RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781193|ref|YP_003065606.1| putative DNA polymerase from
bacteriophage origin [Candidatus Liberibacter asiaticus str. psy62]
(675 letters)
>gnl|CDD|176479 cd08642, DNA_pol_A_pol_I_A, 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
,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 = 378
Score = 180 bits (458), Expect = 2e-45
Identities = 87/264 (32%), Positives = 129/264 (48%), Gaps = 30/264 (11%)
Query: 203 LAHTLNQIVDVERTKLDQELESLTYGLVSSSRCLEKLKTWLFLETGLHLEDLTETTCQRV 262
L + D + +L +E + LT GL + +LK WL + G L + V
Sbjct: 1 LVNAAIACDDQYKEELLEEAKELT-GL-DNPNSPAQLKDWLNEQGGEVDSLLKKDV---V 55
Query: 263 LSSNKKLTPQAIQVFNNRMRASRSAVLKLNTLVEAMNSDGRLRGTLQFLGASRTGRWSGC 322
K +V R S+++V K + A+ SDGR+RG LQF GA+RTGRW+G
Sbjct: 56 ALLLKTAPGDVKRVLELRQELSKTSVKKYEAMERAVCSDGRVRGLLQFYGANRTGRWAGR 115
Query: 323 VFPPQNLPR-------------PSRSHEELDQIITHLPTSITSDPDPLQIISDCVRSCVI 369
+ QNLPR S + L+ + +P ++S +R+ I
Sbjct: 116 LVQVQNLPRNYLKDLDLARELVKSGDFDALELLYGSVP----------DVLSQLIRTAFI 165
Query: 370 ASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNVAPAQVTKDQ- 428
SEG + +V+D + IEARV+AW+AGEQW+L F T +Y + ++ F V ++ K+
Sbjct: 166 PSEGHRFIVSDFSAIEARVIAWLAGEQWRLDVFATHGKIYEASASQMFGVPVEKIGKNSH 225
Query: 429 -RAIGKVMELALGYQGGAKAFQKM 451
R GKV ELALGY G A + M
Sbjct: 226 LRQKGKVAELALGYGGSVGALKAM 249
Score = 111 bits (280), Expect = 6e-25
Identities = 44/83 (53%), Positives = 54/83 (65%), Gaps = 1/83 (1%)
Query: 592 TYGGKLTENIVQAVSRDILAEGMMNATKAGYDIVLTVHDEIVCETPDTDEFNASMLYHLM 651
GGKL ENIVQA++RD LAE M+ KAGYDIV+ VHDE+V E P E + + +M
Sbjct: 297 KLGGKLVENIVQAIARDCLAEAMLRLEKAGYDIVMHVHDEVVIEVP-EGEGSLEEVNEIM 355
Query: 652 TSNPSWAKGLPLKAEGYESKRYR 674
P WA GLPL A+G+ES Y
Sbjct: 356 AQPPPWAPGLPLNADGFESPYYM 378
>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 = 91.3 bits (227), Expect = 7e-19
Identities = 74/387 (19%), Positives = 121/387 (31%), Gaps = 100/387 (25%)
Query: 297 AMNSDGRLRGTLQFL-GASRTGRWSGCVFPPQNLPRPSRSHEELDQIITHLPTSITSDPD 355
DGR +++ G + TGRW+ Q +PR ++
Sbjct: 52 QWVRDGRFHP--EYVPGGTVTGRWASRGGNAQQIPRRDPLGRDI---------------- 93
Query: 356 PLQIISDCVRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYAR 415
R +A G LVVAD + +E RVLA ++G++ +AF G DLY T +
Sbjct: 94 ---------RQAFVADPGWTLVVADASQLELRVLAALSGDEALAEAFGRGGDLYTATASA 144
Query: 416 SFNVAPAQVTKDQRAIGKVMELALGYQGGAKAFQKMASTTGLNLNTFAHLVKTNSAPEEW 475
F V V +R K+ L Y GA T+G++ A L + ++
Sbjct: 145 MFGVP---VGGGERQHAKIANLGAMY--GA--------TSGISARLLAQLRRISTKEAA- 190
Query: 476 EDAENFCRWMQENHPEHAIEDLFIGTACERVKKAWRQKHSRVSELWNELHQAFEQTIENG 535
E F A E V+ A R+ + +T
Sbjct: 191 ALIELFFSRFPAF-----------PKAMEYVEDAARRGERGG----------YVRT---- 225
Query: 536 KAIIARKRRDVPLVYMKKDKNNLILMLPSGRSLVYRDVGNNRSYLNTTTRQLTREYTYGG 595
++ R+ P R S +R G
Sbjct: 226 --LLGRRSP-----------------PPDIRW------TEVVSDPAAASRARRVRRAAGR 260
Query: 596 KLTENIVQAVSRDILAEGMMN------ATKAGYDIVLTVHDEIVCETP-DTDEFNASMLY 648
+VQ + D M+ +V VHDE+V P + E A+++
Sbjct: 261 FARNFVVQGTAADWAKLAMVALRRRLEELALDARLVFFVHDEVVLHCPKEEAEAVAAIVR 320
Query: 649 HLM-TSNPSWAKGLPLKAEGYESKRYR 674
+ +P++ +R
Sbjct: 321 EAAEQAVRLLFGSVPVRFPVKIGVVWR 347
>gnl|CDD|144170 pfam00476, DNA_pol_A, DNA polymerase family A.
