RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5521
(570 letters)
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 230 bits (589), Expect = 5e-69
Identities = 106/248 (42%), Positives = 154/248 (62%), Gaps = 17/248 (6%)
Query: 232 GLDSAKRLLLEAIVYPTRYPELFRGL-LSPWKAILLHGPPGTGKTLLARAVATQCTTTFF 290
GL+ AK L EAI P + PELFR L L P K +LL+GPPGTGKTLLA+AVA + + F
Sbjct: 246 GLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESRSRFI 305
Query: 291 NISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEASRRLKAE 350
++ S L+SKW GESEK +R LF ARK APS IF+DE+D+L S R E + RR+ +
Sbjct: 306 SVKGSELLSKWVGESEKNIRELFEKARKLAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQ 365
Query: 351 LLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAREAMLRHYLP 408
LL +LDG+ E V ++A +N P DLDPA+LR RF++ I++ +PD R + + +L
Sbjct: 366 LLTELDGIEKA-EGVLVIAATNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLR 424
Query: 409 PLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQ----------RVRDTFELLE 458
+ P L ++D L++ EGYSG+DI ++ +E A++ + D + L+
Sbjct: 425 ---DKKPPLAEDVDLEELAEITEGYSGADIAALVREAALEALREARRREVTLDDFLDALK 481
Query: 459 RMNPGLTM 466
++ P +T
Sbjct: 482 KIKPSVTY 489
Score = 114 bits (286), Expect = 5e-27
Identities = 86/227 (37%), Positives = 126/227 (55%), Gaps = 12/227 (5%)
Query: 246 YPTRYPELFRGL-LSPWKAILLHGPPGTGKTLLARAVATQCTTTFFNISASSLVSKWRGE 304
P + PELF+ L + P K +LLHGPPGTGKTLLARA+A F +I+ ++SK+ GE
Sbjct: 2 LPLKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALA-NEGAEFLSINGPEILSKYVGE 60
Query: 305 SEKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEASRRLKAELLMQLDGLNTGEER 364
SE +R LF A K APS IF+DE+DAL +R ++ E RR+ A+LL +DGL +
Sbjct: 61 SELRLRELFEEAEKLAPSIIFIDEIDALAPKRSSDQGEVERRVVAQLLALMDGLK--RGQ 118
Query: 365 VFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAREAMLRHYLPPLVSESPRLCAELD 422
V ++ +N P LDPA R RF++ I +++PD R L L
Sbjct: 119 VIVIGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGRL----EILQIHTRLMF-LGPPGT 173
Query: 423 YPALSKAMEGYSGSDIKSVCKEVAMQRVRDTFELLERMNPGLTMTNT 469
L+ G SG+D+ ++ KE A++ +R +L+ G+T +
Sbjct: 174 GKTLAARTVGKSGADLGALAKEAALRELRRAIDLVGE-YIGVTEDDF 219
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 182 bits (463), Expect = 9e-52
Identities = 95/228 (41%), Positives = 134/228 (58%), Gaps = 14/228 (6%)
Query: 232 GLDSAKRLLLEAIVYPTRYPELFRGL-LSPWKAILLHGPPGTGKTLLARAVATQCTTTFF 290
GLD + + E + P + PELF L + P K +LL+GPPGTGKTLLA+AVA Q TF
Sbjct: 155 GLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTDATFI 214
Query: 291 NISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEASR---RL 347
+ S LV K+ GE +LVR LF LAR+ APS IF+DE+DA+ ++R R R
Sbjct: 215 RVVGSELVQKYIGEGARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRT 274
Query: 348 KAELLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAREAMLR- 404
ELL QLDG + ++AT N P LDPA+LR RF+++I +PD R +L+
Sbjct: 275 MLELLNQLDGFDPRGNVKVIMAT-NRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKI 333
Query: 405 HYLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVRD 452
H + L ++D L++ EG+SG+D+K++C E M +R+
Sbjct: 334 H------TRKMNLADDVDLELLARLTEGFSGADLKAICTEAGMFAIRE 375
>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 = 173 bits (440), Expect = 9e-52
Identities = 64/130 (49%), Positives = 84/130 (64%), Gaps = 1/130 (0%)
Query: 264 ILLHGPPGTGKTLLARAVATQCTTTFFNISASSLVSKWRGESEKLVRVLFTLARKCAPST 323
+LL+GPPGTGKT LA+AVA + F IS S LVSK+ GESEK +R LF A+K AP
Sbjct: 1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCV 60
Query: 324 IFLDELDALMSRRDGEEHEASRRLKAELLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR 383
IF+DE+DAL R SRR+ +LL +LDG + +V ++A +N P LDPA+LR
Sbjct: 61 IFIDEIDALAGSRGSGGDSESRRVVNQLLTELDGFTSSLSKVIVIAATNRPDKLDPALLR 120
Query: 384 -RFEKRIFID 392
RF++ I
Sbjct: 121 GRFDRIIEFP 130
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 181 bits (462), Expect = 1e-51
Identities = 92/230 (40%), Positives = 137/230 (59%), Gaps = 18/230 (7%)
Query: 232 GLDSAKRLLLEAIVYPTRYPELFRGL-LSPWKAILLHGPPGTGKTLLARAVATQCTTTFF 290
GL+ R + EA+ P + PELF + + P K +LL+GPPGTGKTLLA+AVA + TF
Sbjct: 135 GLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFI 194
Query: 291 NISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRR----DGEEHEASRR 346
+ S LV K+ GE +LVR LF LAR+ APS IF+DE+DA+ ++R + E R
Sbjct: 195 RVVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRT 254
Query: 347 LKAELLMQLDGLNT-GEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAREAML 403
L +LL ++DG + G ++ +A +N LDPA+LR RF++ I + +PD R +L
Sbjct: 255 L-MQLLAEMDGFDPRGNVKI--IAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEIL 311
Query: 404 R-HYLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVRD 452
+ H + L ++D L++ EG SG+D+K++C E M +RD
Sbjct: 312 KIH------TRKMNLADDVDLEELAELTEGASGADLKAICTEAGMFAIRD 355
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 168 bits (428), Expect = 3e-47
Identities = 91/228 (39%), Positives = 140/228 (61%), Gaps = 14/228 (6%)
Query: 232 GLDSAKRLLLEAIVYPTRYPELFRGL-LSPWKAILLHGPPGTGKTLLARAVATQCTTTFF 290
GL+ R + EA+ P ++PELF + + P K +LL+GPPGTGKTLLA+AVA + TF
Sbjct: 126 GLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFI 185
Query: 291 NISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRR----DGEEHEASRR 346
+ S LV K+ GE +LVR +F LA++ APS IF+DE+DA+ ++R + E R
Sbjct: 186 RVVGSELVRKYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRT 245
Query: 347 LKAELLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAREAMLR 404
L +LL +LDG + V ++A +N P LDPA+LR RF++ I + +PD R +L+
Sbjct: 246 L-MQLLAELDGFDP-RGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILK 303
Query: 405 HYLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVRD 452
+ + +L ++D A++K EG SG+D+K++C E M +R+
Sbjct: 304 IH-----TRKMKLAEDVDLEAIAKMTEGASGADLKAICTEAGMFAIRE 346
>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 = 173 bits (441), Expect = 2e-46
Identities = 89/226 (39%), Positives = 141/226 (62%), Gaps = 10/226 (4%)
Query: 232 GLDSAKRLLLEAIVYPTRYPELFRGL-LSPWKAILLHGPPGTGKTLLARAVATQCTTTFF 290
GL+ K+ L EA+ +P ++PE+F + + P K +LL GPPGTGKTLLA+AVAT+ F
Sbjct: 457 GLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANFI 516
Query: 291 NISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEA-SRRLKA 349
+ ++SKW GESEK +R +F AR+ AP+ IF DE+DA+ R + + R+
Sbjct: 517 AVRGPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARFDTSVTDRIVN 576
Query: 350 ELLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAREAMLRHYL 407
+LL ++DG+ V ++A +N P LDPA+LR RF++ I + PD AR+ + + +
Sbjct: 577 QLLTEMDGIQELSN-VVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIH- 634
Query: 408 PPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVRDT 453
+ S L ++D L++ EGY+G+DI++VC+E AM +R++
Sbjct: 635 ----TRSMPLAEDVDLEELAEMTEGYTGADIEAVCREAAMAALRES 676
Score = 163 bits (414), Expect = 5e-43
Identities = 90/224 (40%), Positives = 136/224 (60%), Gaps = 11/224 (4%)
Query: 232 GLDSAKRLLLEAIVYPTRYPELFRGL-LSPWKAILLHGPPGTGKTLLARAVATQCTTTFF 290
GL AK + E + P ++PELF L + P K +LL+GPPGTGKTLLA+AVA + F
Sbjct: 182 GLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAYFI 241
Query: 291 NISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEASRRLKAE 350
+I+ ++SK+ GESE+ +R +F A + APS IF+DE+DA+ +R+ E +R+ A+
Sbjct: 242 SINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQ 301
Query: 351 LLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAREAMLRHYLP 408
LL +DGL G RV ++ +N P LDPA+ R RF++ I I +PD AR+ +L+
Sbjct: 302 LLTLMDGLK-GRGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILK---- 356
Query: 409 PLVSESPRLCAE-LDYPALSKAMEGYSGSDIKSVCKEVAMQRVR 451
V AE +D L++ G+ G+D+ ++ KE AM +R
Sbjct: 357 --VHTRNMPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALR 398
>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 = 150 bits (381), Expect = 1e-39
Identities = 85/231 (36%), Positives = 135/231 (58%), Gaps = 21/231 (9%)
Query: 232 GLDSAKRLLLEAIV----YPTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQCTT 287
G+D AK L+E IV P+++ +L G P K +LL GPPGTGKTLLA+AVA +
Sbjct: 59 GIDEAKEELME-IVDFLKNPSKFTKL--GAKIP-KGVLLVGPPGTGKTLLAKAVAGEAGV 114
Query: 288 TFFNISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRD---GEEHEAS 344
FF+IS S V + G VR LF A+K AP IF+DE+DA+ +R G ++
Sbjct: 115 PFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDER 174
Query: 345 RRLKAELLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAREAM 402
+ +LL+++DG V ++A +N P LDPA+LR RF++++ +D+PD RE +
Sbjct: 175 EQTLNQLLVEMDGF-GTNTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEI 233
Query: 403 LR-HYLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVRD 452
L+ H +++ +L ++D A+++ G+SG+D+ ++ E A+ R
Sbjct: 234 LKVH------AKNKKLAPDVDLKAVARRTPGFSGADLANLLNEAALLAARK 278
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 141 bits (356), Expect = 9e-37
Identities = 84/227 (37%), Positives = 129/227 (56%), Gaps = 14/227 (6%)
Query: 232 GLDSAKRLLLEAIVYPTRYPELFRGL-LSPWKAILLHGPPGTGKTLLARAVATQCTTTFF 290
GLD K+ + EA+ P PEL+ + + P + +LL+GPPGTGKT+LA+AVA T TF
Sbjct: 149 GLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTATFI 208
Query: 291 NISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEASR---RL 347
+ S V K+ GE ++VR +F LAR+ APS IF+DE+D++ ++R + A R R+
Sbjct: 209 RVVGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGADREVQRI 268
Query: 348 KAELLMQLDGLNTGEERVFLLATSNVPWD-LDPAMLR--RFEKRIFIDIPDPPAREAMLR 404
ELL Q+DG + ++AT+ D LDPA+LR R +++I +PD + + +
Sbjct: 269 LLELLNQMDGFDQTTNVKVIMATNR--ADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQ 326
Query: 405 HYLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVR 451
++ L E+D E S +DI ++C+E MQ VR
Sbjct: 327 -----TITSKMNLSEEVDLEDFVSRPEKISAADIAAICQEAGMQAVR 368
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 136 bits (343), Expect = 8e-35
Identities = 80/228 (35%), Positives = 132/228 (57%), Gaps = 14/228 (6%)
Query: 232 GLDSAKRLLLEAIVYPTRYPELFRGL-LSPWKAILLHGPPGTGKTLLARAVATQCTTTFF 290
GL+ + + EA+ P +PEL+ + + P K ++L+GPPGTGKTLLA+AVA + + TF
Sbjct: 187 GLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSATFL 246
Query: 291 NISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRR----DGEEHEASRR 346
+ S L+ K+ G+ KLVR LF +A + APS +F+DE+DA+ ++R G E E R
Sbjct: 247 RVVGSELIQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGEKEIQRT 306
Query: 347 LKAELLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAREAMLR 404
+ ELL QLDG ++ + ++AT+ + LDPA++R R +++I PD + +
Sbjct: 307 M-LELLNQLDGFDSRGDVKVIMATNRIE-SLDPALIRPGRIDRKIEFPNPDEKTKRRIFE 364
Query: 405 HYLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVRD 452
+ + L ++D A + SG+DIK++C E + +R+
Sbjct: 365 IHTSKMT-----LAEDVDLEEFIMAKDELSGADIKAICTEAGLLALRE 407
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 133 bits (336), Expect = 2e-34
Identities = 79/237 (33%), Positives = 123/237 (51%), Gaps = 23/237 (9%)
Query: 231 LGLDSAK---RLLLEAIVYPTRYPELFRGLLSPW--KAILLHGPPGTGKTLLARAVATQC 285
+G + AK RL++E + PE F W K +L +GPPGTGKT++A+A+A +
Sbjct: 124 IGQEEAKRKCRLIMEYL----ENPERFG----DWAPKNVLFYGPPGTGKTMMAKALANEA 175
Query: 286 TTTFFNISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDAL-MSRRDGE-EHEA 343
+ A+ L+ + G+ + + L+ ARK AP +F+DELDA+ + RR E +
Sbjct: 176 KVPLLLVKATELIGEHVGDGARRIHELYERARKAAPCIVFIDELDAIALDRRYQELRGDV 235
Query: 344 SRRLKAELLMQLDGLNTGEERVFLLATSNVPWDLDPAMLRRFEKRIFIDIPDPPAREAML 403
S + A LL +LDG+ E V + AT+ P LDPA+ RFE+ I +P+ R +L
Sbjct: 236 SEIVNA-LLTELDGIKENEGVVTIAATNR-PELLDPAIRSRFEEEIEFKLPNDEERLEIL 293
Query: 404 RHYLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKS-VCKEVAMQRVRDTFELLER 459
+Y + L + D L+ +G SG DIK V K + + + E +ER
Sbjct: 294 EYYA-----KKFPLPVDADLRYLAAKTKGMSGRDIKEKVLKTALHRAIAEDREKVER 345
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 128 bits (323), Expect = 2e-31
Identities = 80/228 (35%), Positives = 130/228 (57%), Gaps = 17/228 (7%)
Query: 232 GLDSAKRLLLEAIVY---PTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQCTTT 288
G D AK + E + Y P+R+ +L G P K +L+ GPPGTGKTLLA+A+A +
Sbjct: 156 GCDEAKEEVAELVEYLREPSRFQKL--GGKIP-KGVLMVGPPGTGKTLLAKAIAGEAKVP 212
Query: 289 FFNISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRD---GEEHEASR 345
FF IS S V + G VR +F A+K AP IF+DE+DA+ +R G H+
Sbjct: 213 FFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDERE 272
Query: 346 RLKAELLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAREAML 403
+ ++L+++DG G E + ++A +N P LDPA+LR RF++++ + +PD RE +L
Sbjct: 273 QTLNQMLVEMDGFE-GNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQIL 331
Query: 404 RHYLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVR 451
+ ++ P L ++D +++ G+SG+D+ ++ E A+ R
Sbjct: 332 KVHM----RRVP-LAPDIDAAIIARGTPGFSGADLANLVNEAALFAAR 374
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 116 bits (293), Expect = 1e-27
Identities = 84/231 (36%), Positives = 125/231 (54%), Gaps = 33/231 (14%)
