RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12447
(551 letters)
>gnl|CDD|240301 PTZ00166, PTZ00166, DNA polymerase delta catalytic subunit;
Provisional.
Length = 1054
Score = 437 bits (1127), Expect = e-142
Identities = 186/545 (34%), Positives = 268/545 (49%), Gaps = 146/545 (26%)
Query: 12 RAPPPELNPKEDKIVFQQISIEHY------TGEPIPGMPGSQLKPVPIVRMFGVTMEGNS 65
R P P ++ ++D +VF Q+ ++ G P + G + VPI+R++GVT EG+S
Sbjct: 30 RRPLPPISLQKD-LVFFQLDADYTEKDDKSQGNPHNTVSGVRHVEVPIIRLYGVTKEGHS 88
Query: 66 VCCHVHGFSPYLYVSAPKEFNSTHCRAFKEALNRAIIADMRGNKDEIQEAVLMVEIVQKQ 125
V +VH F PY Y+ AP F + K LN + + + Q VL +EIV+K+
Sbjct: 89 VLVNVHNFFPYFYIEAPPNFLPEDSQKLKRELNAQL--SEQSQFKKYQNTVLDIEIVKKE 146
Query: 126 TVFGFWGEELENFLKITESVFPTFPT-------------------HTYKAFESNIDFDIR 166
++ + G ++FLKIT + P ++ +ESN+ F +R
Sbjct: 147 SLMYYKGNGEKDFLKITVQLPKMVPRLRSLIESGVVVCGGGWDGIRLFQTYESNVPFVLR 206
Query: 167 FMVDNDIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEEIDV 226
F++DN+I G +W+ +P GK+++R K S CQ+E+D S +D++ PE
Sbjct: 207 FLIDNNITGGSWLTLPKGKYKIRPPKKK-------TSTCQIEVDCSYEDLIPLPPE---- 255
Query: 227 STDDIVSHAPEGEWSKVAPLRILSFDIECAGRKGI-FPDPNHDPIIQIANMCISQGASEN 285
GE+ +APLRILSFDIEC KG+ FP+ +DP+IQI+++ +QG E
Sbjct: 256 -----------GEYLTIAPLRILSFDIECIKLKGLGFPEAENDPVIQISSVVTNQGDEEE 304
Query: 286 IFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCA 345
K +FTL CA I G+ V+ F
Sbjct: 305 PLTKFIFTLKECASIAGANVLS-------------F------------------------ 327
Query: 346 PIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFL 405
+TE ELL W+ F+ +DPD TGYNI NFD PYL+NRAK
Sbjct: 328 ----------ETEKELLLAWAEFVIAVDPDFLTGYNIINFDLPYLLNRAK---------- 367
Query: 406 GRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKD 465
L + +F +LGR+K RSVIKD
Sbjct: 368 --------------------------------------ALKLNDFKYLGRIKSTRSVIKD 389
Query: 466 SFIQSKQMGKRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSI 525
S SKQMG RE+K IN EGR+ FD++ ++ R+YKL+SY+LN VS+ FL+EQKEDV +SI
Sbjct: 390 SKFSSKQMGTRESKEINIEGRIQFDVMDLIRRDYKLKSYSLNYVSFEFLKEQKEDVHYSI 449
Query: 526 ISDLQ 530
ISDLQ
Sbjct: 450 ISDLQ 454
>gnl|CDD|99820 cd05777, DNA_polB_delta_exo, DEDDy 3'-5' exonuclease domain of
eukaryotic DNA polymerase delta, a family-B DNA
polymerase. The 3'-5' exonuclease domain of eukaryotic
DNA polymerase delta. DNA polymerase delta is a family-B
DNA polymerase with a catalytic subunit that contains a
DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one
of the three DNA-dependent type B DNA polymerases (alpha
and epsilon are the other two) that have been identified
as essential for nuclear DNA replication in eukaryotes.
DNA polymerase delta is the enzyme responsible for both
elongation and maturation of Okazaki fragments on the
lagging strand. It is also implicated in mismatch repair
(MMR) and base excision repair (BER). The catalytic
subunit displays both polymerase and 3'-5' exonuclease
activities. The exonuclease domain contains three
sequence motifs termed ExoI, ExoII and ExoIII, with a
specific YX(3)D pattern at ExoIII. These motifs are
clustered around the active site and contain four
conserved acidic residues necessary for metal binding
and catalysis. The exonuclease domain of family B
polymerase also contains a beta hairpin structure that
plays an important role in active site switching in the
event of nucleotide misincorporation.
Length = 230
Score = 329 bits (845), Expect = e-111
Identities = 132/291 (45%), Positives = 157/291 (53%), Gaps = 96/291 (32%)
Query: 240 WSKVAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAP 299
WSK+APLRILSFDIECAGRKG+FP+P DP+IQIAN+ QG E
Sbjct: 1 WSKIAPLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEP-------------- 46
Query: 300 IVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTET 359
F++N+FTL TCAPIVG+QV +TE
Sbjct: 47 ----------------------------------FIRNIFTLKTCAPIVGAQVFSFETEE 72
Query: 360 ELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKDSF 419
ELL W F++E+DPDI TGYNI NFD PYL+ RAK L + F FLGR+K+I+S IKD+
Sbjct: 73 ELLLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDT- 131
Query: 420 IQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENK 479
TF SKQMG RE K
Sbjct: 132 -------------------------------TF----------------SSKQMGTRETK 144
Query: 480 TINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSIISDLQ 530
IN EGR+ FDLL V+ R+YKLRSY+LNSVS HFL EQKEDV +SII+DLQ
Sbjct: 145 EINIEGRIQFDLLQVIQRDYKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQ 195
>gnl|CDD|217371 pfam03104, DNA_pol_B_exo1, DNA polymerase family B, exonuclease
domain. This domain has 3' to 5' exonuclease activity
and adopts a ribonuclease H type fold.
