RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15087
(341 letters)
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 183 bits (465), Expect = 1e-53
Identities = 76/207 (36%), Positives = 122/207 (58%), Gaps = 5/207 (2%)
Query: 130 EKLKKVGLDVGNKLNTHELKIAANLIVPEEINGSWKNIAGLEHIKKELNQSVIFPMKNRN 189
+ +G+ + + + + ++ E+ + + +I GLE K+EL +++ P+K
Sbjct: 207 LVGEYIGVTEDDFEEALKKVLPSRGVLFEDEDVTLDDIGGLEEAKEELKEAIETPLKRPE 266
Query: 190 LLKESGLLKPPKGILLYGPPGCGKTMIAKATAKEANVSFINLDISTLTDKLYGESPKLAT 249
L ++ GL +PPKG+LLYGPPG GKT++AKA A E+ FI++ S L K GES K
Sbjct: 267 LFRKLGL-RPPKGVLLYGPPGTGKTLLAKAVALESRSRFISVKGSELLSKWVGESEKNIR 325
Query: 250 AIFSLAEKIQPCIIFIDEIDSLLRSRSSSDHEATAQLKSIFLSKWDGLTTDKNIDIIIMG 309
+F A K+ P IIFIDEIDSL R S+ + ++ L++ DG+ +K ++++
Sbjct: 326 ELFEKARKLAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGI--EKAEGVLVIA 383
Query: 310 ATNRPDDIDPAIAR--RMPKKYHIKLP 334
ATNRPDD+DPA+ R R + ++ LP
Sbjct: 384 ATNRPDDLDPALLRPGRFDRLIYVPLP 410
Score = 92.6 bits (230), Expect = 8e-21
Identities = 60/140 (42%), Positives = 85/140 (60%), Gaps = 5/140 (3%)
Query: 184 PMKNRNLLKESGLLKPPKGILLYGPPGCGKTMIAKATAKEANVSFINLDISTLTDKLYGE 243
P+K L + ++PPKG+LL+GPPG GKT++A+A A E F++++ + K GE
Sbjct: 3 PLK-EPELFKKLGIEPPKGVLLHGPPGTGKTLLARALANE-GAEFLSINGPEILSKYVGE 60
Query: 244 SPKLATAIFSLAEKIQPCIIFIDEIDSLLRSRSSSDHEATAQLKSIFLSKWDGLTTDKNI 303
S +F AEK+ P IIFIDEID+L RSS E ++ + L+ DGL K
Sbjct: 61 SELRLRELFEEAEKLAPSIIFIDEIDALAPKRSSDQGEVERRVVAQLLALMDGL---KRG 117
Query: 304 DIIIMGATNRPDDIDPAIAR 323
+I++GATNRPD +DPA R
Sbjct: 118 QVIVIGATNRPDGLDPAKRR 137
>gnl|CDD|215649 pfam00004, AAA, ATPase family associated with various cellular
activities (AAA). AAA family proteins often perform
chaperone-like functions that assist in the assembly,
operation, or disassembly of protein complexes.
Length = 131
Score = 158 bits (403), Expect = 2e-48
Identities = 58/132 (43%), Positives = 80/132 (60%), Gaps = 2/132 (1%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFINLDISTLTDKLYGESPKLATAIFSLAEKIQPCI 262
+LLYGPPG GKT +AKA AKE FI + S L K GES K +F A+K+ PC+
Sbjct: 1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCV 60
Query: 263 IFIDEIDSLLRSRSSSDHEATAQLKSIFLSKWDGLTTDKNIDIIIMGATNRPDDIDPAIA 322
IFIDEID+L SR S + ++ + L++ DG T+ + +I++ ATNRPD +DPA+
Sbjct: 61 IFIDEIDALAGSRGSGGDSESRRVVNQLLTELDGFTSSLS-KVIVIAATNRPDKLDPALL 119
Query: 323 R-RMPKKYHIKL 333
R R + L
Sbjct: 120 RGRFDRIIEFPL 131
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 159 bits (404), Expect = 2e-45
Identities = 75/188 (39%), Positives = 109/188 (57%), Gaps = 16/188 (8%)
Query: 156 VPEEINGSWKNIAGLEHIKKELNQSVIFPMKNRNLLKESGLLKPPKGILLYGPPGCGKTM 215
V E+ + ++++I GL+ +E+ + V P+KN L +E G+ PPKG+LLYGPPG GKT+
Sbjct: 142 VEEKPDVTYEDIGGLDEQIQEIREVVELPLKNPELFEELGI-DPPKGVLLYGPPGTGKTL 200
Query: 216 IAKATAKEANVSFINLDISTLTDKLYGESPKLATAIFSLAEKIQPCIIFIDEIDSL---- 271
+AKA A + + +FI + S L K GE +L +F LA + P IIFIDEID++
Sbjct: 201 LAKAVANQTDATFIRVVGSELVQKYIGEGARLVRELFELAREKAPSIIFIDEIDAIGAKR 260
Query: 272 LRSRSSSDHEAT---AQLKSIFLSKWDGLTTDKNIDIIIMGATNRPDDIDPAIAR--RMP 326
S +S D E +L L++ DG N+ +I ATNRPD +DPA+ R R
Sbjct: 261 FDSGTSGDREVQRTMLEL----LNQLDGFDPRGNVKVI--MATNRPDILDPALLRPGRFD 314
Query: 327 KKYHIKLP 334
+K LP
Sbjct: 315 RKIEFPLP 322
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 150 bits (382), Expect = 2e-42
Identities = 73/168 (43%), Positives = 100/168 (59%), Gaps = 14/168 (8%)
Query: 163 SWKNIAGLEHIKKELNQSVIFPMKNRNLLKESGLLKPPKGILLYGPPGCGKTMIAKATAK 222
++++I GLE +E+ ++V P+K L +E G+ +PPKG+LLYGPPG GKT++AKA A
Sbjct: 129 TYEDIGGLEEQIREVREAVELPLKKPELFEEVGI-EPPKGVLLYGPPGTGKTLLAKAVAH 187
Query: 223 EANVSFINLDISTLTDKLYGESPKLATAIFSLAEKIQPCIIFIDEIDSL----LRSRSSS 278
E N +FI + S L K GE +L +F LA + P IIFIDEID++ S +S
Sbjct: 188 ETNATFIRVVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTSG 247
Query: 279 DHEAT---AQLKSIFLSKWDGLTTDKNIDIIIMGATNRPDDIDPAIAR 323
D E QL L++ DG N+ II ATNR D +DPAI R
Sbjct: 248 DREVQRTLMQL----LAEMDGFDPRGNVKII--AATNRIDILDPAILR 289
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 147 bits (373), Expect = 2e-41
Identities = 80/186 (43%), Positives = 114/186 (61%), Gaps = 12/186 (6%)
Query: 156 VPEEINGSWKNIAGLEHIKKELNQSVIFPMKNRNLLKESGLLKPPKGILLYGPPGCGKTM 215
V E N S+++I GLE +E+ ++V P+K+ L +E G+ +PPKG+LLYGPPG GKT+
Sbjct: 113 VEERPNVSYEDIGGLEEQIREIREAVELPLKHPELFEEVGI-EPPKGVLLYGPPGTGKTL 171
Query: 216 IAKATAKEANVSFINLDISTLTDKLYGESPKLATAIFSLAEKIQPCIIFIDEIDSL---- 271
+AKA A E N +FI + S L K GE +L IF LA++ P IIFIDEID++
Sbjct: 172 LAKAVAHETNATFIRVVGSELVRKYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKR 231
Query: 272 LRSRSSSDHEATAQLKSIFLSKWDGLTTDKNIDIIIMGATNRPDDIDPAIARRMPKKYH- 330
S +S D E L + L++ DG N+ +I ATNRPD +DPA+ R P ++
Sbjct: 232 TDSGTSGDREVQRTLMQL-LAELDGFDPRGNVKVI--AATNRPDILDPALLR--PGRFDR 286
Query: 331 -IKLPL 335
I++PL
Sbjct: 287 IIEVPL 292
>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This
subfamily of the AAA family ATPases includes two members
each from three archaeal species. It also includes yeast
CDC48 (cell division control protein 48) and the human
ortholog, transitional endoplasmic reticulum ATPase
(valosin-containing protein). These proteins in
eukaryotes are involved in the budding and transfer of
membrane from the transitional endoplasmic reticulum to
the Golgi apparatus.
Length = 733
Score = 143 bits (362), Expect = 6e-38
Identities = 65/170 (38%), Positives = 108/170 (63%), Gaps = 4/170 (2%)
Query: 155 IVPEEINGSWKNIAGLEHIKKELNQSVIFPMKNRNLLKESGLLKPPKGILLYGPPGCGKT 214
++ E N W +I GLE +K+EL ++V +P+K+ + ++ G+ +PPKG+LL+GPPG GKT
Sbjct: 443 VLVEVPNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGI-RPPKGVLLFGPPGTGKT 501
Query: 215 MIAKATAKEANVSFINLDISTLTDKLYGESPKLATAIFSLAEKIQPCIIFIDEIDSLLRS 274
++AKA A E+ +FI + + K GES K IF A + P IIF DEID++ +
Sbjct: 502 LLAKAVATESGANFIAVRGPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPA 561
Query: 275 RSSSDHEA-TAQLKSIFLSKWDGLTTDKNIDIIIMGATNRPDDIDPAIAR 323
R + + T ++ + L++ DG+ + +++++ ATNRPD +DPA+ R
Sbjct: 562 RGARFDTSVTDRIVNQLLTEMDGI--QELSNVVVIAATNRPDILDPALLR 609
Score = 143 bits (362), Expect = 6e-38
Identities = 71/174 (40%), Positives = 108/174 (62%), Gaps = 5/174 (2%)
Query: 163 SWKNIAGLEHIKKELNQSVIFPMKNRNLLKESGLLKPPKGILLYGPPGCGKTMIAKATAK 222
++++I GL+ K+++ + V PMK+ L + G+ +PPKG+LLYGPPG GKT++AKA A
Sbjct: 176 TYEDIGGLKEAKEKIREMVELPMKHPELFEHLGI-EPPKGVLLYGPPGTGKTLLAKAVAN 234
Query: 223 EANVSFINLDISTLTDKLYGESPKLATAIFSLAEKIQPCIIFIDEIDSLLRSRSSSDHEA 282
EA FI+++ + K YGES + IF AE+ P IIFIDEID++ R E
Sbjct: 235 EAGAYFISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEV 294
Query: 283 TAQLKSIFLSKWDGLTTDKNIDIIIMGATNRPDDIDPAIAR--RMPKKYHIKLP 334
++ + L+ DGL +I++GATNRPD +DPA+ R R ++ I++P
Sbjct: 295 EKRVVAQLLTLMDGLKGRGR--VIVIGATNRPDALDPALRRPGRFDREIVIRVP 346
>gnl|CDD|200312 TIGR03689, pup_AAA, proteasome ATPase. In the Actinobacteria, as
shown for Mycobacterium tuberculosis, some proteins are
modified by ligation between an epsilon-amino group of a
lysine side chain and the C-terminal carboxylate of the
ubiquitin-like protein Pup. This modification leads to
protein degradation by the archaeal-like proteasome
found in the Actinobacteria. Members of this protein
family belong to the AAA family of ATPases and tend to
be clustered with the genes for Pup, the Pup ligase
PafA, and structural components of the proteasome. This
protein forms hexameric rings with ATPase activity
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 512
Score = 139 bits (352), Expect = 3e-37
Identities = 79/203 (38%), Positives = 114/203 (56%), Gaps = 28/203 (13%)
Query: 153 NLIVPEEINGSWKNIAGLEHIKKELNQSVIFPMKNRNLLKESGLLKPPKGILLYGPPGCG 212
+L++ E + ++ +I GL +++ +V P + L +E GL KPPKG+LLYGPPGCG
Sbjct: 170 DLVLEEVPDVTYADIGGLGSQIEQIRDAVELPFLHPELYREYGL-KPPKGVLLYGPPGCG 228
Query: 213 KTMIAKATAK------EANVS----FINLDISTLTDKLYGESPKLATAIFS----LAEKI 258
KT+IAKA A A F+N+ L +K GE+ + IF A +
Sbjct: 229 KTLIAKAVANSLAARIGAEGGGKSYFLNIKGPELLNKYVGETERQIRLIFQRAREKASEG 288
Query: 259 QPCIIFIDEIDSLLRSRS---SSDHEATA--QLKSIFLSKWDGLTTDKNIDIIIMGATNR 313
+P I+F DE+DSL R+R SSD E T QL L++ DG+ + N +I++GA+NR
Sbjct: 289 RPVIVFFDEMDSLFRTRGSGVSSDVETTVVPQL----LAEIDGVESLDN--VIVIGASNR 342
Query: 314 PDDIDPAIAR--RMPKKYHIKLP 334
D IDPAI R R+ K I+ P
Sbjct: 343 EDMIDPAILRPGRLDVKIRIERP 365
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 132 bits (334), Expect = 2e-35
Identities = 69/186 (37%), Positives = 108/186 (58%), Gaps = 8/186 (4%)
Query: 154 LIVPEEINGSWKNIAGLEHIKKELNQSVIFPMKNRNLLKESGLLKPPKGILLYGPPGCGK 213
L + E+ + ++ +I GL+ K+E+ ++V P+ L ++ G+ PP+G+LLYGPPG GK
Sbjct: 134 LQMSEKPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGI-DPPRGVLLYGPPGTGK 192
Query: 214 TMIAKATAKEANVSFINLDISTLTDKLYGESPKLATAIFSLAEKIQPCIIFIDEIDSLLR 273
TM+AKA A +FI + S K GE P++ +F LA + P IIFIDE+DS+
Sbjct: 193 TMLAKAVAHHTTATFIRVVGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIAT 252
Query: 274 SRSSSDHEATAQLKSIF---LSKWDGLTTDKNIDIIIMGATNRPDDIDPAIAR--RMPKK 328
R + A +++ I L++ DG N+ +I+ ATNR D +DPA+ R R+ +K
Sbjct: 253 KRFDAQTGADREVQRILLELLNQMDGFDQTTNVKVIM--ATNRADTLDPALLRPGRLDRK 310
Query: 329 YHIKLP 334
LP
Sbjct: 311 IEFPLP 316
>gnl|CDD|233327 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH.
