RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14291
(538 letters)
>gnl|CDD|233044 TIGR00600, rad2, DNA excision repair protein (rad2). All proteins
in this family for which functions are known are flap
endonucleases that generate the 3' incision next to DNA
damage as part of nucleotide excision repair. This
family is related to many other flap endonuclease
families including the fen1 family. 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 = 1034
Score = 230 bits (589), Expect = 7e-66
Identities = 131/391 (33%), Positives = 197/391 (50%), Gaps = 53/391 (13%)
Query: 158 DNIIDAEEKDILEMIRAEEENEIEFEE------EIAGGKEEKTEKIKLTREMLAEQQKIL 211
I + E + +E + E E++ F E + K++ + E + +
Sbjct: 636 LLISNPMEVEPMESEKEESESDGSFIEVDSVSSTLELQVPSKSQPTDESEENAENKVASI 695
Query: 212 DSLVKKKAKSDDVIDVDLTETSTSGFFDYGCDVIKSSTLEKDRDQLLLERGKQTRLASTI 271
+ ++ D+ E+ +++ EKD + K ++
Sbjct: 696 E-----GEHRKEIEDLLFDESEED-------NIVGMIEEEKD-----ADDFKNEWQDISL 738
Query: 272 TEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGTDKKRRPYVSRKM-LEAQELLQLF 330
E + EA L + +AQ + + V+ +M LE+QELL+LF
Sbjct: 739 EELEALEANLLAEQN---------SLKAQKQQQKRIAAE-----VTGQMILESQELLRLF 784
Query: 331 GVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPD 390
G+P+IVAP EAEAQCA L+L + T G ITDDSDIWLFGAR VYKNFF++ V Y D
Sbjct: 785 GIPYIVAPMEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNFFNQNKFVEYYQYVD 844
Query: 391 IRYYFELTREKLIQLALLVGSDYTPGLQGVGPVTALEILAKFSPSDSPNQNYIVESMRRF 450
I L R KLI LA L+GSDYT G+ VGPV+A+EIL +F P D +E + +F
Sbjct: 845 IHNQLGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEILNEF-PGDG------LEPLLKF 897
Query: 451 KNWLA-----KKNKPDTHLT---RKLRNVKLNDDFPNVSVIEAYLKPDINTNVQKLAWGT 502
K W KK + + + T +KLR ++L FPN +V +AYL+P ++ + WG
Sbjct: 898 KEWWHEAQKDKKKRENPNDTKVKKKLRLLQLTPGFPNPAVADAYLRPVVDDSKGSFLWGK 957
Query: 503 PDLDGLRRFAANKFGWSQNRVDQTLIPIMKK 533
PDLD +R F FGW++ + D+ L+P++KK
Sbjct: 958 PDLDKIREFCQRYFGWNREKTDEVLLPVLKK 988
Score = 49.9 bits (119), Expect = 3e-06
Identities = 23/31 (74%), Positives = 24/31 (77%)
Query: 110 MGVNGLWKLLEASGKPVPVETLENKVLAVGI 140
MGV GLWKLLE SG+PV ETLE K LAV I
Sbjct: 1 MGVQGLWKLLECSGRPVSPETLEGKRLAVDI 31
Score = 36.4 bits (84), Expect = 0.044
Identities = 22/80 (27%), Positives = 33/80 (41%), Gaps = 7/80 (8%)
Query: 33 AQRKTLKSKAASNADKVRSDLLKNLLEQQ-LLNDVLGKNEMALPPPSVS---REVDMFEL 88
A+R+ + A+ +A K LL L++Q + K PSV R D++ L
Sbjct: 89 AKRRQRRDGASEDARKTAEKLLATFLKRQAIKTAFNSKKSTPEALPSVQQVPRPQDLYVL 148
Query: 89 PPAPAQTVQD---EEEDTLE 105
PP P + E E E
Sbjct: 149 PPLPEEEKHSSEEESEKEWE 168
>gnl|CDD|189038 cd09868, PIN_XPG, PIN domain of Xeroderma pigmentosum
complementation group G (XPG) nuclease, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. The Xeroderma pigmentosum
complementation group G (XPG) nuclease plays a central
role in nucleotide excision repair (NER) in cleaving DNA
bubble structures or loops. XPG is a member 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). In XPG PIN domains, this arch region can be
quite variable and extensive (400 - 800 residues) in
length and is required for NER activity and for
efficient processing of bubble substrates. Inserted
within the PIN domain of these 5' nucleases is 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. Nucleases within this group
also have a carboxylate-rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+).
Length = 249
Score = 129 bits (327), Expect = 3e-34
Identities = 64/185 (34%), Positives = 78/185 (42%), Gaps = 68/185 (36%)
Query: 238 FDYGCDVIKSSTLEKDRDQ--------------LLL----------ERGKQTRLASTITE 273
FD G +K TL K R Q LL ++ +Q R A IT+
Sbjct: 76 FDGGAPELKRRTLAKRRQQREKAEINAKKTAEKLLASQLKKSAVKSQQQQQERDADEITQ 135
Query: 274 QMSREAQELLQLFGVPFIVAPGEAEAQCASLELGTDKKRRPYVSRKMLEAQELLQLFGVP 333
+M E QELL+LFG+P+IVAP EAEAQCA L QL
Sbjct: 136 EMYDECQELLRLFGIPYIVAPMEAEAQCA----------------------ILNQL---- 169
Query: 334 FIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDIRY 393
GVITDDSD++LFGA+ VYKNFF+ +V Y A DI
Sbjct: 170 ------------------GLVDGVITDDSDVFLFGAKRVYKNFFNGNKYVEYYLAEDIEK 211
Query: 394 YFELT 398
T
Sbjct: 212 ELPFT 216
Score = 59.9 bits (146), Expect = 5e-10
Identities = 21/29 (72%), Positives = 24/29 (82%)
Query: 110 MGVNGLWKLLEASGKPVPVETLENKVLAV 138
MGV GLWKLLE SG+PV +ETLE K LA+
Sbjct: 1 MGVKGLWKLLEPSGRPVRLETLEGKRLAI 29
Score = 55.7 bits (135), Expect = 1e-08
Identities = 24/68 (35%), Positives = 34/68 (50%), Gaps = 6/68 (8%)
Query: 465 TRKLRNVKLNDDFPNVSVIEAYLKPDINTNVQKLAWGTPDLDGLRRFAANKFGWSQNRVD 524
R +N F +E YL DI + WG PDL+ LR F KFGW + + D
Sbjct: 188 KRVYKNF-----FNGNKYVEYYLAEDIEKEL-PFTWGKPDLELLREFCRQKFGWPKEKTD 241
Query: 525 QTLIPIMK 532
+ L+P++K
Sbjct: 242 EILLPVIK 249
>gnl|CDD|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional.
Length = 393
Score = 109 bits (274), Expect = 6e-26
Identities = 60/220 (27%), Positives = 101/220 (45%), Gaps = 29/220 (13%)
Query: 311 KRRPYVSRKMLE-AQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGA 369
KR V+++ E A++LL+L G+P I AP EAEAQCA L V T+D D FG
Sbjct: 130 KRTVRVTKEQNEDAKKLLRLMGIPVIEAPCEAEAQCAELVKKGKVYAVATEDMDALTFGT 189
Query: 370 RTVYKNFF---DKKSHVLRYTAPDIRYYFELTREKLIQLALLVGSDYTPGLQGVGPVTAL 426
+ +N KK + + L+ ++ I L +L G DY ++G+GP TA
Sbjct: 190 PVLLRNLNFSEAKKRPIQEINLSTVLEELGLSMDQFIDLCILCGCDYCDTIKGIGPKTAY 249
Query: 427 EILAKFSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHLTRKLRNVKLNDDFPNVSVIEAY 486
+++ K+ +S+ L K P + ++F E +
Sbjct: 250 KLIKKY------------KSIEEILEHLDKTKYP------------VPENFDYKEARELF 285
Query: 487 LKPDINTNVQ-KLAWGTPDLDGLRRFAANKFGWSQNRVDQ 525
L P++ + L W PD +GL++F + +++ RV++
Sbjct: 286 LNPEVTPAEEIDLKWNEPDEEGLKKFLVKEKNFNEERVEK 325
>gnl|CDD|188624 cd09904, H3TH_XPG, H3TH domain of Xeroderma pigmentosum
complementation group G (XPG) nuclease, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease. The Xeroderma pigmentosum complementation
group G (XPG) nuclease plays a central role in
nucleotide excision repair (NER) in cleaving DNA bubble
structures or loops. XPG is a member of the
structure-specific, 5' nuclease family that catalyzes
hydrolysis of DNA duplex-containing nucleic acid
structures during DNA replication, repair, and
recombination. Members of this subgroup include the
H3TH (helix-3-turn-helix) domains of XPG 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.
