RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15891
(899 letters)
>gnl|CDD|176478 cd08641, DNA_pol_gammaA, Pol gammaA is a family A polymerase that
is responsible for DNA replication and repair in
mitochondria. DNA polymerase gamma (Pol gamma), 5'-3'
polymerase domain (Pol gammaA). Pol gammaA is a family A
polymerase that is responsible for DNA replication and
repair in mitochondria. Family A polymerase functions
primarily to fill DNA gaps that arise during DNA repair,
recombination and replication. DNA-dependent DNA
polymerases can be classified into six main groups based
upon phylogenetic relationships with E. coli polymerase
I (classA), E. coli polymerase II (class B), E.coli
polymerase III (class C), euryarchaeota polymerase II
(class D), human polymerase beta (class X), E. coli
UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum
variant (class Y). Family A polymerases are found
primarily in organisms related to prokaryotes and
include prokaryotic DNA polymerase I, mitochondrial
polymerase gammaA, and several bacteriophage polymerases
including those from odd-numbered phage (T3, T5, and
T7). The structure of these polymerases resembles in
overall morphology a cupped human right hand, with
fingers (which bind an incoming nucleotide and interact
with the single-stranded template), palm (which harbors
the catalytic amino acid residues and also binds an
incoming dNTP) and thumb (which binds double-stranded
DNA) subdomains. Pol gammaA has also the right hand
configuration. Pol gammaA has both polymerase and
proofreading exonuclease activities separated by a
spacer. Pol gamma holoenzyme is a heterotrimer
containing one Pol gammaA subunit and a dimeric Pol
gammaB subunit. Pol gamma is important for mitochondria
DNA maintenance and mutation of the catalytic subunit of
Pol gamma is implicated in more than 30 human diseases.
Length = 425
Score = 627 bits (1618), Expect = 0.0
Identities = 219/403 (54%), Positives = 280/403 (69%), Gaps = 28/403 (6%)
Query: 468 AKRIIEISRMLSYWRNNHERVKKQFVVWLNKKDLPRRLVENIE-SEGRDYGVILPQLIVS 526
AKR +EI++M SYWRN +R+ Q VVW +K +LPR + + + E YG ILPQ++
Sbjct: 47 AKRALEINKMCSYWRNARDRIMSQMVVWDDKSELPRAVSRHPQDDEEPGYGAILPQVVPM 106
Query: 527 GTLTRRAVEATWMTASNAVGERVGSELRAMIQAPDGYSIIGADVDSQELWIASVIGDSYC 586
GT+TRRAVE TW+TASNA RVGSEL+AM+QAP GYS +GADVDSQELWIASV+GD++
Sbjct: 107 GTITRRAVEPTWLTASNAKKNRVGSELKAMVQAPPGYSFVGADVDSQELWIASVLGDAHF 166
Query: 587 AKEHGATPLGWMTLSGQKSNATDMHSITAKAVGISREHAKIINYARIYGAGERFAERLLK 646
HGAT +GWMTL G+KS TD+HS TA +GISR+HAK+ NY RIYGAG+ FAERLL
Sbjct: 167 GGIHGATAIGWMTLQGKKSEGTDLHSKTASILGISRDHAKVFNYGRIYGAGQPFAERLLM 226
Query: 647 QFNPEMSKSDAKSKARKMYTLTKGKKLYRLKDGHLEELIKRVYSKYEAREVCSAYNTSVD 706
QFNP ++ ++A KA++MY TKG + + +T
Sbjct: 227 QFNPRLTPAEATEKAKQMYAATKGIR------------------------IAIQRSTKGK 262
Query: 707 KIFDKPQWYGGTESAMFNRLEEIATSLQPVTPFLNCRLSRALEPVSEDDSKFIQTRINWV 766
++F +P W GG+ES MFN+LEEIA QP TP L ++ AL + ++F+ +RINWV
Sbjct: 263 RLFKRPFWSGGSESIMFNKLEEIAAQSQPRTPVLGACITSALLEPNLVKNEFMTSRINWV 322
Query: 767 VQSGAVDFLHLMLVCMRWLVSR---DTRFVISIHDEIRYLVPDEEKYETALALHVTNLLT 823
VQS AVD+LHLMLV MRWL+ + D RF ISIHDE+RYLV +E+KY ALAL +TNLLT
Sbjct: 323 VQSSAVDYLHLMLVSMRWLIEKYDIDARFCISIHDEVRYLVKEEDKYRAALALQITNLLT 382
Query: 824 RAFCIKKLDMTDIPLSISFFSGVEIDKVLRKESDNDCKTPSNP 866
RA +KL + D+P S++FFS V+ID VLRKE D DC TPSNP
Sbjct: 383 RAMFAQKLGINDLPQSVAFFSAVDIDTVLRKEVDMDCVTPSNP 425
Score = 51.6 bits (124), Expect = 1e-06
Identities = 19/43 (44%), Positives = 28/43 (65%)
Query: 128 STAYLPVNNNWVKYFNESCQTFNDLNVEMKSLLMDKCDQACSL 170
+AYLPVN+NW +Y N + +T+ +L E+K LM + AC L
Sbjct: 1 GSAYLPVNSNWERYLNTAEETYQELQQEVKESLMQLAEDACQL 43
>gnl|CDD|201250 pfam00476, DNA_pol_A, DNA polymerase family A.