HflB(FtsH) is a pleiotropic protein required for correct
cell division in bacteria. It has ATP-dependent zinc
metalloprotease activity. It was formerly designated
cell division protein FtsH [Cellular processes, Cell
division, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 495
Score = 128 bits (325), Expect = 2e-33
Identities = 70/178 (39%), Positives = 102/178 (57%), Gaps = 7/178 (3%)
Query: 149 KIAANLIVPEEINGSWKNIAGLEHIKKELNQSVIFPMKNRNLLKESGLLKPPKGILLYGP 208
K A L+ E+ ++K++AG++ K+EL + V F +KN + + G K PKG+LL GP
Sbjct: 39 KSKAKLLNEEKPKVTFKDVAGIDEAKEELMEIVDF-LKNPSKFTKLGA-KIPKGVLLVGP 96
Query: 209 PGCGKTMIAKATAKEANVSFINLDISTLTDKLYGESPKLATAIFSLAEKIQPCIIFIDEI 268
PG GKT++AKA A EA V F ++ S + G +F A+K PCIIFIDEI
Sbjct: 97 PGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEI 156
Query: 269 DSLLRSRS---SSDHEATAQLKSIFLSKWDGLTTDKNIDIIIMGATNRPDDIDPAIAR 323
D++ R R ++ Q + L + DG T N +I++ ATNRPD +DPA+ R
Sbjct: 157 DAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGT--NTGVIVIAATNRPDVLDPALLR 212
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 124 bits (314), Expect = 3e-32
Identities = 68/184 (36%), Positives = 108/184 (58%), Gaps = 13/184 (7%)
Query: 157 PEEINGSWKNIAGLEHIKKELNQSVIFPMKNRNLLKESGLLKPPKGILLYGPPGCGKTMI 216
P E S+ +I GLE +E+ ++V P+ + L + G+ KPPKG++LYGPPG GKT++
Sbjct: 178 PLE---SYADIGGLEQQIQEIKEAVELPLTHPELYDDIGI-KPPKGVILYGPPGTGKTLL 233
Query: 217 AKATAKEANVSFINLDISTLTDKLYGESPKLATAIFSLAEKIQPCIIFIDEIDSLLRSRS 276
AKA A E + +F+ + S L K G+ PKL +F +AE+ P I+FIDEID++ R
Sbjct: 234 AKAVANETSATFLRVVGSELIQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRY 293
Query: 277 SSDHEATAQLKSI---FLSKWDGLTTDKNIDIIIMGATNRPDDIDPAIAR--RMPKKYHI 331
+ +++ L++ DG D D+ ++ ATNR + +DPA+ R R+ +K I
Sbjct: 294 DATSGGEKEIQRTMLELLNQLDGF--DSRGDVKVIMATNRIESLDPALIRPGRIDRK--I 349
Query: 332 KLPL 335
+ P
Sbjct: 350 EFPN 353
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 117 bits (293), Expect = 7e-29
Identities = 68/191 (35%), Positives = 104/191 (54%), Gaps = 9/191 (4%)
Query: 149 KIAANLIVPEEINGSWKNIAGLEHIKKELNQSVIFPMKNRNLLKESGLLKPPKGILLYGP 208
K A ++ ++I ++ ++AG + K+E+ + V + + K G K PKG+L+ GP
Sbjct: 136 KSKARMLTEDQIKTTFADVAGCDEAKEEVAELVEYLREPSRFQKLGG--KIPKGVLMVGP 193
Query: 209 PGCGKTMIAKATAKEANVSFINLDISTLTDKLYGESPKLATAIFSLAEKIQPCIIFIDEI 268
PG GKT++AKA A EA V F + S + G +F A+K PCIIFIDEI
Sbjct: 194 PGTGKTLLAKAIAGEAKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEI 253
Query: 269 DSLLRSRSS---SDHEATAQLKSIFLSKWDGLTTDKNIDIIIMGATNRPDDIDPAIAR-- 323
D++ R R + H+ Q + L + DG + N II++ ATNRPD +DPA+ R
Sbjct: 254 DAVGRQRGAGLGGGHDEREQTLNQMLVEMDGF--EGNEGIIVIAATNRPDVLDPALLRPG 311
Query: 324 RMPKKYHIKLP 334
R ++ + LP
Sbjct: 312 RFDRQVVVGLP 322
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 114 bits (287), Expect = 4e-28
Identities = 59/164 (35%), Positives = 89/164 (54%), Gaps = 7/164 (4%)
Query: 163 SWKNIAGLEHIKKELNQSVIFPMKNRNLLKESGLLKPPKGILLYGPPGCGKTMIAKATAK 222
++++IAG+E K+E + V F K K PKG+LL GPPG GKT++AKA A
Sbjct: 181 TFRDIAGIEEAKEEFEEVVSFLKKPERFTAVGA--KIPKGVLLVGPPGTGKTLLAKAIAG 238
Query: 223 EANVSFINLDISTLTDKLYGESPKLATAIFSLAEKIQPCIIFIDEIDSLLRSRSS---SD 279
EA V F ++ S + G +F A++ PCI+FIDEID++ R R +
Sbjct: 239 EAEVPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGIGGG 298
Query: 280 HEATAQLKSIFLSKWDGLTTDKNIDIIIMGATNRPDDIDPAIAR 323
++ Q + L++ DG N +I++ ATNR D +D A+ R
Sbjct: 299 NDEREQTLNQLLTEMDGF--KGNKGVIVIAATNRVDILDAALLR 340
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 105 bits (263), Expect = 6e-25
Identities = 77/293 (26%), Positives = 133/293 (45%), Gaps = 14/293 (4%)
Query: 36 TFLYKQYS--ITHTRMSEVTVDSDSYLMHFGKFATTAIVSYFAVNFFFKKYQELFVDRTT 93
Y Q+ ++ ++S V++ DS ++ + Y
Sbjct: 24 QVTYSQFIQLVSGGKVSSVSIKGDSKTVNLKLKDGSKNTVYLPKGVNDPNLVSFLDSNNI 83
Query: 94 NKLMATHQDTNHVQCYFSDPSGTSTFNVLLAITTAYEKLKKVGLDVGNKLNTHELKIAAN 153
+ +D + + S S F +L+ + + + + G G + + K A
Sbjct: 84 TESGFIPEDNSLL---ASLLSTWLPFILLIGLGWFFFRRQAQGGGGGGAFSFGKSK--AK 138
Query: 154 LIVPEEINGSWKNIAGLEHIKKELNQSVIFPMKNRNLLKESGLLKPPKGILLYGPPGCGK 213
L + +++ ++ ++AG++ K+EL++ V F + + PKG+LL GPPG GK
Sbjct: 139 LYLEDQVKVTFADVAGVDEAKEELSELVDFLKNPKKYQALGAKI--PKGVLLVGPPGTGK 196
Query: 214 TMIAKATAKEANVSFINLDISTLTDKLYGESPKLATAIFSLAEKIQPCIIFIDEIDSLLR 273
T++AKA A EA V F ++ S + G +F A+K PCIIFIDEID++ R
Sbjct: 197 TLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGR 256
Query: 274 SR---SSSDHEATAQLKSIFLSKWDGLTTDKNIDIIIMGATNRPDDIDPAIAR 323
R ++ Q + L + DG N +I++ ATNRPD +DPA+ R
Sbjct: 257 QRGAGLGGGNDEREQTLNQLLVEMDGFGG--NEGVIVIAATNRPDVLDPALLR 307
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 102 bits (256), Expect = 1e-24
Identities = 50/136 (36%), Positives = 79/136 (58%), Gaps = 3/136 (2%)
Query: 200 PKGILLYGPPGCGKTMIAKATAKEANVSFINLDISTLTDKLYGESPKLATAIFSLAEKIQ 259
PK +L YGPPG GKTM+AKA A EA V + + + L + G+ + ++ A K
Sbjct: 151 PKNVLFYGPPGTGKTMMAKALANEAKVPLLLVKATELIGEHVGDGARRIHELYERARKAA 210
Query: 260 PCIIFIDEIDSL-LRSRSSSDHEATAQLKSIFLSKWDGLTTDKNIDIIIMGATNRPDDID 318
PCI+FIDE+D++ L R +++ + L++ DG+ +N ++ + ATNRP+ +D
Sbjct: 211 PCIVFIDELDAIALDRRYQELRGDVSEIVNALLTELDGI--KENEGVVTIAATNRPELLD 268
Query: 319 PAIARRMPKKYHIKLP 334
PAI R ++ KLP
Sbjct: 269 PAIRSRFEEEIEFKLP 284
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase fold.
The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons, ATPase
subunits of proteases, helicases, or nucleic-acid
stimulated ATPases. The AAA+ proteins contain several
distinct features in addition to the conserved
alpha-beta-alpha core domain structure and the Walker A
and B motifs of the P-loop NTPases.
Length = 151
Score = 94.1 bits (234), Expect = 2e-23
Identities = 58/156 (37%), Positives = 80/156 (51%), Gaps = 19/156 (12%)
Query: 188 RNLLKESGLLKPPKGILLYGPPGCGKTMIAKATAKEA---NVSFINLDISTLTDKLYGES 244
L+E+ L PPK +LLYGPPG GKT +A+A A E F+ L+ S L + L
Sbjct: 7 IEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAE 66
Query: 245 ---PKLATAIFSLAEKIQPCIIFIDEIDSLLRSRSSSDHEATAQLKSIFLSKWDGLTTDK 301
L +F LAEK +P ++FIDEIDSL R A L + + D +
Sbjct: 67 LFGHFLVRLLFELAEKAKPGVLFIDEIDSLSR-------GAQNALLRVLETLNDLRIDRE 119
Query: 302 NIDIIIMGATNRPD--DIDPAIARRMPKKYHIKLPL 335
N + ++GATNRP D+D A+ R+ I +PL
Sbjct: 120 N--VRVIGATNRPLLGDLDRALYDRLDI--RIVIPL 151
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 78.6 bits (193), Expect = 9e-18
Identities = 39/144 (27%), Positives = 64/144 (44%), Gaps = 24/144 (16%)
Query: 199 PPKGILLYGPPGCGKTMIAKATAKEAN-----VSFINLD------------ISTLTDKLY 241
P + IL+ GPPG GKT +A+A A+E V +I+ + I K
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60
Query: 242 GESPKLATAIFSLAEKIQPCIIFIDEIDSLLRSRSSSDHEATAQLKSIFLSKWDGLTTDK 301
G +LA K++P ++ +DEI SLL + + +L+ + L K
Sbjct: 61 GSGELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLK-------S 113
Query: 302 NIDIIIMGATNRPDDIDPAIARRM 325
++ ++ TN D+ PA+ RR
Sbjct: 114 EKNLTVILTTNDEKDLGPALLRRR 137
>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional.
Length = 489
Score = 73.9 bits (182), Expect = 2e-14
Identities = 53/178 (29%), Positives = 88/178 (49%), Gaps = 13/178 (7%)
Query: 161 NGSWKNIAGLEHIKKELNQ-SVIFPMKNRNLLKESGLLKPPKGILLYGPPGCGKTMIAKA 219
N +I GL+++K L + S F + N GL P+G+LL G G GK++ AKA
Sbjct: 224 NEKISDIGGLDNLKDWLKKRSTSFSKQASNY----GL-PTPRGLLLVGIQGTGKSLTAKA 278
Query: 220 TAKEANVSFINLDISTLTDKLYGESPKLATAIFSLAEKIQPCIIFIDEID-SLLRSRSSS 278
A + + + LD+ L + GES + +AE + PCI++IDEID + S S
Sbjct: 279 IANDWQLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPCILWIDEIDKAFSNSESKG 338
Query: 279 DHEATAQLKSIFLSKWDGLTTDKNIDIIIMGATNRPDDIDPAIAR--RMPKKYHIKLP 334
D T ++ + F++ W ++K + ++ N D + I R R + + + LP
Sbjct: 339 DSGTTNRVLATFIT-W---LSEKKSPVFVVATANNIDLLPLEILRKGRFDEIFFLDLP 392
>gnl|CDD|232949 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit
(clpX). A member of the ATP-dependent proteases, ClpX
has ATP-dependent chaperone activity and is required for
specific ATP-dependent proteolytic activities expressed
by ClpPX. The gene is also found to be involved in
stress tolerance in Bacillus subtilis and is essential
for the efficient acquisition of genes specifying type
IA and IB restriction [Protein fate, Protein folding and
stabilization, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 413
Score = 56.7 bits (137), Expect = 6e-09
Identities = 35/77 (45%), Positives = 43/77 (55%), Gaps = 6/77 (7%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFINLDISTLTDKLY-GES-----PKLATAIFSLAE 256
ILL GP G GKT++A+ A+ NV F D +TLT+ Y GE KL A E
Sbjct: 119 ILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVE 178
Query: 257 KIQPCIIFIDEIDSLLR 273
K Q II+IDEID + R
Sbjct: 179 KAQKGIIYIDEIDKISR 195
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 54.9 bits (133), Expect = 2e-08
Identities = 34/77 (44%), Positives = 43/77 (55%), Gaps = 6/77 (7%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFINLDISTLTDKLY-GES-----PKLATAIFSLAE 256
ILL GP G GKT++A+ AK NV F D +TLT+ Y GE KL A E
Sbjct: 100 ILLIGPTGSGKTLLAQTLAKILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVE 159
Query: 257 KIQPCIIFIDEIDSLLR 273
+ + II+IDEID + R
Sbjct: 160 RAERGIIYIDEIDKIAR 176
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 51.7 bits (125), Expect = 2e-07
Identities = 33/82 (40%), Positives = 46/82 (56%), Gaps = 10/82 (12%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFINLDISTLTDKLY-GE------SPKLATAIFSLA 255
ILL GP G GKT++A+ A+ +V F D +TLT+ Y GE L A + +
Sbjct: 111 ILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDV- 169
Query: 256 EKIQPCIIFIDEIDSLLRSRSS 277
EK Q I++IDEID + +R S
Sbjct: 170 EKAQRGIVYIDEIDKI--ARKS 189
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 51.6 bits (125), Expect = 3e-07
Identities = 25/82 (30%), Positives = 38/82 (46%), Gaps = 19/82 (23%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFINLDISTLTDKLYGESPKLATAIFSLAEKI---- 258
++L+GPPG GKT +A+ A + F L S +T + K + A +
Sbjct: 39 MILWGPPGTGKTTLARIIAGATDAPFEAL--SAVTSGV-----KDLREVIEEARQRRSAG 91
Query: 259 QPCIIFIDEI--------DSLL 272
+ I+FIDEI D+LL
Sbjct: 92 RRTILFIDEIHRFNKAQQDALL 113
>gnl|CDD|219536 pfam07724, AAA_2, AAA domain (Cdc48 subfamily). This Pfam entry
includes some of the AAA proteins not detected by the
pfam00004 model.
Length = 168
Score = 49.1 bits (118), Expect = 4e-07
Identities = 26/88 (29%), Positives = 36/88 (40%), Gaps = 22/88 (25%)
Query: 200 PKG-ILLYGPPGCGKTMIAKATAKEANVS---FINLDISTLT-----DKL---------Y 241
P G L GP G GKT +AKA A+ I +D+S +L Y
Sbjct: 2 PIGSFLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYMEEHSVSRLIGAPPGYVGY 61
Query: 242 GESPKLATAIFSLAEKIQPCIIFIDEID 269
E +L A+ + I+ IDEI+
Sbjct: 62 EEGGQLTEAV----RRKPYSIVLIDEIE 85
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 49.2 bits (118), Expect = 2e-06
Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 11/76 (14%)
Query: 205 LYGPPGCGKTMIAKATAKEANVSFINLDISTLTDKLYGESPKLATAIFSLAEKIQPCIIF 264
L+GPPG GKT +A+ A N +F +S +T + + A + + I+F
Sbjct: 53 LWGPPGTGKTTLARLIAGTTNAAFE--ALSAVTSGVKDLREIIEEARKNRLLGRRT-ILF 109
Query: 265 IDEI--------DSLL 272
+DEI D+LL
Sbjct: 110 LDEIHRFNKAQQDALL 125
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 48.4 bits (116), Expect = 3e-06
Identities = 28/79 (35%), Positives = 40/79 (50%), Gaps = 10/79 (12%)
Query: 198 KPPKGILLYGPPGCGKTMIAKATAKEANVSFINL---DISTLTD--KLYGESPKLATAIF 252
KP K +LLYGPPG GKT +A A A + I L D T ++ GE+ + +F
Sbjct: 37 KPKKALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQRTADVIERVAGEAATSGS-LF 95
Query: 253 SLAEKIQPCIIFIDEIDSL 271
K +I +DE+D +
Sbjct: 96 GARRK----LILLDEVDGI 110
>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam
entry includes some of the AAA proteins not detected by
the pfam00004 model.
Length = 135
Score = 45.4 bits (108), Expect = 5e-06
Identities = 32/142 (22%), Positives = 53/142 (37%), Gaps = 25/142 (17%)
Query: 202 GILLYGPPGCGKTMIAKATAK---EANVSFINLDISTLTDKL-YGESPKLATAIF---SL 254
G+LL GPPG GK+ +A+ A V ++ L T + L + A + L
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIDPGGASWVDGPL 60
Query: 255 AEKIQ-PCIIFIDEIDSLLRSRSSSDHEATAQLKSIF------LSKWDGLTTDKNIDIII 307
+ I +DEI+ R++ D L S+ L + L +
Sbjct: 61 VRAAREGEIAVLDEIN-----RANPD--VLNSLLSLLDERRLLLPEGGELVKAAPDGFRL 113
Query: 308 MGATNRPD----DIDPAIARRM 325
+ N D ++ PA+ R
Sbjct: 114 IATMNPLDRGLNELSPALRSRF 135
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 46.7 bits (111), Expect = 7e-06
Identities = 37/153 (24%), Positives = 62/153 (40%), Gaps = 30/153 (19%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSF--INLDISTLTDKLYGESPKLATAIFSLAEKIQP 260
+LL GPPG GKT++A+A A+ + F I L L G A + + P
Sbjct: 46 VLLEGPPGVGKTLLARALARALGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRFVP 105
Query: 261 --------CIIFIDEIDSLLRSRSSSD-----HEATAQLKSIFLSKWDGLTTDKNIDIII 307
I+ +DEI+ R+ + EA + + + + GLTT + I
Sbjct: 106 GPLFAAVRVILLLDEIN-----RAPPEVQNALLEAL-EERQVTV---PGLTTIRLPPPFI 156
Query: 308 MGATNRPDDID------PAIARRMPKKYHIKLP 334
+ AT P + + A+ R + ++ P
Sbjct: 157 VIATQNPGEYEGTYPLPEALLDRFLLRIYVDYP 189
>gnl|CDD|234053 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family.
Members of this protein family resemble the widely
distributed ATP-dependent protease La, also called Lon
and LonA. It resembles even more closely LonB, which is
a LonA paralog found in genomes if and only if the
species is capable of endospore formation (as in
Bacillus subtilis, Clostridium tetani, and select other
members of the Firmicutes) and expressed specifically in
the forespore compartment. Members of this family are
restricted to a subset of spore-forming species, and are
very likely to participate in the program of endospore
formation. We propose the designation LonC [Protein
fate, Degradation of proteins, peptides, and
glycopeptides, Cellular processes, Sporulation and
germination].
Length = 615
Score = 46.7 bits (111), Expect = 1e-05
Identities = 51/179 (28%), Positives = 76/179 (42%), Gaps = 63/179 (35%)
Query: 200 PKGILLYGPPGCGKTMIAKATAKEA----------NVSFINLDISTL-------TDKLYG 242
P+ I+LYGPPG GKT A+ +EA + F+ +D +TL T+ L G
Sbjct: 175 PQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTLRWDPREVTNPLLG 234
Query: 243 --ESPKLATAIFSLAEKIQP------------CIIFIDEI---DSLLRSR---------- 275
P A LAE P ++FIDEI D LL+++
Sbjct: 235 SVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELDPLLQNKLLKVLEDKRV 294
Query: 276 --SSS-----DHEATAQLKSIFLSKWDGLTTDKN--IDIIIMGATNR-PDDIDPAIARR 324
SSS D +K +F ++ D +++GAT R P++I+PA+ R
Sbjct: 295 EFSSSYYDPDDPNVPKYIKKLF---------EEGAPADFVLIGATTRDPEEINPALRSR 344
>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit. All
proteins in this family for which functions are known
are 5'-3' DNA helicases that, as part of a complex with
RuvA homologs serve as a 5'-3' Holliday junction
helicase. RuvA specifically binds Holliday junctions as
a sandwich of two tetramers and maintains the
configuration of the junction. It forms a complex with
two hexameric rings of RuvB, the subunit that contains
helicase activity. The complex drives ATP-dependent
branch migration of the Holliday junction recombination
intermediate. The endonuclease RuvC resolves junctions
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 305
Score = 45.8 bits (109), Expect = 1e-05
Identities = 37/112 (33%), Positives = 48/112 (42%), Gaps = 17/112 (15%)
Query: 163 SWKNIAGLEHIKKELNQSVIFPMKNRNLLKESGLLKPPKGILLYGPPGCGKTMIAKATAK 222
G E +K++L Q I K R + +LLYGPPG GKT +A A
Sbjct: 2 LLAEFIGQEKVKEQL-QLFIEAAKMRQ--------EALDHLLLYGPPGLGKTTLAHIIAN 52
Query: 223 EANVSFINLDISTLTDKLYGESPKLATAIFSLAEKIQPCIIFIDEIDSLLRS 274
E V NL I T E P AI + E+ ++FIDEI L +
Sbjct: 53 EMGV---NLKI---TSGPALEKPGDLAAILTNLEEGD--VLFIDEIHRLSPA 96
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA
replication, recombination, and repair].