Length = 97
Score = 100 bits (251), Expect = 1e-25
Identities = 40/105 (38%), Positives = 57/105 (54%), Gaps = 21/105 (20%)
Query: 400 EKLIQLALLVGSDYTPGLQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNWL----- 454
+KLI+LALL+GSDYT G+ G+GPV A+EIL++F E + +FK+W
Sbjct: 1 DKLIRLALLLGSDYTEGVSGIGPVNAMEILSEFPG---------EEDLEKFKDWWENAQP 51
Query: 455 AKKNKPDTHLT---RKLRNVKLN----DDFPNVSVIEAYLKPDIN 492
K D RK +N N FP+ +VI AYL P+++
Sbjct: 52 EKSEDSDNDKQEFKRKHKNYLKNLILPPGFPSPAVINAYLNPNVD 96
>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional.
Length = 292
Score = 103 bits (259), Expect = 1e-24
Identities = 61/242 (25%), Positives = 106/242 (43%), Gaps = 46/242 (19%)
Query: 311 KRRPYVSRKMLE-AQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGA 369
+R ++ +++E +++LL L G+P++ AP E EAQ A + V + D D LFGA
Sbjct: 75 QRSSRLTDEIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGA 134
Query: 370 RTVYKNF----FDKKSHVLRYTAPDIRYY--------FELTREKLIQLALLVGSDYTPGL 417
+ +N K Y +TRE+LI +A+LVG+DY PG+
Sbjct: 135 PRLVRNLTISGKRKLPGKNVYVEVKPELIELEEVLKELGITREQLIDIAILVGTDYNPGI 194
Query: 418 QGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHLTRKLRNVKLNDDF 477
+G+GP TAL+++ K + L ++ +
Sbjct: 195 KGIGPKTALKLIKKHG---------------DLEKVLEERGF----------------EI 223
Query: 478 PNVSVI-EAYLKPDINTNVQKLAWGTPDLDGLRRFAANKFGWSQNRVDQTLIPIMKKISQ 536
N I E +L P + + +L W PD +G+ F + +S+ RV + L + K + +
Sbjct: 224 ENYDEIREFFLNPPVTDDY-ELKWKEPDKEGIIEFLVEEHDFSEERVKKALERLEKAVKE 282
Query: 537 RS 538
+
Sbjct: 283 KK 284
>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 = 103 bits (259), Expect = 3e-24
Identities = 60/240 (25%), Positives = 107/240 (44%), Gaps = 44/240 (18%)
Query: 311 KRRPYVSRKMLE-AQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGA 369
+R ++ +++E +++LL L G+P++ AP E EAQ A + V + D D LFGA
Sbjct: 122 QRSSRLTSEIVESSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDVDYVGSQDYDSLLFGA 181
Query: 370 RTVYKNFFDKKSHVLRYTAPDIRYYFEL------------TREKLIQLALLVGSDYTPGL 417
+ +N L + EL TRE+LI +A+LVG+DY G+
Sbjct: 182 PRLVRNLTISGKRKLPGKNIYVEVKPELIELEEVLSELGITREQLIDIAILVGTDYNEGV 241
Query: 418 QGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHLTRKLRNVKLNDDF 477
+G+GP TAL+++ + + L + + + ++R LN
Sbjct: 242 KGIGPKTALKLIKEH---------------GDLEKVLKARGEDIENY-DEIREFFLN--- 282
Query: 478 PNVSVIEAYLKPDINTNVQKLAWGTPDLDGLRRFAANKFGWSQNRVDQTLIPIMKKISQR 537
P V T+ +L W PD +G+ F ++ +S++RV++ L + +
Sbjct: 283 PPV------------TDDYELKWRKPDKEGIIEFLCDEHDFSEDRVERALERLEAAYKSK 330
>gnl|CDD|189026 cd09856, PIN_FEN1-like, PIN domain of Flap Endonuclease-1
(FEN1)-like, structure-specific, divalent-metal-ion
dependent, 5' nucleases. PIN (PilT N terminus) domain
of Flap Endonuclease-1 (FEN1)-like nucleases: FEN1, Gap
endonuclease 1 (GEN1) and Xeroderma pigmentosum
complementation group G (XPG) nuclease 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 30 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. Most nucleases within this
family also have a carboxylate rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+). Some nucleases in this family
have C-terminal extensions that act as interaction sites
for other proteins.
Length = 207
Score = 99.1 bits (247), Expect = 7e-24
Identities = 36/85 (42%), Positives = 54/85 (63%), Gaps = 3/85 (3%)
Query: 310 KKRRPYVSRKML-EAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFG 368
K++ + +M+ E ++LL L G+P++ APGE EAQCA L++ G++++DSD LFG
Sbjct: 86 KRKTNPSTPEMISECRKLLDLMGIPYVQAPGEGEAQCAYLQVSGAVDGILSNDSDTLLFG 145
Query: 369 ARTVYKNF--FDKKSHVLRYTAPDI 391
A VY+NF F K+S V P I
Sbjct: 146 AEKVYRNFTKFYKESFVEVIDLPKI 170
Score = 39.4 bits (92), Expect = 0.002
Identities = 19/88 (21%), Positives = 30/88 (34%), Gaps = 15/88 (17%)
Query: 453 WLAKKNKPDTHLT-----------RKLRNVKLNDDFPNVSVIEAYLKPDINTNVQKLAWG 501
+L D L+ + RN V VI+ P IN V +
Sbjct: 124 YLQVSGAVDGILSNDSDTLLFGAEKVYRNFTKFYKESFVEVIDL---PKIN-KVLSINMA 179
Query: 502 TPDLDGLRRFAANKFGWSQNRVDQTLIP 529
PDL+ + F ++Q+ D+ L
Sbjct: 180 GPDLEYINLFFNELKYFNQSSFDKWLHD 207
Score = 29.4 bits (66), Expect = 4.3
Identities = 9/27 (33%), Positives = 13/27 (48%)
Query: 114 GLWKLLEASGKPVPVETLENKVLAVGI 140
LW+ LE +P E L K +A+
Sbjct: 1 QLWEFLEPQKSRIPKEQLRGKRIAIDA 27
>gnl|CDD|189039 cd09869, PIN_GEN1, PIN domain of Gap Endonuclease 1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. Gap Endonuclease 1 (GEN1) is a
Holliday junction resolvase reported to symmetrically
cleave Holliday junctions and allow religation without
additional processing. GEN1 is a member 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) of variable length (approximately 30 - 50
residues in GEN1 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. Nucleases within this group
also have a carboxylate-rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+).
Length = 233
Score = 91.3 bits (227), Expect = 7e-21
Identities = 40/88 (45%), Positives = 52/88 (59%), Gaps = 2/88 (2%)
Query: 307 GTDKKRRPYVSRKMLEAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWL 366
G+ + RR S + E ELL+L G+P + A GEAEA CA L G IT DSD +L
Sbjct: 107 GSKRNRRSRFSHVLKECVELLELLGIPCLQAAGEAEALCAELNSEGLVDGCITQDSDAFL 166
Query: 367 FGARTVYKNFF--DKKSHVLRYTAPDIR 392
+GARTVY+NF +K +V Y DI+
Sbjct: 167 YGARTVYRNFQMSEKGGYVDCYDMSDIK 194
Score = 36.2 bits (84), Expect = 0.024
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 110 MGVNGLWKLLEASGKPVPVETLENKVLAV 138
MGV GLW +LE K P++ L+ K +AV
Sbjct: 1 MGVKGLWDILEPVKKRKPLDHLQGKRVAV 29
Score = 30.0 bits (68), Expect = 2.5
Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 4/63 (6%)
Query: 469 RNVKLNDDFPNVSVIEAYLKPDINTNVQKLAWGTPDLDGLRRFAANKFGWSQNRVDQTLI 528
RN ++++ V + Y DI + + L+W PDL+ F+ W ++ + L+
Sbjct: 174 RNFQMSEKGGYV---DCYDMSDIKSKLD-LSWRQPDLELFIDFSVVPLHWDESYCREKLL 229
Query: 529 PIM 531
P++
Sbjct: 230 PLL 232
>gnl|CDD|214689 smart00484, XPGI, Xeroderma pigmentosum G I-region. domain in
nucleases.
