RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780545|ref|YP_003064958.1| metalloprotease [Candidatus
Liberibacter asiaticus str. psy62]
(647 letters)
>gnl|CDD|162266 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.
Length = 495
Score = 788 bits (2038), Expect = 0.0
Identities = 306/497 (61%), Positives = 384/497 (77%), Gaps = 4/497 (0%)
Query: 95 LLSYLGSWFPLVLV-VLVWMFLMRQIQGGGARGAMGFGKSKAKLLSGNVGSVTFKDVAGV 153
LL +L S P +L+ V VW F RQ+QGGG A FGKSKAKLL+ VTFKDVAG+
Sbjct: 2 LLGFLFSLLPPILLLVGVWFFFRRQMQGGG-GRAFSFGKSKAKLLNEEKPKVTFKDVAGI 60
Query: 154 DEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEANVPFFTIS 213
DEAKE+L EIVDFL +P KF +LG +IP GVLLVGPPGTGKTLLA+AVAGEA VPFF+IS
Sbjct: 61 DEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSIS 120
Query: 214 GSDFVELFVGVGASRVRDMFEQAKNNSPCIVFVDEIDAVGRHRGIGLGGGNDEREQTLNQ 273
GSDFVE+FVGVGASRVRD+FEQAK N+PCI+F+DEIDAVGR RG GLGGGNDEREQTLNQ
Sbjct: 121 GSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQ 180
Query: 274 LLVEMDGFESSEGVILIAATNRPDVLDAALLRPGRFDRQITVPNPDIVGREHILMVHSRN 333
LLVEMDGF ++ GVI+IAATNRPDVLD ALLRPGRFDRQ+ V PDI GRE IL VH++N
Sbjct: 181 LLVEMDGFGTNTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKN 240
Query: 334 VPLAPNVILKTIARGTPGFSGADLRNLVNEAALMAARRNRRLVTMQEFEDAKDKILMGAE 393
LAP+V LK +AR TPGFSGADL NL+NEAAL+AAR+N+ +TM + E+A D+++ G E
Sbjct: 241 KKLAPDVDLKAVARRTPGFSGADLANLLNEAALLAARKNKTEITMNDIEEAIDRVIAGPE 300
Query: 394 RRSTAMTEEEKKITAYHEAGHAVVACHVPKADPLHKATIIPRGRALGMVMQLPEADRHST 453
++S ++E+EKK+ AYHEAGHA+V + ADP+HK TIIPRG+ALG LPE D++
Sbjct: 301 KKSRVISEKEKKLVAYHEAGHALVGLLLKDADPVHKVTIIPRGQALGYTQFLPEEDKYLY 360
Query: 454 TYVWMTSRLTILMGGRVAEEFTFGEDNVTSGAMSDIEYATKLARVMVTQFGFSNLLGKVS 513
T + +++ +L+GGR AEE FGE VT+GA +DI+ AT +AR MVT++G S+ LG V+
Sbjct: 361 TKSQLLAQIAVLLGGRAAEEIIFGE--VTTGASNDIKQATNIARAMVTEWGMSDKLGPVA 418
Query: 514 YEEGQQEALLSHPVSRPRSISEETAQKIDKEVFRLIEEAYQKAKSIIQEKNDNFVAIAEA 573
Y + L ++ + SEETA++ID+EV R+IEEAY++AK I+ E D +A+A
Sbjct: 419 YGSDGGDVFLGRGFAKAKEYSEETAREIDEEVKRIIEEAYKRAKQILTENRDELELLAKA 478
Query: 574 LLEYETLSGKEIASLIR 590
LLE ET++ +EI L+
Sbjct: 479 LLEKETITREEIKELLA 495
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 679 bits (1753), Expect = 0.0
Identities = 333/598 (55%), Positives = 443/598 (74%), Gaps = 5/598 (0%)
Query: 1 MIALCLIASFSIFQAPSAGQDGVQDISYSQFIKDVDAGRVRKISVIGTHITGFYVNGESS 60
+IA+ L+ S+FQ+ + + + YS F+++V+ +VR+ + G I +
Sbjct: 10 VIAVVLM---SVFQSFGPSESNGRKVDYSTFLQEVNQDQVREARINGREIN-VTKKDSNR 65
Query: 61 FQTYMPLVGSKLLDKLQSKDIEISSRPVNDGSPGLLSYLGSWFPLVLVVLVWMFLMRQIQ 120
+ TY+P+ KLLD L +K++++ P + S L S SWFP++L++ VW+F MRQ+Q
Sbjct: 66 YTTYIPVNDPKLLDNLLTKNVKVVGEPPEEPSL-LASIFISWFPMLLLIGVWIFFMRQMQ 124
Query: 121 GGGARGAMGFGKSKAKLLSGNVGSVTFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRI 180
GGG +GAM FGKSKA++L+ + TF DVAG DEAKE++ E+V++L +P +F++LGG+I
Sbjct: 125 GGGGKGAMSFGKSKARMLTEDQIKTTFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKI 184
Query: 181 PHGVLLVGPPGTGKTLLARAVAGEANVPFFTISGSDFVELFVGVGASRVRDMFEQAKNNS 240
P GVL+VGPPGTGKTLLA+A+AGEA VPFFTISGSDFVE+FVGVGASRVRDMFEQAK +
Sbjct: 185 PKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAA 244
Query: 241 PCIVFVDEIDAVGRHRGIGLGGGNDEREQTLNQLLVEMDGFESSEGVILIAATNRPDVLD 300
PCI+F+DEIDAVGR RG GLGGG+DEREQTLNQ+LVEMDGFE +EG+I+IAATNRPDVLD
Sbjct: 245 PCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLD 304
Query: 301 AALLRPGRFDRQITVPNPDIVGREHILMVHSRNVPLAPNVILKTIARGTPGFSGADLRNL 360
ALLRPGRFDRQ+ V PD+ GRE IL VH R VPLAP++ IARGTPGFSGADL NL
Sbjct: 305 PALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANL 364
Query: 361 VNEAALMAARRNRRLVTMQEFEDAKDKILMGAERRSTAMTEEEKKITAYHEAGHAVVACH 420