Length = 383
Score = 246 bits (629), Expect = 2e-73
Identities = 96/431 (22%), Positives = 148/431 (34%), Gaps = 64/431 (14%)
Query: 420 TDDADTPREIGFIKLPHKDGEHLNVGNPLSRDFINKFSDNSLAGV--DIGAKRIIEISRM 477
+++ K+P GE N+G+P + D R +
Sbjct: 10 SNELGAQLADLEFKIPELAGEEFNLGSPKQLGVLLFEELGLPKTKKTDKTGARSTNADVL 69
Query: 478 LSYWRNNHERVKKQFVVWLNKKDLPRRLVEN-IESEGRDYGVILPQLIVSGTLTRRAVEA 536
S + HE +K K L V+ D G I +GT T R
Sbjct: 70 ESLREDAHEIIKIILEYRQLSK-LQSTYVDKLPLMIDPDDGRIHTSYNQAGTATGRLSST 128
Query: 537 TWMTASNAVGERVGSELRAMIQAPDGYSIIGADVDSQELWIASVIGDSYCAKEHGATPLG 596
+ + G E+RA A GY ++ AD EL I + + E T
Sbjct: 129 DPNLQNIPIRNEYGREIRAAFIAEPGYVLVAADYSQIELRILAHLSGDENLIEAFRTGAD 188
Query: 597 WMTLSGQKSNATDMHSITAKAVGISREHAKIINYARIYGAGERFAERLLKQFNPEMSKSD 656
TL+ D+H +T G R +AK N+ RIYGA + +LL +S+ +
Sbjct: 189 IHTLTAADIFGVDLHEVT----GNQRRNAKTFNFGRIYGASAKGLSQLLG-----ISREE 239
Query: 657 AKSKARKMYTLTKGKKLYRLKDGHLEELIKRVYSKYEAREVCSAYNTSVDKIFDKPQWYG 716
AK K + G K YR E+ K G
Sbjct: 240 AKEFIEKYFERFPGVKRYR------EKTRKEA-------------------------KKG 268
Query: 717 GTESAMFNRLEEIATSLQPVTPFLNCRLSRALEPVSEDDSKFIQTRINWVVQSGAVDFLH 776
G +F R + P N L A E + +N +Q A D L
Sbjct: 269 GYVETLFGRRRYL-----PDIDSRNRSLREAAE----------RAALNTPIQGSAADILK 313
Query: 777 LMLVCMRWLV---SRDTRFVISIHDEIRYLVPDEEKYETALALHVTNLLTRAFCIKKLDM 833
L ++ + + D R + +HDEI + VP EE A+A + L+ RA + +
Sbjct: 314 LAMIKLDEALVEKGLDARMCLQVHDEIVFEVPKEEA--EAVAAQIKELMERAMFLDVPLL 371
Query: 834 TDIPLSISFFS 844
++ ++FS
Sbjct: 372 VEVGQGRNWFS 382
>gnl|CDD|214687 smart00482, POLAc, DNA polymerase A domain.
Length = 207
Score = 173 bits (442), Expect = 1e-49
Identities = 64/271 (23%), Positives = 96/271 (35%), Gaps = 76/271 (28%)
Query: 550 GSELRAMIQAPDGYSIIGADVDSQELWIASVIGDSYCAKEHGATPLGWMTLSGQKSNATD 609
G E+R AP GY ++ AD EL I + + L +N D
Sbjct: 1 GREIRRAFIAPPGYVLVSADYSQIELRILAHLSGD-------------ENLIEAFNNGGD 47
Query: 610 MHSITAKAV---------GISREHAKIINYARIYGAGERFAERLLKQFNPEMSKSDAKSK 660
+H+ TA V R AK IN+ IYG G A+ L +Q +S+++AK
Sbjct: 48 IHTKTAAQVFGVPEEEVTPELRRAAKAINFGIIYGMG---AKGLAEQLG--ISEAEAKEL 102
Query: 661 ARKMYTLTKGKKLYRLKDGHLEELIKRVYSKYEAREVCSAYNTSVDKIFDKPQWYGGTES 720
+K + G + Y I R EA G +
Sbjct: 103 IKKYFARFPGVRRY----------IDRT--LEEA-------------------RRKGYVT 131
Query: 721 AMFNRLEEIATSLQPVTPFLNCRLSRALEPVSEDDSKFIQTRINWVVQSGAVDFLHLMLV 780
+F R I + P L RA +N +Q A D L L ++
Sbjct: 132 TLFGRRRYIPD-IDSRNPVLRAAAERA--------------AVNTPIQGSAADILKLAMI 176
Query: 781 CMRWLVSR---DTRFVISIHDEIRYLVPDEE 808
M + R ++ +HDE+ + VP+EE
Sbjct: 177 KMDEALKEFGLRARLLLQVHDELVFEVPEEE 207
>gnl|CDD|176473 cd06444, DNA_pol_A, Family A polymerase primarily fills DNA gaps
that arise during DNA repair, recombination and
replication. DNA polymerase family A, 5'-3' polymerase
domain. Family A polymerase functions primarily to fill
DNA gaps that arise during DNA repair, recombination and
replication. DNA-dependent DNA polymerases can be
classified into six main groups based upon phylogenetic
relationships with E. coli polymerase I (classA), E.