Length = 332
Score = 43.3 bits (103), Expect = 9e-05
Identities = 35/103 (33%), Positives = 48/103 (46%), Gaps = 23/103 (22%)
Query: 169 GLEHIKKELNQSVIFPMKNRNLLKESGLLKPPKGILLYGPPGCGKTMIAKATAKEANVSF 228
G E +K++L Q I K R + +LL+GPPG GKT +A A E V
Sbjct: 30 GQEKVKEQL-QIFIKAAKKRG--------EALDHVLLFGPPGLGKTTLAHIIANELGV-- 78
Query: 229 INLDISTLTDKLYG---ESPKLATAIFSLAEKIQPCIIFIDEI 268
NL I++ G E P AI + E+ ++FIDEI
Sbjct: 79 -NLKITS------GPALEKPGDLAAILTNLEEGD--VLFIDEI 112
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 41.0 bits (97), Expect = 1e-04
Identities = 19/69 (27%), Positives = 26/69 (37%), Gaps = 7/69 (10%)
Query: 203 ILLYGPPGCGKTMIAKATAKEA---NVSFINLDISTLTDKLYGESPKLATAIFSLAEKIQ 259
I++ GP GKT + KE N+ +INLD L L
Sbjct: 5 IVITGPRQVGKTTLLLQFLKELLSENILYINLDDPRFLRL---ALLDLLEEFLKLLLP-G 60
Query: 260 PCIIFIDEI 268
+F+DEI
Sbjct: 61 KKYLFLDEI 69
>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI.
Magnesium-chelatase is a three-component enzyme that
catalyzes the insertion of Mg2+ into protoporphyrin IX.
This is the first unique step in the synthesis of
(bacterio)chlorophyll. Due to this, it is thought that
Mg-chelatase has an important role in channelling inter-
mediates into the (bacterio)chlorophyll branch in
response to conditions suitable for photosynthetic
growth. ChlI and BchD have molecular weight between
38-42 kDa.
Length = 207
Score = 41.7 bits (99), Expect = 2e-04
Identities = 11/17 (64%), Positives = 14/17 (82%)
Query: 203 ILLYGPPGCGKTMIAKA 219
+L+ GPPG GKTM+AK
Sbjct: 25 LLMIGPPGSGKTMLAKR 41
>gnl|CDD|131948 TIGR02902, spore_lonB, ATP-dependent protease LonB. Members of
this protein are LonB, a paralog of the ATP-dependent
protease La (LonA, TIGR00763). LonB proteins are found
strictly, and almost universally, in endospore-forming
bacteria. This protease was shown, in Bacillus subtilis,
to be expressed specifically in the forespore, during
sporulation, under control of sigma(F). The lonB gene,
despite location immediately upstream of lonA, was shown
to be monocistronic. LonB appears able to act on
sigma(H) for post-translation control, but lonB mutation
did not produce an obvious sporulation defect under the
conditions tested. Note that additional paralogs of LonA
and LonB occur in the Clostridium lineage and this model
selects only one per species as the protein that
corresponds to LonB in B. subtilis [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Cellular processes, Sporulation and germination].
Length = 531
Score = 42.5 bits (100), Expect = 2e-04
Identities = 46/176 (26%), Positives = 69/176 (39%), Gaps = 58/176 (32%)
Query: 200 PKGILLYGPPGCGKTMIAKATAKEA----------NVSFINLDISTL-------TDKLYG 242
P+ +++YGPPG GKT A+ +EA +F+ +D +T D L G
Sbjct: 86 PQHVIIYGPPGVGKTAAARLVLEEAKKNPASPFKEGAAFVEIDATTARFDERGIADPLIG 145
Query: 243 --ESPKLATA-IFSLAEKIQP----------CIIFIDEIDSL-----------LRSR--- 275
P A +A QP ++FIDEI L L R
Sbjct: 146 SVHDPIYQGAGPLGIAGIPQPKPGAVTRAHGGVLFIDEIGELHPVQMNKLLKVLEDRKVF 205
Query: 276 ------SSSDHEATAQLKSIFLSKWDGLTTDKNIDIIIMGATNR-PDDIDPAIARR 324
+S + + + IF +GL D ++GAT R P++I PA+ R
Sbjct: 206 LDSAYYNSENPNIPSHIHDIF---QNGLPA----DFRLIGATTRNPEEIPPALRSR 254
>gnl|CDD|234063 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation
protein. Members of this protein family are found
exclusively in the archaea. This set of DNA binding
proteins shows homology to the origin recognition
complex subunit 1/cell division control protein 6 family
in eukaryotes. Several members may be found in genome
and interact with each other [DNA metabolism, DNA
replication, recombination, and repair].
Length = 365
Score = 41.9 bits (99), Expect = 3e-04
Identities = 25/114 (21%), Positives = 36/114 (31%), Gaps = 38/114 (33%)
Query: 199 PPKGILLYGPPGCGKTMIAKATAKEAN-----------VSFINLDI-STLTDKLYGESPK 246
P + +YG G GKT + K KE ++N I TL L +
Sbjct: 39 RPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLV----E 94
Query: 247 LATAIFSLAEKI----------------------QPCIIFIDEIDSLLRSRSSS 278
LA + E++ II +DEID L+
Sbjct: 95 LANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGDDDDL 148
>gnl|CDD|213527 TIGR00390, hslU, ATP-dependent protease HslVU, ATPase subunit.
This model represents the ATPase subunit of HslVU, while
the proteasome-related peptidase subunit is HslV.
Residues 54-61 of the model contain a P-loop ATP-binding
motif. Cys-287 of E. coli (position 308 in the seed
alignment), studied in MEDLINE:98389714, is Ser in other
members of the seed alignment [Protein fate, Protein
folding and stabilization].
Length = 441
Score = 42.1 bits (99), Expect = 3e-04
Identities = 32/93 (34%), Positives = 48/93 (51%), Gaps = 17/93 (18%)
Query: 155 IVPEEINGSWKNIAGL-EHI--KKELNQSVIFPMKNRNLLKESGLLKP------PKGILL 205
+ P EI +A L ++I + E +SV ++NR + S L + PK IL+
Sbjct: 1 MTPREI------VAELDKYIIGQDEAKKSVAIALRNR--YRRSQLPEELKDEVTPKNILM 52
Query: 206 YGPPGCGKTMIAKATAKEANVSFINLDISTLTD 238
GP G GKT IA+ AK AN FI ++ + T+
Sbjct: 53 IGPTGVGKTEIARRLAKLANAPFIKVEATKFTE 85
Score = 29.0 bits (65), Expect = 3.5
Identities = 55/250 (22%), Positives = 89/250 (35%), Gaps = 61/250 (24%)
Query: 121 VLLAITTAYEKLKKVGLDVGNKLNTHELKIAANLIVPEEINGSWKNIAGLEHIKKELNQS 180
V L EK++ + + +I +L+ P + +E I++E +
Sbjct: 105 VKLVKEEMIEKVRDRAEERAEE------RIVDSLLPPAK-----NQWGNMEEIQEEESVR 153
Query: 181 VIFPMKNRNLLKESGL----------LKPPKGILLYGPPG----------------CGKT 214
R L+E L K P GI + PPG K
Sbjct: 154 ----EAFRKKLREGELDDKEIEIEVSAKMPSGIEIMAPPGMEEMTMNLQSLFQNLGPDKK 209
Query: 215 MIAKATAKEANVSFINLDISTLTDKLYGESPKLATAIFSLAEKIQPCIIFIDEIDSLLRS 274
K KEA + I + + L D ++ E Q IIFIDEID + +
Sbjct: 210 KKRKLKIKEAKKALIAEEAAKLVD-----PEEIKQEAIDRVE--QSGIIFIDEIDKIAKK 262
Query: 275 RSSSDHEATAQ----------LKSIFLSKWDGLTTDKNIDIIIMGATN--RPDDIDPAIA 322
SS + + + S +K+ + TD +I I GA + +P D+ P +
Sbjct: 263 GESSGADVSREGVQRDLLPIVEGSTVNTKYGSVKTD-HILFIAAGAFHLAKPSDLIPELQ 321
Query: 323 RRMPKKYHIK 332
R P + +K
Sbjct: 322 GRFPIRVELK 331
>gnl|CDD|223775 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 40.3 bits (95), Expect = 3e-04
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 199 PPKGILLYGPPGCGKTMIAKATAKEANVSFINLD 232
I+L G G GK+ I +A AK N+ FI+ D
Sbjct: 1 RNMNIVLIGFMGAGKSTIGRALAKALNLPFIDTD 34
>gnl|CDD|233119 TIGR00763, lon, ATP-dependent protease La. This protein is induced
by heat shock and other stresses in E. coli, B.
subtilis, and other species. The yeast member,
designated PIM1, is located in the mitochondrial matrix,
required for mitochondrial function, and also induced by
heat shock [Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 775
Score = 41.5 bits (98), Expect = 5e-04
Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 12/82 (14%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFINLDISTLTD--------KLY-GESP-KLATAIF 252
+ L GPPG GKT + K+ AK N F+ + + D + Y G P ++ +
Sbjct: 350 LCLVGPPGVGKTSLGKSIAKALNRKFVRFSLGGVRDEAEIRGHRRTYVGAMPGRIIQGLK 409
Query: 253 SLAEKIQPCIIFIDEIDSLLRS 274
A+ P + +DEID + S
Sbjct: 410 K-AKTKNP-LFLLDEIDKIGSS 429
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 40.9 bits (97), Expect = 6e-04
Identities = 30/73 (41%), Positives = 39/73 (53%), Gaps = 16/73 (21%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFINLDISTLTDKLYG---ESPK-LATAIFSLAEKI 258
+LLYGPPG GKT +A A E V N+ I++ G E P LA AI + E+
Sbjct: 54 VLLYGPPGLGKTTLANIIANEMGV---NIRITS------GPALEKPGDLA-AILTNLEEG 103
Query: 259 QPCIIFIDEIDSL 271
++FIDEI L
Sbjct: 104 D--VLFIDEIHRL 114
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 41.2 bits (97), Expect = 6e-04
Identities = 46/172 (26%), Positives = 71/172 (41%), Gaps = 50/172 (29%)
Query: 170 LEHIKKELNQSVIFPMKN--RNLLK-----ESGLLKPPKGI---LLYGPPGCGKTMIAKA 219
L++++K L ++ IF L+ +GL P K + L GP G GKT +AK
Sbjct: 444 LKNLEKNL-KAKIFGQDEAIDQLVSAIKRSRAGLGDPNKPVGSFLFVGPTGVGKTELAKQ 502
Query: 220 TAKEANVSFINLDISTLTDK-----LYGESP---------KLATAIFSLAEKIQPCIIFI 265
A+E V + D+S +K L G P L A+ K C++ +
Sbjct: 503 LAEELGVHLLRFDMSEYMEKHTVSRLIGSPPGYVGFEQGGLLTDAV----RKHPHCVLLL 558
Query: 266 DEIDSLLRSRSSSDHEATAQLKSIFLSKWDGLT-TD--------KNIDIIIM 308
DEI+ +A + +I L D T TD +N+ I+IM
Sbjct: 559 DEIE-----------KAHPDIYNILLQVMDYATLTDNNGRKADFRNV-ILIM 598
Score = 32.7 bits (75), Expect = 0.27
Identities = 27/77 (35%), Positives = 34/77 (44%), Gaps = 12/77 (15%)
Query: 204 LLYGPPGCGKTMIAKATAKE----------ANVSFINLDISTLT--DKLYGESPKLATAI 251
LL G PG GKT I + A N +LD+ TL K G+ + A+
Sbjct: 206 LLVGEPGVGKTAIVEGLALRIAEGKVPERLKNAKIYSLDMGTLLAGTKYRGDFEERLKAV 265
Query: 252 FSLAEKIQPCIIFIDEI 268
S EK I+FIDEI
Sbjct: 266 VSEIEKEPNAILFIDEI 282
>gnl|CDD|203260 pfam05496, RuvB_N, Holliday junction DNA helicase ruvB N-terminus.
The RuvB protein makes up part of the RuvABC revolvasome
which catalyzes the resolution of Holliday junctions
that arise during genetic recombination and DNA repair.
Branch migration is catalyzed by the RuvB protein that
is targeted to the Holliday junction by the structure
specific RuvA protein. This family contains the
N-terminal region of the protein.
Length = 231
Score = 39.7 bits (94), Expect = 0.001
Identities = 14/26 (53%), Positives = 17/26 (65%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSF 228
+LLYGPPG GKT +A A E V+
Sbjct: 53 VLLYGPPGLGKTTLANIIANEMGVNI 78
>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 444
Score = 39.6 bits (93), Expect = 0.002
Identities = 17/30 (56%), Positives = 19/30 (63%)
Query: 200 PKGILLYGPPGCGKTMIAKATAKEANVSFI 229
PK IL+ GP G GKT IA+ AK A FI
Sbjct: 50 PKNILMIGPTGVGKTEIARRLAKLAGAPFI 79
Score = 28.0 bits (63), Expect = 8.1
Identities = 19/67 (28%), Positives = 25/67 (37%), Gaps = 7/67 (10%)
Query: 212 GKTMIAKATAKEANVSFINLDISTLTDKLYGESPKLATAIFSLAEKIQPCIIFIDEIDSL 271
K K KEA I + L D ++ AE Q I+FIDEID +
Sbjct: 210 KKKKKRKLKVKEAKKLLIEEEADKLID-----QEEIKQEAIDAAE--QNGIVFIDEIDKI 262
Query: 272 LRSRSSS 278
+ S
Sbjct: 263 AKRGGSG 269
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 37.3 bits (87), Expect = 0.002
Identities = 17/85 (20%), Positives = 32/85 (37%), Gaps = 16/85 (18%)
Query: 203 ILLYGPPGCGKTMIAKATAKEA-NVSFINLDISTLTDKL---------------YGESPK 246
+L G G GKT + + A++ N + ++ +L G + +
Sbjct: 7 GVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLLRKILRALGLPLSGGTTAE 66
Query: 247 LATAIFSLAEKIQPCIIFIDEIDSL 271
L AI ++ ++ IDE L
Sbjct: 67 LLEAILDALKRRGRPLLIIDEAQHL 91
>gnl|CDD|224292 COG1373, COG1373, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 398
Score = 38.9 bits (91), Expect = 0.002
Identities = 19/76 (25%), Positives = 30/76 (39%), Gaps = 2/76 (2%)
Query: 196 LLKPPKGILLYGPPGCGKTMIAKATAKEANVSFINLDISTLTDKLYGESPKLATAIFSLA 255
L P IL+ GP GKT + K K I I+ +L +
Sbjct: 33 LDLRPFIILILGPRQVGKTTLLKLLIKGLLEEIIY--INFDDLRLDRIELLDLLRAYIEL 90
Query: 256 EKIQPCIIFIDEIDSL 271
++ + IF+DEI ++
Sbjct: 91 KEREKSYIFLDEIQNV 106
>gnl|CDD|235364 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU;
Provisional.
Length = 443
Score = 38.9 bits (92), Expect = 0.003
Identities = 18/30 (60%), Positives = 20/30 (66%)
Query: 200 PKGILLYGPPGCGKTMIAKATAKEANVSFI 229
PK IL+ GP G GKT IA+ AK AN FI
Sbjct: 50 PKNILMIGPTGVGKTEIARRLAKLANAPFI 79
Score = 27.7 bits (63), Expect = 9.5
Identities = 7/8 (87%), Positives = 8/8 (100%)
Query: 262 IIFIDEID 269
I+FIDEID
Sbjct: 252 IVFIDEID 259
>gnl|CDD|234654 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 37.5 bits (88), Expect = 0.004
Identities = 12/36 (33%), Positives = 16/36 (44%)
Query: 198 KPPKGILLYGPPGCGKTMIAKATAKEANVSFINLDI 233
I+L G G GK+ I + AK FI+ D
Sbjct: 2 LKGPNIVLIGFMGAGKSTIGRLLAKRLGYDFIDTDH 37
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 38.4 bits (90), Expect = 0.004
Identities = 24/80 (30%), Positives = 37/80 (46%), Gaps = 12/80 (15%)
Query: 204 LLYGPPGCGKTMIAKATAKE----------ANVSFINLDISTL--TDKLYGESPKLATAI 251
+L G PG GKT I + A+ + +LD+ +L K GE + A+
Sbjct: 195 VLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSLDLGSLVAGAKYRGEFEERLKAV 254
Query: 252 FSLAEKIQPCIIFIDEIDSL 271
EK + I+FIDEI ++
Sbjct: 255 LKEVEKSKNVILFIDEIHTI 274
Score = 32.3 bits (74), Expect = 0.42
Identities = 39/144 (27%), Positives = 58/144 (40%), Gaps = 45/144 (31%)
Query: 194 SGLLKP--PKGILLY-GPPGCGKTMIAKATAKE---ANVSFINLDISTLTDKL------- 240
+GL P P G L+ GP G GKT +AKA A+ + I +D+S +K
Sbjct: 512 AGLGDPNRPIGSFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSEYMEKHSVSRLIG 571
Query: 241 -------YGESPKLATAIFSLAEKIQPCIIFIDEIDSLLRSRSSSDHEATAQLKSIFLSK 293
Y E +L A+ + +I +DEI+ +A + ++ L
Sbjct: 572 APPGYVGYEEGGQLTEAV----RRKPYSVILLDEIE-----------KAHPDVFNLLLQV 616
Query: 294 WD--------GLTTD-KNIDIIIM 308
D G T D +N IIIM
Sbjct: 617 LDDGRLTDGQGRTVDFRNT-IIIM 639
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a wide
variety of presumed DNA repair proteins.
Length = 154
Score = 36.9 bits (86), Expect = 0.004
Identities = 31/132 (23%), Positives = 51/132 (38%), Gaps = 33/132 (25%)
Query: 195 GLLKPPKGI-LLYGPPGCGKTMIAKATA---------------KEANVSFINLDIS--TL 236
GLL P G+ LL G PG GK+ +A A + V +++ + S L
Sbjct: 28 GLL-PRGGLTLLAGAPGTGKSTLALDLAAAVATGRPFLGPFPVEPGRVLYLDGEDSEAGL 86
Query: 237 TDKLYGESPKLATAIFSLAEKI-QPCIIFIDEIDSLLRSRSSSDHEATAQLKSIFLSKWD 295
+L A+ E+I P ++ ID + SLL + + A L+ D
Sbjct: 87 RRRLR--------ALGEALEEIEGPDLVVIDPLASLLGGDENDNAAVGA-----LLAALD 133
Query: 296 GLTTDKNIDIII 307
L +++
Sbjct: 134 RLARRTGAAVLL 145
>gnl|CDD|238260 cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the
shikimate pathway, a seven-step biosynthetic pathway
which converts erythrose-4-phosphate to chorismic acid,
found in bacteria, fungi and plants. Chorismic acid is a
important intermediate in the synthesis of aromatic
compounds, such as aromatic amino acids, p-aminobenzoic
acid, folate and ubiquinone. Shikimate kinase catalyses
the phosphorylation of the 3-hydroxyl group of shikimic
acid using ATP.
