RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13355
(314 letters)
>gnl|CDD|235541 PRK05643, PRK05643, DNA polymerase III subunit beta; Validated.
Length = 367
Score = 296 bits (761), Expect = 2e-99
Identities = 124/307 (40%), Positives = 197/307 (64%), Gaps = 5/307 (1%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTA 60
M+ ++ +NA+L LQ+V VE++N +PILSN+L+ K+S +TD E+ I T
Sbjct: 1 MKFTIS--RNALLKALQLVQGAVERRNTIPILSNVLIEAEGGKLSLTATDLEISIETTIP 58
Query: 61 VGYGNSSINIIVAARKFIDILRSLPETEKVTIYI-ENKHMFIKSGKSKFTLQTLDAKEYP 119
+I V A+K +DI+R LP+ ++T+ + EN + IKSGKS+F L TL A+++P
Sbjct: 59 AEVEVEEGSITVPAKKLLDIVRKLPDGAEITLELEENNRLTIKSGKSRFNLPTLPAEDFP 118
Query: 120 IMTLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHR 179
+ + + FTL QKTLK ++ F+++ Q+ RYYLNG+LL + + AV++DGHR
Sbjct: 119 NLP-EIEEEVSFTLPQKTLKRLIEKTQFAMSTQETRYYLNGVLLEIEGNELRAVATDGHR 177
Query: 180 LTYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISK 239
L ++ +++ +IIPRKT+ LQ+LL++ E PVE+ IS+NQI F N SK
Sbjct: 178 LAVRKLELEEGSLGDFSVIIPRKTLLELQKLLDD-EEPVEIFISDNQILFEFGNTIFTSK 236
Query: 240 LIDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVS 299
LIDGKF DY+ VI +++K V+R +LL++L+R SI+SN+K +GV+L + LKI+ +
Sbjct: 237 LIDGKFPDYRRVIPKEFDKKLTVDRKELLQALERASILSNEKSRGVKLSLSEGQLKISAN 296
Query: 300 SSNREKA 306
+ + +A
Sbjct: 297 NPEQGEA 303
>gnl|CDD|238082 cd00140, beta_clamp, Beta clamp domain. The beta subunit
(processivity factor) of DNA polymerase III holoenzyme,
refered to as the beta clamp, forms a ring shaped dimer
that encircles dsDNA (sliding clamp) in bacteria. The
beta-clamp is structurally similar to the trimeric ring
formed by PCNA (found in eukaryotes and archaea) and the
processivity factor (found in bacteriophages T4 and
RB69). This structural correspondence further
substantiates the mechanistic connection between
eukaryotic and prokaryotic DNA replication that has been
suggested on biochemical grounds. .
Length = 365
Score = 265 bits (680), Expect = 3e-87
Identities = 109/307 (35%), Positives = 183/307 (59%), Gaps = 4/307 (1%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTA 60
M+ +N + A+L LQ V +E +N +PILSN+L+ + ++ +TD E+ I T
Sbjct: 1 MKFTIN--REALLEALQKVSRAIESRNTIPILSNVLIEASDGGLTLTATDLEISIKTTIP 58
Query: 61 VGYGNSSINIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPI 120
++ V A+K +DI+R LP+ E+VT+ E + IKSGKS+F+L TL A+E+P
Sbjct: 59 AEEVEEEGSVTVPAKKLLDIVRKLPD-EEVTLETEENRLTIKSGKSRFSLNTLPAEEFPE 117
Query: 121 MTLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRL 180
+ + FT+ LK ++ F+++ + R LNG+LL + + AV++DGHRL
Sbjct: 118 LP-EIENGSSFTIPASELKELIKKTAFAVSTDETRPILNGVLLEIEDNKLRAVATDGHRL 176
Query: 181 TYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISKL 240
++ ++ ++I+PRKT+ L +LLE+ + VE+ IS NQI N S+L
Sbjct: 177 ALREIELESGAEEDFNVIVPRKTLNELLKLLEDDDEEVEISISENQILFKLGNTTFTSRL 236
Query: 241 IDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSS 300
I+G+F DY+ VI ++EKS V+R +LL +L+R+S++SN+K +GV+L I LK++ ++
Sbjct: 237 IEGEFPDYERVIPKEFEKSLTVDREELLEALKRVSLLSNEKNRGVKLEISEGQLKLSANN 296
Query: 301 SNREKAS 307
+A
Sbjct: 297 PEIGEAE 303
>gnl|CDD|214686 smart00480, POL3Bc, DNA polymerase III beta subunit.