Length = 254
Score = 182 bits (464), Expect = 7e-54
Identities = 98/352 (27%), Positives = 133/352 (37%), Gaps = 123/352 (34%)
Query: 158 ESNIDFDIRFMVDNDIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIV 217
E ++D+ RF++DNDIVG W ++ GK + + VS C+ E D DD+
Sbjct: 26 EYDVDYLERFLIDNDIVGFGWYKVKGGKPNCQVR----------VSNCKPEFDCPVDDLS 75
Query: 218 SHAPEEIDVSTDDIVSHAPEGEWSKVAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMC 277
EEI PLR+LSFDIEC KG FP+ DPIIQI+ M
Sbjct: 76 PLPEEEIW------------------PPLRVLSFDIECTSLKGKFPENEKDPIIQISCML 117
Query: 278 ISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKN 337
+G + I +FTL +CA I
Sbjct: 118 YREGEPDPIE-DKLFTLKSCALIEI----------------------------------- 141
Query: 338 VFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
G +V +E ELL ++ FIR+ DPDI TGYN NFD+PY++NRAK L
Sbjct: 142 -----------GGEVYIFPSEKELLRRFFEFIRQYDPDIITGYNGDNFDWPYILNRAKIL 190
Query: 398 GVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVK 457
G+K G +K G + +
Sbjct: 191 GLKMTPEYGVRSSKIGRLKRGGFPRVFSGNGSREKVK----------------------- 227
Query: 458 DIRSVIKDSFIQSKQMGKRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSV 509
I+ GR+ DL V+ R+ KL SY LN+V
Sbjct: 228 -----------------------IS--GRIHLDLYRVIKRDSKLGSYKLNAV 254
Score = 42.0 bits (99), Expect = 4e-04
Identities = 13/28 (46%), Positives = 18/28 (64%)
Query: 59 VTMEGNSVCCHVHGFSPYLYVSAPKEFN 86
T +G SVC +V GF PY Y P+E++
Sbjct: 1 KTDDGVSVCVNVFGFKPYFYCLPPEEYD 28
>gnl|CDD|214691 smart00486, POLBc, DNA polymerase type-B family. DNA polymerase
alpha, delta, epsilon and zeta chain (eukaryota), DNA
polymerases in archaea, DNA polymerase II in e. coli,
mitochondrial DNA polymerases and and virus DNA
polymerases.
Length = 474
Score = 128 bits (323), Expect = 5e-32
Identities = 70/287 (24%), Positives = 105/287 (36%), Gaps = 98/287 (34%)
Query: 245 PLRILSFDIECAGRKGIFPDPN--HDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVG 302
PL+ILSFDIE G FPD D IIQI+ +
Sbjct: 2 PLKILSFDIETYTDGGNFPDAEIFDDEIIQISLVINDGD--------------------- 40
Query: 303 SQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELL 362
+ + +FTL TC I G +V E ELL
Sbjct: 41 ---------------------------KKGANRRILFTLGTCKEIDGIEVYEFNNEKELL 73
Query: 363 DKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKDSFIQS 422
+ FI++ DPDI G+NI NFD PY+I+R + L + + +GR+K
Sbjct: 74 LAFFEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIDPLSKIGRLKIG----------- 122
Query: 423 KQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTIN 482
+R K SK G + +
Sbjct: 123 ------------------------------------LRIPNKKPLFGSKSFGLS-DIKVY 145
Query: 483 FEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSIISDL 529
+GR+ DL + + KL SY L++V+ + L ++K+D+ + I +L
Sbjct: 146 IKGRLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPEL 192
>gnl|CDD|176646 cd05160, DEDDy_DNA_polB_exo, DEDDy 3'-5' exonuclease domain of
family-B DNA polymerases. The 3'-5' exonuclease domain
of family-B DNA polymerases. This domain has a
fundamental role in reducing polymerase errors and is
involved in proofreading activity. Family-B DNA
polymerases contain an N-terminal DEDDy DnaQ-like
exonuclease domain in the same polypeptide chain as the
polymerase domain, similar to family-A DNA polymerases.
This domain contains three sequence motifs termed ExoI,
ExoII and ExoIII, with a specific YX(3)D 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 exonuclease domain of family B polymerase
also contains a beta hairpin structure that plays an
important role in active site switching in the event of
nucleotide misincorporation. Members include Escherichia
coli DNA polymerase II, some eubacterial phage DNA
polymerases, nuclear replicative DNA polymerases (alpha,
delta, epsilon and zeta), and eukaryotic viral and
plasmid-borne enzymes. Nuclear DNA polymerases alpha and
zeta lack the four conserved acidic metal-binding
residues. Family-B DNA polymerases are predominantly
involved in DNA replication and DNA repair.
Length = 199
Score = 117 bits (296), Expect = 1e-30
Identities = 73/283 (25%), Positives = 94/283 (33%), Gaps = 110/283 (38%)
Query: 248 ILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVIC 307
+LSFDIE G P+P+ DPII I S + +F+ T+
Sbjct: 1 VLSFDIETTPPVG-GPEPDRDPIICIT-YADSFDGVKVVFLLKTSTVGDDIEF------- 51
Query: 308 CKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSA 367
I G +V E ELL ++
Sbjct: 52 ---------------------------------------IDGIEVEYFADEKELLKRFFD 72
Query: 368 FIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGK 427
IRE DPDI TGYNI +FD PYL+ RA+ LG
Sbjct: 73 IIREYDPDILTGYNIDDFDLPYLLKRAEALG----------------------------- 103
Query: 428 RENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMG-KRENKTINFEGR 486
I RR S + I +GR
Sbjct: 104 -----IKLTDGIYRR---------------------------SGGEKSSGSTERIAVKGR 131
Query: 487 VCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSIISDL 529
V FDLL R++KL+SYTL++V+ L E KE V II D
Sbjct: 132 VVFDLLAAYKRDFKLKSYTLDAVAEELLGEGKEKVDGEIIEDA 174
>gnl|CDD|223494 COG0417, PolB, DNA polymerase elongation subunit (family B) [DNA
replication, recombination, and repair].
