RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12450
(168 letters)
>gnl|CDD|99916 cd05533, POLBc_delta, DNA polymerase type-B delta subfamily
catalytic domain. Three DNA-dependent DNA polymerases
type B (alpha, delta, and epsilon) have been identified
as essential for nuclear DNA replication in eukaryotes.
Presently, no direct data is available regarding the
strand specificity of DNA polymerase during DNA
replication in vivo. However, mutation analysis supports
the hypothesis that DNA polymerase delta is the enzyme
responsible for both elongation and maturation of
Okazaki fragments on the lagging strand.
Length = 393
Score = 191 bits (488), Expect = 2e-60
Identities = 74/105 (70%), Positives = 86/105 (81%), Gaps = 2/105 (1%)
Query: 60 DQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYS 119
+Q+EGATVIEP KGYY PIATLDF+SLYPSIMMAHNLCYTTLL T KL P+ Y
Sbjct: 1 EQYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAKKLP--PEDYI 58
Query: 120 KTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQ 164
KTP G++F+KSS+RKGLLPEILE LL+ARK+AK DLK+ETD +
Sbjct: 59 KTPNGDYFVKSSVRKGLLPEILEELLAARKRAKKDLKEETDPFKK 103
Score = 67.3 bits (165), Expect = 8e-14
Identities = 21/34 (61%), Positives = 27/34 (79%)
Query: 10 GLETVRRDNSPLVANMINTCLQKLLINRDPDGAV 43
G+ETVRRDN LV N++ TCL K+LI RD +GA+
Sbjct: 247 GIETVRRDNCLLVQNVVETCLNKILIERDVEGAI 280
>gnl|CDD|240301 PTZ00166, PTZ00166, DNA polymerase delta catalytic subunit;
Provisional.
Length = 1054
Score = 184 bits (469), Expect = 2e-54
Identities = 66/124 (53%), Positives = 89/124 (71%), Gaps = 5/124 (4%)
Query: 46 KNFIIPTYHGGQG--EDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLL 103
N++IPT G E+++EGATV+EPKKG+Y +PIATLDF+SLYPSIM+AHNLCY+TL+
Sbjct: 522 LNYVIPTVKYSGGGSEEKYEGATVLEPKKGFYDEPIATLDFASLYPSIMIAHNLCYSTLV 581
Query: 104 TPQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELT 163
P D Y TP G+ F+K +RKG+LP I+E L++ARK+AK ++K E D L
Sbjct: 582 PPNDANNYP--EDTYVTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEKDPLL 639
Query: 164 -QVL 166
+VL
Sbjct: 640 KKVL 643
Score = 58.9 bits (143), Expect = 9e-11
Identities = 18/34 (52%), Positives = 24/34 (70%)
Query: 10 GLETVRRDNSPLVANMINTCLQKLLINRDPDGAV 43
G+ETVRRDN LV M+ T L K+LI +D + A+
Sbjct: 785 GIETVRRDNCLLVQQMVETVLNKILIEKDVESAI 818
>gnl|CDD|215742 pfam00136, DNA_pol_B, DNA polymerase family B. This region of DNA
polymerase B appears to consist of more than one
structural domain, possibly including elongation,
DNA-binding and dNTP binding activities.
Length = 458
Score = 130 bits (328), Expect = 2e-36
Identities = 49/132 (37%), Positives = 75/132 (56%), Gaps = 17/132 (12%)
Query: 45 QKNFIIP---------TYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAH 95
++NFI+P + E ++GATV+EPKKG+Y +P+ LDF+SLYPSI+ AH
Sbjct: 16 ERNFILPDKFELRSLSRQVNIKKE-GYQGATVLEPKKGFYNNPVLVLDFASLYPSIIQAH 74
Query: 96 NLCYTTLLTPQTITKLELTPDQYSKT------PCGNFFLKSSLRKGLLPEILENLLSARK 149
NLCY TL+ +L ++ + F+K +RKG+LP +L +LL+ RK
Sbjct: 75 NLCYETLVDVD-AEAPKLAAERNLEVLHIVVGSLRERFVKKGVRKGILPVLLRDLLAKRK 133
Query: 150 QAKNDLKKETDE 161
+ K +K+ D
Sbjct: 134 EKKKLMKESKDP 145
Score = 44.6 bits (106), Expect = 7e-06
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 10 GLETVRRDNSPLVANMINTCLQKLLINRDPDGAV 43
G++ VRRD V +I L LL ++D + A
Sbjct: 283 GVDLVRRDWCEFVKEVIRKVLDLLLKDKDVEDAA 316
>gnl|CDD|214691 smart00486, POLBc, DNA polymerase type-B family. DNA polymerase
alpha, delta, epsilon and zeta chain (eukaryota), DNA
polymerases in archaea, DNA polymerase II in e. coli,
mitochondrial DNA polymerases and and virus DNA
polymerases.
