Score E
Sequences producing significant alignments: (bits) Value
gnl|CDD|5373 cd00140, POL3Bc, DNA polymerase III beta subun... 417 e-117
gnl|CDD|3918 smart00480, POL3Bc, DNA polymerase III beta su... 385 e-108
gnl|CDD|10462 COG0592, DnaN, DNA polymerase sliding clamp s... 349 6e-97
gnl|CDD|25954 pfam02767, DNA_pol3_beta_2, DNA polymerase II... 147 5e-36
gnl|CDD|1268 pfam00712, DNA_pol3_beta, DNA polymerase III b... 141 3e-34
gnl|CDD|4799 pfam02768, DNA_pol3_beta_3, DNA polymerase III... 139 8e-34
gnl|CDD|24996 pfam06123, CreD, Inner membrane protein CreD.... 28 2.9
gnl|CDD|16795 pfam00668, Condensation, Condensation domain.... 28 3.2
>gnl|CDD|5373 cd00140, POL3Bc, DNA polymerase III beta subunit; the processivity
factor of the holoenzyme forms a ring shaped dimer that
encircles dsDNA (sliding clamp)
Length = 364
Score = 417 bits (1074), Expect = e-117
Identities = 168/366 (45%), Positives = 237/366 (64%), Gaps = 2/366 (0%)
Query: 1 MHFTIQREALLKPLQLVAGVVERRQTLPVLSNVLLVVEGQQLSLTGTDLEVELVGRVVLE 60
Sbjct: 1 MKFTIEREALLKALSKVARVISSRPTIPILSNVLLEAEEDGLTLTGTDLEISIESSIAAE 60
Query: 61 DAAEPGEITVPARKLMDICKSLPNDVLIDIRVEEQKLLVKAGRSRFTLSTLPANDFPTVE 120
Sbjct: 61 IIEEEGSVLVPARKLSDIVRALPDK-DVTLSFEEDKLLITTGKSRFSLPTLDAEDYPHLP 119
Query: 121 EGPGSLNFSIAQSKLRRLIDRTSFAMAQQDVRYYLNGMLLEVNGGTLRSVATDGHRLAMC 180
Sbjct: 120 EIEEGSELTLPQKLLKEGIEQTAFAASTDETRPVLNGVNLETSGDELRLVATDGHRLAVR 179
Query: 181 SLDAQIPSQDRHQVIVPRKGILELARLLTEQDGEVGIVLGQHHIRATTGEFTFTSKLVDG 240
Sbjct: 180 ELKLEIPDED-FNVIVPRKTLNELKKLLTDGEELVSIFISSNQILFELGNFKFTSRLIEG 238
Query: 241 KFPDYERVLPRGGDKLVVGDRQQLREAFSRTAILSNEKYRGIRLQLSNGLLKIQANNPEQ 300
Sbjct: 239 EFPDYKRLIPTEFETKVTIDRKELKKALKRVALLANEKNRGVRLTVSEGQLKLTSNAPEV 298
Query: 301 EEAEEEVQVEYNGGNLEIGFNVSYLLDVLGVIGTEQVRFILSDSNSSALVHEADNDDSAY 360
Sbjct: 299 GEAEEEVDVDYEGEDLEIAFNPKYLLDALKALKSEEIELKFTDSNKPFLLSPNEDEDLKY 358
Query: 361 VVMPMR 366
Sbjct: 359 LIMPMR 364
>gnl|CDD|3918 smart00480, POL3Bc, DNA polymerase III beta subunit;
Length = 346
Score = 385 bits (991), Expect = e-108
Identities = 146/347 (42%), Positives = 224/347 (64%), Gaps = 1/347 (0%)
Query: 17 VAGVVERRQTLPVLSNVLLVVEGQQLSLTGTDLEVELVGRVVLEDAAEPGEITVPARKLM 76
Sbjct: 1 VSRVISSRPTIPILSNILLEAKDDGLTLTATDLEISIKSSIAAEVESEEGSVTVPAKKFL 60
Query: 77 DICKSLPNDVLIDIRVEEQKLLVKAGRSRFTLSTLPANDFPTVEEGPGSLNFSIAQSKLR 136
Sbjct: 61 DIVRKLPDA-EITLSFKEDKLLITSGKSRFNLPTLPAEEFPELPEIEEGVTFELPTSLLK 119
Query: 137 RLIDRTSFAMAQQDVRYYLNGMLLEVNGGTLRSVATDGHRLAMCSLDAQIPSQDRHQVIV 196
Sbjct: 120 EGIEKTAFAVSTDETRYVLNGVNLEISNDELRLVATDGHRLAVREIKLEKEEDDSFSVII 179
Query: 197 PRKGILELARLLTEQDGEVGIVLGQHHIRATTGEFTFTSKLVDGKFPDYERVLPRGGDKL 256
Sbjct: 180 PRKSLNELNKLLTDNEELVNIFISSNQILFELGNVIFTSRLIDGEFPDYKRVIPKEFETK 239
Query: 257 VVGDRQQLREAFSRTAILSNEKYRGIRLQLSNGLLKIQANNPEQEEAEEEVQVEYNGGNL 316
Sbjct: 240 LTVNRKELKEALKRVALLADEKNRSVKLTLSEGQLKLTANSPEVGEAEEEIDVDYEGEDL 299