Length = 154
Score = 36.8 bits (86), Expect = 0.004
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFINLD 232
I+L G G GKT + + AK + F++LD
Sbjct: 2 IVLIGMMGAGKTTVGRLLAKALGLPFVDLD 31
>gnl|CDD|140006 PRK13949, PRK13949, shikimate kinase; Provisional.
Length = 169
Score = 37.0 bits (86), Expect = 0.005
Identities = 16/30 (53%), Positives = 20/30 (66%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFINLD 232
I L G G GKT + KA A+E +SFI+LD
Sbjct: 4 IFLVGYMGAGKTTLGKALARELGLSFIDLD 33
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 36.1 bits (83), Expect = 0.005
Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 4/71 (5%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFINLD----ISTLTDKLYGESPKLATAIFSLAEKI 258
IL+ GPPG GK+ +AK A++ + I+LD L + GE + + L E +
Sbjct: 2 ILITGPPGSGKSTLAKKLAEKLGIPVISLDDLLREEGLAELDDGELDDIDIDLELLEEIL 61
Query: 259 QPCIIFIDEID 269
ID
Sbjct: 62 DELAKQEWVID 72
>gnl|CDD|219014 pfam06414, Zeta_toxin, Zeta toxin. This family consists of several
bacterial zeta toxin proteins. Zeta toxin is thought to
be part of a postregulational killing system in
bacteria. It relies on antitoxin/toxin systems that
secure stable inheritance of low and medium copy number
plasmids during cell division and kill cells that have
lost the plasmid.
Length = 191
Score = 36.9 bits (86), Expect = 0.006
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 200 PKGILLYGPPGCGKTMIAKATAKE-ANVSFINLD 232
P +LL G PG GKT +A+A +E + + +D
Sbjct: 12 PVAVLLGGQPGAGKTELARALLEELGGGNVVRID 45
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 37.6 bits (88), Expect = 0.007
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 201 KGILLYGPPGCGKTMIAK 218
+LL GPPG GKTM+A
Sbjct: 199 HNLLLVGPPGTGKTMLAS 216
>gnl|CDD|224337 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and
secretion].
Length = 407
Score = 37.3 bits (87), Expect = 0.008
Identities = 39/134 (29%), Positives = 55/134 (41%), Gaps = 33/134 (24%)
Query: 182 IFPMKNRNLLK---ESGLLKPPKGILLYGPPGCGKTM-IAKATA------KEANVSFINL 231
F K R LL E+ +++ + I L GP G GKT +AK A K+ V+ I
Sbjct: 182 YFSEKLRKLLLSLIENLIVEQKRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITT 241
Query: 232 D---------ISTLTDKL-----YGESPK-LATAIFSLAEKIQPCIIFIDEIDSLLRSRS 276
D + T D + SPK LA AI +L + +I +D RS
Sbjct: 242 DTYRIGAVEQLKTYADIMGVPLEVVYSPKELAEAIEALRDCD---VILVDTA-----GRS 293
Query: 277 SSDHEATAQLKSIF 290
D E +LK +
Sbjct: 294 QYDKEKIEELKELI 307
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 36.9 bits (86), Expect = 0.012
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 201 KGILLYGPPGCGKTMIAKATAKE 223
+GIL+ GPPG GKT +A A+E
Sbjct: 66 RGILIVGPPGTGKTALAMGIARE 88
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 36.0 bits (84), Expect = 0.020
Identities = 21/57 (36%), Positives = 26/57 (45%), Gaps = 14/57 (24%)
Query: 167 IAGLEHIKKELNQSVIFPMKNRNLLKESGLLKPPKGILLYGPPGCGKTMIAKATAKE 223
I G E I + L V K +N+ P +L GPPG GKT A A A+E
Sbjct: 19 IVGQEEIVERLKSYV----KEKNM---------PH-LLFAGPPGTGKTTAALALARE 61
>gnl|CDD|216186 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family are
found in a variety of single stranded RNA viruses.
Length = 105
Score = 34.1 bits (79), Expect = 0.021
Identities = 13/21 (61%), Positives = 16/21 (76%)
Query: 203 ILLYGPPGCGKTMIAKATAKE 223
I LYGPPGCGK+ +AK A+
Sbjct: 1 IWLYGPPGCGKSTLAKYLARA 21
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 154
Score = 34.9 bits (80), Expect = 0.022
Identities = 17/94 (18%), Positives = 31/94 (32%), Gaps = 11/94 (11%)
Query: 199 PPKGILLYGPPGCGKTMIAKATAKEANVSFINLDISTLTDKLYGESPKLATAIFSLAEKI 258
P +LL GP G GKT + + + V+ D + + A+ L ++
Sbjct: 23 GPPSVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERNPPYA-----FSQALRELLRQL 77
Query: 259 QPCIIFIDEIDSLLRSRSSSDHEATAQLKSIFLS 292
+ E+ + L + A L
Sbjct: 78 ------LRELAAELLLLREALLAALGAELIEGLQ 105
>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus. This family consists of the
C-terminal region of several eukaryotic and archaeal
RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin
or TIP49b) proteins. The N-terminal domain contains the
pfam00004 domain. In zebrafish, the liebeskummer (lik)
mutation, causes development of hyperplastic embryonic
hearts. lik encodes Reptin, a component of a
DNA-stimulated ATPase complex. Beta-catenin and Pontin,
a DNA-stimulated ATPase that is often part of complexes
with Reptin, are in the same genetic pathways. The
Reptin/Pontin ratio serves to regulate heart growth
during development, at least in part via the
beta-catenin pathway. TBP-interacting protein 49 (TIP49)
was originally identified as a TBP-binding protein, and
two related proteins are encoded by individual genes,
tip49a and b. Although the function of this gene family
has not been elucidated, they are supposed to play a
critical role in nuclear events because they interact
with various kinds of nuclear factors and have DNA
helicase activities.TIP49a has been suggested to act as
an autoantigen in some patients with autoimmune
diseases.
Length = 395
Score = 36.1 bits (84), Expect = 0.022
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 201 KGILLYGPPGCGKTMIAKATAKE 223
+ +L+ GPPG GKT +A A +KE
Sbjct: 51 RAVLIAGPPGTGKTALAIAISKE 73
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 35.8 bits (83), Expect = 0.026
Identities = 20/101 (19%), Positives = 37/101 (36%), Gaps = 22/101 (21%)
Query: 200 PKGILLYGPPGCGKTMIAKATAKEANVSFINLDISTLTDKLYGESPKLATAIFSLAEKIQ 259
P I++YGP G GKT K +E S N+++ + ++ + I + K+
Sbjct: 42 PSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNKLGKVP 101
Query: 260 PC----------------------IIFIDEIDSLLRSRSSS 278
I+ +DE+D+L+
Sbjct: 102 LTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGEV 142
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a wide
variety of presumed phage proteins.
Length = 201
Score = 35.0 bits (81), Expect = 0.029
Identities = 26/78 (33%), Positives = 36/78 (46%), Gaps = 9/78 (11%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFINLDISTLTDKLYGES------PKLATAIFSLAE 256
+L+YGPPG GKT +AK T F++LD T G++ L + LAE
Sbjct: 6 VLIYGPPGIGKTSLAK-TLPP-KTLFLDLDAGTTKVLSRGDNVDIRSWQDLRDFLDELAE 63
Query: 257 KIQPC-IIFIDEIDSLLR 273
+ + ID I L R
Sbjct: 64 DLAEYDTLVIDTITKLER 81
>gnl|CDD|238979 cd02021, GntK, Gluconate kinase (GntK) catalyzes the phosphoryl
transfer from ATP to gluconate. The resulting product
gluconate-6-phoshate is an important precursor of
gluconate metabolism. GntK acts as a dimmer composed of
two identical subunits.
Length = 150
Score = 34.2 bits (79), Expect = 0.032
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFINLD 232
I++ G G GK+ + KA A+ FI+ D
Sbjct: 2 IVVMGVSGSGKSTVGKALAERLGAPFIDGD 31
>gnl|CDD|223401 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase
[Translation, ribosomal structure and biogenesis].
Length = 308
Score = 35.3 bits (82), Expect = 0.033
Identities = 15/33 (45%), Positives = 19/33 (57%)
Query: 200 PKGILLYGPPGCGKTMIAKATAKEANVSFINLD 232
PK I++ GP GKT +A A AK I+LD
Sbjct: 3 PKLIVIAGPTASGKTALAIALAKRLGGEIISLD 35
>gnl|CDD|236828 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
Provisional.
Length = 758
Score = 35.6 bits (82), Expect = 0.033
Identities = 27/87 (31%), Positives = 42/87 (48%), Gaps = 12/87 (13%)
Query: 204 LLYGPPGCGKTMIAKATAKE----------ANVSFINLDISTLT--DKLYGESPKLATAI 251
LL G G GKT IA+ A A+ + +LDI +L K G+ K A+
Sbjct: 211 LLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKAL 270
Query: 252 FSLAEKIQPCIIFIDEIDSLLRSRSSS 278
E+ I+FIDEI +++ + ++S
Sbjct: 271 LKQLEQDTNSILFIDEIHTIIGAGAAS 297
Score = 28.3 bits (63), Expect = 7.9
Identities = 14/46 (30%), Positives = 19/46 (41%), Gaps = 5/46 (10%)
Query: 198 KPPKGILLYGPPGCGKTMIAKATAKEANVSFINLDISTLTDKLYGE 243
KP L GP G GKT + +K + + D+S Y E
Sbjct: 486 KPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSE-----YME 526
>gnl|CDD|216270 pfam01057, Parvo_NS1, Parvovirus non-structural protein NS1. This
family also contains the NS2 protein. Parvoviruses
encode two non-structural proteins, NS1 and NS2. The
mRNA for NS2 contains the coding sequence for the first
87 amino acids of NS1, then by an alternative splicing
mechanism mRNA from a different reading frame, encoding
the last 78 amino acids, makes up the full length of the
NS2 mRNA. NS1, is the major non-structural protein. It
is essential for DNA replication. It is an 83-kDa
nuclear phosphoprotein. It has DNA helicase and ATPase
activity.
Length = 271
Score = 34.6 bits (80), Expect = 0.049
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 203 ILLYGPPGCGKTMIAKATAK 222
+ YGP GKT +A+A A
Sbjct: 116 VWFYGPASTGKTNLAQAIAH 135
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 35.0 bits (81), Expect = 0.050
Identities = 24/67 (35%), Positives = 36/67 (53%), Gaps = 6/67 (8%)
Query: 204 LLYGPPGCGKTMIAK--ATAKEANVSFINLDISTLTDKLYGESPKLATAIFSLAEKIQPC 261
+LYGPPG GKT +A+ A A+ S +N ++ + D L E + A L +
Sbjct: 56 ILYGPPGVGKTTLARIIANHTRAHFSSLNAVLAGVKD-LRAE---VDRAKERLERHGKRT 111
Query: 262 IIFIDEI 268
I+FIDE+
Sbjct: 112 ILFIDEV 118
>gnl|CDD|222264 pfam13614, AAA_31, AAA domain. This family includes a wide variety
of AAA domains including some that have lost essential
nucleotide binding residues in the P-loop.
Length = 145
Score = 33.3 bits (77), Expect = 0.061
Identities = 20/88 (22%), Positives = 35/88 (39%), Gaps = 8/88 (9%)
Query: 203 ILLYGP-PGCGKTMIAKATAKE-----ANVSFINLDI-STLTDKLYGESPKLATAIFSLA 255
I +Y P G GKT A A+ V +++L+ S G PK + +
Sbjct: 3 IGVYSPVGGEGKTTFALNLAQSLAEEGPKVLYLDLEEYSGDLALFLGLEPKGLSDLLYYL 62
Query: 256 EKIQPCIIF-IDEIDSLLRSRSSSDHEA 282
+++ +I + +D L R+ D
Sbjct: 63 KRLDSMLIQAMGGLDYLAPPRNPEDLRE 90
>gnl|CDD|235244 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 33.6 bits (78), Expect = 0.072
Identities = 9/24 (37%), Positives = 16/24 (66%)
Query: 207 GPPGCGKTMIAKATAKEANVSFIN 230
GPPG GKT +A+ A++ + ++
Sbjct: 7 GPPGSGKTTVARLLAEKLGLKHVS 30
>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 34.2 bits (79), Expect = 0.073
Identities = 30/99 (30%), Positives = 44/99 (44%), Gaps = 17/99 (17%)
Query: 181 VIFPMKNRNLLK---ESGLLKPPKGILLYGPPGCGKTMIAKATAKE--ANVSFIN---LD 232
I P ++ K + G + P +L PG GKT +AKA E A V F+N
Sbjct: 23 CILPAADKETFKSIVKKGRI--PNMLLHSPSPGTGKTTVAKALCNEVGAEVLFVNGSDCR 80
Query: 233 ISTLTDKLYGESPKLATAIFSLAEKIQPCIIFIDEIDSL 271
I + ++L + A+ + SL +I IDE D L
Sbjct: 81 IDFVRNRL----TRFASTV-SLTGG--GKVIIIDEFDRL 112
>gnl|CDD|116340 pfam07726, AAA_3, ATPase family associated with various cellular
activities (AAA). This Pfam entry includes some of the
AAA proteins not detected by the pfam00004 model.
Length = 131
Score = 32.9 bits (76), Expect = 0.077
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSF 228
+LL G PG KT++A+ A+ + F
Sbjct: 2 VLLEGVPGLAKTLLARTLARSLGLDF 27
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 33.9 bits (78), Expect = 0.079
Identities = 23/77 (29%), Positives = 33/77 (42%), Gaps = 13/77 (16%)
Query: 200 PKGILLYGPPGCGKTMIAKATAKEA---NVSFINLDISTLTDKLYGESPKLATAIFSLAE 256
+ ++L GPPG GKT +A A E +S + + L KL K A L E
Sbjct: 105 GENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDLLSKL-----KAAFDEGRLEE 159
Query: 257 KIQPCII-----FIDEI 268
K+ + ID+I
Sbjct: 160 KLLRELKKVDLLIIDDI 176
>gnl|CDD|238978 cd02020, CMPK, Cytidine monophosphate kinase (CMPK) catalyzes the
reversible phosphorylation of cytidine monophosphate
(CMP) to produce cytidine diphosphate (CDP), using ATP
as the preferred phosphoryl donor.
Length = 147
Score = 33.2 bits (77), Expect = 0.083
Identities = 9/24 (37%), Positives = 16/24 (66%)
Query: 207 GPPGCGKTMIAKATAKEANVSFIN 230
GP G GK+ +AK AK+ + +++
Sbjct: 6 GPAGSGKSTVAKLLAKKLGLPYLD 29
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 34.6 bits (79), Expect = 0.085
Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 3/54 (5%)
Query: 185 MKNRNLLKESGLLKPPKGILLYGPPGCGKTMIAKATAKEANVSFINLDISTLTD 238
+ R +L+ + KP ILL G PG GKT + A A++ I +++S TD
Sbjct: 1531 VNLRRVLRAMQVGKP---ILLEGSPGVGKTSLITALARKTGKKLIRINLSEQTD 1581
Score = 28.8 bits (64), Expect = 5.2
Identities = 18/67 (26%), Positives = 27/67 (40%), Gaps = 1/67 (1%)
Query: 172 HIKKELNQSVIFPMKNRNLLKESGLLKPPKGILLYGPPGCGKTMIAKATAKEANVSFINL 231
H+KK + V L KE+ LK I L G G GK+ + E + +
Sbjct: 122 HVKKPEIR-VGTLETLDRLAKEAVDLKIAVPIYLEGGRGSGKSFLISELCDEGGQRIVEI 180
Query: 232 DISTLTD 238
+ +TD
Sbjct: 181 HLREITD 187
>gnl|CDD|224402 COG1485, COG1485, Predicted ATPase [General function prediction
only].
Length = 367
Score = 34.2 bits (79), Expect = 0.091
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 199 PPKGILLYGPPGCGKTM 215
P +G+ L+G G GKTM
Sbjct: 64 PVRGLYLWGGVGRGKTM 80
>gnl|CDD|238549 cd01129, PulE-GspE, PulE/GspE The type II secretory pathway is the
main terminal branch of the general secretory pathway
(GSP). It is responsible for the export the majority of
Gram-negative bacterial exoenzymes and toxins. PulE is a
cytoplasmic protein of the GSP, which contains an ATP
binding site and a tetracysteine motif. This subgroup
also includes PillB and HofB.
Length = 264
Score = 33.8 bits (78), Expect = 0.094
Identities = 21/55 (38%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 185 MKNRNLLKESGLLKPPKGILLY-GPPGCGKTMIAKATAKEANVSFINLDISTLTD 238
+K NL LL+ P GI+L GP G GKT + E N N I T+ D
Sbjct: 64 LKPENLEIFRKLLEKPHGIILVTGPTGSGKTTTLYSALSELNTPEKN--IITVED 116
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 34.5 bits (80), Expect = 0.097
Identities = 15/29 (51%), Positives = 18/29 (62%), Gaps = 2/29 (6%)
Query: 196 LLKPPKG--ILLYGPPGCGKTMIAKATAK 222
L K KG + L GPPG GKT + K+ AK
Sbjct: 344 LTKKLKGPILCLVGPPGVGKTSLGKSIAK 372
>gnl|CDD|235153 PRK03731, aroL, shikimate kinase II; Reviewed.
Length = 171
Score = 33.0 bits (76), Expect = 0.11
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFINLDIS 234
+ L G GCGKT + A A+ F++ D
Sbjct: 5 LFLVGARGCGKTTVGMALAQALGYRFVDTDQW 36
>gnl|CDD|214396 CHL00206, ycf2, Ycf2; Provisional.
