RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780818|ref|YP_003065231.1| DNA polymerase III subunit
epsilon [Candidatus Liberibacter asiaticus str. psy62]
(245 letters)
>gnl|CDD|180217 PRK05711, PRK05711, DNA polymerase III subunit epsilon;
Provisional.
Length = 240
Score = 258 bits (662), Expect = 1e-69
Identities = 105/243 (43%), Positives = 149/243 (61%), Gaps = 13/243 (5%)
Query: 5 NKMRKIVFDIETTGLDSKN-DRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLH 63
MR+IV D ETTGL+ + RIIEIGAVEL++ T R F V++ P+ R PEAL +H
Sbjct: 2 AIMRQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPD-RLVDPEALAVH 60
Query: 64 GITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKD---PLDP 120
GITDEFL DKP+F+ + EF DF + AE I HNA FD+GF++ E + +D
Sbjct: 61 GITDEFLADKPTFAEVADEFLDFI--RGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTF 118
Query: 121 SRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMMVGGSQ 180
++ DTL++ARR P RN L++LCKRYGI SHR+ HGALLD+ +L++VY+ M GG Q
Sbjct: 119 CKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLHGALLDAEILAEVYL-AMTGG-Q 176
Query: 181 INFGFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKEELDEHD---KTIQTLGKNAIW 237
+ GF + ++ ++T+ I +R + R T EEL H+ + G + +W
Sbjct: 177 TSLGFAMEGETQQQQGEETIQRIV-RQRSRLPVVRATDEELAAHEARLDLLDKKGGSCLW 235
Query: 238 DRY 240
+Y
Sbjct: 236 RKY 238
>gnl|CDD|130473 TIGR01406, dnaQ_proteo, DNA polymerase III, epsilon subunit,
Proteobacterial. This model represents DnaQ, the DNA
polymerase III epsilon subunit, as found in most
Proteobacteria. It consists largely of an exonuclease
domain as described in pfam model pfam00929. In
Gram-positive bacteria, closely related regions are
found both in the Gram-positive type DNA polymerase III
alpha subunit and as an additional N-terminal domain of
a DinG-family helicase. Both are excluded from this
model, as are smaller proteins, also outside the
Proteobacteria, that are similar in size to the epsilon
subunit but as different in sequence as are the
epsilon-like regions found in Gram-positive bacteria.
Length = 225
Score = 218 bits (557), Expect = 1e-57
Identities = 97/232 (41%), Positives = 134/232 (57%), Gaps = 11/232 (4%)
Query: 8 RKIVFDIETTGLD-SKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGIT 66
R+I+ D ETTGLD RI+EIGAVEL++ T F V++ P R EA K+HGIT
Sbjct: 1 RQIILDTETTGLDPKGGHRIVEIGAVELVNRMLTGDNFHVYVNP-ERDMPAEAAKVHGIT 59
Query: 67 DEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRIN---KDPLDPSRI 123
DEFL DKP F I EF DF +E + HNA FDVGF+N EL+R+ K + R+
Sbjct: 60 DEFLADKPKFKEIADEFLDFIG--GSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRV 117
Query: 124 IDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMMVGGSQINF 183
IDTL++AR + P RN L++LCKR+ + SHR+ HGALLD+HLL++VY+ + G +
Sbjct: 118 IDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALLDAHLLAEVYLALTGGQESLLE 177
Query: 184 GFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKEELDEHDKTIQTLGKNA 235
++N K K + L + L + EL H+ + L K +
Sbjct: 178 LAESNSGEAAKPSKS--AEMKLGATLRVL--APREAELQAHEAYLDKLLKKS 225
>gnl|CDD|129663 TIGR00573, dnaq, exonuclease, DNA polymerase III, epsilon subunit
family. All proteins in this family for which functions
are known are components of the DNA polymerase III
complex (epsilon subunit). There is, however, an
outgroup that includes paralogs in some
gamma-proteobacteria and the n-terminal region of DinG
from some low GC gram positive bacteria. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University).
Length = 217
Score = 160 bits (407), Expect = 3e-40
Identities = 82/201 (40%), Positives = 117/201 (58%), Gaps = 9/201 (4%)
Query: 11 VFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFL 70
D ETTGL + +D IIEIGAVE+++ T F ++ P+ R P+A+K+HGITD+ L
Sbjct: 11 TGDNETTGLYAGHD-IIEIGAVEIINRRITGNKFHTYIKPD-RPIDPDAIKIHGITDDML 68
Query: 71 KDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDT---L 127
KDKP F I +F D+ AE + HNA FDVGF+N E ++ K + +IDT L
Sbjct: 69 KDKPDFKEIAEDFADYIR--GAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTL 126
Query: 128 SIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMMVGGSQINFGFKT 187
AR + P RN L++LCKRY IT SHR+ HGAL D+ +L+ +Y +M G Q +G
Sbjct: 127 QYARPEFPGKRNTLDALCKRYEITNSHRALHGALADAFILAKLY-LVMTGK-QTKYGENE 184
Query: 188 NEDRFFKEEKKTVPNISLLKR 208
+ K++ +L +
Sbjct: 185 GQQSRPYHAIKSIVKKDMLLK 205
>gnl|CDD|128755 smart00479, EXOIII, exonuclease domain in DNA-polymerase alpha and
epsilon chain, ribonuclease T and other exonucleases.