coli polymerase II (class B), E.coli polymerase III
(class C), euryarchaeota polymerase II (class D), human
polymerase beta (class X), E. coli UmuC/DinB and
eukaryotic RAP 30/Xeroderma pigmentosum variant (class
Y). Family A polymerases are found primarily in
organisms related to prokaryotes and include prokaryotic
DNA polymerase I, mitochondrial polymerase gamma, and
several bacteriophage polymerases including those from
odd-numbered phage (T3, T5, and T7). Prokaryotic
polymerase I (pol I) has two functional domains located
on the same polypeptide; a 5'-3' polymerase and a 5'-3'
exonuclease. Pol I uses its 5' nuclease activity to
remove the ribonucleotide portion of newly synthesized
Okazaki fragments and the DNA polymerase activity to
fill in the resulting gap. The structure of these
polymerases resembles in overall morphology a cupped
human right hand, with fingers (which bind an incoming
nucleotide and interact with the single-stranded
template), palm (which harbors the catalytic amino acid
residues and also binds an incoming dNTP) and thumb
(which binds double-stranded DNA) subdomains.
Length = 347
Score = 157 bits (400), Expect = 2e-42
Identities = 69/367 (18%), Positives = 112/367 (30%), Gaps = 78/367 (21%)
Query: 469 KRIIEISRMLSYWRNNHERVKKQFVVWLNKKDLPRRLVENIESEGRDYGVILPQLIVSGT 528
++E ++ W N Q+V G P+ + GT
Sbjct: 30 PLLLEYKKLAKLWSANGWPWLDQWV---------------------RDGRFHPEYVPGGT 68
Query: 529 LTRRAVEATWMTASNAVGERVGSELRAMIQAPDGYSIIGADVDSQELWIASVIGDSYCAK 588
+T R + +G ++R A G++++ AD EL + + +
Sbjct: 69 VTGRWASRGGNAQQIPRRDPLGRDIRQAFVADPGWTLVVADASQLELRVLAALSGDEALA 128
Query: 589 EHGATPLGWMTLSGQKSNATDMHSITAKAV------GISREHAKIINYARIYGAGERFAE 642
E D+++ TA A+ G R+HAKI N +YGA +
Sbjct: 129 EAFGR-------------GGDLYTATASAMFGVPVGGGERQHAKIANLGAMYGATSGISA 175
Query: 643 RLLKQFNPEMSKSDAKSKARKMYTLTKGKKLYRLKDGHLEELIKRVYSKYEAREVCSAYN 702
RLL Q +K A K ++ V + AR
Sbjct: 176 RLLAQLRRISTKEAAALIELFFSRFPAFPKA-----------MEYV--EDAARR------ 216
Query: 703 TSVDKIFDKPQWYGGTESAMFNRLEEIATSLQPVTPFLNCRLSRALEPVSEDDSKFIQT- 761
GG + R S P + A + +
Sbjct: 217 ----------GERGGYVRTLLGR-----RSPPPDIRWTEVVSDPAAASRARRVRRAAGRF 261
Query: 762 RINWVVQSGAVDFLHLMLVCMRWL---VSRDTRFVISIHDEIRYLVPDEEKYETALALHV 818
N+VVQ A D+ L +V +R ++ D R V +HDE+ P EE A +
Sbjct: 262 ARNFVVQGTAADWAKLAMVALRRRLEELALDARLVFFVHDEVVLHCPKEEAEAVAAIVRE 321
Query: 819 TNLLTRA 825
Sbjct: 322 AAEQAVR 328
>gnl|CDD|223820 COG0749, PolA, DNA polymerase I - 3'-5' exonuclease and polymerase
domains [DNA replication, recombination, and repair].
