RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780277|ref|YP_003064690.1| DNA polymerase I [Candidatus
Liberibacter asiaticus str. psy62]
(976 letters)
>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 = 602 bits (1555), Expect = e-172
Identities = 205/382 (53%), Positives = 277/382 (72%), Gaps = 6/382 (1%)
Query: 591 DQDLLKQVSAEISKNLLSLEENIYDLSGEKFNLSSPKQLGDILFTKLKFPSGAKTKTGQW 650
D + L+++S E+ K L LEE IY+L+GE+FN++SPKQLG++LF KL P G KTKTG
Sbjct: 1 DTEYLEELSEELEKELAELEEEIYELAGEEFNINSPKQLGEVLFEKLGLPVGKKTKTGYS 60
Query: 651 KTTAQDLEQINCGDNPIIKNILEWRQLSKIKSTYADSLPNHINKRTQRVHTFYSLASTMT 710
T A+ LE++ ++PI++ ILE+R+L+K+KSTY D+LP IN +T R+HT ++ T T
Sbjct: 61 -TDAEVLEKL-ADEHPIVELILEYRELTKLKSTYVDALPKLINPKTGRIHTSFNQTVTAT 118
Query: 711 GRLASLEPNLQNIPIKTDLGQKIRRAFISPPTKKLISADYSQIELRILAHIAKITPLYQV 770
GRL+S +PNLQNIPI+T+ G++IR+AF++ L+SADYSQIELRILAH++ L +
Sbjct: 119 GRLSSSDPNLQNIPIRTEEGREIRKAFVAEEGWVLLSADYSQIELRILAHLSGDEALIEA 178
Query: 771 FENSLDIHRMVAAEIFGVNIEKVSPQMRRHAKTINFSIIYGISPFRLATQLRIPRSEAAD 830
F+N DIH AAE+FGV E+V+P+MRR AK +NF IIYGIS F L+ QL I R EA +
Sbjct: 179 FKNGEDIHTRTAAEVFGVPPEEVTPEMRRIAKAVNFGIIYGISAFGLSQQLGISRKEAKE 238
Query: 831 YIKRYFHRFPGIHEYIEKTKNFVRQNGYVETIFGRRIHYDEINSPKSSIRNINERAAINA 890
YI RYF R+PG+ EY+E+T R+ GYVET+FGRR + EINS ++R ER AIN
Sbjct: 239 YIDRYFARYPGVKEYMEETVEEAREKGYVETLFGRRRYIPEINSKNRNVRAFAERIAINT 298
Query: 891 PIQGSAADITRRAMISVHKSLEDHKLATKMLLQIHDELVFEVPEEEITTASQIIVHSMEK 950
PIQG+AADI + AMI VHK+L++ L +MLLQ+HDELVFEVPEEE+ + ++ ME
Sbjct: 299 PIQGTAADIIKLAMIRVHKALKEEGLKARMLLQVHDELVFEVPEEELEEVAALVKEEMEN 358
Query: 951 ACLPKINLRVPLKVNIKVSNNW 972
A + L VPLKV++ V NW
Sbjct: 359 A----VELSVPLKVDVGVGKNW 376
>gnl|CDD|31092 COG0749, PolA, DNA polymerase I - 3'-5' exonuclease and polymerase
domains [DNA replication, recombination, and repair].
Length = 593
Score = 596 bits (1538), Expect = e-171
Identities = 266/612 (43%), Positives = 386/612 (63%), Gaps = 28/612 (4%)
Query: 368 YTKIVNTKDIQQWVQKLETIGSASFKIITDTMDAFHSKPIAIAISTLDQKDDTSFKVETI 427
Y I + + W+ KL + +F TD +D + + ++++ + E
Sbjct: 3 YGTITDLAVLNAWLTKLNAAANIAFDTETDGLDPHGADLVGLSVA---------SEEEAA 53
Query: 428 FIDLSVHTSQDSTGKNTLTKEILSYLKKFFENEHFLKIGHNIKYDKLVLHRYGISMRGFE 487
+I L Q +L+ LK E+E K+G N+KYD VL GI
Sbjct: 54 YIPLLHGPEQ---------LNVLAALKPLLEDEGIKKVGQNLKYDYKVLANLGIEPGVAF 104
Query: 488 DIMLMSYVLDSGRSSHDIASIAQKWLSYT---RKEILKSRKSSIPIDKISDSQVQEHAIE 544
D ML SY+L+ G +H++ +A+++L ++I K + + + E+A E
Sbjct: 105 DTMLASYLLNPGAGAHNLDDLAKRYLGLETITFEDIAGKGKKQLTFADVKLEKATEYAAE 164
Query: 545 NSNVILQLWLLLRPKLI-VEKLLHVYERLDKPMIDVVSQMEITGIQIDQDLLKQVSAEIS 603
+++ L+L +L P+L+ LL +YE ++ P++ V+++ME GI++D LK++S E+
Sbjct: 165 DADATLRLESILEPELLKTPVLLELYEEIEMPLVRVLARMERNGIKVDVQYLKELSKELG 224
Query: 604 KNLLSLEENIYDLSGEKFNLSSPKQLGDILFTKLKFPSGA-KTKTGQWKTTAQDLEQINC 662
L LEE IY+L+GE+FN++SPKQLG+ILF KL P G KTKTG + T A+ LE++
Sbjct: 225 CELAELEEEIYELAGEEFNINSPKQLGEILFEKLGLPPGLKKTKTGNYSTDAEVLEKLA- 283
Query: 663 GDNPIIKNILEWRQLSKIKSTYADSLPNHINKRTQRVHTFYSLASTMTGRLASLEPNLQN 722
D+P+ K ILE+RQL+K+KSTY D LP IN T R+HT ++ T TGRL+S +PNLQN
Sbjct: 284 DDHPLPKLILEYRQLAKLKSTYTDGLPKLINPDTGRIHTSFNQTGTATGRLSSSDPNLQN 343
Query: 723 IPIKTDLGQKIRRAFISPPTKKLISADYSQIELRILAHIAKITPLYQVFENSLDIHRMVA 782
IPI+++ G+KIR+AF++ LISADYSQIELRILAH+++ L + F DIH A
Sbjct: 344 IPIRSEEGRKIRKAFVAEKGYTLISADYSQIELRILAHLSQDEGLLRAFTEGEDIHTATA 403
Query: 783 AEIFGVNIEKVSPQMRRHAKTINFSIIYGISPFRLATQLRIPRSEAADYIKRYFHRFPGI 842
AE+FGV IE+V+ + RR AK INF +IYG+S F LA QL IPR EA +YI RYF R+PG+
Sbjct: 404 AEVFGVPIEEVTSEQRRKAKAINFGLIYGMSAFGLAQQLGIPRKEAKEYIDRYFERYPGV 463
Query: 843 HEYIEKTKNFVRQNGYVETIFGRRIHYDEINSPKSSIRNINERAAINAPIQGSAADITRR 902
EY+E+TK R++GYVET+FGRR + +INS +R ERAAINAPIQG+AADI +
Sbjct: 464 KEYMERTKEEAREDGYVETLFGRRRYLPDINSSNRVVRAAAERAAINAPIQGTAADIIKL 523
Query: 903 AMISVHKSLEDHKLATKMLLQIHDELVFEVPEEEITTASQIIVHSMEKACLPKINLRVPL 962
AMI V K+L++ KL ++LLQ+HDELVFEVP+EE+ +++ ME A +NL VPL
Sbjct: 524 AMIKVDKALKEEKLKARLLLQVHDELVFEVPKEELEEVKKLLKAIMENA----VNLSVPL 579
Query: 963 KVNIKVSNNWQE 974
+V++ + NW E
Sbjct: 580 EVDVGIGKNWDE 591
>gnl|CDD|144170 pfam00476, DNA_pol_A, DNA polymerase family A.