Length = 169
Score = 137 bits (347), Expect = 3e-33
Identities = 56/167 (33%), Positives = 88/167 (52%), Gaps = 6/167 (3%)
Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEF 69
+V D ETTGLD D IIEI AV++ D + F ++ P+ R + A ++HGIT E
Sbjct: 3 VVIDCETTGLDPGKDEIIEIAAVDV-DGGRIIVVFDTYVKPD-RPITDYATEIHGITPEM 60
Query: 70 LKDKPSFSSIFSEFWDFFNEQNAEWIAHNA-KFDVGFINAELQRINKDPLDPSRIIDTLS 128
L D P+F + E +F + +A NA FD+ F+ E R+ + +IDTL
Sbjct: 61 LDDAPTFEEVLEELLEFLKGKI--LVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLK 118
Query: 129 IARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMM 175
+AR +P + L L +R G+ + R H AL D+ + ++ K++
Sbjct: 119 LARALNPGRKYSLKKLAERLGLEVIGR-AHRALDDARATAKLFKKLV 164
>gnl|CDD|179031 PRK00448, polC, DNA polymerase III PolC; Validated.
Length = 1437
Score = 124 bits (315), Expect = 2e-29
Identities = 60/166 (36%), Positives = 97/166 (58%), Gaps = 8/166 (4%)
Query: 11 VFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFL 70
VFD+ETTGL + D IIEIGAV++ + ++ F+ F+ P G S +L GITD+ +
Sbjct: 423 VFDVETTGLSAVYDEIIEIGAVKIKNGEIIDK-FEFFIKP-GHPLSAFTTELTGITDDMV 480
Query: 71 KDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIA 130
KD PS + +F +F ++ +AHNA FDVGFIN +++ + + +IDTL ++
Sbjct: 481 KDAPSIEEVLPKFKEFC--GDSILVAHNASFDVGFINTNYEKLGLEKIKNP-VIDTLELS 537
Query: 131 RRKHPS-SRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMM 175
R +P + LN+L K++G+ + H H A D+ + + IK +
Sbjct: 538 RFLYPELKSHRLNTLAKKFGVELEHH--HRADYDAEATAYLLIKFL 581
>gnl|CDD|162340 TIGR01405, polC_Gram_pos, DNA polymerase III, alpha chain,
Gram-positive type. The N-terminal region of about 200
amino acids is rich in low-complexity sequence, poorly
alignable, and not included n this model.
Length = 1213
Score = 109 bits (273), Expect = 1e-24
Identities = 59/171 (34%), Positives = 98/171 (57%), Gaps = 16/171 (9%)
Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNR---TFQVFLCPNGRKNSPEALKLHGIT 66
+VFDIETTGL + D IIE GAV++ K R FQ F+ P+ ++ +L GIT
Sbjct: 193 VVFDIETTGLSPQYDEIIEFGAVKV----KNGRIIDKFQFFIKPHEPLSA-FVTELTGIT 247
Query: 67 DEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLD-PSRIID 125
+ L++ P + +F +FF +++ +AHNA FD+GF+N +++ +PL+ P ID
Sbjct: 248 QDMLENAPEIEEVLEKFKEFF--KDSILVAHNASFDIGFLNTNFEKVGLEPLENPV--ID 303
Query: 126 TLSIARRKHPSSRN-DLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMM 175
TL +AR +P ++ L ++CK+ G+ + H A D+ + V+ M+
Sbjct: 304 TLELARALNPEYKSHRLGNICKKLGVDLDDH--HRADYDAEATAKVFKVMV 352
>gnl|CDD|181157 PRK07883, PRK07883, hypothetical protein; Validated.