Length = 345
Score = 218 bits (558), Expect = 3e-69
Identities = 98/288 (34%), Positives = 170/288 (59%), Gaps = 3/288 (1%)
Query: 19 VISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSSINIIVAARKFI 78
V ++ +N +PILSNIL+ + ++ +TD E+ I + + + ++ V A+KF+
Sbjct: 1 VSRVISNRNTIPILSNILLEAKDDGLTLTATDLEISIKSSISAEVEDEEGSVTVPAKKFL 60
Query: 79 DILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKYDFEFTLSQKTL 138
DI+R LP+ +++T+ +E + I SGKS+F L TLDA+E+P + + F L K L
Sbjct: 61 DIVRKLPD-KEITLSVEEDKLVITSGKSRFNLPTLDAEEFPELPFIEE-GVTFELPTKLL 118
Query: 139 KCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNIDKKFSSCSDII 198
K + F+++ + R LNG+ L + V++DGHRL ++ ++ + +I
Sbjct: 119 KEGIEKTAFAVSTDETRPVLNGVNLEISNGELRLVATDGHRLAVREIKLESEEDD-FSVI 177
Query: 199 IPRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISKLIDGKFLDYKYVISNKYEK 258
IPRK++ L +LL + E VE+ IS+NQI N+ S+LIDG+F DYK VI ++E
Sbjct: 178 IPRKSLLELNKLLTDNEELVEIFISSNQILFETGNVIFTSRLIDGEFPDYKRVIPKEFET 237
Query: 259 SFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKA 306
VNR +L +L+R+++++N+K + V+L ++ LK+T +S +A
Sbjct: 238 KLTVNRKELKEALKRVALLANEKNRSVKLTLEEGQLKLTANSPEVGEA 285
>gnl|CDD|223665 COG0592, DnaN, DNA polymerase sliding clamp subunit (PCNA homolog)
[DNA replication, recombination, and repair].
Length = 364
Score = 194 bits (494), Expect = 2e-59
Identities = 90/307 (29%), Positives = 166/307 (54%), Gaps = 8/307 (2%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTA 60
M+ + + +L LQ+V IVE + +PILSN+L+ ++ TD E+ +
Sbjct: 1 MKFSIE--RENLLKALQLVSRIVESRPTIPILSNVLIEAKENGLTLTGTDLEISLEARIP 58
Query: 61 VGYGNSSINIIVAARKFIDILRSLPETEKVTIYIE-NKHMFIKSGKSKFTLQTLDAKEYP 119
+ + V A+K +DI+ LP+ + + + + SGKS F L TL A+++P
Sbjct: 59 AEV-EAEGEVAVPAKKLLDIISKLPDEAVFLVTEDGISLLAVDSGKSAFVLLTLPAEDFP 117
Query: 120 IMTLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHR 179
++ + + EF L + LK I+ F+ + + RY LNG+LL + + V++DGHR
Sbjct: 118 EYPVDEE-EVEFGLPTELLKKIIKRTKFADSLLETRYELNGVLLEIEGTKLRLVATDGHR 176
Query: 180 LTYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISK 239
L ++ I + + +IIP KT+ L +LL++ + VE+ + ++QI+ + SK
Sbjct: 177 LAVEELEIPE-LEEDASVIIPAKTLKELIKLLKDAD--VEIFLVSDQIRFKAGETILFSK 233
Query: 240 LIDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVS 299
LI+G+F DY+ VI ++EK ++R +L +L+R+ +S K +G +L + +K+++
Sbjct: 234 LIEGEFPDYERVIPKEFEKELTLDRLELKEALKRVYSLSYLKDRGKKLSLADGEVKLSLG 293
Query: 300 SSNREKA 306
+ KA
Sbjct: 294 NDEPGKA 300
>gnl|CDD|233078 TIGR00663, dnan, DNA polymerase III, beta subunit. All proteins in
this family for which functions are known are components
of the DNA polymerase III complex (beta subunit). 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 = 367
Score = 183 bits (466), Expect = 2e-55
Identities = 86/304 (28%), Positives = 160/304 (52%), Gaps = 3/304 (0%)
Query: 5 VNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYG 64
E++ +L L V ++ + +PILSNIL+ +K++ +TD ++ + +
Sbjct: 3 FIIERDDLLKELSKVQRVLSNRPTIPILSNILLEVKDDKLTITATDLDISLESQIFTINS 62
Query: 65 NSSINIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLN 124
++ + A+KF+DI+R+LP K+T+ ++N + I S KS+F L TL A+E+P +
Sbjct: 63 EQEGSVTINAKKFLDIVRALP-DSKITLEVKNDKLAITSEKSRFKLPTLSAEEFPNLP-T 120
Query: 125 SKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQ 184
+ + LK +N F+ + + R LNG+L+ + K ++ V++DGHRL +
Sbjct: 121 IEEGVSIEIPSDVLKEAINQTAFAAGEDETRPVLNGVLIEQKGKTLLLVATDGHRLAVCK 180
Query: 185 VNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISKLIDGK 244
+ + +IIP K + L +LL + V +++ + I N + SKLI+G
Sbjct: 181 LKSEVSDEEDFSVIIPAKALNELLKLLSENGSVVLKSLNDQLVYIELGNYKFTSKLIEGN 240
Query: 245 FLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVR-LVIKPNYLKITVSSSNR 303
+ DYK VI + + SF VNR +L +++R+S+++++K V L LK + +
Sbjct: 241 YPDYKSVIPKEQKNSFTVNREELKEAIKRVSLLADEKRNLVLTLSENGKKLKESSDTQEI 300
Query: 304 EKAS 307
+A
Sbjct: 301 GEAE 304
>gnl|CDD|184904 PRK14940, PRK14940, DNA polymerase III subunit beta; Provisional.