Length = 73
Score = 85.7 bits (213), Expect = 1e-20
Identities = 28/56 (50%), Positives = 35/56 (62%)
Query: 329 LFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVL 384
L G+P+IVAP EAEAQCA L +IT+DSD+ LFGA +Y+N F L
Sbjct: 2 LMGIPYIVAPYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKKKL 57
>gnl|CDD|216163 pfam00867, XPG_I, XPG I-region.
Length = 46
Score = 73.2 bits (181), Expect = 1e-16
Identities = 23/42 (54%), Positives = 29/42 (69%)
Query: 329 LFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGAR 370
L G+P++VAP EAEAQCA L VI++DSD+ LFGA
Sbjct: 2 LMGIPYVVAPYEAEAQCAYLVKTGLVDAVISEDSDLLLFGAP 43
>gnl|CDD|223336 COG0258, Exo, 5'-3' exonuclease (including N-terminal domain of
PolI) [DNA replication, recombination, and repair].
Length = 310
Score = 77.8 bits (192), Expect = 9e-16
Identities = 47/183 (25%), Positives = 79/183 (43%), Gaps = 21/183 (11%)
Query: 322 EAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKS 381
LL+L G+ P E AQ A + G+ +I+ D D+ + V K
Sbjct: 108 LGIPLLELMGIE-ADDPIETLAQKAY-KKGDVV-LIISGDKDLLQLVSPNVLVINGKKGE 164
Query: 382 HVLRYTAPDIR-YYFELTREKLIQLALLVG--SDYTPGLQGVGPVTALEILAKFSPSDSP 438
++ + LT E+LI L LVG SD PG++G+GP TAL++L ++ +
Sbjct: 165 PEKFLDLEEVEEKFKGLTPEQLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYGSLEG- 223
Query: 439 NQNYIVESMRRFKNWLAKK---NKPDTHLTRKL----RNVKLNDDFPNVSVIEAYLKPDI 491
+ E++ K +K +K L++ L +V L D + I L P+
Sbjct: 224 ----LYENLDIIKKKTREKLLEDKEKAFLSKPLATIKTDVPLEFDLED---ILELLVPEH 276
Query: 492 NTN 494
+ +
Sbjct: 277 DFS 279
>gnl|CDD|189040 cd09870, PIN_YEN1, PIN domain of Yeast Endonuclease 1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and fungal homologs. Yeast Endonuclease 1
(YEN1) is a Holliday junction resolvase which promotes
reciprocal exchange during mitotic recombination to
maintain genome integrity in budding yeast. YEN1 is a
member 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) of variable length (approximately 15 - 50
residues in YEN1 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. Nucleases within this group
also have a carboxylate-rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+).
Length = 239
Score = 76.2 bits (188), Expect = 1e-15
Identities = 33/99 (33%), Positives = 50/99 (50%), Gaps = 19/99 (19%)
Query: 310 KKRRPYVSRKMLEAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGA 369
KK+ ++ + + +ELL LFG+P+ APGEAEA+CA L+ V+++DSD +FGA
Sbjct: 105 KKKEHWLIKLV---KELLDLFGIPYHTAPGEAEAECARLQRLGIVDAVLSNDSDALMFGA 161
Query: 370 RTVYKNF----------------FDKKSHVLRYTAPDIR 392
V +N + HV Y +IR
Sbjct: 162 TRVIRNPSKEGEDSLASSSNVKSKKDEDHVTVYDLDEIR 200
>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 = 66.9 bits (164), Expect = 4e-14
Identities = 25/88 (28%), Positives = 37/88 (42%), Gaps = 21/88 (23%)
Query: 400 EKLIQLALLVGSDYTPGLQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNWLAKKNK 459
E+ I L +L G DY PGL G+GP TAL+++ ++ S+ + L K
Sbjct: 1 EQFIDLCILSGCDYLPGLPGIGPKTALKLIKEYG------------SLEKVLKALRDDKK 48
Query: 460 PDTHLTRKLRNVKLNDDFPNVSVIEAYL 487
V + DFP E +L
Sbjct: 49 ---------DKVPVPYDFPYKKARELFL 67
>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 = 64.0 bits (157), Expect = 3e-13
Identities = 21/34 (61%), Positives = 28/34 (82%)
Query: 400 EKLIQLALLVGSDYTPGLQGVGPVTALEILAKFS 433
E+LI LALL+G+DY PG+ G+GP TALE+L +F
Sbjct: 1 EQLILLALLLGTDYNPGVPGIGPKTALELLKEFG 34
>gnl|CDD|189037 cd09867, PIN_FEN1, PIN domain of Flap Endonuclease-1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. Flap endonuclease-1 (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. FEN1 belongs to the
FEN1-EXO1-like family of structure-specific, 5'
nucleases. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region (I
domain) of variable length (approximately 45 residues in
FEN1 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. Nucleases
within this group also have a carboxylate-rich active
site that is involved in binding essential divalent
metal ion cofactors (Mg2+/Mn2+). 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 = 261
Score = 66.0 bits (162), Expect = 5e-12
Identities = 27/67 (40%), Positives = 41/67 (61%), Gaps = 1/67 (1%)
Query: 311 KRRPYVSRKMLE-AQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGA 369
KR V+++++E ++LL+L G+P++ AP EAEAQCA L V + D D LFGA
Sbjct: 123 KRTVRVTKEIVEECKKLLRLMGIPYVEAPSEAEAQCAYLVKKGDVYAVASQDYDSLLFGA 182
Query: 370 RTVYKNF 376
+ +N
Sbjct: 183 PRLVRNL 189
Score = 61.0 bits (149), Expect = 2e-10
Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 15/74 (20%)
Query: 246 KSSTLEKDRD---------QLLLERG------KQTRLASTITEQMSREAQELLQLFGVPF 290
KS LEK R+ + E G K + +T+++ E ++LL+L G+P+
Sbjct: 88 KSGELEKRRERREEAEEKLEEAKEEGDAEEARKYAKRTVRVTKEIVEECKKLLRLMGIPY 147
Query: 291 IVAPGEAEAQCASL 304
+ AP EAEAQCA L
Sbjct: 148 VEAPSEAEAQCAYL 161
>gnl|CDD|189027 cd09857, PIN_EXO1, PIN domain of Exonuclease-1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. 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. EXO1 belongs to the FEN1-EXO1-like
family of structure-specific, 5' nucleases. These
nucleases contain a PIN (PilT N terminus) domain with a
helical arch/clamp region (I domain) of variable length
(approximately 43 residues in EXO1 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. Nucleases within this group
also have a carboxylate-rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+). EXO1 nucleases also have
C-terminal Mlh1- and Msh2-binding domains which allow
interaction with MMR and PRR proteins, respectively.
Length = 210
Score = 56.7 bits (138), Expect = 3e-09
Identities = 27/73 (36%), Positives = 39/73 (53%), Gaps = 8/73 (10%)
Query: 316 VSRKMLEAQELLQLF---GVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTV 372
++ +M A EL++ GV +IVAP EA+AQ A L + VIT+DSD+ +G V
Sbjct: 125 ITPEM--AHELIKALRKEGVEYIVAPYEADAQLAYLAKTGYVDAVITEDSDLLAYGCPKV 182
Query: 373 -YKNFFDKKSHVL 384
+K DK
Sbjct: 183 LFK--LDKNGSCQ 193
Score = 31.3 bits (72), Expect = 0.84
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 110 MGVNGLWKLLEASGKPVPVETLENKVLAV 138
MG+ GL L+ +PV + + K +AV
Sbjct: 1 MGIQGLLPFLKPIQRPVHISEYKGKRVAV 29
>gnl|CDD|188626 cd09906, H3TH_YEN1, H3TH domain of Yeast Endonuclease 1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease. Yeast Endonuclease 1 (YEN1): Holliday
junction resolvase which promotes reciprocal exchange
during mitotic recombination to maintain genome
integrity in budding yeast. YEN1 is a member of the
structure-specific, 5' nuclease family that catalyzes
hydrolysis of DNA duplex-containing nucleic acid
structures during DNA replication, repair, and
recombination. Members of this subgroup include the H3TH
(helix-3-turn-helix) domains of YEN1 and other similar
fungal 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.