Length = 383
Score = 79.7 bits (197), Expect = 3e-15
Identities = 101/448 (22%), Positives = 157/448 (35%), Gaps = 132/448 (29%)
Query: 239 LKTWLFLETGLHLEDLTETTCQRVLSSN--KKLTPQA------IQVFNNRMRASRSAVLK 290
L LF E GL T+ T R +++ + L A I + + + V K
Sbjct: 40 LGVLLFEELGLPKTKKTDKTGARSTNADVLESLREDAHEIIKIILEYRQLSKLQSTYVDK 99
Query: 291 LNTLVEAMNSDGRLRGTLQFLGASRTGRWSGCVFPPQNLPRPSRSHEELDQIITHLPTSI 350
L +++ DGR+ + G TGR S QN+P + E+
Sbjct: 100 LPLMID--PDDGRIHTSYNQAGT-ATGRLSSTDPNLQNIPIRNEYGREI----------- 145
Query: 351 TSDPDPLQIISDCVRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYV 410
R+ IA G LV AD + IE R+LA ++G++ ++AF TG D++
Sbjct: 146 --------------RAAFIAEPGYVLVAADYSQIELRILAHLSGDENLIEAFRTGADIHT 191
Query: 411 TTYARSFNVAPAQVTKDQRAIGKVMELALGYQGGAKAFQKMASTTGLNLNTFAHLVKTNS 470
T A F V +VT +QR K Y AK ++ L ++
Sbjct: 192 LTAADIFGVDLHEVTGNQRRNAKTFNFGRIYGASAKGLSQL-----LGISR--------- 237
Query: 471 APEEWEDAENFCRWMQENHP--EHAIEDLFIGTACERVKKAWRQKHSRVSELWNELHQAF 528
E+A+ F E P + E K+A + +
Sbjct: 238 -----EEAKEFIEKYFERFPGVKRYREKTR--------KEAKK--------------GGY 270
Query: 529 EQTIENGKAIIARKRRDVPLVYMKKDKNNLILMLPSGRSLVYRDVGNNRSYLNTTTRQLT 588
+T+ +RR +P + R+ R+ R+ LNT
Sbjct: 271 VETLFG-------RRRYLPDI--------------DSRNRSLRE-AAERAALNT------ 302
Query: 589 REYTYGGKLTENIVQAVSRDILAEGMMNATKAGYD------IVLTVHDEIVCETPDTD-E 641
+Q + DIL M+ +A + + L VHDEIV E P + E
Sbjct: 303 ------------PIQGSAADILKLAMIKLDEALVEKGLDARMCLQVHDEIVFEVPKEEAE 350
Query: 642 FNASMLYHLMTSNPSWAKGL--PLKAEG 667
A+ + LM A L PL E
Sbjct: 351 AVAAQIKELME----RAMFLDVPLLVEV 374
>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 = 78.9 bits (195), Expect = 4e-15
Identities = 42/155 (27%), Positives = 69/155 (44%), Gaps = 32/155 (20%)
Query: 301 DGRLRGTLQFLGASRTGRWSGCVFPP-QNLPRPSRSHEELDQIITHLPTSITSDPDPLQI 359
GR+ + +GA +GR S C P Q +PR
Sbjct: 60 TGRIHPSFNQIGA-ASGRMS-CSNPNLQQIPREREF------------------------ 93
Query: 360 ISDCVRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNV 419
R C +A EG KL++AD + IE R+ A ++G++ + A++ GEDL+ T +
Sbjct: 94 -----RRCFVAPEGNKLIIADYSQIELRIAAEISGDERMISAYQKGEDLHRLTASLITGK 148
Query: 420 APAQVTKDQRAIGKVMELALGYQGGAKAFQKMAST 454
++TK++R + K + L Y AK ++ A T
Sbjct: 149 PIEEITKEERQLAKAVNFGLIYGMSAKGLREYART 183
Score = 29.6 bits (67), Expect = 2.8
Identities = 16/40 (40%), Positives = 19/40 (47%), Gaps = 4/40 (10%)
Query: 602 VQAVSRDILAEGM--MNATKAGYD--IVLTVHDEIVCETP 637
+Q DIL + + D IVL VHDEIV E P
Sbjct: 246 IQGTGADILKLALALLVDRLKDLDAKIVLCVHDEIVLEVP 285
>gnl|CDD|31092 COG0749, PolA, DNA polymerase I - 3'-5' exonuclease and polymerase
domains [DNA replication, recombination, and repair].