Length = 557
Score = 108 bits (271), Expect = 2e-24
Identities = 56/172 (32%), Positives = 78/172 (45%), Gaps = 28/172 (16%)
Query: 11 VFDIETTGLDSKNDRIIEIGAV-----ELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGI 65
V D+ETTG D I EIGAV E+L F + P GR P L GI
Sbjct: 19 VVDLETTGGSPAGDAITEIGAVKVRGGEVLG------EFATLVNP-GRPIPPFITVLTGI 71
Query: 66 TDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIID 125
T + P + F +F + A +AHNA FD+GF+ A R P ++
Sbjct: 72 TTAMVAGAPPIEEVLPAFLEFA--RGAVLVAHNAPFDIGFLRAAAARCGYPWPGP-PVLC 128
Query: 126 TLSIARR-----KHPSSRNDLNSLCKRYGITI--SHRSKHGALLDSHLLSDV 170
T+ +ARR + P+ R L++L + +G T +HR AL D+ DV
Sbjct: 129 TVRLARRVLPRDEAPNVR--LSTLARLFGATTTPTHR----ALDDARATVDV 174
>gnl|CDD|181223 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 928
Score = 89.6 bits (223), Expect = 6e-19
Identities = 52/173 (30%), Positives = 89/173 (51%), Gaps = 9/173 (5%)
Query: 5 NKMRKIVFDIETTGLD-SKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLH 63
R +V D+ETTG K D+II+I AV + D R F F+ P R P +L
Sbjct: 1 MSKRFVVVDLETTGNSPKKGDKIIQIAAVVVEDGEILER-FSSFVNPE-RPIPPFITELT 58
Query: 64 GITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRI 123
GI++E +K P F + E + + A ++AHN FD+ F+N EL+R +
Sbjct: 59 GISEEMVKQAPLFEDVAPEIVELL--EGAYFVAHNVHFDLNFLNEELERAGYTEIH-CPK 115
Query: 124 IDTLSIARRKHPSSRN-DLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMM 175
+DT+ +AR P++ + L L + G+ H H A D+ + ++++++++
Sbjct: 116 LDTVELARILLPTAESYKLRDLSEELGLE--HDQPHRADSDAEVTAELFLQLL 166
>gnl|CDD|181100 PRK07740, PRK07740, hypothetical protein; Provisional.
Length = 244
Score = 86.3 bits (214), Expect = 6e-18
Identities = 50/169 (29%), Positives = 77/169 (45%), Gaps = 8/169 (4%)
Query: 10 IVFDIETTGLD-SKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDE 68
+VFD+ETTG + D I+ IGAV+ TF + P R L+L GIT E
Sbjct: 62 VVFDLETTGFSPQQGDEILSIGAVKTKGGEVETDTFYSLVKP-KRPIPEHILELTGITAE 120
Query: 69 FLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLS 128
+ P + + F+ F +AH+A D F+ L R + P R+IDT+
Sbjct: 121 DVAFAPPLAEVLHRFYAFIG--AGVLVAHHAGHDKAFLRHALWRTYRQPFT-HRLIDTMF 177
Query: 129 IARR-KHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMMV 176
+ + H L+ YGI I R H AL D+ + + ++ ++V
Sbjct: 178 LTKLLAHERDFPTLDDALAYYGIPIPRR--HHALGDALMTAKLWAILLV 224
>gnl|CDD|180524 PRK06309, PRK06309, DNA polymerase III subunit epsilon; Validated.
Length = 232
Score = 83.7 bits (207), Expect = 4e-17
Identities = 54/169 (31%), Positives = 77/169 (45%), Gaps = 11/169 (6%)
Query: 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITD 67
I +D ETTG DRIIEI A T+ +FQ + P EA K+HGIT
Sbjct: 3 ALIFYDTETTGTQIDKDRIIEIAAYN----GVTSESFQTLVNP-EIPIPAEASKIHGITT 57
Query: 68 EFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNA-KFDVGFINAELQRINKDPLDPSRIIDT 126
+ + D P F + +F +F N +AHN FD + E +R +P R ID+
Sbjct: 58 DEVADAPKFPEAYQKFIEFCGTDNI-LVAHNNDAFDFPLLRKECRRHGLEPPT-LRTIDS 115
Query: 127 LSIARRKHPS-SRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKM 174
L A++ P +++L L + YG H AL D L V+ +
Sbjct: 116 LKWAQKYRPDLPKHNLQYLRQVYGFE--ENQAHRALDDVITLHRVFSAL 162
>gnl|CDD|181455 PRK08517, PRK08517, DNA polymerase III subunit epsilon;
Provisional.
Length = 257
Score = 82.4 bits (204), Expect = 1e-16
Identities = 59/165 (35%), Positives = 87/165 (52%), Gaps = 13/165 (7%)
Query: 3 RKNKMRKIVF---DIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEA 59
R ++ VF DIET G K +IIEIGAV++ + +R F+ F+ K PE
Sbjct: 61 RFTPIKDQVFCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDR-FESFV---KAKEVPEY 116
Query: 60 L-KLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPL 118
+ +L GIT E L++ PS + EF F ++ ++AHN FD FI+ L+ I PL
Sbjct: 117 ITELTGITYEDLENAPSLKEVLEEFRLFL--GDSVFVAHNVNFDYNFISRSLEEIGLGPL 174
Query: 119 DPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITI--SHRSKHGAL 161
+R + T+ +A+R S R L+ L + GI I HR+ AL
Sbjct: 175 -LNRKLCTIDLAKRTIESPRYGLSFLKELLGIEIEVHHRAYADAL 218
>gnl|CDD|180525 PRK06310, PRK06310, DNA polymerase III subunit epsilon; Validated.
