-LDYKINNSDLELNIDEELYNNFISKKDNLKLAILR 687
KN+ + L K++F + + S ++D++LY+ F S D + I+R
Sbjct: 120 CLKNLALLRQNPELRE--KLKEVFEEEREFPPST---DVDQQLYDGFFSDADKRLMEIIR 174
Query: 688 SMSPKKLSNVNFCFENKKLEELIFLYRARNFIETLSYKELKRWKKYRISRFYNKKNNLYN 747
SP++L+ + F++K+L EL+F YRARNF ETLS +E +RW++Y R +
Sbjct: 175 ETSPEQLAELELNFDDKRLPELLFRYRARNFPETLSEEEQQRWQEYCQQRLLDPAGGALT 234
Query: 748 INMFYLEIESLLKKA-NEHDTKILNALLMYGK 778
+ + ++E L + ++ +L AL Y +
Sbjct: 235 LEDYEQKLEQLAAEYSDDEKQALLQALYDYAQ 266
>gnl|CDD|234659 PRK00137, rplI, 50S ribosomal protein L9; Reviewed.
Length = 147
Score = 182 bits (464), Expect = 5e-53
Identities = 65/136 (47%), Positives = 95/136 (69%), Gaps = 1/136 (0%)
Query: 174 MQVILLKDIPNLGKLGEIIKVKNGYARNFLIPKNKARHATKFVIKEFEEKRIKLEKTAFT 233
M+VILL+D+ NLGK G++++VK+GYARNFLIP+ KA ATK +K+ E +R +LE A
Sbjct: 1 MKVILLEDVKNLGKKGDVVEVKDGYARNFLIPQGKAVRATKGNLKQLEARRAELEAKAAE 60
Query: 234 IFLNAKKIGEEIKKLNINIIKKSGVDGKLFGSVTNSDIVKELEKKGLKIEKNKIKLPNNS 293
A+ + E+++ L + I K+G DGKLFGSVT DI + L+K+G++I+K KI+LP
Sbjct: 61 ELAEAEALAEKLEGLTVTIKAKAGEDGKLFGSVTTKDIAEALKKQGIEIDKRKIELPGP- 119
Query: 294 IKKIGNYYIDILLHNG 309
IK +G Y + + LH
Sbjct: 120 IKTLGEYEVPVKLHPE 135
>gnl|CDD|145734 pfam02739, 5_3_exonuc_N, 5'-3' exonuclease, N-terminal
resolvase-like domain.
Length = 169
Score = 180 bits (459), Expect = 4e-52
Identities = 71/150 (47%), Positives = 94/150 (62%), Gaps = 5/150 (3%)
Query: 779 IDGSSCIYRAFYALPD--IRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNF 836
IDGSS +RAF+ALP + N P A+YG ++ML KL K + TY+A +FDA F
Sbjct: 6 IDGSSLAFRAFFALPKVPLTNSKGEPTNAVYGFLRMLLKLLKEEKPTYVAVVFDAGAPTF 65
Query: 837 RNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKH 896
R+ LY YKA R K P L QI LI +++ A+G P+L + G EADDVIGTLAK+A K
Sbjct: 66 RHELYEEYKANRAKTPDELPPQIPLIKELLDALGIPVLEVPGYEADDVIGTLAKKA-EKE 124
Query: 897 NLKVIISTNDKDMAQLVS--NKIALINNNK 924
V I + DKD+ QLVS +A++N +
Sbjct: 125 GYDVRIVSGDKDLLQLVSDKVNVAVLNPGR 154
>gnl|CDD|223436 COG0359, RplI, Ribosomal protein L9 [Translation, ribosomal
structure and biogenesis].
Length = 148
Score = 158 bits (403), Expect = 7e-45
Identities = 65/134 (48%), Positives = 92/134 (68%), Gaps = 1/134 (0%)
Query: 174 MQVILLKDIPNLGKLGEIIKVKNGYARNFLIPKNKARHATKFVIKEFEEKRIKLEKTAFT 233
M+VILL+D+ LGK G+I++VK+GYARNFLIPK A ATK +K E +R KLEK A
Sbjct: 1 MKVILLEDVKGLGKKGDIVEVKDGYARNFLIPKGLAVPATKGNLKLLEARRAKLEKKAAE 60
Query: 234 IFLNAKKIGEEIKKLNINIIKKSGVDGKLFGSVTNSDIVKELEKKGLKIEKNKIKLPNNS 293
A+ + E+++ + I K+G DGKLFGSVT+ DI + L+ G K++K KI+LPN
Sbjct: 61 ELAEAEALKEKLEGKTVEIAVKAGEDGKLFGSVTSKDIAEALKAAGFKLDKRKIRLPNG- 119
Query: 294 IKKIGNYYIDILLH 307
IK +G + +++ LH
Sbjct: 120 IKTLGEHEVEVKLH 133
>gnl|CDD|181896 PRK09482, PRK09482, flap endonuclease-like protein; Provisional.
Length = 256
Score = 134 bits (340), Expect = 4e-35
Identities = 72/212 (33%), Positives = 107/212 (50%), Gaps = 5/212 (2%)
Query: 813 LRKLYKNYRATYIACIFD--AKGKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIG 870
L KL ++ + T+ +FD A+ +R+ L P YKA RK MP L + I + +G
Sbjct: 38 LDKLIRHSQPTHAVAVFDGDARSSGWRHQLLPDYKAGRKPMPEALQQGLPAIRAAFEELG 97
Query: 871 WPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALIN--NNKIHDR 928
G EADD+I TLA + V + + I + DK QL+S I + + + D
Sbjct: 98 IDSWHADGNEADDLIATLAVK-VAQAGHQATIVSTDKGYCQLLSPTIQIRDYFQKRWLDA 156
Query: 929 TTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIK 988
I FGV P+++ DY+ L G S +PGV IGPK+A +LLNQ+ SLENI + + +
Sbjct: 157 PFIEQEFGVEPQQLPDYWGLAGISSSKIPGVAGIGPKSAAELLNQFRSLENIYESLDALP 216
Query: 989 GVIGKNLRFALNWLPKLKKILTIKTDCDLTKN 1020
K L +K+ ++TD L N
Sbjct: 217 EKWRKKLEEHKEMARLCRKLAQLQTDLPLGGN 248
>gnl|CDD|129262 TIGR00158, L9, ribosomal protein L9. Ribosomal protein L9 appears
to be universal in, but restricted to, eubacteria and
chloroplast [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 148
Score = 126 bits (319), Expect = 1e-33
Identities = 61/136 (44%), Positives = 87/136 (63%)
Query: 174 MQVILLKDIPNLGKLGEIIKVKNGYARNFLIPKNKARHATKFVIKEFEEKRIKLEKTAFT 233
M+VILL+D+ NLGK G++++VK+GYARNFLIPK A ATK I+ FE +R KLE+
Sbjct: 1 MKVILLEDVANLGKRGDVVEVKDGYARNFLIPKGLAVPATKKNIEFFEARRKKLEEKLAA 60
Query: 234 IFLNAKKIGEEIKKLNINIIKKSGVDGKLFGSVTNSDIVKELEKKGLKIEKNKIKLPNNS 293
A ++ E ++ + I KK G +GKLFGS+T I L+ GL ++K KI+LP+
Sbjct: 61 NKAAAARLKEVLELGTLTISKKVGDEGKLFGSITTKQIADALKAAGLDLDKKKIELPDGV 120
Query: 294 IKKIGNYYIDILLHNG 309
I+ G + + I LH
Sbjct: 121 IRTTGEHEVTIKLHEE 136
>gnl|CDD|179034 PRK00453, rpsF, 30S ribosomal protein S6; Reviewed.
Length = 108
Score = 111 bits (281), Expect = 5e-29
Identities = 36/84 (42%), Positives = 54/84 (64%)
Query: 1 MIERYKKIIISGKGKIHRLEDWGRRSLAYQIKKVIKAHYICFNIEINKKTLLEIETSFRF 60
++ER+K +I G IH++EDWGRR LAY I K+ K HY+ N E + E+E FR
Sbjct: 22 LVERFKGVITENGGTIHKVEDWGRRRLAYPINKLRKGHYVLLNFEAPPAAIAELERLFRI 81
Query: 61 NDAILRYLTIKTKKVETEESSFLR 84
N+ +LR+LT+K ++ E E S ++
Sbjct: 82 NEDVLRFLTVKVEEAEEEPSPMMK 105
>gnl|CDD|240187 cd05560, Xcc1710_like, Xcc1710_like family, specific to
proteobacteria. Xcc1710 is a hypothetical protein from
Xanthomonas campestris pv. campestris str. ATCC 33913,
similar to Mth938, a hypothetical protein encoded by the
Methanobacterium thermoautotrophicum (Mth) genome. Their
three-dimensional structures have been determined, but
their functions are unknown.
Length = 109
Score = 102 bits (257), Expect = 9e-26
Identities = 41/110 (37%), Positives = 60/110 (54%), Gaps = 1/110 (0%)
Query: 1317 TIVAYTNYGVKFRNGIFYTKSFLVSPEIDPIFWSINKYNFLTKKDFIHISKFNPSVVILG 1376
TI AY + V+ N Y S +V+P+ W + ++ LT F + P V++LG
Sbjct: 1 TITAYGDGYVEI-NDQRYEHSLIVTPDELITDWPVARFEDLTAAHFEALLALQPEVILLG 59
Query: 1377 TGNIQHFIHPKLTYILTQKNIGIECMNNQAACRTYNILVSDDIKAMLALI 1426
TG Q F P L L + IG+E M+ QAACRTYNIL+ + + + AL+
Sbjct: 60 TGERQRFPPPALLAPLLARGIGVEVMDTQAACRTYNILMGEGRRVVAALL 109
>gnl|CDD|223437 COG0360, RpsF, Ribosomal protein S6 [Translation, ribosomal
structure and biogenesis].
Length = 112
Score = 102 bits (256), Expect = 1e-25
Identities = 36/94 (38%), Positives = 58/94 (61%), Gaps = 4/94 (4%)
Query: 1 MIERYKKIIISGKGKIHRLEDWGRRSLAYQIKKVIKAHYICFNIEINKKTLLEIETSFRF 60
++E+YK ++ + G+IH++EDWG+R LAY IKK+ + HY+ N E + E+E R
Sbjct: 21 LVEKYKGVLTNNGGEIHKVEDWGKRRLAYPIKKLREGHYVLMNFEAEPAAIAELERLLRI 80
Query: 61 NDAILRYLTIKTKKVETEESSFLRFIQKKEKVLK 94
N+ +LR+L IK +K + E S + KK+ K
Sbjct: 81 NEDVLRHLIIKVEKAKEELS----PMLKKKDQRK 110
>gnl|CDD|178997 PRK00391, rpsR, 30S ribosomal protein S18; Reviewed.