Length = 593
Score = 74.2 bits (182), Expect = 1e-13
Identities = 43/130 (33%), Positives = 62/130 (47%), Gaps = 9/130 (6%)
Query: 325 PPQNLPRPSRSHEELDQIITHLPTSITSDPDPLQIIS------DCVRSCVIASEGKKLVV 378
P P R H +Q T +SDP+ LQ I +R +A +G L+
Sbjct: 310 PKLINPDTGRIHTSFNQTGTATGRLSSSDPN-LQNIPIRSEEGRKIRKAFVAEKGYTLIS 368
Query: 379 ADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNVAPAQVTKDQRAIGKVMELA 438
AD + IE R+LA ++ ++ L+AF GED++ T A F V +VT +QR K +
Sbjct: 369 ADYSQIELRILAHLSQDEGLLRAFTEGEDIHTATAAEVFGVPIEEVTSEQRRKAKAINFG 428
Query: 439 LGYQGGAKAF 448
L Y G AF
Sbjct: 429 LIY--GMSAF 436
>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 = 69.8 bits (172), Expect = 2e-12
Identities = 28/71 (39%), Positives = 44/71 (61%)
Query: 364 VRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNVAPAQ 423
+R +A EG L+ AD + IE R+LA ++G++ ++AF+ GED++ T A F V P +
Sbjct: 141 IRKAFVAEEGWVLLSADYSQIELRILAHLSGDEALIEAFKNGEDIHTRTAAEVFGVPPEE 200
Query: 424 VTKDQRAIGKV 434
VT + R I K
Sbjct: 201 VTPEMRRIAKA 211
Score = 28.9 bits (66), Expect = 4.7
Identities = 14/44 (31%), Positives = 26/44 (59%), Gaps = 3/44 (6%)
Query: 624 IVLTVHDEIVCETPDTD-EFNASMLYHLMTSNPSWAKGLPLKAE 666
++L VHDE+V E P+ + E A+++ M + + +PLK +
Sbjct: 328 MLLQVHDELVFEVPEEELEEVAALVKEEMENAVELS--VPLKVD 369
>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 = 59.9 bits (146), Expect = 2e-09
Identities = 38/149 (25%), Positives = 64/149 (42%), Gaps = 15/149 (10%)
Query: 301 DGRLRGT-LQFLGASRTGRWSGCVFPP-QNLPRPSRSHEELDQIITHLPTSITSDPDPLQ 358
R+ T Q A TGR S P QN+P+ I P+ +
Sbjct: 78 MYRIHPTWNQTGTA--TGRLS-SSEPNLQNVPKDF--------EIKDAPSPPAGSEGDIP 126
Query: 359 IISDCVRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFN 418
IS +R I G+ L+ AD + +E R+LA ++G+ ++ +G D++ A+
Sbjct: 127 TIS--LRHAFIPPPGRVLLSADYSQLELRILAHLSGDPALIELLNSGGDVFKMIAAQWLG 184
Query: 419 VAPAQVTKDQRAIGKVMELALGYQGGAKA 447
+VT ++R K + + Y GAK+
Sbjct: 185 KPVEEVTDEERQQAKQLVYGILYGMGAKS 213
Score = 29.9 bits (68), Expect = 2.4
Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 14/66 (21%)
Query: 601 IVQAVSRDILAEGMMN-----------ATKAGYDIVLTVHDEIVCETPDT--DEFNASML 647
++Q + DI+ M+N +VL +HDE++ E P++ DE A ++
Sbjct: 288 VIQGSAADIMKIAMINIHEKLHSLLPNLPAGRARLVLQIHDELLFEVPESDVDEV-ARII 346
Query: 648 YHLMTS 653
M +
Sbjct: 347 KRSMEN 352
>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 = 55.5 bits (134), Expect = 5e-08
Identities = 48/222 (21%), Positives = 74/222 (33%), Gaps = 60/222 (27%)
Query: 259 CQRVLSSNKKLTPQAIQVFNNRMRASRSAVLKLNTLVEAM-----NSDGRLRGTLQFLGA 313
C S + +A + + L L+T + + +S GR+ +L
Sbjct: 27 CYENGVSGGEEGKEACEAIEALKEIKSISTL-LSTFIIPLQELLNDSTGRIHCSLNIN-- 83
Query: 314 SRTGRWSGCVFPP--QNLPRPSRSHEELDQIITHLPTSITSDPDPLQIISDCVRSCVIAS 371
+ TGR S P QN P + D +I R IAS
Sbjct: 84 TETGRLSS--RNPNLQNQPAL--------------------EKDRYKI-----RKAFIAS 116