Length = 593
Score = 65.7 bits (161), Expect = 5e-11
Identities = 64/356 (17%), Positives = 106/356 (29%), Gaps = 59/356 (16%)
Query: 527 GTLTRRAVEATWMTASNAVGERVGSELRAMIQAPDGYSIIGADVDSQE--LWIASVIGDS 584
GT+T AV W+T NA + + P G ++G V S+E +I + G
Sbjct: 4 GTITDLAVLNAWLTKLNAAAN-IAFDTETDGLDPHGADLVGLSVASEEEAAYIPLLHGPE 62
Query: 585 YCAKEHGATPLGWMTLSGQKS---NAT-DMHSITAKAVGI---SREHAKIINYARIYGAG 637
A + G K N D +GI + +Y GAG
Sbjct: 63 QL--NVLAALKPLLEDEGIKKVGQNLKYDYK--VLANLGIEPGVAFDTMLASYLLNPGAG 118
Query: 638 ERFAERLLKQFNPEMSKSDAKSKARKMYTLTKGKKLYRLKDGHLEELIKRVYSKYEAREV 697
+ L K++ L+ E++ +
Sbjct: 119 AHNLDDLAKRY-------------------------LGLETITFEDIAGKGKK------- 146
Query: 698 CSAYNTSVDKIFDKPQWYGGTESAMFNRLEEIATSLQPVTPFLNCRLSRALE-PVSEDDS 756
T D +K Y ++ RLE I TP L L +E P+ +
Sbjct: 147 ---QLTFADVKLEKATEYAAEDADATLRLESILEPELLKTPVL-LELYEEIEMPLVRVLA 202
Query: 757 KFIQTRINWVVQSGAVDFLHLMLVCMRWLVSR-----DTRFVISIHDEIRYLVPDEEKYE 811
+ + I VQ L + L F I+ ++ ++ ++
Sbjct: 203 RMERNGIKVDVQYLKELSKEL-GCELAELEEEIYELAGEEFNINSPKQLGEILFEKLGLP 261
Query: 812 TAL-ALHVTNLLTRAFCIKKL-DMTDIPLSISFFSGVEIDKVLRKESDNDCKTPSN 865
L N T A ++KL D +P I + + K + P
Sbjct: 262 PGLKKTKTGNYSTDAEVLEKLADDHPLPKLILEYRQLAKLKSTYTDGLPKLINPDT 317
Score = 29.5 bits (67), Expect = 8.9
Identities = 37/141 (26%), Positives = 54/141 (38%), Gaps = 41/141 (29%)
Query: 550 GSELRAMIQAPDGYSIIGADVDSQ-ELWIASVIGDSYCAKEHGATPLGWMTLSGQKS--- 605
G ++R A GY++I AD SQ EL I + H LS +
Sbjct: 351 GRKIRKAFVAEKGYTLISADY-SQIELRILA----------H---------LSQDEGLLR 390
Query: 606 ---NATDMHSITAKAV------GISREH---AKIINYARIYGAGERFAERLLKQFNPEMS 653
D+H+ TA V ++ E AK IN+ IYG A L +Q +
Sbjct: 391 AFTEGEDIHTATAAEVFGVPIEEVTSEQRRKAKAINFGLIYGMS---AFGLAQQLG--IP 445
Query: 654 KSDAKSKARKMYTLTKGKKLY 674
+ +AK + + G K Y
Sbjct: 446 RKEAKEYIDRYFERYPGVKEY 466
>gnl|CDD|176480 cd08643, DNA_pol_A_pol_I_B, Polymerase I functions primarily to
fill DNA gaps that arise during DNA repair,
recombination and replication. Family A polymerase
functions primarily to fill DNA gaps that arise during
DNA repair, recombination and replication. DNA-dependent
DNA polymerases can be classified in six main groups
based upon phylogenetic relationships with E. coli
polymerase I (classA), E. coli polymerase II (class B),
E.coli polymerase III (class C), euryarchaaeota
polymerase II (class D), human polymerase beta (class
x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma
pigmentosum variant (class Y). Family A polymerase are
found primarily in organisms related to prokaryotes and
include prokaryotic DNA polymerase I ,mitochondrial
polymerase delta, and several bacteriphage polymerases
including those from odd-numbered phage (T3, T5, and
T7). Prokaryotic Pol Is have two functional domains
located on the same polypeptide; a 5'-3' polymerase and
5'-3' exonuclease. Pol I uses its 5' nuclease activity
to remove the ribonucleotide portion of newly
synthesized Okazaki fragments and DNA polymerase
activity to fill in the resulting gap. A combination of
phylogenomic and signature sequence-based (or phonetic)
approaches is used to understand the evolutionary
relationships among bacteria. DNA polymerase I is one of
the conserved proteins that is used to search for
protein signatures. The structure of these polymerases
resembles in overall morphology a cupped human right
hand, with fingers (which bind an incoming nucleotide
and interact with the single-stranded template), palm
(which harbors the catalytic amino acid residues and
also binds an incoming dNTP) and thumb (which binds
double-stranded DNA) subdomains.
Length = 429
Score = 55.1 bits (133), Expect = 8e-08
Identities = 42/136 (30%), Positives = 62/136 (45%), Gaps = 27/136 (19%)
Query: 509 IESEGRDYGVILPQLIVSGTLTRRAVEATWMTAS-NAVGERVGSELRAMIQAPDGYSIIG 567
+ +GR +G + +G +T RA + A AVG G E R + P G+S++G
Sbjct: 136 VHEDGRIHGAVNT----NGAVTGRATHFSPNMAQVPAVGSPYGKECRELFGVPPGWSLVG 191
Query: 568 ADVDSQEL-----WIASVIGDSYCAKEHGATPLGWMTLSGQKSNATDMHSITAKAVGI-S 621
AD EL ++A G +Y K G D+H A+A+G+ S
Sbjct: 192 ADASGLELRCLAHYLARYDGGAYTRKVLG----------------GDIHWANAQAMGLLS 235
Query: 622 REHAKIINYARIYGAG 637
R+ AK YA +YGAG
Sbjct: 236 RDGAKTFIYAFLYGAG 251
>gnl|CDD|176476 cd08639, DNA_pol_A_Aquificae_like, Phylum Aquificae Pol A is
different from Escherichia coli Pol A by three
signature sequences. Family A polymerase functions
primarily to fill DNA gaps that arise during DNA repair,
recombination and replication. DNA-dependent DNA
polymerases can be classified in six main groups based
upon phylogenetic relationships with E. coli polymerase
I (classA), E. coli polymerase II (class B), E.coli
polymerase III (class C), euryarchaaeota polymerase II
(class D), human polymerase beta (class x), E. coli
UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum
variant (class Y). Family A polymerase are found
primarily in organisms related to prokaryotes and
include prokaryotic DNA polymerase I ,mitochondrial
polymerase delta, and several bacteriphage polymerases
including those from odd-numbered phage (T3, T5, and
T7). Prokaryotic Pol Is have two functional domains
located on the same polypeptide; a 5'-3' polymerase and
5'-3' exonuclease. Pol I uses its 5' nuclease activity
to remove the ribonucleotide portion of newly
synthesized Okazaki fragments and DNA polymerase
activity to fill in the resulting gap. A combination of
phylogenomic and signature sequence-based (or phonetic)
approaches is used to understand the evolutionary
relationships among bacteria. DNA polymerase I is one of
the conserved proteins that is used for phylogenetic
anaylsis of bacteria. Species of the phylum Aquificae
grow in extreme thermophilic environments. The Aquificae
are non-spore-forming, Gram-negative rods and strictly
thermophilic. Phylum Aquificae Pol A is different from
E. coli Pol I by three signature sequences consisting of
a 2 amino acids (aa) insert, a 5-6 aa insert and a 6 aa
deletion. These signature sequences may provide a
molecular marker for the family Aquificaceae and related
species.