Length = 79
Score = 99.5 bits (249), Expect = 5e-25
Identities = 29/60 (48%), Positives = 41/60 (68%)
Query: 109 KRQQQNPLFKRKKFCRFTVMNIKQIDYKDIETLKDFIQENGKIMAARLTGTCSHYQRQIT 168
+++ + F+RKK CRF I+ IDYKD+E LK FI E GKI+ R+TGT + +QRQ+
Sbjct: 3 RKKARRRFFRRKKVCRFCAEKIEYIDYKDVELLKKFISERGKILPRRITGTSAKHQRQLA 62
>gnl|CDD|188618 cd09898, H3TH_53EXO, H3TH domain of the 5'-3' exonuclease of Taq DNA
polymerase I and homologs. H3TH (helix-3-turn-helix)
domains of the 5'-3' exonuclease (53EXO) of mutli-domain
DNA polymerase I and single domain protein homologs are
included in this family. Taq DNA polymerase I contains a
polymerase domain for synthesizing a new DNA strand and a
53EXO domain for cleaving RNA primers or damaged DNA
strands. Taq's 53EXO recognizes and endonucleolytically
cleaves a structure-specific DNA substrate that has a
bifurcated downstream duplex and an upstream
template-primer duplex that overlaps the downstream
duplex by 1 bp. The 53EXO cleaves the unpaired 5'-arm of
the overlap flap DNA substrate. 5'-3' exonucleases are
members of the structure-specific, 5' nuclease family
that catalyzes hydrolysis of DNA duplex-containing
nucleic acid structures during DNA replication, repair,
and recombination. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region/I
domain (not included here) and inserted within the PIN
domain is an atypical helix-hairpin-helix-2 (HhH2)-like
region. This atypical HhH2 region, the H3TH domain, has
an extended loop with at least three turns between the
first two helices, and only three of the four helices
appear to be conserved. Both the H3TH domain and the
helical arch/clamp region are involved in DNA binding.
Studies suggest that a glycine-rich loop in the H3TH
domain contacts the phosphate backbone of the template
strand in the downstream DNA duplex. The nucleases within
this family have a carboxylate rich active site that is
involved in binding essential divalent metal ion
cofactors (i. e., Mg2+ or Mn2+ or Zn2+) required for
nuclease activity. The first metal binding site is
composed entirely of Asp/Glu residues from the PIN
domain, whereas, the second metal binding site is
composed generally of two Asp residues from the PIN
domain and two Asp residues from the H3TH domain.
Together with the helical arch and network of amino acids
interacting with metal binding ions, the H3TH region
defines a positively charged active-site DNA-binding
groove in structure-specific 5' nucleases.
Length = 73
Score = 96.3 bits (241), Expect = 5e-24
Identities = 35/73 (47%), Positives = 49/73 (67%)
Query: 939 PEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFA 998
PE+I+DY +L+GD SDN+PGV IGPKTA KLL +Y SLENI+ N + +KG + + L
Sbjct: 1 PEQIIDYLALVGDSSDNIPGVPGIGPKTAAKLLQEYGSLENILANLDELKGKLREKLEEN 60
Query: 999 LNWLPKLKKILTI 1011
+K+ T+
Sbjct: 61 KEQALLSRKLATL 73
>gnl|CDD|214378 CHL00160, rpl9, ribosomal protein L9; Provisional.
Length = 153
Score = 98.3 bits (245), Expect = 1e-23
Identities = 51/141 (36%), Positives = 85/141 (60%), Gaps = 4/141 (2%)
Query: 170 IRKNMQVILLKDIPNLGKLGEIIKVKNGYARNFLIPKNKARHATKFVIKEFEEKRIKLEK 229
+K +QVIL ++I LGK G +IKVK+GYARN+LIP A+ AT+ +K+ + + L+
Sbjct: 2 SKKKIQVILKENIQKLGKSGTVIKVKSGYARNYLIPNKMAKVATQGSLKQQKMYQKILDL 61
Query: 230 TAFTIFLNAKKIGEEIKKLN-INIIKKSGVDGKLFGSVTNSDIVKELEKK-GLKIEKNKI 287
K+ + ++++ ++ KK G + ++FGSVT +I + ++ K + +EK I
Sbjct: 62 KLKEAKEKCLKVKQLLEEIQKFSVKKKVGENNQIFGSVTEKEISQIIKNKTNIDLEKQNI 121
Query: 288 KLPNNSIKKIGNYYIDILLHN 308
+LP IK IG Y I+I L +
Sbjct: 122 ELPE--IKTIGIYNIEIKLTS 140
>gnl|CDD|216458 pfam01367, 5_3_exonuc, 5'-3' exonuclease, C-terminal SAM fold.
Length = 100
Score = 95.7 bits (239), Expect = 2e-23
Identities = 45/104 (43%), Positives = 65/104 (62%), Gaps = 4/104 (3%)
Query: 937 VSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLR 996
++PE+I+DY +L+GD SDN+PGV IG KTA KLL +Y SLENI N + +KG + + L
Sbjct: 1 LTPEQIIDYKALVGDSSDNIPGVPGIGEKTAAKLLKEYGSLENIYENLDKLKGKLREKLL 60
Query: 997 FALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQ 1040
+K+ TIKTD L + E L L+P D++ L++
Sbjct: 61 NGKEDAFLSRKLATIKTDVPLELTL----EDLRLKPPDKEELIE 100
>gnl|CDD|226260 COG3737, COG3737, Uncharacterized conserved protein [Function
unknown].
Length = 127
Score = 94.8 bits (236), Expect = 9e-23
Identities = 38/127 (29%), Positives = 59/127 (46%), Gaps = 4/127 (3%)
Query: 1303 KKMELKKIINTKHQTIVAYTNYGVKFRNGIFYTKSFLVSPEIDPIFWSINKYNFLTKKDF 1362
K M ++ I AY G +F + + S LV P+ W + + LT +DF
Sbjct: 3 KGMLFREAHFPGRAPIDAYGAGGFRF-ADMSHRGSLLVLPD-GVCDWEVATLSDLTPEDF 60
Query: 1363 IHISKF--NPSVVILGTGNIQHFIHPKLTYILTQKNIGIECMNNQAACRTYNILVSDDIK 1420
+ + ++++GTG F PKL L I +E M+ AA RTYN+L+S+ +
Sbjct: 61 ERVLAEAPDVEILLIGTGARLRFPPPKLRAALKAAGISVEPMSTGAAVRTYNVLLSEGRR 120
Query: 1421 AMLALIL 1427
ALI
Sbjct: 121 VAAALIA 127
>gnl|CDD|216388 pfam01250, Ribosomal_S6, Ribosomal protein S6.
Length = 92
Score = 91.4 bits (228), Expect = 5e-22
Identities = 30/72 (41%), Positives = 48/72 (66%)
Query: 1 MIERYKKIIISGKGKIHRLEDWGRRSLAYQIKKVIKAHYICFNIEINKKTLLEIETSFRF 60
+IE+YKK+I G++ ++EDWG+R LAY IKK + +Y+ N E + + E+E R
Sbjct: 21 LIEKYKKLIEENGGEVVKVEDWGKRKLAYPIKKKREGYYVLINFEAEPEAIAELERRLRI 80
Query: 61 NDAILRYLTIKT 72
N+ +LR+LT+K
Sbjct: 81 NEDVLRFLTVKL 92
>gnl|CDD|223316 COG0238, RpsR, Ribosomal protein S18 [Translation, ribosomal
structure and biogenesis].
Length = 75
Score = 89.2 bits (222), Expect = 2e-21
Identities = 30/63 (47%), Positives = 43/63 (68%)
Query: 106 FKQKRQQQNPLFKRKKFCRFTVMNIKQIDYKDIETLKDFIQENGKIMAARLTGTCSHYQR 165
K ++ P F+R+K CRFT I++IDYKD+E LK FI E GKI+ R+TGT + +QR
Sbjct: 1 MNAKFGRRAPFFRRRKVCRFTAEGIEEIDYKDVELLKRFISERGKILPRRITGTSAKHQR 60
Query: 166 QIT 168
++
Sbjct: 61 RLA 63
>gnl|CDD|146531 pfam03948, Ribosomal_L9_C, Ribosomal protein L9, C-terminal domain.
Length = 86
Score = 89.4 bits (223), Expect = 2e-21
Identities = 31/71 (43%), Positives = 49/71 (69%), Gaps = 1/71 (1%)
Query: 237 NAKKIGEEIKKLNINIIKKSGVDGKLFGSVTNSDIVKELEKKGLKIEKNKIKLPNNSIKK 296
A+ + E+++ L + I K+G DGKLFGSVT DI + L+ +G++I+K KI+LP IK
Sbjct: 3 EAEALAEKLEGLTVTIKAKAGEDGKLFGSVTTKDIAEALKAQGIEIDKKKIELPEP-IKT 61
Query: 297 IGNYYIDILLH 307
+G Y +++ LH
Sbjct: 62 LGEYEVEVKLH 72
>gnl|CDD|201708 pfam01281, Ribosomal_L9_N, Ribosomal protein L9, N-terminal domain.
Length = 48
Score = 86.8 bits (216), Expect = 7e-21
Identities = 28/48 (58%), Positives = 37/48 (77%)
Query: 174 MQVILLKDIPNLGKLGEIIKVKNGYARNFLIPKNKARHATKFVIKEFE 221
M+VILL+D+ LGK G+I++VK GYARNFL+PK A +AT +KE E
Sbjct: 1 MKVILLEDVEGLGKKGDIVEVKPGYARNFLLPKGLAVYATPENLKELE 48
>gnl|CDD|238152 cd00248, Mth938-like, Mth938-like domain. The members of this family
include: Mth938, 2P1, Xcr35, Rpa2829, and several
uncharacterized sequences. Mth938 is a hypothetical
protein encoded by the Methanobacterium
thermoautotrophicum (Mth) genome. This protein
crystallizes as a dimer, although it is monomeric in
solution, with one disulfide bond in each monomer. 2P1
is a partially characterized nuclear protein which is
homologous to E3-3 from rat and known to be alternately
spliced. Xcr35 and Rpa2829 are hypothetical proteins of
unknown function from the Xanthomonas campestris and
Rhodopseudomonas palustris genomes, respectively, for
which the crystal structures have been determined.