Length = 2281
Score = 34.1 bits (78), Expect = 0.11
Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 183 FPMKNRNLLKESGLLKPPKGILLYGPPGCGKTMIAKATAKEANVSFINLDISTLTDK 239
FP + L P +GIL+ G G G++ + K A + V FI + ++ D
Sbjct: 1614 FPSHGKPFSLRLALS-PSRGILVIGSIGTGRSYLVKYLATNSYVPFITVFLNKFLDN 1669
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 33.8 bits (78), Expect = 0.12
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 16/52 (30%)
Query: 204 LLYGPPGCGKTMIAKATAKEANVSFINLDISTLTDKLYGESPKLATAIFSLA 255
L+ GPPG GKT +A A+E LYG+ + F++A
Sbjct: 40 LVQGPPGSGKTAAVRALARE----------------LYGDPWENNFTEFNVA 75
>gnl|CDD|238540 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes
the NTP binding domain of F1 and V1 H+ATPases, DnaB and
related helicases as well as bacterial RecA and related
eukaryotic and archaeal recombinases. This group also
includes bacterial conjugation proteins and related DNA
transfer proteins involved in type II and type IV
secretion.
Length = 165
Score = 32.9 bits (75), Expect = 0.12
Identities = 27/103 (26%), Positives = 43/103 (41%), Gaps = 27/103 (26%)
Query: 203 ILLYGPPGCGKTMIAKATAKEA-----NVSFINLDIST--LTDKLYGESPKLA---TAIF 252
IL++GP G GKT +A A V +++++ LT++L GES K A I
Sbjct: 2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLIIV 61
Query: 253 S-----------------LAEKIQPCIIFIDEIDSLLRSRSSS 278
L E+ +I +DE+ L+R+
Sbjct: 62 FATADDPAAARLLSKAERLRERGGDDLIILDELTRLVRALREI 104
>gnl|CDD|188437 TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA. This
model represents the AAA family ATPase, EccA, of the
actinobacterial flavor of type VII secretion systems.
Species such as Mycobacterium tuberculosis have several
instances of this system per genome, designated EccA1,
EccA2, etc [Protein fate, Protein and peptide secretion
and trafficking].
Length = 557
Score = 33.3 bits (76), Expect = 0.18
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 203 ILLYGPPGCGKTMIAKATAK 222
+L GPPG GKT IA+ AK
Sbjct: 315 MLFAGPPGTGKTTIARVVAK 334
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 31.6 bits (72), Expect = 0.20
Identities = 12/32 (37%), Positives = 16/32 (50%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFINLDIS 234
IL+ G PG GKT +AK A+ +L
Sbjct: 1 ILITGTPGSGKTTLAKELAERLGDVLRDLAKE 32
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 32.9 bits (76), Expect = 0.21
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 198 KPPKGILLYGPPGCGKTMIAKATAKE 223
K + +L YG G GKT ++ AKE
Sbjct: 181 KNNENLLFYGNTGTGKTFLSNCIAKE 206
>gnl|CDD|238544 cd01124, KaiC, KaiC is a circadian clock protein primarily found in
cyanobacteria KaiC is a RecA-like ATPase, having both
Walker A and Walker B motifs. A related protein is found
in archaea.
Length = 187
Score = 32.3 bits (74), Expect = 0.21
Identities = 23/136 (16%), Positives = 34/136 (25%), Gaps = 46/136 (33%)
Query: 203 ILLYGPPGCGKTMIA--------------------------KATAK---------EANVS 227
LL G PG GKT A A+ E
Sbjct: 2 TLLSGGPGTGKTTFALQFLYAGLARGEPGLYVTLEESPEELIENAESLGWDLERLEDEGL 61
Query: 228 FINLDISTLTDKLYGESPKLAT--AIFSLAEKIQPCIIFIDEIDSLLRSRSSSD----HE 281
+D S +L + E+ + + ID + LL S+
Sbjct: 62 LAIVDADPDEIGPAESSLRLELIQRLKDAIEEFKAKRVVIDSVSGLLLMEQSTARLEIRR 121
Query: 282 ATAQLK-----SIFLS 292
LK ++ S
Sbjct: 122 LLFALKRFGVTTLLTS 137
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 33.1 bits (76), Expect = 0.23
Identities = 15/31 (48%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 191 LKESGLLKPPKGILLYGPPGCGKTMIAKATA 221
LKE L + +GIL+ G PG GK+ A+A A
Sbjct: 255 LKER-LEERAEGILIAGAPGAGKSTFAQALA 284
>gnl|CDD|235570 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 32.9 bits (76), Expect = 0.23
Identities = 52/222 (23%), Positives = 90/222 (40%), Gaps = 62/222 (27%)
Query: 129 YEKLKKVGLDVGNKLNTHELKIAANLI--VPEEINGSWKNIAGLEHIKKELNQSVIFPMK 186
Y++LK+ GL K+ L+ +P +W+ + LE + + P++
Sbjct: 167 YKRLKRSGLS-----PEIAEKLLKLLLEHMPPRERTAWRYL--LELLANMI------PVR 213
Query: 187 NRNLLKESGLLKPPKGILLYGPPGCGKTM-IAKATAKEA------NVSFINLD------I 233
++LK+ G+ + L GP G GKT +AK A+ A V+ I LD +
Sbjct: 214 VEDILKQGGV------VALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDTYRIGAV 267
Query: 234 STLTDKLYGE----------SPK-LATAIFSLAEKIQPCIIFIDEIDSLLRSRSSSDHEA 282
L K Y + PK LA A+ L + +I ID RS D
Sbjct: 268 EQL--KTYAKIMGIPVEVVYDPKELAKALEQLRDCD---VILIDTA-----GRSQRDKRL 317
Query: 283 TAQLKSIFLSKWDGLTTDKNIDI-IIMGATNRPDDIDPAIAR 323
+LK+ + + + ID+ +++ AT + +D+
Sbjct: 318 IEELKA-LIEF-----SGEPIDVYLVLSATTKYEDLKDIYKH 353
>gnl|CDD|216360 pfam01202, SKI, Shikimate kinase.
Length = 158
Score = 31.8 bits (73), Expect = 0.26
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 209 PGCGKTMIAKATAKEANVSFINLD 232
G GK+ I + AK + FI+ D
Sbjct: 1 MGAGKSTIGRLLAKALGLPFIDTD 24
>gnl|CDD|129690 TIGR00602, rad24, checkpoint protein rad24. All proteins in this
family for which functions are known are involved in DNA
damage tolerance (likely cell cycle checkpoints).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 = 637
Score = 33.0 bits (75), Expect = 0.26
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 198 KPPKGILLYGPPGCGKTMIAKATAKEANVSFI 229
P + +L+ GP GCGK+ K +KE +
Sbjct: 108 APKRILLITGPSGCGKSTTIKILSKELGIQVQ 139
>gnl|CDD|215599 PLN03140, PLN03140, ABC transporter G family member; Provisional.
Length = 1470
Score = 32.9 bits (75), Expect = 0.28
Identities = 16/33 (48%), Positives = 22/33 (66%), Gaps = 1/33 (3%)
Query: 190 LLKE-SGLLKPPKGILLYGPPGCGKTMIAKATA 221
+LK+ SG++KP + LL GPP GKT + A A
Sbjct: 180 ILKDASGIIKPSRMTLLLGPPSSGKTTLLLALA 212
>gnl|CDD|233355 TIGR01313, therm_gnt_kin, carbohydrate kinase, thermoresistant
glucokinase family. This model represents a subfamily
of proteins that includes thermoresistant and
thermosensitve isozymes of gluconate kinase
(gluconokinase) in E. coli and other related proteins;
members of this family are often named by similarity to
the thermostable isozyme. These proteins show homology
to shikimate kinases and adenylate kinases but not to
gluconate kinases from the FGGY family of carbohydrate
kinases.
Length = 163
Score = 31.6 bits (72), Expect = 0.30
Identities = 12/30 (40%), Positives = 14/30 (46%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFINLD 232
+L G G GK+ IA A A FI D
Sbjct: 1 FVLMGVAGSGKSTIASALAHRLGAKFIEGD 30
>gnl|CDD|217429 pfam03215, Rad17, Rad17 cell cycle checkpoint protein.
Length = 490
Score = 32.7 bits (74), Expect = 0.31
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFI 229
+LL GP GCGK+ K +KE + I
Sbjct: 48 LLLTGPSGCGKSTTVKVLSKELGIEII 74
>gnl|CDD|224027 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 179
Score = 31.5 bits (72), Expect = 0.32
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFIN 230
I + G PG GKT +A+ A+ + ++
Sbjct: 3 ITISGLPGSGKTTVARELAEHLGLKLVS 30
>gnl|CDD|235335 PRK05057, aroK, shikimate kinase I; Reviewed.
Length = 172
Score = 31.6 bits (72), Expect = 0.32
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 201 KGILLYGPPGCGKTMIAKATAKEANVSFINLD 232
+ I L GP G GK+ I + A++ N+ F + D
Sbjct: 5 RNIFLVGPMGAGKSTIGRQLAQQLNMEFYDSD 36
>gnl|CDD|233761 TIGR02173, cyt_kin_arch, cytidylate kinase, putative. Proteins in
this family are believed to be cytidylate kinase.
Members of this family are found in the archaea and in
spirochaetes, and differ considerably from the common
bacterial form of cytidylate kinase described by
TIGR00017.
Length = 171
Score = 31.6 bits (72), Expect = 0.32
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFI 229
I + GPPG GKT +AK A++ ++ I
Sbjct: 3 ITISGPPGSGKTTVAKILAEKLSLKLI 29
>gnl|CDD|220642 pfam10236, DAP3, Mitochondrial ribosomal death-associated protein
3. This is a family of conserved proteins which were
originally described as death-associated-protein-3
(DAP-3). The proteins carry a P-loop DNA-binding motif,
and induce apoptosis. DAP3 has been shown to be a
pro-apoptotic factor in the mitochondrial matrix and to
be crucial for mitochondrial biogenesis and so has also
been designated as MRP-S29 (mitochondrial ribosomal
protein subunit 29).
Length = 274
Score = 32.2 bits (74), Expect = 0.35
Identities = 9/27 (33%), Positives = 13/27 (48%)
Query: 189 NLLKESGLLKPPKGILLYGPPGCGKTM 215
LKE+ K +L G G GK++
Sbjct: 12 KKLKEADASKKVVRFVLTGERGSGKSV 38
>gnl|CDD|215651 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
nucleotide-binding domain. This family includes the ATP
synthase alpha and beta subunits, the ATP synthase
associated with flagella and the termination factor Rho.
Length = 213
Score = 31.7 bits (73), Expect = 0.35
Identities = 9/29 (31%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 203 ILLYGPPGCGKTMIAKATAK--EANVSFI 229
I ++G G GKT++ A+ +A+V +
Sbjct: 18 IGIFGGSGTGKTVLLGMIARNAKADVVEV 46
>gnl|CDD|222927 PHA02774, PHA02774, E1; Provisional.
Length = 613
Score = 32.6 bits (75), Expect = 0.36
Identities = 21/64 (32%), Positives = 28/64 (43%), Gaps = 19/64 (29%)
Query: 159 EINGSWKNIA------GLEHIKKELNQSVIFPMKNRNLLKESGLLKPPKG-ILLYGPPGC 211
E G WK I G+E I F ++ LK G P K +++YGPP
Sbjct: 398 EGEGDWKPIVKFLRYQGVEFI--------SFLTALKDFLK--G--IPKKNCLVIYGPPDT 445
Query: 212 GKTM 215
GK+M
Sbjct: 446 GKSM 449
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 32.1 bits (74), Expect = 0.38
Identities = 15/31 (48%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 191 LKESGLLKPPKGILLYGPPGCGKTMIAKATA 221
LKE L + +GIL+ G PG GK+ A+A A
Sbjct: 249 LKER-LEERAEGILIAGAPGAGKSTFAQALA 278
>gnl|CDD|215967 pfam00519, PPV_E1_C, Papillomavirus helicase. This protein is a
DNA helicase that is required for initiation of viral
DNA replication. This protein forms a complex with the
E2 protein pfam00508.
Length = 432
Score = 32.1 bits (74), Expect = 0.39
Identities = 20/64 (31%), Positives = 27/64 (42%), Gaps = 19/64 (29%)
Query: 159 EINGSWKNIA------GLEHIKKELNQSVIFPMKNRNLLKESGLLKPPKG-ILLYGPPGC 211
E G WK I G+E I F ++ LK P K +++YGPP
Sbjct: 226 EGEGDWKPIVKFLRYQGIEFI--------SFLSALKDFLKG----IPKKNCLVIYGPPDT 273
Query: 212 GKTM 215
GK+M
Sbjct: 274 GKSM 277
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 32.3 bits (74), Expect = 0.40
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 203 ILLYGPPGCGKTMIAKATA 221
+++ G PG GK+M+AKA A
Sbjct: 53 VMMIGSPGTGKSMLAKAMA 71
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. ABC transporters are a large
family of proteins involved in the transport of a wide
variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and GTP-binding
and hydrolyzing proteins.
Length = 157
Score = 31.1 bits (71), Expect = 0.43
Identities = 30/148 (20%), Positives = 54/148 (36%), Gaps = 35/148 (23%)
Query: 197 LKPPKG--ILLYGPPGCGKTMIAKATAKEANVS-----FINLDISTLTDKLY-------- 241
L G + L GP G GK+ + +A A + DI+ L +
Sbjct: 20 LTLKAGEIVALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAKLPLEELRRRIGYVP 79
Query: 242 ----GESPKLATAIFSLAEKIQPCIIFIDEIDSLLRSRSSSDHEATAQLKSIFLSKWDGL 297
G+ ++A A +L P ++ +DE S L D + +L +
Sbjct: 80 QLSGGQRQRVALAR-ALLL--NPDLLLLDEPTSGL------DPASRERLLELLRE----- 125
Query: 298 TTDKNIDIIIMGATNRPDDIDPAIARRM 325
++ +II T+ P+ + A R +
Sbjct: 126 LAEEGRTVII--VTHDPELAELAADRVI 151
>gnl|CDD|134335 PRK00625, PRK00625, shikimate kinase; Provisional.
Length = 173
Score = 31.3 bits (71), Expect = 0.43
Identities = 19/49 (38%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 201 KGILLYGPPGCGKTMIAKATAKEANVSFINLD---ISTLTDKLYGESPK 246
I L G P GKT KA AK ++ F + D +S LY SPK
Sbjct: 1 MQIFLCGLPTVGKTSFGKALAKFLSLPFFDTDDLIVSNYHGALY-SSPK 48
>gnl|CDD|222307 pfam13671, AAA_33, AAA domain. This family of domains contain only
a P-loop motif, that is characteristic of the AAA
superfamily. Many of the proteins in this family are
just short fragments so there is no Walker B motif.
Length = 143
Score = 30.7 bits (70), Expect = 0.44
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFINLDISTLTDKLYGESPK 246
IL+ G PG GK+ A+ +E ++ D TL +L G+ P
Sbjct: 2 ILMVGLPGSGKSTFARRLLRELGAVVLSSD--TLRKRLRGDGPP 43
>gnl|CDD|179660 PRK03839, PRK03839, putative kinase; Provisional.
Length = 180
Score = 30.8 bits (70), Expect = 0.57
Identities = 12/41 (29%), Positives = 21/41 (51%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFINLDISTLTDKLYGE 243
I + G PG GKT ++K A++ +++L L + E
Sbjct: 3 IAITGTPGVGKTTVSKLLAEKLGYEYVDLTEFALKKGIGEE 43
>gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal
end matches very strongly a pfam Mg_chelatase domain
[Unknown function, General].
Length = 499
Score = 31.7 bits (72), Expect = 0.57
Identities = 11/16 (68%), Positives = 14/16 (87%)
Query: 203 ILLYGPPGCGKTMIAK 218
+LL+GPPG GKTM+A
Sbjct: 214 LLLFGPPGSGKTMLAS 229
>gnl|CDD|238687 cd01393, recA_like, RecA is a bacterial enzyme which has roles in
homologous recombination, DNA repair, and the induction
of the SOS response. RecA couples ATP hydrolysis to DNA
strand exchange. While prokaryotes have a single RecA
protein, eukaryotes have multiple RecA homologs such as
Rad51, DMC1 and Rad55/57. Archaea have the RecA-like
homologs radA and radB.
Length = 226
Score = 31.0 bits (71), Expect = 0.64
Identities = 10/27 (37%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 200 PKGIL--LYGPPGCGKTMIAKATAKEA 224
P G + ++G G GKT + A EA
Sbjct: 17 PTGRITEIFGEFGSGKTQLCLQLAVEA 43
>gnl|CDD|238688 cd01394, radB, RadB. The archaeal protein radB shares similarity
radA, the archaeal functional homologue to the bacterial
RecA. The precise function of radB is unclear.
Length = 218
Score = 30.9 bits (70), Expect = 0.64
Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 5/31 (16%)
Query: 205 LYGPPGCGKTMIAKATAKEA-----NVSFIN 230
+YGPPG GKT IA A E V++I+
Sbjct: 24 VYGPPGTGKTNIAIQLAVETAGQGKKVAYID 54
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 31.1 bits (71), Expect = 0.66
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 202 GILLYGPPGCGKTMIAKATAKE 223
G+LL+G G GKT +A A E
Sbjct: 116 GLLLWGSVGTGKTYLAACIANE 137
>gnl|CDD|183044 PRK11231, fecE, iron-dicitrate transporter ATP-binding subunit;
Provisional.
Length = 255
Score = 31.1 bits (71), Expect = 0.69
Identities = 16/55 (29%), Positives = 22/55 (40%), Gaps = 7/55 (12%)
Query: 197 LKPPKG--ILLYGPPGCGKTMIAKA-----TAKEANVSFINLDISTLTDKLYGES 244
L P G L GP GCGK+ + K T + V + IS L+ +
Sbjct: 23 LSLPTGKITALIGPNGCGKSTLLKCFARLLTPQSGTVFLGDKPISMLSSRQLARR 77
>gnl|CDD|232966 TIGR00416, sms, DNA repair protein RadA. The gene protuct codes
for a probable ATP-dependent protease involved in both
DNA repair and degradation of proteins, peptides,
glycopeptides. Also known as sms. Residues 11-28 of the
SEED alignment contain a putative Zn binding domain.
Residues 110-117 of the seed contain a putative ATP
binding site both documented in Haemophilus and in
Listeria monocytogenes. for E.coli see ( J. BACTERIOL.