Length = 324
Score = 46.1 bits (110), Expect = 5e-05
Identities = 37/127 (29%), Positives = 53/127 (41%), Gaps = 26/127 (20%)
Query: 551 SELRAMIQAPDGYSIIGADVDSQELWIASVI-GDSYCAKEHGATPLGWMTLSGQKSNATD 609
E R AP+G +I AD EL IA+ I GD M + QK D
Sbjct: 91 REFRRCFVAPEGNKLIIADYSQIELRIAAEISGDER------------MISAYQKGE--D 136
Query: 610 MHSITAKAV-GIS--------REHAKIINYARIYGAGER-FAERLLKQFNPEMSKSDAKS 659
+H +TA + G R+ AK +N+ IYG + E + EMS +A+
Sbjct: 137 LHRLTASLITGKPIEEITKEERQLAKAVNFGLIYGMSAKGLREYARTNYGVEMSLEEAE- 195
Query: 660 KARKMYT 666
K R+ +
Sbjct: 196 KFRESFF 202
>gnl|CDD|237876 PRK14975, PRK14975, bifunctional 3'-5' exonuclease/DNA polymerase;
Provisional.
Length = 553
Score = 45.4 bits (108), Expect = 1e-04
Identities = 68/344 (19%), Positives = 107/344 (31%), Gaps = 111/344 (32%)
Query: 499 KDLPRRLVENIESEGRDY---GVILPQLIVSGTLTRRAVEATWMTASNAVGERVGSELRA 555
+ L + L N + + G P+ + G +T R + +++ ++R+
Sbjct: 264 RKLSKLLSANGWAWLDYWVRDGRFHPEYVPGGVVTGR------WASRGPNAQQIPRDIRS 317
Query: 556 MIQAPDGYSIIGADVDSQELWIASVI-GDSYCAKEHGATPLGWMTLSGQKSNATDMHSIT 614
A G+ ++ AD EL + + GD + D+H +T
Sbjct: 318 AFVADPGWKLVVADASQIELRVLAAYSGDE-----------RMIEAFRT---GGDLHRLT 363
Query: 615 A-------KAVGISREHAKIINYARIYGAGERF----------AERLLKQFNPEMSKSDA 657
A + R AK N+ IYGA + A RLL++
Sbjct: 364 ASVGFGKPEEEKEERALAKAANFGAIYGATSKGLQEYAKNYGEAARLLERL--------- 414
Query: 658 KSKARKMYTLTKGKKLYRLKDGHLEELIKRVYSKYEAREVCSAYNTSVDKIFDKPQWYGG 717
R+ Y R E R V + G
Sbjct: 415 ----RRAYP--------RAVGWV--ERAAREGE--RGGVVRT--------------LLG- 443
Query: 718 TESAMFNRLEEIATSLQPVTPFLNCRLSRALEPVSEDDSKFIQTRINWVVQSGAVDFLHL 777
R TS P + R +R+ TR N+ VQ A D+ L
Sbjct: 444 -------R-----TSPPPGFAWRARRRARSRGR---------FTR-NFPVQGTAADWAKL 481
Query: 778 MLVCMRWLVSR-----DTRFVISIHDEIRYLVPDEEKYETALAL 816
L +R R D V +HDE+ P+EE E A A+
Sbjct: 482 ALALLR---RRLAEGLDAELVFFVHDEVVVECPEEEAEEVAAAI 522
>gnl|CDD|176474 cd08637, DNA_pol_A_pol_I_C, Polymerase I functions primarily to
fill DNA gaps that arise during DNA repair,
recombination and replication. Family A polymerase
(polymerase I) functions primarily to fill DNA gaps that
arise during DNA repair, recombination and replication.