Length = 367
Score = 137 bits (346), Expect = 9e-38
Identities = 89/298 (29%), Positives = 153/298 (51%), Gaps = 18/298 (6%)
Query: 8 EKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSS 67
EK A+L + + I+ K L ILSN+L+ ++ +TDT+V T V
Sbjct: 6 EKEALLKEISIAQEIISTKKALSILSNVLLAAQDGSLTIKATDTKVSFETSIPV------ 59
Query: 68 INII------VAARKFIDILRSLPETEKVTIYIENKHMFIKS--GKSKFTLQTLDAKEYP 119
NI+ V KF+ IL SLP E + + + ++ + I K F L+T+ + +P
Sbjct: 60 -NILAEGSTTVFCDKFVGILSSLPTGE-IELELCDEQLVITPPNKKISFQLKTISHESFP 117
Query: 120 IMTLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHR 179
N F + K L+ ++N F+++ + RY++NG+ + FQ NII V++DG R
Sbjct: 118 CFPENEG-GVSFAIPTKDLREMINQTIFAVSDDETRYFMNGVYVEFQYGNIICVATDGRR 176
Query: 180 LTYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISK 239
L Y + + S +I+P K + + + L + N V L I++ I F + S
Sbjct: 177 LAYIKKKGESSPQEFSGVIVPPKILGIINKKLSPEGN-VTLCITSQNIFFFFGGYKFSSV 235
Query: 240 LIDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKIT 297
LI+G+F +YK VI + E+SF V R +L+ +L+R+S++ K + + L I+ L ++
Sbjct: 236 LIEGQFPNYKRVIPDHQERSFCVGRVELMEALKRVSLLVEQKSRRIFLTIQQGLLTLS 293
>gnl|CDD|184907 PRK14943, PRK14943, DNA polymerase III subunit beta; Provisional.
Length = 374
Score = 130 bits (329), Expect = 3e-35
Identities = 89/317 (28%), Positives = 158/317 (49%), Gaps = 27/317 (8%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTA 60
M+ +N K+ L+ L+ V+++V K +PILSN+L+ + +IS +T+ ++ I
Sbjct: 1 MKFKIN--KDHFLNGLRQVLNVVSSKTTMPILSNVLIEAENGQISLTTTNLDLGIRCVIK 58
Query: 61 VGYGNSSINIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPI 120
+ + +K I+R LPE E +N ++SG S+F + + A+E+P
Sbjct: 59 ANVLREG-TVTLPVKKLATIVRELPEAEVQVDANQNNQAKVESGGSQFKIMGIPAEEFPP 117
Query: 121 MTLNSKYDFE----FTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSD 176
+ FE F L Q L+ +L V ++ + + RY LNG+ +F+ + V++D
Sbjct: 118 LP-----SFEQATVFQLEQSELRDMLKSVEYAQSTDETRYILNGVYFNFRDGKLTLVATD 172
Query: 177 GHRLTYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIF----- 231
G RL + ++ D I+P KTV L+RLL+ +LKI N + F
Sbjct: 173 GRRLALAETELEFPEDQAGDAILPAKTVGELRRLLDKGG---KLKIRFNDRQAAFEISIG 229
Query: 232 -------SNIEIISKLIDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKG 284
++ +ISKL++G + +Y+ VI + ++ + R LL + R +++S+DK
Sbjct: 230 EDSSGLANDTYLISKLVEGNYPNYRQVIPKETKERIKLERELLLECVHRAALVSSDKSNS 289
Query: 285 VRLVIKPNYLKITVSSS 301
V+L N L+I SS
Sbjct: 290 VKLKFSENLLEIASSSE 306
>gnl|CDD|202381 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 = 98.9 bits (247), Expect = 7e-26
Identities = 42/116 (36%), Positives = 67/116 (57%)
Query: 132 TLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNIDKKF 191
TL QK LK ++ F++ + + RY LNG+ L + + V++DGHRL ++ + +
Sbjct: 1 TLPQKVLKELIEQTAFAMGRDETRYVLNGVNLETEGNELRLVATDGHRLAVRKLELSVEN 60
Query: 192 SSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISKLIDGKFLD 247
+I+PRKT+ L +LL + V+L+I QI+ F N+ S+LIDGKF D
Sbjct: 61 PDIFSVIVPRKTLLELAKLLTDNGELVKLQIGEGQIRFEFGNVIFTSRLIDGKFPD 116
Score = 30.7 bits (70), Expect = 0.36
Identities = 16/104 (15%), Positives = 41/104 (39%), Gaps = 17/104 (16%)
Query: 25 KKNILPILSNILVCKNSEKISFLSTD--------TEVQITTYTAVGYGNSSINIIVAARK 76
+ +L+ + + ++ ++TD E+ + ++IV +
Sbjct: 20 RDETRYVLNGVNLETEGNELRLVATDGHRLAVRKLELSVEN-------PDIFSVIVPRKT 72
Query: 77 FIDILRSLPET-EKVTIYIENKHMFIKSGKSKFTLQTLDAKEYP 119
+++ + L + E V + I + + G FT + +D K +P
Sbjct: 73 LLELAKLLTDNGELVKLQIGEGQIRFEFGNVIFTSRLIDGK-FP 115
>gnl|CDD|184905 PRK14941, PRK14941, DNA polymerase III subunit beta; Provisional.