VNEAAL AAR N+R+V+M EFE AKDKI+MGAERRS MTE +K+ TAYHEAGHA++
Sbjct: 365 VNEAALFAARGNKRVVSMVEFEKAKDKIMMGAERRSMVMTEAQKESTAYHEAGHAIIGRL 424
Query: 421 VPKADPLHKATIIPRGRALGMVMQLPEADRHSTTYVWMTSRLTILMGGRVAEEFTFGEDN 480
VP+ DP+HK TIIPRGRALG+ LPE D S + + S+++ L GGR+AEE +G ++
Sbjct: 425 VPEHDPVHKVTIIPRGRALGVTFFLPEGDAISASRQKLESQISTLYGGRLAEEIIYGPEH 484
Query: 481 VTSGAMSDIEYATKLARVMVTQFGFSNLLGKVSYEEGQQEALLSHPVSRPRSISEETAQK 540
V++GA +DI+ AT LAR MVTQ+GFS LG + Y E + E L V++ + +S+ETA+
Sbjct: 485 VSTGASNDIKVATNLARNMVTQWGFSEKLGPLLYAEEEGEVFLGRSVAKAKHMSDETARI 544
Query: 541 IDKEVFRLIEEAYQKAKSIIQEKNDNFVAIAEALLEYETLSGKEIASLIRGEKISRPS 598
ID+EV LIE Y +A+ ++ + D A+ +AL++YET+ +I L+ + P+
Sbjct: 545 IDQEVKALIERNYNRARQLLTDNMDILHAMKDALMKYETIDAPQIDDLMARRDVRPPA 602
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 307 bits (790), Expect = 5e-84
Identities = 121/260 (46%), Positives = 169/260 (65%), Gaps = 1/260 (0%)
Query: 144 SVTFKDVAGVDEAKEDLQEIVDF-LCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVA 202
+VT++D+ G++E +++E V+ L P+ F+ +G P GVLL GPPGTGKTLLA+AVA
Sbjct: 127 NVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVA 186
Query: 203 GEANVPFFTISGSDFVELFVGVGASRVRDMFEQAKNNSPCIVFVDEIDAVGRHRGIGLGG 262
E N F + GS+ V+ F+G GA VR++FE A+ +P I+F+DEIDA+ R
Sbjct: 187 HETNATFIRVVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTS 246
Query: 263 GNDEREQTLNQLLVEMDGFESSEGVILIAATNRPDVLDAALLRPGRFDRQITVPNPDIVG 322
G+ E ++TL QLL EMDGF+ V +IAATNR D+LD A+LRPGRFDR I VP PD G
Sbjct: 247 GDREVQRTLMQLLAEMDGFDPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEG 306
Query: 323 REHILMVHSRNVPLAPNVILKTIARGTPGFSGADLRNLVNEAALMAARRNRRLVTMQEFE 382
R IL +H+R + LA +V L+ +A T G SGADL+ + EA + A R +R VTM++F
Sbjct: 307 RLEILKIHTRKMNLADDVDLEELAELTEGASGADLKAICTEAGMFAIRDDRTEVTMEDFL 366
Query: 383 DAKDKILMGAERRSTAMTEE 402
A +K++ E+ S
Sbjct: 367 KAIEKVMGKEEKDSMEEPGV 386
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 264 bits (677), Expect = 4e-71
Identities = 121/246 (49%), Positives = 164/246 (66%), Gaps = 1/246 (0%)
Query: 145 VTFKDVAGVDEAKEDLQEIVDF-LCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAG 203
V+++D+ G++E +++E V+ L P+ F+ +G P GVLL GPPGTGKTLLA+AVA
Sbjct: 119 VSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAH 178
Query: 204 EANVPFFTISGSDFVELFVGVGASRVRDMFEQAKNNSPCIVFVDEIDAVGRHRGIGLGGG 263
E N F + GS+ V ++G GA VR++FE AK +P I+F+DEIDA+ R G
Sbjct: 179 ETNATFIRVVGSELVRKYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSG 238
Query: 264 NDEREQTLNQLLVEMDGFESSEGVILIAATNRPDVLDAALLRPGRFDRQITVPNPDIVGR 323
+ E ++TL QLL E+DGF+ V +IAATNRPD+LD ALLRPGRFDR I VP PD GR
Sbjct: 239 DREVQRTLMQLLAELDGFDPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGR 298
Query: 324 EHILMVHSRNVPLAPNVILKTIARGTPGFSGADLRNLVNEAALMAARRNRRLVTMQEFED 383
IL +H+R + LA +V L+ IA+ T G SGADL+ + EA + A R R VTM +F
Sbjct: 299 LEILKIHTRKMKLAEDVDLEAIAKMTEGASGADLKAICTEAGMFAIREERDYVTMDDFIK 358
Query: 384 AKDKIL 389
A +K+L
Sbjct: 359 AVEKVL 364
>gnl|CDD|162267 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 = 231 bits (591), Expect = 4e-61
Identities = 111/266 (41%), Positives = 166/266 (62%), Gaps = 3/266 (1%)
Query: 142 VGSVTFKDVAGVDEAKEDLQEIVDF-LCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARA 200
V +V + D+ G++E K++L+E V++ L P+ F+++G R P GVLL GPPGTGKTLLA+A
Sbjct: 447 VPNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKA 506
Query: 201 VAGEANVPFFTISGSDFVELFVGVGASRVRDMFEQAKNNSPCIVFVDEIDAVGRHRGIGL 260
VA E+ F + G + + +VG +R++F +A+ +P I+F DEIDA+ RG
Sbjct: 507 VATESGANFIAVRGPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARF 566
Query: 261 GGGNDEREQTLNQLLVEMDGFESSEGVILIAATNRPDVLDAALLRPGRFDRQITVPNPDI 320