Query: 232 GLDSAKRLLLEAIVY---PTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQCTTT 288
G+D AK L E + + P +Y L G P K +LL GPPGTGKTLLA+AVA +
Sbjct: 154 GVDEAKEELSELVDFLKNPKKYQAL--GAKIP-KGVLLVGPPGTGKTLLAKAVAGEAGVP 210
Query: 289 FFNISASSLVSKW---RGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRD---GEEHE 342
FF+IS S V + G S VR LF A+K AP IF+DE+DA+ +R G ++
Sbjct: 211 FFSISGSDFV-EMFVGVGASR--VRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGND 267
Query: 343 ASRRLKAELLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPARE 400
+ +LL+++DG E + + AT N P LDPA+LR RF+++I +++PD RE
Sbjct: 268 EREQTLNQLLVEMDGFGGNEGVIVIAAT-NRPDVLDPALLRPGRFDRQILVELPDIKGRE 326
Query: 401 AMLRHY-----LPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVA 446
+L+ + L V D +++ G+SG+D+ ++ E A
Sbjct: 327 QILKVHAKNKPLAEDV----------DLKKIARGTPGFSGADLANLLNEAA 367
>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 = 109 bits (273), Expect = 4e-25
Identities = 67/196 (34%), Positives = 105/196 (53%), Gaps = 19/196 (9%)
Query: 232 GLDSAKRLLLEAIVYPTRYPELFRGL-LSPWKAILLHGPPGTGKTLLARAVATQC----- 285
GL S + +A+ P +PEL+R L P K +LL+GPPG GKTL+A+AVA
Sbjct: 186 GLGSQIEQIRDAVELPFLHPELYREYGLKPPKGVLLYGPPGCGKTLIAKAVANSLAARIG 245
Query: 286 -----TTTFFNISASSLVSKWRGESEKLVRVLFTLARKCA----PSTIFLDELDALM-SR 335
+ F NI L++K+ GE+E+ +R++F AR+ A P +F DE+D+L +R
Sbjct: 246 AEGGGKSYFLNIKGPELLNKYVGETERQIRLIFQRAREKASEGRPVIVFFDEMDSLFRTR 305
Query: 336 RDGEEHEASRRLKAELLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDI 393
G + + +LL ++DG+ + V ++ SN +DPA+LR R + +I I+
Sbjct: 306 GSGVSSDVETTVVPQLLAEIDGVE-SLDNVIVIGASNREDMIDPAILRPGRLDVKIRIER 364
Query: 394 PDPPAREAMLRHYLPP 409
PD A + YL
Sbjct: 365 PDAEAAADIFAKYLTD 380
>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 = 99.5 bits (248), Expect = 1e-24
Identities = 57/172 (33%), Positives = 77/172 (44%), Gaps = 34/172 (19%)
Query: 232 GLDSAKRLLLEAIVYPTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQCT---TT 288
G + A L EA+ L P K +LL+GPPGTGKT LARA+A +
Sbjct: 2 GQEEAIEALREAL------------ELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAP 49
Query: 289 FFNISASSLVSKWRGESEK---LVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEASR 345
F ++AS L+ LVR+LF LA K P +F+DE+D+L SR
Sbjct: 50 FLYLNASDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSL-----------SR 98
Query: 346 RLKAELLMQLDGLNTG---EERVFLLATSNVPWDLDPAM--LRRFEKRIFID 392
+ LL L+ LN E V ++ +N P D R + RI I
Sbjct: 99 GAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIP 150
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 107 bits (270), Expect = 2e-24
Identities = 82/278 (29%), Positives = 137/278 (49%), Gaps = 32/278 (11%)
Query: 232 GLDSAKRLLLEAIVYPTRYPELFRGL-LSPWKAILLHGPPGTGKTLLARAVATQCTTTFF 290
G++ AK E +V + PE F + K +LL GPPGTGKTLLA+A+A + FF
Sbjct: 187 GIEEAKEEF-EEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAEVPFF 245
Query: 291 NISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRD---GEEHEASRRL 347
+IS S V + G VR LF A++ +P +F+DE+DA+ +R G ++ +
Sbjct: 246 SISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGIGGGNDEREQT 305
Query: 348 KAELLMQLDGL--NTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAREAML 403
+LL ++DG N G V ++A +N LD A+LR RF+++I + +PD R +L
Sbjct: 306 LNQLLTEMDGFKGNKG---VIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLDIL 362
Query: 404 RHYL--PPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVR--------DT 453
+ + L + +++ G+SG+D+ ++ E A+ R
Sbjct: 363 KVHARNKKLSPDVSLE-------LIARRTPGFSGADLANLLNEAAILTARRKKATITMKE 415
Query: 454 FEL-LERMNPGLTMTNTSLSGSMTNI--NNTGHGMTGS 488
+ ++R+ GL T S + I + GH + G+
Sbjct: 416 IDTAIDRVIAGLEGTPLEDSKNKRLIAYHEVGHAIVGT 453
>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 = 81.3 bits (200), Expect = 4e-18
Identities = 46/154 (29%), Positives = 70/154 (45%), Gaps = 24/154 (15%)
Query: 260 PWKAILLHGPPGTGKTLLARAVATQCTTT---FFNISASSL--------------VSKWR 302
P + IL+ GPPG+GKT LARA+A + I + K
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60
Query: 303 GESEKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEASRRLKAELLMQLDGLNTGE 362
G E +R+ LARK P + LDE+ +L+ E L ++L L E
Sbjct: 61 GSGELRLRLALALARKLKPDVLILDEITSLLDA------EQEALLLLLEELRLLLLLKSE 114
Query: 363 ERVFLLATSNVPWDLDPAMLR-RFEKRIFIDIPD 395
+ + ++ T+N DL PA+LR RF++RI + +
Sbjct: 115 KNLTVILTTNDEKDLGPALLRRRFDRRIVLLLIL 148
>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional.
Length = 489
Score = 67.4 bits (165), Expect = 7e-12
Identities = 57/197 (28%), Positives = 97/197 (49%), Gaps = 15/197 (7%)
Query: 256 GLLSPWKAILLHGPPGTGKTLLARAVATQCTTTFFNISASSLVSKWRGESEKLVRVLFTL 315
GL +P + +LL G GTGK+L A+A+A + L GESE +R + +
Sbjct: 255 GLPTP-RGLLLVGIQGTGKSLTAKAIANDWQLPLLRLDVGKLFGGIVGESESRMRQMIRI 313
Query: 316 ARKCAPSTIFLDELDALMSRRDGE-EHEASRRLKAELLMQLDGLNTGEER--VFLLATSN 372
A +P +++DE+D S + + + + R+ A + L E++ VF++AT+N
Sbjct: 314 AEALSPCILWIDEIDKAFSNSESKGDSGTTNRVLATFITWL-----SEKKSPVFVVATAN 368
Query: 373 VPWDLDPAMLR--RFEKRIFIDIPDPPAREAMLRHYLPPLVSESPRLCAELDYPALSKAM 430
L +LR RF++ F+D+P RE + + +L P+ + D LSK
Sbjct: 369 NIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKF---RPKSWKKYDIKKLSKLS 425
Query: 431 EGYSGSDIKSVCKEVAM 447
+SG++I+ E AM
Sbjct: 426 NKFSGAEIEQSIIE-AM 441
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 49.7 bits (119), Expect = 2e-06
Identities = 48/233 (20%), Positives = 78/233 (33%), Gaps = 64/233 (27%)
Query: 202 MDQSKREIMRLKPRPHFVQSTILFSVPHTLGLDSAKRLLLEAIVYPTRYPELFRGLLSPW 261
+++ + R+ ++S + +G + L L A++
Sbjct: 1 LEEIMAPLERVAEILGKIRSELE---KVVVGDEEVIELALLALL--AGGH---------- 45
Query: 262 KAILLHGPPGTGKTLLARAVATQCTTTFFNIS------ASSLVSKW--------RGESEK 307
+LL GPPG GKTLLARA+A F I S L+ + GE
Sbjct: 46 --VLLEGPPGVGKTLLARALARALGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRF 103
Query: 308 LVRVLFTLARKCAPSTIFLDELDA-----------LMSRRDGEEHEASRRLKAELLMQLD 356
+ LF R + LDE++ + R ++
Sbjct: 104 VPGPLFAAVR----VILLLDEINRAPPEVQNALLEALEERQVTVPG-LTTIRL------- 151
Query: 357 GLNTGEERVFLLATSNVPWD-----LDPAMLRRFEKRIFIDIPDPPAREAMLR 404
++AT N L A+L RF RI++D PD E ++
Sbjct: 152 -----PPPFIVIATQNPGEYEGTYPLPEALLDRFLLRIYVDYPDSEEEERIIL 199
>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 = 43.1 bits (102), Expect = 5e-05
Identities = 38/147 (25%), Positives = 54/147 (36%), Gaps = 38/147 (25%)
Query: 264 ILLHGPPGTGKTLLAR--AVATQCTTTFF-----NISASSLVSKWR---GESEKLVRVLF 313
+LL GPPGTGK+ LA A A F+ + + L + G + + L
Sbjct: 2 VLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIDPGGASWVDGPLV 61
Query: 314 TLARKCAPSTIFLDELDALMSRRDGEEHEASRRLKAELLMQLD-----GLNTGEERVF-- 366
AR+ LDE++ A+ + LL LD GE
Sbjct: 62 RAARE--GEIAVLDEIN-----------RANPDVLNSLLSLLDERRLLLPEGGELVKAAP 108
Query: 367 ----LLATSNVP----WDLDPAMLRRF 385
L+AT N +L PA+ RF
Sbjct: 109 DGFRLIATMNPLDRGLNELSPALRSRF 135
>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 = 45.6 bits (108), Expect = 6e-05
Identities = 44/174 (25%), Positives = 70/174 (40%), Gaps = 21/174 (12%)
Query: 231 LGLDSAKR--LLLEAIVYPTRYPELFRGLLSPWKA--ILLHGPPGTGKTLLARAVATQ-C 285
+GL+ KR L++ RGL + +L GPPGTGKT +AR VA C
Sbjct: 279 IGLERVKRQVAALKSST-AMALARAERGLPVAQTSNHMLFAGPPGTGKTTIARVVAKIYC 337
Query: 286 TTTFF------NISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRDGE 339
+S + L+ ++ GESE + A +FLDE L+ G+
Sbjct: 338 GLGVLRKPLVREVSRADLIGQYIGESEAKTNEIIDSALGGV---LFLDEAYTLVETGYGQ 394
Query: 340 EHEASRRLKAELLMQLDGLNTGEERVFLLATSNVPWD----LDPAMLRRFEKRI 389
+ LL +++ N + V + A D ++ + RF + I
Sbjct: 395 KDPFGLEAIDTLLARME--NDRDRLVVIGAGYRKDLDKFLEVNEGLRSRFTRVI 446
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 43.9 bits (105), Expect = 2e-04
Identities = 16/33 (48%), Positives = 21/33 (63%)
Query: 264 ILLHGPPGTGKTLLARAVATQCTTTFFNISASS 296
++L GPPGTGKT LAR +A F +SA +
Sbjct: 39 MILWGPPGTGKTTLARIIAGATDAPFEALSAVT 71
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 43.8 bits (104), Expect = 2e-04
Identities = 16/24 (66%), Positives = 19/24 (79%)
Query: 259 SPWKAILLHGPPGTGKTLLARAVA 282
P KA+LL+GPPG GKT LA A+A
Sbjct: 37 KPKKALLLYGPPGVGKTSLAHALA 60
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 41.2 bits (97), Expect = 0.001
Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 262 KAILLHGPPGTGKTLLARAVATQC--TTTFFNISASSLVSKWRGESEKLVRVL 312
+ IL+ GPPGTGKT LA +A + F IS S + S ++E L + L
Sbjct: 66 RGILIVGPPGTGKTALAMGIARELGEDVPFVAISGSEIYSLEVKKTEALTQAL 118
>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 = 40.4 bits (95), Expect = 0.003
Identities = 51/225 (22%), Positives = 86/225 (38%), Gaps = 43/225 (19%)
Query: 262 KAILLHGPPGTGKTLLARAVATQCTTTFFNISASSL--VSKWRGESEKLV-----RVLFT 314
+ L GPPG GKT L +++A F S + ++ RG V R++
Sbjct: 348 PILCLVGPPGVGKTSLGKSIAKALNRKFVRFSLGGVRDEAEIRGHRRTYVGAMPGRIIQG 407
Query: 315 LAR-KCAPSTIFLDELD------------ALMSRRDGEEHEASRRLKAELLMQLDGLNTG 361
L + K LDE+D AL+ D E++ A ++ L
Sbjct: 408 LKKAKTKNPLFLLDEIDKIGSSFRGDPASALLEVLDPEQNNAFSDHYLDVPFDL------ 461
Query: 362 EERVFLLATSNVPWDLDPAMLRRFEKRIFIDIPD--PPAREAMLRHYLPPLVSESPRLC- 418
+V +AT+N + +L R E I++ + + + YL P E L
Sbjct: 462 -SKVIFIATANSIDTIPRPLLDRME---VIELSGYTEEEKLEIAKKYLIPKALEDHGLKP 517
Query: 419 AELDYP--ALSKAMEGY---SG-----SDIKSVCKEVAMQRVRDT 453
EL AL ++ Y +G I+ +C++ A++ V
Sbjct: 518 DELKITDEALLLLIKYYTREAGVRNLERQIEKICRKAAVKLVEQG 562
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 36.6 bits (85), Expect = 0.003
Identities = 19/91 (20%), Positives = 29/91 (31%), Gaps = 24/91 (26%)
Query: 257 LLSPWKAILLHGPPGTGKTLLARAVATQCTTTFFNISASSLVSKWRGESEKLVRVLFTLA 316
S ++ G PGTGKT A A+ + L++ R VL
Sbjct: 6 AASGRSLFVVDGGPGTGKTATAAAI------------IARLLAAGR-------SVLV--- 43
Query: 317 RKCAPSTIFLDELDALMSRRDGEEHEASRRL 347
AP+ L ++ D + L
Sbjct: 44 --VAPTGRAARRLRERLAALDLADASTLHAL 72
>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 = 38.7 bits (91), Expect = 0.003
Identities = 21/80 (26%), Positives = 32/80 (40%), Gaps = 13/80 (16%)
Query: 264 ILLHGPPGTGKTLLARAVA-----TQCTTTFFNISA---SSLVSKWRGESEKLVRV---- 311
L GP G GKT LA+A+A + ++S VS+ G V
Sbjct: 6 FLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYMEEHSVSRLIGAPPGYVGYEEGG 65
Query: 312 -LFTLARKCAPSTIFLDELD 330
L R+ S + +DE++
Sbjct: 66 QLTEAVRRKPYSIVLIDEIE 85
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 37.3 bits (86), Expect = 0.003
Identities = 28/144 (19%), Positives = 48/144 (33%), Gaps = 37/144 (25%)
Query: 264 ILLHGPPGTGKTLLARAVATQCTTTFFNISASSLVSKWRGESEKLVRVLFTLARKCAPST 323
IL+ GPPG+GK+ LA+ +A + ++ +
Sbjct: 2 ILITGPPGSGKSTLAKKLAEKLGIPVISLDDLLREEGLAELDD----------------- 44
Query: 324 IFLDELDALMSRRDGEEHEASRRLKAELLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR 383
ELD + + E K E ++ +T E R L
Sbjct: 45 ---GELDDIDIDLELLEEILDELAKQEWVIDGVRESTLELR-----------------LE 84
Query: 384 RFEKRIFIDIPDPPAREAMLRHYL 407
+ +F+D+P P R +L+ L
Sbjct: 85 EADLVVFLDLPLPACRFRLLKRRL 108
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 40.0 bits (94), Expect = 0.004
Identities = 14/30 (46%), Positives = 20/30 (66%)
Query: 265 LLHGPPGTGKTLLARAVATQCTTTFFNISA 294
+L+GPPG GKT LAR +A F +++A
Sbjct: 56 ILYGPPGVGKTTLARIIANHTRAHFSSLNA 85
>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 = 39.2 bits (92), Expect = 0.005
Identities = 19/40 (47%), Positives = 26/40 (65%), Gaps = 2/40 (5%)
Query: 262 KAILLHGPPGTGKTLLARAVATQC--TTTFFNISASSLVS 299
+A+L+ GPPGTGKT LA A++ + T F IS S + S
Sbjct: 51 RAVLIAGPPGTGKTALAIAISKELGEDTPFCPISGSEVYS 90
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 35.7 bits (83), Expect = 0.012
Identities = 15/85 (17%), Positives = 30/85 (35%), Gaps = 16/85 (18%)
Query: 264 ILLHGPPGTGKTLLARAVATQ---CTTTFFNISASS--------LVSKW-----RGESEK 307
+L G G+GKT L R +A Q + + ++ G + +
Sbjct: 7 GVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLLRKILRALGLPLSGGTTAE 66
Query: 308 LVRVLFTLARKCAPSTIFLDELDAL 332
L+ + ++ + +DE L
Sbjct: 67 LLEAILDALKRRGRPLLIIDEAQHL 91
>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 = 36.4 bits (84), Expect = 0.013
Identities = 19/98 (19%), Positives = 31/98 (31%), Gaps = 16/98 (16%)
Query: 263 AILLHGPPGTGKTLLARAVATQC-------------TTTFFNISASSLVSKWRGESEKLV 309
++LL GP GTGKT L R + F+ + L+ + E +
Sbjct: 26 SVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERNPPYAFSQALRELLRQLLRELAAEL 85
Query: 310 RVLFTLARKCAPSTIFLDELDALMSRRDGEEHEASRRL 347
+L + + D + E A R
Sbjct: 86 LLLREALLAALGAELIEGLQDLV---ELLERLLARARP 120
>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 = 35.3 bits (82), Expect = 0.013
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 264 ILLHGPPGTGKTLLARAVATQCTTTFFNISASSLVSK 300
I L+GPPG GK+ LA+ +A S+ S+
Sbjct: 1 IWLYGPPGCGKSTLAKYLARALLKHLGLPKKDSVYSR 37
>gnl|CDD|219837 pfam08430, Fork_head_N, Forkhead N-terminal region. The region
described in this family is found towards the N-terminus
of various eukaryotic fork head/HNF-3-related
transcription factors (which contain the pfam00250
domain). These proteins play key roles in embryogenesis,
maintenance of differentiated cell states, and
tumorigenesis.