Length = 474
Score = 116 bits (292), Expect = 4e-31
Identities = 48/133 (36%), Positives = 75/133 (56%), Gaps = 15/133 (11%)
Query: 44 TQKNFIIPTYHGGQGED---------QFEGATVIEPKKGYYADPIATLDFSSLYPSIMMA 94
+ N+I+P+ + ++EG V+EPKKG+Y +P+ LDF+SLYPSI++A
Sbjct: 259 KKNNYILPSKELYDFKGSEPDLKKKVKYEGGKVLEPKKGFYDNPVLVLDFNSLYPSIIIA 318
Query: 95 HNLCYTTLLTPQTITKLELTP------DQYSKTPCGNFFLKSSLRKGLLPEILENLLSAR 148
HNLCY+TL+ + + F+K ++RKG+LP++L+ LL R
Sbjct: 319 HNLCYSTLVGVGEVVIKGDLIIPEDLLTIKYEKGNKYRFVKKNIRKGILPKLLKKLLDKR 378
Query: 149 KQAKNDLKKETDE 161
K+ K +KKE DE
Sbjct: 379 KEIKKLMKKEKDE 391
>gnl|CDD|223494 COG0417, PolB, DNA polymerase elongation subunit (family B) [DNA
replication, recombination, and repair].
Length = 792
Score = 112 bits (283), Expect = 1e-29
Identities = 41/122 (33%), Positives = 59/122 (48%), Gaps = 12/122 (9%)
Query: 47 NFIIPTYHGGQGE-DQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTP 105
+IP + E +++G V+EP+ G Y + + LDFSSLYPSI++ +N+ TL+
Sbjct: 391 GELIPNK-EERPERKKYKGGLVLEPEPGLYEN-VLVLDFSSLYPSIIIKYNISPDTLVEE 448
Query: 106 QTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQV 165
+P G KG LPEILE LL R + K +KKE D +
Sbjct: 449 DC---------SDDYSPPGVGHGFCKREKGFLPEILEELLDRRDEIKKKMKKEKDPSERK 499
Query: 166 LY 167
L
Sbjct: 500 LL 501
Score = 44.0 bits (104), Expect = 1e-05
Identities = 16/33 (48%), Positives = 18/33 (54%)
Query: 10 GLETVRRDNSPLVANMINTCLQKLLINRDPDGA 42
GLETVRRD LV L+ LL RD + A
Sbjct: 630 GLETVRRDWPELVKEFQREVLEVLLSGRDVEEA 662
>gnl|CDD|99912 cd00145, POLBc, DNA polymerase type-B family catalytic domain.
DNA-directed DNA polymerases elongate DNA by adding
nucleotide triphosphate (dNTP) residues to the 5'-end of
the growing chain of DNA. DNA-directed DNA polymerases
are multifunctional with both synthetic (polymerase) and
degradative modes (exonucleases) and play roles in the
processes of DNA replication, repair, and recombination.
DNA-dependent DNA polymerases can be classified in six
main groups based upon their phylogenetic relationships
with E. coli polymerase I (class A), 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 B
DNA polymerases include E. coli DNA polymerase II, some
eubacterial phage DNA polymerases, nuclear replicative
DNA polymerases (alpha, delta, epsilon, and zeta), and
eukaryotic viral and plasmid-borne enzymes. DNA
polymerase is made up of distinct domains and
sub-domains. The polymerase domain of DNA polymerase
type B (Pol domain) is responsible for the
template-directed polymerization of dNTPs onto the
growing primer strand of duplex DNA that is usually
magnesium dependent. In general, the architecture of the
Pol domain has been likened to a right hand with
fingers, thumb, and palm sub-domains with a deep groove
to accommodate the nucleic acid substrate. There are a
few conserved motifs in the Pol domain of family B DNA
polymerases. The conserved aspartic acid residues in the
DTDS motifs of the palm sub-domain is crucial for
binding to divalent metal ion and is suggested to be
important for polymerase catalysis.