+R +NQLL EMDG + V++IAATNRPD+LD ALLRPGRFDR I VP PD
Sbjct: 567 DTSVTDR--IVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDE 624
Query: 321 VGREHILMVHSRNVPLAPNVILKTIARGTPGFSGADLRNLVNEAALMAARRNRRLVTMQE 380
R+ I +H+R++PLA +V L+ +A T G++GAD+ + EAA+ A R + ++
Sbjct: 625 EARKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVCREAAMAALRESIGSPAKEK 684
Query: 381 FEDAKDKILMGAERRSTAMTEEEKKI 406
E +++ L + E KK+
Sbjct: 685 LEVGEEEFLKDLKVEMRHFLEALKKV 710
Score = 215 bits (548), Expect = 4e-56
Identities = 111/231 (48%), Positives = 152/231 (65%), Gaps = 4/231 (1%)
Query: 142 VGSVTFKDVAGVDEAKEDLQEIVDF-LCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARA 200
V VT++D+ G+ EAKE ++E+V+ + P+ F+ LG P GVLL GPPGTGKTLLA+A
Sbjct: 172 VPKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKA 231
Query: 201 VAGEANVPFFTISGSDFVELFVGVGASRVRDMFEQAKNNSPCIVFVDEIDAVGRHRGIGL 260
VA EA F +I+G + + + G R+R++F++A+ N+P I+F+DEIDA+ R
Sbjct: 232 VANEAGAYFISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVT 291
Query: 261 GGGNDEREQTLNQLLVEMDGFESSEGVILIAATNRPDVLDAALLRPGRFDRQITVPNPDI 320
G + ++ + QLL MDG + VI+I ATNRPD LD AL RPGRFDR+I + PD
Sbjct: 292 G---EVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDK 348
Query: 321 VGREHILMVHSRNVPLAPNVILKTIARGTPGFSGADLRNLVNEAALMAARR 371
R+ IL VH+RN+PLA +V L +A T GF GADL L EAA+ A RR
Sbjct: 349 RARKEILKVHTRNMPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRR 399
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 208 bits (531), Expect = 4e-54
Identities = 101/245 (41%), Positives = 155/245 (63%), Gaps = 1/245 (0%)
Query: 146 TFKDVAGVDEAKEDLQEIVDF-LCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGE 204
++ D+ G+++ ++++E V+ L P+ + +G + P GV+L GPPGTGKTLLA+AVA E
Sbjct: 181 SYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANE 240
Query: 205 ANVPFFTISGSDFVELFVGVGASRVRDMFEQAKNNSPCIVFVDEIDAVGRHRGIGLGGGN 264
+ F + GS+ ++ ++G G VR++F A+ N+P IVF+DEIDA+G R GG
Sbjct: 241 TSATFLRVVGSELIQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGE 300
Query: 265 DEREQTLNQLLVEMDGFESSEGVILIAATNRPDVLDAALLRPGRFDRQITVPNPDIVGRE 324
E ++T+ +LL ++DGF+S V +I ATNR + LD AL+RPGR DR+I PNPD +
Sbjct: 301 KEIQRTMLELLNQLDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKR 360
Query: 325 HILMVHSRNVPLAPNVILKTIARGTPGFSGADLRNLVNEAALMAARRNRRLVTMQEFEDA 384
I +H+ + LA +V L+ SGAD++ + EA L+A R R VT +F A
Sbjct: 361 RIFEIHTSKMTLAEDVDLEEFIMAKDELSGADIKAICTEAGLLALRERRMKVTQADFRKA 420
Query: 385 KDKIL 389
K+K+L
Sbjct: 421 KEKVL 425
>gnl|CDD|185633 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 204 bits (521), Expect = 6e-53
Identities = 95/242 (39%), Positives = 145/242 (59%), Gaps = 1/242 (0%)
Query: 144 SVTFKDVAGVDEAKEDLQEIVDF-LCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVA 202
VT+ D+ G+D K++++E V+ L P+ ++++G P GVLL GPPGTGKT+LA+AVA
Sbjct: 141 DVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVA 200
Query: 203 GEANVPFFTISGSDFVELFVGVGASRVRDMFEQAKNNSPCIVFVDEIDAVGRHRGIGLGG 262
F + GS+FV+ ++G G VRD+F A+ N+P I+F+DE+D++ R G
Sbjct: 201 HHTTATFIRVVGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTG 260
Query: 263 GNDEREQTLNQLLVEMDGFESSEGVILIAATNRPDVLDAALLRPGRFDRQITVPNPDIVG 322
+ E ++ L +LL +MDGF+ + V +I ATNR D LD ALLRPGR DR+I P PD
Sbjct: 261 ADREVQRILLELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQ 320
Query: 323 REHILMVHSRNVPLAPNVILKTIARGTPGFSGADLRNLVNEAALMAARRNRRLVTMQEFE 382
+ I + + L+ V L+ S AD+ + EA + A R+NR ++ ++FE
Sbjct: 321 KRLIFQTITSKMNLSEEVDLEDFVSRPEKISAADIAAICQEAGMQAVRKNRYVILPKDFE 380
Query: 383 DA 384
Sbjct: 381 KG 382
>gnl|CDD|163401 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.