Length = 109
Score = 85.4 bits (212), Expect = 1e-19
Identities = 33/110 (30%), Positives = 52/110 (47%), Gaps = 3/110 (2%)
Query: 1318 IVAYTNYGVKFRNGIFYTKSFLVSPEIDPIFWSINKYNFLTKKDFIHISKFN-PSVVILG 1376
I Y G + G Y LV P+ + W + L + + + + P ++++G
Sbjct: 2 IDGYGPGGFRI-AGQVYRGPLLVLPD-GVVPWDGTSLSDLDPEALLPLLAEDRPDILLIG 59
Query: 1377 TGNIQHFIHPKLTYILTQKNIGIECMNNQAACRTYNILVSDDIKAMLALI 1426
TG F+ L L IG+E M+ AACRTYN+L+S+ + ALI
Sbjct: 60 TGAEIAFLPRALRAALRAAGIGVEVMSTGAACRTYNVLLSEGRRVAAALI 109
>gnl|CDD|218085 pfam04430, DUF498, Protein of unknown function (DUF498/DUF598). This
is a large family of uncharacterized proteins found in
all domains of life. The structure shows a novel fold
with three beta sheets. A dimeric form is found in the
crystal structure. It was suggested that the cleft in
between the two monomers might bing nucleic acid.
Length = 109
Score = 81.1 bits (201), Expect = 3e-18
Identities = 41/112 (36%), Positives = 59/112 (52%), Gaps = 7/112 (6%)
Query: 1318 IVAYTNYGVKFRNGIFYTKSFLVSPEIDPIFWSINKYNF--LTKKDF--IHISKFNPSVV 1373
I Y G + NG+ Y S LV P D I W + +F L+ +D + +P V+
Sbjct: 1 IDGYGPGGFRI-NGVRYEGSLLVLP--DGIVWDWDVGSFEDLSPEDLALLLALAPDPEVL 57
Query: 1374 ILGTGNIQHFIHPKLTYILTQKNIGIECMNNQAACRTYNILVSDDIKAMLAL 1425
I+GTG F+ P+L L + IG+E M+ AACRTYN+L S+ + AL
Sbjct: 58 IIGTGARLRFLPPELREALRKLGIGVEVMDTGAACRTYNVLASEGRRVAAAL 109
>gnl|CDD|129270 TIGR00166, S6, ribosomal protein S6. The ribosomal protein S6
ortholog family, including yeast MRP17, shows more than
two-fold length variation from 95 residues in Bacillus
subtilis to 215 in Mycoplasma pneumoniae. This length
variation comes primarily from poorly conserved
C-terminal extensions that are particularly long in the
Mycoplasmas. MRP17 protein is a component of the small
ribosomal subunit in mitochondria, and is shown here to
be an ortholog of S6 [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 93
Score = 79.7 bits (197), Expect = 7e-18
Identities = 33/74 (44%), Positives = 45/74 (60%)
Query: 1 MIERYKKIIISGKGKIHRLEDWGRRSLAYQIKKVIKAHYICFNIEINKKTLLEIETSFRF 60
IERYKK+I +I R EDWG+R LAY IKK ++AHY+ N + + E E + R
Sbjct: 20 QIERYKKVITLNGAEIVRSEDWGKRRLAYPIKKQLRAHYVLMNFSGEAQVIKEFERTARI 79
Query: 61 NDAILRYLTIKTKK 74
ND ++R L IK +
Sbjct: 80 NDNVIRSLIIKLEH 93
>gnl|CDD|173004 PRK14538, PRK14538, putative bifunctional signaling protein/50S
ribosomal protein L9; Provisional.
Length = 838
Score = 89.5 bits (222), Expect = 7e-18
Identities = 59/159 (37%), Positives = 83/159 (52%), Gaps = 10/159 (6%)
Query: 172 KNMQVILLKDIPNLGKLGEIIKVKNGYARNFLIPKNKARHATKFVIKEFEEKRIKLEKTA 231
KNM++ILL DI N GK EIIKV NGY NFLI KA A K + + ++K+I ++
Sbjct: 687 KNMEIILLTDIKNKGKKHEIIKVNNGYG-NFLIQNKKALLADKENLAKIKKKKILEQEKK 745
Query: 232 FTIFLNAKKIGEEIKKLNINIIKKSGVDGKLFGSVTNSDIVKELEKK-GLKIEKNKIKLP 290
L KK+ EI I + + G GK++G +T IV+E K + I++ KI L
Sbjct: 746 RNHELLMKKLKSEIDNKKITLDIQLGPKGKIYGKITLKQIVEEFHKIHNITIDRKKISL- 804
Query: 291 NNSIKKIGNYYIDILLHNGNSTFLWYDYETFGLNVRRDR 329
N I +G Y +D+ L + TF LNV +
Sbjct: 805 ENEIISVGIYPVDVFLTDQIKA-------TFFLNVIERK 836
>gnl|CDD|232851 TIGR00165, S18, ribosomal protein S18. This ribosomal small
subunit protein is found in all eubacteria so far, as
well as in chloroplasts. YER050C from Saccharomyces
cerevisiae and a related protein from Caenorhabditis
elegans appear to be homologous and may represent
mitochondrial forms. The trusted cutoff is set high
enough that these two candidate S18 proteins are not
categorized automatically [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 70
Score = 76.3 bits (188), Expect = 6e-17
Identities = 29/52 (55%), Positives = 39/52 (75%)
Query: 117 FKRKKFCRFTVMNIKQIDYKDIETLKDFIQENGKIMAARLTGTCSHYQRQIT 168
F+RKK+CRFT I+ IDYKD++ LK FI E GKI+ R+TGT + YQR++
Sbjct: 2 FRRKKYCRFTAEGIQFIDYKDLDLLKKFISERGKILPRRITGTSAKYQRRLA 53
>gnl|CDD|189019 cd00008, PIN_53EXO-like, PIN domains of the 5'-3' exonucleases of
DNA polymerase I, bacteriophage T4 RNase H and T5-5'
nucleases, and homologs. PIN (PilT N terminus) domains
of the 5'-3' exonucleases (53EXO) of mutli-domain DNA
polymerase I and single domain protein homologs, as well
as, the PIN domains of bacteriophage T5-5'nuclease
(T5FEN or 5'-3'exonuclease), bacteriophage T4 RNase H
(T4FEN), bacteriophage T3 (T3 phage
exodeoxyribonuclease) and other similar nucleases are
included in this family. The 53EXO of DNA polymerase I
recognizes and endonucleolytically cleaves a
structure-specific DNA substrate that has a bifurcated
downstream duplex and an upstream template-primer duplex
that overlaps the downstream duplex by 1 bp. The
T5-5'nuclease is a 5'-3'exodeoxyribonuclease that also
exhibits endonucleolytic activity on flap structures
(branched duplex DNA containing a free single-stranded
5'end). T4 RNase H, which removes the RNA primers that
initiate lagging strand fragments, has 5'- 3'exonuclease
activity on DNA/DNA and RNA/DNA duplexes and has
endonuclease activity on flap or forked DNA structures.
These nucleases are members of the structure-specific,
5' nuclease family that catalyzes hydrolysis of DNA
duplex-containing nucleic acid structures during DNA
replication, repair, and recombination. They contain a
PIN domain with a helical arch/clamp region (I domain)
of variable length (approximately 16 to 30 residues in
53EXO-like PIN domains) and a H3TH (helix-3-turn-helix)
domain, an atypical helix-hairpin-helix-2-like region.
Both the H3TH domain (not included here) and the helical
arch/clamp region are involved in DNA binding. The
active site of the 53EXO of Taq DNA polymerase I
includes a set of conserved acidic residues that are
essential for binding three divalent metal ions (two
Mn2+ ions and one Zn2+ ion) required for nuclease
activity. T5-5'nuclease requires at least two bound
divalent metal ions for nuclease activity and is
reported to be able to use Mg2+, Mn2+ or Co2+ as
co-factors.
Length = 160
Score = 76.9 bits (189), Expect = 4e-16
Identities = 34/147 (23%), Positives = 58/147 (39%), Gaps = 11/147 (7%)
Query: 779 IDGSSCIYRAFYAL-PDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFR 837
+DG++ +R + I+ + ++ L K+Y A + D FR
Sbjct: 4 VDGTNLAFRTKHNNSKKKEKIN--LSPFASSYVSSIQSLAKSYSARTTIVLGDKGKSVFR 61
Query: 838 NILYPSYKATR-------KKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAK 890
P YK R K + + ++ KA +P I+G EADD+ L K
Sbjct: 62 LEHLPEYKGNRDEKYAEEKALDEQFFEYLKDAFELCKATTFPTFTIRGYEADDMAAYLVK 121
Query: 891 QAVTKHNLKVIISTNDKDMAQLVSNKI 917
+ V I + D D QL+++K+
Sbjct: 122 KI-GHEGDHVWIISTDGDWDQLLTDKV 147
>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 = 68.9 bits (169), Expect = 2e-13
Identities = 45/183 (24%), Positives = 61/183 (33%), Gaps = 24/183 (13%)
Query: 314 LWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITP 373
+ D ET GL+ +D + AA+ N I Y K P+ L A ITP
Sbjct: 1 VVIDCETTGLDPEKDEIIEIAAVSIVGGEN-IGPVFDTYVK--PERLITDEATEFHGITP 57
Query: 374 QFCLNNGIPEYKFASIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNN 433
+ P ++ FLK I VG+N FD + R L P
Sbjct: 58 EML--RNAPSFEEVLEAFLEFLKKLKILVGHNAS-FDVGFLLYDDLRFLKLPM------- 107
Query: 434 CSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNLSH-KKAHDALSDVRAT 492
+ I G L+ L+ L ++AH AL D RAT
Sbjct: 108 ----------PKLNDVIDTLILDKATYKGFKRRSLDALAEKLGLEKIQRAHRALDDARAT 157
Query: 493 LGL 495
L
Sbjct: 158 AEL 160
>gnl|CDD|201589 pfam01084, Ribosomal_S18, Ribosomal protein S18.
Length = 54
Score = 62.5 bits (153), Expect = 2e-12
Identities = 20/42 (47%), Positives = 28/42 (66%)
Query: 127 VMNIKQIDYKDIETLKDFIQENGKIMAARLTGTCSHYQRQIT 168
I+ IDYKD+E L+ FI E GKI+ R+TG C+ QR++
Sbjct: 1 ADKIEYIDYKDVELLRRFISERGKILPRRITGLCAKQQRKLA 42
>gnl|CDD|188616 cd00080, H3TH_StructSpec-5'-nucleases, H3TH domains of
structure-specific 5' nucleases (or flap
endonuclease-1-like) involved in DNA replication, repair,
and recombination. The 5' nucleases of this superfamily
are capable of both 5'-3' exonucleolytic activity and
cleaving bifurcated or branched DNA, in an
endonucleolytic, structure-specific manner, and are
involved in DNA replication, repair, and recombination.