Length = 383
Score = 397 bits (1021), Expect = e-110
Identities = 187/384 (48%), Positives = 253/384 (65%), Gaps = 5/384 (1%)
Query: 590 IDQDLLKQVSAEISKNLLSLEENIYDLSGEKFNLSSPKQLGDILFTKLKFPSGAKT-KTG 648
+D + L+++S E+ L LE I +L+GE+FNL SPKQLG +LF +L P KT KTG
Sbjct: 1 VDVEYLEELSNELGAQLADLEFKIPELAGEEFNLGSPKQLGVLLFEELGLPKTKKTDKTG 60
Query: 649 QWKTTAQDLEQINCGDNPIIKNILEWRQLSKIKSTYADSLPNHINKRTQRVHTFYSLAST 708
T A LE + + IIK ILE+RQLSK++STY D LP I+ R+HT Y+ A T
Sbjct: 61 ARSTNADVLESLREDAHEIIKIILEYRQLSKLQSTYVDKLPLMIDPDDGRIHTSYNQAGT 120
Query: 709 MTGRLASLEPNLQNIPIKTDLGQKIRRAFISPPTKKLISADYSQIELRILAHIAKITPLY 768
TGRL+S +PNLQNIPI+ + G++IR AFI+ P L++ADYSQIELRILAH++ L
Sbjct: 121 ATGRLSSTDPNLQNIPIRNEYGREIRAAFIAEPGYVLVAADYSQIELRILAHLSGDENLI 180
Query: 769 QVFENSLDIHRMVAAEIFGVNIEKVSPQMRRHAKTINFSIIYGISPFRLATQLRIPRSEA 828
+ F DIH + AA+IFGV++ +V+ RR+AKT NF IYG S L+ L I R EA
Sbjct: 181 EAFRTGADIHTLTAADIFGVDLHEVTGNQRRNAKTFNFGRIYGASAKGLSQLLGISREEA 240
Query: 829 ADYIKRYFHRFPGIHEYIEKTKNFVRQNGYVETIFGRRIHYDEINSPKSSIRNINERAAI 888
++I++YF RFPG+ Y EKT+ ++ GYVET+FGRR + +I+S S+R ERAA+
Sbjct: 241 KEFIEKYFERFPGVKRYREKTRKEAKKGGYVETLFGRRRYLPDIDSRNRSLREAAERAAL 300
Query: 889 NAPIQGSAADITRRAMISVHKSLEDHKLATKMLLQIHDELVFEVPEEEITTASQIIVHSM 948
N PIQGSAADI + AMI + ++L + L +M LQ+HDE+VFEVP+EE + I M
Sbjct: 301 NTPIQGSAADILKLAMIKLDEALVEKGLDARMCLQVHDEIVFEVPKEEAEAVAAQIKELM 360
Query: 949 EKACLPKINLRVPLKVNIKVSNNW 972
E+A + L VPL V + NW
Sbjct: 361 ERA----MFLDVPLLVEVGQGRNW 380
>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 = 328 bits (842), Expect = 6e-90
Identities = 136/346 (39%), Positives = 202/346 (58%), Gaps = 29/346 (8%)
Query: 651 KTTAQDLEQINCGDNPIIKNILEWRQLSKIKSTYADSLPNHI--NKRTQ--RVHTFYSLA 706
T+ + LEQ+ +P+ K ILE+R+LSK+ +TY + L + Q R+H ++
Sbjct: 30 STSKEVLEQLK-RLHPLPKLILEYRKLSKLLTTYVEPLLLLCKLSSSLQMYRIHPTWNQT 88
Query: 707 STMTGRLASLEPNLQNIP----IKTDLGQK-----------IRRAFISPPTKKLISADYS 751
T TGRL+S EPNLQN+P IK +R AFI PP + L+SADYS
Sbjct: 89 GTATGRLSSSEPNLQNVPKDFEIKDAPSPPAGSEGDIPTISLRHAFIPPPGRVLLSADYS 148
Query: 752 QIELRILAHIAKITPLYQVFENSLDIHRMVAAEIFGVNIEKVSPQMRRHAKTINFSIIYG 811
Q+ELRILAH++ L ++ + D+ +M+AA+ G +E+V+ + R+ AK + + I+YG
Sbjct: 149 QLELRILAHLSGDPALIELLNSGGDVFKMIAAQWLGKPVEEVTDEERQQAKQLVYGILYG 208
Query: 812 ISPFRLATQLRIPRSEAADYIKRYFHRFPGIHEYIEKTKNFVRQNGYVETIFGRRIHYDE 871
+ LA QL + EA +I+ + + +PG+ +I +T R+NG+VET+ GRR + E
Sbjct: 209 MGAKSLAEQLGVSEEEAKQFIESFKNAYPGVRRFIRETIERARRNGFVETLTGRRRYLPE 268
Query: 872 INSPKSSIRNINERAAINAPIQGSAADITRRAMISVHKSLEDHKLATK-----MLLQIHD 926
INS SS R ER A+N IQGSAADI + AMI++H+ L ++LQIHD
Sbjct: 269 INSGNSSERAQAERQAVNTVIQGSAADIMKIAMINIHEKLHSLLPNLPAGRARLVLQIHD 328
Query: 927 ELVFEVPEEEITTASQIIVHSMEKACLPKINLRVPLKVNIKVSNNW 972
EL+FEVPE ++ ++II SME A L VPL V + + +W
Sbjct: 329 ELLFEVPESDVDEVARIIKRSMENAA----KLSVPLPVKVSIGKSW 370
>gnl|CDD|28892 cd00008, 53EXOc, 5'-3' exonuclease; T5 type 5'-3' exonuclease
domains may co-occur with DNA polymerase I (Pol I)
domains, or be part of Pol I containing complexes. They
digest dsDNA and ssDNA, releasing mono-,di- and
tri-nucleotides, as well as oligonucleotides, and have
also been reported to possess RNase H activity. Also
called 5' nuclease family, involved in
structure-specific cleavage of flaps formed by Pol I
activity (similar to mammalian flap endonuclease I,
FEN-1). A single nucleic acid strand may be threaded
through the 5' nuclease enzyme before cleavage occurs.
The domain binds two divalent metal ions which are
necessary for activity..
Length = 240
Score = 278 bits (712), Expect = 6e-75
Identities = 122/245 (49%), Positives = 166/245 (67%), Gaps = 5/245 (2%)
Query: 5 NHLFLVDGSSFIYRAFYATPLLSRKHDGLPVNAIAGFCNMLWKLLQNSRKESIASHFAVI 64
L L+DGSS YRA++A P L GLP NA+ GF NML KL+ KE ++ AV+
Sbjct: 1 KRLLLIDGSSLAYRAYFALPPLKNSPKGLPTNAVYGFLNMLLKLI----KEYKPTYVAVV 56
Query: 65 FDYPAVTFRNEIYPDYKANRPKIPEMLLPQLPLVRLATQAFGIPAIEIQGFEADDIIATY 124
FD TFR+E+YP+YKANR K+PE L Q+PL++ +A GIP +EI+G+EADD+I T
Sbjct: 57 FDAGGKTFRHELYPEYKANRKKMPEELREQIPLIKELLEALGIPVLEIEGYEADDVIGTL 116
Query: 125 TYIAEKEGFAVTIISTDKDLMQLVSPTTCLYDTVKEEKIDIEHVIKKWGIPPEKMVCLQA 184
AE EG+ V I+S DKDL+QLVS + +K++ + E+VI+K+G+ P +++ +A
Sbjct: 117 AKKAEAEGYKVVIVSGDKDLLQLVSDNVKVVSPMKKKLVTEENVIEKYGVTPAQIIDYKA 176
Query: 185 LTGDSIDNIPGIPGIGYKTAALLLQEYGNLENILINASRIKQKKRRENILEYAETARLSR 244
L GDS DNIPG+PGIG KTAA LL+EYG+LE IL N +IK K RE + E E A LS+
Sbjct: 177 LMGDSSDNIPGVPGIGEKTAAKLLKEYGSLEGILENLDKIKG-KLREKLEEGKEMAFLSK 235
Query: 245 KLVML 249
+L +
Sbjct: 236 RLATI 240
>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 = 262 bits (672), Expect = 3e-70
Identities = 103/327 (31%), Positives = 161/327 (49%), Gaps = 23/327 (7%)
Query: 664 DNPIIKNILEWRQLSKIKSTYADSLPNHINKRTQRVHTFYSLASTMTGRLASLEPNLQNI 723
+P + +LE+++L+K+ S R R H Y T+TGR AS N Q I
Sbjct: 25 AHPAVPLLLEYKKLAKLWSANGWPWL-DQWVRDGRFHPEYVPGGTVTGRWASRGGNAQQI 83