Length = 792
Score = 126 bits (318), Expect = 2e-30
Identities = 90/386 (23%), Positives = 121/386 (31%), Gaps = 128/386 (33%)
Query: 51 VPIVRMFGVTMEGNSVCCHVHGFSPYLYVSAPKEFNSTHCRAFKEALNRAIIADMRGNKD 110
P+VR+FG T G SV V F PY YV+ E I+
Sbjct: 8 FPLVRIFGDTDSGKSVVKLVATFRPYFYVTLDNSR--------PEDYVLKILNRRL---- 55
Query: 111 EIQEAVLMVEIVQKQTVFGFWGEELENFLKI----------TESVFPTFPTHTYKAFESN 160
+ + + E+ + G E+E LKI FE++
Sbjct: 56 --DDVLELEEVENVPDPYL--GREVE-VLKIYARDPQAVRKLREKVKRELEGVVDIFEAD 110
Query: 161 IDFDIRFMVDNDIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHA 220
I F +R+++D I W+ V +DI
Sbjct: 111 IPFAMRYLIDKGIRPMVWV------------------------------SVDVEDI---- 136
Query: 221 PEEIDVSTDDIVSHAPEGEWSKVAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQ 280
I S E PLR+L+FDIE G FPD DPII I+ I
Sbjct: 137 --------GSIHSLFLEHREDVRPPLRVLAFDIETLSEPGKFPDGEKDPIIMIS-YAIEA 187
Query: 281 GASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFT 340
+ G
Sbjct: 188 EGGLIE-------VFIYTSGEG-------------------------------------- 202
Query: 341 LNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVK 400
V +E ELL+++ IRE DPD+ GYN NFD+PYL RA+ LG+
Sbjct: 203 ---------FSVEVVISEAELLERFVELIREYDPDVIVGYNGDNFDWPYLAERAERLGIP 253
Query: 401 NFTFLGRVKDIRSVIKDSFIQSKQMG 426
LGR V K F S Q+G
Sbjct: 254 --LRLGRDGSELRVRKSGF--SSQVG 275
Score = 84.0 bits (208), Expect = 5e-17
Identities = 47/192 (24%), Positives = 67/192 (34%), Gaps = 65/192 (33%)
Query: 341 LNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVK 400
+ G V +E ELL+++ IRE DPD+ GYN NFD+PYL RA+ LG+
Sbjct: 194 VFIYTSGEGFSVEVVISEAELLERFVELIREYDPDVIVGYNGDNFDWPYLAERAERLGIP 253
Query: 401 NFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIR 460
LGR
Sbjct: 254 --------------------------------------------------LRLGRDGSEL 263
Query: 461 SVIKDSFIQSKQMGKRENKTINFEGRVCFDLL-FVLLREYKLRSYTLNSVSYHFLQEQK- 518
V K F + GR+ DL + R L+SY+L +VS L E K
Sbjct: 264 RVRKSGFS-------------SQVGRLHIDLYPALRRRPLNLKSYSLEAVSEALLGEGKR 310
Query: 519 EDVQHSIISDLQ 530
ED+ + + ++
Sbjct: 311 EDIPYDSMEEIW 322
>gnl|CDD|99821 cd05778, DNA_polB_zeta_exo, inactive DEDDy 3'-5' exonuclease domain
of eukaryotic DNA polymerase zeta, a family-B DNA
polymerase. The 3'-5' exonuclease domain of eukaryotic
DNA polymerase zeta. DNA polymerase zeta is a family-B
DNA polymerase which is distantly related to DNA
polymerase delta. It plays a major role in translesion
replication and the production of either spontaneous or
induced mutations. In addition, DNA polymerase zeta also
appears to be involved in somatic hypermutability in B
lymphocytes, an important element for the production of
high affinity antibodies in response to an antigen. The
catalytic subunit contains both polymerase and 3'-5'
exonuclease domains, but only exhibits polymerase
activity. The DnaQ-like 3'-5' exonuclease domain
contains three sequence motifs termed ExoI, ExoII and
ExoIII, without the four conserved acidic residues that
are crucial for metal binding and catalysis.
Length = 231
Score = 74.6 bits (184), Expect = 3e-15
Identities = 59/285 (20%), Positives = 91/285 (31%), Gaps = 86/285 (30%)
Query: 246 LRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQV 305
L ILS ++ R + PDP DPI I CI V A VG +
Sbjct: 4 LTILSLEVHVNTRGDLLPDPEFDPISAIF-YCIDDD---------VSPFILDANKVGV-I 52
Query: 306 ICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKW 365
I + ++ + I V V +E EL ++
Sbjct: 53 IVDELKSN-------ASNGRIRSGLSGIPV-EVVE----------------SELELFEEL 88
Query: 366 SAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTF-LGRVKDIRSVIKDSFIQSKQ 424
+R DPDI +GY IQ + YLI RA LG+ + + RV S
Sbjct: 89 IDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLLDEISRVP------------SDS 136
Query: 425 MGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFE 484
GK ++ + G I
Sbjct: 137 NGKFGDRDDEW--------------------------------------GYTHTSGIKIV 158
Query: 485 GRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSIISDL 529
GR ++ ++ E L +YTL +V YH L ++ + +++
Sbjct: 159 GRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEW 203
>gnl|CDD|99823 cd05780, DNA_polB_Kod1_like_exo, DEDDy 3'-5' exonuclease domain of
Pyrococcus kodakaraensis Kod1 and similar archaeal
family-B DNA polymerases. The 3'-5' exonuclease domain
of archaeal family-B DNA polymerases with similarity to
Pyrococcus kodakaraensis Kod1, including polymerases
from Desulfurococcus (D. Tok Pol) and Thermococcus
gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are
thermostable enzymes that exhibit both polymerase and
3'-5' exonuclease activities. They are family-B DNA
polymerases. Their amino termini harbor a DEDDy-type
DnaQ-like 3'-5' exonuclease domain that contains three
sequence motifs termed ExoI, ExoII and ExoIII, with a
specific YX(3)D pattern at ExoIII. These motifs are
clustered around the active site and are involved in
metal binding and catalysis. The exonuclease domain of
family B polymerases contains a beta hairpin structure
that plays an important role in active site switching in
the event of nucleotide misincorporation. Members of
this subfamily show similarity to eukaryotic DNA
polymerases involved in DNA replication. Some archaea
possess multiple family-B DNA polymerases. Phylogenetic
analyses of eubacterial, archaeal, and eukaryotic
family-B DNA polymerases support independent gene
duplications during the evolution of archaeal and
eukaryotic family-B DNA polymerases.