Query: 317 EIGFNVSYLLDVLGVIGTEQVRFILSDSNSSALVHEADNDDSAYVVM 363
Sbjct: 300 EIAFNPKYLLDALKALKSEEIELKFTDSSSPFLISPPDDEDLKYLIM 346
>gnl|CDD|10462 COG0592, DnaN, DNA polymerase sliding clamp subunit (PCNA homolog)
[DNA replication, recombination, and repair]
Length = 364
Score = 349 bits (897), Expect = 6e-97
Identities = 169/368 (45%), Positives = 235/368 (63%), Gaps = 5/368 (1%)
Query: 1 MHFTIQREALLKPLQLVAGVVERRQTLPVLSNVLLVVEGQQLSLTGTDLEVELVGRVVLE 60
Sbjct: 1 MKFSIERENLLKALQLVSRIVESRPTIPILSNVLIEAKENGLTLTGTDLEISLEARIPAE 60
Query: 61 DAAEPGEITVPARKLMDICKSLPNDVLIDIRVEEQKLL-VKAGRSRFTLSTLPANDFPTV 119
Sbjct: 61 VEAE-GEVAVPAKKLLDIISKLPDEAVFLVTEDGISLLAVDSGKSAFVLLTLPAEDFPEY 119
Query: 120 EEGPGSLNFSIAQSKLRRLIDRTSFAMAQQDVRYYLNGMLLEVNGGTLRSVATDGHRLAM 179
Sbjct: 120 PVDEEEVEFGLPTELLKKIIKRTKFADSLLETRYELNGVLLEIEGTKLRLVATDGHRLAV 179
Query: 180 CSLDAQIPSQDRHQVIVPRKGILELARLLTEQDGEVGIVLGQHHIRATTGEFTFTSKLVD 239
Sbjct: 180 EELEIPELEED-ASVIIPAKTLKELIKLLK--DADVEIFLVSDQIRFKAGETILFSKLIE 236
Query: 240 GKFPDYERVLPRGGDKLVVGDRQQLREAFSRTAILSNEKYRGIRLQLSNGLLKIQANNPE 299
Sbjct: 237 GEFPDYERVIPKEFEKELTLDRLELKEALKRVYSLSYLKDRGKKLSLADGEVKLSLGNDE 296
Query: 300 QEEAEEEVQVEYNGGNLEIGFNVSYLLDVLGVIGTEQVRFILSDSNSSALVHEADNDDSA 359
Sbjct: 297 PGKAEEEIDVGYTGEELKIGFNLAYLLDVLKALDSEEVQFGFNDSSSPFLIRPEENDDFK 356
Query: 360 YVVMPMRL 367
Sbjct: 357 YLIMPMRL 364
>gnl|CDD|25954 pfam02767, DNA_pol3_beta_2, DNA polymerase III beta subunit, central
domain. A dimer of the beta subunit of DNA polymerase
beta forms a ring which encircles duplex DNA. Each
monomer contains three domains of identical topology and
DNA clamp fold
Length = 116
Score = 147 bits (372), Expect = 5e-36
Identities = 54/115 (46%), Positives = 74/115 (64%)
Query: 130 IAQSKLRRLIDRTSFAMAQQDVRYYLNGMLLEVNGGTLRSVATDGHRLAMCSLDAQIPSQ 189
Sbjct: 2 LPSKVLKELIEQTAFAMGRDETRPVLTGVNLETEGNELRLVATDGHRLAVRKLELSVENN 61
Query: 190 DRHQVIVPRKGILELARLLTEQDGEVGIVLGQHHIRATTGEFTFTSKLVDGKFPD 244
Sbjct: 62 DIFSVIVPRKTLLELAKLLTDNGEMVKIQIGEGQIRFEFGNVIFTSRLIDGKYPD 116
>gnl|CDD|1268 pfam00712, DNA_pol3_beta, DNA polymerase III beta subunit, N-terminal
domain. A dimer of the beta subunit of DNA polymerase
beta forms a ring which encircles duplex DNA. Each
monomer contains three domains of identical topology and
DNA clamp fold
Length = 119
Score = 141 bits (357), Expect = 3e-34
Identities = 57/120 (47%), Positives = 83/120 (69%), Gaps = 1/120 (0%)
Query: 1 MHFTIQREALLKPLQLVAGVVERRQTLPVLSNVLLVVEGQQLSLTGTDLEVELVGRVVLE 60
Sbjct: 1 MKFTIERDVLLKALSKVARVVSNRPTIPILSGILLNVKDDRLSLTGTDLEISIESSIAAE 60
Query: 61 DAAEPGEITVPARKLMDICKSLPNDVLIDIRVEEQKLLVKAGRSRFTLSTLPANDFPTVE 120
Sbjct: 61 ISSEPGSVLIPARLLLDIVRALPDK-DVKLSVNEDRLLIISGNSRFSLPTLPAEDYPNLP 119
>gnl|CDD|4799 pfam02768, DNA_pol3_beta_3, DNA polymerase III beta subunit,
C-terminal domain. A dimer of the beta subunit of DNA
polymerase beta forms a ring which encircles duplex DNA.