Query: 372 EGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTT------------------- 412
G L+VAD + +E R+LA M + ++AF G D + T
Sbjct: 117 PGNTLIVADYSQLELRLLAHMTRCKSMIEAFNAGGDFHSRTASGMYPHVAEAVANGEVLL 176
Query: 413 --YARSFNVAP--AQVTKDQRAIGKVMELALGYQGGAKAFQK 450
+ AP K +R KV+ ++ Y A K
Sbjct: 177 EWKSEGKPPAPLLKDKFKSERRKAKVLNFSIAYGKTAHGLAK 218
Score = 31.6 bits (72), Expect = 0.76
Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 5/50 (10%)
Query: 621 GYDIVLTVHDEIVCETP-DTDEFNASMLYHLMTSNPSWAKGL--PLKAEG 667
G+ ++L +HDE++ E P + + ++ M NP + L PL+ +G
Sbjct: 316 GWKLLLQIHDEVILEGPEEKADEALKIVKDCM-ENP-FFGPLDVPLEVDG 363
>gnl|CDD|99834 cd06130, DNA_pol_III_epsilon_like, an uncharacterized bacterial
subgroup of the DEDDh 3'-5' exonuclease domain family
with similarity to the epsilon subunit of DNA polymerase
III. This subfamily is composed of uncharacterized
bacterial proteins with similarity to the epsilon
subunit of DNA polymerase III (Pol III), a multisubunit
polymerase which is the main DNA replicating enzyme in
bacteria, functioning as the chromosomal replicase. The
Pol III holoenzyme is a complex of ten different
subunits, three of which (alpha, epsilon, and theta)
compose the catalytic core. The Pol III epsilon subunit,
encoded by the dnaQ gene, is a DEDDh-type 3'-5'
exonuclease which is responsible for the proofreading
activity of the polymerase, increasing the fidelity of
DNA synthesis. It contains three conserved sequence
motifs termed ExoI, ExoII and ExoIII, with a specific
Hx(4)D conserved pattern at ExoIII. These motifs are
clustered around the active site and contain four
conserved acidic residues that serve as ligands for the
two metal ions required for catalysis. The epsilon
subunit of Pol III also functions as a stabilizer of the
holoenzyme complex.
Length = 156
Score = 52.1 bits (126), Expect = 5e-07
Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 7/76 (9%)
Query: 51 PVMPQVLKEALEN-TDVTIVAHNSYFERTVLKAC---FNLDIPIHRWICTLVLARS--NG 104
P P+V E +VAHN+ F+R+VL+A + L P ++++CT+ LAR
Sbjct: 62 PTFPEVWPEIKPFLGGSLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPL 121
Query: 105 LPS-ALKAVGEALKLS 119
LP+ L V E L +
Sbjct: 122 LPNHKLNTVAEHLGIE 137
>gnl|CDD|144991 pfam01612, 3_5_exonuc, 3'-5' exonuclease. This domain is
responsible for the 3'-5' exonuclease proofreading
activity of E. coli DNA polymerase I (polI) and other
enzymes, it catalyses the hydrolysis of unpaired or
mismatched nucleotides. This domain consists of the
amino-terminal half of the Klenow fragment in E. coli
polI it is also found in the Werner syndrome helicase
(WRN), focus forming activity 1 protein (FFA-1) and
ribonuclease D (RNase D). Werner syndrome is a human
genetic disorder causing premature aging; the WRN
protein has helicase activity in the 3'-5' direction.