Length = 137
Score = 35.7 bits (82), Expect = 0.015
Identities = 13/69 (18%), Positives = 26/69 (37%), Gaps = 3/69 (4%)
Query: 465 TMTNTSLSGSMTNINNTGHGMTGSKNNHSHSNLNASVSGQ---SMNINMKNHSNNHSISS 521
+ + + SM ++N G T + +S N++ M+ + N + +
Sbjct: 11 SSVSGGMVYSMNSMNTYGPMNTSQGSANSSMNMSGYAGPGAMNGMSSSSMNGMSPGYGGA 70
Query: 522 HSMTGMAQM 530
S GM M
Sbjct: 71 GSPMGMMGM 79
Score = 29.2 bits (65), Expect = 3.2
Identities = 10/74 (13%), Positives = 23/74 (31%), Gaps = 6/74 (8%)
Query: 460 MNPGLTMTNTSLSGSMTNINN---TGHGMTGSKNNHSHSNLNASVSGQSMNINMKNHSNN 516
+M + + G M + M+G + + +++S S M+
Sbjct: 15 GGMVYSMNSMNTYGPMNTSQGSANSSMNMSGYAGPGAMNGMSSS-SMNGMSPGYG--GAG 71
Query: 517 HSISSHSMTGMAQM 530
+ M+ M
Sbjct: 72 SPMGMMGMSSMGTS 85
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 37.4 bits (88), Expect = 0.015
Identities = 12/19 (63%), Positives = 15/19 (78%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
+LL+GPPG GKT LA +A
Sbjct: 54 VLLYGPPGLGKTTLANIIA 72
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA
replication, recombination, and repair].
Length = 332
Score = 37.2 bits (87), Expect = 0.017
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
+LL GPPG GKT LA +A
Sbjct: 55 VLLFGPPGLGKTTLAHIIA 73
>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 37.3 bits (87), Expect = 0.018
Identities = 28/113 (24%), Positives = 49/113 (43%), Gaps = 13/113 (11%)
Query: 241 LEAIVYPTRYPELFRGLLSPWK--AILLHGP-PGTGKTLLARAVATQCTTTFFNISASSL 297
++ + P E F+ ++ + +LLH P PGTGKT +A+A+ + ++ S
Sbjct: 20 IDECILPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEVGAEVLFVNGSDC 79
Query: 298 -VSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEASRRLKA 349
+ R L R T++ I +DE D L +A R L++
Sbjct: 80 RIDFVRNR---LTRFASTVSLTGGGKVIIIDEFDRLGL------ADAQRHLRS 123
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 37.3 bits (87), Expect = 0.019
Identities = 32/151 (21%), Positives = 58/151 (38%), Gaps = 42/151 (27%)
Query: 264 ILLHGPPGTGKTLLARAVATQ--------------CTT--TFFNISASSLVSKWRGESE- 306
I+++GP GTGKT + V + C T + + S +++K
Sbjct: 45 IIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQV-LSKILNKLGKVPLT 103
Query: 307 -----KLVRVLFTLARKCAPSTIF-LDELDALMSRRDGEEHEASRRLKAELLMQLDGLNT 360
++++ L+ K + I LDE+DAL+ + E+L L
Sbjct: 104 GDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKD------------GEVLYSLLRAPG 151
Query: 361 -GEERVFLLATSNVPWDLDPAMLRRFEKRIF 390
+ +V ++A SN D L + R+
Sbjct: 152 ENKVKVSIIAVSN-----DDKFLDYLDPRVK 177
>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 = 35.2 bits (82), Expect = 0.022
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
+LL G PG KTLLAR +A
Sbjct: 2 VLLEGVPGLAKTLLARTLA 20
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 37.0 bits (86), Expect = 0.027
Identities = 35/143 (24%), Positives = 64/143 (44%), Gaps = 28/143 (19%)
Query: 152 PPVRKLDVRDYPEEWKPFVEIITQEICTR-DVNTHWTDVIE-LSQAYESYLQMDQSKREI 209
PP+ K + P EWK V + + + TR ++ ++IE + +S++++D+ +
Sbjct: 160 PPMAK---KGKPGEWK-LVRL-SDKPLTREELEEIAREIIERAKRDPDSFIEIDRPGATV 214
Query: 210 MRLK------PRPHF---VQSTILFSVPHTLGLDSAKRLLLEAIVYPTRYPELFRGLLSP 260
++L+ RP F + T + V +L LE +L L
Sbjct: 215 VQLRNYRIVIARPPFSDRWEITAVRPV---------VKLSLE---DYGLSDKLKERLEER 262
Query: 261 WKAILLHGPPGTGKTLLARAVAT 283
+ IL+ G PG GK+ A+A+A
Sbjct: 263 AEGILIAGAPGAGKSTFAQALAE 285
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 36.8 bits (86), Expect = 0.029
Identities = 16/29 (55%), Positives = 18/29 (62%)
Query: 266 LHGPPGTGKTLLARAVATQCTTTFFNISA 294
L GPPGTGKT LAR +A F +SA
Sbjct: 53 LWGPPGTGKTTLARLIAGTTNAAFEALSA 81
>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 = 36.7 bits (85), Expect = 0.030
Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 8/72 (11%)
Query: 229 HTLGLDSAKRLLLEAIVYPTRY-----PELFRGLLSPWKAILLHGPPGTGKTLLARAVAT 283
+ +G D AK+ + AI RY PE + ++P K IL+ GP G GKT +AR +A
Sbjct: 13 YIIGQDEAKKSV--AIALRNRYRRSQLPEELKDEVTP-KNILMIGPTGVGKTEIARRLAK 69
Query: 284 QCTTTFFNISAS 295
F + A+
Sbjct: 70 LANAPFIKVEAT 81
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 35.8 bits (83), Expect = 0.043
Identities = 38/148 (25%), Positives = 55/148 (37%), Gaps = 53/148 (35%)
Query: 265 LLHGPPGTGKTLLARAVATQCTTTFFNISASSLVSKWRGESEKLVRVLFTLARKCAPSTI 324
LL G GTGKT LA + A+ L EK V V+F +
Sbjct: 118 LLWGSVGTGKTYLAACI------------ANEL-------IEKGVPVIFV-------NFP 151
Query: 325 -FLDELDALMSRRDGE-EHEASRRLK-AELLMQLDGLNT------GEERVF--------- 366
L+ + + E E+E R L A+LL+ LD L E+V+
Sbjct: 152 QLLNRIKSTYKSSGKEDENEIIRSLVNADLLI-LDDLGAERDTEWAREKVYNIIDSRYRK 210
Query: 367 ---LLATSNVPWDLDPAMLRR-FEKRIF 390
+ T+N L L+ + KRI+
Sbjct: 211 GLPTIVTTN----LSLEELKNQYGKRIY 234
>gnl|CDD|236828 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
Provisional.
Length = 758
Score = 36.4 bits (84), Expect = 0.043
Identities = 45/154 (29%), Positives = 71/154 (46%), Gaps = 29/154 (18%)
Query: 265 LLHGPPGTGKTLLARAVA------------TQCTTTFFNISASSLVSKWRGESEKLVRVL 312
LL G G GKT +A +A CT +I + +K+RG+ EK + L
Sbjct: 211 LLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKAL 270
Query: 313 FTLARKCAPSTIFLDELDALM--SRRDGEEHEASRRLKAELLMQLDGLNTGEERVFLLAT 370
+ S +F+DE+ ++ G + +A A L+ L L++G+ RV T
Sbjct: 271 LKQLEQDTNSILFIDEIHTIIGAGAASGGQVDA-----ANLIKPL--LSSGKIRVIGSTT 323
Query: 371 ----SNVPWDLDPAMLRRFEKRIFIDIPDPPARE 400
SN+ ++ D A+ RRF+K IDI +P E
Sbjct: 324 YQEFSNI-FEKDRALARRFQK---IDITEPSIEE 353
>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 = 35.6 bits (83), Expect = 0.044
Identities = 10/20 (50%), Positives = 16/20 (80%)
Query: 264 ILLHGPPGTGKTLLARAVAT 283
+L+ GPPG+GKT+LA+ +
Sbjct: 25 LLMIGPPGSGKTMLAKRLPG 44
>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 = 34.9 bits (81), Expect = 0.052
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 263 AILLHGPPGTGKTLLARAVA 282
A L GP G GK LLA A+A
Sbjct: 16 AYLFAGPEGVGKELLALALA 35
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 36.1 bits (84), Expect = 0.055
Identities = 40/159 (25%), Positives = 70/159 (44%), Gaps = 29/159 (18%)
Query: 265 LLHGPPGTGKT----LLARAVATQCTTTF------FNISASSLVS--KWRGESEKLVRVL 312
+L G PG GKT LA+ + +++ SLV+ K+RGE E+ ++ +
Sbjct: 195 VLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSLDLGSLVAGAKYRGEFEERLKAV 254
Query: 313 FTLARKCAPSTIFLDELDALM--SRRDGEEHEASRRLKAELL---MQLDGLNTGEE--RV 365
K +F+DE+ ++ +G +A+ LK L ++ G T +E +
Sbjct: 255 LKEVEKSKNVILFIDEIHTIVGAGATEGGAMDAANLLKPALARGELRCIGATTLDEYRKY 314
Query: 366 FLLATSNVPWDLDPAMLRRFEKRIFIDIPDPPAREAMLR 404
+ D A+ RRF+K + +D P A+LR
Sbjct: 315 I---------EKDAALERRFQK-VLVDEPSVEDTIAILR 343
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 35.9 bits (84), Expect = 0.057
Identities = 13/19 (68%), Positives = 16/19 (84%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
ILL GP G+GKTLLA+ +A
Sbjct: 111 ILLIGPTGSGKTLLAQTLA 129
>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 = 34.5 bits (80), Expect = 0.061
Identities = 34/119 (28%), Positives = 52/119 (43%), Gaps = 22/119 (18%)
Query: 264 ILLHGPPGTGKTLLARAVATQC----TTTFFNISASSLVSKWRGE--SEKLVRVLFTLAR 317
+LL GPPG GKT LA A+ Q + F LV + + +L R L LA+
Sbjct: 50 LLLLGPPGVGKTHLACALGHQACRAGYSVLF-TRTPDLVEQLKRARGDGRLARTLQRLAK 108
Query: 318 KCAPSTIFLDELDALMSRRDGEEHEASRRLKAELLMQLDGLNTGEERVFLLATSNVPWD 376
+ LD++ L ++ A LL +L ++ ER + TSN+P+
Sbjct: 109 ---ADLLILDDIGYLPLSQEA----------AHLLFEL--ISDRYERRSTILTSNLPFG 152
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 35.1 bits (81), Expect = 0.071
Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 13/74 (17%)
Query: 264 ILLHGPPGTGKTLLARAVATQC-----TTTFFNISASSLVSKW---RGESEKLVRVLFTL 315
++L GPPG GKT LA A+ + + F L+SK E ++L L
Sbjct: 108 LVLLGPPGVGKTHLAIAIGNELLKAGISVLFITA--PDLLSKLKAAFDEGRLEEKLLREL 165
Query: 316 ARKCAPSTIFLDEL 329
+ +D++
Sbjct: 166 ---KKVDLLIIDDI 176
>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 = 34.4 bits (79), Expect = 0.076
Identities = 39/161 (24%), Positives = 50/161 (31%), Gaps = 33/161 (20%)
Query: 264 ILLHGPPGTGKTLLARAVATQCTTTFFNI-------SASSLVSKWRGESEK--------- 307
IL+ GP G+GKT LA +A T + L + GES K
Sbjct: 2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLIIV 61
Query: 308 --------LVRVLFTLARKCAPS---TIFLDELDALMSRRDGEEHEASRRLKAELLMQLD 356
R+L R I LDEL + R E E E L +L
Sbjct: 62 FATADDPAAARLLSKAERLRERGGDDLIILDELTR-LVRALREIREGYPGELDEELRELL 120
Query: 357 GL--NTGEERVFLLATSNVPWDLDPAMLRRFEKRIFIDIPD 395
G V ++ T VP + DI D
Sbjct: 121 ERARKGG---VTVIFTLQVPSGDKGDPRLTRGAQNLEDIAD 158
>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 = 35.0 bits (81), Expect = 0.080
Identities = 10/27 (37%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 263 AILLHGPPGTGKTLLARAVATQCTTTF 289
+ +GP TGKT LA+A+A +
Sbjct: 115 TVWFYGPASTGKTNLAQAIA-HAVPLY 140
>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 = 34.7 bits (81), Expect = 0.086
Identities = 12/19 (63%), Positives = 15/19 (78%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
+LL+GPPG GKT LA +A
Sbjct: 53 VLLYGPPGLGKTTLANIIA 71
>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 = 33.8 bits (78), Expect = 0.10
Identities = 21/57 (36%), Positives = 26/57 (45%), Gaps = 7/57 (12%)
Query: 234 DSAKRLLLEAIVYPTRYPE---LFRGLLSPWKAILLHGPPGTGKTLL----ARAVAT 283
+ ++ L A P L +GLL LL G PGTGK+ L A AVAT
Sbjct: 3 EPSELLPSSAEDLDAPPPPLRWLVKGLLPRGGLTLLAGAPGTGKSTLALDLAAAVAT 59
>gnl|CDD|215758 pfam00158, Sigma54_activat, Sigma-54 interaction domain.