Length = 374
Score = 97.9 bits (244), Expect = 4e-23
Identities = 71/300 (23%), Positives = 144/300 (48%), Gaps = 14/300 (4%)
Query: 19 VISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSSINIIVAARKFI 78
V + K+I P NI + + K++ +TD E+ IT T V +S NI + AR
Sbjct: 17 VAQAIPAKSIDPRFENIHLTLENGKLTLFATDGELSITAKTEVESSDSG-NIGIRARTLQ 75
Query: 79 DILRSLPETEKVTIYIENKHM------FIKSGKSKFTLQ-TLDAKEYPIMTLNSKYDFEF 131
D LRS+ +TE VT IE + + I + K ++ + ++K +D
Sbjct: 76 DFLRSMYDTE-VTFSIERQEISDHGTVHIATDKGRYKIPCLFESKP---EKQEKNFDISL 131
Query: 132 TLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNIDKKF 191
L L ++ F+ + +R + G+L + I AVS+DGHRL + N
Sbjct: 132 DLETSELLDLIQKTIFACSVDGMRPAMMGVLFELEGNTITAVSTDGHRLVRCRKNSSVGV 191
Query: 192 SSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISKLIDGKFLDYKYV 251
I++P + + LQ+L +++ + + ++ I N+ + + LI + +Y+ V
Sbjct: 192 EEKQKIVVPARVLSILQKLAQHETVTMSIDSERRFVRFICGNVVLDAALIVEPYPNYEAV 251
Query: 252 ISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKASSTDL 311
I + +K ++NR+ + S++R+ S+ + +++ ++ + LK+ ++N +++ +L
Sbjct: 252 IPVENDKKLVINRSNIYDSVKRVGRFSS--IGDIKISVEGSVLKVMAENTNEGESAQEEL 309
>gnl|CDD|216076 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 = 120
Score = 84.2 bits (209), Expect = 3e-20
Identities = 37/115 (32%), Positives = 69/115 (60%)
Query: 8 EKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSS 67
E++ +L LQ V ++ + +PILS IL+ +++S TD E+ I + + +
Sbjct: 6 ERDQLLKALQKVARVLSNRPTIPILSGILLEVKDDQLSLTGTDLEISIESTISAEIESEP 65
Query: 68 INIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMT 122
++++ ARKF+DI+R+LP+ + V + + + I SG S+F+L TL A++YP +
Sbjct: 66 GSVLIPARKFLDIVRALPDDKDVKLSVNEDRLLIISGNSRFSLPTLPAEDYPNLP 120
>gnl|CDD|184909 PRK14945, PRK14945, DNA polymerase III subunit beta; Provisional.
Length = 362
Score = 88.6 bits (220), Expect = 6e-20
Identities = 51/213 (23%), Positives = 105/213 (49%), Gaps = 7/213 (3%)
Query: 69 NIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKYD 128
++V A F I+R+LP E V + + + ++SG S+ LQT + YP ++ S
Sbjct: 66 RVVVPAHLFFQIVRNLP-GELVELEFQGGELEVRSGSSRTKLQTAPPEGYPELSFPS--Q 122
Query: 129 FEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNID 188
+ LS L L V ++ + ++ + G+ L + + AV+SDG+RL Y +
Sbjct: 123 GDVRLSAGELAKALTHVRYAASNEEFQAIFRGVKLEHSPQGLRAVASDGYRLAIYDLPAS 182
Query: 189 KKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISKLIDGKFLDY 248
+ ++IP ++ L R+L++ + L + + + + + KL++G+F DY
Sbjct: 183 QGQGR--KLVIPARSADELVRVLKDGDE-ASLALGEGVLTLTTGGVRMNLKLMEGEFPDY 239
Query: 249 KYVISNKYEKSFLVNRNKLLRSLQRISIISNDK 281
+ VI ++ + L ++ R++++S D+
Sbjct: 240 ERVIPQDFKLQVTLPAEALREAVNRVAVLS-DR 271
>gnl|CDD|135998 PRK06673, PRK06673, DNA polymerase III subunit beta; Validated.