The superfamily includes the H3TH (helix-3-turn-helix)
domains of Flap Endonuclease-1 (FEN1), Exonuclease-1
(EXO1), Mkt1, Gap Endonuclease 1 (GEN1) and Xeroderma
pigmentosum complementation group G (XPG) nuclease. Also
included are the H3TH domains of the 5'-3' exonucleases
of DNA polymerase I and single domain protein homologs,
as well as, the bacteriophage T4 RNase H, T5-5'nuclease,
and other homologs. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region/I
domain (not included here) and inserted within the
C-terminal region of the PIN domain is an atypical
helix-hairpin-helix-2 (HhH2)-like region. This atypical
HhH2 region, the H3TH domain, has an extended loop with
at least three turns between the first two helices, and
only three of the four helices appear to be conserved.
Both the H3TH domain and the helical arch/clamp region
are involved in DNA binding. Studies suggest that a
glycine-rich loop in the H3TH domain contacts the
phosphate backbone of the template strand in the
downstream DNA duplex. Typically, the nucleases within
this superfamily have a carboxylate rich active site that
is involved in binding essential divalent metal ion
cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for
nuclease activity. The first metal binding site is
composed entirely of Asp/Glu residues from the PIN
domain, whereas, the second metal binding site is
composed generally of two Asp residues from the PIN
domain and one or two Asp residues from the H3TH domain.
Together with the helical arch and network of amino acids
interacting with metal binding ions, the H3TH region
defines a positively charged active-site DNA-binding
groove in structure-specific 5' nucleases.
Length = 71
Score = 58.9 bits (143), Expect = 7e-11
Identities = 30/72 (41%), Positives = 42/72 (58%), Gaps = 2/72 (2%)
Query: 940 EKIVDYFSLIG-DMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFA 998
E+ +D +L+G D SDN PGV IGPKTA KL +Y SLE I+ N + +KG + L
Sbjct: 1 EQFIDLCALVGCDYSDN-PGVPGIGPKTAAKLALKYGSLEGILENLDELKGKKREKLEEP 59
Query: 999 LNWLPKLKKILT 1010
+ +K+ T
Sbjct: 60 KEYAFLSRKLAT 71
>gnl|CDD|189030 cd09860, PIN_T4-like, PIN domain of bacteriophage T3, T4 RNase H,
T5-5'nuclease, and homologs. PIN (PilT N terminus)
domain of bacteriophage T5-5'nuclease (5'-3' exonuclease
or T5FEN), bacteriophage T4 RNase H (T4FEN),
bacteriophage T3 (T3 phage exodeoxyribonuclease) and
other similar 5' nucleases are included in this family.
T5-5'nuclease is a 5'-3'exodeoxyribonuclease that also
exhibits endonucleolytic activity on flap structures
(branched duplex DNA containing a free single-stranded
5'end). T4 RNase H, which removes the RNA primers that
initiate lagging strand fragments, has 5'- 3'exonuclease
activity on DNA/DNA and RNA/DNA duplexes and has
endonuclease activity on flap or forked DNA structures.
Bacteriophage T3 is believed to function in the removal
of DNA-linked RNA primers and is essential for phage DNA
replication and also necessary for host DNA degradation
and phage genetic recombination. These nucleases are
members of the structure-specific, 5' nuclease family
that catalyzes hydrolysis of DNA duplex-containing
nucleic acid structures during DNA replication, repair,
and recombination. They have a PIN domain with a helical
arch/clamp region (I domain) of variable length
(approximately 20 to 30 residues in PIN T5-like domains)
and a H3TH (helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA/RNA binding. The active site
includes a set of conserved acidic residues that are
essential for binding divalent metal ions required for
nuclease activity. In the T5-5'nuclease,
structure-specific endonuclease activity requires
binding of a single metal ion in the high-affinity,
metal binding site 1, whereas exonuclease activity
requires both, the high-affinity, metal binding site 1
and the low-affinity, metal binding site 2 to be
occupied by a divalent cofactor. The T5-5'nuclease is
reported to be able to bind several metal ions
including, Mg2+, Mn2+, Zn2+ and Co2+, as co-factors.
Length = 170
Score = 61.6 bits (150), Expect = 9e-11
Identities = 40/147 (27%), Positives = 64/147 (43%), Gaps = 13/147 (8%)
Query: 779 IDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRN 838
IDG+ + A Y+ V A +G + +++ K Y+ ++D K +R
Sbjct: 5 IDGNQLGFAAMYS-NFKDESGIMEVMARHGLLDSIKRNAKRYKYAIPIVLWD-GRKYWRR 62
Query: 839 ILYPSYKATRKKMP-------YNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQ 891
L P YKA R K P Y + I +M + + + I G EADDV L K+
Sbjct: 63 DLLPYYKANRDKTPDKRAWEGYFEAQKP-YIEEMKENMPVIQIRIPGAEADDVAAVLVKK 121
Query: 892 -AVTKHNLKVIISTNDKDMAQLVSNKI 917
+ H KV++ ++D D QL +
Sbjct: 122 LSAFGH--KVLLISSDGDWTQLHKPNV 146
>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 = 60.0 bits (146), Expect = 2e-10
Identities = 38/183 (20%), Positives = 62/183 (33%), Gaps = 29/183 (15%)
Query: 317 DYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQFC 376
D ET GL+ ++DR + A++ D + ++ P P A I IT +
Sbjct: 4 DTETTGLDPKKDRIIEIGAVKVDGGIEIVE-RFETLVNP--GRPIPPEATAIHGITDE-M 59
Query: 377 LNNGIPEYKFASIIEKI--FLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNC 434
L + P F ++ + FL + V +N FD R P W
Sbjct: 60 LADAPP---FEEVLPEFLEFLGGRVL-VAHN-ASFDLRFLNRELRRLGGPPLPNPW---- 110
Query: 435 SRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNLSHKKAHDALSDVRATLG 494
D + + + P + + L + + AH AL+D AT
Sbjct: 111 --IDTLRLARRLL---------PGLRSHRLGLLLAER---YGIPLEGAHRALADALATAE 156
Query: 495 LAR 497
L
Sbjct: 157 LLL 159
>gnl|CDD|197623 smart00279, HhH2, Helix-hairpin-helix class 2 (Pol1 family) motifs.
Length = 36
Score = 56.3 bits (137), Expect = 3e-10
Identities = 23/36 (63%), Positives = 30/36 (83%)
Query: 939 PEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQY 974
PE+ +DY L+GD SDN+PGVK IGPKTA+KLL ++
Sbjct: 1 PEQFIDYAILVGDYSDNIPGVKGIGPKTALKLLREF 36
>gnl|CDD|184031 PRK13401, PRK13401, 30S ribosomal protein S18; Provisional.
Length = 82
Score = 56.3 bits (136), Expect = 8e-10
Identities = 20/55 (36%), Positives = 29/55 (52%)
Query: 119 RKKFCRFTVMNIKQIDYKDIETLKDFIQENGKIMAARLTGTCSHYQRQITFIRKN 173
+ K + I+ +DYKD L+ FI + GKI + R+TG QRQ+ KN
Sbjct: 12 KAKKNLLDSLGIESVDYKDTALLRTFISDRGKIRSRRVTGLTVQQQRQVATAIKN 66
>gnl|CDD|222794 PHA00439, PHA00439, exonuclease.
Length = 286
Score = 56.7 bits (137), Expect = 2e-08
Identities = 44/175 (25%), Positives = 68/175 (38%), Gaps = 25/175 (14%)
Query: 806 LYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRK--KMP--YNLILQINL 861
L +IK + K ++ I F N+R + P+YKA RK + P Y L+ +
Sbjct: 48 LEDSIKSYKTRKKAWKDAPIVLAFTDS-VNWRKEVVPTYKANRKAKRKPVGYRKFLEELM 106
Query: 862 IHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALIN 921
+ K+I P G+E DDV+G + K ++ + DKD + +
Sbjct: 107 AREEWKSILEP-----GLEGDDVMGIIGTNPSLFGFKKAVLVSCDKDFKTIPNCDFLWCT 161
Query: 922 NNKIHDRTTIISRFGVSPEKIVDYFSLI----GDMSDNLPGVKKIGPKTAVKLLN 972
I +T PE D + L GD +D G+ G TA L
Sbjct: 162 TGNILTQT---------PET-ADRWHLFQTIKGDSTDGYSGIPGWG-DTAEAFLE 205
>gnl|CDD|184030 PRK13400, PRK13400, 30S ribosomal protein S18; Provisional.
Length = 147
Score = 53.1 bits (127), Expect = 6e-08
Identities = 26/79 (32%), Positives = 37/79 (46%), Gaps = 5/79 (6%)
Query: 101 NNKNRFKQKRQQQNPLFKRKKFCRFTVMNIKQIDYKDIETLKDFIQENGKIMAARLTGTC 160
N R + R ++K C F + +IDYKD L +I + GKI R TGTC
Sbjct: 8 NRPARGGRGRYT-----PKRKICSFCAEKVSRIDYKDSAKLARYISDRGKIEPRRRTGTC 62
Query: 161 SHYQRQITFIRKNMQVILL 179
+ +QR + K + I L
Sbjct: 63 ARHQRALANAIKRARFIAL 81
>gnl|CDD|177046 CHL00123, rps6, ribosomal protein S6; Validated.
Length = 97
Score = 50.8 bits (122), Expect = 1e-07
Identities = 24/71 (33%), Positives = 39/71 (54%)
Query: 2 IERYKKIIISGKGKIHRLEDWGRRSLAYQIKKVIKAHYICFNIEINKKTLLEIETSFRFN 61
IE YKK++ K +++ G+R L+Y+I K YI N N K + +E + + +
Sbjct: 27 IENYKKLLRKRGAKNISVQNRGKRKLSYKINKYEDGIYIQMNYSGNGKLVNSLEKALKLD 86
Query: 62 DAILRYLTIKT 72
+ +LRYLT K
Sbjct: 87 ENVLRYLTFKK 97
>gnl|CDD|234639 PRK00109, PRK00109, Holliday junction resolvase-like protein;
Reviewed.
Length = 138
Score = 47.8 bits (115), Expect = 3e-06
Identities = 12/43 (27%), Positives = 25/43 (58%)
Query: 1260 IGIAFGNTLIKHAKPLKIIHSITNKAKFNEISKLVEKWKPNTV 1302
IG+A + L A+PL+ I ++ + KL+++W+P+ +
Sbjct: 16 IGVAVSDPLGGTAQPLETIKRNNGTPDWDRLEKLIKEWQPDGL 58
>gnl|CDD|222882 PHA02567, rnh, RnaseH; Provisional.