Length = 323
Score = 102 bits (256), Expect = 8e-27
Identities = 42/108 (38%), Positives = 55/108 (50%), Gaps = 10/108 (9%)
Query: 61 QFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSK 120
+EG V +P G Y + + LDF SLYPSI++ +NL TTL+ I E
Sbjct: 2 PYEGGYVFDPIPGLY-ENVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPE-------- 52
Query: 121 TPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKK-ETDELTQVLY 167
G F RKGLLP ILE LL+ R +AK +K + +VLY
Sbjct: 53 DYIGVGFRSPKDRKGLLPRILEELLNFRDEAKKRMKAAKLAPEERVLY 100
Score = 36.6 bits (85), Expect = 0.003
Identities = 14/34 (41%), Positives = 17/34 (50%)
Query: 10 GLETVRRDNSPLVANMINTCLQKLLINRDPDGAV 43
GLET RRD+ PLV L+ +L AV
Sbjct: 231 GLETRRRDSPPLVKKFQKEVLELILEEERKVEAV 264
>gnl|CDD|99917 cd05534, POLBc_zeta, DNA polymerase type-B zeta subfamily catalytic
domain. DNA polymerase (Pol) zeta is a member of the
eukaryotic B-family of DNA polymerases and distantly
related to DNA Pol delta. Pol zeta plays a major role in
translesion replication and the production of either
spontaneous or induced mutations. Apart from its role in
translesion replication, Pol zeta also appears to be
involved in somatic hypermutability in B lymphocytes, an
important element for the production of high affinity
antibodies in response to an antigen.
Length = 451
Score = 95.4 bits (238), Expect = 1e-23
Identities = 45/115 (39%), Positives = 63/115 (54%), Gaps = 20/115 (17%)
Query: 67 VIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLL--------------------TPQ 106
V+EP+ G+Y+DP+ LDF SLYPSIM+A+N CY+T L P
Sbjct: 41 VMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLGRVEELNGGGKFGFLGVKLYLPP 100
Query: 107 TITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDE 161
L L D + +P G F+K S+RKG+LP++LE +L R K +KK D+
Sbjct: 101 PPLDLLLLKDDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKKYKDD 155
Score = 36.4 bits (85), Expect = 0.004
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 10 GLETVRRDNSPLVANMINTCLQKLLINRD 38
G+ETVRRD P V ++ L+ L +D
Sbjct: 299 GIETVRRDGCPAVQKILEKSLRILFETKD 327
>gnl|CDD|99915 cd05532, POLBc_alpha, DNA polymerase type-B alpha subfamily
catalytic domain. Three DNA-dependent DNA polymerases
type B (alpha, delta, and epsilon) have been identified
as essential for nuclear DNA replication in eukaryotes.
DNA polymerase (Pol) alpha is almost exclusively
required for the initiation of DNA replication and the
priming of Okazaki fragments during elongation. In most
organisms no specific repair role, other than check
point control, has been assigned to this enzyme. Pol
alpha contains both polymerase and exonuclease domains,
but lacks exonuclease activity suggesting that the
exonuclease domain may be for structural purposes only.
Length = 400
Score = 91.9 bits (229), Expect = 2e-22
Identities = 36/107 (33%), Positives = 54/107 (50%), Gaps = 10/107 (9%)
Query: 55 GGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELT 114
+ + ++ G V+EPKKG Y I LDF+SLYPSI+ +N+C+TT+ + +
Sbjct: 1 KKKKKAKYAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRADPDDEDDEE 60
Query: 115 PDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDE 161
P S KG+LP I+ L+ R+Q K +K E D
Sbjct: 61 PPLPP----------SDQEKGILPRIIRKLVERRRQVKKLMKSEKDP 97
Score = 30.6 bits (70), Expect = 0.35
Identities = 12/36 (33%), Positives = 19/36 (52%)
Query: 10 GLETVRRDNSPLVANMINTCLQKLLINRDPDGAVTQ 45
GL+ VRRD PL + N L ++L ++ + V
Sbjct: 235 GLDIVRRDWCPLSKEIGNYVLDQILSDKSREDIVEN 270
>gnl|CDD|235595 PRK05762, PRK05762, DNA polymerase II; Reviewed.