The FFA-1 protein is required for formation of a
replication foci and also has helicase activity; it is a
homologue of the WRN protein. RNase D is a 3'-5'
exonuclease involved in tRNA processing. Also found in
this family is the autoantigen PM/Scl thought to be
involved in polymyositis-scleroderma overlap syndrome.
Length = 172
Score = 43.8 bits (104), Expect = 2e-04
Identities = 29/152 (19%), Positives = 50/152 (32%), Gaps = 25/152 (16%)
Query: 30 VILFAFGFDDHPVELWDCVHDPVMPQVLKEALENTDVTIVAHNSYFERTVLKACFNLDIP 89
L + + D + + LK LE+ ++T V HN+ F+ VL F I
Sbjct: 41 GCLIQISTGEGAYII-DPLALGDDLEGLKRLLEDPNITKVGHNAKFDLEVLARDF--GIK 97
Query: 90 IHRWICTLVLARSNGLPSALKAVGEALKLSSQKMEEGKELIARFCKGET---HECLYDRN 146
+ T++ A G P + L +L ++ E +C R
Sbjct: 98 LENLFDTMLAAYLLGYP-------RSHSL--------DDLAEKYLGVELDKSEQCADWRA 142
Query: 147 KPNHREAWRLFGEYCKGDVTVTREIFKRLEPL 178
+P E Y D ++ +L
Sbjct: 143 RPLSEEQ----LRYAAEDADYLLRLYDKLRKE 170
>gnl|CDD|176648 cd06127, DEDDh, DEDDh 3'-5' exonuclease domain family. DEDDh
exonucleases, part of the DnaQ-like (or DEDD)
exonuclease superfamily, catalyze the excision of
nucleoside monophosphates at the DNA or RNA termini in
the 3'-5' direction. These proteins contain four
invariant acidic residues in three conserved sequence
motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases
are classified as such because of the presence of
specific Hx(4)D conserved pattern at the ExoIII motif.
The four conserved acidic residues are clustered around
the active site and serve as ligands for the two metal
ions required for catalysis. Most DEDDh exonucleases are
the proofreading subunits (epsilon) or domains of
bacterial DNA polymerase III, the main replicating
enzyme in bacteria, which functions as the chromosomal
replicase. Other members include other DNA and RNA
exonucleases such as RNase T, Oligoribonuclease, and RNA
exonuclease (REX), among others.
Length = 159
Score = 42.7 bits (101), Expect = 3e-04
Identities = 19/55 (34%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 51 PVMPQVLKEALE-NTDVTIVAHNSYFERTVLKACF---NLDIPIHRWICTLVLAR 101
P +VL E LE +VAHN+ F+ L + WI TL LAR
Sbjct: 64 PPFEEVLPEFLEFLGGRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLAR 118
>gnl|CDD|28891 cd00007, 35EXOc, 3'-5' exonuclease. The 35EXOc domain is
responsible for the 3'-5' exonuclease proofreading
activity of prokaryotic DNA polymerase I (pol I) and
other enzymes, it catalyses the hydrolysis of unpaired
or mismatched nucleotides. This domain consists of the
amino-terminal half of the Klenow fragment in E. coli
pol I. 35EXOc is also found in the Werner syndrome
helicase (WRN), focus forming activity 1 protein (FFA-1)
and ribonuclease D (RNase D)..
Length = 155
Score = 40.0 bits (93), Expect = 0.002
Identities = 24/153 (15%), Positives = 45/153 (29%), Gaps = 21/153 (13%)
Query: 30 VILFAFGFDDHPVELWDCVHDPVMPQVLKEALENTDVTIVAHNSYFERTVLKACFNLDIP 89
++ + D + + LKE LE+ D+T V H++ F+ VL
Sbjct: 19 LVGIQIATAGEAAYIPDELELEEDLEALKELLEDEDITKVGHDAKFDLVVLARDGIELPG 78
Query: 90 IHRWICTLVLARSNGLPSALKAVGEALKLSSQKMEEG-KELIARFCKGET---HECLYDR 145
T++ A L+ + +L + E +
Sbjct: 79 NI--FDTMLAAY---------------LLNPGEGSHSLDDLAKEYLGIELDKDEQIYGKG 121
Query: 146 NKPNHREAWRLFGEYCKGDVTVTREIFKRLEPL 178
K R EY D ++++L
Sbjct: 122 AKTFARPLSEELLEYAAEDADALLRLYEKLLEE 154
>gnl|CDD|31188 COG0847, DnaQ, DNA polymerase III, epsilon subunit and related
3'-5' exonucleases [DNA replication, recombination, and
repair].