Query: 724 PIKTDLGQKIRRAFISPPTKKLISADYSQIELRILAHIAKITPLYQVFENSLDIHRMVAA 783
P + LG+ IR+AF++ P L+ AD SQ+ELR+LA ++ L + F D++ A+
Sbjct: 84 PRRDPLGRDIRQAFVADPGWTLVVADASQLELRVLAALSGDEALAEAFGRGGDLYTATAS 143
Query: 784 EIFGVNIEKVSPQMRRHAKTINFSIIYG----ISPFRLATQLRIPRSEAADYIKRYFHRF 839
+FGV V R+HAK N +YG IS LA RI EAA I+ +F RF
Sbjct: 144 AMFGV---PVGGGERQHAKIANLGAMYGATSGISARLLAQLRRISTKEAAALIELFFSRF 200
Query: 840 PGIHEYIEKTKNFVRQ---NGYVETIFGRRIH-----------YDEINSPKSSIRNINER 885
P + +E ++ R+ GYV T+ GRR S +R R
Sbjct: 201 PAFPKAMEYVEDAARRGERGGYVRTLLGRRSPPPDIRWTEVVSDPAAASRARRVRRAAGR 260
Query: 886 AAINAPIQGSAADITRRAMISVHKSLEDHKLATKMLLQIHDELVFEVPEEEITTASQIIV 945
A N +QG+AAD + AM+++ + LE+ L +++ +HDE+V P+EE + I+
Sbjct: 261 FARNFVVQGTAADWAKLAMVALRRRLEELALDARLVFFVHDEVVLHCPKEEAEAVAAIVR 320
Query: 946 HSMEKACLPKINLRVPLKVNIKVSNNW 972
+ E + + VP++ +K+ W
Sbjct: 321 EAAE-QAVRLLFGSVPVRFPVKIGVVW 346
>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 = 256 bits (656), Expect = 2e-68
Identities = 119/330 (36%), Positives = 173/330 (52%), Gaps = 26/330 (7%)
Query: 668 IKNILEWRQLSKIKSTYADSLPNHINKRTQRVHTFYSLASTMTGRLASLEPNLQNIPIKT 727
I+ + E + +S + ST+ L +N T R+H ++ +T TGRL+S PNLQN P
Sbjct: 45 IEALKEIKSISTLLSTFIIPLQELLNDSTGRIHCSLNI-NTETGRLSSRNPNLQNQPALE 103
Query: 728 DLGQKIRRAFISPPTKKLISADYSQIELRILAHIAKITPLYQVFENSLDIHRMVAAEIFG 787
KIR+AFI+ P LI ADYSQ+ELR+LAH+ + + + F D H A+ ++
Sbjct: 104 KDRYKIRKAFIASPGNTLIVADYSQLELRLLAHMTRCKSMIEAFNAGGDFHSRTASGMYP 163
Query: 788 VNIEKVSPQM-----------------------RRHAKTINFSIIYGISPFRLATQLRIP 824
E V+ RR AK +NFSI YG + LA ++
Sbjct: 164 HVAEAVANGEVLLEWKSEGKPPAPLLKDKFKSERRKAKVLNFSIAYGKTAHGLAKDWKVK 223
Query: 825 RSEAADYIKRYFHRFPGIHEYIEKTKNFVRQNGYVETIFGRRIHYDEINSPKSSIRNINE 884
EA + ++ P + ++ +KTK R+ GY T+ GR + +I S R E
Sbjct: 224 LKEAERTVDAWYSDRPEVEQWQKKTKKEARERGYTRTLLGRYRYLPDIKSRNRKKRGHAE 283
Query: 885 RAAINAPIQGSAADITRRAMISVHKSLEDHKLATKMLLQIHDELVFEVPEEEITTASQII 944
RAAIN PIQGSAADI +AM+ ++++L +L K+LLQIHDE++ E PEE+ A +I+
Sbjct: 284 RAAINTPIQGSAADIAMKAMLRIYRNLRLKRLGWKLLLQIHDEVILEGPEEKADEALKIV 343
Query: 945 VHSMEKACLPKINLRVPLKVNIKVSNNWQE 974
ME L VPL+V+ V NW E
Sbjct: 344 KDCMENP--FFGPLDVPLEVDGSVGYNWYE 371
>gnl|CDD|30607 COG0258, Exo, 5'-3' exonuclease (including N-terminal domain of
PolI) [DNA replication, recombination, and repair].
Length = 310
Score = 242 bits (619), Expect = 3e-64
Identities = 126/299 (42%), Positives = 179/299 (59%), Gaps = 13/299 (4%)
Query: 1 MQKENHLFLVDGSSFIYRAFYATPLLSRKHDGLPVNAIAGFCNMLWKLLQNSRKESIASH 60
M K L L+DGSS +YRA +A P G P A++GF ML++L++ +H
Sbjct: 7 MNKSGKLLLIDGSSLLYRALHALPQPLGNPLGDPTGAVSGFLGMLYRLIRLLE----PTH 62
Query: 61 FAVIFDYPAVTFRNEIYPDYKANRPKI-PEMLLPQLPLVRLATQAFGIPAIEIQGFEADD 119
V+FD TFR+E+ +YKANR K P+ L PQ+P++ A GIP +E+ G EADD
Sbjct: 63 PVVVFDGKPPTFRHELLEEYKANREKEMPDELAPQIPILTELLVALGIPLLELMGIEADD 122
Query: 120 IIATYTYIAEKEGFAVTIISTDKDLMQLVSPTTCLYDTVK---EEKIDIEHVIKKW-GIP 175
I T A K+G V IIS DKDL+QLVSP + + K E+ +D+E V +K+ G+
Sbjct: 123 PIETLAQKAYKKGDVVLIISGDKDLLQLVSPNVLVINGKKGEPEKFLDLEEVEEKFKGLT 182
Query: 176 PEKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENILINASRIKQKKRRENILE 235
PE+++ L+AL GDS DNIPG+ GIG KTA LLQEYG+LE + N IK KK RE +LE
Sbjct: 183 PEQLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYGSLEGLYENLDIIK-KKTREKLLE 241
Query: 236 YAETARLSRKLVMLRTDVPITIPLEHLI---LEDCNGPRLISFLKALEFTKLINRVATT 291
E A LS+ L ++TDVP+ LE ++ + + + +L+ L F +L+ + +
Sbjct: 242 DKEKAFLSKPLATIKTDVPLEFDLEDILELLVPEHDFSKLLEERVELGFKRLLKAIGSV 300
>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 = 237 bits (607), Expect = 1e-62
Identities = 112/340 (32%), Positives = 190/340 (55%), Gaps = 37/340 (10%)
Query: 649 QWKTTAQDLEQ--------INCGDNPIIKNILEWRQLSKIKSTYADSLPNHINKRTQRVH 700
+WK ++LE+ + ++P ++ +LE+R+L+K+ ST+ + LP HI+ T R+H
Sbjct: 5 RWKELEKELERERQEAAKELYIEEHPAVRLLLEYRKLNKLISTFGEKLPKHIHPVTGRIH 64
Query: 701 TFYSLASTMTGRLASLEPNLQNIPIKTDLGQKIRRAFISPPTKKLISADYSQIELRILAH 760
++ +GR++ PNLQ IP + + RR F++P KLI ADYSQIELRI A
Sbjct: 65 PSFNQIGAASGRMSCSNPNLQQIPREREF----RRCFVAPEGNKLIIADYSQIELRIAAE 120
Query: 761 IAKITPLYQVFENSLDIHRMVAAEIFGVNIEKVSPQMRRHAKTINFSIIYGISPFRLATQ 820
I+ + ++ D+HR+ A+ I G IE+++ + R+ AK +NF +IYG+S L
Sbjct: 121 ISGDERMISAYQKGEDLHRLTASLITGKPIEEITKEERQLAKAVNFGLIYGMSAKGLREY 180
Query: 821 LR----IPRS--EAADYIKRYFHRFPGIHEYIEKTKNFVRQNGYVE--TIFGRRIHYDEI 872
R + S EA + + +F + GI + + ++ G +E T+ GRR ++
Sbjct: 181 ARTNYGVEMSLEEAEKFRESFFFFYKGIL----RWHHRLKAKGPIEVRTLLGRRRVFEYF 236
Query: 873 NSPKSSIRNINERAAINAPIQGSAADITRRAMISVHKSLEDHKLATKMLLQIHDELVFEV 932
+ A+N PIQG+ ADI + A+ + L+D L K++L +HDE+V EV
Sbjct: 237 TFTE----------ALNYPIQGTGADILKLALALLVDRLKD--LDAKIVLCVHDEIVLEV 284
Query: 933 PEEEITTASQIIVHSMEKACLPKINLRVPLKVNIKVSNNW 972
PE+E A +I+ SME+A + +VP++V + +S++W
Sbjct: 285 PEDEAEEAKKILESSMEEAGKRILK-KVPVEVEVSISDSW 323
>gnl|CDD|145734 pfam02739, 5_3_exonuc_N, 5'-3' exonuclease, N-terminal
resolvase-like domain.