Length = 304
Score = 50.4 bits (121), Expect = 3e-06
Identities = 28/111 (25%), Positives = 50/111 (45%), Gaps = 12/111 (10%)
Query: 813 LRKLYKNYRATY---IACIFDAKGKNFRNILYPSYKATRKK----MPYNLILQINLIHQM 865
+R K ++ Y + ++K +R + YK RKK P++ I+++
Sbjct: 52 IRYNVKKFKEEYPEIVLAFDNSKSGYWRRDIAWYYKKNRKKDREESPWDWEGLFEAINKI 111
Query: 866 VKAI----GWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQL 912
V I + ++ I EADD+I L K+ + V+I ++D D QL
Sbjct: 112 VDEIKENMPYKVMKIDKAEADDIIAVLTKKFSAE-GRPVLIVSSDGDFTQL 161
>gnl|CDD|217659 pfam03652, UPF0081, Uncharacterized protein family (UPF0081).
Length = 134
Score = 46.3 bits (111), Expect = 1e-05
Identities = 12/43 (27%), Positives = 24/43 (55%)
Query: 1260 IGIAFGNTLIKHAKPLKIIHSITNKAKFNEISKLVEKWKPNTV 1302
IG+A + L A PL+ I E+++L+++W+P+ +
Sbjct: 13 IGVAISDPLGILASPLETIRRKNGNPDLEELAELIKEWQPDGI 55
>gnl|CDD|240161 cd05125, Mth938_2P1-like, Mth938_2P1-like domain. This model contains
sequences that are similar to 2P1, a partially
characterized nuclear protein, which is homologous to
E3-3 from rat and known to be alternatively spliced. Its
function is unknown. This family is part of the Mth938
family, for which structures, but no functional data are
available.
Length = 114
Score = 44.9 bits (107), Expect = 2e-05
Identities = 16/57 (28%), Positives = 30/57 (52%)
Query: 1370 PSVVILGTGNIQHFIHPKLTYILTQKNIGIECMNNQAACRTYNILVSDDIKAMLALI 1426
P ++++GTG + P+L + I +E ++ + AC T+N L + + ALI
Sbjct: 55 PEILVIGTGRKSRPLSPELRKYFKKLGIAVEVVDTRNACATFNFLAEEGRRVAAALI 111
>gnl|CDD|177016 CHL00077, rps18, ribosomal protein S18.
Length = 86
Score = 43.4 bits (103), Expect = 4e-05
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 2/61 (3%)
Query: 108 QKRQQQNPLFKRKKFCRFTVMNIKQIDYKDIETLKDFIQENGKIMAARLTGTCSHYQRQI 167
++ +++ R++ + IDYK++ L FI E GKI++ R+T QR I
Sbjct: 5 KRPFRKSKRSFRRRLPPIQSGDR--IDYKNMSLLSRFISEQGKILSRRVTRLTLKQQRLI 62
Query: 168 T 168
T
Sbjct: 63 T 63
>gnl|CDD|214685 smart00479, EXOIII, exonuclease domain in DNA-polymerase alpha and
epsilon chain, ribonuclease T and other exonucleases.
Length = 169
Score = 45.4 bits (108), Expect = 4e-05
Identities = 47/195 (24%), Positives = 73/195 (37%), Gaps = 28/195 (14%)
Query: 312 TFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKI 371
T + D ET GL+ +D + AA+ D I Y KP I I
Sbjct: 1 TLVVIDCETTGLDPGKDEIIEIAAVDVD--GGEIIEVFDTYVKPDRPITDYATE--IHGI 56
Query: 372 TPQFCLNNGIPEYKFASIIEKIF-LKPGTISVGYNTILFDDEITRFMFWRNLINPYEREW 430
TP+ L++ F ++E++ G I V N+ FD F L + R
Sbjct: 57 TPEM-LDDAPT---FEEVLEELLEFLRGRILVAGNSAHFD-----LRF---LKLEHPRLG 104
Query: 431 KNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNLSH-KKAHDALSDV 489
+ +I+ +K +P G P + L+ L+ L ++AH AL D
Sbjct: 105 IKQPPKLPVIDTLKLARATNP----------GLPKYSLKKLAKRLLLEVIQRAHRALDDA 154
Query: 490 RATLGLARLIRNNNP 504
RAT L + +
Sbjct: 155 RATAKLFKKLLERLE 169
>gnl|CDD|188621 cd09901, H3TH_FEN1-like, H3TH domains of Flap endonuclease-1
(FEN1)-like structure specific 5' nucleases: FEN1
(eukaryotic) and EXO1. The 5' nucleases within this
family are capable of both 5'-3' exonucleolytic activity
and cleaving bifurcated or branched DNA, in an
endonucleolytic, structure-specific manner, and are
involved in DNA replication, repair, and recombination.
This family includes the H3TH (helix-3-turn-helix)
domains of eukaryotic Flap Endonuclease-1 (FEN1),
Exonuclease-1 (EXO1), and other eukaryotic homologs.
These nucleases contain a PIN (PilT N terminus) domain
with a helical arch/clamp region/I domain (not included
here) and inserted within the PIN domain is an atypical
helix-hairpin-helix-2 (HhH2)-like region. This atypical
HhH2 region, the H3TH domain, has an extended loop with
at least three turns between the first two helices, and
only three of the four helices appear to be conserved.
Both the H3TH domain and the helical arch/clamp region
are involved in DNA binding. Studies suggest that a
glycine-rich loop in the H3TH domain contacts the
phosphate backbone of the template strand in the
downstream DNA duplex. The nucleases within this family
have a carboxylate rich active site that is involved in
binding essential divalent metal ion cofactors (i. e.,
Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease
activity. The first metal binding site is composed
entirely of Asp/Glu residues from the PIN domain,
whereas, the second metal binding site is composed
generally of two Asp residues from the PIN domain and
one Asp residue from the H3TH domain. Together with the
helical arch and network of amino acids interacting with
metal binding ions, the H3TH region defines a positively
charged active-site DNA-binding groove in
structure-specific 5' nucleases.
Length = 73
Score = 42.1 bits (100), Expect = 7e-05
Identities = 13/30 (43%), Positives = 20/30 (66%)
Query: 954 DNLPGVKKIGPKTAVKLLNQYNSLENIINN 983
D LP + IGPKTA KL+ ++ S+E ++
Sbjct: 13 DYLPSIPGIGPKTAYKLIKKHKSIEKVLKA 42
>gnl|CDD|188627 cd09907, H3TH_FEN1-Euk, H3TH domain of Flap Endonuclease-1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease: Eukaryotic homologs. Members of this subgroup
include the H3TH (helix-3-turn-helix) domains of
eukaryotic Flap endonuclease-1 (FEN1), 5' nucleases.
FEN1 is involved in multiple DNA metabolic pathways,
including DNA replication processes (5' flap DNA
endonuclease activity and double stranded DNA
5'-exonuclease activity) and DNA repair processes
(long-patch base excision repair) in eukaryotes and
archaea. Interaction between FEN1 and PCNA
(Proliferating cell nuclear antigen) is an essential
prerequisite to FEN1's DNA replication functionality and
stimulates FEN1 nuclease activity by 10-50 fold. These
nucleases contain a PIN (PilT N terminus) domain with a
helical arch/clamp region/I domain (not included here)
and inserted within the PIN domain is an atypical
helix-hairpin-helix-2 (HhH2)-like region. This atypical
HhH2 region, the H3TH domain, has an extended loop with
at least three turns between the first two helices, and
only three of the four helices appear to be conserved.
Both the H3TH domain and the helical arch/clamp region
are involved in DNA binding. Studies suggest that a
glycine-rich loop in the H3TH domain contacts the
phosphate backbone of the template strand in the
downstream DNA duplex. The nucleases within this
subfamily have a carboxylate rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+ or Mn2+) required for nuclease activity.
The first metal binding site is composed entirely of
Asp/Glu residues from the PIN domain, whereas, the
second metal binding site is composed generally of two
Asp residues from the PIN domain and one Asp residue
from the H3TH domain. Together with the helical arch and
network of amino acids interacting with metal binding
ions, the H3TH region defines a positively charged
active-site DNA-binding groove in structure-specific 5'
nucleases. Also, FEN1 has a C-terminal extension
containing residues forming the consensus PIP-box -
Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1 to PCNA.
Length = 70
Score = 41.4 bits (98), Expect = 1e-04
Identities = 19/58 (32%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 940 EKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRF 997
E+ +D L+G D +K IGPKTA+KL+ ++ S+E I+ N + K + ++ +
Sbjct: 1 EQFIDLCILLG--CDYCESIKGIGPKTALKLIKKHKSIEKILENIDKSKYPVPEDWPY 56
>gnl|CDD|188617 cd09897, H3TH_FEN1-XPG-like, H3TH domains of Flap endonuclease-1
(FEN1)-like structure specific 5' nucleases. The 5'
nucleases within this family are capable of both 5'-3'
exonucleolytic activity and cleaving bifurcated or
branched DNA, in an endonucleolytic, structure-specific
manner, and are involved in DNA replication, repair, and
recombination. This family includes the H3TH
(helix-3-turn-helix) domains of Flap Endonuclease-1
(FEN1), Exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1
(GEN1), Xeroderma pigmentosum complementation group G
(XPG) nuclease, and other eukaryotic and archaeal
homologs. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region/I
domain (not included here) and inserted within the PIN
domain is an atypical helix-hairpin-helix-2 (HhH2)-like
region. This atypical HhH2 region, the H3TH domain, has
an extended loop with at least three turns between the
first two helices, and only three of the four helices
appear to be conserved. Both the H3TH domain and the
helical arch/clamp region are involved in DNA binding.
Studies suggest that a glycine-rich loop in the H3TH
domain contacts the phosphate backbone of the template
strand in the downstream DNA duplex. With the except of
the Mkt1-like proteins, the nucleases within this family
have a carboxylate rich active site that is involved in
binding essential divalent metal ion cofactors (i. e.,
Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease
activity. The first metal binding site is composed
entirely of Asp/Glu residues from the PIN domain,
whereas, the second metal binding site is composed
generally of two Asp residues from the PIN domain and
one Asp residue from the H3TH domain. Together with the
helical arch and network of amino acids interacting with
metal binding ions, the H3TH region defines a positively
charged active-site DNA-binding groove in
structure-specific 5' nucleases.
Length = 68
Score = 41.4 bits (98), Expect = 1e-04
Identities = 21/49 (42%), Positives = 30/49 (61%), Gaps = 2/49 (4%)
Query: 940 EKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIK 988
E+ +D L G D LPG+ IGPKTA+KL+ +Y SLE ++ + K
Sbjct: 1 EQFIDLCILSG--CDYLPGLPGIGPKTALKLIKEYGSLEKVLKALRDDK 47
>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional.