Length = 250
Score = 79.1 bits (195), Expect = 1e-15
Identities = 49/155 (31%), Positives = 79/155 (50%), Gaps = 6/155 (3%)
Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEF 69
+ D ETTGLD K DRIIE A+ + + + + + P R S E+ ++H I+D
Sbjct: 10 VCLDCETTGLDVKKDRIIEFAAIR-FTFDEVIDSVEFLINPE-RVVSAESQRIHHISDAM 67
Query: 70 LKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPL-DPSRIIDTLS 128
L+DKP + +F + FF E + + H+ FD+ ++ E +RI + L IIDTL
Sbjct: 68 LRDKPKIAEVFPQIKGFFKEGDY-IVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLR 126
Query: 129 IARRKHPSSRNDLNSLCKRYGITISHRSKHGALLD 163
+A+ S N L +L + + + H A+ D
Sbjct: 127 LAKEYGDSPNNSLEALAVHF--NVPYDGNHRAMKD 159
>gnl|CDD|162341 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase,
putative. This model represents a family of proteins in
Gram-positive bacteria. The N-terminal region of about
200 amino acids resembles the epsilon subunit of E. coli
DNA polymerase III and the homologous region of the
Gram-positive type DNA polymerase III alpha subunit. The
epsilon subunit contains an exonuclease domain. The
remainder of this protein family resembles a predicted
ATP-dependent helicase, the DNA damage-inducible protein
DinG of E. coli.
Length = 850
Score = 78.3 bits (193), Expect = 2e-15
Identities = 51/168 (30%), Positives = 87/168 (51%), Gaps = 8/168 (4%)
Query: 8 RKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITD 67
R V D+ETTG D+II+IG V +++ + TF + PN P +L GI+D
Sbjct: 1 RYAVVDLETTGTQLSFDKIIQIGIV-VVEDGEIVDTFHTDVNPN-EPIPPFIQELTGISD 58
Query: 68 EFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTL 127
L+ P FS + E +D ++ ++AHN FD+ F+ L+ +PL P IDT+
Sbjct: 59 NMLQQAPYFSQVAQEIYDLL--EDGIFVAHNVHFDLNFLAKALKDCGYEPL-PKPRIDTV 115
Query: 128 SIARRKHPSSRN-DLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKM 174
+A+ P+ + L+ L + G+T H + H A D+ +++ + +
Sbjct: 116 ELAQIFFPTEESYQLSELSEALGLT--HENPHRADSDAQATAELLLLL 161
>gnl|CDD|180706 PRK06807, PRK06807, DNA polymerase III subunit epsilon; Validated.
Length = 313
Score = 73.7 bits (181), Expect = 5e-14
Identities = 49/170 (28%), Positives = 78/170 (45%), Gaps = 19/170 (11%)
Query: 10 IVFDIETTGLDSKNDRIIEIGAV-----ELLDYSKTNRTFQVFLCPNGRKNSPEALKLHG 64
+V D ETTG + ND+II++ AV EL+D F ++ P R L G
Sbjct: 11 VVIDFETTGFNPYNDKIIQVAAVKYRNHELVD------QFVSYVNPE-RPIPDRITSLTG 63
Query: 65 ITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRII 124
IT+ + D P+ + F F + +AHNA FD+ F+ + + + +++I
Sbjct: 64 ITNYRVSDAPTIEEVLPLFLAFLHTNVI--VAHNASFDMRFLKSNVNMLGLPEPK-NKVI 120
Query: 125 DTLSIARRKHPSSRNDLNSLCKRY-GITISHRSKHGALLDSHLLSDVYIK 173
DT+ +A++ + N KR GI + S H A D + VY K
Sbjct: 121 DTVFLAKKYMKHAPNHKLETLKRMLGIRL---SSHNAFDDCITCAAVYQK 167
>gnl|CDD|180377 PRK06063, PRK06063, DNA polymerase III subunit epsilon;
Provisional.
Length = 313
Score = 68.6 bits (168), Expect = 1e-12
Identities = 48/164 (29%), Positives = 77/164 (46%), Gaps = 15/164 (9%)
Query: 11 VFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFL 70
V D+ET+G RII + + L ++ L P G P +HG+T E L
Sbjct: 19 VVDVETSGFRPGQARIISLAVLGLDADGNVEQSVVTLLNP-GVDPGP--THVHGLTAEML 75
Query: 71 KDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKD-PLDPSRIIDTLSI 129
+ +P F+ I E + + +AHN FD F+ AE +R + P+D + T+ +
Sbjct: 76 EGQPQFADIAGEVAELLRGRTL--VAHNVAFDYSFLAAEAERAGAELPVD-QVMC-TVEL 131
Query: 130 ARR---KHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDV 170
ARR P+ R L +L +G+ R H AL D+ +L+ +
Sbjct: 132 ARRLGLGLPNLR--LETLAAHWGVP-QQRP-HDALDDARVLAGI 171
>gnl|CDD|181680 PRK09182, PRK09182, DNA polymerase III subunit epsilon; Validated.