Length = 105
Score = 51.5 bits (124), Expect = 2e-08
Identities = 29/103 (28%), Positives = 44/103 (42%), Gaps = 13/103 (12%)
Query: 399 REKLIQLALLVGSDY-TPGLQGVGPVTALEILAKFSPSDSP-------NQNYIVESMRRF 450
R ++ ALL G DY T GL G G TALE LAK DS ++ + + +
Sbjct: 1 RGGMVLFALLSGGDYDTVGLPGCGKKTALE-LAKLGFGDSLLEAAEDLSEEELESFLEEW 59
Query: 451 KNWLAK--KNKPDTHLTRKLRNVKLN--DDFPNVSVIEAYLKP 489
+ L + + R + L+ + FP+ V+ Y P
Sbjct: 60 RERLLEELRTNGRGLFGRNYPALSLSIPEGFPDPDVLLYYTHP 102
>gnl|CDD|189022 cd09852, PIN_SF, PIN (PilT N terminus) domain: Superfamily. PIN_SF
The PIN (PilT N terminus) domain belongs to a large
nuclease superfamily with representatives from
eukaryota, eubacteria, and archaea. PIN domains were
originally named for their sequence similarity to the
N-terminal domain of an annotated pili biogenesis
protein, PilT, a domain fusion between a PIN-domain and
a PilT ATPase domain. The structural properties of the
PIN domain indicate its putative active center,
consisting of invariant acidic amino acid residues
(putative metal-binding residues) is geometrically
similar in the active center of structure-specific 5'
nucleases (also known as Flap endonuclease-1-like),
PIN-domain ribonucleases of eukaryotic rRNA editing
proteins, and bacterial toxins of toxin-antitoxin (TA)
operons. Seen here, are two major divisions in the PIN
domain superfamily. The first major division, the
structure-specific 5' nuclease family, is represented by
FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4
RNase H nuclease PIN domains. These 5' nucleases are
involved in DNA replication, repair, and recombination.
They are capable of both 5'-3' exonucleolytic activity
and cleaving bifurcated DNA, in an endonucleolytic,
structure-specific manner. Unique to FEN1-like
nucleases, the PIN domain has a helical arch/clamp
region (I domain) of variable length (approximately 16
to 800 residues) and, inserted within the C-terminal
region of the PIN domain, 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, these nucleases have a carboxylate
rich active site that is involved in binding essential
divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or
Co2+). The second major division of the PIN domain
superfamily, the VapC-Smg6 family, includes such
eukaryotic ribonucleases as, Smg6, an essential factor
in nonsense-mediated mRNA decay; Rrp44, the catalytic
subunit of the exosome; and Nob1, a ribosome assembly
factor critical in pre-rRNA processing. A large
percentage of members in this family are bacterial
ribonuclease toxins of TA operons such as Mycobacterium
tuberculosis VapC and Neisseria gonorrhoeae FitB, as
well as, archaeal homologs, Pyrobaculum aerophilum
Pea0151 and P. aerophilum Pae2754. Also included are the
eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U
three-associated protein 24) and Utp23-like proteins.
Components of the small subunit processome, Fcf1/Utp24
and Utp23 are essential proteins involved in pre-rRNA
processing and 40S ribosomal subunit assembly.
Length = 120
Score = 51.4 bits (123), Expect = 4e-08
Identities = 33/110 (30%), Positives = 52/110 (47%), Gaps = 5/110 (4%)
Query: 267 LASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGTDKKRRPYV-SRKMLEAQE 325
L +TE R++ + L + I+ + A+ LE +R+ + +L E
Sbjct: 8 LFRLLTEIRLRKSLKRLLEGDITVII-VFDVVAELLKLEAQKGLRRKKGRVAELLLRDLE 66
Query: 326 LLQLFGVPFIVAPG---EAEAQCASLELGNHTQGVITDDSDIWLFGARTV 372
LL L G+P + APG EA+AQ A+L H +IT+DSD+ V
Sbjct: 67 LLDLMGIPVVHAPGDLYEADAQIAALAKKGHVVALITNDSDLRQKAKPGV 116
>gnl|CDD|197623 smart00279, HhH2, Helix-hairpin-helix class 2 (Pol1 family) motifs.
Length = 36
Score = 47.4 bits (114), Expect = 1e-07
Identities = 18/36 (50%), Positives = 26/36 (72%), Gaps = 2/36 (5%)
Query: 399 REKLIQLALLVG--SDYTPGLQGVGPVTALEILAKF 432
E+ I A+LVG SD PG++G+GP TAL++L +F
Sbjct: 1 PEQFIDYAILVGDYSDNIPGVKGIGPKTALKLLREF 36
>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 = 47.8 bits (114), Expect = 2e-07
Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 10/76 (13%)
Query: 400 EKLIQLALLVGSDYT--PGLQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNWLAKK 457
E+ I L LVG DY+ PG+ G+GP TA ++ K+ + I+E++ K +K
Sbjct: 1 EQFIDLCALVGCDYSDNPGVPGIGPKTAAKLALKY-----GSLEGILENLDELKGKKREK 55
Query: 458 ---NKPDTHLTRKLRN 470
K L+RKL
Sbjct: 56 LEEPKEYAFLSRKLAT 71
>gnl|CDD|188625 cd09905, H3TH_GEN1, H3TH domain of Gap Endonuclease 1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease. Gap Endonuclease 1 (GEN1): Holliday junction
resolvase reported to symmetrically cleave Holliday
junctions and allow religation without additional
processing. GEN1 is a member of the structure-specific,
5' nuclease family that catalyzes hydrolysis of DNA
duplex-containing nucleic acid structures during DNA
replication, repair, and recombination. Members of this
subgroup include the H3TH (helix-3-turn-helix) domains
of GEN1 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.
Length = 108
Score = 48.5 bits (116), Expect = 3e-07
Identities = 39/117 (33%), Positives = 51/117 (43%), Gaps = 35/117 (29%)
Query: 399 REKLIQLALLVGSDYTP-GLQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNW---- 453
REKLI LALL G DY P G+ GVG AL ++ S E + R +NW
Sbjct: 1 REKLIALALLCGCDYNPKGVPGVGKERALRLVNIVSSD---------EVLDRLRNWRATS 51
Query: 454 -------LAKKNKPDT----HLTRKLRNVK----------LNDDFPNVSVIEAYLKP 489
L KK+K HL +K ++K L+ FPN +IE +L
Sbjct: 52 DPSSPQELKKKDKNHCSNCGHLGKKQEHIKSGCEDCDKALLDPGFPNEEIIEEFLSR 108
>gnl|CDD|189020 cd00128, PIN_FEN1_EXO1-like, PIN domains of Flap Endonuclease-1
(FEN1)-like and Exonuclease-1 (EXO1)-like nucleases,
structure-specific, divalent-metal-ion dependent, 5'
nucleases. PIN (PilT N terminus) domain of Flap
Endonuclease-1 (FEN1) and Exonuclease-1 (EXO1)-like
nucleases: FEN1, EXO1, Mkt1, Gap endonuclease 1 (GEN1)
and Xeroderma pigmentosum complementation group G (XPG)
nuclease 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 30 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. Most
nucleases within this family also have a carboxylate
rich active site that is involved in binding essential
divalent metal ion cofactors (Mg2+/Mn2+). Some nucleases
in this family have C-terminal extensions that act as
interaction sites for other proteins.
Length = 209
Score = 47.5 bits (113), Expect = 4e-06
Identities = 24/66 (36%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 311 KRRPYVSRKMLE-AQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGA 369
KR ++ K + + LL L G+P++VAP EAEAQ A L H IT+D+D ++G
Sbjct: 117 KRNVTITPKAYQNCKILLSLEGIPYVVAPYEAEAQLAYLAKSGHVIAAITEDTDCLMYGV 176
Query: 370 RTVYKN 375
+
Sbjct: 177 PRFIRG 182
Score = 42.9 bits (101), Expect = 1e-04
Identities = 19/42 (45%), Positives = 26/42 (61%)
Query: 263 KQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASL 304
K + TIT + + + LL L G+P++VAP EAEAQ A L
Sbjct: 114 KPFKRNVTITPKAYQNCKILLSLEGIPYVVAPYEAEAQLAYL 155
>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 = 44.1 bits (105), Expect = 4e-06
Identities = 14/33 (42%), Positives = 21/33 (63%)
Query: 400 EKLIQLALLVGSDYTPGLQGVGPVTALEILAKF 432
E+ I L +L G DY P + G+GP TA +++ K
Sbjct: 1 EQFIDLCILSGCDYLPSIPGIGPKTAYKLIKKH 33
>gnl|CDD|214690 smart00485, XPGN, Xeroderma pigmentosum G N-region. domain in
nucleases.