Length = 169
Score = 196 bits (500), Expect = 3e-50
Identities = 75/173 (43%), Positives = 102/173 (58%), Gaps = 9/173 (5%)
Query: 5 NHLFLVDGSSFIYRAFYATPLLS-RKHDGLPVNAIAGFCNMLWKLLQNSRKESIASHFAV 63
L L+DGSS +RAF+A P + G P NA+ GF ML KLL+ + + AV
Sbjct: 1 KKLLLIDGSSLAFRAFFALPKVPLTNSKGEPTNAVYGFLRMLLKLLKEEKPT----YVAV 56
Query: 64 IFDYPAVTFRNEIYPDYKANRPKIPEMLLPQLPLVRLATQAFGIPAIEIQGFEADDIIAT 123
+FD A TFR+E+Y +YKANR K P+ L PQ+PL++ A GIP +E+ G+EADD+I T
Sbjct: 57 VFDAGAPTFRHELYEEYKANRAKTPDELPPQIPLIKELLDALGIPVLEVPGYEADDVIGT 116
Query: 124 YTYIAEKEGFAVTIISTDKDLMQLVSPTT----CLYDTVKEEKIDIEHVIKKW 172
AEKEG+ V I+S DKDL+QLVS + E V++K+
Sbjct: 117 LAKKAEKEGYDVRIVSGDKDLLQLVSDKVNVAVLNPGRTEFTLYTPEEVVEKY 169
>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 = 120 bits (303), Expect = 2e-27
Identities = 55/189 (29%), Positives = 104/189 (55%), Gaps = 17/189 (8%)
Query: 396 TDTMDAFHSKPIAIAISTLDQKDDTSFKVETIFIDLSVHTSQDSTGKNTLTKEILSYLKK 455
T ++D ++ + I+ + + ++ +I L H D G+ +E+L+ LK
Sbjct: 14 TTSLDPMQAELVGISFAV---EPGEAY-----YIPLG-H---DYGGEQLPREEVLAALKP 61
Query: 456 FFENEHFLKIGHNIKYDKLVLHRYGISMRG-FEDIMLMSYVLDSGRSSHDIASIAQKWLS 514
E+ K+G N+K+D VL +GI +RG D ML SY+L+ GR H + +A+++L
Sbjct: 62 LLEDPSIKKVGQNLKFDLHVLANHGIELRGPAFDTMLASYLLNPGRRRHGLDDLAERYLG 121
Query: 515 Y---TRKEILKSRKSSIPIDKISDSQVQEHAIENSNVILQLWLLLRPKLI-VEKLLHVYE 570
+ + ++++ K I D++ + E+A E++++ L+L+ LL+PKL LL +YE
Sbjct: 122 HKTISFEDLVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPKLKEEPGLLELYE 181
Query: 571 RLDKPMIDV 579
++ P+I V
Sbjct: 182 EIEMPLIPV 190
>gnl|CDD|110372 pfam01367, 5_3_exonuc, 5'-3' exonuclease, C-terminal SAM fold.
Length = 100
Score = 109 bits (275), Expect = 4e-24
Identities = 49/89 (55%), Positives = 64/89 (71%), Gaps = 1/89 (1%)
Query: 174 IPPEKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENILINASRIKQKKRRENI 233
+ PE+++ +AL GDS DNIPG+PGIG KTAA LL+EYG+LENI N ++K K RE +
Sbjct: 1 LTPEQIIDYKALVGDSSDNIPGVPGIGEKTAAKLLKEYGSLENIYENLDKLK-GKLREKL 59
Query: 234 LEYAETARLSRKLVMLRTDVPITIPLEHL 262
L E A LSRKL ++TDVP+ + LE L
Sbjct: 60 LNGKEDAFLSRKLATIKTDVPLELTLEDL 88
>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 = 102 bits (256), Expect = 5e-22
Identities = 84/386 (21%), Positives = 147/386 (38%), Gaps = 55/386 (14%)
Query: 621 FNLSSPKQLGDILFTKLKFPSGAKTKTGQWKTTAQDLEQINCGDNPIIKNILEWRQLSKI 680
FN SS K + L K + T++G+ K L ++ D P K + E+ + K
Sbjct: 65 FNPSSRKHIAKRLKAKYGWEPQEFTESGEPKVDEDVLSKL---DYPEAKLLAEYLLVQKR 121
Query: 681 KSTYADSLPN---HINKRTQRVHTFYSLASTMTGRLASLEPNLQNIP-IKTDLGQKIRRA 736
AD N + R+H + +TGR PN+ +P + + G++ R
Sbjct: 122 LGQLADG-NNAWLKLVHEDGRIHGAVNTNGAVTGRATHFSPNMAQVPAVGSPYGKECREL 180
Query: 737 FISPPTKKLISADYSQIELRILAHIAKITPLYQVFENSLDIHRMVAAEIFGVNIEKVSPQ 796
F PP L+ AD S +ELR LAH ++ +++ +I N + +
Sbjct: 181 FGVPPGWSLVGADASGLELRCLAH------YLARYDGGAYTRKVLGGDIHWANAQAMGLL 234
Query: 797 MRRHAKTINFSIIYGISPFRLATQLRIPRSEAADYI------------------------ 832
R AKT ++ +YG +L + A +
Sbjct: 235 SRDGAKTFIYAFLYGAGDEKLGQIVGDDLRTAKNLNAEWPQTKKGTIKKIADKAKGRVVR 294
Query: 833 KRYFHRFPGIHEYIEKTKNFVRQNGYVETIFGRRIHYDEINSPKSSIRNINERAAINAPI 892
+ P + + I+K K ++ G++ + GRRI +R + AA+N +
Sbjct: 295 ANFLKGLPALGKLIKKVKEAAKKRGHLVGLDGRRIR----------VR--SAHAALNTLL 342
Query: 893 QGSAADITRRAMISVHKSLEDHKLAT----KMLLQIHDELVFEVPEEEITTASQIIVHSM 948
Q + A + ++ ++ + L + +HDE+ E + +I V +
Sbjct: 343 QSAGAILMKKWLVLLDDELTAKGGVWGGDFEYCAWVHDEVQIECRKGIAEEVGKIAVEAA 402
Query: 949 EKACLPKINLRVPLKVNIKVSNNWQE 974
EKA N R PL + NW E
Sbjct: 403 EKAGE-HFNFRCPLAGEFDIGRNWAE 427
>gnl|CDD|176652 cd06140, DNA_polA_I_Bacillus_like_exo, inactive DEDDy 3'-5'
exonuclease domain of Bacillus stearothermophilus DNA
polymerase I and similar family-A DNA polymerases.
Bacillus stearothermophilus-like Polymerase I (Pol I), a
subgroup of the family-A DNA polymerases, contains an
inactive DnaQ-like 3'-5' exonuclease domain in the same
polypeptide chain as the polymerase region. The
exonuclease-like domain of these proteins possess the
same fold as the Klenow fragment (KF) of Escherichia
coli Pol I, but does not contain the four critical
metal-binding residues necessary for activity. The
function of this domain is unknown. It might act as a
spacer between the polymerase and the 5'-3' exonuclease
domains. Some members of this subgroup, such as those
from Bacillus sphaericus and Thermus aquaticus, are
thermostable DNA polymerases.