Length = 294
Score = 63.8 bits (156), Expect = 4e-11
Identities = 37/104 (35%), Positives = 46/104 (44%), Gaps = 10/104 (9%)
Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQV-----FLCPNGRKNSPEALKLHG 64
++ D ETTGLD + D IIEIG V +Y R V L R PE +L G
Sbjct: 40 VILDTETTGLDPRKDEIIEIGMV-AFEYDDDGRIGDVLDTFGGLQQPSRPIPPEITRLTG 98
Query: 65 ITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINA 108
ITDE + + +I D IAHNA FD F+
Sbjct: 99 ITDEMVAGQ----TIDPAAVDALIAPADLIIAHNAGFDRPFLER 138
>gnl|CDD|181176 PRK07942, PRK07942, DNA polymerase III subunit epsilon;
Provisional.
Length = 232
Score = 63.1 bits (154), Expect = 6e-11
Identities = 38/150 (25%), Positives = 65/150 (43%), Gaps = 11/150 (7%)
Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEF 69
FD+ETTG+D + RI+ A+ ++D + +L G + EA +HGIT E+
Sbjct: 9 AAFDLETTGVDPETARIVT-AALVVVDADGEVVESREWLADPGVEIPEEASAVHGITTEY 67
Query: 70 LKDK-----PSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRII 124
+ + I + + + NA +D+ ++ EL+R L P +I
Sbjct: 68 ARAHGRPAAEVLAEIADALREAWAR-GVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVI 126
Query: 125 DTLSIARRKHP---SSRNDLNSLCKRYGIT 151
D I + R L +LC+ YG+
Sbjct: 127 DPYVIDKAVDRYRKGKRT-LTALCEHYGVR 155
>gnl|CDD|130365 TIGR01298, RNaseT, ribonuclease T. in gamma-subdivision
Proteobacteria such as Escherichia coli and Xylella
fastidiosa. Ribonuclease T is homologous to the DNA
polymerase III alpha chain. It can liberate AMP from the
common C-C-A terminus of uncharged tRNA. It appears also
to be involved in RNA maturation. It also acts as a 3'
to 5' single-strand DNA-specific exonuclease; it is
distinctive for its ability to remove residues near a
double-stranded stem. Ribonuclease T is a high copy
suppressor in E. coli of a uv-repair defect caused by
deletion of three other single-stranded DNA
exonucleases.
Length = 200
Score = 60.6 bits (147), Expect = 4e-10
Identities = 50/171 (29%), Positives = 77/171 (45%), Gaps = 19/171 (11%)
Query: 10 IVFDIETTGLDSKNDRIIEIGAVEL-LD-----YSKTNRTFQVFLCPNGRKNSPEALKLH 63
+V D+ET G ++K D ++EI A+ L +D + T F V G PEAL+
Sbjct: 11 VVVDVETGGFNAKTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFE-GANIQPEALEFT 69
Query: 64 GIT-DEFLK----DKPSFSSIFSEFWDFFNE---QNAEWIAHNAKFDVGFINAELQRIN- 114
GI D L+ + + IF Q A + HNA FD+GF+NA ++R +
Sbjct: 70 GIDLDHPLRGAVSEYEALHEIFKVVRKAMKASGCQRAILVGHNANFDLGFLNAAVERTSL 129
Query: 115 -KDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDS 164
++P P DT ++A + + L C+ G H AL D+
Sbjct: 130 KRNPFHPFSTFDTATLAGLAY--GQTVLAKACQAAGXDFDSTQAHSALYDT 178
>gnl|CDD|181671 PRK09145, PRK09145, DNA polymerase III subunit epsilon; Validated.
Length = 202
Score = 57.6 bits (140), Expect = 3e-09
Identities = 39/178 (21%), Positives = 82/178 (46%), Gaps = 25/178 (14%)
Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNR-----TFQVFLCPNGRKNSPEALKLHG 64
+ D ETTGLD + I+ I AV++ + NR ++ + P + S E++K+H
Sbjct: 32 VALDCETTGLDPRRAEIVSIAAVKI----RGNRILTSERLELLVRPP-QSLSAESIKIHR 86
Query: 65 ITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRII 124
+ + L+D S + F N + + +FDV +N ++ + PL P+ +I
Sbjct: 87 LRHQDLEDGLSEEEALRQLLAFIG--NRPLVGYYLEFDVAMLNRYVRPLLGIPL-PNPLI 143
Query: 125 DTLSIARRK--------HPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKM 174
+ ++ K + R +++ K + + R H AL D+ + + +++++
Sbjct: 144 EVSALYYDKKERHLPDAYIDLR--FDAILKHLDLPVLGR--HDALNDAIMAALIFLRL 197
>gnl|CDD|181186 PRK07983, PRK07983, exodeoxyribonuclease X; Provisional.