Length = 292
Score = 44.8 bits (107), Expect = 2e-04
Identities = 19/46 (41%), Positives = 33/46 (71%), Gaps = 2/46 (4%)
Query: 936 GVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENII 981
G++ E+++D L+G +D PG+K IGPKTA+KL+ ++ LE ++
Sbjct: 173 GITREQLIDIAILVG--TDYNPGIKGIGPKTALKLIKKHGDLEKVL 216
>gnl|CDD|234306 TIGR03674, fen_arch, flap structure-specific endonuclease.
Endonuclease that cleaves the 5'-overhanging flap
structure that is generated by displacement synthesis
when DNA polymerase encounters the 5'-end of a
downstream Okazaki fragment. Has 5'-endo-/exonuclease
and 5'-pseudo-Y-endonuclease activities. Cleaves the
junction between single and double-stranded regions of
flap DNA.
Length = 338
Score = 43.8 bits (104), Expect = 4e-04
Identities = 20/49 (40%), Positives = 33/49 (67%), Gaps = 2/49 (4%)
Query: 933 SRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENII 981
S G++ E+++D L+G +D GVK IGPKTA+KL+ ++ LE ++
Sbjct: 217 SELGITREQLIDIAILVG--TDYNEGVKGIGPKTALKLIKEHGDLEKVL 263
>gnl|CDD|223916 COG0847, DnaQ, DNA polymerase III, epsilon subunit and related
3'-5' exonucleases [DNA replication, recombination, and
repair].
Length = 243
Score = 42.9 bits (101), Expect = 5e-04
Identities = 33/182 (18%), Positives = 55/182 (30%), Gaps = 27/182 (14%)
Query: 316 YDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKITPQF 375
D ET GLN ++DR + A+ T ++ P+ P I IT +
Sbjct: 18 IDLETTGLNPKKDRIIEIGAV-TLEDGRIVERSFHTLVN--PERPIPPEIFKIHGITDEM 74
Query: 376 CLNNGIPEYKFASIIEKIFLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREWKNNCS 435
+ ++ F+ + V +N FD R R I
Sbjct: 75 LADAPKFAEVLPEFLD--FIGGLRLLVAHN-AAFDVGFLRVESERLGIEIPGDPVL---- 127
Query: 436 RWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNL--SHKKAHDALSDVRATL 493
D + + + + G L+ L+ + + H AL D A
Sbjct: 128 --DTLALARRHFP-------------GFDRSSLDALAERLGIDRNPFHPHRALFDALALA 172
Query: 494 GL 495
L
Sbjct: 173 EL 174
>gnl|CDD|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional.
Length = 393
Score = 42.7 bits (101), Expect = 0.001
Identities = 22/68 (32%), Positives = 38/68 (55%), Gaps = 2/68 (2%)
Query: 930 TIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKG 989
T++ G+S ++ +D L G D +K IGPKTA KL+ +Y S+E I+ + + K
Sbjct: 213 TVLEELGLSMDQFIDLCILCG--CDYCDTIKGIGPKTAYKLIKKYKSIEEILEHLDKTKY 270
Query: 990 VIGKNLRF 997
+ +N +
Sbjct: 271 PVPENFDY 278
>gnl|CDD|189023 cd09853, PIN_StructSpec-5'-nucleases, PIN domains of
structure-specific 5' nucleases (or flap
endonuclease-1-like) involved in DNA replication,
repair, and recombination. Structure-specific 5'
nucleases are capable of both 5'-3' exonucleolytic
activity and cleaving bifurcated or branched DNA, in an
endonucleolytic, structure-specific manner. The family
includes the PIN (PilT N terminus) domains of Flap
Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap
Endonuclease 1 (GEN1), and Xeroderma pigmentosum
complementation group G (XPG) nuclease. Also included
are the PIN domains of the 5'-3' exonucleases of DNA
polymerase I and single domain protein homologs, as well
as, the bacteriophage T4- and T5-5' nucleases, and other
homologs. These nucleases contain a PIN domain with a
helical arch/clamp region (I domain) of variable length
(approximately 16 to 800 residues) and a H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA binding. With the exception of Mkt1,
the nucleases within this family have a carboxylate rich
active site that is involved in binding essential
divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or
Co2+).
Length = 163
Score = 39.9 bits (93), Expect = 0.003
Identities = 35/158 (22%), Positives = 60/158 (37%), Gaps = 19/158 (12%)
Query: 779 IDGSSCIYRAFYAL---PDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKN 835
IDGS+ Y+ + + + +F G Y I + KNY A +FD
Sbjct: 4 IDGSNLGYQFLHNNRKDKEKGELTSFASGYFYTIISLA----KNYSAITPIVVFDGGKPV 59
Query: 836 FRNILYPSYKATR-----------KKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDV 884
R P YK R K++ + +++K +G P I+ EA+D+
Sbjct: 60 LRLEHLPEYKENRDEAEAEATEEEKRLDEQTFEYLKDCKELLKLMGIPYFDIRPSEAEDM 119
Query: 885 IGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINN 922
L K V + + D D L ++K++ +
Sbjct: 120 AAYLVK-KGGHLYDVVALISTDGDWLTLGTDKVSRFSF 156
>gnl|CDD|188623 cd09903, H3TH_FEN1-Arc, H3TH domain of Flap Endonuclease-1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease: Archaeal homologs. Members of this subgroup
include the H3TH (helix-3-turn-helix) domains of
archaeal Flap endonuclease-1 (FEN1), 5' nucleases. FEN1
is involved in multiple DNA metabolic pathways,
including DNA replication processes (5' flap DNA
endonuclease activity and double stranded DNA
5'-exonuclease activity) and DNA repair processes
(long-patch base excision repair) in eukaryotes and
archaea. Interaction between FEN1 and PCNA
(Proliferating cell nuclear antigen) is an essential
prerequisite to FEN1's DNA replication functionality and
stimulates FEN1 nuclease activity by 10-50 fold. These
nucleases contain a PIN (PilT N terminus) domain with a
helical arch/clamp region/I domain (not included here)
and inserted within the PIN domain is an atypical
helix-hairpin-helix-2 (HhH2)-like region. This atypical
HhH2 region, the H3TH domain, has an extended loop with
at least three turns between the first two helices, and
only three of the four helices appear to be conserved.
Both the H3TH domain and the helical arch/clamp region
are involved in DNA binding. Studies suggest that a
glycine-rich loop in the H3TH domain contacts the
phosphate backbone of the template strand in the
downstream DNA duplex. The nucleases within this
subfamily have a carboxylate rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+ or Mn2+) required for nuclease activity.
The first metal binding site is composed entirely of
Asp/Glu residues from the PIN domain, whereas, the
second metal binding site is composed generally of two
Asp residues from the PIN domain and one Asp residue
from the H3TH domain. Together with the helical arch and
network of amino acids interacting with metal binding
ions, the H3TH region defines a positively charged
active-site DNA-binding groove in structure-specific 5'
nucleases. Also, FEN1 has a C-terminal extension
containing residues forming the consensus PIP-box -
Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1 to PCNA.
Length = 65
Score = 36.0 bits (84), Expect = 0.007
Identities = 20/43 (46%), Positives = 30/43 (69%), Gaps = 3/43 (6%)
Query: 940 EKIVDYFSLIGDMSD-NLPGVKKIGPKTAVKLLNQYNSLENII 981
E+++D L+G +D N GVK IGPKTA+KL+ +Y LE ++
Sbjct: 1 EQLIDIAILVG--TDYNPGGVKGIGPKTALKLVKEYGDLEKVL 41
>gnl|CDD|188620 cd09900, H3TH_XPG-like, H3TH domains of Flap endonuclease-1
(FEN1)-like structure specific 5' nucleases: FEN1
(archaeal), GEN1, YEN1, and XPG. The 5' nucleases
within this family are capable of both 5'-3'
exonucleolytic activity and cleaving bifurcated or
branched DNA, in an endonucleolytic, structure-specific
manner, and are involved in DNA replication, repair, and
recombination. This family includes the H3TH
(helix-3-turn-helix) domains of archaeal Flap
Endonuclease-1 (FEN1), Gap Endonuclease 1 (GEN1), Yeast
Endonuclease 1 (YEN1), Xeroderma pigmentosum
complementation group G (XPG) nuclease, and other
eukaryotic and archaeal homologs. These nucleases
contain a PIN (PilT N terminus) domain with a helical
arch/clamp region/I domain (not included here) and
inserted within the PIN domain is an atypical
helix-hairpin-helix-2 (HhH2)-like region. This atypical
HhH2 region, the H3TH domain, has an extended loop with
at least three turns between the first two helices, and
only three of the four helices appear to be conserved.
Both the H3TH domain and the helical arch/clamp region
are involved in DNA binding. Studies suggest that a
glycine-rich loop in the H3TH domain contacts the
phosphate backbone of the template strand in the
downstream DNA duplex. With the except of the Mkt1-like
proteins, the nucleases within this family have a
carboxylate rich active site that is involved in binding
essential divalent metal ion cofactors (i. e., Mg2+,
Mn2+, Zn2+, or Co2+) required for nuclease activity. The
first metal binding site is composed entirely of Asp/Glu
residues from the PIN domain, whereas, the second metal
binding site is composed generally of two Asp residues
from the PIN domain and one Asp residue from the H3TH
domain. Together with the helical arch and network of
amino acids interacting with metal binding ions, the
H3TH region defines a positively charged active-site
DNA-binding groove in structure-specific 5' nucleases.
Length = 52
Score = 35.5 bits (83), Expect = 0.008
Identities = 17/45 (37%), Positives = 28/45 (62%), Gaps = 3/45 (6%)
Query: 940 EKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNS-LENIINN 983
E+++ L+G +D PGV IGPKTA++LL ++ LE + +
Sbjct: 1 EQLILLALLLG--TDYNPGVPGIGPKTALELLKEFGEDLEKFLES 43
>gnl|CDD|188619 cd09899, H3TH_T4-like, H3TH domain of bacteriophage T3, T4 RNase H,
T5-5' nucleases, and homologs. H3TH
(helix-3-turn-helix) domains of bacteriophage
T5-5'nuclease (5'-3' exonuclease or T5FEN),
bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3
phage exodeoxyribonuclease) and other similar 5'
nucleases are included in this family. The T5-5'nuclease
is a 5'-3' exodeoxyribonuclease that also exhibits
endonucleolytic activity on flap structures (branched
duplex DNA containing a free single-stranded 5'end). T4
RNase H, which removes the RNA primers that initiate
lagging strand fragments, has 5'- 3' exonuclease
activity on DNA/DNA and RNA/DNA duplexes and has
endonuclease activity on flap or forked DNA structures.