Length = 512
Score = 139 bits (352), Expect = 2e-33
Identities = 89/277 (32%), Positives = 139/277 (50%), Gaps = 25/277 (9%)
Query: 142 VGSVTFKDVAGVDEAKEDLQEIVD--FLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLAR 199
V VT+ D+ G+D E +++ V+ FL P+ ++ + P GVLL GPPG GKTL+A+
Sbjct: 176 VPDVTYADIGGLDSQIEQIRDAVELPFL-HPELYREYDLKPPKGVLLYGPPGCGKTLIAK 234
Query: 200 AVA------GEANVP----FFTISGSDFVELFVGVGASRVRDMFEQAK----NNSPCIVF 245
AVA A F I G + + +VG ++R +F++A+ + P IVF
Sbjct: 235 AVANSLAQRIGAETGDKSYFLNIKGPELLNKYVGETERQIRLIFQRAREKASDGRPVIVF 294
Query: 246 VDEIDAVGRHRGIGLGGGNDEREQTLNQLLVEMDGFESSEGVILIAATNRPDVLDAALLR 305
DE+D++ R RG G+ +D + QLL E+DG ES + VI+I A+NR D++D A+LR
Sbjct: 295 FDEMDSIFRTRGSGVS--SDVETTVVPQLLSELDGVESLDNVIVIGASNREDMIDPAILR 352
Query: 306 PGRFDRQITVPNPDIVGREHILMVH-SRNVPLAPNVILKTIARGTPGFSGADLRNLVNEA 364
PGR D +I + PD I + + ++PL ++ R A L +
Sbjct: 353 PGRLDVKIRIERPDAEAAADIFSKYLTDSLPLDADLAEFDGDREAT---AAALIQRAVD- 408
Query: 365 ALMAARRNRRLVTMQEFEDAKDKILMGAERRSTAMTE 401
L A R V + + ++L + S AM
Sbjct: 409 HLYATSEENRYVEVTY-ANGSTEVLYFKDFVSGAMIA 444
>gnl|CDD|128665 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 = 85.1 bits (210), Expect = 5e-17
Identities = 46/156 (29%), Positives = 66/156 (42%), Gaps = 26/156 (16%)
Query: 181 PHGVLLVGPPGTGKTLLARAVAGEANVP---FFTISGSDFVE--------------LFVG 223
+L+VGPPG+GKT LARA+A E P I G D +E G
Sbjct: 2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASG 61
Query: 224 VGASRVRDMFEQAKNNSPCIVFVDEIDAVGRHRGIGLGGGNDEREQTLNQLLVEMDGFES 283
G R+R A+ P ++ +DEI ++ E L + L + +S
Sbjct: 62 SGELRLRLALALARKLKPDVLILDEITSLLDAEQ--------EALLLLLEELRLLLLLKS 113
Query: 284 SEGVILIAATNRPDVLDAALLRPGRFDRQITVPNPD 319
+ + +I TN L ALLR RFDR+I +
Sbjct: 114 EKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
>gnl|CDD|183986 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 66.3 bits (163), Expect = 2e-11
Identities = 30/84 (35%), Positives = 43/84 (51%), Gaps = 17/84 (20%)
Query: 177 GGRIPHGVLLVGPPGTGKTLLARAVAGEANVPFFTISGSDFVELFVGVGASRVRDMFEQA 236
GR+ ++L GPPGTGKT LAR +AG + PF +S G +R++ E+A
Sbjct: 33 AGRLSS-MILWGPPGTGKTTLARIIAGATDAPFEALSAVTS-------GVKDLREVIEEA 84
Query: 237 KNNS----PCIVFVDEIDAVGRHR 256
+ I+F+DEI HR
Sbjct: 85 RQRRSAGRRTILFIDEI-----HR 103
Score = 27.7 bits (63), Expect = 9.3
Identities = 25/102 (24%), Positives = 38/102 (37%), Gaps = 40/102 (39%)
Query: 301 AALLRPGRFDRQITVPNPDIVGREHIL--------MVHSRNVPLAPNVIL-------KT- 344
A +RP D ++VG+EH+L M+ + + ++IL KT
Sbjct: 3 AERMRPKTLD--------EVVGQEHLLGPGKPLRRMIEAGRL---SSMILWGPPGTGKTT 51
Query: 345 ----IARGT--------PGFSG-ADLRNLVNEAALMAARRNR 373
IA T SG DLR ++ EA + R
Sbjct: 52 LARIIAGATDAPFEALSAVTSGVKDLREVIEEARQRRSAGRR 93
>gnl|CDD|179778 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 58.0 bits (141), Expect = 8e-09
Identities = 33/110 (30%), Positives = 52/110 (47%), Gaps = 18/110 (16%)
Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEA 205
T DV G ++AKE L+E ++ L G+ +LL GPPG GKT LA A+A +
Sbjct: 12 TLSDVVGNEKAKEQLREWIE--------SWLKGKPKKALLLYGPPGVGKTSLAHALANDY 63
Query: 206 NVPFFTISGSDF-----VELFVGVGASRVRDMFEQAKNNSPCIVFVDEID 250
++ SD +E G A+ +F + ++ +DE+D
Sbjct: 64 GWEVIELNASDQRTADVIERVAG-EAATSGSLFGARRK----LILLDEVD 108
>gnl|CDD|163057 TIGR02881, spore_V_K, stage V sporulation protein K. Members of
this protein family are the stage V sporulation protein
K (SpoVK), a close homolog of the Rubisco expression
protein CbbX (TIGR02880) and a members of the ATPase
family associated with various cellular activities
(pfam00004). Members are strictly limited to bacterial
endospore-forming species, but are not universal in this
group and are missing from the Clostridium group.
Length = 261
Score = 54.7 bits (132), Expect = 7e-08
Identities = 65/249 (26%), Positives = 107/249 (42%), Gaps = 36/249 (14%)
Query: 147 FKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVL---LVGPPGTGKTLLARAVAG 203
+ G+DE K ++EI ++ +K K G + VL G PGTGKT +AR +
Sbjct: 5 LSRMVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGK 64
Query: 204 ---EANV----PFFTISGSDFVELFVGVGASRVRDMFEQAKNNSPCIVFVDEIDAVGRHR 256
E NV + +D V ++G A + R++ ++A ++F+DE ++ R
Sbjct: 65 LFKEMNVLSKGHLIEVERADLVGEYIGHTAQKTREVIKKALGG---VLFIDEAYSLAR-- 119
Query: 257 GIGLGGGNDEREQTLNQLLVEMDGFESSEGVILIAATNRPDVLDAAL-LRPG---RFDRQ 312
GG D ++ ++ L+ M+ ++ +LI A D +D L L PG RF
Sbjct: 120 ----GGEKDFGKEAIDTLVKGME--DNRNEFVLILA-GYSDEMDYFLSLNPGLRSRFPIS 172
Query: 313 ITVPNPDIVGREHIL--MVHSRNVPLAPNV------ILKTIARGTPG-FSGADL-RNLVN 362
I P+ + I MV R L L + + + FS A RN++
Sbjct: 173 IDFPDYTVEELMEIAERMVKEREYKLTEEAKWKLREHLYKVDQLSSREFSNARYVRNIIE 232
Query: 363 EAALMAARR 371
+A A R
Sbjct: 233 KAIRRQAVR 241
>gnl|CDD|162028 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.