Length = 168
Score = 33.9 bits (79), Expect = 0.11
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 264 ILLHGPPGTGKTLLARAV 281
+L+ G GTGK L ARA+
Sbjct: 25 VLITGESGTGKELFARAI 42
>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 = 34.7 bits (80), Expect = 0.12
Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 264 ILLHGPPGTGKTLLARAVATQCTTTFFNISASSLV-SKWRGES-----EKLVRVLFTLAR 317
ILL GP G+GKTLLA+ +A F A++L + + GE KL++
Sbjct: 119 ILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVE 178
Query: 318 KCAPSTIFLDELDALMSRRDG 338
K I++DE+D + + +
Sbjct: 179 KAQKGIIYIDEIDKISRKSEN 199
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 34.4 bits (79), Expect = 0.13
Identities = 16/35 (45%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 247 PTRYP---ELFRGLLSPWKAILLHGPPGTGKTLLA 278
PT P E+ G L +L+ GPPGTGKT+ A
Sbjct: 6 PTGIPGLDEILGGGLPRGSVVLITGPPGTGKTIFA 40
>gnl|CDD|225821 COG3283, TyrR, Transcriptional regulator of aromatic amino acids
metabolism [Transcription / Amino acid transport and
metabolism].
Length = 511
Score = 34.7 bits (80), Expect = 0.13
Identities = 44/173 (25%), Positives = 67/173 (38%), Gaps = 44/173 (25%)
Query: 264 ILLHGPPGTGKTLLARA------------VATQCTTTFFNISASSLVSKWRGESEKLVRV 311
+L+ G GTGK LLA+A +A C + + + S L G+ K
Sbjct: 230 LLITGETGTGKDLLAKACHLASPRHSKPFLALNCASLPEDAAESELFGHAPGDEGKK--G 287
Query: 312 LFTLARKCAPSTIFLDELDALMSRRDGEEHEASRRLKAELLMQL-DGL--NTGEER---- 364
F A T+ LDE+ E S RL+A+LL L DG GE+
Sbjct: 288 FFEQANG---GTVLLDEIG-----------EMSPRLQAKLLRFLNDGTFRRVGEDHEVHV 333
Query: 365 -VFLLATSNVPWDLDPAMLRRFEKRIF-----IDIPDPPAREAMLRHYLPPLV 411
V ++ + V + +F + +F + + PP RE + PL
Sbjct: 334 DVRVICATQVNLV-ELVQKGKFREDLFYRLNVLTLNLPPLRERP--QDIMPLA 383
>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 = 34.2 bits (79), Expect = 0.15
Identities = 12/19 (63%), Positives = 15/19 (78%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
+LL+GPPG GKT LA +A
Sbjct: 33 LLLYGPPGLGKTTLAHIIA 51
>gnl|CDD|116541 pfam07931, CPT, Chloramphenicol phosphotransferase-like protein.
The members of this family are all similar to
chloramphenicol 3-O phosphotransferase (CPT) expressed
by Streptomyces venezuelae. Chloramphenicol (Cm) is a
metabolite produced by this bacterium that can inhibit
ribosomal peptidyl transferase activity and therefore
protein production. By transferring a phosphate group to
the C-3 hydroxyl group of Cm, CPT inactivates this
potentially lethal metabolite.
Length = 174
Score = 33.5 bits (77), Expect = 0.16
Identities = 10/37 (27%), Positives = 19/37 (51%)
Query: 262 KAILLHGPPGTGKTLLARAVATQCTTTFFNISASSLV 298
+ ILL+G +GK+ +ARA+ + + + V
Sbjct: 2 RIILLNGGSSSGKSSIARALQDILDGPWLHFGVDAFV 38
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 34.1 bits (79), Expect = 0.18
Identities = 13/19 (68%), Positives = 16/19 (84%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
ILL GP G+GKTLLA+ +A
Sbjct: 100 ILLIGPTGSGKTLLAQTLA 118
>gnl|CDD|222258 pfam13604, AAA_30, 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. There is a Walker A and
Walker B.
Length = 195
Score = 33.3 bits (77), Expect = 0.19
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 252 ELFRGLL-SPWKAILLHGPPGTGKTLLARAVA 282
E R +L S + ++ GP GTGKT +A
Sbjct: 8 EAVRHVLTSGDRVAVVQGPAGTGKTTSLKAAR 39
>gnl|CDD|183114 PRK11388, PRK11388, DNA-binding transcriptional regulator DhaR;
Provisional.
Length = 638
Score = 34.3 bits (79), Expect = 0.22
Identities = 61/251 (24%), Positives = 106/251 (42%), Gaps = 52/251 (20%)
Query: 264 ILLHGPPGTGKTLLARA------------VATQCTTTFFNISASSLVSKWRGESEKLVRV 311
+LL G G GK LLA+A +A C A + R +SE
Sbjct: 351 VLLCGEEGVGKALLAQAIHNESERAAGPYIAVNCQLYPDEALAEEFLGSDRTDSENGRLS 410
Query: 312 LFTLARKCAPSTIFLDELDALMSRRDGEEHEAS--RRLKAELLMQLDGLNTGEERVFLLA 369
F LA T+FL++++ L E +++ + LK ++ +LD V ++A
Sbjct: 411 KFELAHG---GTLFLEKVEYLSP-----ELQSALLQVLKTGVITRLDSRRLIPVDVRVIA 462
Query: 370 TSNVPWDLDPAML---RRFEKRIFI-----DIPDPPAREAMLRHYLPPLVS-------ES 414
T+ D AML RF ++++ +I PP R R +P LV+ +
Sbjct: 463 TTTA----DLAMLVEQNRFSRQLYYALHAFEITIPPLRMR--REDIPALVNNKLRSLEKR 516
Query: 415 PRLCAELDYPALSKAME-GYSGSD--IKSVCKEVAMQ------RVRDTFELLERMNPGLT 465
++D AL++ + + G+D ++SV + +A+ R+ D E L
Sbjct: 517 FSTRLKIDDDALARLVSYRWPGNDFELRSVIENLALSSDNGRIRLSDLPEHLFTEQATDD 576
Query: 466 MTNTSLSGSMT 476
++ T LS S++
Sbjct: 577 VSATRLSTSLS 587
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 33.7 bits (78), Expect = 0.27
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 264 ILLHGPPGTGKTLLARAVATQCTTTFFNIS 293
+ L GPPG GKT L +++A F IS
Sbjct: 353 LCLVGPPGVGKTSLGKSIAKALGRKFVRIS 382
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 32.0 bits (73), Expect = 0.30
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
IL+ G PG+GKT LA+ +A
Sbjct: 1 ILITGTPGSGKTTLAKELA 19
>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 444
Score = 33.4 bits (77), Expect = 0.32
Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 8/72 (11%)
Query: 229 HTLGLDSAKRLLLEAIVYPTRY-----PELFRGLLSPWKAILLHGPPGTGKTLLARAVAT 283
+ +G D AK+ + AI R+ E R ++P K IL+ GP G GKT +AR +A
Sbjct: 16 YIIGQDEAKKAV--AIALRNRWRRMQLEEELRDEVTP-KNILMIGPTGVGKTEIARRLAK 72
Query: 284 QCTTTFFNISAS 295
F + A+
Sbjct: 73 LAGAPFIKVEAT 84
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 32.1 bits (74), Expect = 0.36
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
I++ G P TGKT L A+A
Sbjct: 2 IVITGGPSTGKTTLLEALA 20
>gnl|CDD|223993 COG1066, Sms, Predicted ATP-dependent serine protease
[Posttranslational modification, protein turnover,
chaperones].
Length = 456
Score = 33.3 bits (77), Expect = 0.36
Identities = 19/45 (42%), Positives = 21/45 (46%), Gaps = 4/45 (8%)
Query: 242 EAIVYPTRYPELFR---GLLSPWKAILLHGPPGTGK-TLLARAVA 282
E T EL R G L P IL+ G PG GK TLL + A
Sbjct: 71 EEPRISTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAA 115
>gnl|CDD|223718 COG0645, COG0645, Predicted kinase [General function prediction
only].
Length = 170
Score = 32.0 bits (73), Expect = 0.39
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 264 ILLHGPPGTGKTLLARAVATQC 285
+L+ G PG+GK+ LAR +A
Sbjct: 4 VLVGGLPGSGKSTLARGLAELL 25
>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 = 33.2 bits (76), Expect = 0.39
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 12/56 (21%)
Query: 226 SVPHTLGLDSAKRLLLEAIVYPTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAV 281
+ +G + A + LL + P +P+ I+L+GPPG GKT AR
Sbjct: 152 AFSEIVGQERAIKALLAKVASP--FPQ----------HIILYGPPGVGKTTAARLA 195
>gnl|CDD|224857 COG1946, TesB, Acyl-CoA thioesterase [Lipid metabolism].
Length = 289
Score = 32.7 bits (75), Expect = 0.42
Identities = 11/42 (26%), Positives = 15/42 (35%), Gaps = 3/42 (7%)
Query: 130 PEEVEFANIVITPVTKLAQHSPPPVRKLDVRDYPEEWKPFVE 171
PE + + KL H P VR + P E +P
Sbjct: 127 PEGLPSETQIAQ---KLLPHLPEIVRAKFELERPIEIRPVNL 165
>gnl|CDD|180471 PRK06209, PRK06209, glutamate-1-semialdehyde 2,1-aminomutase;
Provisional.
Length = 431
Score = 33.1 bits (76), Expect = 0.43
Identities = 14/25 (56%), Positives = 18/25 (72%), Gaps = 2/25 (8%)
Query: 348 KAELLMQLDGL-NTGEERVFLLATS 371
K E M+L GL +T ERVFLL+T+
Sbjct: 265 KREY-MELGGLEHTDRERVFLLSTT 288
>gnl|CDD|190347 pfam02562, PhoH, PhoH-like protein. PhoH is a cytoplasmic protein
and predicted ATPase that is induced by phosphate
starvation.
Length = 205
Score = 32.4 bits (75), Expect = 0.44
Identities = 11/21 (52%), Positives = 12/21 (57%)
Query: 264 ILLHGPPGTGKTLLARAVATQ 284
+ GP GTGKT LA A A
Sbjct: 22 VFGIGPAGTGKTYLAVAAAVD 42
>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 = 31.8 bits (73), Expect = 0.45
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 264 ILLHGPPGTGKTLLARAVATQCTTTFFN 291
I++ G G+GK+ + +A+A + F +
Sbjct: 2 IVVMGVSGSGKSTVGKALAERLGAPFID 29
>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 = 31.9 bits (73), Expect = 0.55
Identities = 9/11 (81%), Positives = 10/11 (90%)
Query: 265 LLHGPPGTGKT 275
L+ GPPGTGKT
Sbjct: 21 LIQGPPGTGKT 31
>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 = 31.5 bits (72), Expect = 0.56
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 13/68 (19%)
Query: 264 ILLHGPPGTGKTLLARAVATQCTTTFFNISASSLVSKWRGE-----------SEKLVRVL 312
IL+ G PG+GK+ AR + + +S+ +L + RG+ S ++ + L
Sbjct: 2 ILMVGLPGSGKSTFARRLLRELGAVV--LSSDTLRKRLRGDGPPDISYYARASGRVYQRL 59
Query: 313 FTLARKCA 320
LAR+
Sbjct: 60 LELAREAL 67
>gnl|CDD|233208 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein. [Transport and binding proteins, Other].
Length = 1394
Score = 32.8 bits (75), Expect = 0.59
Identities = 12/44 (27%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 256 GLLSPWKAILLHGPPGTGKTLLARAVATQCTTTFFNISASSLVS 299
GL+ P + ++ G PG+G + L + +A T F+I +++
Sbjct: 82 GLIKPGELTVVLGRPGSGCSTLLKTIA--SNTDGFHIGVEGVIT 123
>gnl|CDD|237926 PRK15213, PRK15213, fimbrial outer membrane usher protein PefC;
Provisional.
Length = 797
Score = 32.8 bits (75), Expect = 0.61
Identities = 13/55 (23%), Positives = 23/55 (41%), Gaps = 1/55 (1%)
Query: 468 NTSLSGSMTNINNTGHGMTGSKNNHSHSNLNASVSGQSMNINMK-NHSNNHSISS 521
N+ +SGS+ + + G ++ S+LNAS N +H + S
Sbjct: 569 NSGVSGSLNDRLSYGLNTNRDRDGGRSSSLNASYGFDRAQTNGMLSHQGGGNTSG 623
Score = 30.9 bits (70), Expect = 2.0
Identities = 14/65 (21%), Positives = 30/65 (46%), Gaps = 7/65 (10%)
Query: 468 NTSLSGSMTNINNTGHGMTGSKNNHSHSNLNASVSGQSMNINM----KNHSNNHSISSHS 523
SLS ++ ++ +G +N+ ++ +AS+ S++I K H ++ S+S
Sbjct: 506 TVSLSTTIKGVSVNLNGSYSKRNSLGENDYSASL---SISIPFTLFDKRHYSSTSVSYSR 562
Query: 524 MTGMA 528
G
Sbjct: 563 SGGTG 567
>gnl|CDD|225806 COG3267, ExeA, Type II secretory pathway, component ExeA (predicted
ATPase) [Intracellular trafficking and secretion].
Length = 269
Score = 32.0 bits (73), Expect = 0.70
Identities = 45/194 (23%), Positives = 73/194 (37%), Gaps = 33/194 (17%)
Query: 264 ILLHGPPGTGKTLLARAVA------TQCTTTFFN--ISASSLVSKW--RGESEKLVRV-- 311
+ + G G+GKT+L RA+ +S ++L+ ES+ V V
Sbjct: 54 LAVTGEVGSGKTVLRRALLASLNEDQVAVVVIDKPTLSDATLLEAIVADLESQPKVNVNA 113
Query: 312 -LFTLARKCA--------PSTIFLDELDALMSRRDGEEHEASRRLKAELLMQLDGLNTGE 362
L + R+ A P + +DE L EA R LL L+ ++
Sbjct: 114 VLEQIDRELAALVKKGKRPVVLMVDEAHDLN----DSALEALR-----LLTNLEEDSSKL 164
Query: 363 ERVFLLATSNVPWDLDPAMLRRFEKRIFIDIPDPPAREAMLRHYLPPLV---SESPRLCA 419
+ L+ + L +LR E+RI I I PP EA YL + L +
Sbjct: 165 LSIVLIGQPKLRPRLRLPVLRELEQRIDIRIELPPLTEAETGLYLRHRLEGAGLPEPLFS 224
Query: 420 ELDYPALSKAMEGY 433
+ + +A +G
Sbjct: 225 DDALLLIHEASQGI 238
>gnl|CDD|226646 COG4178, COG4178, ABC-type uncharacterized transport system,
permease and ATPase components [General function
prediction only].