Length = 178
Score = 95.4 bits (238), Expect = 8e-20
Identities = 40/140 (28%), Positives = 71/140 (50%), Gaps = 7/140 (5%)
Query: 444 TLTKEILSYLKKFFENEHFLKIGHNIKYDKLVLHRYGISMRGFE-DIMLMSYVLDSGRSS 502
L L+ LK++ E+E K+GH+ K + L R+GI + G D ML +Y+LD RSS
Sbjct: 39 ELALLDLAALKEWLEDEKIPKVGHDAKRAYVALKRHGIELAGVAFDTMLAAYLLDPTRSS 98
Query: 503 HDIASIAQKWLSY---TRKEILKSRKSSIPIDKISDSQVQEHAIENSNVILQLWLLLRPK 559
+D+A +A+++L + +E+ D + + EH + I +L L +
Sbjct: 99 YDLADLAKRYLGRELPSDEEVYGKGAKFAVPD---EEVLAEHLARKAAAIARLAPKLEEE 155
Query: 560 LIVEKLLHVYERLDKPMIDV 579
L + L +Y ++ P+ +V
Sbjct: 156 LEENEQLELYYEVELPLAEV 175
>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 = 80.0 bits (197), Expect = 3e-15
Identities = 42/167 (25%), Positives = 77/167 (46%), Gaps = 22/167 (13%)
Query: 396 TDTMDAFHSKPIAIAISTLDQKDDTSFKVETIFIDLSVHTSQDSTGKNTLTKEILSYLKK 455
T ++ K + I I+T + +I + E L LK+
Sbjct: 9 TTGLNYHRGKLVGIQIATAGEA---------AYIPDELELE-----------EDLEALKE 48
Query: 456 FFENEHFLKIGHNIKYDKLVLHRYGISMRGF-EDIMLMSYVLDSGRSSHDIASIAQKWLS 514
E+E K+GH+ K+D +VL R GI + G D ML +Y+L+ G SH + +A+++L
Sbjct: 49 LLEDEDITKVGHDAKFDLVVLARDGIELPGNIFDTMLAAYLLNPGEGSHSLDDLAKEYLG 108
Query: 515 Y-TRKEILKSRKSSIPIDKISDSQVQEHAIENSNVILQLWLLLRPKL 560
K+ K + + ++ E+A E+++ +L+L+ L +L
Sbjct: 109 IELDKDEQIYGKGAKTFARPLSEELLEYAAEDADALLRLYEKLLEEL 155
>gnl|CDD|28961 cd00080, HhH2_motif, Helix-hairpin-helix class 2 (Pol1 family)
motif. HhH2 domains are found in Rad2 family of
prokaryotic and eukaryotic replication and repair
nucleases, i.e., DNA polymerase I, Taq DNA polymerase,
DNA repair protein Rad2 endonuclease, flap endonuclease,
exonuclease I and IX, 5'-3' exonuclease and also
bacteriophage Rnase H. These nucleases degrade RNA-DNA
or DNA-DNA duplexes, or both and play essential roles in
DNA duplication, repair, and recombination..
Length = 75
Score = 78.4 bits (193), Expect = 8e-15
Identities = 41/78 (52%), Positives = 54/78 (69%), Gaps = 3/78 (3%)
Query: 170 KKWGIPPEKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENILINASRIKQKKR 229
+K G+ PE+ + L L GD DNIPG+PGIG KTA LL+EYG+LEN+L N +IK
Sbjct: 1 EKLGLTPEQFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGSLENLLENLDKIKL--- 57
Query: 230 RENILEYAETARLSRKLV 247
RE +LE+ E A+LS+ L
Sbjct: 58 REKLLEHKELAKLSKLLA 75
>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 = 67.7 bits (166), Expect = 2e-11
Identities = 36/114 (31%), Positives = 62/114 (54%), Gaps = 7/114 (6%)
Query: 450 LSYLKKFFENEHFLKIGHNIKYDKLVLHR-YGISMRGFEDIMLMSYVLDSGRSSHDIASI 508
L LK+ E+ + K+GHN K+D VL R +GI + D ML +Y+L R SH + +
Sbjct: 64 LEGLKRLLEDPNITKVGHNAKFDLEVLARDFGIKLENLFDTMLAAYLLGYPR-SHSLDDL 122
Query: 509 AQKWLSY-TRKEILKSRKSSIPIDKISDSQVQEHAIENSNVILQLWLLLRPKLI 561
A+K+L K + +S+ Q++ +A E+++ +L+L+ LR +L
Sbjct: 123 AEKYLGVELDKSEQCADWR---ARPLSEEQLR-YAAEDADYLLRLYDKLRKELE 172
>gnl|CDD|176649 cd06128, DNA_polA_exo, DEDDy 3'-5' exonuclease domain of family-A
DNA polymerases. The 3'-5' exonuclease domain of
family-A DNA polymerases has a fundamental role in
reducing polymerase errors and is involved in
proofreading activity. Family-A DNA polymerases contain
a DnaQ-like exonuclease domain in the same polypeptide
chain as the polymerase domain, similar to family-B DNA
polymerases. The exonuclease domain contains three
conserved sequence motifs termed ExoI, ExoII and ExoIII,
which are clustered around the active site and contain
four invariant acidic residues that serve as ligands for
the two metal ions required for catalysis. The Klenow
fragment (KF) of Escherichia coli Pol I, the Thermus
aquaticus (Taq) Pol I, and Bacillus stearothermophilus
(BF) Pol I are examples of family-A DNA polymerases.
They are involved in nucleotide excision repair and in
the processing of Okazaki fragments that are generated
during lagging strand synthesis. The N-terminal domains
of BF Pol I and Taq Pol I resemble the fold of the 3'-5'
exonuclease domain of KF without the proofreading
activity of KF. The four critical metal-binding residues
are not conserved in BF Pol I and Taq Pol I, and they
are unable to bind metals necessary for exonuclease
activity.
Length = 151
Score = 65.1 bits (158), Expect = 8e-11
Identities = 40/110 (36%), Positives = 63/110 (57%), Gaps = 1/110 (0%)
Query: 450 LSYLKKFFENEHFLKIGHNIKYDKLVLHRYGISMRGF-EDIMLMSYVLDSGRSSHDIASI 508
L LK E+E LK+G N+KYD+++L YGI +RG D ML +Y+LD HD+ S+
Sbjct: 42 LELLKPLLEDEKALKVGQNLKYDRVILANYGIELRGIAFDTMLEAYLLDPVAGRHDMDSL 101
Query: 509 AQKWLSYTRKEILKSRKSSIPIDKISDSQVQEHAIENSNVILQLWLLLRP 558
A++WL + + ++I+ + E+A E++ V LQL L + P
Sbjct: 102 AERWLKEKTITFEEIAGKGLTFNQIALEEAGEYAAEDAAVTLQLHLKMWP 151
>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 = 63.0 bits (154), Expect = 4e-10
Identities = 90/360 (25%), Positives = 143/360 (39%), Gaps = 83/360 (23%)
Query: 622 NLSSPKQLGDILFTK-LKFPSGAKTKTGQWKTTAQDLEQINCGDNPIIKNILEWRQ-LSK 679
N +SP QL D L + + S K K L + GD +K +LE RQ LSK
Sbjct: 28 NPNSPAQLKDWLNEQGGEVDSLLK------KDVVALLLKTAPGD---VKRVLELRQELSK 78
Query: 680 IKSTYADSLPNHINKRTQRVH---TFYSLASTMTGRLASLEPNLQNIP------------ 724
+++ + RV FY A+ TGR A +QN+P
Sbjct: 79 TSVKKYEAMERAVCS-DGRVRGLLQFYG-ANR-TGRWAGRLVQVQNLPRNYLKDLDLARE 135
Query: 725 ----------------IKTDLGQKIRRAFISPPTKKLISADYSQIELRILAHIAKITPLY 768
+ L Q IR AFI + I +D+S IE R++A +A
Sbjct: 136 LVKSGDFDALELLYGSVPDVLSQLIRTAFIPSEGHRFIVSDFSAIEARVIAWLAGEQWRL 195
Query: 769 QVFENSLDIHRMVAAEIFGVNIEKVSP--QMRRHAKTINFSIIYGISPFRL----ATQLR 822
VF I+ A+++FGV +EK+ +R+ K ++ YG S L A ++
Sbjct: 196 DVFATHGKIYEASASQMFGVPVEKIGKNSHLRQKGKVAELALGYGGSVGALKAMGALEMG 255
Query: 823 IPRSEAADYIKRYFHRFPGIHEY---IEKT-KNFVRQNGYVETIFGRRIHYDEINSPKSS 878
+ E + + + P I + ++K K V++ V+ K
Sbjct: 256 LTEDELPGIVDAWRNANPNIVKLWWDVDKAAKKAVKERKTVKL------------GGK-L 302
Query: 879 IRNINERAAINAPIQGSAADITRRAMISVHKSLEDHKLATKMLLQIHDELVFEVPEEEIT 938
+ NI +Q A D AM+ + K+ D +++ +HDE+V EVPE E +
Sbjct: 303 VENI---------VQAIARDCLAEAMLRLEKAGYD------IVMHVHDEVVIEVPEGEGS 347
>gnl|CDD|176656 cd09018, DEDDy_polA_RNaseD_like_exo, DEDDy 3'-5' exonuclease domain
of family-A DNA polymerases, RNase D, WRN, and similar
proteins. DEDDy 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. They contain four invariant acidic
residues in three conserved sequence motifs termed ExoI,
ExoII and ExoIII. DEDDy exonucleases are classified as
such because of the presence of a specific YX(3)D
pattern at ExoIII. The four conserved acidic residues
serve as ligands for the two metal ions required for
catalysis. This family of DEDDy exonucleases includes
the proofreading domains of family A DNA polymerases, as
well as RNases such as RNase D and yeast Rrp6p. The
Egalitarian (Egl) and Bacillus-like DNA Polymerase I
subfamilies do not possess a completely conserved YX(3)D
pattern at the ExoIII motif. In addition, the
Bacillus-like DNA polymerase I subfamily has inactive
3'-5' exonuclease domains which do not possess the
metal-binding residues necessary for activity.