Length = 786
Score = 85.3 bits (212), Expect = 7e-20
Identities = 35/112 (31%), Positives = 50/112 (44%), Gaps = 10/112 (8%)
Query: 47 NFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQ 106
++ P GE G V++ K G Y D + LDF SLYPSI+ N+ L
Sbjct: 387 GYVAPNLGERPGEA-SPGGYVMDSKPGLY-DSVLVLDFKSLYPSIIRTFNIDPDGL---- 440
Query: 107 TITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKE 158
+ L P++ G F + K LPEI+E L R +AK ++ K
Sbjct: 441 -VEGLAQPPEESVAGFLGARFSR---EKHFLPEIVERLWEGRDEAKREMNKP 488
>gnl|CDD|99919 cd05536, POLBc_B3, DNA polymerase type-B B3 subfamily catalytic
domain. Archaeal proteins that are involved in DNA
replication are similar to those from eukaryotes. Some
members of the archaea also possess multiple family B
DNA polymerases (B1, B2 and B3). So far there is no
specific function(s) has been assigned for different
members of the archaea type B DNA polymerases.
Phylogenetic analyses of eubacterial, archaeal, and
eukaryotic family B DNA polymerases are support
independent gene duplications during the evolution of
archaeal and eukaryotic family B DNA polymerases.
Structural comparison of the thermostable DNA polymerase
type B to its mesostable homolog suggests several
adaptations to high temperature such as shorter loops,
disulfide bridges, and increasing electrostatic
interaction at subdomain interfaces.
Length = 371
Score = 80.1 bits (198), Expect = 2e-18
Identities = 38/100 (38%), Positives = 57/100 (57%), Gaps = 10/100 (10%)
Query: 62 FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKT 121
+EG V+EP+KG + + I LDFSSLYPSIM+ +N ++P T+ + E D +
Sbjct: 4 YEGGIVLEPEKGLHEN-IVVLDFSSLYPSIMIKYN------ISPDTLVR-EGCEDCDVEP 55
Query: 122 PCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDE 161
G+ F K G +P +LE+LL R++ K +KK E
Sbjct: 56 QVGHKFRKD--PPGFIPSVLEDLLEERRRIKEKMKKLDPE 93
>gnl|CDD|233037 TIGR00592, pol2, DNA polymerase (pol2). All proteins in this
superfamily for which functions are known are DNA
polymerases.This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1172
Score = 63.9 bits (155), Expect = 2e-12
Identities = 34/106 (32%), Positives = 53/106 (50%), Gaps = 13/106 (12%)
Query: 62 FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKT 121
+ G V+EPK G Y + +DF+SLYPSI+ N+C+TT+ +L PD
Sbjct: 796 YAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQQKVDEDELPELPD----- 850
Query: 122 PCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVLY 167
S L G+LP L L+ RK+ K +K++ + ++ Y
Sbjct: 851 --------SELEMGILPRELRKLVERRKEVKKLMKQDLNPDLRLQY 888
Score = 33.1 bits (75), Expect = 0.063
Identities = 31/123 (25%), Positives = 45/123 (36%), Gaps = 18/123 (14%)
Query: 62 FEGATVIEP--KKGYY--ADPIATLDFS--SLYPSIMMAHNLCYTTLLTPQTITKLELTP 115
+EG V P +KG P+ LDFS SL PSI+ + + P
Sbjct: 485 YEGGYVKPPNVEKGLDKTPPPLVVLDFSMKSLNPSIIRNEI-VSIPDTLHREFALDKPPP 543
Query: 116 DQ-YSKTPC-GNFFLKSSLR-------KGLLPEILENLLSARKQAKNDLK--KETDELTQ 164
+ Y PC G S G P ++E+L + R K + K+ D
Sbjct: 544 EPPYDVHPCVGTRPKDCSFPLDLKGEFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEI 603
Query: 165 VLY 167
V +
Sbjct: 604 VGH 606
Score = 29.6 bits (66), Expect = 0.99
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 10 GLETVRRDNSPLVANMINTCLQKLLINRDPDGAVT 44
GL+ VRRD SPL L +L ++D + AV
Sbjct: 1022 GLDIVRRDWSPLAKETGKKVLDTILSDKDVEEAVE 1056
>gnl|CDD|99914 cd05531, POLBc_B2, DNA polymerase type-B B2 subfamily catalytic
domain. Archaeal proteins that are involved in DNA
replication are similar to those from eukaryotes. Some
archaeal members also possess multiple family B DNA
polymerases (B1, B2 and B3). So far there is no specific
function(s) has been assigned for different members of
the archaea type B DNA polymerases. Phylogenetic
analyses of eubacterial, archaeal, and eukaryotic family
B DNA polymerases are support independent gene
duplications during the evolution of archaeal and
eukaryotic family B DNA polymerases.