Length = 376
Score = 83.6 bits (206), Expect = 4e-18
Identities = 73/322 (22%), Positives = 152/322 (47%), Gaps = 17/322 (5%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTA 60
M+ +VN + L V + K I+PILS I + + I+ +++++ + I +
Sbjct: 1 MEFIVNHKH--FTQALSEVSKAISTKAIIPILSGIKITADQSGITLIASNSNIFIEKFIP 58
Query: 61 VGYGNSSI-------NIIVAARKFIDILRSLPETEKVTIYIENKHMF-IKSGKSKFTLQT 112
+ I I+V A+ FI+I++ +P + I +N+ I+SG+ L
Sbjct: 59 SAIDDEQITTILQAGTIVVPAKYFIEIIKKMPS--DIVIKSKNEQTITIQSGEITLNLNG 116
Query: 113 LDAKEYPIMTLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIA 172
A E+P + + E + K L F++A+ + R L G+ + +I
Sbjct: 117 FPANEFPNVPQIDDHT-EIQIETKQLIDAFKQTVFAVAKNESRPVLTGVHIELDHNKLIC 175
Query: 173 VSSDGHRLTYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFS 232
++D HRL + I + + I+P T+ L +L+ + V + +S + I F
Sbjct: 176 AATDSHRLAIRETLISTNMKA--NCIVPSATINELLKLMNSNLEFVSIYLSESHIIFTFG 233
Query: 233 NIEIISKLIDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISND-KLKGVRL-VIK 290
+ S+LI+GK+ + +I N+++ ++R ++L+ + R S+++++ V L ++
Sbjct: 234 TTTLYSRLIEGKYPNISTLIPNEFQTVINIDRQRMLQGVDRSSLLASEWANNNVNLEIVN 293
Query: 291 PNYLKITVSSSNREKASSTDLI 312
+ ++I+ ++S K S T I
Sbjct: 294 ESTIQISSNASQIGKISETQQI 315
>gnl|CDD|184906 PRK14942, PRK14942, DNA polymerase III subunit beta; Provisional.
Length = 373
Score = 78.8 bits (194), Expect = 2e-16
Identities = 82/312 (26%), Positives = 150/312 (48%), Gaps = 21/312 (6%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLS-TDTEVQITTYT 59
M++ VNT + L + V ++ + I ILSN+ + + EK FLS TD E+ I T
Sbjct: 1 MKIKVNTSE--FLKAIHAVEGVISVREIKSILSNLKI-EAEEKEVFLSATDLEISIKTSV 57
Query: 60 AVGYGNSSINIIVAARKFIDILRSLP-ETEKVTIYIENKHMFI-----KSGKS--KFTLQ 111
G + A++ +++ ET +++ + I SGK+ K +
Sbjct: 58 PATVGQKG-TASLPAKQLSSFFKTIHFETTLLSLEESDSESSIVYITDASGKNDYKSKIS 116
Query: 112 TLDAKEYPIMTLNSKYDFEFTLSQKTLKCILNMV---YFSIAQQDIRYYLNGLLLSFQKK 168
+DA+E I T+ SK D E +S + I +M+ ++IA +D R+ NGL +
Sbjct: 117 GMDAEE--IKTI-SKVD-ESQVSSFPSQLINDMIRKTSYAIAHEDQRFIFNGLYMIPDGT 172
Query: 169 NIIAVSSDGHRLTYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIK 228
+I V +DG RL + + II+P K V + +++ E + + + QI
Sbjct: 173 KLIFVGTDGRRLCKIERTLPSPLQFKDSIIVPAKAVREISKMIATSETG-NIGLIDEQIY 231
Query: 229 IIFSNIEIISKLIDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLV 288
+ +NIE++ KLI+G F +Y+ VI + + S +++ + SL+++ + + + VRL
Sbjct: 232 VSANNIELLCKLIEGNFPNYEQVIPKQTKFSVRISKEEFQVSLRQVLTAAEEPSRQVRLT 291
Query: 289 IKPNYLKITVSS 300
N L + +
Sbjct: 292 FSKNNLNLFAQT 303
>gnl|CDD|184908 PRK14944, PRK14944, DNA polymerase III subunit beta; Provisional.