Length = 150
Score = 59.6 bits (144), Expect = 4e-09
Identities = 36/110 (32%), Positives = 61/110 (55%), Gaps = 2/110 (1%)
Query: 450 LSYLKKFFENEHFLKIGHNIKYDKLVLHRYGISMRG-FEDIMLMSYVLDSGRSSHDIASI 508
L LK E+E LK+G N+KYD+ +L Y I +RG D ML +Y+L+S D+ S+
Sbjct: 42 LELLKPLLEDEKALKVGQNLKYDRGILLNYFIELRGIAFDTMLEAYILNSVAGRWDMDSL 101
Query: 509 AQKWLSYTRKEILKSRKSSIPIDKISDSQVQEHAIENSNVILQLWLLLRP 558
++WL + + +S + ++ + +A E+++V LQ+ L L P
Sbjct: 102 VERWLGHKLIK-FESIAGKLWFNQPLTEEQGRYAAEDADVTLQIHLKLWP 150
>gnl|CDD|29030 cd00128, XPG, Xeroderma pigmentosum G N- and I-regions (XPGN,
XPGI); contains the HhH2 motif; domain in nucleases. XPG
is a eukaryotic enzyme that functions in
nucleotide-excision repair and transcription-coupled
repair of oxidative DNA damage.
Functionally/structurally related to FEN-1; divalent
metal ion-dependent exo- and endonuclease, and bacterial
and bacteriophage 5'3' exonucleases..
Length = 316
Score = 51.0 bits (122), Expect = 1e-06
Identities = 44/132 (33%), Positives = 68/132 (51%), Gaps = 14/132 (10%)
Query: 103 QAFGIPAIEIQGFEADDIIATYTYIAEKEGFAVTIISTDKDLMQLVSPTTCLYDTVKE-- 160
+ GIP I +EA+ A Y+ K+G II+ D DL+ +P
Sbjct: 138 RLMGIPYIVA-PYEAE---AQCAYL-AKKGLVDAIITEDSDLLLFGAPRVYRNLFDSGAK 192
Query: 161 --EKIDIEHVIKKWGIPPEKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENIL 218
E+ID+E ++K+ G+ EK++ L L G D GIPGIG TA L+++YG++E +
Sbjct: 193 PVEEIDLEKILKELGLTREKLIDLAILLG--CDYTEGIPGIGPVTALKLIKKYGDIEKDI 250
Query: 219 INASRIKQKKRR 230
R+K+K R
Sbjct: 251 ---ERLKKKLYR 259
>gnl|CDD|37730 KOG2519, KOG2519, KOG2519, 5'-3' exonuclease [Replication,
recombination and repair].
Length = 449
Score = 44.2 bits (104), Expect = 2e-04
Identities = 30/124 (24%), Positives = 50/124 (40%), Gaps = 17/124 (13%)
Query: 130 KEGFAVTIISTDKDLMQLVSPTTCLYDTVKEEK------IDIEHVIKKWGIPPEKMVCLQ 183
K G + + D D + +P + D+ +++ G+ E + L
Sbjct: 164 KAGKVYAVATEDSDALTFGAPVKLRHLIHSLASGLPVSEYDMSRILEGLGLSRESFIDLC 223
Query: 184 ALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENILINASRIKQKKRRENILEYAETARLS 243
L G D P I GIG K A L++++G++ENIL + ++ EY S
Sbjct: 224 LLLG--CDYCPTIRGIGPKKALKLIRQHGDIENIL---------EINSDLKEYPIPEDWS 272
Query: 244 RKLV 247
KL
Sbjct: 273 YKLA 276
>gnl|CDD|176653 cd06141, WRN_exo, DEDDy 3'-5' exonuclease domain of WRN and similar
proteins. WRN is a unique RecQ DNA helicase exhibiting
an exonuclease activity. It contains a DEDDy-type
DnaQ-like 3'-5' exonuclease domain possessing 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. Mutations in the
WRN gene cause Werner syndrome, an autosomal recessive
disorder associated with premature aging and increased
susceptibility to cancer and type II diabetes. WRN
interacts with key proteins involved in DNA replication,
recombination, and repair. It is believed to maintain
genomic stability and life span by participating in DNA
processes. WRN is stimulated by Ku70/80, an important
regulator of genomic stability.
Length = 170
Score = 38.7 bits (91), Expect = 0.007
Identities = 16/38 (42%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 453 LKKFFENEHFLKIGHNIKYDKLVLHR-YGISMRGFEDI 489
LK+ E+ LK+G IK D L R +GI +RG D+
Sbjct: 65 LKQLLEDPSILKVGVGIKGDARKLARDFGIEVRGVVDL 102
>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 = 36.5 bits (85), Expect = 0.034
Identities = 46/194 (23%), Positives = 73/194 (37%), Gaps = 50/194 (25%)
Query: 776 DIHRMVAAEIFGVNIEKVSPQMRRHAKTINFSIIYGIS-PF--RLATQL--RIPRSEAAD 830
D+H A I G++ R HAK N+ IYG PF RL Q R+ +EA +
Sbjct: 189 DLHSK-TASILGIS--------RDHAKVFNYGRIYGAGQPFAERLLMQFNPRLTPAEATE 239
Query: 831 YIKRYFHRFPGIHEYIEKTKNFVRQNGYVETIFGRRIHYDEINS--------------PK 876
K+ + GI I+++ R +F R S P+
Sbjct: 240 KAKQMYAATKGIRIAIQRSTKGKR-------LFKRPFWSGGSESIMFNKLEEIAAQSQPR 292
Query: 877 SS------IRNINERAA---------INAPIQGSAADITRRAMISVHKSLEDHKLATKML 921
+ + E IN +Q SA D ++S+ +E + + +
Sbjct: 293 TPVLGACITSALLEPNLVKNEFMTSRINWVVQSSAVDYLHLMLVSMRWLIEKYDIDARFC 352
Query: 922 LQIHDELVFEVPEE 935
+ IHDE+ + V EE
Sbjct: 353 ISIHDEVRYLVKEE 366
>gnl|CDD|38861 KOG3657, KOG3657, KOG3657, Mitochondrial DNA polymerase gamma,
catalytic subunit [Replication, recombination and
repair].
Length = 1075
Score = 35.4 bits (81), Expect = 0.080
Identities = 53/272 (19%), Positives = 97/272 (35%), Gaps = 73/272 (26%)
Query: 729 LGQKIRRAFISPPTKKLISADYSQIELRIL-----AHIAKI---TPLYQVF-----ENSL 775
+G +++ +PP +L+ AD EL I A + T + +
Sbjct: 719 IGSELKAMVQAPPGYRLVGADVDSQELWIAALLGDASAEGVHGKTAFGWMTLAGSKSDGT 778
Query: 776 DIHRMVAAEIFGVNIEKVSPQMRRHAKTINFSIIYGI-SPF--RLATQL--RIPRSEAAD 830
D+H A+++ +S R HAK N++ IYG F +L + + +SEA
Sbjct: 779 DLHSKTASQL------GIS---RNHAKVFNYARIYGAGQTFAEKLLMRFNPSLTQSEAKS 829
Query: 831 ---------------YIKRYFH-----------RFPGIHEYIEKTKNFVR-----QNGYV 859
+K GI+ +N V G
Sbjct: 830 KASQLFKLTKGDRAKRLKVEVRMVENSLVCKILTIDGIYLIYSIYENEVEPRRLWVGGTE 889
Query: 860 ETIFGRRIHYDEINSPKS---------SIRNINERAA------INAPIQGSAADITRRAM 904
++F + + P++ S+ + E IN +Q SA D +
Sbjct: 890 SSMFNKLESIATAHDPRTPVLGCQISRSLEKLPEGEPKFLPSRINWVVQSSAVDFLHLLL 949
Query: 905 ISVHKSLEDHKLATKMLLQIHDELVFEVPEEE 936
+S+ + +K+ + + IHDE+ + V EE+
Sbjct: 950 VSMQWLCDTYKIDARFCISIHDEVRYLVKEED 981
>gnl|CDD|37729 KOG2518, KOG2518, KOG2518, 5'-3' exonuclease [Replication,
recombination and repair].