DNA-dependent DNA polymerases can be classified in six
main groups based upon phylogenetic relationships with
E. coli polymerase I (classA), E. coli polymerase II
(class B), E.coli polymerase III (class C),
euryarchaaeota polymerase II (class D), human polymerase
beta (class x), E. coli UmuC/DinB and eukaryotic RAP
30/Xeroderma pigmentosum variant (class Y). Family A
polymerase are found primarily in organisms related to
prokaryotes and include prokaryotic DNA polymerase I
(pol I) ,mitochondrial polymerase delta, and several
bacteriphage polymerases including those from
odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is
have two functional domains located on the same
polypeptide; a 5'-3' polymerase and 5'-3' exonuclease.
Pol I uses its 5' nuclease activity to remove the
ribonucleotide portion of newly synthesized Okazaki
fragments and DNA polymerase activity to fill in the
resulting gap. A combination of phylogenomic and
signature sequence-based (or phonetic) approaches is
used to understand the evolutionary relationships among
bacteria. DNA polymerase I is one of the conserved
proteins that is used to search for protein signatures.
The structure of these polymerases resembles in overall
morphology a cupped human right hand, with fingers
(which bind an incoming nucleotide and interact with the
single-stranded template), palm (which harbors the
catalytic amino acid residues and also binds an incoming
dNTP) and thumb (which binds double-stranded DNA)
subdomains.
Length = 377
Score = 36.2 bits (85), Expect = 0.065
Identities = 34/123 (27%), Positives = 53/123 (43%), Gaps = 37/123 (30%)
Query: 550 GSELRAMIQAPDGYSIIGADVDSQ-ELWI-ASVIGDS--YCAKEHGATPLGWMTLSGQKS 605
G E+R A +G+ ++ AD SQ EL I A + GD A ++G
Sbjct: 138 GREIRKAFVAEEGWVLLSADY-SQIELRILAHLSGDEALIEAFKNGE------------- 183
Query: 606 NATDMHSITAKAV-GIS--------REHAKIINYARIYGAGE-RFAERLLKQFNPEMSKS 655
D+H+ TA V G+ R AK +N+ IYG +++L +S+
Sbjct: 184 ---DIHTRTAAEVFGVPPEEVTPEMRRIAKAVNFGIIYGISAFGLSQQL------GISRK 234
Query: 656 DAK 658
+AK
Sbjct: 235 EAK 237
>gnl|CDD|176475 cd08638, DNA_pol_A_theta, DNA polymerase theta is a low-fidelity
family A enzyme implicated in translesion synthesis and
in somatic hypermutation. DNA polymerase theta is a
low-fidelity family A enzyme implicated in translesion
synthesis (TLS) and in somatic hypermutation (SHM).
DNA-dependent DNA polymerases can be classified in six
main groups based upon phylogenetic relationships with
E. coli polymerase I (classA), E. coli polymerase II
(class B), E.coli polymerase III (class C),
euryarchaaeota polymerase II (class D), human polymerase
beta (class x), E. coli UmuC/DinB and eukaryotic RAP
30/Xeroderma pigmentosum variant (class Y). Family A
polymerase functions primarily to fill DNA gaps that
arise during DNA repair, recombination and replication.
Pol theta is an exception among family A polymerases and
generates processive single base substitutions. Family A
polymerase are found primarily in organisms related to
prokaryotes and include prokaryotic DNA polymerase I
(pol I) ,mitochondrial polymerase delta, and several
bacteriphage polymerases including those from
odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is
have two functional domains located on the same
polypeptide; a 5'-3' polymerase and 5'-3' exonuclease.
Pol I uses its 5' nuclease activity to remove the
ribonucleotide portion of newly synthesized Okazaki
fragments and DNA polymerase activity to fill in the
resulting gap. Polymerase theta mostly has
amino-terminal helicase domain, a carboxy-terminal
polymerase domain and an intervening space region.
Length = 373
Score = 34.1 bits (79), Expect = 0.31
Identities = 32/118 (27%), Positives = 48/118 (40%), Gaps = 33/118 (27%)
Query: 553 LRAMIQAPDGYSIIGADVDSQ-ELWI-ASVIGDSYCAKEHGATPLGWMTLSGQKSNATDM 610
LR P G ++ AD SQ EL I A + GD L ++ D+
Sbjct: 130 LRHAFIPPPGRVLLSADY-SQLELRILAHLSGDP--------------ALIELLNSGGDV 174
Query: 611 H-SITAKAVGIS--------REHAKIINYARIYGAG-ERFAERLLKQFNPEMSKSDAK 658
I A+ +G R+ AK + Y +YG G + AE+L +S+ +AK
Sbjct: 175 FKMIAAQWLGKPVEEVTDEERQQAKQLVYGILYGMGAKSLAEQL------GVSEEEAK 226
Score = 29.1 bits (66), Expect = 9.9
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 8/53 (15%)
Query: 763 INWVVQSGAVDFLHL-MLVCMR-------WLVSRDTRFVISIHDEIRYLVPDE 807
+N V+Q A D + + M+ L + R V+ IHDE+ + VP+
Sbjct: 285 VNTVIQGSAADIMKIAMINIHEKLHSLLPNLPAGRARLVLQIHDELLFEVPES 337
>gnl|CDD|163257 TIGR03425, urea_degr_2, urea carboxylase-associated protein 2. A
number of bacteria degrade urea as a nitrogen source by
the urea carboxylase/allophanate hydrolase pathway,
which uses biotin and consumes ATP, rather than my means
of the nickel-dependent enzyme urease. This model
represents one of a pair of homologous, tandem
uncharacterized genes found together with the urea
carboxylase and allophanate hydrolase genes.