Length = 219
Score = 55.9 bits (135), Expect = 1e-08
Identities = 48/171 (28%), Positives = 75/171 (43%), Gaps = 29/171 (16%)
Query: 11 VFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFL 70
V D ET GL I+EI +V+++D N + P R SP+A+ +H IT+ +
Sbjct: 4 VIDTETCGLQGG---IVEIASVDVIDGKIVN-PMSHLVRP-DRPISPQAMAIHRITEAMV 58
Query: 71 KDKPSFSSIFSEFWDFFNEQNAEW-IAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSI 129
DKP + + +EW +AHNA FD + P P I T+ +
Sbjct: 59 ADKPWIEDVIPHY------YGSEWYVAHNASFDRRVL----------PEMPGEWICTMKL 102
Query: 130 ARRKHPSSRNDLNSLCKRYGITIS-----HRSKHGALLDSHLLSDVYIKMM 175
ARR P + +L K + + H H AL D ++ + + I +M
Sbjct: 103 ARRLWPGIKYSNMALYKSRKLNVQTPPGLH--HHRALYDCYITAALLIDIM 151
>gnl|CDD|181672 PRK09146, PRK09146, DNA polymerase III subunit epsilon; Validated.
Length = 239
Score = 51.5 bits (124), Expect = 2e-07
Identities = 37/132 (28%), Positives = 55/132 (41%), Gaps = 21/132 (15%)
Query: 13 DIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGR--------KNSPEALKLHG 64
D ETTGLD++ D I+ IG V T Q C R E++ +HG
Sbjct: 53 DFETTGLDAEQDAIVSIGLVPF--------TLQRIRCRQARHWVVKPRRPLEEESVVIHG 104
Query: 65 ITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQ-RINKDPLDPSRI 123
IT L+D P I E + + + H + + F++ L+ RI + P +
Sbjct: 105 ITHSELQDAPDLERILDELLEALAGK--VVVVHYRRIERDFLDQALRNRIGEGIEFP--V 160
Query: 124 IDTLSIARRKHP 135
IDT+ I R
Sbjct: 161 IDTMEIEARIQR 172
>gnl|CDD|180459 PRK06195, PRK06195, DNA polymerase III subunit epsilon; Validated.
Length = 309
Score = 49.4 bits (118), Expect = 9e-07
Identities = 31/110 (28%), Positives = 51/110 (46%), Gaps = 7/110 (6%)
Query: 56 SPEALKLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINK 115
P + +HGI ++D+ F I+ + +FN IAHNA FD+ + L+ N
Sbjct: 47 MPINIGIHGIRPHMVEDELEFDKIWEKIKHYFNNNLV--IAHNASFDISVLRKTLELYNI 104
Query: 116 DPLDPSRIIDTLSIARRKHPSSRN-DLNSLCKRYGITISHRSKHGALLDS 164
P+ I T+ +A+ + + N LN++ G H H AL D+
Sbjct: 105 -PMPSFEYICTMKLAKNFYSNIDNARLNTVNNFLGYEFKH---HDALADA 150
>gnl|CDD|179951 PRK05168, PRK05168, ribonuclease T; Provisional.
Length = 211
Score = 47.5 bits (114), Expect = 3e-06
Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 29/143 (20%)
Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPN-----------GRKNSPE 58
+V D+ET G ++K D ++EI AV L + Q +L P+ G PE
Sbjct: 20 VVIDVETAGFNAKTDALLEIAAV-TLKMDE-----QGWLYPDETLHFHVEPFEGANLEPE 73
Query: 59 ALKLHGITDEF------LKDKPSFSSIFSEFWDFFNEQN---AEWIAHNAKFDVGFINAE 109
AL +GI D + +K + IF A +AHNA FD+ F+ A
Sbjct: 74 ALAFNGI-DPDNPLRGAVSEKEALHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAA 132
Query: 110 LQR--INKDPLDPSRIIDTLSIA 130
+R + ++P P DT +++
Sbjct: 133 AERAGLKRNPFHPFSTFDTATLS 155
>gnl|CDD|180905 PRK07246, PRK07246, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 820
Score = 45.8 bits (109), Expect = 1e-05
Identities = 44/181 (24%), Positives = 85/181 (46%), Gaps = 20/181 (11%)
Query: 1 MIRKNKMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEAL 60
M +K + V D+E TG N II++G V +++ + ++ + P+ E L
Sbjct: 1 MTQKKLRKYAVVDLEATGAGP-NASIIQVGIV-IIEGGEIIDSYTTDVNPH------EPL 52
Query: 61 KLH-----GITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINK 115
H GITD+ L P FS + +D ++ ++AHN KFD + L
Sbjct: 53 DEHIKHLTGITDQQLAQAPDFSQVARHIYDLI--EDCIFVAHNVKFDANLLAEALFLEGY 110
Query: 116 DPLDPSRIIDTLSIARRKHPS-SRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKM 174
+ P +DT+ +A+ P+ + L+ L + I ++ H A+ D+ +++++K+
Sbjct: 111 ELRTPR--VDTVELAQVFFPTLEKYSLSHLSRELNIDLAD--AHTAIADARATAELFLKL 166
Query: 175 M 175
+
Sbjct: 167 L 167
>gnl|CDD|180158 PRK05601, PRK05601, DNA polymerase III subunit epsilon; Validated.