178:5045-5048(1996)) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 454
Score = 31.3 bits (71), Expect = 0.70
Identities = 30/126 (23%), Positives = 48/126 (38%), Gaps = 22/126 (17%)
Query: 203 ILLYGPPGCGK-TMIAKATAK-------------EANVSFINLDISTL---TDKLYGESP 245
IL+ G PG GK T++ + + E ++ I + L LY S
Sbjct: 97 ILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVSGEESLQQIKMRAIRLGLPEPNLYVLSE 156
Query: 246 KLATAIFSLAEKIQPCIIFIDEIDSLLRSRSSSDHEATAQLKSI--FLSKWDGLTTDKNI 303
I + E+ P ID I +L SS + +Q++ L + L + I
Sbjct: 157 TNWEQICANIEEENPQACVIDSIQTLYSPDISSAPGSVSQVRECTAELMR---LAKTRGI 213
Query: 304 DIIIMG 309
I I+G
Sbjct: 214 AIFIVG 219
>gnl|CDD|240262 PTZ00088, PTZ00088, adenylate kinase 1; Provisional.
Length = 229
Score = 30.9 bits (70), Expect = 0.75
Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 197 LKPPKGILLYGPPGCGKTMIAKATAKEANVSFINLDISTLTDKLYGESP 245
LK P I+L+G PG GK A+ +K+ N+ IN+ + L +++ ++
Sbjct: 3 LKGPLKIVLFGAPGVGKGTFAEILSKKENLKHINMG-NILREEIKAKTT 50
>gnl|CDD|238713 cd01428, ADK, Adenylate kinase (ADK) catalyzes the reversible
phosphoryl transfer from adenosine triphosphates (ATP)
to adenosine monophosphates (AMP) and to yield adenosine
diphosphates (ADP). This enzyme is required for the
biosynthesis of ADP and is essential for homeostasis of
adenosine phosphates.
Length = 194
Score = 30.7 bits (70), Expect = 0.79
Identities = 13/28 (46%), Positives = 17/28 (60%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFIN 230
ILL GPPG GK A+ AK+ + I+
Sbjct: 2 ILLLGPPGSGKGTQAERLAKKYGLPHIS 29
>gnl|CDD|213213 cd03246, ABCC_Protease_Secretion, ATP-binding cassette domain of
PrtD, subfamily C. This family represents the ABC
component of the protease secretion system PrtD, a
60-kDa integral membrane protein sharing 37% identity
with HlyB, the ABC component of the alpha-hemolysin
secretion pathway, in the C-terminal domain. They export
degradative enzymes by using a type I protein secretion
system and lack an N-terminal signal peptide, but
contain a C-terminal secretion signal. The Type I
secretion apparatus is made up of three components, an
ABC transporter, a membrane fusion protein (MFP), and an
outer membrane protein (OMP). For the HlyA transporter
complex, HlyB (ABC transporter) and HlyD (MFP) reside in
the inner membrane of E. coli. The OMP component is
TolC, which is thought to interact with the MFP to form
a continuous channel across the periplasm from the
cytoplasm to the exterior. HlyB belongs to the family of
ABC transporters, which are ubiquitous, ATP-dependent
transmembrane pumps or channels. The spectrum of
transport substrates ranges from inorganic ions,
nutrients such as amino acids, sugars, or peptides,
hydrophobic drugs, to large polypeptides, such as HlyA.
Length = 173
Score = 30.3 bits (69), Expect = 0.80
Identities = 28/123 (22%), Positives = 45/123 (36%), Gaps = 28/123 (22%)
Query: 178 NQSVIFPMKNRNLLKESGL-LKPPKGILLYGPPGCGKTMIAKATA-----KEANVSFINL 231
N S +P +L+ ++P + + + GP G GK+ +A+ V
Sbjct: 5 NVSFRYPGAEPPVLRNVSFSIEPGESLAIIGPSGSGKSTLARLILGLLRPTSGRVRLDGA 64
Query: 232 DISTLTDKLYGE------------SPKLATAIFS--------LAEKI--QPCIIFIDEID 269
DIS G+ S +A I S LA + P I+ +DE +
Sbjct: 65 DISQWDPNELGDHVGYLPQDDELFSGSIAENILSGGQRQRLGLARALYGNPRILVLDEPN 124
Query: 270 SLL 272
S L
Sbjct: 125 SHL 127
>gnl|CDD|238554 cd01134, V_A-ATPase_A, V/A-type ATP synthase catalytic subunit A.
These ATPases couple ATP hydrolysis to the build up of a
H+ gradient, but V-type ATPases do not catalyze the
reverse reaction. The Vacuolar (V-type) ATPase is found
in the membranes of vacuoles, the golgi apparatus and in
other coated vesicles in eukaryotes. Archaea have a
protein which is similar in sequence to V-ATPases, but
functions like an F-ATPase (called A-ATPase). A similar
protein is also found in a few bacteria.
Length = 369
Score = 30.7 bits (70), Expect = 0.97
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 207 GPPGCGKTMIAKATAKEANVSFI 229
GP GCGKT+I ++ +K +N +
Sbjct: 164 GPFGCGKTVIQQSLSKYSNSDIV 186
>gnl|CDD|225369 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA
replication, recombination, and repair].
Length = 515
Score = 30.8 bits (70), Expect = 1.1
Identities = 19/63 (30%), Positives = 27/63 (42%), Gaps = 13/63 (20%)
Query: 163 SWKNIAGLEHIKKELNQSVIFPMKNRNLLKESGLLKPPKGILLYGPPGCGKTMIAKATAK 222
++ ++ G EH+ K L N L+ + L GP G GKT IA+ AK
Sbjct: 14 TFDDVVGQEHVVKTL----------SNALENG---RIAHAYLFSGPRGVGKTTIARILAK 60
Query: 223 EAN 225
N
Sbjct: 61 ALN 63
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 30.7 bits (69), Expect = 1.3
Identities = 19/56 (33%), Positives = 23/56 (41%), Gaps = 13/56 (23%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFINLDISTLTDKLYGESPKLATAIFSLAEKI 258
+LL GPPG GKTM+A I+ L L E + AI SL
Sbjct: 213 LLLIGPPGTGKTMLASR-------------INGLLPDLSNEEALESAAILSLVNAE 255
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 29.8 bits (68), Expect = 1.3
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 203 ILLYGPPGCGKTMIAKATAK 222
I++ G P GKT + +A A
Sbjct: 2 IVITGGPSTGKTTLLEALAA 21
>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 30.3 bits (69), Expect = 1.4
Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 188 RNLLKESGLLKPPKGILLYGPPGCGKTMIAKATAKEANVSFINL 231
+ + + G P + +YG G GKT + +A EA + N
Sbjct: 103 KAVAENPGGAYNP--LFIYGGVGLGKTHLLQAIGNEALANGPNA 144
>gnl|CDD|233120 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
This model represents a set of proteins with extensive
C-terminal homology to the ATP-dependent protease La,
product of the lon gene of E. coli. The model is based
on a seed alignment containing only archaeal members,
but several bacterial proteins match the model well.
Because several species, including Thermotoga maritima
and Treponema pallidum, contain both a close homolog of
the lon protease and nearly full-length homolog of the
members of this family, we suggest there may also be a
functional division between the two families. Members of
this family from Pyrococcus horikoshii and Pyrococcus
abyssi each contain a predicted intein [Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 608
Score = 30.6 bits (69), Expect = 1.4
Identities = 13/25 (52%), Positives = 18/25 (72%)
Query: 198 KPPKGILLYGPPGCGKTMIAKATAK 222
K + +LL G PG GK+M+AKA A+
Sbjct: 35 KQKRNVLLIGEPGVGKSMLAKAMAE 59
>gnl|CDD|234203 TIGR03420, DnaA_homol_Hda, DnaA regulatory inactivator Hda.
Members of this protein family are Hda (Homologous to
DnaA). These proteins are about half the length of DnaA
and homologous over length of Hda. In the model species
Escherichia coli, the initiation of DNA replication
requires DnaA bound to ATP rather than ADP; Hda helps
facilitate the conversion of DnaA-ATP to DnaA-ADP [DNA
metabolism, DNA replication, recombination, and repair].
Length = 226
Score = 29.9 bits (68), Expect = 1.5
Identities = 14/72 (19%), Positives = 32/72 (44%), Gaps = 13/72 (18%)
Query: 203 ILLYGPPGCGKTMIAKA---TAKEANVSFINLDISTLTDKLYGESPKLATAIFSLAEKIQ 259
+ L+G G GK+ + +A A+E S I L + E + + E+
Sbjct: 41 LYLWGESGSGKSHLLQAACAAAEERGKSAIYLPL--------AELAQADPEVLEGLEQAD 92
Query: 260 PCIIFIDEIDSL 271
++ +D+++++
Sbjct: 93 --LVCLDDVEAI 102
>gnl|CDD|131688 TIGR02640, gas_vesic_GvpN, gas vesicle protein GvpN. Members of
this family are the GvpN protein associated with the
production of gas vesicles produced in some prokaryotes
to give cells buoyancy. This family belongs to a larger
family of ATPases (pfam07728) [Cellular processes,
Other].
Length = 262
Score = 30.1 bits (68), Expect = 1.6
Identities = 19/59 (32%), Positives = 25/59 (42%), Gaps = 2/59 (3%)
Query: 187 NRNLLKESGLLKPPKGILLYGPPGCGKTMIAKATAKEAN--VSFINLDISTLTDKLYGE 243
R + LK + L GP G GKT +A A++ + V IN D T L G
Sbjct: 8 KRVTSRALRYLKSGYPVHLRGPAGTGKTTLAMHVARKRDRPVMLINGDAELTTSDLVGS 66
>gnl|CDD|235638 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau;
Validated.
Length = 605
Score = 30.2 bits (68), Expect = 1.6
Identities = 22/63 (34%), Positives = 27/63 (42%), Gaps = 13/63 (20%)
Query: 163 SWKNIAGLEHIKKELNQSVIFPMKNRNLLKESGLLKPPKGILLYGPPGCGKTMIAKATAK 222
++K I G E IKK L ++ N K + GP G GKT IAK AK
Sbjct: 14 NFKQIIGQELIKKILVNAI-----LNN--------KLTHAYIFSGPRGIGKTSIAKIFAK 60
Query: 223 EAN 225
N
Sbjct: 61 AIN 63
>gnl|CDD|233793 TIGR02237, recomb_radB, DNA repair and recombination protein RadB.
This family consists exclusively of archaeal RadB
protein, a homolog of bacterial RecA (TIGR02012),
eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and
archaeal RadA (TIGR02236).
Length = 209
Score = 29.7 bits (67), Expect = 1.6
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 7/37 (18%)
Query: 201 KGIL--LYGPPGCGKTMIAKATAKEA-----NVSFIN 230
+G + +YGPPG GKT I A A V +I+
Sbjct: 11 RGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYID 47
>gnl|CDD|225363 COG2804, PulE, Type II secretory pathway, ATPase PulE/Tfp pilus
assembly pathway, ATPase PilB [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 500
Score = 30.4 bits (69), Expect = 1.7
Identities = 22/70 (31%), Positives = 31/70 (44%), Gaps = 4/70 (5%)
Query: 170 LEHIKKELNQSVIFPMKNRNLLKESGLLKPPKGILLY-GPPGCGKTMIAKATAKEANVSF 228
L+ + L+ + M L + LL P+G++L GP G GKT A E N
Sbjct: 228 LDKDQVILDLEKL-GMSPFQLARLLRLLNRPQGLILVTGPTGSGKTTTLYAALSELNTPE 286
Query: 229 INLDISTLTD 238
N I T+ D
Sbjct: 287 RN--IITIED 294
>gnl|CDD|218685 pfam05673, DUF815, Protein of unknown function (DUF815). This
family consists of several bacterial proteins of unknown
function.
Length = 248
Score = 29.8 bits (68), Expect = 1.7
Identities = 26/108 (24%), Positives = 43/108 (39%), Gaps = 23/108 (21%)
Query: 163 SWKNIAGLEHIKKELNQSVIFPMKN-RNLLKESGLLKPPKGILLYGPPGCGKTMIAKATA 221
++ G++ K+ L ++N L GL P +LL+G G GK+ + KA
Sbjct: 26 DLDDLVGIDRQKEAL-------LRNTEQFLA--GL--PANNVLLWGARGTGKSSLVKALL 74
Query: 222 KE---ANVSFINLDISTLTDKLYGESPKLATAIFSLAEKIQPCIIFID 266
E + I +D L D L P + + + I+F D
Sbjct: 75 NEYADQGLRLIEVDKDDLGD-L----PDIVDLLRGRPYR---FILFCD 114
>gnl|CDD|226970 COG4619, COG4619, ABC-type uncharacterized transport system, ATPase
component [General function prediction only].
Length = 223
Score = 29.8 bits (67), Expect = 1.7
Identities = 13/41 (31%), Positives = 20/41 (48%), Gaps = 5/41 (12%)
Query: 197 LKPPKGILLYGPPGCGKTMIAKATAKEANVSFINLDISTLT 237
++ + I + GP GCGK+ + K A S I+ TL
Sbjct: 26 VRAGEFIAITGPSGCGKSTLLKIVA-----SLISPTSGTLL 61
>gnl|CDD|223544 COG0468, RecA, RecA/RadA recombinase [DNA replication,
recombination, and repair].
Length = 279
Score = 29.9 bits (68), Expect = 1.8
Identities = 10/27 (37%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 200 PKGIL--LYGPPGCGKTMIAKATAKEA 224
P+G + +YGP GKT +A A
Sbjct: 58 PRGRITEIYGPESSGKTTLALQLVANA 84
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 30.0 bits (68), Expect = 1.8
Identities = 35/163 (21%), Positives = 55/163 (33%), Gaps = 46/163 (28%)
Query: 128 AYEKLKKVGLDVGNKLNTHELKIAANLIVPEEINGSWKNIAGLEHIKKELNQSVIFPMKN 187
E+L + G+ ++ L + +W+ + E ++ L
Sbjct: 140 LLERLLEAGVS-----EELARELLEKLPEDLDAEDAWRWL--REALEGMLPVKPE----E 188
Query: 188 RNLLKESGLLKPPKGILLYGPPGCGKT-----MIAKATAKEAN--VSFINLD---IST-- 235
+L+ I L GP G GKT + A+ + V+ I D I
Sbjct: 189 DPILER------GGVIALVGPTGVGKTTTLAKLAARFVLEHGKKKVALITTDTYRIGAVE 242
Query: 236 -LTDKLYGE----------SPK-LATAIFSLAEKIQPCIIFID 266
L K Y E PK LA A+ L +K +I ID
Sbjct: 243 QL--KTYAEILGVPVKVARDPKELAEALDRLRDKD---LILID 280
>gnl|CDD|216619 pfam01637, Arch_ATPase, Archaeal ATPase. This family contain a
conserved P-loop motif that is involved in binding ATP.
This family is almost exclusively found in
archaebacteria and particularly in Methanococcus
jannaschii that encodes sixteen members of this family.
Length = 223
Score = 29.5 bits (67), Expect = 1.8
Identities = 23/137 (16%), Positives = 45/137 (32%), Gaps = 36/137 (26%)
Query: 203 ILLYGPPGCGKTMIAKATAKEAN------VSFINL-DISTLTDKLYGESPKLATAIFSLA 255
I++YGP CGKT + + +E + + L + E+ +LA A+
Sbjct: 23 IVVYGPRRCGKTALLREFLEELRELGYRVIYYDPLRREFEEKLDRFEEAKRLAEALGDAL 82
Query: 256 EKIQP-----------------------CIIFIDEIDSLLRSRSSSDHEATAQLKSIFLS 292
KI I IDE+ + + + L+
Sbjct: 83 PKIGIAKSKLAFLSLTLLFELLKRKGKKIAIIIDEVQYAIGLNGA------ESYVKLLLN 136
Query: 293 KWDGLTTDKNIDIIIMG 309
D + ++ +++ G
Sbjct: 137 LIDYPPKEYHLIVVLCG 153
>gnl|CDD|233087 TIGR00678, holB, DNA polymerase III, delta' subunit. This model
describes the N-terminal half of the delta' subunit of
DNA polymerase III. Delta' is homologous to the gamma
and tau subunits, which form an outgroup for
phylogenetic comparison. The gamma/tau branch of the
tree is much more tighly conserved than the delta'
branch, and some members of that branch score more
highly against this model than some proteins
classisified as delta'. The noise cutoff is set to
detect weakly scoring delta' subunits rather than to
exclude gamma/tau subunits. At position 126-127 of the
seed alignment, this family lacks the HM motif of
gamma/tau; at 132 it has a near-invariant A vs. an
invariant F in gamma/tau [DNA metabolism, DNA
replication, recombination, and repair].
Length = 188
Score = 29.5 bits (67), Expect = 1.8
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 198 KPPKGILLYGPPGCGKTMIAKATAK 222
+ L GP G GK ++A A AK
Sbjct: 12 RLAHAYLFAGPEGVGKELLALALAK 36
>gnl|CDD|215758 pfam00158, Sigma54_activat, Sigma-54 interaction domain.
Length = 168
Score = 29.3 bits (67), Expect = 1.8
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 203 ILLYGPPGCGKTMIAKA 219
+L+ G G GK + A+A
Sbjct: 25 VLITGESGTGKELFARA 41
>gnl|CDD|225327 COG2607, COG2607, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 287
Score = 30.0 bits (68), Expect = 1.8
Identities = 31/134 (23%), Positives = 52/134 (38%), Gaps = 39/134 (29%)
Query: 165 KNIAGLEHIKKELNQSVIFPMKN-RNLLKESGLLKPPKGILLYGPPGCGKTMIAKATAKE 223
++ G++ K+ L ++N + GL P +LL+G G GK+ + KA E
Sbjct: 60 ADLVGVDRQKEAL-------VRNTEQFAE--GL--PANNVLLWGARGTGKSSLVKALLNE 108
Query: 224 ANVSFINL------DISTLTDKLYGESPKLATAIFSLAEKIQPCIIFIDEIDSLLRSRSS 277
+ L D++TL D L L + + I+F D++ S
Sbjct: 109 YADEGLRLVEVDKEDLATLPD-LVEL----------LRARPEKFILFCDDL--------S 149
Query: 278 SDHEATA--QLKSI 289
+ A LKS
Sbjct: 150 FEEGDDAYKALKSA 163
>gnl|CDD|206669 cd01882, BMS1, Bms1, an essential GTPase, promotes assembly of
preribosomal RNA processing complexes. Bms1 is an
essential, evolutionarily conserved, nucleolar protein.