Length = 233
Score = 30.7 bits (70), Expect = 2.6
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 831 LDMTDIPLSISFFSGVEID 849
L D+ +++FFS V +D
Sbjct: 132 LGRRDLVPNVNFFSKVAVD 150
>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 = 30.8 bits (70), Expect = 3.7
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 14/60 (23%)
Query: 609 DMHSITAKAV-GISREH--------AKIINYARIYGAGERFAERLLKQFNPEMSKSDAKS 659
D+H+ TA + G+ E AK IN+ +YG A L ++ +S+ +AK
Sbjct: 691 DIHTETASRLFGVEIEDVTPNMRRIAKTINFGVVYGMS---AFGLAQELG--ISRKEAKE 745
>gnl|CDD|147470 pfam05290, Baculo_IE-1, Baculovirus immediate-early protein (IE-0).
The Autographa californica multinucleocapsid nuclear
polyhedrosis virus (AcMNPV) ie-1 gene product (IE-1) is
thought to play a central role in stimulating early
viral transcription. IE-1 has been demonstrated to
activate several early viral gene promoters and to
negatively regulate the promoters of two other AcMNPV
regulatory genes, ie-0 and ie-2. It is thought that that
IE-1 negatively regulates the expression of certain
genes by binding directly, or as part of a complex, to
promoter regions containing a specific IE-1-binding
motif (5'-ACBYGTAA-3') near their mRNA start sites.
Length = 141
Score = 29.7 bits (67), Expect = 3.9
Identities = 17/73 (23%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 351 LEQLKQLYNNITKQDNCEANVDNAQNSLRDSVETNISFIDCSKS-AKRLEVIANVLDKKK 409
L+QL+++ C V Q +L + + ++ K+ +R++V+ NV + K
Sbjct: 21 LKQLRKILKLFVNDYCCSKLVKQNQAALDTLITRSQKYLHVIKAINERMQVM-NVFLEPK 79
Query: 410 LAEAS-STDTSTD 421
L + + DTS +
Sbjct: 80 LYQCNICQDTSAE 92
>gnl|CDD|235656 PRK05964, PRK05964, adenosylmethionine--8-amino-7-oxononanoate
transaminase; Provisional.
Length = 423
Score = 30.6 bits (70), Expect = 4.5
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 8/43 (18%)
Query: 456 FSDNSLAGVDIGAKRIIEISRM-LSYWRNNHERVKKQFVVWLN 497
FSD+ V++ K M L YWRN E + +F+
Sbjct: 107 FSDSGSVAVEVALK-------MALQYWRNRGEPGRSRFLSLRG 142
>gnl|CDD|148740 pfam07305, DUF1454, Protein of unknown function (DUF1454). This
family consists of several Enterobacterial sequences of
around 200 residues in length which are often known as
YiiQ proteins. The function of this family is unknown.
Length = 200
Score = 29.9 bits (67), Expect = 4.6
Identities = 11/44 (25%), Positives = 24/44 (54%)
Query: 638 ERFAERLLKQFNPEMSKSDAKSKARKMYTLTKGKKLYRLKDGHL 681
+ L++ F P +S++ ++ K + + T KGK+ Y +G +
Sbjct: 125 LEYMAALIRHFTPTLSQAQSQQKLQNLLTAGKGKRYYSHTEGAI 168
>gnl|CDD|220559 pfam10088, DUF2326, Uncharacterized protein conserved in bacteria
(DUF2326). This domain, found in various hypothetical
bacterial proteins, has no known function.
Length = 140
Score = 29.2 bits (66), Expect = 5.1
Identities = 13/47 (27%), Positives = 20/47 (42%), Gaps = 5/47 (10%)
Query: 458 DNSLAGVDIGAKRIIEISRMLSYWRNNHERVKKQFVVWLNKKDLPRR 504
D GVD R ++L E+ Q++V +NK LP+
Sbjct: 70 DGLFEGVD---DRQKA--KLLKLINEYAEKRGIQYIVTINKDKLPKD 111
>gnl|CDD|223235 COG0157, NadC, Nicotinate-nucleotide pyrophosphorylase [Coenzyme
metabolism].
Length = 280
Score = 29.8 bits (68), Expect = 5.7
Identities = 11/43 (25%), Positives = 19/43 (44%), Gaps = 2/43 (4%)
Query: 613 ITAKAVGISREHAKIINYARIYG--AGERFAERLLKQFNPEMS 653
IT +A+ A+ + A+ G AG AE + + P +
Sbjct: 23 ITTEALIPEDRKAEAVIIAKEAGVVAGLDVAEEVFELLGPSIE 65
>gnl|CDD|222962 PHA03036, PHA03036, DNA polymerase; Provisional.