Length = 243
Score = 39.0 bits (90), Expect = 0.004
Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 5/67 (7%)
Query: 40 HPVELWDCVHDPVMPQVLKEALE--NTDVTIVAHNSYFERTVLKACF---NLDIPIHRWI 94
H + P +VL E L+ +VAHN+ F+ L+ ++IP +
Sbjct: 68 HGITDEMLADAPKFAEVLPEFLDFIGGLRLLVAHNAAFDVGFLRVESERLGIEIPGDPVL 127
Query: 95 CTLVLAR 101
TL LAR
Sbjct: 128 DTLALAR 134
>gnl|CDD|176651 cd06139, DNA_polA_I_Ecoli_like_exo, DEDDy 3'-5' exonuclease domain
of Escherichia coli DNA polymerase I and similar
bacterial family-A DNA polymerases. Escherichia
coli-like Polymerase I (Pol I), a subgroup of family-A
DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5'
exonuclease domain in the same polypeptide chain as the
polymerase domain. The exonuclease domain contains three
conserved 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 3'-5'
exonuclease domain of DNA polymerases has a fundamental
role in reducing polymerase errors and is involved in
proofreading activity. E. coli DNA Pol I is involved in
genome replication but is not the main replicating
enzyme. It is also implicated in DNA repair.
Length = 193
Score = 38.7 bits (91), Expect = 0.005
Identities = 29/142 (20%), Positives = 49/142 (34%), Gaps = 19/142 (13%)
Query: 55 QVLKEALENTDVTIVAHNSYFERTVLKACFNLDIPIHRWIC-TLVLAR---SNGLPSALK 110
LK LE+ + V N F+ VL N I + T++ + L
Sbjct: 57 AALKPLLEDPSIKKVGQNLKFDLHVLA---NHGIELRGPAFDTMLASYLLNPGRRRHGLD 113
Query: 111 AVGEALKLSSQKMEEGKELIARFCKGETHECLYDRNKPNHREAWRLFGEYCKGDVTVTRE 170
+ A + K ++L+ KG+ E EY D +T
Sbjct: 114 DL--AERYLGHKTISFEDLVG---KGKKQITFDQV----PLEKA---AEYAAEDADITLR 161
Query: 171 IFKRLEPLSSKEQELWYLDQTI 192
+++ L+P +E L L + I
Sbjct: 162 LYELLKPKLKEEPGLLELYEEI 183
>gnl|CDD|99835 cd06131, DNA_pol_III_epsilon_Ecoli_like, DEDDh 3'-5' exonuclease
domain of the epsilon subunit of Escherichia coli DNA
polymerase III and similar proteins. This subfamily is
composed of the epsilon subunit of Escherichia coli DNA
polymerase III (Pol III) and similar proteins. Pol III
is the main DNA replicating enzyme in bacteria,
functioning as the chromosomal replicase. It is a
holoenzyme complex of ten different subunits, three of
which (alpha, epsilon, and theta) compose the catalytic
core. The Pol III epsilon subunit, encoded by the dnaQ
gene, is a DEDDh-type 3'-5' exonuclease which is
responsible for the proofreading activity of the
polymerase, increasing the fidelity of DNA synthesis. It
contains three conserved sequence motifs termed ExoI,
ExoII and ExoIII, with a specific Hx(4)D conserved
pattern at ExoIII. These motifs are clustered around the
active site and contain four conserved acidic residues
that serve as ligands for the two metal ions required
for catalysis. The epsilon subunit of Pol III also
functions as a stabilizer of the holoenzyme complex.