Length = 352
Score = 59.7 bits (145), Expect = 4e-11
Identities = 31/98 (31%), Positives = 48/98 (48%), Gaps = 11/98 (11%)
Query: 64 GATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPC 123
G V +P+ G Y + +A +DFSS+YPSI++ +N ++P+TI +
Sbjct: 7 GGLVFQPEPGLYEN-VAQIDFSSMYPSIIVKYN------ISPETIN----CRCCECRDHV 55
Query: 124 GNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDE 161
R+G LPE+LE LL R + K K+E
Sbjct: 56 YLGHRICLKRRGFLPEVLEPLLERRLEYKRLKKEEDPY 93
Score = 28.1 bits (63), Expect = 2.5
Identities = 10/31 (32%), Positives = 13/31 (41%)
Query: 10 GLETVRRDNSPLVANMINTCLQKLLINRDPD 40
G+E RRD P V L L + P+
Sbjct: 217 GIELRRRDTPPFVKKFQEEALDILASAKTPE 247
>gnl|CDD|235594 PRK05761, PRK05761, DNA polymerase I; Reviewed.
Length = 787
Score = 55.5 bits (134), Expect = 2e-09
Identities = 24/95 (25%), Positives = 41/95 (43%), Gaps = 8/95 (8%)
Query: 64 GATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPC 123
G V +P G + + + LDF+SLYPSI++ NL T+ P+ + + + C
Sbjct: 409 GGLVFQPPPGIFFN-VYVLDFASLYPSIIVKWNLSPETVRIPECKCHYDDEVPELGHSVC 467
Query: 124 GNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKE 158
+ R GL ++ L R + K+
Sbjct: 468 DD-------RPGLTSVLVGLLRDFRVKIYKKKAKD 495
>gnl|CDD|177369 PHA02528, 43, DNA polymerase; Provisional.
Length = 881
Score = 53.5 bits (129), Expect = 8e-09
Identities = 31/122 (25%), Positives = 53/122 (43%), Gaps = 24/122 (19%)
Query: 46 KNFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTP 105
+ +IP + + ++ GA V EP G Y + + D +SLYPSI+ N ++P
Sbjct: 362 EKIVIPE-NKSHKKQKYAGAFVKEPVPGAY-RWVVSFDLTSLYPSIIRQVN------ISP 413
Query: 106 QTIT--------------KLELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQA 151
+TI D+YS +P G + K +G++P ++ + RK
Sbjct: 414 ETIAGTFHVAPVHEYINKTAPRPSDEYSCSPNGWMYRKD--IRGVIPTEIKKVFDQRKIY 471
Query: 152 KN 153
K
Sbjct: 472 KK 473
>gnl|CDD|99913 cd05530, POLBc_B1, DNA polymerase type-B B1 subfamily catalytic
domain. Archaeal proteins that are involved in DNA
replication are similar to those from eukaryotes. Some
archaeal members also possess multiple family B DNA
polymerases (B1, B2 and B3). So far there is no specific
function(s) has been assigned for different members of
the archaea type B DNA polymerases. Phylogenetic
analyses of eubacterial, archaeal, and eukaryotic family
B DNA polymerases are support independent gene
duplications during the evolution of archaeal and
eukaryotic family B DNA polymerases.