Length = 375
Score = 61.8 bits (150), Expect = 8e-11
Identities = 54/239 (22%), Positives = 119/239 (49%), Gaps = 6/239 (2%)
Query: 70 IIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKYDF 129
I R FI+I++ + ++ +EN + IK+ ++ L+ +D + + +
Sbjct: 70 IACLGRYFIEIIKKINDSLIKMTVMENNFLVIKTEFCEYKLKLMDLCNFLELDFFFEKKE 129
Query: 130 EFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNIDK 189
F + K I+ + S ++ + R L GL L +QK + A+++D R++ ++ +D
Sbjct: 130 FFEIKTHFFKKIIKEINISTSKNEKRPILTGLNLIYQKNLLKALATDSFRMSQKKIKLDF 189
Query: 190 KFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIF--SNIEIISKLIDGKFLD 247
+ + +I+IP K++ L ++LE ++ LKI ++ KI N+ + L++G +
Sbjct: 190 NYHN-FNIVIPNKSLEELSKILEYYQSK-NLKIYSDSKKIFLKIDNLWFQTSLLEGNYPQ 247
Query: 248 YKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKL--KGVRLVIKPNYLKITVSSSNRE 304
+ + + S +N++ L+++L+R+S++ + + V I I +SSSN
Sbjct: 248 IQEIKLTNFPFSIHLNKDDLMKALERVSLLFSKEQNNTNVVKFILTKEKSIEISSSNES 306
>gnl|CDD|236089 PRK07761, PRK07761, DNA polymerase III subunit beta; Validated.
Length = 376
Score = 54.5 bits (132), Expect = 2e-08
Identities = 25/93 (26%), Positives = 48/93 (51%), Gaps = 6/93 (6%)
Query: 29 LPILSNILVCKNSEKISFLSTDTEV--QITTYTAVGYGNSSINIIVAARKFIDILRSLPE 86
+P+L+ +L+ + ++ D EV ++T V ++V+ R DI RSLP
Sbjct: 27 VPVLAGVLLEADDGGLTLSGFDYEVSARVTIEAEVDEPGR---VLVSGRLLADITRSLPN 83
Query: 87 TEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYP 119
+ V I ++ + + G ++FTL T+ ++YP
Sbjct: 84 -KPVDISVDGSRVTLTCGSARFTLPTMPVEDYP 115
>gnl|CDD|237861 PRK14947, PRK14947, DNA polymerase III subunit beta; Provisional.
Length = 384
Score = 53.2 bits (128), Expect = 5e-08
Identities = 77/332 (23%), Positives = 140/332 (42%), Gaps = 39/332 (11%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQIT-TYT 59
M L VN K ++ LQ +I+ K L I + +S +STD+ ++ TY
Sbjct: 1 MYLKVN--KEDVIDGLQKAANIIPAKTGAAYLRTIWLKAEDGTLSIMSTDSNIEFRGTYP 58
Query: 60 AVGYGNSSINIIVAARKFIDILRSLPETEKVTIYI--ENKHMFIKSGKSKFTLQTLDA-- 115
A V R F+D++R LP E +T+ + + ++ I+ G+ K+ L D
Sbjct: 59 AEVTEPGLAG--VQGRAFVDLVRKLPPGE-ITLKLDASSGNLLIEQGRRKYKLPVNDPSW 115
Query: 116 ----KEYPIMTLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNII 171
+P + S L+ +++ + F I+ +D + L + N I
Sbjct: 116 FQNFSAFP-------AEGAVVWSGDFLQELIDRIAFCISDEDAMEAIACLKIKPVADNAI 168
Query: 172 AVSS-DGH---RLTYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQI 227
V +GH L + +I K I+I +K + L++ L E +EL IS
Sbjct: 169 EVCGLNGHQFALLRFLNDDIHAKLPQ-EGILIQKKYLLELKKWLGADE--IELSISEK-- 223
Query: 228 KIIFSNI---EIIS-KLIDGKFLDYKYVISNKYEK--SFL-VNRNKLLRSLQRISIISND 280
++ F E S L ++ DY +S S L V+R + + +L RI I + D
Sbjct: 224 RLFFRTGDGKETFSLPLSYYQYPDYMNFLSKLQGDDVSNLEVDRKECMDALDRILIFNTD 283
Query: 281 KLKGVRLVIKPNYLKITVSSSNREKASSTDLI 312
+ P ++++S+ ++ S+T+ +
Sbjct: 284 NNRCTYFDFGPG--ELSLSAQGQDVGSATESL 313
>gnl|CDD|111641 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 = 43.8 bits (104), Expect = 1e-05
Identities = 16/58 (27%), Positives = 36/58 (62%)
Query: 249 KYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKA 306
+ V+ ++E V+ +L ++L R+++++N+K +GVRL + LK+T ++ +A
Sbjct: 1 RRVLPKEFETKITVDNKELKKALARVALLANEKNRGVRLSFEEGQLKLTANNPEIGRA 58
>gnl|CDD|184910 PRK14946, PRK14946, DNA polymerase III subunit beta; Provisional.