Length = 99
Score = 44.9 bits (107), Expect = 4e-06
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 110 MGVNGLWKLLEASGKPVPVETLENKVLAV 138
MG+ GLW LL+ + VP+E L K LA+
Sbjct: 1 MGIKGLWPLLKPVVREVPLEALRGKTLAI 29
>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 = 43.7 bits (104), Expect = 5e-06
Identities = 17/36 (47%), Positives = 29/36 (80%), Gaps = 1/36 (2%)
Query: 400 EKLIQLALLVGSDYTP-GLQGVGPVTALEILAKFSP 434
E+LI +A+LVG+DY P G++G+GP TAL+++ ++
Sbjct: 1 EQLIDIAILVGTDYNPGGVKGIGPKTALKLVKEYGD 36
>gnl|CDD|214682 smart00475, 53EXOc, 5'-3' exonuclease.
Length = 259
Score = 44.9 bits (107), Expect = 4e-05
Identities = 46/175 (26%), Positives = 80/175 (45%), Gaps = 20/175 (11%)
Query: 324 QELLQLFGVPFIVAPG-EAEAQCASL-----ELGNHTQGVITDDSD-IWLFGARTVYKNF 376
+ELL G+P + G EA+ A+L G + +++ D D + L + +
Sbjct: 90 KELLDALGIPVLEVEGYEADDVIATLAKKAEAEGYEVR-IVSGDKDLLQLVSDKVSVLDP 148
Query: 377 FDKKSHVLRYTAPDIRYYFELTREKLIQLALLVG--SDYTPGLQGVGPVTALEILAKFSP 434
YT ++ + LT E++I L+G SD PG+ G+G TA ++L +F
Sbjct: 149 TKGIKEFELYTPENVIEKYGLTPEQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEFGS 208
Query: 435 SDSPNQNYIVESMRRFKNWLAKK---NKPDTHLTRKLRNVKLNDDFPNVSVIEAY 486
++ I+E++ + K L +K +K D L+RKL + D P +E
Sbjct: 209 LEN-----ILENLDKLKKKLREKLLAHKEDAKLSRKL--ATIETDVPLEVDLEDL 256
>gnl|CDD|221785 pfam12813, XPG_I_2, XPG domain containing. This family is largely
of fungal proteins and is related to the XP-G protein
family.
Length = 223
Score = 44.3 bits (105), Expect = 5e-05
Identities = 38/170 (22%), Positives = 62/170 (36%), Gaps = 19/170 (11%)
Query: 320 MLEA-QELLQ--LFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYK-N 375
M+ A E L+ +GV +V PGEA+ CASL V+T DSD+ +
Sbjct: 5 MVPAVVEALKYRNWGVITVVVPGEADVYCASL-ARKLGCAVLTGDSDLLVHDLGPDGSVI 63
Query: 376 FFDKKSHVLRYTAPDIR---YYFELTREKL-IQLALLVGSDYTPGLQGVGPVTALEILAK 431
F + IR Y ++L + L+ + P + L K
Sbjct: 64 FLQSIEVTSTASYRGIRATLYRPANIAKRLGLPSLPLLAFELKR-----DPHSTFYKLIK 118
Query: 432 FSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHL-TRKLRNVKLNDDFPNV 480
+ +VE R ++ +L + P TR + ++ P V
Sbjct: 119 RAKVSDK----VVEKSRSYQEFLREYLNPSLASATRAILAFVEEEEAPEV 164
>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 = 43.9 bits (104), Expect = 2e-04
Identities = 33/119 (27%), Positives = 57/119 (47%), Gaps = 9/119 (7%)
Query: 323 AQELLQLFGVPFIVAPG-EAEAQCASL-----ELGNHTQGVITDDSDIWLFGARTVYKNF 376
+ELL G+P + G EA+ A+L + G + +I+ D D+ + V
Sbjct: 89 IKELLDALGIPILEVEGYEADDVIATLAKQAEKEGYEVR-IISGDKDLLQLVSDNVKVLI 147
Query: 377 FDKKSHVLRYTAPDIRYYFELTREKLIQLALLVG--SDYTPGLQGVGPVTALEILAKFS 433
K+ T + + +T ++L+ L LVG SD PG++G+G TA ++L +F
Sbjct: 148 PKGKTSFTEITPEYVVEKYGVTPDQLVDLKALVGDSSDNIPGVKGIGEKTAAKLLQEFG 206
>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 = 39.1 bits (92), Expect = 3e-04
Identities = 14/33 (42%), Positives = 23/33 (69%)
Query: 400 EKLIQLALLVGSDYTPGLQGVGPVTALEILAKF 432
E+ I L +L+G DY ++G+GP TAL+++ K
Sbjct: 1 EQFIDLCILLGCDYCESIKGIGPKTALKLIKKH 33
>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 = 39.1 bits (92), Expect = 3e-04
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 400 EKLIQLALLVGSDYTPGLQGVGPVTALEILAKFS 433
EK + +L G DY P L G+G A +++ +
Sbjct: 1 EKFRHMCILSGCDYLPSLPGIGLKKAYKLVRRHR 34
>gnl|CDD|216458 pfam01367, 5_3_exonuc, 5'-3' exonuclease, C-terminal SAM fold.
Length = 100
Score = 38.7 bits (91), Expect = 7e-04
Identities = 29/92 (31%), Positives = 46/92 (50%), Gaps = 14/92 (15%)
Query: 397 LTREKLIQLALLVG--SDYTPGLQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNWL 454
LT E++I LVG SD PG+ G+G TA ++L ++ ++ I E++ + K L
Sbjct: 1 LTPEQIIDYKALVGDSSDNIPGVPGIGEKTAAKLLKEYGSLEN-----IYENLDKLKGKL 55
Query: 455 AKK---NKPDTHLTRKL----RNVKLNDDFPN 479
+K K D L+RKL +V L +
Sbjct: 56 REKLLNGKEDAFLSRKLATIKTDVPLELTLED 87
>gnl|CDD|235591 PRK05755, PRK05755, DNA polymerase I; Provisional.
Length = 880
Score = 41.2 bits (98), Expect = 0.001
Identities = 45/208 (21%), Positives = 81/208 (38%), Gaps = 49/208 (23%)
Query: 324 QELLQLFGVPFIVAPG-EAE------AQCASLELGNHTQGVITDDSD--------IWLFG 368
+ELL+ G+P + G EA+ A+ A G ++T D D +
Sbjct: 92 RELLRALGIPLLELEGYEADDVIGTLAKQAE-AAGYEVL-IVTGDKDLLQLVDDNV---- 145
Query: 369 ARTVYKNFFDKKSHVLRYTAPDIRYYFELTREKLIQLALLVG--SDYTPGLQGVGPVTAL 426
T+ K+ ++ + +T E++I L+G SD PG+ G+G TA
Sbjct: 146 --TLLDTMGVSKNE--ELDPEEVVEKYGVTPEQIIDYLALMGDSSDNIPGVPGIGEKTAA 201
Query: 427 EILAKFSPSDSPNQNYIVESMRRFKNWLAKK---NKPDTHLTRKLRNVKLNDDFPNVSVI 483
++L ++ + + E++ K +K NK L+RKL + D P
Sbjct: 202 KLLQEYGSLEG-----LYENLDEIKGKKKEKLRENKEQAFLSRKL--ATIKTDVP----- 249
Query: 484 EAYLKPDINTNVQKLAWGTPDLDGLRRF 511
+ +++ L PD + L
Sbjct: 250 -------LEVDLEDLELQPPDREKLIAL 270
>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 = 38.0 bits (88), Expect = 0.004
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 238 FDYGCDVIKSSTL---EKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPFIVA- 293
FD G V++ L +++RD+ E ++ + T + ++ +ELL+L G+P+
Sbjct: 53 FDGGKPVLRLEHLPEYKENRDEAEAEATEEEKRLDEQTFEYLKDCKELLKLMGIPYFDIR 112
Query: 294 PGEAEAQCASL 304
P EAE A L
Sbjct: 113 PSEAEDMAAYL 123
>gnl|CDD|216098 pfam00752, XPG_N, XPG N-terminal domain.