Length = 1004
Score = 30.4 bits (69), Expect = 6.1
Identities = 15/65 (23%), Positives = 29/65 (44%)
Query: 448 LSRDFINKFSDNSLAGVDIGAKRIIEISRMLSYWRNNHERVKKQFVVWLNKKDLPRRLVE 507
++ + + +G +II+I ++SY+ N ER K +WL K+ R + +
Sbjct: 42 VTDELYKSLAPPPFESRFLGNMKIIDIDEIISYYVNIEERKKTTADLWLIKEPKKRNIEK 101
Query: 508 NIESE 512
E
Sbjct: 102 AFMDE 106
>gnl|CDD|176477 cd08640, DNA_pol_A_plastid_like, DNA polymerase A type from
plastids of higher plants possibly involve in DNA
replication or in the repair of errors occurring during
replication. DNA polymerase A type from plastids of
higher plants possibly involve in DNA replication or in
the repair of errors occurring during replication.
Family A polymerase functions primarily to fill DNA gaps
that arise during DNA repair, recombination and
replication. DNA-dependent DNA polymerases can be
classified in six main groups based upon phylogenetic
relationships with E. coli polymerase I (classA), E.
coli polymerase II (class B), E.coli polymerase III
(class C), euryarchaaeota polymerase II (class D), human
polymerase beta (class x), E. coli UmuC/DinB and
eukaryotic RAP 30/Xeroderma pigmentosum variant (class
Y). Family A polymerase are found primarily in organisms
related to prokaryotes and include prokaryotic DNA
polymerase I ,mitochondrial polymerase delta, and
several bacteriphage polymerases including those from
odd-numbered phage (T3, T5, and T7). The
three-dimensional structure of plastid DNA polymerase
has substantial similarity to Pol I. The structure of
Pol I resembles in overall morphology a cupped human
right hand, with fingers (which bind an incoming
nucleotide and interact with the single-stranded
template), palm (which harbors the catalytic amino acid
residues and also binds an incoming dNTP) and thumb
(which binds double-stranded DNA) subdomains.
Length = 371
Score = 30.1 bits (68), Expect = 6.2
Identities = 24/81 (29%), Positives = 36/81 (44%), Gaps = 9/81 (11%)
Query: 763 INWVVQSGAVDFLHL-MLVCMRWLVSRDTRF--VISIHDEIRYLVPDEEKYETALALHVT 819
IN +Q A D ML R L + + ++ IHDE+ P EEK + AL + V
Sbjct: 287 INTPIQGSAADIAMKAMLRIYRNLRLKRLGWKLLLQIHDEVILEGP-EEKADEALKI-VK 344
Query: 820 NLLTRAFCIKKLDMTDIPLSI 840
+ + F D+PL +
Sbjct: 345 DCMENPFFGP----LDVPLEV 361
>gnl|CDD|99748 cd06502, TA_like, Low-specificity threonine aldolase (TA). This
family belongs to pyridoxal phosphate (PLP)-dependent
aspartate aminotransferase superfamily (fold I). TA
catalyzes the conversion of L-threonine or
L-allo-threonine to glycine and acetaldehyde in a
secondary glycine biosynthetic pathway.
Length = 338
Score = 29.6 bits (67), Expect = 6.6
Identities = 28/134 (20%), Positives = 43/134 (32%), Gaps = 27/134 (20%)
Query: 537 TWMTASNAVGERVGSELRAMIQAPDGYSIIGADVDSQEL--WIASVIGDSYCAKEHGATP 594
T + + L AM A G + G D + +L A + G A
Sbjct: 6 TVTGPTPEM-------LEAMAAANVGDDVYGEDPTTAKLEARAAELFGK--EA------- 49
Query: 595 LGWMTLSGQKSNATDMHSITAK--AVGISREHAKIINYARIYGAGERFAERLLKQFNPE- 651
SG +N + + T +V I E A I GA E + L E
Sbjct: 50 -ALFVPSGTAANQLALAAHTQPGGSV-ICHETAHIYTDEA--GAPEFLSGVKLLPVPGEN 105
Query: 652 --MSKSDAKSKARK 663
++ D ++ R
Sbjct: 106 GKLTPEDLEAAIRP 119
>gnl|CDD|182031 PRK09694, PRK09694, helicase Cas3; Provisional.
Length = 878
Score = 29.8 bits (67), Expect = 9.4
Identities = 19/74 (25%), Positives = 29/74 (39%), Gaps = 10/74 (13%)
Query: 718 TESAMFNRLEEIATSLQPVTPFL----NCRLSRALEPVSEDDSKFIQTRINWVV------ 767
T +AM +RLE +A+ L P + N R + + + + WV
Sbjct: 343 TANAMLSRLEALASKLFPSPNLILAHGNSRFNHLFQSLKSRAATEQGQEEAWVQCCEWLS 402
Query: 768 QSGAVDFLHLMLVC 781
QS FL + VC
Sbjct: 403 QSNKRVFLGQIGVC 416
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
0.317 0.134 0.398
Gapped
Lambda K H
0.267 0.0766 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 46,025,731
Number of extensions: 4559968
Number of successful extensions: 4265
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4234
Number of HSP's successfully gapped: 39
Length of query: 899
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 793
Effective length of database: 6,236,078
Effective search space: 4945209854
Effective search space used: 4945209854
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: 41 (21.7 bits)
S2: 64 (28.4 bits)