Length = 366
Score = 36.0 bits (83), Expect = 0.021
Identities = 46/276 (16%), Positives = 106/276 (38%), Gaps = 18/276 (6%)
Query: 32 LSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSSINIIVAARKFID------ILRSLP 85
LS + + +ST++E+ ++ I I ID I++
Sbjct: 29 LSGFFLKLTRSGLFIISTNSELSYKSFIN---KKDLIEINDVGSCLIDGVFLKNIIKKS- 84
Query: 86 ETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKYDFEFTLSQKTLKCILNMV 145
+++ + + + ++F+ D+ +P + K + T++ K LK +
Sbjct: 85 -DNQISFELIGSELKVFWEDAQFSKTLRDSSFFPEINFEQK-GIKLTVNAKNLKRAIKNT 142
Query: 146 YFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNIDKKFSSCSDIIIPRKTVF 205
F+ + L+ + L + + ++D R ++ I S I I
Sbjct: 143 AFATTNNPNQPILSAINLKSEDNFLHFSATDTIRFASEKIEISNP----SRIDISISAKN 198
Query: 206 TLQRLLENKENPVELKISNNQIKIIFSNIEIISKLIDGKFLDYKYVISNKYE--KSFLVN 263
+ + +EL I +++I + N+ I S++ ++ D V+ E S +
Sbjct: 199 LKDFIPPELDKDIELFIESSKISYTYDNLTIQSRIFTIEYKDISNVLPKDSEILYSLTIE 258
Query: 264 RNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVS 299
+ ++L + + +II+ K + + N LK +S
Sbjct: 259 KKEILDLIDKATIITPGKDNVINFSLSKNELKGYIS 294
>gnl|CDD|236673 PRK10340, ebgA, cryptic beta-D-galactosidase subunit alpha;
Reviewed.
Length = 1021
Score = 34.3 bits (79), Expect = 0.083
Identities = 25/123 (20%), Positives = 44/123 (35%), Gaps = 20/123 (16%)
Query: 156 YYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKE 215
+LN ++ K + S GH + YQ + + + TL+ E
Sbjct: 671 AFLN---ITVTKDSRTRYSEAGHSIATYQFPLKENTAQPVPFAPNNARPLTLE------E 721
Query: 216 NPVELKISNNQIKIIFSNI--EIISKLIDG--------KFLDYKYVISN-KYEKSFLVNR 264
+ + + I FS + ++ S ++G K +K +I N K E L
Sbjct: 722 DRLSCTVRGYNFAITFSKVSGKLTSWQVNGESLLTREPKINFFKPMIDNHKQEYEGLWQP 781
Query: 265 NKL 267
N L
Sbjct: 782 NHL 784
>gnl|CDD|233103 TIGR00722, ttdA_fumA_fumB, hydro-lyases, Fe-S type,
tartrate/fumarate subfamily, alpha region. A number of
Fe-S cluster-containing hydro-lyases share a conserved
motif, including argininosuccinate lyase,
adenylosuccinate lyase, aspartase, class I fumarate
hydratase (fumarase), and tartrate dehydratase (see
PROSITE:PDOC00147). This model represents a subset of
closely related proteins or modules, including the E.
coli tartrate dehydratase alpha chain and the N-terminal
region of the class I fumarase (where the C-terminal
region is homologous to the tartrate dehydratase beta
chain). The activity of archaeal proteins in this
subfamily has not been established.
Length = 273
Score = 30.1 bits (68), Expect = 1.3
Identities = 11/44 (25%), Positives = 20/44 (45%), Gaps = 4/44 (9%)
Query: 197 IIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISKL 240
+P V ++ + +E+ I+ ++ I NIEI KL
Sbjct: 14 TRLPEDVVDAIKEAYDREESE----IAKINLEAILDNIEIAEKL 53
>gnl|CDD|223498 COG0421, SpeE, Spermidine synthase [Amino acid transport and
metabolism].
Length = 282
Score = 29.6 bits (67), Expect = 2.0
Identities = 10/40 (25%), Positives = 20/40 (50%)
Query: 69 NIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKF 108
+I ARK++ + +V I I++ F++ + KF
Sbjct: 111 AVIELARKYLPEPSGGADDPRVEIIIDDGVEFLRDCEEKF 150
>gnl|CDD|216028 pfam00621, RhoGEF, RhoGEF domain. Guanine nucleotide exchange
factor for Rho/Rac/Cdc42-like GTPases Also called
Dbl-homologous (DH) domain. It appears that pfam00169
domains invariably occur C-terminal to RhoGEF/DH
domains.