Length = 604
Score = 32.3 bits (74), Expect = 0.70
Identities = 27/100 (27%), Positives = 39/100 (39%), Gaps = 24/100 (24%)
Query: 189 VIELSQAYESYLQMDQSKREIMRLKPRPHFVQSTILFSVPHTLGLD------SAKRLLLE 242
+ E QA E+ QMD K R R F + H + L+ + LL
Sbjct: 359 LAEFRQALEA-AQMDTEKPA--RTGRRIDFDDN-----ADHGITLENLSLRTPDGQTLLS 410
Query: 243 AIVYPTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVA 282
+ F + P + +L+ G G GKT L RA+A
Sbjct: 411 ELN--------FE--VRPGERLLITGESGAGKTSLLRALA 440
>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 = 32.5 bits (74), Expect = 0.71
Identities = 11/16 (68%), Positives = 14/16 (87%)
Query: 264 ILLHGPPGTGKTLLAR 279
+LL GPPG+GKT+LA
Sbjct: 214 LLLFGPPGSGKTMLAS 229
>gnl|CDD|237421 PRK13539, PRK13539, cytochrome c biogenesis protein CcmA;
Provisional.
Length = 207
Score = 31.8 bits (73), Expect = 0.71
Identities = 16/34 (47%), Positives = 22/34 (64%), Gaps = 3/34 (8%)
Query: 252 ELFRGL---LSPWKAILLHGPPGTGKTLLARAVA 282
LF GL L+ +A++L GP G+GKT L R +A
Sbjct: 16 VLFSGLSFTLAAGEALVLTGPNGSGKTTLLRLIA 49
>gnl|CDD|240609 cd12796, LbR_Ice_bind, Ice-binding protein, left-handed beta-roll.
The ice-binding protein of the grass Lolium perenne
(LpIBP) discourages the recrystallization of ice.
Ice-binding proteins produced by organisms to prevent
the growing of ice are termed to anti-freeze proteins.
LpIBP consists of an unusual left-handed beta roll.
Ice-binding is mediated by a flat beta-sheet on one side
of the helix.
Length = 114
Score = 30.4 bits (69), Expect = 0.81
Identities = 16/62 (25%), Positives = 33/62 (53%), Gaps = 8/62 (12%)
Query: 468 NTSLSGSMTNINNTGHGMTGSKN-----NHSHSNLNASVSGQSMNINMKNHS---NNHSI 519
N ++SG+ + + + +TG+ N N+ S N +VSG + ++ N++ +NH +
Sbjct: 47 NNTVSGNNHVVTGSNNVVTGNGNTVSGSNNVVSGSNNTVSGGNNTVSGSNNTVSGSNHIV 106
Query: 520 SS 521
S
Sbjct: 107 SG 108
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 32.3 bits (74), Expect = 0.82
Identities = 10/19 (52%), Positives = 17/19 (89%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
+++ G PGTGK++LA+A+A
Sbjct: 53 VMMIGSPGTGKSMLAKAMA 71
>gnl|CDD|198283 cd10420, SH2_STAT5b, Src homology 2 (SH2) domain found in signal
transducer and activator of transcription (STAT) 5b
proteins. STAT5 is a member of the STAT family of
transcription factors. Two highly related proteins,
STAT5a and STAT5b are encoded by separate genes, but are
90% identical at the amino acid level. Both STAT5a and
STAT5b are ubiquitously expressed and functionally
interchangeable. Mice lacking either STAT5a or STAT5b
have mild defects in prolactin dependent mammary
differentiation or sexually dimorphic growth
hormone-dependent effects, respectively. Mice lacking
both STAT5a and STAT5b exhibit a perinatal lethal
phenotype and have multiple defects, including anemia
and a virtual absence of B and T lymphocytes. STAT
proteins mediate the signaling of cytokines and a number
of growth factors from the receptors of these
extracellular signaling molecules to the cell nucleus.
STATs are specifically phosphorylated by
receptor-associated Janus kinases, receptor tyrosine
kinases, or cytoplasmic tyrosine kinases. The
phosphorylated STAT molecules dimerize by reciprocal
binding of their SH2 domains to the phosphotyrosine
residues. These dimeric STATs translocate into the
nucleus, bind to specific DNA sequences, and regulate
the transcription of their target genes. However there
are a number of unphosphorylated STATs that travel
between the cytoplasm and nucleus and some STATs that
exist as dimers in unstimulated cells that can exert
biological functions independent of being activated.
There are seven mammalian STAT family members which have
been identified: STAT1, STAT2, STAT3, STAT4, STAT5
(STAT5A and STAT5B), and STAT6. There are 6 conserved
domains in STAT: N-terminal domain (NTD), coiled-coil
domain (CCD), DNA-binding domain (DBD), alpha-helical
linker domain (LD), SH2 domain, and transactivation
domain (TAD). NTD is involved in dimerization of
unphosphorylated STATs monomers and for the
tetramerization between STAT1, STAT3, STAT4 and STAT5 on
promoters with two or more tandem STAT binding sites.
It also plays a role in promoting interactions with
transcriptional co-activators such as CREB binding
protein (CBP)/p300, as well as being important for
nuclear import and deactivation of STATs involving
tyrosine de-phosphorylation. CCD interacts with other
proteins, such as IFN regulatory protein 9 (IRF-9/p48)
with STAT1 and c-JUN with STAT3 and is also thought to
participate in the negative regulation of these
proteins. Distinct genes are bound to STATs via their
DBD domain. This domain is also involved in nuclear
translocation of activated STAT1 and STAT3
phosphorylated dimers upon cytokine stimulation. LD
links the DNA-binding and SH2 domains and is important
for the transcriptional activation of STAT1 in response
to IFN-gamma. It also plays a role in protein-protein
interactions and has also been implicated in the
constitutive nucleocytoplasmic shuttling of
unphosphorylated STATs in resting cells. The SH2 domain
is necessary for receptor association and tyrosine
phosphodimer formation. Residues within this domain may
be particularly important for some cellular functions
mediated by the STATs as well as residues adjacent to
this domain. The TAD interacts with several proteins,
namely minichromosome maintenance complex component 5
(MCM5), breast cancer 1 (BRCA1) and CBP/p300. TAD also
contains a modulatory phosphorylation site that
regulates STAT activity and is necessary for maximal
transcription of a number of target genes. The conserved
tyrosine residue present in the C-terminus is crucial
for dimerization via interaction with the SH2 domain
upon the interaction of the ligand with the receptor.
STAT activation by tyrosine phosphorylation also
determines nuclear import and retention, DNA binding to
specific DNA elements in the promoters of responsive
genes, and transcriptional activation of STAT dimers. In
addition to the SH2 domain there is a coiled-coil
domain, a DNA binding domain, and a transactivation
domain in the STAT proteins. In general SH2 domains are
involved in signal transduction. They typically bind
pTyr-containing ligands via two surface pockets, a pTyr
and hydrophobic binding pocket, allowing proteins with
SH2 domains to localize to tyrosine phosphorylated
sites.
Length = 145
Score = 30.8 bits (69), Expect = 0.84
Identities = 27/94 (28%), Positives = 36/94 (38%), Gaps = 30/94 (31%)
Query: 362 EERVFLLATSNVPWDLDPAMLRRFEKRIFID-----------IPDPPAREAMLRHYLPPL 410
+ER+F W+L P R F R D PD P E ++Y
Sbjct: 64 QERMF--------WNLMPFTTRDFSIRSLADRLGDLNYLIYVFPDRPKDEVYSKYY---- 111
Query: 411 VSESPRLCAELDYPALSKAMEGYSGSDIKSVCKE 444
+P C PA +KA++GY IK V E
Sbjct: 112 ---TPVPCE----PATAKAVDGYVKPQIKQVVPE 138
>gnl|CDD|180215 PRK05707, PRK05707, DNA polymerase III subunit delta'; Validated.
Length = 328
Score = 31.6 bits (72), Expect = 0.96
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 263 AILLHGPPGTGKTLLARAVA 282
A LLHGP G GK LA +A
Sbjct: 24 AYLLHGPAGIGKRALAERLA 43
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 31.7 bits (73), Expect = 1.1
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 251 PELFRGLLSPWKAILLHGPPGTGKTLLARAVAT 283
+L L + IL+ G PG GK+ A+A+A
Sbjct: 247 EKLKERLEERAEGILIAGAPGAGKSTFAQALAE 279
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 31.6 bits (71), Expect = 1.1
Identities = 13/21 (61%), Positives = 16/21 (76%)
Query: 262 KAILLHGPPGTGKTLLARAVA 282
K I+L GPPG GKT +AR +A
Sbjct: 195 KNIILQGPPGVGKTFVARRLA 215
>gnl|CDD|236982 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
Length = 345
Score = 31.3 bits (72), Expect = 1.1
Identities = 9/31 (29%), Positives = 17/31 (54%)
Query: 252 ELFRGLLSPWKAILLHGPPGTGKTLLARAVA 282
+ + + ++L G G+GKT L +A+A
Sbjct: 132 DTLEEAPAQFPLVVLGGNTGSGKTELLQALA 162
>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 = 31.7 bits (72), Expect = 1.2
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 8/55 (14%)
Query: 265 LLHGPPGTGKTLLARAVATQ--------CTTTFFNISASSLVSKWRGESEKLVRV 311
L+HGPPGTGKT + Q T NI+ +L+ + +K+VR+
Sbjct: 177 LIHGPPGTGKTRTLVELIRQLVKRGLRVLVTAPSNIAVDNLLERLALCDQKIVRL 231
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 31.5 bits (72), Expect = 1.2
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 7/36 (19%)
Query: 265 LLHGPPGTGKTLLARAVATQC-------TTTFFNIS 293
L+ GPPG+GKT RA+A + T FN++
Sbjct: 40 LVQGPPGSGKTAAVRALARELYGDPWENNFTEFNVA 75
>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 = 31.5 bits (72), Expect = 1.3
Identities = 26/122 (21%), Positives = 44/122 (36%), Gaps = 42/122 (34%)
Query: 264 ILLHGPPGTGKTLLARAVATQ-----------CTTTFFN---IS-----ASSLVSKWRGE 304
+ ++G GTGKT + + V + T + N + L ++ RG
Sbjct: 43 VFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLVELANQLRGS 102
Query: 305 ----------SEKLVRVLFTLARKCAPSTIF-LDELDALMSRRDGEEHEASRRLKAELLM 353
+ ++ R L+ + S I LDE+D L+ D +LL
Sbjct: 103 GEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGDDD------------DLLY 150
Query: 354 QL 355
QL
Sbjct: 151 QL 152
>gnl|CDD|213194 cd03227, ABC_Class2, ATP-binding cassette domain of non-transporter
proteins. ABC-type Class 2 contains systems involved in
cellular processes other than transport. These families
are characterized by the fact that the ABC subunit is
made up of duplicated, fused ABC modules (ABC2). No
known transmembrane proteins or domains are associated
with these proteins.
Length = 162
Score = 30.4 bits (69), Expect = 1.3
Identities = 24/133 (18%), Positives = 42/133 (31%), Gaps = 30/133 (22%)
Query: 265 LLHGPPGTGKTLLARAVA-----------------TQCTTTFFNIS-ASSLVSKWRGESE 306
++ GP G+GK+ + A+ C + + + GE E
Sbjct: 25 IITGPNGSGKSTILDAIGLALGGAQSATRRRSGVKAGCIVAAVSAELIFTRLQLSGGEKE 84
Query: 307 KL-VRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEASRRLKAELLMQLDGLNTG---- 361
+ ++ LA LDE+D + RDG + L +L L
Sbjct: 85 LSALALILALASLKPRPLYILDEIDRGLDPRDG------QALAEAILEHLVKGAQVIVIT 138
Query: 362 -EERVFLLATSNV 373
+ LA +
Sbjct: 139 HLPELAELADKLI 151
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 31.5 bits (71), Expect = 1.4
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 11/50 (22%)
Query: 264 ILLHGPPGTGKTLLARAV-----------ATQCTTTFFNISASSLVSKWR 302
+LL GPPGTGKT+LA + A + ++A S+ +WR
Sbjct: 213 LLLIGPPGTGKTMLASRINGLLPDLSNEEALESAAILSLVNAESVQKQWR 262
>gnl|CDD|235898 PRK06964, PRK06964, DNA polymerase III subunit delta'; Validated.
Length = 342
Score = 31.3 bits (71), Expect = 1.4
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 263 AILLHGPPGTGKTLLARAVA 282
A+LLHG G GK A+ +A
Sbjct: 23 ALLLHGQAGIGKLDFAQHLA 42
>gnl|CDD|113356 pfam04582, Reo_sigmaC, Reovirus sigma C capsid protein.
Length = 326
Score = 31.0 bits (70), Expect = 1.4
Identities = 15/73 (20%), Positives = 34/73 (46%), Gaps = 7/73 (9%)
Query: 436 SDIKSVCKEVAMQRVRDTFELLERMNPGLTMTNTSLSGSMTNINNTGHGMTGSKNNHSHS 495
+ + + V Q ++ + + L L++T ++ +++++ T H + S
Sbjct: 77 ATLNGLITTV--QALQTSVDSLSSELADLSLTVSAHDAAISDLQTTVHANSTDI-----S 129
Query: 496 NLNASVSGQSMNI 508
NL +SVS +NI
Sbjct: 130 NLKSSVSANGLNI 142
>gnl|CDD|237908 PRK15095, PRK15095, FKBP-type peptidyl-prolyl cis-trans isomerase;
Provisional.
Length = 156
Score = 30.4 bits (69), Expect = 1.4
Identities = 21/80 (26%), Positives = 32/80 (40%), Gaps = 13/80 (16%)
Query: 337 DGEEHEASRR-------------LKAELLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR 383
DG E++R L L QL GL G+++ F L P +++
Sbjct: 21 DGSTAESTRNNGKPALFRLGDGSLSEGLEQQLLGLKVGDKKTFSLEPEAAFGVPSPDLIQ 80
Query: 384 RFEKRIFIDIPDPPAREAML 403
F +R F+D +P ML
Sbjct: 81 YFSRRDFMDAGEPEIGAIML 100
>gnl|CDD|216001 pfam00577, Usher, Type VII secretion system (T7SS), usher protein.
The chaperone-usher (CU) pathway or Type VII secretion
system (T7SS) in Gram-negative (diderm) bacteria is
responsible for the secretion and assembly of prepilins
for fimbriae biogenesis, the prototypical Type 1 pili.
Following the prepilins export to the periplasm by the
Sec translocon, the biogenesis of fimbriae requires a
two-component assembly and transport system which is
composed of a periplasmic chaperone and an outer
membrane protein, which has been termed a molecular
'usher'. The usher protein is rather large (from 86 to
100 Kd) and seems to be mainly composed of
membrane-spanning beta-sheets, a structure reminiscent
of porins. Although the degree of sequence similarity of
these proteins is not very high they share a number of
characteristics. One of these is the presence of two
pairs of cysteines, the first one located in the
N-terminal part and the second at the C-terminal
extremity that are probably involved in disulphide
bonds. The best conserved region is located in the
central part of these proteins.