Length = 775
Score = 53.8 bits (130), Expect = 1e-07
Identities = 38/120 (31%), Positives = 60/120 (50%), Gaps = 17/120 (14%)
Query: 148 KDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEANV 207
+D G+ + KE I+++L + ++ G I + LVGPPG GKT L +++A N
Sbjct: 320 EDHYGLKKVKE---RILEYLAVQKLRGKMKGPI---LCLVGPPGVGKTSLGKSIAKALNR 373
Query: 208 PFFTIS-G--SDFVEL------FVGVGASRVRDMFEQAKNNSPCIVFVDEIDAVGR-HRG 257
F S G D E+ +VG R+ ++AK +P + +DEID +G RG
Sbjct: 374 KFVRFSLGGVRDEAEIRGHRRTYVGAMPGRIIQGLKKAKTKNPLFL-LDEIDKIGSSFRG 432
>gnl|CDD|148219 pfam06480, FtsH_ext, FtsH Extracellular. This domain is found in
the FtsH family of proteins. FtsH is the only
membrane-bound ATP-dependent protease universally
conserved in prokaryotes. It only efficiently degrades
proteins that have a low thermodynamic stability - e.g.
it lacks robust unfoldase activity. This feature may be
key and implies that this could be a criterion for
degrading a protein. In Oenococcus oeni FtsH is involved
in protection against environmental stress. and shows
increased expression under heat or osmotic stress. These
two lines of evidence suggest that it is a fundamental
prokaryotic self-protection mechanism that checks if
proteins are correctly folded (personal obs: Yeats C).
The precise function of this N-terminal region is
unclear.
Length = 104
Score = 52.2 bits (125), Expect = 4e-07
Identities = 27/99 (27%), Positives = 51/99 (51%), Gaps = 15/99 (15%)
Query: 2 IALCLIASFSIFQAPSAGQDGVQDISYSQFIKDVDAGRVRKISVIGTHIT-------GFY 54
I L L+ F +F S+ ++ISYS+F++ ++AG+V+K+ + IT G
Sbjct: 7 ILLVLLLLFLLFLLSSSSS--TKEISYSEFLELLEAGKVKKVVIDDDEITKPTGDVAGKL 64
Query: 55 VNGESSFQTYMPLVGS------KLLDKLQSKDIEISSRP 87
+G ++P + S KL + L K +++S++P
Sbjct: 65 KDGSKFTTYFIPTLPSVDSFLEKLEEALVEKGVKVSAKP 103
>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 = 51.2 bits (123), Expect = 9e-07
Identities = 31/81 (38%), Positives = 42/81 (51%), Gaps = 18/81 (22%)
Query: 139 SGNVGSVTFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLA 198
G VG ++ AGV IV+ + K ++ GR VL+ GPPGTGKT LA
Sbjct: 24 EGLVGQEKAREAAGV---------IVEMI----KEGKIAGR---AVLIAGPPGTGKTALA 67
Query: 199 RAVAGE--ANVPFFTISGSDF 217
A++ E + PF ISGS+
Sbjct: 68 IAISKELGEDTPFCPISGSEV 88
>gnl|CDD|149019 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam
entry includes some of the AAA proteins not detected by
the pfam00004 model.
Length = 139
Score = 49.2 bits (118), Expect = 3e-06
Identities = 40/144 (27%), Positives = 53/144 (36%), Gaps = 22/144 (15%)
Query: 183 GVLLVGPPGTGKTLLARAVAGE-ANVPFFTISGSDFVE--------LFVGVGASRVRDMF 233
GVLLVGPPGTGK+ LA +A +N P F + + S V
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIANGTTSWVDGPL 60
Query: 234 EQAKNNSPCIVFVDEIDAVGRH-RGIGLGGGNDEREQTLN---QLLVEMDGFESSEGVIL 289
+A I +DEI+ L ++ R + V D F ++ L
Sbjct: 61 VRAA-REGEIAVLDEINRANPDVLNSLLSLLDERRLLLPEGGELVKVAPDDF--AKRFRL 117
Query: 290 IAATNRPD----VLDAALLRPGRF 309
IA N D L AL RF
Sbjct: 118 IATMNPLDRGLNELSPALRS--RF 139
>gnl|CDD|177379 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 48.1 bits (115), Expect = 8e-06
Identities = 17/39 (43%), Positives = 24/39 (61%)
Query: 178 GRIPHGVLLVGPPGTGKTLLARAVAGEANVPFFTISGSD 216
GRIP+ +L PGTGKT +A+A+ E ++GSD
Sbjct: 40 GRIPNMLLHSPSPGTGKTTVAKALCNEVGAEVLFVNGSD 78
>gnl|CDD|161849 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.
Length = 413
Score = 45.9 bits (109), Expect = 3e-05
Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 6/77 (7%)
Query: 184 VLLVGPPGTGKTLLARAVAGEANVPFFTISGSDFVEL-FVGVGASRVRDMFEQA-----K 237
+LL+GP G+GKTLLA+ +A NVPF + E +VG + QA +
Sbjct: 119 ILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVE 178
Query: 238 NNSPCIVFVDEIDAVGR 254
I+++DEID + R
Sbjct: 179 KAQKGIIYIDEIDKISR 195
>gnl|CDD|178847 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 45.1 bits (108), Expect = 5e-05
Identities = 25/79 (31%), Positives = 31/79 (39%), Gaps = 25/79 (31%)
Query: 184 VLLVGPPGTGKTLLARAVAGEANVPFFTISG------SDFVELFVGVGASRVRDMFEQAK 237
VLL GPPG GKT LA +A E V SG D + + D
Sbjct: 54 VLLYGPPGLGKTTLANIIANEMGVNIRITSGPALEKPGDLAAILTNLEE---GD------ 104
Query: 238 NNSPCIVFVDEIDAVGRHR 256
++F+DEI HR
Sbjct: 105 -----VLFIDEI-----HR 113
>gnl|CDD|180029 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 44.0 bits (105), Expect = 1e-04
Identities = 15/26 (57%), Positives = 21/26 (80%)
Query: 184 VLLVGPPGTGKTLLARAVAGEANVPF 209
+LL+GP G+GKTLLA+ +A +VPF
Sbjct: 111 ILLIGPTGSGKTLLAQTLARILDVPF 136
>gnl|CDD|161852 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 PubMed:98389714, is Ser in other
members of the seed alignment.