Length = 195
Score = 64.7 bits (158), Expect = 5e-12
Identities = 70/284 (24%), Positives = 96/284 (33%), Gaps = 119/284 (41%)
Query: 246 LRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQV 305
L+ILSFDIE +G P+P DPII I+ A E G++V
Sbjct: 3 LKILSFDIEVLNHEGE-PNPEKDPIIMISF------ADEG----------------GNKV 39
Query: 306 ICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKW 365
I K + FV+ V KTE E++ ++
Sbjct: 40 ITWKKF-------------------DLPFVEVV-----------------KTEKEMIKRF 63
Query: 366 SAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKDSFIQSKQM 425
++E DPD+ YN NFDFPYL RA
Sbjct: 64 IEIVKEKDPDVIYTYNGDNFDFPYLKKRA------------------------------- 92
Query: 426 GKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEG 485
E LG++ LGR S I+ ++ G N + +G
Sbjct: 93 -----------------EKLGIE-LD-LGR--------DGSEIKIQRGGFN-NAS-EIKG 123
Query: 486 RVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSIISDL 529
R+ DL V R L YTL V +KEDV I++
Sbjct: 124 RIHVDLYPVARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEA 167
>gnl|CDD|235595 PRK05762, PRK05762, DNA polymerase II; Reviewed.
Length = 786
Score = 66.4 bits (163), Expect = 2e-11
Identities = 20/53 (37%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 355 CKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGR 407
E LL+K++A+ E DPD+ G+N+ FD L RA+ G+ LGR
Sbjct: 200 VADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIP-LR-LGR 250
Score = 44.1 bits (105), Expect = 2e-04
Identities = 30/204 (14%), Positives = 59/204 (28%), Gaps = 59/204 (28%)
Query: 52 PIVRMFGVTMEGNSVCCHVHGFSPYLYVSAPKEFNSTHCRAFKEALNRAIIADMRGNKDE 111
P V ++ T EG V F PY + E + L I +
Sbjct: 20 PEVELWLATDEGPRVVLLDPQFRPYFIPAEQDE-------RAESLLAGEIGVRLS----- 67
Query: 112 IQEAVLMVEIVQKQTVFGFWGEELENFLKITESVFPTFPTHTYKAFESNIDFDIRFMVDN 171
+ + + ++ V G + + +E++I F R++++
Sbjct: 68 ---PLALKDFHRRP-VLG----LYCRQHRQLTRLPKRLREGGVDVYEADIRFPERYLMER 119
Query: 172 DIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEEIDVSTDDI 231
I C W G+ + + +L+
Sbjct: 120 FITPCVWFS---GEVEQYTTD-------GVLRNARLK----------------------- 146
Query: 232 VSHAPEGEWSKVAPLRILSFDIEC 255
P ++ PL+++S DIE
Sbjct: 147 ----PAPDYRP--PLKVVSLDIET 164
>gnl|CDD|99819 cd05776, DNA_polB_alpha_exo, inactive DEDDy 3'-5' exonuclease
domain of eukaryotic DNA polymerase alpha, a family-B
DNA polymerase. The 3'-5' exonuclease domain of
eukaryotic DNA polymerase alpha. DNA polymerase alpha
is a family-B DNA polymerase with a catalytic subunit
that contains a DnaQ-like 3'-5' exonuclease domain. It
is one of the three DNA-dependent type B DNA polymerases
(delta and epsilon are the other two) that have been
identified as essential for nuclear DNA replication in
eukaryotes. DNA polymerase alpha is almost exclusively
required for the initiation of DNA replication and the
priming of Okazaki fragments during elongation. It
associates with DNA primase and is the only enzyme able
to start DNA synthesis de novo. The catalytic subunit
contains both polymerase and 3'-5' exonuclease domains,
but only exhibits polymerase activity. The 3'-5'
exonuclease domain contains three sequence motifs termed
ExoI, ExoII and ExoIII, without the four conserved
acidic residues that are crucial for metal binding and
catalysis. This explains why in most organisms, that no
specific repair role, other than check point control,
has been assigned to this enzyme. The exonuclease domain
may have a structural role.
Length = 234
Score = 61.1 bits (149), Expect = 1e-10
Identities = 22/78 (28%), Positives = 45/78 (57%), Gaps = 2/78 (2%)
Query: 350 SQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVK 409
++V + E LL+ + A ++++DPD+ G++++ FD L++R + L V +++ +GR+K
Sbjct: 74 TKVRIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLK 133
Query: 410 DIRSVIKDSFIQSKQMGK 427
RSV K +
Sbjct: 134 --RSVWPKKKGGGKFGER 149
>gnl|CDD|99827 cd05784, DNA_polB_II_exo, DEDDy 3'-5' exonuclease domain of
Escherichia coli DNA polymerase II and similar bacterial
family-B DNA polymerases. The 3'-5' exonuclease domain
of Escherichia coli DNA polymerase II (Pol II) and
similar bacterial proteins. Pol II is a family-B DNA
polymerase. Family-B DNA polymerases contain an
N-terminal DEDDy DnaQ-like exonuclease domain in the
same polypeptide chain as the polymerase domain, similar
to family-A DNA polymerases. This exonuclease domain
contains three sequence motifs termed ExoI, ExoII and
ExoIII, with a specific YX(3)D pattern at ExoIII. These
motifs are clustered around the active site and are
involved in metal binding and catalysis. The exonuclease
domain has a fundamental role in the proofreading
activity of polII. It contains a beta hairpin structure
that plays an important role in active site switching in
the event of a nucleotide misincorporation. Pol II is
involved in a variety of cellular activities, such as
the repair of DNA damaged by UV irradiation or
oxidation. It plays a pivotal role in
replication-restart, a process that bypasses DNA damage
in an error-free manner. Pol II is also involved in
lagging strand synthesis.