Length = 372
Score = 51.6 bits (124), Expect = 2e-08
Identities = 35/108 (32%), Positives = 53/108 (49%), Gaps = 16/108 (14%)
Query: 62 FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKT 121
+ GA V+EP G + + + LDF+SLYPSI+ NL Y T+ P K P+
Sbjct: 13 YRGAIVLEPPPGIFFN-VVVLDFASLYPSIIKVWNLSYETVNCPHCECKTNEVPE----- 66
Query: 122 PCGNFFLKSSLRKGLLPEILENLLSAR-----KQAKNDLKKETDELTQ 164
G++ K R G+ +I+ L R K+AK+ K +E+ Q
Sbjct: 67 -VGHWVCKK--RPGITSQIIGLLRDLRVKIYKKKAKD--KSLDEEMRQ 109
>gnl|CDD|222962 PHA03036, PHA03036, DNA polymerase; Provisional.
Length = 1004
Score = 51.6 bits (124), Expect = 3e-08
Identities = 28/127 (22%), Positives = 53/127 (41%), Gaps = 22/127 (17%)
Query: 62 FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTL-------------LTPQTI 108
+EG V PK+ + + + D++SLYP++ + NL TL + Q +
Sbjct: 530 YEGGKVFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETLVGVVVNDNRLEAEINKQEL 589
Query: 109 TKLELTPDQYSKTPCGN--------FFLKSSLRKGLLPEILENLLSARKQAKNDLKKETD 160
+ P Y C + +G++P++L+ L R + K LK+ T
Sbjct: 590 RRKYPYPR-YIYVHCEPRSPDLVSEIAVFDRRIEGIIPKLLKTFLEERARYKKLLKEATS 648
Query: 161 ELTQVLY 167
+ + +Y
Sbjct: 649 SVEKAIY 655
>gnl|CDD|99920 cd05537, POLBc_Pol_II, DNA polymerase type-II subfamily catalytic
domain. Bacteria contain five DNA polymerases (I, II,
III, IV and V). DNA polymerase II (Pol II) is a
prototype for the B-family of polymerases. The role of
Pol II in a variety of cellular activities, such as
repair of DNA damaged by UV irradiation or oxidation has
been proven by genetic studies. DNA polymerase III is
the main enzyme responsible for replication of the
bacterial chromosome; however, In vivo studies have also
shown that Pol II is able to participate in chromosomal
DNA replication with larger role in lagging-strand
replication.
Length = 371
Score = 50.0 bits (120), Expect = 9e-08
Identities = 27/91 (29%), Positives = 42/91 (46%), Gaps = 8/91 (8%)
Query: 64 GATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPC 123
G V++ K G Y + + LDF SLYPSI+ + L+ P+
Sbjct: 5 GGYVMDSKPGLYKN-VLVLDFKSLYPSIIRTFLIDPLGLIEGL----KAPDPEDLIPGFL 59
Query: 124 GNFFLKSSLRKGLLPEILENLLSARKQAKND 154
G F S K +LP+++ L +AR +AK +
Sbjct: 60 GARF---SREKHILPDLIARLWAARDEAKRE 87
Score = 26.5 bits (59), Expect = 8.2
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 10 GLETVRRDNSPLVANMINTCLQKLLINRDP 39
GLETVR D +PL A L + + N +P
Sbjct: 238 GLETVRSDWTPL-ARQFQKELYERVFNDEP 266
>gnl|CDD|164925 PHA02524, 43A, DNA polymerase subunit A; Provisional.
Length = 498
Score = 41.5 bits (97), Expect = 9e-05
Identities = 36/119 (30%), Positives = 54/119 (45%), Gaps = 12/119 (10%)
Query: 42 AVTQKNFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLC--- 98
++ + N +IP + F GA V EP G Y + + D +SLYPSI+ N+
Sbjct: 358 SLVESNVVIPAMKASP-KQSFPGAYVKEPVPGGYRYGL-SFDLTSLYPSILRLLNISPEM 415
Query: 99 YTTLLTP----QTITKLELTP-DQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAK 152
+ +P I K+ P DQ+S P G + K + G+LP E + RK K
Sbjct: 416 IAGMFSPARLEDYINKVAPKPSDQFSCAPNGMMYKKGVV--GVLPNETEKVFLQRKSEK 472
>gnl|CDD|223049 PHA03334, PHA03334, putative DNA polymerase catalytic subunit;
Provisional.