Length = 441
Score = 42.9 bits (101), Expect = 3e-04
Identities = 24/61 (39%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 180 IPHGVLLVGPPGTGKTLLARAVAGEANVPFFTISGSDFVEL-FVGVGA-SRVRDMFEQAK 237
P +L++GP G GKT +AR +A AN PF + + F E+ +VG S VRD+ + A
Sbjct: 46 TPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGRDVESMVRDLTDAAV 105
Query: 238 N 238
Sbjct: 106 K 106
>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit.
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.
Length = 305
Score = 41.9 bits (99), Expect = 6e-04
Identities = 21/77 (27%), Positives = 31/77 (40%), Gaps = 20/77 (25%)
Query: 184 VLLVGPPGTGKTLLARAVAGEANVPFFTISG------SDFVELFVGVGASRVRDMFEQAK 237
+LL GPPG GKT LA +A E V SG D + + +
Sbjct: 33 LLLYGPPGLGKTTLAHIIANEMGVNLKITSGPALEKPGDLAAILTNL----------EEG 82
Query: 238 NNSPCIVFVDEIDAVGR 254
+ ++F+DEI +
Sbjct: 83 D----VLFIDEIHRLSP 95
>gnl|CDD|179026 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 41.8 bits (99), Expect = 6e-04
Identities = 34/119 (28%), Positives = 53/119 (44%), Gaps = 33/119 (27%)
Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEA 205
T ++ G +E E L+ V +PH +L GPPGTGKT A A+A E
Sbjct: 15 TLDEIVGQEEIVERLKSYVK-----------EKNMPH-LLFAGPPGTGKTTAALALARE- 61
Query: 206 NVPFFTISGSDFVELFVGVGAS----------RVRDMFEQAK--NNSPC-IVFVDEIDA 251
+ G D+ E F+ + AS ++++ F + +P I+F+DE D
Sbjct: 62 ------LYGEDWRENFLELNASDERGIDVIRNKIKE-FARTAPVGGAPFKIIFLDEADN 113
>gnl|CDD|161993 TIGR00678, holB, DNA polymerase III, delta' subunit. 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.
Length = 188
Score = 41.5 bits (98), Expect = 6e-04
Identities = 14/26 (53%), Positives = 16/26 (61%)
Query: 177 GGRIPHGVLLVGPPGTGKTLLARAVA 202
GR+ H L GP G GK LLA A+A
Sbjct: 10 KGRLAHAYLFAGPEGVGKELLALALA 35
>gnl|CDD|116338 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 = 41.0 bits (97), Expect = 0.001
Identities = 25/88 (28%), Positives = 37/88 (42%), Gaps = 15/88 (17%)
Query: 184 VLLVGPPGTGKTLLARAVAGEANV---PFFTISGSDFVE-----LFVG-----VGASRVR 230
L +GP G GKT LA+A+A I S+++E +G VG
Sbjct: 6 FLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYMEEHSVSRLIGAPPGYVGYEEGG 65
Query: 231 DMFEQAKNNSPCIVFVDEIDAVGRHRGI 258
+ E + IV +DEI+ H G+
Sbjct: 66 QLTEAVRRKPYSIVLIDEIEKA--HPGV 91
>gnl|CDD|183503 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 40.7 bits (96), Expect = 0.001
Identities = 29/92 (31%), Positives = 40/92 (43%), Gaps = 22/92 (23%)
Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEA 205
+D+ G DE E L VD +PH +L+ GPPG+GKT RA+A E
Sbjct: 13 LLEDILGQDEVVERLSRAVD-----------SPNLPH-LLVQGPPGSGKTAAVRALAREL 60
Query: 206 NVPFFTISGSDFVELFVGVGASRVRDMFEQAK 237
+ ++F E V D F+Q K
Sbjct: 61 ---YGDPWENNFTEF-------NVADFFDQGK 82
>gnl|CDD|162839 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.
Length = 355
Score = 39.5 bits (93), Expect = 0.002
Identities = 21/57 (36%), Positives = 27/57 (47%), Gaps = 11/57 (19%)
Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVA 202
TF+DV G + + L+ + GRI H L GP GTGKT +AR A
Sbjct: 12 TFEDVIGQEHIVQTLKNAIKN-----------GRIAHAYLFSGPRGTGKTSIARIFA 57
>gnl|CDD|183985 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 39.7 bits (93), Expect = 0.003
Identities = 24/77 (31%), Positives = 35/77 (45%), Gaps = 17/77 (22%)
Query: 185 LLVGPPGTGKTLLARAVAGEANVPFFTISGSDFVELFVGVGASRVRDMFEQAKN-----N 239
+L GPPG GKT LAR +A F +++ V G +R ++AK
Sbjct: 56 ILYGPPGVGKTTLARIIANHTRAHFSSLNA-------VLAGVKDLRAEVDRAKERLERHG 108
Query: 240 SPCIVFVDEIDAVGRHR 256
I+F+DE+ HR
Sbjct: 109 KRTILFIDEV-----HR 120
>gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal
end matches very strongly a pfam Mg_chelatase domain.