Length = 167
Score = 32.5 bits (75), Expect = 0.39
Identities = 15/43 (34%), Positives = 19/43 (44%), Gaps = 6/43 (13%)
Query: 65 DVTIVAHNSYFERTVLKACFNLD------IPIHRWICTLVLAR 101
+V HN+ F+ L A +L I R I TL LAR
Sbjct: 81 GAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALAR 123
>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 = 32.0 bits (73), Expect = 0.51
Identities = 11/26 (42%), Positives = 13/26 (50%)
Query: 365 RSCVIASEGKKLVVADLAGIEARVLA 390
R G LV AD +G+E R LA
Sbjct: 178 RELFGVPPGWSLVGADASGLELRCLA 203
>gnl|CDD|39364 KOG4162, KOG4162, KOG4162, Predicted calmodulin-binding protein
[Signal transduction mechanisms].
Length = 799
Score = 31.5 bits (71), Expect = 0.68
Identities = 22/90 (24%), Positives = 36/90 (40%), Gaps = 9/90 (10%)
Query: 161 CKGDVTVTREIFKRLEPLSSKEQELWYLDQTINDRGYCVDVALAHTLNQIVDVERTKLDQ 220
G V E F++ P S E E WY A + + + E K +
Sbjct: 335 RCGQFEVLAEQFEQALPFSFGEHERWYQ------LALSYSAAGSDSKAVNLLRESLKKSE 388
Query: 221 ELESLTYGLVSSSRCLEKLKTWLFLETGLH 250
+ ++ L++S C+E+LK +E GL
Sbjct: 389 QPSDISVLLMASKLCIERLKL---VEEGLD 415
>gnl|CDD|32445 COG2264, PrmA, Ribosomal protein L11 methylase [Translation,
ribosomal structure and biogenesis].
Length = 300
Score = 30.3 bits (68), Expect = 1.8
Identities = 12/56 (21%), Positives = 20/56 (35%), Gaps = 5/56 (8%)
Query: 457 LNLNTFAHLVKTNSAPEEWEDAENFCRWMQENHPEHAIEDLFIGTACERVKKAWRQ 512
L FAH+++ E+WE W + HP E I + + +
Sbjct: 80 ALLELFAHVIEQEEDEEDWERE-----WKKYFHPVRIGERFVIVPSWREYPEPSDE 130
>gnl|CDD|145226 pfam01937, DUF89, Protein of unknown function DUF89. This family
has no known function.
Length = 314
Score = 29.2 bits (66), Expect = 3.7
Identities = 11/50 (22%), Positives = 18/50 (36%), Gaps = 6/50 (12%)
Query: 19 CGICKYAEDVCVILFAFGFDDHPVELWDCVHDPVMPQVLKEALENTDVTI 68
G+ + D +I F ++ W+ M L E L D+ I
Sbjct: 227 AGLDELLADGKLIDSGSDFWTPGLDYWE------MSPELYEELSKADLVI 270
>gnl|CDD|176453 cd00424, PolY, Y-family of DNA polymerases. Y-family DNA
polymerases are a specialized subset of polymerases that
facilitate translesion synthesis (TLS), a process that
allows the bypass of a variety of DNA lesions. Unlike
replicative polymerases, TLS polymerases lack
proofreading activity and have low fidelity and low
processivity. They use damaged DNA as templates and
insert nucleotides opposite the lesions. The active
sites of TLS polymerases are large and flexible to allow
the accomodation of distorted bases. Most TLS
polymerases are members of the Y-family, including Pol
eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is
found exclusively in bacteria. In eukaryotes, the
B-family polymerase Pol zeta also functions as a TLS
polymerase. Expression of Y-family polymerases is often
induced by DNA damage and is believed to be highly
regulated. TLS is likely induced by the
monoubiquitination of the replication clamp PCNA, which
provides a scaffold for TLS polymerases to bind in order
to access the lesion. Because of their high error
rates, TLS polymerases are potential targets for cancer
treatment and prevention.
Length = 343
Score = 28.9 bits (65), Expect = 5.4
Identities = 33/133 (24%), Positives = 44/133 (33%), Gaps = 19/133 (14%)
Query: 203 LAHTLNQIVDVERTKLDQELESLTYGLVSSSRCLEKLKTWLFLETGLHLEDLTETTCQRV 262
A +N I D+ D L G VS R + G+ E L+ ++
Sbjct: 190 EAVGINPIGDLLAASPDALLALW--GGVSGER-------LWYALRGIDDEPLSPPRPRKS 240
Query: 263 LSSNKKLTPQAIQVFNNRMRASRSAVLKLNTLVEAMNSDGRLRGTLQFLGASRTGRWSGC 322
S + L N A L L L + DGR L+ + GRWSG
Sbjct: 241 FSHERVLPRD----SRNAEDARPLLRLLLEKLARRLRRDGRGATRLRLWLRTVDGRWSGH 296
Query: 323 VFPPQNLPRPSRS 335
PSRS
Sbjct: 297 ------ADIPSRS 303
>gnl|CDD|111839 pfam02993, MCPVI, Minor capsid protein VI. This minor capsid
protein may act as a link between the external capsid
and the internal DNA-protein core. The C-terminal 11
residues may function as a protease cofactor leading to
enzyme activation.