Length = 100
Score = 34.6 bits (80), Expect = 0.021
Identities = 13/30 (43%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 111 GVNGLWKLLE--ASGKPVPVETLENKVLAV 138
G+ GL +L+ A +PV +E LE K LA+
Sbjct: 1 GIKGLLPILKPVALIRPVDIEALEGKTLAI 30
>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 = 33.5 bits (78), Expect = 0.023
Identities = 15/35 (42%), Positives = 23/35 (65%), Gaps = 2/35 (5%)
Query: 400 EKLIQLALLVG--SDYTPGLQGVGPVTALEILAKF 432
E++I LVG SD PG+ G+GP TA ++L ++
Sbjct: 2 EQIIDYLALVGDSSDNIPGVPGIGPKTAAKLLQEY 36
>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682). The
members of this family are all hypothetical eukaryotic
proteins of unknown function. One member is described as
being an adipocyte-specific protein, but no evidence of
this was found.
Length = 322
Score = 32.6 bits (75), Expect = 0.45
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 10/68 (14%)
Query: 154 RRKEDNIIDAEEKDIL---EMIRAEEENEIEFEEEIAGGKEEKTEKIKLTREMLAEQQKI 210
RK D + EE+ IL E R EE E + E++ KEE+ K+ ++ E+Q+
Sbjct: 258 LRKVDKTREEEEEKILKAAEEERQEEAQEKKEEKK----KEEREAKL---AKLSPEEQRK 310
Query: 211 LDSLVKKK 218
L+ +KK
Sbjct: 311 LEEKERKK 318
>gnl|CDD|200379 TIGR04128, exoso_Fjoh_1448, exosortase family protein XrtF.
Members of this protein family are exosortase-related
proteins found always in association with a member of
family TIGR04127, a small, hydrophobic, uncharacterized
protein limited to the Bacteriodetes. Exosortases are
proposed transpeptidases with a cysteine active site
(3.4.22.-), but usually are associated with specific
C-terminal target motifs (PEP-CTERM, PEF-CTERM,
PGF-CTERM, etc).
Length = 174
Score = 31.9 bits (73), Expect = 0.47
Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 11/70 (15%)
Query: 271 ITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGTDKKRRPYVSRKMLE---AQELL 327
IT ++ + + LL FG + P E S++L + YV+R ++E A ++
Sbjct: 43 ITHMVAHQTESLLNAFGYDANIEPHPNE---PSMKLYVNNN---YVAR-VVEGCNAISVI 95
Query: 328 QLFGVPFIVA 337
LF + F++A
Sbjct: 96 ILF-ISFVLA 104
>gnl|CDD|237877 PRK14976, PRK14976, 5'-3' exonuclease; Provisional.
Length = 281
Score = 32.2 bits (74), Expect = 0.52
Identities = 26/93 (27%), Positives = 50/93 (53%), Gaps = 5/93 (5%)
Query: 408 LVG--SDYTPGLQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHLT 465
LVG SD G++G+GP TA+++L K+ ++ +N I + ++ KN L + K L+
Sbjct: 185 LVGDSSDNIKGVKGIGPKTAIKLLNKYGNIENIYEN-IDKIKKKIKNKL-SEAKEKALLS 242
Query: 466 RKLRNVKLNDDFPNVSVIEAYLKPDINTNVQKL 498
+KL +K + + + + LK ++K+
Sbjct: 243 KKLATIKTDVPL-DFQIEDIKLKKLDQPELKKI 274
>gnl|CDD|214854 smart00849, Lactamase_B, Metallo-beta-lactamase superfamily. Apart
from the beta-lactamases a number of other proteins
contain this domain. These proteins include
thiolesterases, members of the glyoxalase II family,
that catalyse the hydrolysis of S-D-lactoyl-glutathione
to form glutathione and D-lactic acid and a competence
protein that is essential for natural transformation in
Neisseria gonorrhoeae and could be a transporter
involved in DNA uptake. Except for the competence
protein these proteins bind two zinc ions per molecule
as cofactor.
Length = 177
Score = 31.8 bits (72), Expect = 0.55
Identities = 29/144 (20%), Positives = 41/144 (28%), Gaps = 25/144 (17%)
Query: 279 AQELLQLFGVPFIVAPGEAEAQCASLELGTDKKRRPYVSRKM--LEAQELLQL--FGVPF 334
ELL+ G P G AE L L + + L+ + L L +
Sbjct: 52 LPELLEAPGAPVYAPEGTAELLKDLLALLGELGAEAEPAPPDRTLKDGDELDLGGGELEV 111
Query: 335 IVAPGEAEAQCASLELGNHTQG--VITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDIR 392
I PG HT G V+ LF ++ R
Sbjct: 112 IHTPG-------------HTPGSIVLYLPEGKILFTGDLLFAG------GDGRTLVDGGD 152
Query: 393 YYFELTREKLIQLALLVGSDYTPG 416
E L++L L+ PG
Sbjct: 153 AAASDALESLLKLLKLLPKLVVPG 176
>gnl|CDD|235239 PRK04172, pheS, phenylalanyl-tRNA synthetase subunit alpha;
Provisional.
Length = 489
Score = 32.5 bits (75), Expect = 0.57
Identities = 16/70 (22%), Positives = 29/70 (41%), Gaps = 11/70 (15%)
Query: 147 RASALLDRRKEDNIIDAEEKDILE-----MIRAEEENEIEFE------EEIAGGKEEKTE 195
+A L ++ + + + K + E ++ +E E E E + G E K E
Sbjct: 137 KALKALAEGDKEELSEEDLKVLKELKKRKLVEEKERTERSVELTDAGLELLKEGIELKEE 196
Query: 196 KIKLTREMLA 205
+LT E+L
Sbjct: 197 ITQLTPELLK 206
>gnl|CDD|146016 pfam03179, V-ATPase_G, Vacuolar (H+)-ATPase G subunit. This family
represents the eukaryotic vacuolar (H+)-ATPase
(V-ATPase) G subunit. V-ATPases generate an acidic
environment in several intracellular compartments.
Correspondingly, they are found as membrane-attached
proteins in several organelles. They are also found in
the plasma membranes of some specialised cells.
V-ATPases consist of peripheral (V1) and membrane
integral (V0) heteromultimeric complexes. The G subunit
is part of the V1 subunit, but is also thought to be
strongly attached to the V0 complex. It may be involved
in the coupling of ATP degradation to H+ translocation.
Length = 105
Score = 30.2 bits (69), Expect = 0.66
Identities = 21/64 (32%), Positives = 31/64 (48%), Gaps = 9/64 (14%)
Query: 165 EKDILEMIRAEEENEI-EFEEEIAGGKEEKTEKI-KLTREMLAEQQKILDSLVKKKAKSD 222
EK+I E RA+ E E EFE E +G + E +KI K T E + E ++ +
Sbjct: 39 EKEI-EEYRAQREAEFKEFEAEHSGSRGELEKKIEKETEEKIDELKRSF------NKNKE 91
Query: 223 DVID 226
V+
Sbjct: 92 AVVQ 95
>gnl|CDD|181896 PRK09482, PRK09482, flap endonuclease-like protein; Provisional.
Length = 256
Score = 31.4 bits (72), Expect = 0.97
Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 385 RY-TAPDIRYYFELTREKLIQLALLVG--SDYTPGLQGVGPVTALEILAKFS 433
R+ AP I F + ++L L G S PG+ G+GP +A E+L +F
Sbjct: 152 RWLDAPFIEQEFGVEPQQLPDYWGLAGISSSKIPGVAGIGPKSAAELLNQFR 203
>gnl|CDD|114751 pfam06047, SynMuv_product, Ras-induced vulval development
antagonist. This family is from synthetic multi-vulval
genes which encode chromatin-associated proteins
involved in transcriptional repression. This protein has
a role in antagonising Ras-induced vulval development.
Length = 105
Score = 30.1 bits (68), Expect = 1.00
Identities = 17/38 (44%), Positives = 22/38 (57%), Gaps = 6/38 (15%)
Query: 155 RKEDNIIDAEEKDILEMIRAEE----ENEI--EFEEEI 186
RKE+ + AEEK L M EE EN+I +F+E I
Sbjct: 65 RKENQVYSAEEKRALAMFNYEERAKRENKILSQFKELI 102
>gnl|CDD|140176 PTZ00147, PTZ00147, plasmepsin-1; Provisional.