Length = 1545
Score = 37.5 bits (87), Expect = 0.002
Identities = 30/126 (23%), Positives = 41/126 (32%), Gaps = 38/126 (30%)
Query: 64 GATVIEPKKGY-----YADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITK-------- 110
G V P G Y TLDF+SLYPS M N+ ++ P +
Sbjct: 635 GGYVFAPLTGLTFAGPYQGTELTLDFASLYPSNMCDANISPEAIVDPDCTARVRGWVVFD 694
Query: 111 ------------LELTPDQY-SKTPCGNFFL---KSSLRKGLLPEILENLLSARKQAKND 154
L T + + P F SSL + LS R + K
Sbjct: 695 WKKIDRGFGKATLMYTILRTKPEEPSWRRFTTYTTSSLN---------HYLSMRTEYKGA 745
Query: 155 LKKETD 160
+K+ D
Sbjct: 746 MKQAKD 751
>gnl|CDD|99921 cd05538, POLBc_Pol_II_B, DNA polymerase type-II B subfamily
catalytic domain. Bacteria contain five DNA polymerases
(I, II, III, IV and V). DNA polymerase II (Pol II) is a
prototype for the B-family of polymerases. The role of
Pol II in a variety of cellular activities, such as
repair of DNA damaged by UV irradiation or oxidation
has been proved by genetic studies. DNA polymerase III
is the main enzyme responsible for replication of the
bacterial chromosome; however, In vivo studies have
also shown that Pol II is able to participate in
chromosomal DNA replication with larger role in
lagging-strand replication.
Length = 347
Score = 34.4 bits (79), Expect = 0.016
Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 61 QFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLC 98
+FEG G PI D +SLYPSIM+A+ +C
Sbjct: 2 KFEGGYAYVFITGVLG-PIVHADVASLYPSIMLAYRIC 38
>gnl|CDD|193501 cd03880, M28_QC_like, M28 Zn-Peptidase Glutaminyl Cyclase.
Peptidase M28 family; Glutaminyl Cyclase (QC; EC
2.3.2.5) subfamily. QC is involved in N-terminal
glutamine cyclization of many endocrine peptides and is
typically abundant in brain tissue. N-terminal
glutamine residue cyclization is an important
post-translational event in the processing of numerous
bioactive proteins, including neuropeptides, hormones,
and cytokines during their maturation in the secretory
pathway. The N-terminal pGlu protects them from
exopeptidase degradation and/or enables them to have
proper conformation for binding to the receptors. QCs
are highly conserved from yeast to human. In humans,
several genetic diseases, such as osteoporosis, appear
to result from mutations of the QC gene. N-terminal
glutamate cyclization into pyroglutamate (pGlu) is a
reaction that may be related to the formation of
several plaque-forming peptides, such as amyloid-(A)
peptides and collagen-like Alzheimer amyloid plaque
component, which play a pivotal role in Alzheimer's
disease.
Length = 304
Score = 30.6 bits (70), Expect = 0.33
Identities = 22/81 (27%), Positives = 32/81 (39%), Gaps = 9/81 (11%)
Query: 12 ETVRRDNSPLVANMINTCLQKLLINRDPD--GAVTQKNFIIPTYHG-GQG----EDQFEG 64
ET+R + P + L+ +LI R P G +N II + G D F
Sbjct: 1 ETLRLLSDPTDNTHLRNLLKPILIPRVPGTPGHKKVRNHIIDFFRSLLPGWTVELDNFTE 60
Query: 65 ATVIEPKKGYYADPIATLDFS 85
T I + + IATL+
Sbjct: 61 KTPIGEVT--FTNIIATLNPP 79
>gnl|CDD|182166 PRK09955, rihB, ribonucleoside hydrolase 2; Provisional.
Length = 313
Score = 30.3 bits (68), Expect = 0.47
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 75 YADP-IATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLE 112
+ADP A + F+S P +MM +L T+ TP I ++E
Sbjct: 168 FADPEAARVVFTSGVPLVMMGLDLTNQTVCTPDVIARME 206
>gnl|CDD|184766 PRK14610, PRK14610, 4-diphosphocytidyl-2-C-methyl-D-erythritol
kinase; Provisional.