Bacteriophage T3 is believed to function in the removal
of DNA-linked RNA primers and is essential for phage DNA
replication and also necessary for host DNA degradation
and phage genetic recombination. These nucleases are
members of the structure-specific, 5' nuclease family
that catalyzes hydrolysis of DNA duplex-containing
nucleic acid structures during DNA replication, repair,
and recombination. They contain a PIN (PilT N terminus)
domain with a helical arch/clamp region/I domain (not
included here) and inserted within the PIN domain is an
atypical helix-hairpin-helix-2 (HhH2)-like region. This
atypical HhH2 region, the H3TH domain, has an extended
loop with at least three turns between the first two
helices, and only three of the four helices appear to be
conserved. Both the H3TH domain and the helical
arch/clamp region are involved in DNA binding. Studies
suggest that a glycine-rich loop in the H3TH domain
contacts the phosphate backbone of the template strand
in the downstream DNA duplex. The nucleases within this
family have a carboxylate rich active site that is
involved in binding essential divalent metal ion
cofactors required for nuclease activity. The first
metal binding site (MBS-1) is composed entirely of
Asp/Glu residues from the PIN domain, whereas, the
second metal binding site (MBS-2) is composed generally
of two Asp residues from the PIN domain and two Asp
residues from the H3TH domain. In the T5-5'nuclease,
structure-specific endonuclease activity requires
binding of a single metal ion in the high-affinity,
MBS-1, whereas exonuclease activity requires both, the
high-affinity, MBS-1 and the low-affinity, MBS-2 to be
occupied by a divalent cofactor. The T5-5'nuclease is
reported to be able to bind several metal ions
including, Mg2+, Mn2+, Zn2+ and Co2+, as co-factors.
Together with the helical arch and network of amino
acids interacting with metal binding ions, the H3TH
region defines a positively charged active-site
DNA-binding groove in structure-specific 5' nucleases.
Length = 74
Score = 35.5 bits (82), Expect = 0.015
Identities = 15/38 (39%), Positives = 20/38 (52%)
Query: 948 LIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNAN 985
L GD DN+ GV IG A KLL + + +II+
Sbjct: 11 LAGDTKDNIAGVPGIGTGRATKLLEEIGDVADIIDALL 48
>gnl|CDD|223886 COG0816, COG0816, Predicted endonuclease involved in recombination
(possible Holliday junction resolvase in Mycoplasmas and
B. subtilis) [DNA replication, recombination, and
repair].
Length = 141
Score = 36.8 bits (86), Expect = 0.023
Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 1260 IGIAFGNTLIKHAKPLKIIHSITN-KAKFNEISKLVEKWKPNTV 1302
IG+A + L A PL+ I FN + KLV++++ +TV
Sbjct: 14 IGVAVSDILGSLASPLETIKRKNGKPQDFNALLKLVKEYQVDTV 57
>gnl|CDD|99838 cd06135, Orn, DEDDh 3'-5' exonuclease domain of oligoribonuclease
and similar proteins. Oligoribonuclease (Orn) is a
DEDDh-type DnaQ-like 3'-5' exoribonuclease that is
responsible for degrading small oligoribonucleotides to
mononucleotides. It contains 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. Orn is essential
for Escherichia coli survival. The human homolog, also
called Sfn (small fragment nuclease), is able to
hydrolyze short single-stranded RNA and DNA oligomers.
It plays a role in cellular nucleotide recycling.
Length = 173
Score = 36.4 bits (85), Expect = 0.046
Identities = 14/34 (41%), Positives = 18/34 (52%)
Query: 313 FLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTID 346
+W D E GL+ +DR + A I TD LN I
Sbjct: 1 LVWIDLEMTGLDPEKDRILEIACIITDGDLNIIA 34
>gnl|CDD|188628 cd09908, H3TH_EXO1, H3TH domain of Exonuclease-1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease. Exonuclease-1 (EXO1) is involved in multiple,
eukaryotic DNA metabolic pathways, including DNA
replication processes (5' flap DNA endonuclease activity
and double stranded DNA 5'-exonuclease activity), DNA
repair processes (DNA mismatch repair (MMR) and
post-replication repair (PRR), recombination, and
telomere integrity. EXO1 functions in the MMS2
error-free branch of the PRR pathway in the maintenance
and repair of stalled replication forks. Studies also
suggest that EXO1 plays both structural and catalytic
roles during MMR-mediated mutation avoidance. Members of
this subgroup include the H3TH (helix-3-turn-helix)
domains of EXO1 and other similar eukaryotic 5'
nucleases. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region/I
domain (not included here) and inserted within the PIN
domain is an atypical helix-hairpin-helix-2 (HhH2)-like
region. This atypical HhH2 region, the H3TH domain, has
an extended loop with at least three turns between the
first two helices, and only three of the four helices
appear to be conserved. Both the H3TH domain and the
helical arch/clamp region are involved in DNA binding.
Studies suggest that a glycine-rich loop in the H3TH
domain contacts the phosphate backbone of the template
strand in the downstream DNA duplex. These nucleases
have a carboxylate rich active site that is involved in
binding essential divalent metal ion cofactors (Mg2+ or
Mn2+) required for nuclease activity. The first metal
binding site is composed entirely of Asp/Glu residues
from the PIN domain, whereas, the second metal binding
site is composed generally of two Asp residues from the
PIN domain and one Asp residue from the H3TH domain.
Together with the helical arch and network of amino
acids interacting with metal binding ions, the H3TH
region defines a positively charged active-site
DNA-binding groove in structure-specific 5' nucleases.
EXO1 nucleases also have C-terminal Mlh1- and
Msh2-binding domains which allow interaction with MMR
and PRR proteins, respectively.
Length = 73
Score = 34.1 bits (79), Expect = 0.051
Identities = 11/29 (37%), Positives = 18/29 (62%)
Query: 954 DNLPGVKKIGPKTAVKLLNQYNSLENIIN 982
D LP + IG K A KL+ ++ ++E +I
Sbjct: 13 DYLPSLPGIGLKKAYKLVRRHRTIEKVIK 41
>gnl|CDD|128971 smart00732, YqgFc, Likely ribonuclease with RNase H fold. YqgF
proteins are likely to function as an alternative to RuvC
in most bacteria, and could be the principal holliday
junction resolvases in low-GC Gram-positive bacteria. In
Spt6p orthologues, the catalytic residues are substituted
indicating that they lack enzymatic functions.
Length = 99
Score = 34.1 bits (79), Expect = 0.077
Identities = 15/44 (34%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 1260 IGIAFGNTLIKHAKPLKIIHSITNKAK-FNEISKLVEKWKPNTV 1302
IG+A + K A PL++I TNK + KL++K++P+ +
Sbjct: 13 IGVAVVDETGKLADPLEVIP-RTNKEADAARLKKLIKKYQPDLI 55
>gnl|CDD|236148 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 928
Score = 35.3 bits (82), Expect = 0.31
Identities = 12/31 (38%), Positives = 14/31 (45%)
Query: 462 GKPSFKLEHLSFVNNLSHKKAHDALSDVRAT 492
S+KL LS L H + H A SD T
Sbjct: 128 TAESYKLRDLSEELGLEHDQPHRADSDAEVT 158
>gnl|CDD|237749 PRK14543, PRK14543, nucleoside diphosphate kinase; Provisional.
Length = 169
Score = 32.9 bits (75), Expect = 0.53
Identities = 21/64 (32%), Positives = 31/64 (48%), Gaps = 7/64 (10%)
Query: 252 IIKKSGVDGKLFGSVTNSDIVKELEKKGLKIEKNKIKLPNNSIKKIGNYYIDILLHNGNS 311
IIK GV L G ++V E+ GLKI K+ L + S+ + Y DI + +G
Sbjct: 11 IIKPDGVRRGLIG-----NVVSRFERVGLKIVAAKMLLVDRSMAEKHYLYDDIAVRHGE- 64
Query: 312 TFLW 315
+W
Sbjct: 65 -AVW 67
>gnl|CDD|180525 PRK06310, PRK06310, DNA polymerase III subunit epsilon; Validated.
Length = 250
Score = 33.3 bits (76), Expect = 0.69
Identities = 40/179 (22%), Positives = 73/179 (40%), Gaps = 29/179 (16%)
Query: 313 FLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTIDNPIMLYCKPAPDFLPDPRACLITKIT 372
F+ D ET GL+V++DR +FAAIR + + + + P + + I I+
Sbjct: 9 FVCLDCETTGLDVKKDRIIEFAAIRFT--FDEVIDSVEFLINPERVVSAESQR--IHHIS 64
Query: 373 PQFCLNNGIPEYKFASIIEKI--FLKPGTISVGYNTILFDDEITRFMFWRNLINPYEREW 430
+ + K A + +I F K G VG++ + FD ++
Sbjct: 65 DAMLRD----KPKIAEVFPQIKGFFKEGDYIVGHS-VGFDLQVL---------------- 103
Query: 431 KNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNLSHKKAHDALSDV 489
R + K +Y++ + Y ++ P+ LE L+ N+ + H A+ DV
Sbjct: 104 SQESERIGETFLSKHYYIIDTLRLAKEYGDS--PNNSLEALAVHFNVPYDGNHRAMKDV 160
>gnl|CDD|217573 pfam03462, PCRF, PCRF domain. This domain is found in peptide
chain release factors.
Length = 115
Score = 31.4 bits (72), Expect = 0.98
Identities = 11/38 (28%), Positives = 17/38 (44%)
Query: 748 INMFYLEIESLLKKANEHDTKILNALLMYGKIDGSSCI 785
E+E L K+ E + ++LN LL D + I
Sbjct: 12 REEAEEELEELEKELEELEKELLNLLLPLDPYDDKNAI 49
>gnl|CDD|172564 PRK14074, rpsF, 30S ribosomal protein S6; Provisional.
Length = 257
Score = 32.6 bits (74), Expect = 1.1
Identities = 16/58 (27%), Positives = 26/58 (44%)
Query: 18 RLEDWGRRSLAYQIKKVIKAHYICFNIEINKKTLLEIETSFRFNDAILRYLTIKTKKV 75
+ E WG AY I K+ HY I + E + N+ I+R+L+++ K
Sbjct: 183 KYEYWGLLDFAYPINKMKSGHYCIMCISSTSSIMDEFVRRMKLNENIIRHLSVQVDKF 240
>gnl|CDD|185064 PRK15109, PRK15109, antimicrobial peptide ABC transporter
periplasmic binding protein SapA; Provisional.