Length = 193
Score = 59.5 bits (145), Expect = 2e-10
Identities = 21/70 (30%), Positives = 29/70 (41%), Gaps = 2/70 (2%)
Query: 338 VFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
V + + E LL A+ + DPDI G+N+ NFD L RA+
Sbjct: 31 VLMVGDPEDDAPDNIEWFADEKSLLLALIAWFAQYDPDIIIGWNVINFDLRLLQRRAEAH 90
Query: 398 GVKNFTFLGR 407
G+ LGR
Sbjct: 91 GLP-LR-LGR 98
>gnl|CDD|99824 cd05781, DNA_polB_B3_exo, DEDDy 3'-5' exonuclease domain of
Sulfurisphaera ohwakuensis DNA polymerase B3 and similar
archaeal family-B DNA polymerases. The 3'-5'
exonuclease domain of archaeal proteins with similarity
to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a
family-B DNA polymerase. Family-B DNA polymerases
contain an N-terminal DEDDy DnaQ-like exonuclease domain
in the same polypeptide chain as the polymerase domain,
similar to family-A DNA polymerases. B3 exhibits both
polymerase and 3'-5' exonuclease activities. This
exonuclease domain contains three sequence motifs termed
ExoI, ExoII and ExoIII, with a specific YX(3)D pattern
at ExoIII. These motifs are clustered around the active
site and are involved in metal binding and catalysis.
The exonuclease domain of family B polymerases also
contains a beta hairpin structure that plays an
important role in active site switching in the event of
nucleotide misincorporation. Archaeal proteins that are
involved in DNA replication are similar to those from
eukaryotes. Some archaea possess multiple family-B DNA
polymerases. B3 is mainly found in crenarchaea.
Phylogenetic analyses of eubacterial, archaeal, and
eukaryotic family B-DNA polymerases support independent
gene duplications during the evolution of archaeal and
eukaryotic family-B DNA polymerases.
Length = 188
Score = 55.4 bits (134), Expect = 6e-09
Identities = 19/33 (57%), Positives = 25/33 (75%)
Query: 368 FIRELDPDIFTGYNIQNFDFPYLINRAKHLGVK 400
+++E DPDI GYN FD+PYL+ RA+ LGVK
Sbjct: 58 YVKEYDPDIIVGYNSNAFDWPYLVERARVLGVK 90
Score = 38.5 bits (90), Expect = 0.004
Identities = 14/30 (46%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 245 PLRILSFDIECAGRKGIFPDPNHDPIIQIA 274
L+ L+FDIE + G P+P DPII I+
Sbjct: 2 DLKTLAFDIEVYSKYG-TPNPRRDPIIVIS 30
>gnl|CDD|177369 PHA02528, 43, DNA polymerase; Provisional.
Length = 881
Score = 55.9 bits (135), Expect = 4e-08
Identities = 41/154 (26%), Positives = 61/154 (39%), Gaps = 44/154 (28%)
Query: 246 LRILSFDIECAGRKGIFPDPNH--DPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGS 303
+RI + DIE G FPDP I I + +V F L +
Sbjct: 106 IRIANLDIEVTAEDG-FPDPEEAKYEIDAI---THYDSIDDRFYV---FDLGS------- 151
Query: 304 QVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLD 363
+++W A G + I K V+ + TE E+L
Sbjct: 152 -----------VEEWDA----KGDEVPQEILDKVVY-------------MPFDTEREMLL 183
Query: 364 KWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
++ F E P IFTG+N++ FD PY+INR K++
Sbjct: 184 EYINFWEENTPVIFTGWNVELFDVPYIINRIKNI 217
>gnl|CDD|99828 cd05785, DNA_polB_like2_exo, Uncharacterized bacterial subgroup of
the DEDDy 3'-5' exonuclease domain of family-B DNA
polymerases. A subfamily of the 3'-5' exonuclease
domain of family-B DNA polymerases. This subfamily is
composed of uncharacterized bacterial family-B DNA
polymerases. Family-B DNA polymerases contain an
N-terminal DEDDy DnaQ-like exonuclease domain in the
same polypeptide chain as the polymerase domain, similar
to family-A DNA polymerases. This exonuclease domain
contains three sequence motifs termed ExoI, ExoII and
ExoIII, with a specific YX(3)D pattern at ExoIII. These
motifs are involved in metal binding and catalysis. The
exonuclease domain of family-B DNA polymerases has a
fundamental role in proofreading activity. It contains a
beta hairpin structure that plays an important role in
active site switching in the event of a nucleotide
misincorporation. Family-B DNA polymerases are
predominantly involved in DNA replication and DNA
repair.
Length = 207
Score = 52.0 bits (125), Expect = 1e-07
Identities = 22/44 (50%), Positives = 27/44 (61%)
Query: 357 TETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVK 400
E ELL++ A IRE DPD+ G+NI FD PYL R + GV
Sbjct: 57 AEKELLEELVAIIRERDPDVIEGHNIFRFDLPYLRRRCRRHGVP 100
>gnl|CDD|99822 cd05779, DNA_polB_epsilon_exo, DEDDy 3'-5' exonuclease domain of
eukaryotic DNA polymerase epsilon, a family-B DNA
polymerase. The 3'-5' exonuclease domain of eukaryotic
DNA polymerase epsilon. DNA polymerase epsilon is a
family-B DNA polymerase with a catalytic subunit that
contains a DEDDy-type DnaQ-like 3'-5' exonuclease
domain. It is one of the three DNA-dependent type B DNA
polymerases (alpha and delta are the other two) that
have been identified as essential for nuclear DNA
replication in eukaryotes. DNA polymerase epsilon plays
a role in elongating the leading strand during DNA
replication. It is also involved in DNA repair. The
catalytic subunit contains both polymerase and 3'-5'
exonuclease activities. The N-terminal exonuclease
domain contains three sequence motifs termed ExoI, ExoII
and ExoIII, with a specific YX(3)D pattern at ExoIII.
These motifs are clustered around the active site and
are involved in metal binding and catalysis. DNA
polymerase epsilon also carries a unique large
C-terminal domain with an unknown function. Phylogenetic
analyses indicate that it is orthologous to the archaeal
DNA polymerase B3 rather than to the eukaryotic alpha,
delta, or zeta polymerases. The exonuclease domain of
family-B polymerases contains a beta hairpin structure
that plays an important role in active site switching in
the event of nucleotide misincorporation.