Each monomer contains three domains of identical topology
and DNA clamp fold
Length = 121
Score = 139 bits (353), Expect = 8e-34
Identities = 52/121 (42%), Positives = 76/121 (62%)
Query: 246 ERVLPRGGDKLVVGDRQQLREAFSRTAILSNEKYRGIRLQLSNGLLKIQANNPEQEEAEE 305
Sbjct: 1 KRVIPKEFKTKITVDNKELKKALARVALLADERNRGVRLSFEEGQLKLTAGNPEIGRAEE 60
Query: 306 EVQVEYNGGNLEIGFNVSYLLDVLGVIGTEQVRFILSDSNSSALVHEADNDDSAYVVMPM 365
Sbjct: 61 EVDVDYIGEPLEIAFNPSYLLDALKALKSEEIELQFTDSTKPALISPPGDDSLKYVIMPM 120
Query: 366 R 366
Sbjct: 121 R 121
>gnl|CDD|24996 pfam06123, CreD, Inner membrane protein CreD. This family consists of
several bacterial CreD or Cet inner membrane proteins.
Dominant mutations of the cet gene of Escherichia coli
result in tolerance to colicin E2 and increased amounts
of an inner membrane protein with an Mr of 42,000. The
cet gene is shown to be in the same operon as the phoM
gene, which is required in a phoR background for
expression of the structural gene for alkaline
phosphatase, phoA. Although the Cet protein is not
required for phoA expression, it has been suggested that
the Cet protein has an enhancing effect on the
transcription of phoA
Length = 432
Score = 28.3 bits (63), Expect = 2.9
Identities = 38/173 (21%), Positives = 63/173 (36%), Gaps = 27/173 (15%)
Query: 10 LLKPLQLVAGVVERRQTL--PVLSNVLLVVEGQQLSLTGTDLEVELVGRVVLEDAAEPGE 67
Sbjct: 14 LLIPLLLIRGLIDERARYRNEVIERIAQSWGGSQ-KLIGPLLVIP-YTETVETVEQEDKR 71
Query: 68 ITVPARKLMDICKSLPN--DVLIDIRVEEQKLLVKAGR---------SRFTLSTLPANDF 116
Sbjct: 72 VTV-ERKRQGELYILPEKLNVDGDMKVEVRKRGIYQAQVYHGDLKLKGEFDVPSLDELNA 130
Query: 117 PTVEEGPGSLNFSIAQSKLRRLIDRTSFAMAQQDVRYYLNGMLLEVNGGTLRS 169
Sbjct: 131 PTITLGKPFLVLGVSDA---RGIGKVP--------KLQVNGAELTFEPGSRNL 172
>gnl|CDD|16795 pfam00668, Condensation, Condensation domain. This domain is found in
many multi-domain enzymes which synthesise peptide
antibiotics. This domain catalyses a condensation
reaction to form peptide bonds in non- ribosomal peptide
biosynthesis. It is usually found to the carboxy side of
a phosphopantetheine binding domain (pfam00550). It has
been shown that mutations in the HHXXXDG motif abolish
activity suggesting this is part of the active site
Length = 300
Score = 28.3 bits (63), Expect = 3.2
Identities = 20/113 (17%), Positives = 35/113 (30%), Gaps = 10/113 (8%)
Query: 117 PTVEEGPGSLNFSIAQSKLRRLID-----RTSFAMAQQDVRYYLNGMLLEVNGGTLRSVA 171
Sbjct: 30 QFVLRLPGGLDPERLEKALKRLVERHDALRTRFLRDEGEPVQVVLE---ADEPDLKVLDD 86
Query: 172 TDGHRLAMCSLDAQIPSQDRHQVIVPRKGILELARLLTEQDGEVGIVLGQHHI 224
Sbjct: 87 L--SVTAEEEEILEALAQDLQQPFDLEKGPLFRVALFKLEEDRHRLLFSIHHL 137
Lambda K H
0.318 0.137 0.376
Gapped
Lambda K H
0.267 0.0511 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 1100, Extension: 100
Number of Hits to DB: 5,808,811
Number of Sequences: 0
Number of extensions: 546156
Number of successful extensions: 155
Number of sequences better than 10.0: 1
Number of HSP's better than 10.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 147
length of query: 0
length of database: 5,506,404
effective HSP length: 95
effective length of query: -95
effective length of database: 3,792,699
effective search space: -360306405
effective search space used: 1031614128
T: 11
A: 40
X1: 1600 (734.1 bits)
X2: 3800 (1463.8 bits)
X3: 6400 (2465.3 bits)
S1: 4100 (1884.0 bits)
S2: 58 (26.6 bits)