Length = 552
Score = 31.4 bits (72), Expect = 1.6
Identities = 13/80 (16%), Positives = 25/80 (31%), Gaps = 20/80 (25%)
Query: 467 TNTSLSGSMTNINNTGHGM-------------------TGSKNNHSHSNLNASVSGQSMN 507
++ S S +N T S S +LN S G
Sbjct: 382 AYSTYSYSRSNNGGTTSNTGVSGSLFEDDRLSYGVNAGRSSDGKESSGSLNLSYRGDYGE 441
Query: 508 IN-MKNHSNNHSISSHSMTG 526
++ ++S ++ S++G
Sbjct: 442 LSGSYSYSRDYRQLGASLSG 461
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a wide
variety of presumed phage proteins.
Length = 201
Score = 30.7 bits (70), Expect = 1.6
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 5/48 (10%)
Query: 259 SPWKAILLHGPPGTGKT-LLARAVATQCTTTFFNISASSLVSKWRGES 305
K +L++GPPG GKT L T F ++ A + RG++
Sbjct: 2 KNIK-VLIYGPPGIGKTSLAKTLPP---KTLFLDLDAGTTKVLSRGDN 45
>gnl|CDD|235715 PRK06147, PRK06147, 3-oxoacyl-(acyl carrier protein) synthase;
Validated.
Length = 348
Score = 30.8 bits (70), Expect = 1.7
Identities = 20/59 (33%), Positives = 27/59 (45%), Gaps = 2/59 (3%)
Query: 380 AMLRRFEKRIFIDIPDPPAREAMLRHYLPPLVSESPRLCAELDYPALSKAMEGYSGSDI 438
A L F++ FID P LPP RL AE+ PA+++A+EG D
Sbjct: 29 ARLDNFQETRFIDPPGGEWLIGA-PVPLPPPWRGPERL-AEMAAPAIAEALEGLPALDA 85
>gnl|CDD|224616 COG1702, PhoH, Phosphate starvation-inducible protein PhoH,
predicted ATPase [Signal transduction mechanisms].
Length = 348
Score = 31.1 bits (71), Expect = 1.8
Identities = 11/18 (61%), Positives = 11/18 (61%)
Query: 267 HGPPGTGKTLLARAVATQ 284
GP GTGKT LA A A
Sbjct: 149 IGPAGTGKTYLAVAKAVD 166
>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 = 30.5 bits (69), Expect = 1.8
Identities = 13/30 (43%), Positives = 15/30 (50%)
Query: 255 RGLLSPWKAILLHGPPGTGKTLLARAVATQ 284
L + L GP GTGKT LA VA +
Sbjct: 15 LRYLKSGYPVHLRGPAGTGKTTLAMHVARK 44
>gnl|CDD|99810 cd06214, PA_degradation_oxidoreductase_like, NAD(P) binding domain
of ferredoxin reductase like phenylacetic acid (PA)
degradation oxidoreductase. PA oxidoreductases of E.
coli hydroxylate PA-CoA in the second step of PA
degradation. Members of this group typically fuse a
ferredoxin reductase-like domain with an iron-sulfur
binding cluster domain. Ferredoxins catalyze electron
transfer between an NAD(P)-binding domain of the
alpha/beta class and a discrete (usually N-terminal)
domain which vary in orientation with respect to the
NAD(P) binding domain. The N-terminal portion may
contain a flavin prosthetic group, as in flavoenzymes,
or use flavin as a substrate. Ferredoxin-NADP+
(oxido)reductase is an FAD-containing enzyme that
catalyzes the reversible electron transfer between
NADP(H) and electron carrier proteins such as ferredoxin
and flavodoxin. Isoforms of these flavoproteins (i.e.
having a non-covalently bound FAD as a prosthetic group)
are present in chloroplasts, mitochondria, and bacteria
and participate in a wide variety of redox metabolic
pathways. The C-terminal domain contains most of the
NADP(H) binding residues and the N-terminal domain
interacts non-covalently with the isoalloxazine rings of
the flavin molecule which lies largely in a large gap
betweed the two domains. Ferredoxin-NADP+ reductase
first accepts one electron from reduced ferredoxin to
form a flavin semiquinone intermediate. The enzyme then
accepts a second electron to form FADH2 which then
transfers two electrons and a proton to NADP+ to form
NADPH.
Length = 241
Score = 30.6 bits (70), Expect = 1.8
Identities = 16/58 (27%), Positives = 20/58 (34%), Gaps = 15/58 (25%)
Query: 313 FTL--ARKCAPSTIFLDELDAL-------------MSRRDGEEHEASRRLKAELLMQL 355
TL + S IF +EL L +SR G+ RL A L L
Sbjct: 139 VTLVYGNRTEASVIFREELADLKARYPDRLTVIHVLSREQGDPDLLRGRLDAAKLNAL 196
>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 = 30.9 bits (70), Expect = 1.8
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 264 ILLHGPPGTGKTLLARAV---ATQCTTTFFNISA 294
++++GPPG GKT AR V A + + F A
Sbjct: 89 VIIYGPPGVGKTAAARLVLEEAKKNPASPFKEGA 122
>gnl|CDD|214810 smart00763, AAA_PrkA, PrkA AAA domain. This is a family of PrkA
bacterial and archaeal serine kinases approximately 630
residues long. This is the N-terminal AAA domain.
Length = 361
Score = 30.7 bits (70), Expect = 1.9
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 255 RGLLSPWKAILLHGPPGTGKTLLARAV 281
+GL + + L GP G GK+ L +
Sbjct: 72 QGLEERKQILYLLGPVGGGKSSLVECL 98
>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 = 30.7 bits (70), Expect = 1.9
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 252 ELFRGLLSPWKAILLHGPPGTGKTLLA 278
E+ +G + + +L+ G PGTGKT+
Sbjct: 10 EILKGGIPRGRVVLITGGPGTGKTIFG 36
>gnl|CDD|224160 COG1239, ChlI, Mg-chelatase subunit ChlI [Coenzyme metabolism].
Length = 423
Score = 30.8 bits (70), Expect = 1.9
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 264 ILLHGPPGTGKTLLARAVAT 283
L+ G GT K+ LARA+A
Sbjct: 41 ALIAGEKGTAKSTLARALAD 60
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 31.1 bits (71), Expect = 2.0
Identities = 20/56 (35%), Positives = 25/56 (44%), Gaps = 9/56 (16%)
Query: 232 GLDSAKRLLLEAIVYPTRYPELFRGLLSPWKAI---LLHGPPGTGKTLLARAVATQ 284
G D A L+ AI GL P K + L GP G GKT LA+ +A +
Sbjct: 457 GQDEAIDQLVSAIKRS------RAGLGDPNKPVGSFLFVGPTGVGKTELAKQLAEE 506
>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 = 30.0 bits (68), Expect = 2.1
Identities = 15/72 (20%), Positives = 26/72 (36%), Gaps = 25/72 (34%)
Query: 264 ILLHGPPGTGKTLLARAVATQCTTTFFNISASSLVSKW-RGESEKLVRVLF-----TLAR 317
++L G G+GKT L + + W +G+ + +F L+R
Sbjct: 3 VILQGEAGSGKTTLLQ----------------KIALLWAQGKLPQDFDFVFFLPCRELSR 46
Query: 318 KCAPSTIFLDEL 329
S L +L
Sbjct: 47 SGEAS---LADL 55
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 31.0 bits (70), Expect = 2.1
Identities = 45/159 (28%), Positives = 72/159 (45%), Gaps = 29/159 (18%)
Query: 265 LLHGPPGTGKTLLARAVATQCTT----------TFFNISASSLV--SKWRGE-SEKLVRV 311
+L G PG GKT + +A + + +LV +K+RGE E+L V
Sbjct: 203 VLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGV 262
Query: 312 LFTLARKCAPSTIFLDELDALM--SRRDGEEHEASRRLKAELL---MQLDGLNTGEE-RV 365
L LA++ +F+DEL ++ + DG +A LK L + G T +E R
Sbjct: 263 LNDLAKQEGNVILFIDELHTMVGAGKADG-AMDAGNMLKPALARGELHCVGATTLDEYRQ 321
Query: 366 FLLATSNVPWDLDPAMLRRFEKRIFIDIPDPPAREAMLR 404
++ + D A+ RRF+K +F+ P A+LR
Sbjct: 322 YI--------EKDAALERRFQK-VFVAEPSVEDTIAILR 351
>gnl|CDD|215599 PLN03140, PLN03140, ABC transporter G family member; Provisional.
Length = 1470
Score = 31.0 bits (70), Expect = 2.2
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 256 GLLSPWKAILLHGPPGTGKTLLARAVA 282
G++ P + LL GPP +GKT L A+A
Sbjct: 186 GIIKPSRMTLLLGPPSSGKTTLLLALA 212
>gnl|CDD|213190 cd03223, ABCD_peroxisomal_ALDP, ATP-binding cassette domain of
peroxisomal transporter, subfamily D. Peroxisomal
ATP-binding cassette transporter (Pat) is involved in
the import of very long-chain fatty acids (VLCFA) into
the peroxisome. The peroxisomal membrane forms a
permeability barrier for a wide variety of metabolites
required for and formed during fatty acid
beta-oxidation. To communicate with the cytoplasm and
mitochondria, peroxisomes need dedicated proteins to
transport such hydrophilic molecules across their
membranes. X-linked adrenoleukodystrophy (X-ALD) is
caused by mutations in the ALD gene, which encodes ALDP
(adrenoleukodystrophy protein ), a peroxisomal integral
membrane protein that is a member of the ATP-binding
cassette (ABC) transporter protein family. The disease
is characterized by a striking and unpredictable
variation in phenotypic expression. Phenotypes include
the rapidly progressive childhood cerebral form (CCALD),
the milder adult form, adrenomyeloneuropathy (AMN), and
variants without neurologic involvement (i.e.
asymptomatic).
Length = 166
Score = 29.8 bits (68), Expect = 2.2
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 258 LSPWKAILLHGPPGTGKTLLARAVA 282
+ P +L+ GP GTGK+ L RA+A
Sbjct: 24 IKPGDRLLITGPSGTGKSSLFRALA 48
>gnl|CDD|224142 COG1221, PspF, Transcriptional regulators containing an AAA-type
ATPase domain and a DNA-binding domain [Transcription /
Signal transduction mechanisms].
Length = 403
Score = 30.4 bits (69), Expect = 2.3
Identities = 39/180 (21%), Positives = 61/180 (33%), Gaps = 51/180 (28%)
Query: 262 KAILLHGPPGTGKTLLARAVATQCT----TTF--FN---ISASSLVSKWRGESEKLVRVL 312
+L+ G GTGK L AR + F FN S + ++ G +
Sbjct: 102 LPVLIIGETGTGKELFARLIHALSARRAEAPFIAFNCAAYSENLQEAELFG----HEKGA 157
Query: 313 FTLARKCAPS--------TIFLDELDALMSRRDGEEHEASRRLKAELLMQLDGL---NTG 361
FT A+ T+FLDE+ H + +LL L+ G
Sbjct: 158 FTGAQGGKAGLFEQANGGTLFLDEI-----------HRLPPEGQEKLLRVLEEGEYRRVG 206
Query: 362 EERVF-----LLATSNVPWDLDPAMLRR---FEKRIFIDIPDPPARE------AMLRHYL 407
+ L+ + DL+ A+L + + I PP RE + H+L
Sbjct: 207 GSQPRPVDVRLICATTE--DLEEAVLAGADLTRRLNILTITLPPLRERKEDILLLAEHFL 264
>gnl|CDD|183452 PRK12337, PRK12337, 2-phosphoglycerate kinase; Provisional.
Length = 475
Score = 30.5 bits (69), Expect = 2.4
Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 3/36 (8%)
Query: 249 RYPELFRGLLSPWKA--ILLHGPPGTGKTLLARAVA 282
RY L R + P + +L+ G G GK++LA A+A
Sbjct: 242 RY-RLLRSIRRPPRPLHVLIGGVSGVGKSVLASALA 276
>gnl|CDD|131577 TIGR02525, plasmid_TraJ, plasmid transfer ATPase TraJ. Members of
this protein family are predicted ATPases associated
with plasmid transfer loci in bacteria. This family is
most similar to the DotB ATPase of a type-IV
secretion-like system of obligate intracellular
pathogens Legionella pneumophila and Coxiella burnetii
(TIGR02524) [Mobile and extrachromosomal element
functions, Plasmid functions].
Length = 372
Score = 30.5 bits (69), Expect = 2.4
Identities = 26/88 (29%), Positives = 41/88 (46%), Gaps = 18/88 (20%)
Query: 211 RLKPRPHFVQSTILFSVPHTLGLDSAKRLLLEAIVYPTRYP---------ELFRGLLSPW 261
R++ R +F+Q+TI L++A L L I P+ P +LF LL
Sbjct: 99 RVRFRCNFIQATI-------GKLETAISLTLRVI--PSDIPDLKQMGIEPDLFNSLLPAA 149
Query: 262 KAILLHGPPGTGKTLLARAVATQCTTTF 289
L+ G G+GK+ LA ++ C T+
Sbjct: 150 GLGLICGETGSGKSTLAASIYQHCGETY 177
>gnl|CDD|178120 PLN02504, PLN02504, nitrilase.
Length = 346
Score = 30.5 bits (69), Expect = 2.4
Identities = 19/46 (41%), Positives = 26/46 (56%), Gaps = 6/46 (13%)
Query: 215 RPHFVQ-STILFSVPHTLGLDSAKRLLLEAIVYPTR---YPELFRG 256
R VQ ST+ + P TL D A+RL+ EA Y ++ +PE F G
Sbjct: 26 RATVVQASTVFYDTPATL--DKAERLIAEAAAYGSQLVVFPEAFIG 69
>gnl|CDD|226372 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 30.2 bits (68), Expect = 2.7
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 261 WKAILLHGPPGTGKTLLARAVA 282
W L+ GPP GKT L R +A
Sbjct: 137 WLNTLIIGPPQVGKTTLLRDIA 158
>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 = 29.9 bits (68), Expect = 2.8
Identities = 13/20 (65%), Positives = 15/20 (75%)
Query: 262 KAILLHGPPGTGKTLLARAV 281
A+LL G PG GKT LARA+
Sbjct: 13 VAVLLGGQPGAGKTELARAL 32
>gnl|CDD|221320 pfam11927, DUF3445, Protein of unknown function (DUF3445). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria and eukaryotes.
Proteins in this family are typically between 264 to 418
amino acids in length. This protein has a conserved RLP
sequence motif. This protein has two completely
conserved R residues that may be functionally important.
Length = 245
Score = 29.8 bits (68), Expect = 3.1
Identities = 19/87 (21%), Positives = 30/87 (34%), Gaps = 16/87 (18%)
Query: 183 NTHWTDVIELSQAYESYLQMDQSKREIMRLKPRPHFVQSTILFSVPHTLGLDSAKRLLLE 242
D IEL Y + + ++ P +L +P + A LLE
Sbjct: 5 KLDPEDWIELDNTYADRMAE---RARLLAEHP------DRVLALLPEA---EPAAWELLE 52
Query: 243 AIV--YPTRYPELFRGLLSPWKAILLH 267
++ P RYP+ F L+ H
Sbjct: 53 LVLEYLPARYPQYFS--LTRDGDRTWH 77
>gnl|CDD|236134 PRK07940, PRK07940, DNA polymerase III subunit delta'; Validated.