Length = 238
Score = 28.6 bits (64), Expect = 6.1
Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 188 LDQTINDRGYCVDVA--LAHTLNQIVDVERTKLDQELESL 225
L Q + D G V ++ +VD+ R K++++LE L
Sbjct: 66 LRQGLKDSGLQRKVVEGAGQGIHGLVDIGRQKVEKDLEKL 105
>gnl|CDD|35829 KOG0609, KOG0609, KOG0609, Calcium/calmodulin-dependent serine
protein kinase/membrane-associated guanylate kinase
[Signal transduction mechanisms].
Length = 542
Score = 28.0 bits (62), Expect = 7.9
Identities = 26/114 (22%), Positives = 46/114 (40%), Gaps = 24/114 (21%)
Query: 215 RTKLDQELESLTYGLVSSSRCLEKLKTWLFLETGLHLEDLTET---TCQRVLSSNK---- 267
R E++ + Y VS ++ FLE G + +L T + + V++S K
Sbjct: 377 RPPRSDEVDGVEYHFVSKEEMEADIRAGKFLEYGEYEGNLYGTSLDSVRNVIASGKICVL 436
Query: 268 KLTPQAIQVFNN----------------RMRASRSAVLKLNTLVEAMNSDGRLR 305
+ PQA++V +RA R V ++T+V +D L+
Sbjct: 437 DVEPQALKVLRTAEFKPYVIFIAPPSLEELRALR-KVAVMSTIVAKQFTDEDLQ 489
>gnl|CDD|38861 KOG3657, KOG3657, KOG3657, Mitochondrial DNA polymerase gamma,
catalytic subunit [Replication, recombination and
repair].
Length = 1075
Score = 28.1 bits (62), Expect = 8.8
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 151 REAWRLFGEYCKGDVTVTREIFKRLEPL 178
RE ++ YC DV T ++F RL PL
Sbjct: 355 RENFQPLMNYCARDVIATHQVFFRLFPL 382
>gnl|CDD|144091 pfam00370, FGGY_N, FGGY family of carbohydrate kinases, N-terminal
domain. This domain adopts a ribonuclease H-like fold
and is structurally related to the C-terminal domain.
Length = 245
Score = 28.0 bits (63), Expect = 9.6
Identities = 18/71 (25%), Positives = 25/71 (35%), Gaps = 19/71 (26%)
Query: 421 PAQVTKDQRAIGKVMELALGYQGGAKAFQKMASTTGLNLNTFAHLVKTNSAPEEWEDAEN 480
PA + D R V L GGA ++ TG + L K
Sbjct: 94 PAILWNDTRTAEIVENLK--ELGGADKLYEI---TGNTIWPGFTLSKL------------ 136
Query: 481 FCRWMQENHPE 491
RW++E+ PE
Sbjct: 137 --RWLKEHEPE 145
>gnl|CDD|147383 pfam05170, AsmA, AsmA family. The AsmA gene, whose product is
involved in the assembly of outer membrane proteins in
Escherichia coli. AsmA mutations were isolated as
extragenic suppressors of an OmpF assembly mutant. AsmA
may have a role in LPS biogenesis.
Length = 537
Score = 27.8 bits (62), Expect = 9.8
Identities = 6/32 (18%), Positives = 11/32 (34%)
Query: 509 AWRQKHSRVSELWNELHQAFEQTIENGKAIIA 540
W+ + R+S L + NG +
Sbjct: 270 RWQTGNVRLSGNLKSLTANLDDLSFNGLKWVG 301
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.319 0.133 0.403
Gapped
Lambda K H
0.267 0.0672 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 8,115,569
Number of extensions: 424426
Number of successful extensions: 1080
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1070
Number of HSP's successfully gapped: 37
Length of query: 675
Length of database: 6,263,737
Length adjustment: 100
Effective length of query: 575
Effective length of database: 4,102,837
Effective search space: 2359131275
Effective search space used: 2359131275
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 (27.4 bits)