Length = 377
Score = 42.9 bits (101), Expect = 9e-05
Identities = 37/146 (25%), Positives = 52/146 (35%), Gaps = 31/146 (21%)
Query: 14 IETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDK 73
I+T+G+ R+I I AV L + F L P P LHG++ E
Sbjct: 53 IQTSGIHPSTSRLITIDAVTLTADGEEVEHFHAVLNP---GEDPGPFHLHGLSAEEFAQG 109
Query: 74 PSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSR----------- 122
FS I + + I HNA GFI +E +R +R
Sbjct: 110 KRFSQILKPLDRLIDGR--TLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGR 167
Query: 123 ---------------IIDTLSIARRK 133
I+DTL+ ARR+
Sbjct: 168 GRRRQRVGHIPKPVVIVDTLATARRQ 193
>gnl|CDD|180037 PRK05359, PRK05359, oligoribonuclease; Provisional.
Length = 181
Score = 38.2 bits (90), Expect = 0.002
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 13 DIETTGLDSKNDRIIEIGAV 32
D+E TGLD + DRIIEI +
Sbjct: 9 DLEMTGLDPERDRIIEIATI 28
>gnl|CDD|128750 smart00474, 35EXOc, 3'-5' exonuclease. 3\' -5' exonuclease
proofreading domain present in DNA polymerase I, Werner
syndrome helicase, RNase D and other enzymes.
Length = 172
Score = 33.5 bits (77), Expect = 0.054
Identities = 29/147 (19%), Positives = 50/147 (34%), Gaps = 38/147 (25%)
Query: 4 KNKMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLH 63
+ ++ D ETTGL+S + +++ I + G
Sbjct: 18 RAAGGEVALDTETTGLNSYSGKLVLIQ-----------------ISVTG----------- 49
Query: 64 GITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRI 123
F+ D + D ++ + HNAKFD+ L R ++ I
Sbjct: 50 --EGAFIIDPLALGDDLEILKDLLEDETITKVGHNAKFDLHV----LARFG---IELENI 100
Query: 124 IDTLSIARRK-HPSSRNDLNSLCKRYG 149
DT+ A S++ L +L K Y
Sbjct: 101 FDTMLAAYLLLGGPSKHGLATLLKEYL 127
>gnl|CDD|183390 PRK12268, PRK12268, methionyl-tRNA synthetase; Reviewed.
Length = 556
Score = 30.6 bits (70), Expect = 0.36
Identities = 10/41 (24%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 183 FGFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKEELDE 223
G + E ++ K +P + + +PLF +I E+++E
Sbjct: 508 LGGENIEKLTWESLKPLLPGHPI-NKPEPLFKKIDDEQIEE 547
>gnl|CDD|180237 PRK05755, PRK05755, DNA polymerase I; Provisional.
Length = 880
Score = 29.3 bits (67), Expect = 0.98
Identities = 15/67 (22%), Positives = 27/67 (40%), Gaps = 12/67 (17%)
Query: 85 DFFNEQNAEWIAHNAKFDVGFI---NAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDL 141
+ + + N K+D+ + EL+ I DT+ + P R+ L
Sbjct: 364 PLLEDPAIKKVGQNLKYDLHVLARYGIELRGI---------AFDTMLASYLLDPGRRHGL 414
Query: 142 NSLCKRY 148
+SL +RY
Sbjct: 415 DSLAERY 421
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A''
subunit; Provisional.
Length = 1321
Score = 28.1 bits (62), Expect = 1.9
Identities = 10/40 (25%), Positives = 19/40 (47%)
Query: 116 DPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHR 155
+ + RII+ I R +S++++ L K Y T +
Sbjct: 901 EAFNLERIIEKQKIEDRGKGASKDEIEELAKEYTKTFNAN 940
>gnl|CDD|178839 PRK00071, nadD, nicotinic acid mononucleotide adenylyltransferase;
Provisional.
Length = 203
Score = 27.5 bits (62), Expect = 3.1
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 7/44 (15%)
Query: 95 IAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSR 138
IA N +F V + EL+R PS IDTL R ++P
Sbjct: 66 IADNPRFSVS--DIELERPG-----PSYTIDTLRELRARYPDVE 102
>gnl|CDD|162964 TIGR02660, nifV_homocitr, homocitrate synthase NifV. This family
consists of the NifV clade of homocitrate synthases,
most of which are found in operons for nitrogen
fixation. Members are closely homologous to enzymes that
include 2-isopropylmalate synthase, (R)-citramalate
synthase, and homocitrate synthases associated with
other processes. The homocitrate made by this enzyme
becomes a part of the iron-molybdenum cofactor of
nitrogenase.
Length = 365
Score = 27.6 bits (62), Expect = 3.2
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 2/48 (4%)
Query: 117 PLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDS 164
P DP + + I KH S R L + + GI +S + ALL +
Sbjct: 299 PFDPELVGRSRRIVIGKH-SGRAALINALAQLGIPLS-EEEAAALLPA 344
>gnl|CDD|185356 PRK15459, PRK15459, flagella synthesis chaperone protein FlgN;
Provisional.