Length = 547
Score = 32.4 bits (74), Expect = 1.9
Identities = 8/24 (33%), Positives = 17/24 (70%)
Query: 293 SIKKIGNYYIDILLHNGNSTFLWY 316
S++K+ NY ++ L +++FLW+
Sbjct: 159 SVRKLDNYTVEFRLAQPDASFLWH 182
>gnl|CDD|223097 COG0018, ArgS, Arginyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 577
Score = 32.6 bits (75), Expect = 1.9
Identities = 23/110 (20%), Positives = 45/110 (40%), Gaps = 6/110 (5%)
Query: 177 ILLKDIPNLGKLGE-IIKVKNGYARNFLIPKNKARHATKFVIKEFEEKRIKLEKTAFTIF 235
L G LGE +K+ + + +AR E ++ +L + +
Sbjct: 184 ALGLTPEPDGYLGEYYVKIAKDLEEDPGNDEEEAREE--VEKLESGDEEAELWRKFVDLS 241
Query: 236 LNAKKIGEEIKKLNINIIKKSGVDGKLFGSVTNSDIVKELEKKGLKIEKN 285
L + I E + +L + +G+ F + +V++LE+KGL E +
Sbjct: 242 L--EGIKETLDRLGVKFDVYD-SEGESFYNGKVEKVVEDLEEKGLLYEDD 288
>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 = 31.2 bits (71), Expect = 2.0
Identities = 18/72 (25%), Positives = 23/72 (31%), Gaps = 4/72 (5%)
Query: 638 ASSILNNTYIWKKIFLDYKINNSDLELNIDEELYNNFISKKDNLKLAILRSMSPKKLSNV 697
L Y I+ Y S ELNID L N + + SM + L V
Sbjct: 61 DRESLAQAY---HIYNTYLAPGSPCELNIDHNLRNRITTIMTEKIVGEDDSM-AESLQGV 116
Query: 698 NFCFENKKLEEL 709
FE +
Sbjct: 117 EALFEEAQNAVF 128
>gnl|CDD|223183 COG0105, Ndk, Nucleoside diphosphate kinase [Nucleotide transport
and metabolism].
Length = 135
Score = 30.6 bits (70), Expect = 2.2
Identities = 15/39 (38%), Positives = 18/39 (46%), Gaps = 5/39 (12%)
Query: 252 IIKKSGVDGKLFGSVTNSDIVKELEKKGLKIEKNKIKLP 290
IIK V L G +I+ EKKGLKI K+
Sbjct: 8 IIKPDAVKRGLIG-----EIISRFEKKGLKIVALKMVQL 41
>gnl|CDD|184199 PRK13639, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 275
Score = 31.6 bits (72), Expect = 2.4
Identities = 10/31 (32%), Positives = 22/31 (70%)
Query: 895 KHNLKVIISTNDKDMAQLVSNKIALINNNKI 925
K + +IIST+D D+ + ++K+ ++++ KI
Sbjct: 185 KEGITIIISTHDVDLVPVYADKVYVMSDGKI 215
>gnl|CDD|184752 PRK14573, PRK14573, bifunctional D-alanyl-alanine synthetase
A/UDP-N-acetylmuramate--L-alanine ligase; Provisional.
Length = 809
Score = 31.7 bits (72), Expect = 3.6
Identities = 28/115 (24%), Positives = 49/115 (42%), Gaps = 23/115 (20%)
Query: 665 NIDEELYNNFISKKDNLKLAILRSMSPKKLSNVNFCFENKKLEEL-------IFLYRARN 717
NID E +NF ++ L LA ++ + +K+ +N CF N L + + +
Sbjct: 178 NIDNEHLSNFEGDRELL-LASIQDFA-RKVQQINKCFYNGDCPRLKGCLQGHSYGFSSSC 235
Query: 718 FIETLSYKELKRWKKYRISRFYNKKNNLYNINMFYLEIESLLKKANEHDTKILNA 772
+ LSY + + W+ Y ++F Y +IE L H+ + NA
Sbjct: 236 DLHILSYYQ-EGWRSYFSAKFLGVV---------YQDIE--LNLVGMHN--VANA 276
>gnl|CDD|235429 PRK05359, PRK05359, oligoribonuclease; Provisional.
Length = 181
Score = 30.5 bits (70), Expect = 3.8
Identities = 14/37 (37%), Positives = 18/37 (48%)
Query: 310 NSTFLWYDYETFGLNVRRDRPFQFAAIRTDIMLNTID 346
+W D E GL+ RDR + A I TD LN +
Sbjct: 2 EDNLIWIDLEMTGLDPERDRIIEIATIVTDADLNILA 38
>gnl|CDD|213193 cd03226, ABC_cobalt_CbiO_domain2, Second domain of the ATP-binding
cassette component of cobalt transport system. Domain
II of the ABC component of a cobalt transport family
found in bacteria, archaea, and eukaryota. The
transition metal cobalt is an essential component of
many enzymes and must be transported into cells in
appropriate amounts when needed. The CbiMNQO family ABC
transport system is involved in cobalt transport in
association with the cobalamin (vitamin B12)
biosynthetic pathways. Most cobalt (Cbi) transport
systems possess a separate CbiN component, the
cobalt-binding periplasmic protein, and they are encoded
by the conserved gene cluster cbiMNQO. Both the CbiM and
CbiQ proteins are integral cytoplasmic membrane
proteins, and the CbiO protein has the linker peptide
and the Walker A and B motifs commonly found in the
ATPase components of the ABC-type transport systems.
Length = 205
Score = 30.7 bits (70), Expect = 3.9
Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 5/44 (11%)
Query: 883 DVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNKIH 926
++I LA Q VI+ T+D + V +++ L+ N I
Sbjct: 167 ELIRELAAQGKA-----VIVITHDYEFLAKVCDRVLLLANGAIV 205
>gnl|CDD|224860 COG1949, Orn, Oligoribonuclease (3'->5' exoribonuclease) [RNA
processing and modification].
Length = 184
Score = 30.4 bits (69), Expect = 4.0
Identities = 14/31 (45%), Positives = 17/31 (54%)
Query: 315 WYDYETFGLNVRRDRPFQFAAIRTDIMLNTI 345
W D E GL+ RDR + A I TD LN +
Sbjct: 10 WIDLEMTGLDPERDRIIEIATIVTDANLNIL 40
>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 = 30.8 bits (70), Expect = 4.9
Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 3/53 (5%)
Query: 555 PMNKNILITWNLLHDPKKFLLNDINKIRDYLCFKKNSFKEDIPIS-MIHLNRS 606
N++ L H FL +I I DY C + + +P IHL+RS
Sbjct: 87 VPNQSSGSGTTLEHCLDDFLSTEI--IDDYKCDRCQTVIVRLPQILCIHLSRS 137
>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 = 5.0
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 465 SFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIR 500
S++L LS L+H+ H A SD +AT L L+
Sbjct: 127 SYQLSELSEALGLTHENPHRADSDAQATAELLLLLF 162
>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 = 30.5 bits (69), Expect = 6.6
Identities = 11/52 (21%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 544 YISLMWPICIHPMNKNILITWNLLHDPKKFLLNDINKIRDYLCFKKNSFKED 595
Y+SL+ P + P+ + L+ W+ L DP + ++ + + + L +
Sbjct: 23 YLSLLAPALVAPLLRLELLEWDPLEDP-TYGVDILKRWKALLELDSSDDTGG 73
>gnl|CDD|216035 pfam00632, HECT, HECT-domain (ubiquitin-transferase). The name
HECT comes from Homologous to the E6-AP Carboxyl
Terminus.
Length = 298
Score = 30.0 bits (68), Expect = 8.3
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 647 IWKKIFLDYKINNSDLELNIDEELYNNFISKKDN 680
WKK+ L I DLE +D ELY + S +
Sbjct: 66 FWKKL-LGKPITLEDLEE-VDPELYRSLKSLLEL 97
>gnl|CDD|234600 PRK00053, alr, alanine racemase; Reviewed.
Length = 363
Score = 30.1 bits (69), Expect = 8.6
Identities = 21/95 (22%), Positives = 36/95 (37%), Gaps = 17/95 (17%)
Query: 872 PILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNKIH---DR 928
PILI+ G + + + +NL + + + + + K L K+H D
Sbjct: 77 PILILGGFFPAEDLPLIIA-----YNLTTAV--HSLEQLEALE-KAELGKPLKVHLKID- 127
Query: 929 TTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIG 963
T + R GV PE+ + P V+ G
Sbjct: 128 -TGMHRLGVRPEEAEAALERL----LACPNVRLEG 157
>gnl|CDD|180686 PRK06769, PRK06769, hypothetical protein; Validated.
Length = 173
Score = 29.3 bits (66), Expect = 9.6
Identities = 15/49 (30%), Positives = 25/49 (51%)
Query: 231 AFTIFLNAKKIGEEIKKLNINIIKKSGVDGKLFGSVTNSDIVKELEKKG 279
+FT+F K +++K +I I + G G T +D V+EL+ G
Sbjct: 26 SFTLFPFTKASLQKLKANHIKIFSFTNQPGIADGIATIADFVQELKGFG 74
>gnl|CDD|213197 cd03230, ABC_DR_subfamily_A, ATP-binding cassette domain of the
drug resistance transporter and related proteins,
subfamily A. This family of ATP-binding proteins
belongs to a multi-subunit transporter involved in drug
resistance (BcrA and DrrA), nodulation, lipid transport,
and lantibiotic immunity. In bacteria and archaea, these
transporters usually include an ATP-binding protein and
one or two integral membrane proteins. Eukaryotic
systems of the ABCA subfamily display ABC domains that
are quite similar to this family. The ATP-binding domain
shows the highest similarity between all members of the
ABC transporter 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 = 173
Score = 29.3 bits (67), Expect = 9.7
Identities = 9/43 (20%), Positives = 27/43 (62%), Gaps = 5/43 (11%)
Query: 883 DVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNKI 925
+++ L K+ T +++S++ + A+ + +++A++NN +I
Sbjct: 136 ELLRELKKEGKT-----ILLSSHILEEAERLCDRVAILNNGRI 173
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
0.322 0.139 0.414
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: 74,288,324
Number of extensions: 7730891
Number of successful extensions: 8000
Number of sequences better than 10.0: 1
Number of HSP's gapped: 7904
Number of HSP's successfully gapped: 205
Length of query: 1428
Length of database: 10,937,602
Length adjustment: 109
Effective length of query: 1319
Effective length of database: 6,103,016
Effective search space: 8049878104
Effective search space used: 8049878104
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 (21.9 bits)
S2: 65 (29.0 bits)