Length = 499
Score = 37.9 bits (88), Expect = 0.008
Identities = 23/57 (40%), Positives = 28/57 (49%), Gaps = 14/57 (24%)
Query: 147 FKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAG 203
KD+ G AK L EI GG H +LL GPPG+GKT+LA + G
Sbjct: 191 LKDIKGQQHAKRAL-EIA----------AAGG---HNLLLFGPPGSGKTMLASRLQG 233
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 36.9 bits (85), Expect = 0.015
Identities = 14/22 (63%), Positives = 18/22 (81%)
Query: 182 HGVLLVGPPGTGKTLLARAVAG 203
H +LL+GPPGTGKT+LA + G
Sbjct: 211 HNLLLIGPPGTGKTMLASRING 232
>gnl|CDD|148381 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 = 36.1 bits (84), Expect = 0.030
Identities = 14/25 (56%), Positives = 16/25 (64%), Gaps = 2/25 (8%)
Query: 176 LGGRIPHG--VLLVGPPGTGKTLLA 198
L G IP G VL+ G PGTGKT+
Sbjct: 12 LKGGIPEGRVVLITGGPGTGKTIFG 36
>gnl|CDD|180989 PRK07471, PRK07471, DNA polymerase III subunit delta'; Validated.
Length = 365
Score = 35.8 bits (83), Expect = 0.035
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 177 GGRIPHGVLLVGPPGTGKTLLARAVA 202
GR+ H L+ GP G GK LA +A
Sbjct: 37 SGRLHHAWLIGGPQGIGKATLAYRMA 62
>gnl|CDD|181233 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 35.8 bits (83), Expect = 0.040
Identities = 13/22 (59%), Positives = 15/22 (68%)
Query: 183 GVLLVGPPGTGKTLLARAVAGE 204
G+LL G GTGKT LA +A E
Sbjct: 116 GLLLWGSVGTGKTYLAACIANE 137
>gnl|CDD|163076 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.
Length = 365
Score = 35.3 bits (82), Expect = 0.044
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 176 LGGRIPHGVLLVGPPGTGKTLLARAV 201
L G P V + G GTGKT + + V
Sbjct: 35 LRGSRPSNVFIYGKTGTGKTAVTKYV 60
>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.
Length = 531
Score = 35.1 bits (81), Expect = 0.051
Identities = 27/79 (34%), Positives = 37/79 (46%), Gaps = 18/79 (22%)
Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEA 205
+F ++ G +E + L+ LC P P V++ GPPG GKT AR V EA
Sbjct: 63 SFDEIIGQEEGIKALKAA---LCGPN---------PQHVIIYGPPGVGKTAAARLVLEEA 110
Query: 206 N----VPFFTISGSDFVEL 220
PF G+ FVE+
Sbjct: 111 KKNPASPF--KEGAAFVEI 127
>gnl|CDD|162400 TIGR01526, nadR_NMN_Atrans, nicotinamide-nucleotide
adenylyltransferase, NadR type. 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 = 35.2 bits (81), Expect = 0.051
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 3/54 (5%)
Query: 170 PQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEANVPFFTISGSDFVELFVG 223
P++ + + V ++G TGK+ L +A N ++VE +G
Sbjct: 154 PREVRPFFVKT---VAILGGESTGKSTLVNKLAAVFNTTSAWEYAREYVEEKLG 204
>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).
Length = 262
Score = 35.2 bits (81), Expect = 0.054
Identities = 23/56 (41%), Positives = 28/56 (50%), Gaps = 6/56 (10%)
Query: 184 VLLVGPPGTGKTLLARAVAGEANVPFFTISG------SDFVELFVGVGASRVRDMF 233
V L GP GTGKT LA VA + + P I+G SD V + G +V D F
Sbjct: 24 VHLRGPAGTGKTTLAMHVARKRDRPVMLINGDAELTTSDLVGSYAGYTRKKVHDQF 79
>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 = 0.055
Identities = 13/19 (68%), Positives = 14/19 (73%)
Query: 184 VLLVGPPGTGKTLLARAVA 202
VLL G PG KTLLAR +A
Sbjct: 2 VLLEGVPGLAKTLLARTLA 20
>gnl|CDD|184914 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 35.2 bits (81), Expect = 0.058
Identities = 16/35 (45%), Positives = 19/35 (54%), Gaps = 4/35 (11%)
Query: 178 GRIPHGVLLVGPPGTGKT----LLARAVAGEANVP 208
GR+ H L GP G GKT +LA+AV N P
Sbjct: 35 GRVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDP 69
>gnl|CDD|182842 PRK10923, glnG, nitrogen regulation protein NR(I); Provisional.
Length = 469
Score = 34.8 bits (80), Expect = 0.076
Identities = 32/97 (32%), Positives = 47/97 (48%), Gaps = 21/97 (21%)
Query: 171 QKFKRLGGRIPHG---VLLVGPPGTGKTLLARAV---AGEANVPFFTISGS----DFV-- 218
Q R+ GR+ VL+ G GTGK L+A A+ + A PF ++ + D +
Sbjct: 148 QDVFRIIGRLSRSSISVLINGESGTGKELVAHALHRHSPRAKAPFIALNMAAIPKDLIES 207
Query: 219 ELF-----VGVGASRVRD-MFEQAKNNSPCIVFVDEI 249
ELF GA+ +R FEQA + +F+DEI
Sbjct: 208 ELFGHEKGAFTGANTIRQGRFEQADGGT---LFLDEI 241
>gnl|CDD|184312 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 34.6 bits (80), Expect = 0.076
Identities = 11/19 (57%), Positives = 18/19 (94%)
Query: 184 VLLVGPPGTGKTLLARAVA 202
V+++G PGTGK++LA+A+A
Sbjct: 53 VMMIGSPGTGKSMLAKAMA 71
>gnl|CDD|162958 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA.