Length = 140
Score = 27.6 bits (61), Expect = 3.5
Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 1/71 (1%)
Query: 96 AHNAKFDVGFIN-AELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISH 154
+G IN ++LQRI + +D L RRK ++ N +N + I+
Sbjct: 24 QEQQHLSMGQINGSQLQRITEQKSSLLATLDYLEQQRRKEQNTANSVNDDISQRWQEITE 83
Query: 155 RSKHGALLDSH 165
+++ L+ H
Sbjct: 84 KTQQLRQLNQH 94
>gnl|CDD|180906 PRK07247, PRK07247, DNA polymerase III subunit epsilon;
Validated.
Length = 195
Score = 27.1 bits (60), Expect = 4.7
Identities = 24/89 (26%), Positives = 38/89 (42%), Gaps = 21/89 (23%)
Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLD---------YSKTNRTFQVFLCPNGRKNSPEAL 60
I FD+E ++ + II++ AV+ D Y T+ Q F+ NG
Sbjct: 8 IAFDLEFNTVNGVS-HIIQVSAVKYDDHKEVDSFDSYVYTDVPLQSFI--NG-------- 56
Query: 61 KLHGITDEFLKDKPSFSSIFSEFWDFFNE 89
L GIT + + D P + + F +F E
Sbjct: 57 -LTGITADKIADAPKVEEVLAAFKEFVGE 84
>gnl|CDD|129482 TIGR00387, glcD, glycolate oxidase, subunit GlcD. This protein,
the glycolate oxidase GlcD subunit, is similar in
sequence to that of several D-lactate dehydrogenases,
including that of E. coli. The glycolate oxidase has
been found to have some D-lactate dehydrogenase
activity.
Length = 413
Score = 27.0 bits (60), Expect = 5.1
Identities = 9/35 (25%), Positives = 18/35 (51%)
Query: 118 LDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITI 152
L P +I+ ++ R K P + + + ++Y TI
Sbjct: 290 LSPLYLIEDGTVPRSKLPEALRGIADIARKYDFTI 324
>gnl|CDD|180528 PRK06321, PRK06321, replicative DNA helicase; Provisional.
Length = 472
Score = 26.7 bits (59), Expect = 5.3
Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 2/43 (4%)
Query: 186 KTNEDRFFKEEKKTVPNI--SLLKRDKPLFTRITKEELDEHDK 226
+ ED F+ E K + + K DKP+ + EEL ++
Sbjct: 43 QLQEDDFYFLEHKIIFRVLQDAFKSDKPIDVHLAGEELKRRNQ 85
>gnl|CDD|184421 PRK13961, PRK13961, phosphoribosylaminoimidazole-succinocarboxamide
synthase; Provisional.
Length = 296
Score = 26.7 bits (60), Expect = 5.5
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 207 KRDKPLFTRITKEELDEHDKTI 228
K +P+FT TK EL +HD+ I
Sbjct: 144 KLPEPIFTPATKAELGDHDENI 165
>gnl|CDD|177834 PLN02178, PLN02178, cinnamyl-alcohol dehydrogenase.
Length = 375
Score = 26.5 bits (58), Expect = 7.2
Identities = 18/46 (39%), Positives = 24/46 (52%)
Query: 162 LDSHLLSDVYIKMMVGGSQINFGFKTNEDRFFKEEKKTVPNISLLK 207
LD + V + MVGGSQI +T E F + K V +I L+K
Sbjct: 279 LDLPIFPLVLGRKMVGGSQIGGMKETQEMLEFCAKHKIVSDIELIK 324
>gnl|CDD|148491 pfam06898, YqfD, Putative stage IV sporulation protein YqfD. This
family consists of several putative bacterial stage IV
sporulation (SpoIV) proteins. YqfD of Bacillus subtilis
is known to be essential for efficient sporulation
although its exact function is unknown.
Length = 383
Score = 26.2 bits (58), Expect = 7.8
Identities = 15/72 (20%), Positives = 27/72 (37%), Gaps = 4/72 (5%)
Query: 168 SDVYIKMMVGGSQINFGFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKEELDEHDKT 227
+ +GG ++ F+ NE F++ K L + K L I +E E
Sbjct: 269 KITKHYLSIGGKKLPLKFRKNE---FEKYDKEEDEKPLFLKWK-LPISIVRETYYEVQDK 324
Query: 228 IQTLGKNAIWDR 239
+ L K ++
Sbjct: 325 VVKLTKEEAVEK 336
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.319 0.136 0.398
Gapped
Lambda K H
0.267 0.0743 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,009,717
Number of extensions: 250508
Number of successful extensions: 583
Number of sequences better than 10.0: 1
Number of HSP's gapped: 526
Number of HSP's successfully gapped: 53
Length of query: 245
Length of database: 5,994,473
Length adjustment: 91
Effective length of query: 154
Effective length of database: 4,028,145
Effective search space: 620334330
Effective search space used: 620334330
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: 56 (25.3 bits)