Length = 204
Score = 50.0 bits (120), Expect = 5e-07
Identities = 21/65 (32%), Positives = 30/65 (46%)
Query: 356 KTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVI 415
E LL ++ IRE+ P I YN FD+P++ RA G+ +G KD
Sbjct: 71 PDEKALLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEY 130
Query: 416 KDSFI 420
K +I
Sbjct: 131 KSRYI 135
>gnl|CDD|99826 cd05783, DNA_polB_B1_exo, DEDDy 3'-5' exonuclease domain of
Sulfolobus solfataricus DNA polymerase B1 and similar
archaeal family-B DNA polymerases. The 3'-5'
exonuclease domain of Sulfolobus solfataricus DNA
polymerase B1 and similar archaeal proteins. B1 is a
family-B DNA polymerase. Family-B DNA polymerases
contain an N-terminal DEDDy DnaQ-like exonuclease domain
in the same polypeptide chain as the polymerase domain,
similar to family-A DNA polymerases. B1displays
thermostable polymerase and 3'-5' exonuclease
activities. This exonuclease domain contains three
sequence motifs termed ExoI, ExoII and ExoIII, with a
specific YX(3)D pattern at ExoIII. These motifs are
clustered around the active site and are involved in
metal binding and catalysis. The exonuclease domain of
family-B polymerases also contains a beta hairpin
structure that plays an important role in active site
switching in the event of nucleotide misincorporation.
Family-B DNA polymerases from thermophilic archaea are
unique in that they are able to recognize the presence
of uracil in the template strand, leading to the
stalling of DNA synthesis. This is an additional
safeguard mechanism against increased levels of
deaminated bases during genome duplication at high
temperatures. S. solfataricus B1 also interacts with DNA
polymerase Y and may contribute to genome stability
mechanisms.
Length = 204
Score = 40.4 bits (95), Expect = 0.001
Identities = 23/71 (32%), Positives = 28/71 (39%), Gaps = 7/71 (9%)
Query: 336 KNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIREL------DPDIFTGYNIQNFDFPY 389
K V L ++ E E D IRE P + T +N NFD PY
Sbjct: 44 KRVLVLKREGVEGLEGLLPEGAEVEFFDSEKELIREAFKIISEYPIVLT-FNGDNFDLPY 102
Query: 390 LINRAKHLGVK 400
L NRA LG+
Sbjct: 103 LYNRALKLGIP 113
>gnl|CDD|233037 TIGR00592, pol2, DNA polymerase (pol2). All proteins in this
superfamily for which functions are known are DNA
polymerases.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 = 1172
Score = 40.8 bits (95), Expect = 0.002
Identities = 46/185 (24%), Positives = 61/185 (32%), Gaps = 48/185 (25%)
Query: 345 APIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTF 404
P GS V E ++ ++ I + D D+ N NFD YL +R
Sbjct: 257 KPTTGSYVESVSEEISMIKRFWDVIDQEDTDVEITVNGDNFDLVYLADR----------- 305
Query: 405 LGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIK 464
Q Q ++ D E LGV F GR D S
Sbjct: 306 ----------------QVFQF--------YWDAYEDPAEKLGVV-LLF-GRDVDHVSP-- 337
Query: 465 DSFIQSKQMGKRENKTINF---EGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDV 521
K N+ + F EG++ FDL V R L Y L VS L +KE
Sbjct: 338 ------CVQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKF 391
Query: 522 QHSII 526
+ I
Sbjct: 392 RAKPI 396
Score = 35.8 bits (82), Expect = 0.064
Identities = 49/273 (17%), Positives = 88/273 (32%), Gaps = 66/273 (24%)
Query: 148 TFPTHTYKAFESNIDFDIRFMVDNDIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQL 207
TF H + + N+ RF++ I G W+ + P S C+
Sbjct: 440 TFW-HVFGSNTGNL---ERFLLLRKIKGPCWLAV----------KGPDELEYPRRSWCKY 485
Query: 208 EIDVSTDDIVSHAPEEIDVSTDDIVSHAPEGEWSKVAPLRILSFDIECAGRKGIFPDPNH 267
E V +G PL +L F + K + P
Sbjct: 486 EGGYVKPPNVE------------------KGLDKTPPPLVVLDFSM-----KSLNPSIIR 522
Query: 268 DPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQ 327
+ I+ I + + A + + + ++ C VG++ C +L
Sbjct: 523 NEIVSIPDTLHREFALDKPPPEPPYDVHPC---VGTRPKDCSFPLDL------------- 566
Query: 328 GASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDF 387
E K S V TE L+ K+ A ++++DPD G++ Q
Sbjct: 567 -KGEFPGKKP------------SLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRAL 613
Query: 388 PYLINRAKHLGVKNFTFLGRVKDIRSVIKDSFI 420
L NR L + ++ +GR++ +
Sbjct: 614 KVLANRINDLKIPTWSKIGRLRRSPKFGRRFGE 646
>gnl|CDD|235594 PRK05761, PRK05761, DNA polymerase I; Reviewed.