Length = 556
Score = 34.2 bits (78), Expect = 0.18
Identities = 55/261 (21%), Positives = 94/261 (36%), Gaps = 39/261 (14%)
Query: 10 VDGSSFIYRAFYATPLLSRKHDGLPVNAIAGFCNMLWKLLQNSRKESIASHFAVIFD--- 66
VDG +++R A + G P + F KLL + + I ++FD
Sbjct: 29 VDGYCWLHRG--ALACAEKLAKGKPTDRYIQFFIKRVKLLLSYGIKPI-----LVFDGDP 81
Query: 67 YPAVTFRNEIYPDYKANRPKIPEMLLPQLPLVRLATQAFG-------------IPAIEIQ 113
P+ + + E LL A + F I + Q
Sbjct: 82 LPSKKETERKRRERRKKNLDAAEQLL-AEGKESNARECFQRCVDITPEMAHKLIQYLRSQ 140
Query: 114 GFEADDIIATYTYIA-----EKEGFAVTIISTDKDLMQLVSPT--TCLYDTVKEEKIDIE 166
E I+A Y A E+EG II+ D DL+ + +I+
Sbjct: 141 NVEY--IVAPYEADAQLAYLEREGIVDAIITEDSDLLVFGCKKVIFKMDSFGNGLEINRS 198
Query: 167 HVIKKWGI----PPEKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENILINAS 222
+ + + EK + L+G D + +PG+G TA LL +Y + ++I+
Sbjct: 199 KLPECKPLGDKFTEEKFRRMCILSG--CDYLSSLPGVGLATAHKLLSKYNTPDRVIISHL 256
Query: 223 RIKQKKRRENILEYAETARLS 243
K+ ++ +E E A L+
Sbjct: 257 LKKKLTVPDDYIENFERANLT 277
>gnl|CDD|132972 cd06641, STKc_MST3, Catalytic domain of the Protein
Serine/Threonine Kinase, Mammalian Ste20-like protein
kinase 3. Serine/threonine kinases (STKs), mammalian
Ste20-like protein kinase 3 (MST3) subfamily, catalytic
(c) domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The MST3 subfamily is
part of a larger superfamily that includes the catalytic
domains of other protein STKs, protein tyrosine kinases,
RIO kinases, aminoglycoside phosphotransferase, choline
kinase, and phosphoinositide 3-kinase. MST3
phosphorylates the STK NDR and may play a role in cell
cycle progression and cell morphology. It may also
regulate paxillin and consequently, cell migration. MST3
is present in human placenta, where it plays an
essential role in the oxidative stress-induced apoptosis
of trophoblasts in normal spontaneous delivery.
Dysregulation of trophoblast apoptosis may result in
pregnancy complications such as preeclampsia and
intrauterine growth retardation.
Length = 277
Score = 31.2 bits (70), Expect = 1.5
Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 6/79 (7%)
Query: 376 DIQQWVQKLETIGSASFKIITDTMDAFHSKPIAIAISTLDQKDDTSFKVETIFIDLSVHT 435
D ++ KLE IG SF + +D K +AI I L++ +D ++E I +++V +
Sbjct: 1 DPEELFTKLEKIGKGSFGEVFKGIDNRTQKVVAIKIIDLEEAED---EIEDIQQEITVLS 57
Query: 436 SQDSTGKNTLTKEILSYLK 454
DS +TK SYLK
Sbjct: 58 QCDSP---YVTKYYGSYLK 73
>gnl|CDD|30621 COG0272, Lig, NAD-dependent DNA ligase (contains BRCT domain type
II) [DNA replication, recombination, and repair].
Length = 667
Score = 30.9 bits (70), Expect = 1.5
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 195 GIPGIGYKTAALLLQEYGNLENIL 218
GI +G TA L + +G LE +L
Sbjct: 515 GIRHVGETTAKSLARHFGTLEALL 538
>gnl|CDD|31234 COG1031, COG1031, Uncharacterized Fe-S oxidoreductase [Energy
production and conversion].
Length = 560
Score = 30.3 bits (68), Expect = 2.9
Identities = 21/95 (22%), Positives = 36/95 (37%), Gaps = 11/95 (11%)
Query: 225 KQKKRRENILEYAETARLSRKLVMLRTDVPITIPLEHLILEDCNG-----------PRLI 273
K +K ++ + R L ML+ VP L + +E G P L+
Sbjct: 418 KAEKHKKLFAAFKRKVREEIDLPMLKRVVPKGTVLRDVRVEVYEGGLTFGRQLGSYPLLV 477
Query: 274 SFLKALEFTKLINRVATTYDCDAANIEPVVLDINT 308
LE + ++ V + + PV LD+N+
Sbjct: 478 GIPGRLELGRYVDVVVVDHGARSVTAIPVPLDVNS 512
>gnl|CDD|30715 COG0366, AmyA, Glycosidases [Carbohydrate transport and
metabolism].
Length = 505
Score = 30.3 bits (67), Expect = 2.9
Identities = 16/102 (15%), Positives = 29/102 (28%), Gaps = 1/102 (0%)
Query: 802 KTINFSIIYGISPFRLATQLRIPRSEAADYIKRYFHRFPGIHEYIEKTKNFVRQNGY-VE 860
+ F + G+ FRL I + + IHEY+ + V G +
Sbjct: 182 DVVKFWLDKGVDGFRLDAAKHISKDFGLPPSEENLTFLEEIHEYLREENPDVLIYGEAIT 241
Query: 861 TIFGRRIHYDEINSPKSSIRNINERAAINAPIQGSAADITRR 902
+ E + +S N + G +
Sbjct: 242 DVGEAPGAVKEDFADNTSFTNPELSMLFDFSHVGLDFEALAP 283
>gnl|CDD|146299 pfam03586, Herpes_UL36, Herpesvirus UL36 tegument protein. The
UL36 open reading frame (ORF) encodes the largest herpes
simplex virus type 1 (HSV-1) protein, a 270-kDa
polypeptide designated VP1/2, which is also a component
of the virion tegument. A null mutation in the UL36 gene
of herpes simplex virus type 1 results in accumulation
of unenveloped DNA-filled capsids in the cytoplasm of
infected cells. This family only covers a small central
part of this large protein.
Length = 253
Score = 30.0 bits (68), Expect = 3.1
Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 8/81 (9%)
Query: 783 AEIFGVNIEKVSPQMR------RHAKTINFSIIYGISPFRLATQL-RIPR-SEAADYIKR 834
+FGV++E + +R HA +I Y + L+ L +P ++ D+ +R
Sbjct: 106 ETLFGVDVEPLMRLLRIAGGILEHAAAGGGNIDYYDAVGTLSGDLLAVPELAKYVDFYRR 165
Query: 835 YFHRFPGIHEYIEKTKNFVRQ 855
+ F +E + V Q
Sbjct: 166 GYEEFEEELARLEALRADVLQ 186
>gnl|CDD|35422 KOG0201, KOG0201, KOG0201, Serine/threonine protein kinase [Signal
transduction mechanisms].
Length = 467
Score = 30.0 bits (67), Expect = 3.5
Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 383 KLETIGSASFKIITDTMDAFHSKPIAIAISTLDQKDDTSFKVETIFIDLSVHTSQDSTGK 442
KLE IG SF + +D K +AI I L++ +D ++E I ++SV + DS
Sbjct: 17 KLELIGRGSFGEVYKAIDNKTKKVVAIKIIDLEEAED---EIEDIQQEISVLSQCDSP-- 71
Query: 443 NTLTKEILSYLKKF 456
+T+ SYLK
Sbjct: 72 -NITEYYGSYLKGT 84
>gnl|CDD|37415 KOG2204, KOG2204, KOG2204, Mannosyl-oligosaccharide
alpha-1,2-mannosidase and related glycosyl hydrolases
[Carbohydrate transport and metabolism].