Its depletion interferes with processing of the 35S
pre-rRNA at sites A0, A1, and A2, and the formation of
40S subunits. Bms1, the putative endonuclease Rc11, and
the essential U3 small nucleolar RNA form a stable
subcomplex that is believed to control an early step in
the formation of the 40S subumit. The C-terminal domain
of Bms1 contains a GTPase-activating protein (GAP) that
functions intramolecularly. It is believed that Rc11
activates Bms1 by acting as a guanine-nucleotide
exchange factor (GEF) to promote GDP/GTP exchange, and
that activated (GTP-bound) Bms1 delivers Rc11 to the
preribosomes.
Length = 231
Score = 29.6 bits (67), Expect = 1.9
Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 8/59 (13%)
Query: 184 PMKNRNLLKESGLLKPPKGILLYGPPGCGKTMIAKATAKE---ANVSFINLDISTLTDK 239
P+ +R + PP +++ GPPG GK+ + ++ K N+S I I+ +T K
Sbjct: 28 PVVDRTPEEP-----PPLVVVVVGPPGVGKSTLIRSLIKRYTKQNLSDIKGPITIVTGK 81
>gnl|CDD|110677 pfam01695, IstB_IS21, IstB-like ATP binding protein. This protein
contains an ATP/GTP binding P-loop motif. It is found
associated with IS21 family insertion sequences. The
function of this protein is unknown, but it may perform
a transposase function.
Length = 178
Score = 29.2 bits (66), Expect = 2.0
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 202 GILLYGPPGCGKTMIAKATAKEA 224
+LL GPPG GKT +A A +A
Sbjct: 49 NLLLLGPPGVGKTHLACALGHQA 71
>gnl|CDD|233208 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein. [Transport and binding proteins, Other].
Length = 1394
Score = 30.1 bits (68), Expect = 2.2
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 194 SGLLKPPKGILLYGPPGCGKTMIAKATA 221
GL+KP + ++ G PG G + + K A
Sbjct: 81 DGLIKPGELTVVLGRPGSGCSTLLKTIA 108
>gnl|CDD|213267 cd03300, ABC_PotA_N, ATP-binding cassette domain of the polyamine
transporter. PotA is an ABC-type transporter and the
ATPase component of the
spermidine/putrescine-preferential uptake system
consisting of PotA, -B, -C, and -D. PotA has two domains
with the N-terminal domain containing the ATPase
activity and the residues required for homodimerization
with PotA and heterdimerization with PotB. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds,
like sugars, ions, peptides, and more complex organic
molecules. The nucleotide binding domain shows the
highest similarity between all members of the family.
ABC transporters are a subset of nucleotide hydrolases
that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing proteins.
Length = 232
Score = 29.5 bits (67), Expect = 2.4
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 11/52 (21%)
Query: 170 LEHIKKELNQSVIFPMKNRNLLKESGLLKPPKGILLYGPPGCGKT----MIA 217
LE++ K V + +L + G + L GP GCGKT +IA
Sbjct: 3 LENVSKFYGGFVA--LDGVSLDIKEG-----EFFTLLGPSGCGKTTLLRLIA 47
>gnl|CDD|131251 TIGR02196, GlrX_YruB, Glutaredoxin-like protein, YruB-family. This
glutaredoxin-like protein family contains the conserved
CxxC motif and includes the Clostridium pasteurianum
protein YruB which has been cloned from a rubredoxin
operon. Somewhat related to NrdH, it is unknown whether
this protein actually interacts with
glutathione/glutathione reducatase, or, like NrdH, some
other reductant system.
Length = 74
Score = 27.3 bits (61), Expect = 2.4
Identities = 7/33 (21%), Positives = 13/33 (39%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFINLDIST 235
+ +Y P C AK ++F +D+
Sbjct: 2 VKVYTTPWCPPCKKAKEYLTSKGIAFEEIDVEK 34
>gnl|CDD|182529 PRK10536, PRK10536, hypothetical protein; Provisional.
Length = 262
Score = 29.4 bits (66), Expect = 2.5
Identities = 25/81 (30%), Positives = 36/81 (44%), Gaps = 11/81 (13%)
Query: 158 EEINGSWKNIAGLEHI---KKELNQSVIFPMKNRNLLKESGL--LKPPKGILLYGPPGCG 212
EE S + G+E I + + S I RN + L ++ + I G GCG
Sbjct: 30 EESVTSLVQMGGVEAIGMARDSRDTSPILA---RNEAQAHYLKAIESKQLIFATGEAGCG 86
Query: 213 KTMIAKATAKEANVSFINLDI 233
KT I+ A A EA I+ D+
Sbjct: 87 KTWISAAKAAEA---LIHKDV 104
>gnl|CDD|236333 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau;
Validated.
Length = 709
Score = 29.7 bits (66), Expect = 2.5
Identities = 21/63 (33%), Positives = 28/63 (44%), Gaps = 13/63 (20%)
Query: 163 SWKNIAGLEHIKKELNQSVIFPMKNRNLLKESGLLKPPKGILLYGPPGCGKTMIAKATAK 222
++ ++ G EH+ K L +N L E L LL G G GKT IA+ AK
Sbjct: 14 TFADLVGQEHVVKAL----------QNALDEGRL---HHAYLLTGTRGVGKTTIARILAK 60
Query: 223 EAN 225
N
Sbjct: 61 SLN 63
>gnl|CDD|218719 pfam05729, NACHT, NACHT domain. This NTPase domain is found in
apoptosis proteins as well as those involved in MHC
transcription activation. This family is closely related
to pfam00931.
Length = 165
Score = 28.8 bits (65), Expect = 2.6
Identities = 6/16 (37%), Positives = 10/16 (62%)
Query: 203 ILLYGPPGCGKTMIAK 218
++L G G GKT + +
Sbjct: 3 VILQGEAGSGKTTLLQ 18
>gnl|CDD|233847 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau.
This model represents the well-conserved first ~ 365
amino acids of the translation of the dnaX gene. The
full-length product of the dnaX gene in the model
bacterium E. coli is the DNA polymerase III tau subunit.
A translational frameshift leads to early termination
and a truncated protein subunit gamma, about 1/3 shorter
than tau and present in roughly equal amounts. This
frameshift mechanism is not necessarily universal for
species with DNA polymerase III but appears conserved in
the exterme thermophile Thermus thermophilis [DNA
metabolism, DNA replication, recombination, and repair].
Length = 355
Score = 29.5 bits (67), Expect = 2.7
Identities = 12/22 (54%), Positives = 13/22 (59%)
Query: 204 LLYGPPGCGKTMIAKATAKEAN 225
L GP G GKT IA+ AK N
Sbjct: 40 LFSGPRGTGKTSIARIFAKALN 61
>gnl|CDD|236482 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 29.1 bits (66), Expect = 2.7
Identities = 13/26 (50%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 201 KGIL--LYGPPGCGKTMIAKATAKEA 224
+G + +YGPPG GKT I A EA
Sbjct: 22 RGTITQIYGPPGSGKTNICLQLAVEA 47
>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain.
Length = 285
Score = 29.2 bits (66), Expect = 2.9
Identities = 9/27 (33%), Positives = 13/27 (48%), Gaps = 3/27 (11%)
Query: 196 LLKPPKGIL---LYGPPGCGKTMIAKA 219
LL+ + + G G GKT +AK
Sbjct: 12 LLEMSDNLGVVGIVGMGGVGKTTLAKQ 38
>gnl|CDD|224847 COG1936, COG1936, Predicted nucleotide kinase (related to CMP and
AMP kinases) [Nucleotide transport and metabolism].
Length = 180
Score = 28.8 bits (65), Expect = 2.9
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 203 ILLYGPPGCGKTMIAKATAK 222
I + G PG GKT + K +
Sbjct: 3 IAITGTPGVGKTTVCKLLRE 22
>gnl|CDD|223455 COG0378, HypB, Ni2+-binding GTPase involved in regulation of
expression and maturation of urease and hydrogenase
[Posttranslational modification, protein turnover,
chaperones / Transcription].
Length = 202
Score = 29.1 bits (66), Expect = 2.9
Identities = 20/58 (34%), Positives = 28/58 (48%), Gaps = 7/58 (12%)
Query: 185 MKNRNLLKESGLLKPPKGILLYGPPGCGKT-MIAKATA---KEANVSFINLDISTLTD 238
KN L +++ +P I + GPPG GKT +I K E ++ I DI T D
Sbjct: 1 SKNDRLAEKN---RPMLRIGVGGPPGSGKTALIEKTLRALKDEYKIAVITGDIYTKED 55
>gnl|CDD|163057 TIGR02881, spore_V_K, stage V sporulation protein K. Members of
this protein family are the stage V sporulation protein
K (SpoVK), a close homolog of the Rubisco expression
protein CbbX (TIGR02880) and a members of the ATPase
family associated with various cellular activities
(pfam00004). Members are strictly limited to bacterial
endospore-forming species, but are not universal in this
group and are missing from the Clostridium group
[Cellular processes, Sporulation and germination].
Length = 261
Score = 29.3 bits (66), Expect = 3.0
Identities = 37/118 (31%), Positives = 54/118 (45%), Gaps = 21/118 (17%)
Query: 169 GLEHIK---KELNQSVIFPMKNRNLLKESGLLKPPKGIL---LYGPPGCGKTMIAKATAK 222
GL+ +K KE+ + I + R KE GL K K +L G PG GKT +A+ K
Sbjct: 10 GLDEVKALIKEI-YAWIQINEKR---KEEGL-KTSKQVLHMIFKGNPGTGKTTVARILGK 64
Query: 223 ---EANV----SFINLDISTLTDKLYGESPKLATAIFSLAEKIQPCIIFIDEIDSLLR 273
E NV I ++ + L + G + A + +K ++FIDE SL R
Sbjct: 65 LFKEMNVLSKGHLIEVERADLVGEYIGHT---AQKTREVIKKALGGVLFIDEAYSLAR 119
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 29.3 bits (65), Expect = 3.0
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 201 KGILLYGPPGCGKTMIAKATA 221
K I+L GPPG GKT +A+ A
Sbjct: 195 KNIILQGPPGVGKTFVARRLA 215
>gnl|CDD|226646 COG4178, COG4178, ABC-type uncharacterized transport system,
permease and ATPase components [General function
prediction only].
Length = 604
Score = 29.6 bits (67), Expect = 3.1
Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 187 NRNLLKESGL-LKPPKGILLYGPPGCGKTMIAKATA 221
+ LL E ++P + +L+ G G GKT + +A A
Sbjct: 405 GQTLLSELNFEVRPGERLLITGESGAGKTSLLRALA 440
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 29.3 bits (66), Expect = 3.1
Identities = 8/35 (22%), Positives = 15/35 (42%)
Query: 195 GLLKPPKGILLYGPPGCGKTMIAKATAKEANVSFI 229
+ + ++ P G GKT++A E S +
Sbjct: 50 KNRRTERRGVIVLPTGAGKTVVAAEAIAELKRSTL 84
>gnl|CDD|132351 TIGR03308, phn_thr-fam, phosphonate metabolim protein,
transferase hexapeptide repeat family. This family of
proteins contains copies of the Bacterial transferase
hexapeptide repeat family (pfam00132) and is only found
in operons encoding the phosphonate C-P lyase system
(GenProp0232). Many C-P lyase operons, however, lack a
homolog of this protein.
Length = 204
Score = 28.6 bits (64), Expect = 3.4
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 8/32 (25%)
Query: 47 TRMSEVTVDSDSYLMH--------FGKFATTA 70
TR+ EV + SY+M GKF + A
Sbjct: 32 TRLREVALGDYSYVMRDCDIIYTTIGKFCSIA 63
>gnl|CDD|225804 COG3265, GntK, Gluconate kinase [Carbohydrate transport and
metabolism].
Length = 161
Score = 28.4 bits (64), Expect = 3.6
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 207 GPPGCGKTMIAKATAKEANVSFINLD 232
G G GK+ + A A+ FI+ D
Sbjct: 2 GVSGSGKSTVGSALAERLGAKFIDGD 27
>gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional.
Length = 259
Score = 28.9 bits (65), Expect = 3.7
Identities = 26/80 (32%), Positives = 37/80 (46%), Gaps = 11/80 (13%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFINLDISTLTDKLYGESPKLATAIFS--LAEKIQP 260
I+L GP G GKT +A A EA + I + +T D L +L+TA +Q
Sbjct: 105 IVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTTAADLLL----QLSTAQRQGRYKTTLQR 160
Query: 261 CI-----IFIDEIDSLLRSR 275
+ + IDEI L S+
Sbjct: 161 GVMAPRLLIIDEIGYLPFSQ 180
>gnl|CDD|226372 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 29.0 bits (65), Expect = 3.7
Identities = 18/78 (23%), Positives = 37/78 (47%), Gaps = 8/78 (10%)
Query: 146 HELKIAANLIVPEEINGSWKNIAGLE-HIKKELNQSVIFPMKNRNLLKESGLLKPPKGIL 204
H + +A N+ + E + ++I+ L + +++ P+ L ++G L L
Sbjct: 89 HRVGLAGNVTLEEGKVKTIRDISSLNIRVARQVF-GTANPLIK--DLYQNGWLN----TL 141
Query: 205 LYGPPGCGKTMIAKATAK 222
+ GPP GKT + + A+
Sbjct: 142 IIGPPQVGKTTLLRDIAR 159
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 29.3 bits (65), Expect = 3.7
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 197 LKPPKGILLYGPPGCGKTMIAKATAKEANVSFIN 230
L PP + + GPPG GK+ + ++ + I+
Sbjct: 66 LPPPFIVAVVGPPGTGKSTLIRSLVRRFTKQTID 99
>gnl|CDD|213512 TIGR00174, miaA, tRNA dimethylallyltransferase. Alternate names
include delta(2)-isopentenylpyrophosphate transferase,
IPP transferase, 2-methylthio-N6-isopentyladenosine tRNA
modification enzyme. Catalyzes the first step in the
modification of an adenosine near the anticodon to
2-methylthio-N6-isopentyladenosine. Understanding of
substrate specificity has changed [Protein synthesis,
tRNA and rRNA base modification].
Length = 287
Score = 28.5 bits (64), Expect = 4.3
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 203 ILLYGPPGCGKTMIAKATAKEANVSFINLD 232
I L GP GK+ ++ A++ N I++D
Sbjct: 2 IFLMGPTASGKSQLSIQLAQKLNAEIISVD 31
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 29.1 bits (66), Expect = 4.4
Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 2/20 (10%)
Query: 200 PKG--ILLYGPPGCGKTMIA 217
PKG L+ G G GKT+ A
Sbjct: 29 PKGRPTLVSGTAGTGKTLFA 48
>gnl|CDD|226905 COG4525, TauB, ABC-type taurine transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 259
Score = 28.6 bits (64), Expect = 4.5
Identities = 12/38 (31%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 180 SVIFPMKNRNLLKESGL-LKPPKGILLYGPPGCGKTMI 216
S+ + K R+ L++ L + + +++ GP GCGKT +
Sbjct: 10 SLSYEGKPRSALEDVSLTIASGELVVVLGPSGCGKTTL 47
>gnl|CDD|213199 cd03232, ABCG_PDR_domain2, Second domain of the pleiotropic drug
resistance-like (PDR) subfamily G of ATP-binding
cassette transporters. The pleiotropic drug resistance
(PDR) is a well-described phenomenon occurring in fungi
and shares several similarities with processes in
bacteria and higher eukaryotes. This PDR subfamily
represents domain I of its (ABC-IM)2 organization. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds
including sugars, ions, peptides, and more complex
organic molecules. The nucleotide binding domain shows
the highest similarity between all members of the
family. ABC transporters are a subset of nucleotide
hydrolases that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing proteins.
Length = 192
Score = 28.4 bits (64), Expect = 4.8
Identities = 19/53 (35%), Positives = 22/53 (41%), Gaps = 11/53 (20%)
Query: 163 SWKNIAGLEHIKKELNQSVIFPMKNRNLLKE-SGLLKPPKGILLYGPPGCGKT 214
+WKN LN +V R LL SG +KP L G G GKT
Sbjct: 5 TWKN----------LNYTVPVKGGKRQLLNNISGYVKPGTLTALMGESGAGKT 47
>gnl|CDD|110723 pfam01745, IPT, Isopentenyl transferase. Isopentenyl transferase /
dimethylallyl transferase synthesises
isopentenyladensosine 5'-monophosphate, a cytokinin that
induces shoot formation on host plants infected with the
Ti plasmid.
Length = 232
Score = 28.5 bits (64), Expect = 4.8
Identities = 13/29 (44%), Positives = 15/29 (51%)
Query: 204 LLYGPPGCGKTMIAKATAKEANVSFINLD 232
L++G GKT A A AKE I LD
Sbjct: 5 LIWGATCTGKTAEAIALAKETGWPVIVLD 33
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 28.8 bits (65), Expect = 5.0
Identities = 20/45 (44%), Positives = 24/45 (53%), Gaps = 8/45 (17%)
Query: 195 GLLKP--PKGI-LLYGPPGCGKTMIAKATAK-----EANVSFINL 231
GL P P G+ LL GP G GKT A A A+ E N+ IN+
Sbjct: 588 GLEDPRKPLGVFLLVGPSGVGKTETALALAELLYGGEQNLITINM 632
Score = 28.8 bits (65), Expect = 5.4
Identities = 25/84 (29%), Positives = 35/84 (41%), Gaps = 19/84 (22%)
Query: 204 LLYGPPGCGKTMIAKATAKE----------ANVSFINLDISTLTDKLYGESPK------L 247
+L G G GKT + + A NV ++LD+ L G S K L
Sbjct: 212 ILTGEAGVGKTAVVEGLALRIAAGDVPPALRNVRLLSLDLGLL---QAGASVKGEFENRL 268
Query: 248 ATAIFSLAEKIQPCIIFIDEIDSL 271
+ I + QP I+FIDE +L
Sbjct: 269 KSVIDEVKASPQPIILFIDEAHTL 292
>gnl|CDD|178279 PLN02674, PLN02674, adenylate kinase.