Length = 179
Score = 29.1 bits (66), Expect = 2.3
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 204 VFTLQRLLENKENPVELK--ISNNQIKIIFSNIEIISKL 240
V L+ L+E P+ +S +IK IFSNIE I +L
Sbjct: 13 VRDLKILVEVFLKPLRESPILSEEEIKTIFSNIEEILEL 51
>gnl|CDD|132604 TIGR03565, alk_sulf_monoox, alkanesulfonate monooxygenase,
FMNH(2)-dependent. Members of this protein family are
monooxygenases that catalyze desulfonation of aliphatic
sulfonates such as methane sulfonate. This enzyme uses
reduced FMN, although various others members of the same
luciferase-like monooxygenase family (pfam00296) are
F420-dependent enzymes [Central intermediary metabolism,
Sulfur metabolism].
Length = 346
Score = 29.2 bits (66), Expect = 2.6
Identities = 10/36 (27%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 73 AARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKF 108
A +F+ + R L E V + KH+ +++ K F
Sbjct: 128 ATDEFLRVWRRLLAGETVD--FDGKHIKVENAKLLF 161
>gnl|CDD|236619 PRK09737, PRK09737, EcoKI restriction-modification system protein
HsdS; Provisional.
Length = 461
Score = 29.1 bits (65), Expect = 3.7
Identities = 15/64 (23%), Positives = 24/64 (37%), Gaps = 2/64 (3%)
Query: 246 LDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLV--IKPNYLKITVSSSNR 303
L V+ + + V R + + Q I +I L R+ I P YL + S +
Sbjct: 281 LKLGDVLFCRGNEPLEVGRCAIWKEPQDIPVIYQKALIRARVKDDIIPEYLVYNLKSPDS 340
Query: 304 EKAS 307
S
Sbjct: 341 RNIS 344
>gnl|CDD|234874 PRK00955, PRK00955, hypothetical protein; Provisional.
Length = 620
Score = 28.8 bits (65), Expect = 4.8
Identities = 10/36 (27%), Positives = 21/36 (58%), Gaps = 6/36 (16%)
Query: 69 NIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSG 104
N+ V ++++++LR + + V K +FI+SG
Sbjct: 381 NLDVDHKEYLELLRKVRKLPGV------KKVFIRSG 410
>gnl|CDD|240410 PTZ00418, PTZ00418, Poly(A) polymerase; Provisional.
Length = 593
Score = 28.2 bits (63), Expect = 6.1
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 61 VGYGNSSINIIVAARKFIDILRSLPETEK 89
Y NS+ ++ A R F+DI+ + PE EK
Sbjct: 482 NVYNNSTFDLRYAIRDFVDIINNWPEMEK 510
>gnl|CDD|237784 PRK14669, uvrC, excinuclease ABC subunit C; Provisional.
Length = 624
Score = 28.0 bits (62), Expect = 7.4
Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 75 RKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPI--MTLNSKY 127
R+ +DI L + EK + +EN IK K +F + D K YP +TL KY
Sbjct: 58 REAVDIDYILVDNEKEALALENN--LIKQYKPRFNILLRDDKTYPYVKLTLGEKY 110
>gnl|CDD|144538 pfam00981, Rota_NS53, Rotavirus RNA-binding Protein 53 (NS53).
This protein is also known as NSP1. NS53 is encoded by
gene 5. It is made in low levels in the infected cells
and is a component of early replication. The protein is
known to accumulate on the cytoskeleton of the infected
cell. NS53 is an RNA binding protein that contains a
characteristic cysteine rich region.
Length = 488
Score = 27.7 bits (62), Expect = 9.7
Identities = 23/104 (22%), Positives = 46/104 (44%), Gaps = 16/104 (15%)
Query: 205 FTLQRLLENKENPVELK-ISNNQIKIIFSNIEIISKLIDGKFLDYKYVISNKYEKSFLVN 263
F+ LEN NP + ++ N ++ F+ E ++D Y + Y + + V+
Sbjct: 228 FSKN-TLENLHNPTSKRQVTRNCTEMDFNWNEECKLIVDKN--KYLEALKTSYTEHYSVS 284
Query: 264 RNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKAS 307
L + ++ +S +IKPNY ++S++ + AS
Sbjct: 285 DRCLGFTKYKLFELSK--------LIKPNY----IASNHWQPAS 316
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
0.320 0.135 0.364
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,383,783
Number of extensions: 1499770
Number of successful extensions: 1421
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1356
Number of HSP's successfully gapped: 81
Length of query: 314
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 217
Effective length of database: 6,635,264
Effective search space: 1439852288
Effective search space used: 1439852288
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: 59 (26.4 bits)