Length = 453
Score = 31.0 bits (70), Expect = 1.6
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 8/61 (13%)
Query: 440 QNYIVESMRRFKNWLAKKNKPDTHLTRKLRNVKLNDDFPNVSVIEAYLKPDINTNVQKLA 499
+NYI ES++ F L KK+ +L + NV+L D NV +Y + + N QK
Sbjct: 103 KNYIKESVKFFNKGLTKKS----YLGSEFDNVELK-DLANVM---SYGEAKLGDNGQKFN 154
Query: 500 W 500
+
Sbjct: 155 F 155
>gnl|CDD|130844 TIGR01784, T_den_put_tspse, conserved hypothetical protein
(putative transposase or invertase). Several lines of
evidence suggest that members of this family (loaded as
a fragment mode model to find part-length matches) are
associated with transposition, inversion, or
recombination. Members are found in small numbers of
genomes, but in large copy numbers in many of those
species, including over 30 full length and fragmentary
members in Treponema denticola. The strongest
similarities are usually within rather than between
species. PSI-BLAST shows similarity to proteins
designated as possible transposases, DNA invertases
(resolvases), and recombinases. In the oral pathogenic
spirochete Treponema denticola, full-length members are
often found near transporters or other membrane
proteins. This family includes members of the putative
transposase family pfam04754.
Length = 270
Score = 30.4 bits (69), Expect = 2.0
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 5/60 (8%)
Query: 151 LLDRRKEDNIIDAEEKDILEMIRAEEENEIEFEEEIAGGKEEKTEKIKLTREMLAEQQKI 210
LL KE + + EK + + I AEEE + EE I G E K++ +++L +
Sbjct: 199 LLLSSKELELYEQREKYMTDAISAEEEGK---EEGIEEGILE--AKLETAKKLLKNGLTL 253
>gnl|CDD|183702 PRK12723, PRK12723, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 388
Score = 30.6 bits (69), Expect = 2.4
Identities = 24/99 (24%), Positives = 42/99 (42%), Gaps = 16/99 (16%)
Query: 154 RRKEDNIIDAEEKDILEMIRAEEENEIE--------FEEEIAGGKE-------EKTEKIK 198
+++ N+ D E++ IL+ I+ EE + IE + E+A KE K E I
Sbjct: 60 GQQQINVED-EKRKILQSIKKEENSSIEDVLKEVKSLKNELAHKKEEINHPTILKIEDIL 118
Query: 199 LTREMLAEQQKILDSLVKKKAKSDDVIDVDLTETSTSGF 237
+ K ++ +KK+ D+ D D S +
Sbjct: 119 RENDFSESYIKDINEFIKKEFSLSDLDDYDKVRDSVIIY 157
>gnl|CDD|219124 pfam06658, DUF1168, Protein of unknown function (DUF1168). This
family consists of several hypothetical eukaryotic
proteins of unknown function.
Length = 142
Score = 29.2 bits (66), Expect = 2.5
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 10/74 (13%)
Query: 154 RRKEDNIIDAEEKDILEMIRAEEENEIEFEEEIAGGK---EEKTEKIKLTREMLAEQQKI 210
RR+E ++ + E + E E+E EF+++ K EEKT K + R+ ++QK
Sbjct: 45 RRREYERLELMD----EKWKKETEDE-EFQQKREEKKRKDEEKTAKKRAKRQK--KKQKK 97
Query: 211 LDSLVKKKAKSDDV 224
KK +
Sbjct: 98 KKKKKAKKGNKKEE 111
>gnl|CDD|235971 PRK07219, PRK07219, DNA topoisomerase I; Validated.
Length = 822
Score = 30.0 bits (68), Expect = 4.5
Identities = 15/50 (30%), Positives = 29/50 (58%), Gaps = 6/50 (12%)
Query: 170 EMIRAEEENEIEFEEEIAGGKEEKTEKIKLTREMLAEQQKILDSLVKKKA 219
E + A+ E +++ I GK++K + + +REML ++IL L +K+
Sbjct: 539 EEMTAQLEADMQ---AIEDGKKKKEDVTEESREML---KEILSELKEKRK 582
>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family.
This model family represents the major capsid protein
component of the heads (capsids) of bacteriophage HK97,
phi-105, P27, and related phage. This model represents
one of several analogous families lacking detectable
sequence similarity. The gene encoding this component is
typically located in an operon encoding the small and
large terminase subunits, the portal protein and the
prohead or maturation protease [Mobile and
extrachromosomal element functions, Prophage functions].
Length = 384
Score = 29.6 bits (67), Expect = 4.7
Identities = 15/73 (20%), Positives = 33/73 (45%), Gaps = 6/73 (8%)
Query: 151 LLDRRKEDNIIDAEEKDILEMIRAEEENEIEFEEEIAGGKEEKTEKIKLTREMLAEQQKI 210
L + R+ + K++ ++ E+ E E E+ +E+ +K+ + +++
Sbjct: 1 LKELREA---LAELAKELRKLTEDEKLAEAEEEKAEYDALKEEIDKLD---AEIDRLEEL 54
Query: 211 LDSLVKKKAKSDD 223
LD L K A S +
Sbjct: 55 LDELEAKPAASGE 67
>gnl|CDD|233288 TIGR01139, cysK, cysteine synthase A. This model distinguishes
cysteine synthase A (CysK) from cysteine synthase B
(CysM). CysM differs in having a broader specificity
that also allows the use of thiosulfate to produce
cysteine thiosulfonate [Amino acid biosynthesis, Serine
family].
Length = 298
Score = 29.3 bits (66), Expect = 5.3
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 266 RLASTITEQMSREAQELLQLFGVPFIVAPGE 296
+L T+ E MS E ++LL+ +G ++ PG
Sbjct: 82 KLILTMPETMSIERRKLLKAYGAELVLTPGA 112
>gnl|CDD|220019 pfam08795, DUF1796, Putative papain-like cysteine peptidase
(DUF1796).
Length = 162
Score = 28.4 bits (64), Expect = 5.6
Identities = 10/33 (30%), Positives = 14/33 (42%)
Query: 432 FSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHL 464
P DS + +RRF+ +LA N L
Sbjct: 85 NDPVDSEYYRFKARYVRRFRRFLATINSSKPVL 117
>gnl|CDD|235574 PRK05711, PRK05711, DNA polymerase III subunit epsilon;
Provisional.
Length = 240
Score = 29.1 bits (66), Expect = 5.7
Identities = 24/96 (25%), Positives = 33/96 (34%), Gaps = 27/96 (28%)
Query: 150 ALLDRRKEDN--------IIDAEEKDIL-----EMIRAEEENEIEFEEEIAGGKEEKTEK 196
AL R DN ++DAE IL M + E E + E+T +
Sbjct: 141 ALCKRYGIDNSHRTLHGALLDAE---ILAEVYLAMTGGQTSLGFAMEGETQQQQGEETIQ 197
Query: 197 -----------IKLTREMLAEQQKILDSLVKKKAKS 221
++ T E LA + LD L KK
Sbjct: 198 RIVRQRSRLPVVRATDEELAAHEARLDLLDKKGGSC 233
>gnl|CDD|234701 PRK00252, alaS, alanyl-tRNA synthetase; Reviewed.
Length = 865
Score = 29.3 bits (67), Expect = 5.7
Identities = 15/63 (23%), Positives = 25/63 (39%), Gaps = 24/63 (38%)
Query: 168 ILEMIRAEEEN---------EIEFEEEIAGGKEEKT---EK-----------IKLTREML 204
I ++++AEEE ++ EE +A K K E + LT E+
Sbjct: 342 IEKVLKAEEERFLKTLERGLKL-LEEALAKLKAGKVLSGEDAFKLYDTYGFPLDLTAEIA 400
Query: 205 AEQ 207
E+
Sbjct: 401 RER 403
>gnl|CDD|236295 PRK08570, rpl19e, 50S ribosomal protein L19e; Reviewed.
Length = 150
Score = 28.3 bits (64), Expect = 6.3
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 444 VESMRRFKNWLAKKNKPDTHLTRKL-RNVKLNDDFPNVSVIEAYLK 488
+ ++RR+ L + K D RKL R K +F +VS ++ Y++
Sbjct: 99 IRALRRYLRELRDEGKIDRKTYRKLYRKAKGG-EFRSVSHLKTYIE 143
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 29.4 bits (67), Expect = 6.6
Identities = 17/68 (25%), Positives = 32/68 (47%), Gaps = 11/68 (16%)
Query: 159 NIIDAEEKDILEMIRAEEENEIEFEEEIAGGKEEKTEKIKLTREMLAEQQKILDSLVKKK 218
+I +++ + E+I + EE E E E +K + +L E +K+ + L +KK
Sbjct: 509 KLIGEDKEKLNELIASLEELERELE-----------QKAEEAEALLKEAEKLKEELEEKK 557
Query: 219 AKSDDVID 226
K + D
Sbjct: 558 EKLQEEED 565
>gnl|CDD|224515 COG1599, RFA1, Single-stranded DNA-binding replication protein A
(RPA), large (70 kD) subunit and related ssDNA-binding
proteins [DNA replication, recombination, and repair].