Length = 625
Score = 29.6 bits (66), Expect = 4.3
Identities = 14/39 (35%), Positives = 18/39 (46%), Gaps = 4/39 (10%)
Query: 606 LLSLEENIYDLSGEKFNLSSPKQLGDILFTKLKFPSGAK 644
LLS Y LSGE+ L ++GD L P+G
Sbjct: 271 LLSA----YALSGEEMFLEKAPEIGDKLLPAFNTPTGIP 305
>gnl|CDD|37048 KOG1837, KOG1837, KOG1837, Uncharacterized conserved protein
[Function unknown].
Length = 1621
Score = 29.6 bits (66), Expect = 4.4
Identities = 13/90 (14%), Positives = 32/90 (35%), Gaps = 1/90 (1%)
Query: 298 NIEPVVLDINTTENKGIAIETEIDRDTTIKT-SQFSSLSDQTSKINSEQTPQKLFLERLQ 356
E +LDI ++ I++ + I+ ++ +++ Q + +
Sbjct: 445 LKEYQILDIIQFASEAISLTQSEESIEIIEEELPSCKKIKLSASERAQKLAQLSIFAKRE 504
Query: 357 KLSQYPINNDSYTKIVNTKDIQQWVQKLET 386
+ PIN + + N D +W+
Sbjct: 505 VFNGDPINKATEGLMGNPWDKVEWLSNEMA 534
>gnl|CDD|132971 cd06640, STKc_MST4, Catalytic domain of the Protein
Serine/Threonine Kinase, Mammalian Ste20-like protein
kinase 4. Serine/threonine kinases (STKs), mammalian
Ste20-like protein kinase 4 (MST4) subfamily, catalytic
(c) domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The MST4 subfamily is
part of a larger superfamily that includes the catalytic
domains of other protein STKs, protein tyrosine kinases,
RIO kinases, aminoglycoside phosphotransferase, choline
kinase, and phosphoinositide 3-kinase. MST4 is sometimes
referred to as MASK (MST3 and SOK1-related kinase). It
plays a role in mitogen-activated protein kinase (MAPK)
signaling during cytoskeletal rearrangement,
morphogenesis, and apoptosis. It influences cell growth
and transformation by modulating the extracellular
signal-regulated kinase (ERK) pathway. MST4 may also
play a role in tumor formation and progression. It
localizes in the Golgi apparatus by interacting with the
Golgi matrix protein GM130 and may play a role in cell
migration.
Length = 277
Score = 29.6 bits (66), Expect = 4.7
Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 6/79 (7%)
Query: 376 DIQQWVQKLETIGSASFKIITDTMDAFHSKPIAIAISTLDQKDDTSFKVETIFIDLSVHT 435
D ++ KLE IG SF + +D + +AI I L++ +D ++E I +++V +
Sbjct: 1 DPEELFTKLERIGKGSFGEVFKGIDNRTQQVVAIKIIDLEEAED---EIEDIQQEITVLS 57
Query: 436 SQDSTGKNTLTKEILSYLK 454
DS +TK SYLK
Sbjct: 58 QCDSP---YVTKYYGSYLK 73
>gnl|CDD|38827 KOG3621, KOG3621, KOG3621, WD40 repeat-containing protein [General
function prediction only].
Length = 726
Score = 29.6 bits (66), Expect = 4.7
Identities = 10/54 (18%), Positives = 18/54 (33%)
Query: 157 TVKEEKIDIEHVIKKWGIPPEKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQE 210
T +++I + E+ +C L S+ P G+G E
Sbjct: 455 TQPPRRVEIFKRAGEMDGGFEQSICHTTLEKTSVGEPPFASGVGIVEIGHETHE 508
>gnl|CDD|32437 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 29.4 bits (66), Expect = 5.0
Identities = 17/58 (29%), Positives = 23/58 (39%), Gaps = 1/58 (1%)
Query: 195 GIPGIGYKTAALLLQEYGNLENILINASRIKQKKRRENILEYAETARLSRKLVMLRTD 252
G PG G T A L+ N ++A K I+E A RL + +L D
Sbjct: 55 GPPGTGKTTLARLIAGTTNAAFEALSAV-TSGVKDLREIIEEARKNRLLGRRTILFLD 111
>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 = 29.5 bits (67), Expect = 5.1
Identities = 20/94 (21%), Positives = 35/94 (37%), Gaps = 21/94 (22%)
Query: 402 FHSKPIAIAISTLDQKDDTSFKVETIFIDLSVHTSQDSTGKNTLTKEILSYLKKFFENEH 461
FH K ++I+ D KV T+ KE+L + E ++
Sbjct: 50 FH-KVVSISAL-YRDDDGGFLKVRTLD-GAD-------------EKELLEDFFQLIEKKN 93
Query: 462 FLKIGHNIK-YDKLVLH----RYGISMRGFEDIM 490
+ N + +D VLH +G+S + D+
Sbjct: 94 PRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLG 127
>gnl|CDD|132973 cd06642, STKc_STK25-YSK1, Catalytic domain of the Protein
Serine/Threonine Kinase, STK25 or Yeast
Sps1/Ste20-related kinase 1. Serine/threonine kinases
(STKs), STK25 subfamily, catalytic (c) domain. STKs
catalyze the transfer of the gamma-phosphoryl group from
ATP to serine/threonine residues on protein substrates.
The STK25 subfamily is part of a larger superfamily that
includes the catalytic domains of other protein STKs,
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. STK25 is also called Ste20/oxidant stress
response kinase 1 (SOK1) or yeast Sps1/Ste20-related
kinase 1 (YSK1). STK25 is localized in the Golgi
apparatus through its interaction with the Golgi matrix
protein GM130. It may play a role in the regulation of
cell migration and polarization. STK25 binds and
phosphorylates CCM3 (cerebral cavernous malformation 3),
also called PCD10 (programmed cell death 10), and may
play a role in apoptosis. Human STK25 is a candidate
gene responsible for pseudopseudohypoparathyroidism
(PPHP), a disease that shares features with the Albright
hereditary osteodystrophy (AHO) phenotype.
Length = 277
Score = 28.9 bits (64), Expect = 8.3
Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 6/79 (7%)
Query: 376 DIQQWVQKLETIGSASFKIITDTMDAFHSKPIAIAISTLDQKDDTSFKVETIFIDLSVHT 435
D ++ KLE IG SF + +D + +AI I L++ +D ++E I +++V +
Sbjct: 1 DPEELFTKLERIGKGSFGEVYKGIDNRTKEVVAIKIIDLEEAED---EIEDIQQEITVLS 57
Query: 436 SQDSTGKNTLTKEILSYLK 454
DS +T+ SYLK
Sbjct: 58 QCDSP---YITRYYGSYLK 73
>gnl|CDD|36279 KOG1061, KOG1061, KOG1061, Vesicle coat complex AP-1/AP-2/AP-4,
beta subunit [Intracellular trafficking, secretion, and
vesicular transport].
Length = 734
Score = 28.3 bits (63), Expect = 9.9
Identities = 22/93 (23%), Positives = 45/93 (48%), Gaps = 4/93 (4%)
Query: 511 KWLSYTRKEILKSRKSSIPIDKISDSQVQEHAIENSNVILQLWLLLRPKLIVEKLLHVYE 570
K+L + + K + S+S++Q A+ N N+ILQ RP+++ ++ +
Sbjct: 268 KYLKQVNELLFKKVAPPLVTLLSSESEIQYVALRNINLILQ----KRPEILKVEIKVFFC 323
Query: 571 RLDKPMIDVVSQMEITGIQIDQDLLKQVSAEIS 603
+ + P+ + ++EI + L QV AE+
Sbjct: 324 KYNDPIYVKLEKLEILIELANDANLAQVLAELK 356
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 0.135 0.381
Gapped
Lambda K H
0.267 0.0657 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 11,448,157
Number of extensions: 614262
Number of successful extensions: 1591
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1537
Number of HSP's successfully gapped: 65
Length of query: 976
Length of database: 6,263,737
Length adjustment: 103
Effective length of query: 873
Effective length of database: 4,038,010
Effective search space: 3525182730
Effective search space used: 3525182730
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 (21.7 bits)
S2: 62 (27.8 bits)