Length = 787
Score = 40.4 bits (95), Expect = 0.003
Identities = 19/47 (40%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 357 TETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFT 403
+E ELL + I E P + +N NFD PYL NRA LG+
Sbjct: 209 SEKELLAELFDIILEYPPVVT--FNGDNFDLPYLYNRALKLGIPKEE 253
Score = 36.2 bits (84), Expect = 0.049
Identities = 27/165 (16%), Positives = 53/165 (32%), Gaps = 44/165 (26%)
Query: 114 EAVLMVEIVQKQTVFGFWGEELENFLKIT-----------ESVFPTFPTHTYKAFESNID 162
+ +EIV+K ++ KI SV +A+E++I
Sbjct: 77 PSFDHLEIVEKYDGLRDKKVKV---TKIVVKDPLAVRRLRLSVRDIP-----RAWEADIK 128
Query: 163 FDIRFMVDNDIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPE 222
++ R++ DN ++ ++ G EI + D A +
Sbjct: 129 YEFRYIYDNGLIPGMPYDVKNGLES------------VEPEILVEEIKKAFKDERKLAED 176
Query: 223 EIDVSTDDIVSHAPEGEWSKVAPLRILSFDIECAGR-KGIFPDPN 266
+ + I ++ ++ DIE KG PD +
Sbjct: 177 WLPIFEAPIPK------------IKRIAIDIEVYTPAKGRIPDDS 209
>gnl|CDD|212730 cd11796, SH3_DNMBP_N3, Third N-terminal Src homology 3 domain of
Dynamin Binding Protein, also called Tuba. DNMBP or
Tuba is a cdc42-specific guanine nucleotide exchange
factor (GEF) that contains four N-terminal SH3 domains,
a central RhoGEF [or Dbl homology (DH)] domain followed
by a Bin/Amphiphysin/Rvs (BAR) domain, and two
C-terminal SH3 domains. It provides a functional link
between dynamin and key regulatory proteins of the actin
cytoskeleton. It plays an important role in regulating
cell junction configuration. The four N-terminal SH3
domains of DNMBP binds the GTPase dynamin, which plays
an important role in the fission of endocytic vesicles.
SH3 domains are protein interaction domains that bind to
proline-rich ligands with moderate affinity and
selectivity, preferentially to PxxP motifs. They play
versatile and diverse roles in the cell including the
regulation of enzymes, changing the subcellular
localization of signaling pathway components, and
mediating the formation of multiprotein complex
assemblies.
Length = 51
Score = 31.6 bits (72), Expect = 0.079
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 12/51 (23%)
Query: 215 DIVSHAPEEIDVSTDDIV--SHAPEGEWSKVAPLRILSFDIECAGRKGIFP 263
D+ + EE+D+ D+V + + W F E GR+GIFP
Sbjct: 7 DLSAQLDEELDLREGDVVTITGILDKGW----------FRGELNGRRGIFP 47
>gnl|CDD|222962 PHA03036, PHA03036, DNA polymerase; Provisional.
Length = 1004
Score = 33.1 bits (76), Expect = 0.42
Identities = 54/268 (20%), Positives = 87/268 (32%), Gaps = 86/268 (32%)
Query: 249 LSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICC 308
L DIEC K FP +P+ I+ I E FTL
Sbjct: 163 LFLDIECHFDKK-FPSVFINPVSHISCCYIDLSGKEKR-----FTL-------------- 202
Query: 309 KTETELL---DKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKW 365
++L + A R + S + ++I C +E LL +
Sbjct: 203 -INEDMLSEDEIEEAVKRGYYEIESLLDMDYSK------------ELILC-SEIVLL-RI 247
Query: 366 SAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKDSFIQSKQM 425
+ + EL+ D +N NFD Y+ NR ++ I +
Sbjct: 248 AKKLLELEFDYVVTFNGHNFDLRYISNR------------------LELLTGEKIIFR-- 287
Query: 426 GKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTI---N 482
+ D +ET+ + + + + K +G N T N
Sbjct: 288 ------------SPDGKETVHL-------------CIYERNLSSHKGVGGVANTTYHINN 322
Query: 483 FEGRVCFDLLFVLLREYKLRSYTLNSVS 510
G + FDL + + KL SY L+S+S
Sbjct: 323 NNGTIFFDLYTFIQKTEKLDSYKLDSIS 350
>gnl|CDD|164925 PHA02524, 43A, DNA polymerase subunit A; Provisional.
Length = 498
Score = 32.3 bits (73), Expect = 0.65
Identities = 13/38 (34%), Positives = 21/38 (55%)
Query: 356 KTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINR 393
+ E +LL + + PD+ G+N + FD PY+I R
Sbjct: 178 EDEVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITR 215
>gnl|CDD|176647 cd06125, DnaQ_like_exo, DnaQ-like (or DEDD) 3'-5' exonuclease
domain superfamily. The DnaQ-like exonuclease
superfamily is a structurally conserved group of 3'-5'
exonucleases, which catalyze the excision of nucleoside
monophosphates at the DNA or RNA termini in the 3'-5'
direction. It is also called the DEDD superfamily, after
the four invariant acidic residues present in the
catalytic site of its members. The superfamily consists
of DNA- and RNA-processing enzymes such as the
proofreading domains of DNA polymerases, other DNA
exonucleases, RNase D, RNase T, Oligoribonuclease and
RNA exonucleases (REX). The DnaQ-like exonuclease domain
contains three conserved sequence motifs termed ExoI,
ExoII and ExoIII, which 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 conservation patterns of the three motifs
may vary among different subfamilies. DnaQ-like
exonucleases are classified as DEDDy or DEDDh
exonucleases depending on the variation of motif III as
YX(3)D or HX(4)D, respectively. The significance of the
motif differences is still unclear. Almost all RNase
families in this superfamily are present only in
eukaryotes and bacteria, but not in archaea, suggesting
a later origin, which in some cases are accompanied by
horizontal gene transfer.
Length = 96
Score = 30.1 bits (68), Expect = 0.86
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 367 AFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIR 412
+R+ I G+N +FD P+L NR LG+K G D
Sbjct: 37 DILRDKPLAILVGHNG-SFDLPFLNNRCAELGLKYPLLAGSWIDTI 81
>gnl|CDD|99825 cd05782, DNA_polB_like1_exo, Uncharacterized bacterial subgroup of
the DEDDy 3'-5' exonuclease domain of family-B DNA
polymerases. A subfamily of the 3'-5' exonuclease
domain of family-B DNA polymerases. This subfamily is
composed of uncharacterized bacterial family-B DNA
polymerases. Family-B DNA polymerases contain an
N-terminal DEDDy DnaQ-like exonuclease domain in the
same polypeptide chain as the polymerase domain, similar
to family-A DNA polymerases. This exonuclease domain
contains three sequence motifs termed ExoI, ExoII and
ExoIII, with a specific YX(3)D pattern at ExoIII. These
motifs are involved in metal binding and catalysis. The
exonuclease domain of family-B DNA polymerases has a
fundamental role in proofreading activity. It contains a
beta hairpin structure that plays an important role in
active site switching in the event of a nucleotide
misincorporation. Family-B DNA polymerases are
predominantly involved in DNA replication and DNA
repair.