Length = 394
Score = 30.3 bits (69), Expect = 3.2
Identities = 13/24 (54%), Positives = 17/24 (70%), Gaps = 2/24 (8%)
Query: 265 LLHGPPGTGKTLLARAVAT--QCT 286
L GPPG+G+++ ARA A QCT
Sbjct: 40 LFTGPPGSGRSVAARAFAAALQCT 63
>gnl|CDD|237555 PRK13914, PRK13914, invasion associated secreted endopeptidase;
Provisional.
Length = 481
Score = 30.2 bits (67), Expect = 3.2
Identities = 29/130 (22%), Positives = 56/130 (43%), Gaps = 12/130 (9%)
Query: 414 SPRLCAELDYPALSK-----AMEGYSGSDIKSVCKEVAMQRVRDTFELLERMNPG---LT 465
+P+ + + PA K E + + + KE Q+ E P T
Sbjct: 251 TPKAEVKTEAPAAEKQAAPVVKENTNTNTATTEKKETTTQQQTAPKAPTEAAKPAPAPST 310
Query: 466 MTNTSLSGSMTNI-NNTGHGMTGSKNNHSHSNLNASVSGQSMNINMKNHSNNHSISSHSM 524
TN + + + TN N + T SKN ++++N N + + N N S+N++ +S +
Sbjct: 311 NTNANKTNTNTNTNTNNTNTSTPSKNTNTNTNSNTN---TNSNTNANQGSSNNNSNSSAS 367
Query: 525 TGMAQMKTHI 534
+A+ + H+
Sbjct: 368 AIIAEAQKHL 377
>gnl|CDD|235825 PRK06547, PRK06547, hypothetical protein; Provisional.
Length = 172
Score = 29.3 bits (66), Expect = 3.3
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 2/43 (4%)
Query: 264 ILLHGPPGTGKTLLARAVATQCTTTFFNISASSLVSKWRGESE 306
+L+ G G+GKT LA A+A T F + L W G +
Sbjct: 18 VLIDGRSGSGKTTLAGALA--ARTGFQLVHLDDLYPGWHGLAA 58
>gnl|CDD|233448 TIGR01526, nadR_NMN_Atrans, nicotinamide-nucleotide
adenylyltransferase, NadR type. The NadR protein of E.
coli and closely related bacteria is both enzyme and
regulatory protein. The first 60 or so amino acids,
N-terminal to the region covered by this model, is a
DNA-binding helix-turn-helix domain (pfam01381)
responsible for repressing the nadAB genes of NAD de
novo biosynthesis. The NadR homologs in Mycobacterium
tuberculosis, Haemophilus influenzae, and others appear
to lack the repressor domain. NadR has recently been
shown to act as an enzyme of the salvage pathway of NAD
biosynthesis, nicotinamide-nucleotide
adenylyltransferase; members of this family are presumed
to share this activity. E. coli NadR has also been found
to regulate the import of its substrate, nicotinamide
ribonucleotide, but it is not known if the other members
of this model share that activity.
Length = 325
Score = 29.8 bits (67), Expect = 3.4
Identities = 34/149 (22%), Positives = 45/149 (30%), Gaps = 29/149 (19%)
Query: 246 YPTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQCTTTFFNISASSLVSKWRGES 305
+ P R AIL G TGK+ L +A TT A V + G
Sbjct: 149 HWKHIPREVRPFFVKTVAIL--GGESTGKSTLVNKLAAVFNTTSAWEYAREYVEEKLGGD 206
Query: 306 EKLV-----------RVLFTLARKCAPSTIFLDELDALMSR-----RDGEEHEASRRLKA 349
E L + A + A F+D D + ++ +G EH A
Sbjct: 207 EALQYSDYAQIALGQQRYIDYAVRHAHKIAFIDT-DFITTQVFAKQYEGREHPFLDSDIA 265
Query: 350 ELLMQLDGLNTGEERVFLLATSNVPWDLD 378
E L LL N W D
Sbjct: 266 EYPFDL----------TLLLKPNTEWVDD 284
>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 = 29.5 bits (67), Expect = 3.4
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 264 ILLHGPPGTGKTLLARAVATQCTTTFFNISASSLV 298
ILL GPPG+GK A +A + +IS L+
Sbjct: 2 ILLLGPPGSGKGTQAERLAKK--YGLPHISTGDLL 34
>gnl|CDD|225114 COG2204, AtoC, Response regulator containing CheY-like receiver,
AAA-type ATPase, and DNA-binding domains [Signal
transduction mechanisms].
Length = 464
Score = 30.0 bits (68), Expect = 3.4
Identities = 22/78 (28%), Positives = 34/78 (43%), Gaps = 14/78 (17%)
Query: 264 ILLHGPPGTGKTLLARAVATQCTTT---FFNISASSLVSKWRGESE--KLVRVLFTLARK 318
+L+ G GTGK L+ARA+ F ++ ++ + + ESE + FT A
Sbjct: 167 VLITGESGTGKELVARAIHQASPRAKGPFIAVNCAA-IPENLLESELFGHEKGAFTGAIT 225
Query: 319 CAPS--------TIFLDE 328
T+FLDE
Sbjct: 226 RRIGRFEQANGGTLFLDE 243
>gnl|CDD|238541 cd01121, Sms, Sms (bacterial radA) DNA repair protein. This protein
is not related to archael radA any more than is to other
RecA-like NTPases. Sms has a role in recombination and
recombinational repair and is responsible for the
stabilization or processing of branched DNA molecules.
Length = 372
Score = 29.9 bits (68), Expect = 3.5
Identities = 18/46 (39%), Positives = 21/46 (45%), Gaps = 3/46 (6%)
Query: 246 YPTRYPELFR---GLLSPWKAILLHGPPGTGKTLLARAVATQCTTT 288
PT EL R G L P IL+ G PG GK+ L VA +
Sbjct: 64 IPTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAKR 109
>gnl|CDD|225822 COG3284, AcoR, Transcriptional activator of acetoin/glycerol
metabolism [Secondary metabolites biosynthesis,
transport, and catabolism / Transcription].
Length = 606
Score = 30.0 bits (68), Expect = 3.7
Identities = 19/59 (32%), Positives = 25/59 (42%), Gaps = 3/59 (5%)
Query: 224 LFSVPHTLGLDSAKRLLLEAIVYPTRYPELFRGLLSPWKA-ILLHGPPGTGKTLLARAV 281
S P G SA L T + R ++ +LL G GTGK +LARA+
Sbjct: 300 HLSAPRAKGNASAAAPPLLDPSRATLLRKAER--VAATDLPVLLQGETGTGKEVLARAI 356
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 29.9 bits (68), Expect = 3.7
Identities = 12/16 (75%), Positives = 14/16 (87%)
Query: 264 ILLHGPPGTGKTLLAR 279
+LL GPPGTGKT+LA
Sbjct: 201 LLLVGPPGTGKTMLAS 216
>gnl|CDD|226969 COG4618, ArpD, ABC-type protease/lipase transport system, ATPase
and permease components [General function prediction
only].
Length = 580
Score = 29.9 bits (68), Expect = 4.1
Identities = 24/106 (22%), Positives = 39/106 (36%), Gaps = 30/106 (28%)
Query: 185 HWTDVIELSQAY---ESYLQMDQSKREIMRLKPRPHFVQSTILFSVPHTLGLDSAKRLLL 241
+W + Q+Y L + E M L P P L +
Sbjct: 298 NWKQFVAARQSYKRLNELLAELPAAAERMPL-PAPQG-------------------ALSV 337
Query: 242 EAIVY---PTRYPELFRGL---LSPWKAILLHGPPGTGKTLLARAV 281
E + + P L +G+ L +A+ + GP G+GK+ LAR +
Sbjct: 338 ERLTAAPPGQKKPIL-KGISFALQAGEALGIIGPSGSGKSTLARLL 382
>gnl|CDD|178971 PRK00306, PRK00306, 50S ribosomal protein L29; Reviewed.
Length = 66
Score = 27.1 bits (61), Expect = 4.6
Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 8/45 (17%)
Query: 72 ILQEYEDYYQLRFNKQPKITKKLDTSHPIDKRSDREVKRSLARVK 116
+L+ ++ + LRF K T +L+ +H + REV+R +AR+K
Sbjct: 18 LLELKKELFNLRFQK---ATGQLENTHRL-----REVRRDIARIK 54
>gnl|CDD|214396 CHL00206, ycf2, Ycf2; Provisional.
Length = 2281
Score = 29.9 bits (67), Expect = 4.7
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 258 LSPWKAILLHGPPGTGKTLLARAVAT 283
LSP + IL+ G GTG++ L + +AT
Sbjct: 1627 LSPSRGILVIGSIGTGRSYLVKYLAT 1652
>gnl|CDD|225892 COG3356, COG3356, Predicted membrane protein [Function unknown].
Length = 578
Score = 29.7 bits (67), Expect = 4.7
Identities = 17/44 (38%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 96 TSHPIDKRSDREVKRSLARVKSA----PPHKSASLPVKPEEVEF 135
TSH + S REV + + V+SA ++AS P K E EF
Sbjct: 288 TSHDFNPVSRREVDKIVEAVRSALDEMTDTEAASRPRKVERGEF 331
>gnl|CDD|220440 pfam09848, DUF2075, Uncharacterized conserved protein (DUF2075).
This domain, found in various prokaryotic proteins
(including putative ATP/GTP binding proteins), has no
known function.
Length = 348
Score = 29.5 bits (67), Expect = 4.8
Identities = 11/28 (39%), Positives = 18/28 (64%), Gaps = 1/28 (3%)
Query: 262 KAILL-HGPPGTGKTLLARAVATQCTTT 288
KA+ L G PGTGKT++A + + + +
Sbjct: 1 KAVFLVTGGPGTGKTVVALNLFAELSDS 28
>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 = 28.7 bits (65), Expect = 4.8
Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 5/49 (10%)
Query: 239 LLLEAI--VYPTRYPELFRGL---LSPWKAILLHGPPGTGKTLLARAVA 282
L +E + YP P + R + + P +++ + GP G+GK+ LAR +
Sbjct: 1 LEVENVSFRYPGAEPPVLRNVSFSIEPGESLAIIGPSGSGKSTLARLIL 49
>gnl|CDD|227707 COG5420, COG5420, Uncharacterized conserved small protein
containing a coiled-coil domain [Function unknown].
Length = 71
Score = 27.2 bits (60), Expect = 4.9
Identities = 9/34 (26%), Positives = 24/34 (70%), Gaps = 1/34 (2%)
Query: 181 DVNTHWTDVIELS-QAYESYLQMDQSKREIMRLK 213
+ WT+++ ++ + +E+Y ++D +KRE+ +L+
Sbjct: 35 GLPVKWTEIMAVAEKTFEAYAELDAAKRELAKLE 68
>gnl|CDD|223873 COG0802, COG0802, Predicted ATPase or kinase [General function
prediction only].
Length = 149
Score = 28.8 bits (65), Expect = 5.0
Identities = 11/26 (42%), Positives = 13/26 (50%)
Query: 257 LLSPWKAILLHGPPGTGKTLLARAVA 282
L +LL G G GKT L R +A
Sbjct: 21 ALKAGDVVLLSGDLGAGKTTLVRGIA 46
>gnl|CDD|225713 COG3172, NadR, Predicted ATPase/kinase involved in NAD metabolism
[Coenzyme metabolism].
Length = 187
Score = 28.9 bits (65), Expect = 5.0
Identities = 31/133 (23%), Positives = 43/133 (32%), Gaps = 27/133 (20%)
Query: 262 KAILLHGPPGTGKTLLARAVATQCTTTFFNISASSLVSKWRGESEKLV-----------R 310
K + + G +GK+ L +A TT V + G E L
Sbjct: 9 KTVAILGGESSGKSTLVNKLANIFNTTSAWEYGREYVFEHLGGDEALQYSDYAKIALGQA 68
Query: 311 VLFTLARKCAPSTIFLDELDALMSR-----RDGEEHEASRRLKAELLMQLDGLNTGEERV 365
A + A F+D D L ++ +G EH + L AE L
Sbjct: 69 AYEDAAVRYANKVAFIDT-DFLTTQAFCKKYEGREHPFLQALIAEYRFDL---------- 117
Query: 366 FLLATSNVPWDLD 378
LL N PW D
Sbjct: 118 TLLLEPNTPWVAD 130
>gnl|CDD|215428 PLN02798, PLN02798, nitrilase.
Length = 286
Score = 29.3 bits (66), Expect = 5.2
Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 9/51 (17%)
Query: 244 IVYPTRYPELFRGLLSPWKAILLHGPPG----TG----KTLL-ARAVATQC 285
+ Y R+PEL++ L A +L P TG + LL ARA+ TQC
Sbjct: 162 VCYDLRFPELYQQLRFEHGAQVLLVPSAFTKPTGEAHWEVLLRARAIETQC 212
>gnl|CDD|226132 COG3604, FhlA, Transcriptional regulator containing GAF, AAA-type
ATPase, and DNA binding domains [Transcription / Signal
transduction mechanisms].
Length = 550
Score = 29.6 bits (67), Expect = 5.2
Identities = 20/83 (24%), Positives = 32/83 (38%), Gaps = 14/83 (16%)
Query: 201 QMDQSKREIMRLKPRPHFVQSTILFSVPHTLGLDSAKRLLLEAI--VYPTRYPELFRGLL 258
++ K + S ++ V +G A R LL+ I V +
Sbjct: 196 ELSSLKERLEEENLALEEQLSEVVLEVGGIIGRSPAMRQLLKEIEVVAKSDST------- 248
Query: 259 SPWKAILLHGPPGTGKTLLARAV 281
+L+ G GTGK L+ARA+
Sbjct: 249 -----VLIRGETGTGKELVARAI 266
>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 = 28.8 bits (65), Expect = 5.3
Identities = 10/15 (66%), Positives = 10/15 (66%)
Query: 264 ILLHGPPGTGKTLLA 278
LL G PGTGKT A
Sbjct: 2 TLLSGGPGTGKTTFA 16
>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 = 29.4 bits (66), Expect = 5.4
Identities = 11/19 (57%), Positives = 16/19 (84%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
+LL G PG GK++LA+A+A
Sbjct: 40 VLLIGEPGVGKSMLAKAMA 58
>gnl|CDD|173868 cd08503, PBP2_NikA_DppA_OppA_like_17, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 460
Score = 29.5 bits (67), Expect = 5.4
Identities = 14/30 (46%), Positives = 14/30 (46%), Gaps = 3/30 (10%)
Query: 375 WDLDPAMLRRFEKRIFIDIPDPPAREAMLR 404
W L R E FIDIPDP AR L
Sbjct: 183 WKPGRPYLDRIE---FIDIPDPAARVNALL 209
>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 = 28.7 bits (65), Expect = 5.4
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
I+L G G GKT + R +A
Sbjct: 2 IVLIGMMGAGKTTVGRLLA 20
>gnl|CDD|220564 pfam10094, DUF2332, Uncharacterized protein conserved in bacteria
(DUF2332). Members of this family of hypothetical
bacterial proteins have no known function.