Length = 283
Score = 29.3 bits (66), Expect = 0.84
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 4/42 (9%)
Query: 114 TPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDL 155
T ++K C F S LP ++LL K+A+NDL
Sbjct: 177 TRKVFNKYECKAF----SEPIDNLPVAQDDLLELLKEARNDL 214
>gnl|CDD|213284 cd05917, FACL_like_2, Uncharacterized subfamily of fatty acid CoA
ligase (FACL). Fatty acyl-CoA ligases catalyze the
ATP-dependent activation of fatty acids in a two-step
reaction. The carboxylate substrate first reacts with
ATP to form an acyl-adenylate intermediate, which then
reacts with CoA to produce an acyl-CoA ester. This is a
required step before free fatty acids can participate in
most catabolic and anabolic reactions.
Length = 347
Score = 27.5 bits (62), Expect = 3.4
Identities = 18/45 (40%), Positives = 21/45 (46%), Gaps = 11/45 (24%)
Query: 37 RDPDGAVTQKNFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIAT 81
DPDG +P G GE G +V+ KGYY DP AT
Sbjct: 187 VDPDGG------EVPP--GEVGEICVRGYSVM---KGYYNDPEAT 220
>gnl|CDD|234062 TIGR02924, ICDH_alpha, isocitrate dehydrogenase. This family of
mainly alphaproteobacterial enzymes is a member of the
isocitrate/isopropylmalate dehydrogenase superfamily
described by pfam00180. Every member of the seed of this
model appears to have a TCA cycle lacking only a
determined isocitrate dehydrogenase. The precise
identity of the cofactor (NADH -- 1.1.1.41 vs. NADPH --
1.1.1.42) is unclear [Energy metabolism, TCA cycle].
Length = 473
Score = 27.0 bits (60), Expect = 5.8
Identities = 12/33 (36%), Positives = 21/33 (63%)
Query: 135 GLLPEILENLLSARKQAKNDLKKETDELTQVLY 167
G+ PEI+E +L K+A+ + ET E+ + +Y
Sbjct: 10 GIGPEIMEAVLLILKEAEAPIDIETIEIGEKVY 42
>gnl|CDD|238619 cd01294, DHOase, Dihydroorotase (DHOase) catalyzes the reversible
interconversion of carbamoyl aspartate to
dihydroorotate, a key reaction in the pyrimidine
biosynthesis. In contrast to the large polyfunctional
CAD proteins of higher organisms, this group of DHOases
is monofunctional and mainly dimeric.
Length = 335
Score = 26.5 bits (59), Expect = 8.1
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 3/37 (8%)
Query: 2 LRHVTWRDGLETVRRDNSPLVANMINTCLQKLLINRD 38
L H+T D +E V+ N + A + LL+ RD
Sbjct: 167 LEHITTADAVEYVKSCNENVAATIT---PHHLLLTRD 200
>gnl|CDD|177847 PLN02196, PLN02196, abscisic acid 8'-hydroxylase.
Length = 463
Score = 26.4 bits (58), Expect = 8.5
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 124 GNFFLKSSLRKGLLPEILENLLSARKQAKND 154
G F KS + L +IL +LS R+Q +
Sbjct: 215 GTLFHKSMKARKELAQILAKILSKRRQNGSS 245
>gnl|CDD|165325 PHA03027, PHA03027, hypothetical protein; Provisional.
Length = 325
Score = 26.2 bits (57), Expect = 9.1
Identities = 7/34 (20%), Positives = 17/34 (50%)
Query: 127 FLKSSLRKGLLPEILENLLSARKQAKNDLKKETD 160
+L ++ E+ + L+A + K D +++ D
Sbjct: 289 EENQNLEDEIIEEVFIDKLTANDKIKKDEEEKKD 322
>gnl|CDD|235474 PRK05451, PRK05451, dihydroorotase; Provisional.
Length = 345
Score = 26.2 bits (59), Expect = 9.1
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 4 HVTWRDGLETVRRDNSPLVANMINTCLQKLLINRD 38
H+T +D ++ VR N L A + T LLINR+
Sbjct: 175 HITTKDAVDYVREANDNLAATI--T-PHHLLINRN 206
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.135 0.402
Gapped
Lambda K H
0.267 0.0626 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,398,335
Number of extensions: 747853
Number of successful extensions: 706
Number of sequences better than 10.0: 1
Number of HSP's gapped: 684
Number of HSP's successfully gapped: 50
Length of query: 168
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 78
Effective length of database: 6,945,742
Effective search space: 541767876
Effective search space used: 541767876
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.2 bits)