Length = 407
Score = 29.0 bits (65), Expect = 7.2
Identities = 17/98 (17%), Positives = 35/98 (35%), Gaps = 9/98 (9%)
Query: 140 ILYFTQGRASALLDRRKEDNIIDAEEKDILEMIRAEEENEIEFEEEIAGGKEEKTEKIKL 199
L G+ L + +I+ E + L+ I E+ + I + L
Sbjct: 304 GLDDLTGKIRVTLWGDATEVLINEESVEALKGINVEDASGIALSALDTEAVALEIWYDIL 363
Query: 200 TREM-----LAEQQKILDSLVKKKAKSDDVIDVDLTET 232
+ + E + ++++LV +S DVD+
Sbjct: 364 GKYLRVTGDAREDRYLIENLV----ESSTWDDVDVRAE 397
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 29.3 bits (65), Expect = 7.2
Identities = 18/115 (15%), Positives = 50/115 (43%), Gaps = 1/115 (0%)
Query: 153 DRRKEDNII-DAEEKDILEMIRAEEENEIEFEEEIAGGKEEKTEKIKLTREMLAEQQKIL 211
+++ + + +AEE E ++ +E E + EE+ +EE K + ++ E +K
Sbjct: 1687 EKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKA 1746
Query: 212 DSLVKKKAKSDDVIDVDLTETSTSGFFDYGCDVIKSSTLEKDRDQLLLERGKQTR 266
+ K + + + + E + + + L+++ ++ +E K+ +
Sbjct: 1747 EEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEKRRMEVDKKIK 1801
>gnl|CDD|215969 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A.
Length = 427
Score = 29.0 bits (66), Expect = 7.3
Identities = 19/64 (29%), Positives = 27/64 (42%), Gaps = 2/64 (3%)
Query: 151 LLDRRKEDNIIDAEEK-DILEMIRAEEENEIEFEEEIAGGKEEKTEKIKLTREMLAEQ-Q 208
+ RRKE + EE+ ILE + E I G + K K +L E+ Q
Sbjct: 320 VYKRRKEYLLEKLEERLHILEGLLKALNKIDFVIEVIRGSIDLKKAKKELIEELSEIQAD 379
Query: 209 KILD 212
+LD
Sbjct: 380 YLLD 383
>gnl|CDD|223403 COG0326, HtpG, Molecular chaperone, HSP90 family [Posttranslational
modification, protein turnover, chaperones].
Length = 623
Score = 29.2 bits (66), Expect = 7.4
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 4/54 (7%)
Query: 164 EEKDILEMIRAEEENEIEFEEEIAGGKEEKTEKIKLTREMLAEQQKILDSLVKK 217
E K + + + + E+ EE+ A +EEK E + +L ++IL VK
Sbjct: 472 EGKPFKSITKGDLDLELLEEEDEADSEEEKKE----FKPLLERVKEILGDKVKD 521
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 29.3 bits (66), Expect = 7.4
Identities = 34/133 (25%), Positives = 55/133 (41%), Gaps = 28/133 (21%)
Query: 163 AEEKDILEMIRAE-EENEIEFEEEIAGGKEEKTEKIKLTREM---LAEQQKILDSLVKKK 218
AE K+ LE +RAE EE + EF E K+ + + KL RE+ E ++ + L +
Sbjct: 360 AELKEELEDLRAELEEVDKEFAETRDELKDYREKLEKLKREINELKRELDRLQEELQRLS 419
Query: 219 AKSDD------VIDVDLTETSTSGFFDYGCDVIKSSTLEKDRDQLLLERGKQTRLASTIT 272
+ D I+ + E LE++++ LE KQ +
Sbjct: 420 EELADLNAAIAGIEAKINE------------------LEEEKEDKALEIKKQEWKLEQLA 461
Query: 273 EQMSREAQELLQL 285
+S+ QEL L
Sbjct: 462 ADLSKYEQELYDL 474
>gnl|CDD|216074 pfam00710, Asparaginase, Asparaginase.
Length = 318
Score = 28.7 bits (65), Expect = 8.1
Identities = 32/157 (20%), Positives = 45/157 (28%), Gaps = 50/157 (31%)
Query: 19 YVLPSVALPIQRVGAQRKTLKSKAASNADKVRSDLLKNLLEQQLLNDVLGKNEMALPPPS 78
+L ++ P+ GAQR AD SD +NLL + + +A P +
Sbjct: 96 LMLENLDKPVVLTGAQR---------PADAPSSDGPENLL-----DALR----VAASPDA 137
Query: 79 VSREV----------------------DMFELPPAPAQTVQDEEEDTLENIYIMGVNGLW 116
R V D F P L + V
Sbjct: 138 RGRGVLVVFNDKLHRGRRVTKTHTSSLDAFASPNFGP----------LGEVGEGRVKFFR 187
Query: 117 KLLEASGKPVPVETLENKVLAVGILYFTQGRASALLD 153
L P+ + V ILY G + LLD
Sbjct: 188 DPLRRRRGAFPLRLPDKLDPRVAILYLYPGMDAELLD 224
>gnl|CDD|132767 cd07306, Porin3_VDAC, Voltage-dependent anion channel of the outer
mitochondrial membrane. The voltage-dependent anion
channel (VDAC) regulates the flux of mostly anionic
metabolites through the outer mitochondrial membrane,
which is highly permeable to small molecules. VDAC is
the most abundant protein in the outer membrane, and
membrane potentials can toggle VDAC between open or
high-conducting and closed or low-conducting forms. VDAC
binds to and is regulated in part by hexokinase, an
interaction that renders mitochondria less susceptible
to pro-apoptotic signals, most likely by intefering with
VDAC's capability to respond to Bcl-2 family proteins.
While VDAC appears to play a key role in mitochondrially
induced cell death, a proposed involvement in forming
the mitochondrial permeability transition pore, which is
characteristic for damaged mitochondria and apoptosis,
has been challenged by more recent studies.
Length = 276
Score = 28.3 bits (64), Expect = 8.7
Identities = 36/165 (21%), Positives = 54/165 (32%), Gaps = 45/165 (27%)
Query: 365 WLFGARTVY---KNFFDKKSHVLRYTAPDIRYYFELTREKLIQLALLVGSDYTPGLQGVG 421
+L GA VY K+ F K + L YT D +L K L GS + V
Sbjct: 143 FLLGAEVVYDTAKSKFTKYNFALGYTNGDFELSLKLNNGK-----TLRGSYF----HKVS 193
Query: 422 PVTALEILAKFSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHLTRKLRNVKLNDDFPNVS 481
P L + AK + N+ + + D K K+N+D +
Sbjct: 194 P--RLAVGAKVTWYSGTNETTFA---------VGGQYALDPDALVKA---KVNNDG-QLG 238
Query: 482 -VIEAYLKPDI------NTNVQKLAWGTPDLDGLRRFAANKFGWS 519
+ L+P + + + L G KFG S
Sbjct: 239 LSYQHKLRPGVTLTLSAGFDAKNLNQGGH-----------KFGLS 272
>gnl|CDD|219925 pfam08598, Sds3, Sds3-like. Repression of gene transcription is
mediated by histone deacetylases containing
repressor-co-repressor complexes, which are recruited to
promoters of target genes via interactions with
sequence-specific transcription factors. The
co-repressor complex contains a core of at least seven
proteins. This family represents the conserved region
found in Sds3, Dep1 and BRMS1-homologue p40 proteins.
Length = 184
Score = 28.0 bits (63), Expect = 8.9
Identities = 20/81 (24%), Positives = 34/81 (41%), Gaps = 14/81 (17%)
Query: 145 QGRASALLDRRKEDNIIDAEEKDILEMIRAEEEN-----EIEFEEEIAGGKEEKTEKIKL 199
QG L+ K+ ++ D L++ E E E+E E K+E ++ +L
Sbjct: 38 QGTHPEYLEPLKD---LEERRDDRLKVAELRREYKLECIEREYEAERQAAKQEFEKEKRL 94
Query: 200 TREMLAEQQKILDSLVKKKAK 220
RE L L+ L +K +
Sbjct: 95 LRERL------LEELEEKIYR 109
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
0.315 0.133 0.376
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,865,799
Number of extensions: 2806380
Number of successful extensions: 3108
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3038
Number of HSP's successfully gapped: 200
Length of query: 538
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 436
Effective length of database: 6,413,494
Effective search space: 2796283384
Effective search space used: 2796283384
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 61 (27.3 bits)