Length = 342
Score = 29.2 bits (66), Expect = 5.7
Identities = 17/72 (23%), Positives = 23/72 (31%), Gaps = 8/72 (11%)
Query: 378 DPAMLRRFEKRIFIDIPDPPAREAMLR-----HYLPPLVSESPRLCAELDYPALSKAMEG 432
D L +RI DP LR H L L +P L A YP+ A +
Sbjct: 30 DLEALGAVGRRIAGWEGDPAGDAVPLRLLGALHAL-VLRGRAPPLAAV--YPSADDADDE 86
Query: 433 YSGSDIKSVCKE 444
++
Sbjct: 87 ALWPAVRDALAR 98
>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 = 29.1 bits (66), Expect = 6.1
Identities = 10/20 (50%), Positives = 15/20 (75%), Gaps = 1/20 (5%)
Query: 264 ILLHGPPGTGKT-LLARAVA 282
+L G G+GK+ LLA+A+A
Sbjct: 26 FVLTGERGSGKSVLLAQAMA 45
>gnl|CDD|178806 PRK00030, minC, septum formation inhibitor; Provisional.
Length = 292
Score = 29.3 bits (65), Expect = 6.2
Identities = 14/44 (31%), Positives = 26/44 (59%)
Query: 409 PLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVRD 452
P+V ++ R+ A +D+PAL +A+ ++ I V + +Q RD
Sbjct: 49 PVVIDATRVDAPVDWPALLQALADHNLPPIGVVAEGANLQGARD 92
>gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional.
Length = 259
Score = 28.9 bits (65), Expect = 6.3
Identities = 39/144 (27%), Positives = 60/144 (41%), Gaps = 44/144 (30%)
Query: 264 ILLHGPPGTGKTLLARAV---ATQC--TTTFFNISASSLV-----SKWRGE-SEKLVRVL 312
I+L GP G GKT LA A+ A + F +A+ L+ ++ +G L R +
Sbjct: 105 IVLLGPSGVGKTHLAIALGYEAVRAGIKVRF--TTAADLLLQLSTAQRQGRYKTTLQRGV 162
Query: 313 FTLARKCAPSTIFLDELDAL-MSRRDGEEHEASRRLKAELLMQLDGLNTGEERVFLLATS 371
AP + +DE+ L S+ + A L Q+ + E+ ++ TS
Sbjct: 163 M------APRLLIIDEIGYLPFSQEE-----------ANLFFQV--IAKRYEKGSMILTS 203
Query: 372 NVP---WD--------LDPAMLRR 384
N+P WD L AML R
Sbjct: 204 NLPFGQWDQTFAGDAALTSAMLDR 227
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 29.1 bits (66), Expect = 6.3
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 259 SPWKAILLHGPPGTGKTLLARAVA 282
+ +L +G GTGKT L+ +A
Sbjct: 181 KNNENLLFYGNTGTGKTFLSNCIA 204
>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 = 29.0 bits (65), Expect = 6.3
Identities = 16/65 (24%), Positives = 30/65 (46%), Gaps = 3/65 (4%)
Query: 266 LHGPPGTGKTLLARAVATQCTTTFFNISASSLVSKWRGESEKLVRVLFTLARKCAPSTIF 325
++GPPGTGKT +A +A + + + + SE+ ++ + A S I
Sbjct: 24 VYGPPGTGKTNIAIQLAVETAGQGKKV---AYIDTEGLSSERFRQIAGDRPERAASSIIV 80
Query: 326 LDELD 330
+ +D
Sbjct: 81 FEPMD 85
>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 = 28.8 bits (65), Expect = 6.4
Identities = 10/40 (25%), Positives = 17/40 (42%), Gaps = 1/40 (2%)
Query: 262 KAILLHGPPGTGKT-LLARAVATQCTTTFFNISASSLVSK 300
+LL GP +GKT L + + +T +I +
Sbjct: 1 PTVLLLGPSDSGKTALFTKLTTGKVRSTVTSIEPNVASFY 40
>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 = 28.2 bits (64), Expect = 6.5
Identities = 7/15 (46%), Positives = 12/15 (80%)
Query: 268 GPPGTGKTLLARAVA 282
GP G+GK+ +A+ +A
Sbjct: 6 GPAGSGKSTVAKLLA 20
>gnl|CDD|234132 TIGR03167, tRNA_sel_U_synt, tRNA 2-selenouridine synthase. The
Escherichia coli YbbB protein was shown to encode a
selenophosphate-dependent tRNA 2-selenouridine synthase,
essential for modification of some tRNAs to replace a
sulfur atom with selenium. This enzyme works with SelD,
the selenium donor protein, which also acts in
selenocysteine incorporation. Although the members of
this protein family show a fairly deep split, sequences
from both sides of the split are supported by
co-occurence with, and often proximity to, the selD gene
[Protein synthesis, tRNA and rRNA base modification].
Length = 311
Score = 29.1 bits (66), Expect = 6.5
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 257 LLSPWKAILLHGPPGTGKTLL 277
L P+ I+L G G+GKT L
Sbjct: 123 LPQPFPLIVLGGMTGSGKTEL 143
>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 29.2 bits (66), Expect = 6.6
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
+ ++G G GKT L +A+
Sbjct: 116 LFIYGGVGLGKTHLLQAIG 134
>gnl|CDD|182412 PRK10365, PRK10365, transcriptional regulatory protein ZraR;
Provisional.
Length = 441
Score = 29.2 bits (65), Expect = 6.6
Identities = 14/26 (53%), Positives = 21/26 (80%), Gaps = 1/26 (3%)
Query: 257 LLSPWKA-ILLHGPPGTGKTLLARAV 281
L++P +A +L+HG GTGK L+ARA+
Sbjct: 157 LVAPSEATVLIHGDSGTGKELVARAI 182
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 29.1 bits (66), Expect = 6.7
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
+L GPPGTGKT A A+A
Sbjct: 41 LLFAGPPGTGKTTAALALA 59
>gnl|CDD|226350 COG3829, RocR, Transcriptional regulator containing PAS, AAA-type
ATPase, and DNA-binding domains [Transcription / Signal
transduction mechanisms].
Length = 560
Score = 29.2 bits (66), Expect = 6.8
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 264 ILLHGPPGTGKTLLARAV 281
+L+ G GTGK L ARA+
Sbjct: 271 VLILGESGTGKELFARAI 288
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 28.4 bits (64), Expect = 7.0
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
IL+ GPPG GK+ LA+ +A
Sbjct: 3 ILILGPPGAGKSTLAKKLA 21
>gnl|CDD|237937 PRK15304, PRK15304, putative fimbrial outer membrane usher protein;
Provisional.
Length = 801
Score = 29.3 bits (66), Expect = 7.3
Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 9/79 (11%)
Query: 469 TSLSGSM-TNINNTGHGMTGSKNNHSHSNLNASVSGQSMNINMKNHSNNHSISSHSMT-- 525
S +GS+ +N++ T + + + N NA++SG I H + S +++
Sbjct: 583 NSFNGSLNSNLHYTQLSVGAGTDGDDNRNYNATLSG---GIAA--HDQGVTFSPYTIKDT 637
Query: 526 -GMAQMKTHIKLKTITTQQ 543
+A++ + I T Q
Sbjct: 638 FAIARLDEPVAGVEIATPQ 656
>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 29.1 bits (65), Expect = 7.5
Identities = 11/33 (33%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 50 CLQEEARLSEHYSLCDNVDLATILQEYEDYYQL 82
CL+E + E Y++ + + L L+ +ED+Y L
Sbjct: 30 CLKEPN-VFEKYAVRNALKLRGTLKFWEDFYIL 61
>gnl|CDD|225358 COG2768, COG2768, Uncharacterized Fe-S center protein [General
function prediction only].
Length = 354
Score = 29.0 bits (65), Expect = 7.6
Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 2/41 (4%)
Query: 461 NPGLTMTNTSLSGSMTNINNTGHGMTGSKNNHSHSNLNASV 501
P +T TNT GS N + H ++N ++ A +
Sbjct: 74 KPFVTDTNTLYEGSRHNAVD--HLRNATENGATYIVTGAPL 112
>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT
(nicotinate-mononucleotide:5, 6-dimethylbenzimidazole
phosphoribosyltransferase) [Coenzyme metabolism].
Length = 620
Score = 29.0 bits (65), Expect = 7.8
Identities = 25/87 (28%), Positives = 35/87 (40%), Gaps = 18/87 (20%)
Query: 324 IFLDELDALMSRRDGEEHEASRRLKAELLMQLDGLNTGEERVF------LLATSNVPWD- 376
+F E D ++ + + RL+A L QL L+ R+ L+A N WD
Sbjct: 319 VFTREFDEIVLAEELCDEAELDRLRAFLDKQLAHLSGVVGRLANRLQRRLMAQQNRSWDF 378
Query: 377 ------LDPAMLRRFEKRIFIDIPDPP 397
LD A L R+ ID P P
Sbjct: 379 DLEEGYLDGARL----VRLIID-PMQP 400
>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 = 28.2 bits (63), Expect = 7.9
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
I + GPPG+GKT +A+ +A
Sbjct: 3 ITISGPPGSGKTTVAKILA 21
>gnl|CDD|234175 TIGR03348, VI_IcmF, type VI secretion protein IcmF. Members of
this protein family are IcmF homologs and tend to be
associated with type VI secretion systems [Cellular
processes, Pathogenesis].
Length = 1169
Score = 29.2 bits (66), Expect = 8.2
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 3/22 (13%)
Query: 260 PWKAILLHGPPGTGKT-LLARA 280
PW ++ GPPG+GKT LL +
Sbjct: 112 PWYLVI--GPPGSGKTTLLQNS 131
>gnl|CDD|224985 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport
and metabolism].
Length = 299
Score = 28.9 bits (65), Expect = 8.2
Identities = 10/29 (34%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 254 FRGLLSPWKAILLHGPPGTGKTLLARAVA 282
R + P IL+ G G GK+ +A +A
Sbjct: 83 IRKMKRP-LIILIGGASGVGKSTIAGELA 110
>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 = 28.7 bits (65), Expect = 8.7
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 263 AILLHGPPGTGKTLLARAVA 282
A L GP GTGKT +AR A
Sbjct: 38 AYLFSGPRGTGKTSIARIFA 57
>gnl|CDD|221143 pfam11593, Med3, Mediator complex subunit 3 fungal. Mediator is a
large complex of up to 33 proteins that is conserved
from plants to fungi to humans - the number and
representation of individual subunits varying with
species. It is arranged into four different sections, a
core, a head, a tail and a kinase-activity part, and the
number of subunits within each of these is what varies
with species. Overall, Mediator regulates the
transcriptional activity of RNA polymerase II but it
would appear that each of the four different sections
has a slightly different function. Mediator subunit
Hrs1/Med3 is a physical target for Cyc8-Tup1, a yeast
transcriptional co-repressor.
Length = 381
Score = 28.8 bits (64), Expect = 8.8
Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 4/62 (6%)
Query: 460 MNPGLTMTNTSLSGSMTNI---NNTGHGMTGSKNNHSHSNLN-ASVSGQSMNINMKNHSN 515
N G MT ++ +G+M N N+ GMT S + + +N+ A++ S+N+ + N
Sbjct: 280 QNNGGQMTPSANNGNMNNQSRENSMNQGMTPSASMINLNNITPANILNMSLNLAFDLNQN 339
Query: 516 NH 517
Sbjct: 340 QT 341
>gnl|CDD|218431 pfam05099, TerB, Tellurite resistance protein TerB. This family
contains the TerB tellurite resistance proteins from a a
number of bacteria.
Length = 140
Score = 27.5 bits (62), Expect = 9.0
Identities = 21/78 (26%), Positives = 30/78 (38%), Gaps = 11/78 (14%)
Query: 331 ALMSRRDGEEHEASRRLKAELLMQLDGLNTGEE----RVFLLATSNVPWDLDPAMLRRFE 386
A +++ DG+ E R+ LL GL+ E + A P DL F
Sbjct: 31 AEVAKADGQVDEEERQAIRRLLRSRFGLDPEEAAALIELAEEAEQEAP-DLY-----EFT 84
Query: 387 KRIFIDIPDPPAREAMLR 404
+ I D D R A+L
Sbjct: 85 RAIK-DHFDYEQRLALLE 101
>gnl|CDD|234057 TIGR02915, PEP_resp_reg, PEP-CTERM-box response regulator
transcription factor. Members of this protein family
share full-length homology with (but do not include) the
acetoacetate metabolism regulatory protein AtoC (see
SP|Q06065). These proteins have a Fis family DNA binding
sequence (pfam02954), a response regulator receiver
domain (pfam00072), and sigma-54 interaction domain
(pfam00158) [Regulatory functions, DNA interactions].
Length = 445
Score = 28.6 bits (64), Expect = 9.1
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 264 ILLHGPPGTGKTLLARAV 281
+LL G GTGK +LARA+
Sbjct: 165 VLLLGESGTGKEVLARAL 182
>gnl|CDD|238243 cd00427, Ribosomal_L29_HIP, Ribosomal L29 protein/HIP. L29 is a
protein of the large ribosomal Subunit. A homolog,
called heparin/heparan sulfate interacting protein
(HIP), has also been identified in mammals. L29 is
located on the surface of the large ribosomal subunit,
where it participates in forming a protein ring that
surrounds the polypeptide exit channel, providing
structural support for the ribosome. L29 is involved in
forming the translocon binding site, along with L19,
L22, L23, L24, and L31e. In addition, L29 and L23 form
the interaction site for trigger factor (TF) on the
ribosomal surface, adjacent to the exit tunnel. L29
forms numerous interactions with L23 and with the 23S
rRNA. In some eukaryotes, L29 is referred to as L35,
which is distinct from L35 found in bacteria and some
eukaryotes (primarily plastids and mitochondria). The
mammalian homolog, HIP, is found on the surface of many
tissues and cell lines. It is believed to play a role in
cell adhesion and modulation of blood coagulation. It
has also been shown to inhibit apoptosis in cancer
cells.
Length = 57
Score = 25.9 bits (58), Expect = 9.1
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 8/47 (17%)
Query: 70 ATILQEYEDYYQLRFNKQPKITKKLDTSHPIDKRSDREVKRSLARVK 116
+ + ++ + LRF K T +L+ H I R+V++ +AR+K
Sbjct: 13 EKLDELKKELFNLRFQKA---TGQLENPHRI-----RKVRKDIARIK 51
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 28.9 bits (65), Expect = 9.4
Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 3/30 (10%)
Query: 256 GLLSPWKAI---LLHGPPGTGKTLLARAVA 282
GL +P + I L GP G GKT L +A+A
Sbjct: 531 GLKNPNRPIASFLFSGPTGVGKTELTKALA 560
>gnl|CDD|215175 PLN02309, PLN02309, 5'-adenylylsulfate reductase.
Length = 457
Score = 28.6 bits (64), Expect = 9.9
Identities = 10/41 (24%), Positives = 16/41 (39%)
Query: 394 PDPPAREAMLRHYLPPLVSESPRLCAELDYPALSKAMEGYS 434
P AR+AM+ + D+ L+K +E S
Sbjct: 57 AQPAARQAMIPSAATAVAEVPEEEGEVEDFEKLAKELENAS 97
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
0.317 0.131 0.381
Gapped
Lambda K H
0.267 0.0740 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 28,759,421
Number of extensions: 2826053
Number of successful extensions: 3318
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3233
Number of HSP's successfully gapped: 206
Length of query: 570
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 468
Effective length of database: 6,413,494
Effective search space: 3001515192
Effective search space used: 3001515192
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 62 (27.6 bits)