Length = 244
Score = 28.3 bits (63), Expect = 5.6
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 198 KPPKGILLYGPPGCGK 213
KP K ++L GPPG GK
Sbjct: 29 KPDKRLILIGPPGSGK 44
>gnl|CDD|221912 pfam13086, AAA_11, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 220
Score = 28.1 bits (63), Expect = 5.6
Identities = 9/18 (50%), Positives = 10/18 (55%)
Query: 197 LKPPKGILLYGPPGCGKT 214
L L+ GPPG GKT
Sbjct: 14 LSSSDITLIQGPPGTGKT 31
>gnl|CDD|238483 cd00983, recA, RecA is a bacterial enzyme which has roles in
homologous recombination, DNA repair, and the induction
of the SOS response. RecA couples ATP hydrolysis to DNA
strand exchange.
Length = 325
Score = 28.4 bits (64), Expect = 5.8
Identities = 16/37 (43%), Positives = 19/37 (51%), Gaps = 7/37 (18%)
Query: 200 PKG--ILLYGPPGCGKTMIAKATAKEA-----NVSFI 229
PKG I +YGP GKT +A EA V+FI
Sbjct: 53 PKGRIIEIYGPESSGKTTLALHAIAEAQKLGGTVAFI 89
>gnl|CDD|232945 TIGR00376, TIGR00376, DNA helicase, putative. The gene product may
represent a DNA helicase. Eukaryotic members of this
family have been characterized as binding certain
single-stranded G-rich DNA sequences (GGGGT and GGGCT).
A number of related proteins are characterized as
helicases [DNA metabolism, DNA replication,
recombination, and repair].
Length = 637
Score = 28.6 bits (64), Expect = 5.9
Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 20/71 (28%)
Query: 148 LKIAANLIVPEEINGSWKNIAGLEHIKKELNQS----VIFPMKNRNLLKESGLLKPPKGI 203
L+ P + I + LN+S V+F + +++L
Sbjct: 133 LEFILGREAPSKA----SEIHDFQFFDPNLNESQKEAVLFALSSKDLF------------ 176
Query: 204 LLYGPPGCGKT 214
L++GPPG GKT
Sbjct: 177 LIHGPPGTGKT 187
>gnl|CDD|213200 cd03233, ABCG_PDR_domain1, First domain of the pleiotropic drug
resistance-like subfamily G of ATP-binding cassette
transporters. The pleiotropic drug resistance (PDR) is
a well-described phenomenon occurring in fungi and
shares several similarities with processes in bacteria
and higher eukaryotes. This PDR subfamily represents
domain I of its (ABC-IM)2 organization. ABC transporters
are a large family of proteins involved in the transport
of a wide variety of different compounds including
sugars, ions, peptides, and more complex organic
molecules. The nucleotide-binding domain shows the
highest similarity between all members of the family.
ABC transporters are a subset of nucleotide hydrolases
that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing proteins.
Length = 202
Score = 28.0 bits (63), Expect = 6.3
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 194 SGLLKPPKGILLYGPPGCGKTMIAKATAK 222
SG++KP + +L+ G PG G + + KA A
Sbjct: 27 SGVVKPGEMVLVLGRPGSGCSTLLKALAN 55
>gnl|CDD|136670 PRK08181, PRK08181, transposase; Validated.
Length = 269
Score = 28.0 bits (62), Expect = 6.4
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 203 ILLYGPPGCGKTMIAKA 219
+LL+GPPG GK+ +A A
Sbjct: 109 LLLFGPPGGGKSHLAAA 125
>gnl|CDD|216999 pfam02367, UPF0079, Uncharacterized P-loop hydrolase UPF0079. This
uncharacterized family contains a P-loop.
Length = 123
Score = 27.2 bits (61), Expect = 6.5
Identities = 11/27 (40%), Positives = 14/27 (51%)
Query: 196 LLKPPKGILLYGPPGCGKTMIAKATAK 222
LLK +LL G G GKT + A+
Sbjct: 11 LLKAGDVVLLSGDLGAGKTTFVRGLAQ 37
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 28.4 bits (63), Expect = 6.8
Identities = 12/45 (26%), Positives = 19/45 (42%), Gaps = 3/45 (6%)
Query: 196 LLKPPKGILLYGPPGCGKTMIAKATAKEA---NVSFINLDISTLT 237
L + + GPPG GK M+ + + V + N T+T
Sbjct: 1490 ALNTLRSYIYCGPPGSGKEMLMCPSLRSELITEVKYFNFSTCTMT 1534
>gnl|CDD|227162 COG4825, COG4825, Uncharacterized membrane-anchored protein
conserved in bacteria [Function unknown].
Length = 395
Score = 28.3 bits (63), Expect = 6.9
Identities = 17/60 (28%), Positives = 33/60 (55%), Gaps = 9/60 (15%)
Query: 121 VLLAITTAYEKLKKVGLD----VGN--KLNTHELKIAANLIVPEEINGSWKNIAGLEHIK 174
VL+ + A + L+K G VG+ +++T L+ A +++P + +G + GLE I+
Sbjct: 209 VLIGVDGAADVLRKAGYKPQLIVGDPDQISTEALRCGAKVVLPADADG---HAPGLERIQ 265
>gnl|CDD|225114 COG2204, AtoC, Response regulator containing CheY-like receiver,
AAA-type ATPase, and DNA-binding domains [Signal
transduction mechanisms].
Length = 464
Score = 28.4 bits (64), Expect = 6.9
Identities = 29/130 (22%), Positives = 51/130 (39%), Gaps = 28/130 (21%)
Query: 203 ILLYGPPGCGKTMIAKA---TAKEANVSFINLDISTLTD-----KLYGESPKLAT-AIFS 253
+L+ G G GK ++A+A + A FI ++ + + + +L+G T AI
Sbjct: 167 VLITGESGTGKELVARAIHQASPRAKGPFIAVNCAAIPENLLESELFGHEKGAFTGAITR 226
Query: 254 ---LAEKIQPCIIFIDEIDSLLRS------RSSSDHEATAQLKSIFLSKWDGLTTDKNID 304
E+ +F+DEI + R + E + G +D
Sbjct: 227 RIGRFEQANGGTLFLDEIGEMPLELQVKLLRVLQEREFE------RV----GGNKPIKVD 276
Query: 305 IIIMGATNRP 314
+ I+ ATNR
Sbjct: 277 VRIIAATNRD 286
>gnl|CDD|181235 PRK08118, PRK08118, topology modulation protein; Reviewed.
Length = 167
Score = 27.7 bits (62), Expect = 7.0
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 201 KGILLYGPPGCGKTMIAKATAKEANVSFINLD 232
K I+L G G GK+ +A+ ++ N+ +LD
Sbjct: 2 KKIILIGSGGSGKSTLARQLGEKLNIPVHHLD 33
>gnl|CDD|132613 TIGR03574, selen_PSTK, L-seryl-tRNA(Sec) kinase, archaeal. Members
of this protein are L-seryl-tRNA(Sec) kinase. This
enzyme is part of a two-step pathway in Eukaryota and
Archaea for performing selenocysteine biosynthesis by
changing serine misacylated on selenocysteine-tRNA to
selenocysteine. This enzyme performs the first step,
phosphorylation of the OH group of the serine side
chain. This family represents archaeal proteins with
this activity [Protein synthesis, tRNA aminoacylation].
Length = 249
Score = 27.8 bits (62), Expect = 7.0
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 203 ILLYGPPGCGKTMIAKATAKE 223
I+L G PG GK+ +K AK+
Sbjct: 2 IILTGLPGVGKSTFSKELAKK 22
>gnl|CDD|182331 PRK10247, PRK10247, putative ABC transporter ATP-binding protein
YbbL; Provisional.
Length = 225
Score = 27.8 bits (62), Expect = 7.2
Identities = 21/82 (25%), Positives = 35/82 (42%), Gaps = 12/82 (14%)
Query: 165 KNIAGLEHIKKELNQSVIFPMKNRNLLKESGLLKPPKGILLYGPPGCGKTMIAKATA--- 221
+ L+++ + I + N + +G K L+ GP GCGK+ + K A
Sbjct: 5 SPLLQLQNVGYLAGDAKI--LNNISFSLRAGEFK-----LITGPSGCGKSTLLKIVASLI 57
Query: 222 --KEANVSFINLDISTLTDKLY 241
+ F DISTL ++Y
Sbjct: 58 SPTSGTLLFEGEDISTLKPEIY 79
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 27.7 bits (62), Expect = 7.4
Identities = 22/92 (23%), Positives = 35/92 (38%), Gaps = 19/92 (20%)
Query: 203 ILLYGPPGCGKT----------MIAKATAKEANVSFINLDIS-----TLTDKLYGESPKL 247
+LL GP GKT + + T+ E NV+ + S TL D KL
Sbjct: 3 VLLLGPSDSGKTALFTKLTTGKVRSTVTSIEPNVASFYSNSSKGKKLTLVD--VPGHEKL 60
Query: 248 ATAIFSLAEKIQPCIIFIDEIDSLLRSRSSSD 279
+ + I+F+ +DS ++ D
Sbjct: 61 RDKLLEYLKASLKAIVFV--VDSATFQKNIRD 90
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 28.3 bits (63), Expect = 7.6
Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 13/82 (15%)
Query: 204 LLYGPPGCGKTMIAKATAKE----------ANVSFINLDISTLT--DKLYGE-SPKLATA 250
+L G PG GKT I + A+ + LD+ L K GE +L
Sbjct: 203 VLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGV 262
Query: 251 IFSLAEKIQPCIIFIDEIDSLL 272
+ LA++ I+FIDE+ +++
Sbjct: 263 LNDLAKQEGNVILFIDELHTMV 284
>gnl|CDD|219519 pfam07693, KAP_NTPase, KAP family P-loop domain. The KAP (after
Kidins220/ARMS and PifA) family of predicted NTPases are
sporadically distributed across a wide phylogenetic
range in bacteria and in animals. Many of the
prokaryotic KAP NTPases are encoded in plasmids and tend
to undergo disruption to form pseudogenes. A unique
feature of all eukaryotic and certain bacterial KAP
NTPases is the presence of two or four transmembrane
helices inserted into the P-loop NTPase domain. These
transmembrane helices anchor KAP NTPases in the membrane
such that the P-loop domain is located on the
intracellular side.
Length = 301
Score = 28.1 bits (63), Expect = 7.6
Identities = 32/146 (21%), Positives = 44/146 (30%), Gaps = 30/146 (20%)
Query: 189 NLLKESGLLKPPKGILLYGPPGCGKT-MIAKATA--KEANVSFINLDI------------ 233
LL E L P I LYG G GKT + KE F +
Sbjct: 10 KLLVEPSL-APGFVIGLYGAWGSGKTSFLNLLEDELKEFPEEFHIVYFDPWLFSGQDDAV 68
Query: 234 ----STLTDKLYGESPKLATAIFSLAEKIQPCIIFIDEID--------SLLRSRSSSDHE 281
+ L D L E LAT + K ++ +I L +S
Sbjct: 69 ASLLAALADALEEEYSALATKLL--IGKKLLALVIGAKIGGNFGVGTALALTGLVASVEG 126
Query: 282 ATAQLKSIFLSKWDGLTTDKNIDIII 307
+ +L SI K ++ I
Sbjct: 127 KSLKLLSIEPLKKLQTEIEELRTDIA 152
>gnl|CDD|224077 COG1155, NtpA, Archaeal/vacuolar-type H+-ATPase subunit A [Energy
production and conversion].
Length = 588
Score = 28.0 bits (63), Expect = 7.6
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 207 GPPGCGKTMIAKATAKEANVSFI 229
GP G GKT+ +K A+ +
Sbjct: 231 GPFGSGKTVSQHTLSKLADGDIV 253
>gnl|CDD|221003 pfam11150, DUF2927, Protein of unknown function (DUF2927). This
family is conserved in Proteobacteria. Several members
are described as being putative lipoproteins, but
otherwise the function is not known.
Length = 212
Score = 27.6 bits (62), Expect = 7.8
Identities = 8/39 (20%), Positives = 15/39 (38%), Gaps = 4/39 (10%)
Query: 302 NIDIIIMGATNRPDDIDPAIARRMPKKYHIKLPLLSSFS 340
N ++ + DD+ I R +P +P +S
Sbjct: 76 NFHVLFVSR----DDMANRIRRLLPGAACAVVPNVSRLP 110
>gnl|CDD|224616 COG1702, PhoH, Phosphate starvation-inducible protein PhoH,
predicted ATPase [Signal transduction mechanisms].
Length = 348
Score = 28.0 bits (63), Expect = 7.9
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 207 GPPGCGKTMIAKATAKEA 224
GP G GKT +A A A +A
Sbjct: 150 GPAGTGKTYLAVAKAVDA 167
>gnl|CDD|219158 pfam06745, KaiC, KaiC. This family represents a conserved region
within bacterial and archaeal proteins, most of which
are hypothetical. More than one copy is sometimes found
in each protein. This family includes KaiC, which is one
of the Kai proteins among which direct protein-protein
association may be a critical process in the generation
of circadian rhythms in cyanobacteria.
Length = 231
Score = 27.6 bits (62), Expect = 8.3
Identities = 9/21 (42%), Positives = 13/21 (61%), Gaps = 2/21 (9%)
Query: 200 PKG--ILLYGPPGCGKTMIAK 218
P+G +L+ G PG GKT+
Sbjct: 17 PRGRVVLITGGPGTGKTIFGL 37
>gnl|CDD|223873 COG0802, COG0802, Predicted ATPase or kinase [General function
prediction only].
Length = 149
Score = 27.2 bits (61), Expect = 8.8
Identities = 11/27 (40%), Positives = 14/27 (51%)
Query: 196 LLKPPKGILLYGPPGCGKTMIAKATAK 222
LK +LL G G GKT + + AK
Sbjct: 21 ALKAGDVVLLSGDLGAGKTTLVRGIAK 47
>gnl|CDD|238977 cd02019, NK, Nucleoside/nucleotide kinase (NK) is a protein
superfamily consisting of multiple families of enzymes
that share structural similarity and are functionally
related to the catalysis of the reversible phosphate
group transfer from nucleoside triphosphates to
nucleosides/nucleotides, nucleoside monophosphates, or
sugars. Members of this family play a wide variety of
essential roles in nucleotide metabolism, the
biosynthesis of coenzymes and aromatic compounds, as
well as the metabolism of sugar and sulfate.
Length = 69
Score = 25.8 bits (57), Expect = 8.9
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 203 ILLYGPPGCGKTMIAKATAKE 223
I + G G GK+ +AK A++
Sbjct: 2 IAITGGSGSGKSTVAKKLAEQ 22
>gnl|CDD|238543 cd01123, Rad51_DMC1_radA, Rad51_DMC1_radA,B. This group of
recombinases includes the eukaryotic proteins RAD51,
RAD55/57 and the meiosis-specific protein DMC1, and the
archaeal proteins radA and radB. They are closely
related to the bacterial RecA group. Rad51 proteins
catalyze a similiar recombination reaction as RecA,
using ATP-dependent DNA binding activity and a
DNA-dependent ATPase. However, this reaction is less
efficient and requires accessory proteins such as
RAD55/57 .
Length = 235
Score = 27.5 bits (62), Expect = 8.9
Identities = 5/13 (38%), Positives = 8/13 (61%)
Query: 205 LYGPPGCGKTMIA 217
++G G GKT +
Sbjct: 24 IFGEFGSGKTQLC 36
>gnl|CDD|224047 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 27.6 bits (62), Expect = 9.0
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 5/35 (14%)
Query: 185 MKNRNLLKESGLLKPPKGILLYGPPGCGKTMIAKA 219
+K+ +L E G + +LL GP G GK+ + K
Sbjct: 20 LKDVSLEIEKG-----ERVLLIGPNGSGKSTLLKL 49
>gnl|CDD|234626 PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase;
Reviewed.
Length = 307
Score = 27.8 bits (63), Expect = 9.5
Identities = 14/35 (40%), Positives = 18/35 (51%)
Query: 198 KPPKGILLYGPPGCGKTMIAKATAKEANVSFINLD 232
PK I++ GP GKT +A AK N I+ D
Sbjct: 2 MKPKVIVIVGPTASGKTALAIELAKRLNGEIISAD 36
>gnl|CDD|236353 PRK08939, PRK08939, primosomal protein DnaI; Reviewed.
Length = 306
Score = 27.5 bits (62), Expect = 9.6
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 201 KGILLYGPPGCGKTMIAKATAKE 223
KG+ LYG G GK+ + A A E
Sbjct: 157 KGLYLYGDFGVGKSYLLAAIANE 179
>gnl|CDD|224434 COG1517, COG1517, CRISPR system related protein [Defense
mechanisms].
Length = 406
Score = 27.8 bits (62), Expect = 9.7
Identities = 16/78 (20%), Positives = 24/78 (30%), Gaps = 10/78 (12%)
Query: 130 EKLKKVGLDVGNKLNTHELKIAANLIVPEE---------INGSWKNIAGLEHIKKELNQS 180
E LK+V L+ L + +I K E+ +
Sbjct: 298 EDLKEVLLEDIKLLTEI-GVNSDPIIKRRISKILNSYKLQLEERKIKLEGTIEDSEIRKM 356
Query: 181 VIFPMKNRNLLKESGLLK 198
IF + RN L +GL
Sbjct: 357 NIFEREERNFLAHAGLEV 374
>gnl|CDD|219839 pfam08433, KTI12, Chromatin associated protein KTI12. This is a
family of chromatin associated proteins which interact
with the Elongator complex, a component of the
elongating form of RNA polymerase II. The Elongator
complex has histone acetyltransferase activity.
Length = 266
Score = 27.6 bits (62), Expect = 9.8
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 8/63 (12%)
Query: 203 ILLYGPPGCGKTMIAKATAKEA-----NVSFINLDISTLTDKLYGESPK---LATAIFSL 254
I+L G P GK+ AK AK +V I+ + + Y +S K L ++ S
Sbjct: 2 IILTGLPSSGKSTRAKELAKYLEEKGYDVIVISDESLGIESDDYKDSKKEKFLRGSLRSA 61
Query: 255 AEK 257
++
Sbjct: 62 VKR 64
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
0.319 0.134 0.390
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,219,191
Number of extensions: 1653618
Number of successful extensions: 2217
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2157
Number of HSP's successfully gapped: 240
Length of query: 341
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 243
Effective length of database: 6,590,910
Effective search space: 1601591130
Effective search space used: 1601591130
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 (27.0 bits)