Length = 208
Score = 31.4 bits (72), Expect = 0.89
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVK 400
E ELL+ + I + +P +N + FD P L RA GV
Sbjct: 78 EKELLEDFFQLIEKKNP-RLVSFNGRGFDLPVLHLRALIHGVS 119
>gnl|CDD|238547 cd01127, TrwB, Bacterial conjugation protein TrwB, ATP binding
domain. TrwB is a homohexamer encoded by conjugative
plasmids in Gram-negative bacteria. TrwB also has an all
alpha domain which has been hypothesized to be
responsible for DNA binding. TrwB is a component of Type
IV secretion and is responsible for the horizontal
transfer of DNA between bacteria.
Length = 410
Score = 31.2 bits (71), Expect = 1.7
Identities = 22/97 (22%), Positives = 35/97 (36%), Gaps = 22/97 (22%)
Query: 132 GEELENFLKITESVFPTFPTHTYKAFESNIDFDIRFMVDNDIVG-------------CNW 178
EEL FL T + P + K S IR ++ + +W
Sbjct: 171 LEELREFLAGTPAASLFSP-NAEKTAAS-----IRAVLSTYLRALRFLPMGKEPFSIRDW 224
Query: 179 I--EIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVST 213
+ E PPG + + RP +S L++ V+T
Sbjct: 225 VRDEDPPGFLFITSNADMRASLRPLIS-TWLDVAVNT 260
>gnl|CDD|225394 COG2838, Icd, Monomeric isocitrate dehydrogenase [Energy production
and conversion].
Length = 744
Score = 30.9 bits (70), Expect = 2.2
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 436 EGNSDRRETLGVKNF 450
EGNSDRR VKN+
Sbjct: 142 EGNSDRRAPKAVKNY 156
>gnl|CDD|182154 PRK09935, PRK09935, transcriptional regulator FimZ; Provisional.
Length = 210
Score = 28.7 bits (64), Expect = 5.8
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 443 ETLGVKNFTFLGRVKDIRSVIKDSFIQSK 471
+ G FTFL R+K I+S +K F+ SK
Sbjct: 58 DLPGTDGFTFLKRIKQIQSTVKVLFLSSK 86
Score = 28.7 bits (64), Expect = 6.8
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 398 GVKNFTFLGRVKDIRSVIKDSFIQSK 423
G FTFL R+K I+S +K F+ SK
Sbjct: 61 GTDGFTFLKRIKQIQSTVKVLFLSSK 86
>gnl|CDD|198455 cd10487, EphR_LBD_A10, Ligand Binding Domain of Ephrin type-A
Receptor 10. Ephrin receptors (EphRs) comprise the
largest subfamily of receptor tyrosine kinases (RTKs).
Class EphA receptors bind GPI-anchored ephrin-A ligands.
There are ten vertebrate EphA receptors (EphA1-10),
which display promiscuous interactions with six ephrin-A
ligands. EphA10, which contains an inactive tyr kinase
domain, may function to attenuate signals of
co-clustered active receptors. EphA10 is mainly
expressed in the testis. EphRs contain a ligand binding
domain and two fibronectin repeats extracellularly, a
transmembrane segment, and a cytoplasmic tyrosine kinase
domain. Binding of the ephrin ligand to EphR requires
cell-cell contact since both are anchored to the plasma
membrane. The resulting downstream signals occur
bidirectionally in both EphR-expressing cells (forward
signaling) and ephrin-expressing cells (reverse
signaling). Ephrin/EphR interaction results in cell-cell
repulsion or adhesion.
Length = 173
Score = 28.1 bits (62), Expect = 7.8
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 264 DPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKT 310
+PN + +Q IS+G + IF++ FTL C I G C +T
Sbjct: 47 EPNQNNWLQTG--WISRGRGQRIFIELQFTLRDCNSIPGVAGTCKET 91
>gnl|CDD|112770 pfam03971, IDH, Monomeric isocitrate dehydrogenase.
NADP(+)-dependent isocitrate dehydrogenase (ICD) is an
important enzyme of the intermediary metabolism, as it
controls the carbon flux within the citric acid cycle
and supplies the cell with 2-oxoglutarate EC:1.1.1.42
and NADPH for biosynthetic purposes.
Length = 735
Score = 29.1 bits (65), Expect = 8.4
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 436 EGNSDRRETLGVKNF 450
EGNSDRR VKN+
Sbjct: 136 EGNSDRRAPKAVKNY 150
>gnl|CDD|213521 TIGR00281, TIGR00281, segregation and condensation protein B.
Shown to be required for chromosome segregation and
condensation in B. subtilis [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 186
Score = 28.3 bits (63), Expect = 8.7
Identities = 15/40 (37%), Positives = 25/40 (62%), Gaps = 5/40 (12%)
Query: 92 AFKEALNRAIIADMRGNK-----DEIQEAVLMVEIVQKQT 126
A+K+ + RA I ++RG K D++ E L+VE+ +K T
Sbjct: 97 AYKQPITRARINEIRGVKSYQIVDDLVEKGLVVELGRKDT 136
>gnl|CDD|129282 TIGR00178, monomer_idh, isocitrate dehydrogenase, NADP-dependent,
monomeric type. The monomeric type of isocitrate
dehydrogenase has been found so far in a small number of
species, including Azotobacter vinelandii,
Corynebacterium glutamicum, Rhodomicrobium vannielii,
and Neisseria meningitidis. It is NADP-specific [Energy
metabolism, TCA cycle].
Length = 741
Score = 28.7 bits (64), Expect = 8.9
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 436 EGNSDRRETLGVKNF 450
EGNSDRR L VKN+
Sbjct: 140 EGNSDRRAPLSVKNY 154
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
0.321 0.137 0.418
Gapped
Lambda K H
0.267 0.0626 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 28,118,728
Number of extensions: 2744582
Number of successful extensions: 2114
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2092
Number of HSP's successfully gapped: 63
Length of query: 551
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 449
Effective length of database: 6,413,494
Effective search space: 2879658806
Effective search space used: 2879658806
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 (21.8 bits)
S2: 61 (27.5 bits)