Length = 731
Score = 34.6 bits (80), Expect = 0.078
Identities = 24/78 (30%), Positives = 34/78 (43%), Gaps = 14/78 (17%)
Query: 185 LLVGPPGTGKTLLARAVAGEANVPFFTISGSDFVE-----LFVGVGASRVRDMFEQ---- 235
L GP G GKT LA+ +A V S+++E +G V FEQ
Sbjct: 488 LFTGPTGVGKTELAKQLAEALGVHLERFDMSEYMEKHTVSRLIGAPPGYVG--FEQGGLL 545
Query: 236 --AKNNSP-CIVFVDEID 250
A P C++ +DEI+
Sbjct: 546 TEAVRKHPHCVLLLDEIE 563
>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
Length = 319
Score = 34.7 bits (80), Expect = 0.083
Identities = 36/116 (31%), Positives = 52/116 (44%), Gaps = 32/116 (27%)
Query: 149 DVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEANVP 208
D+ G ++A LQ I G +P+ ++L GPPGTGKT A+A E
Sbjct: 14 DIVGNEDAVSRLQVIAR-----------DGNMPN-LILSGPPGTGKTTSILALAHE---- 57
Query: 209 FFTISGSDFVELFVGVGASR------VRD---MFEQAKNNSPC----IVFVDEIDA 251
+ G ++ E + + AS VR+ MF Q K P IV +DE D+
Sbjct: 58 ---LLGPNYKEAVLELNASDDRGIDVVRNKIKMFAQKKVTLPPGRHKIVILDEADS 110
>gnl|CDD|179962 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU;
Provisional.
Length = 443
Score = 34.7 bits (81), Expect = 0.084
Identities = 26/61 (42%), Positives = 35/61 (57%), Gaps = 6/61 (9%)
Query: 180 IPHGVLLVGPPGTGKTLLARAVAGEANVPFFTISGSDFVELFVG-VG---ASRVRDMFEQ 235
P +L++GP G GKT +AR +A AN PF + + F E VG VG S +RD+ E
Sbjct: 49 TPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTE--VGYVGRDVESIIRDLVEI 106
Query: 236 A 236
A
Sbjct: 107 A 107
>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 504
Score = 34.4 bits (79), Expect = 0.088
Identities = 21/62 (33%), Positives = 27/62 (43%), Gaps = 11/62 (17%)
Query: 145 VTFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGE 204
+TF +V G + KE L + GR+ H L GP G GKT AR +A
Sbjct: 11 ITFDEVVGQEHVKEVLLAALR-----------QGRLGHAYLFSGPRGVGKTTTARLIAMA 59
Query: 205 AN 206
N
Sbjct: 60 VN 61
>gnl|CDD|180779 PRK06964, PRK06964, DNA polymerase III subunit delta'; Validated.
Length = 342
Score = 34.3 bits (79), Expect = 0.091
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 169 DPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVA 202
D + + L R+PH +LL G G GK A+ +A
Sbjct: 9 DWNRLQALRARLPHALLLHGQAGIGKLDFAQHLA 42
>gnl|CDD|180856 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau;
Validated.
Length = 725
Score = 34.4 bits (79), Expect = 0.100
Identities = 20/61 (32%), Positives = 27/61 (44%), Gaps = 11/61 (18%)
Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEA 205
TF D+ G D + L+ I+ +I H L GP GTGKT +A+ A
Sbjct: 16 TFDDIVGQDHIVQTLKNIIKS-----------NKISHAYLFSGPRGTGKTSVAKIFANAL 64
Query: 206 N 206
N
Sbjct: 65 N 65
>gnl|CDD|184925 PRK14961, PRK14961, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 363
Score = 34.4 bits (79), Expect = 0.10
Identities = 33/123 (26%), Positives = 43/123 (34%), Gaps = 37/123 (30%)
Query: 170 PQKFKR---------------LGGRIPHGVLLVGPPGTGKTLLARAVAGEANVPF----- 209
PQ F+ GRI H LL G G GKT +AR +A N
Sbjct: 12 PQYFRDIIGQKHIVTAISNGLSLGRIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGITSN 71
Query: 210 --------FTISGSDFVELFVGVGASR--VRDMFEQAKN--NSPC-----IVFVDEIDAV 252
I ++L ASR V +M E N SP + +DE+ +
Sbjct: 72 PCRKCIICKEIEKGLCLDLIEIDAASRTKVEEMREILDNIYYSPSKSRFKVYLIDEVHML 131
Query: 253 GRH 255
RH
Sbjct: 132 SRH 134
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 34.3 bits (78), Expect = 0.11
Identities = 49/167 (29%), Positives = 73/167 (43%), Gaps = 32/167 (19%)
Query: 173 FKRLGGRIPHGVLLVGPPGTGKTLLARAVA----GE-----ANVPFF--TISGSDFVELF 221
KRL I ++L GPPG GKT +AR +A GE N+ F + S DF++ +
Sbjct: 188 LKRL--TIKKNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGY 245
Query: 222 V--GVGASRVRDMF----EQAKNN--SPCIVFVDEIDAVGRHRGIG---LGGGNDEREQT 270
GVG R +F +QAK + +DEI+ + G + +D+R +
Sbjct: 246 RPNGVGFRRKDGIFYNFCQQAKEQPEKKYVFIIDEINRANLSKVFGEVMMLMEHDKRGEN 305
Query: 271 LNQLLV----EMDGFESSEGVILIAATNRPD----VLDAALLRPGRF 309
+ L + + F E V +I N D V+D AL R F
Sbjct: 306 WSVPLTYSENDEERFYVPENVYIIGLMNTADRSLAVVDYALRRRFSF 352
>gnl|CDD|180215 PRK05707, PRK05707, DNA polymerase III subunit delta'; Validated.
Length = 328
Score = 34.3 bits (79), Expect = 0.11
Identities = 14/25 (56%), Positives = 15/25 (60%)
Query: 178 GRIPHGVLLVGPPGTGKTLLARAVA 202
GR PH LL GP G GK LA +A
Sbjct: 19 GRHPHAYLLHGPAGIGKRALAERLA 43
>gnl|CDD|183133 PRK11432, fbpC, ferric transporter ATP-binding subunit;
Provisional.
Length = 351
Score = 33.9 bits (78), Expect = 0.12
Identities = 38/120 (31%), Positives = 53/120 (44%), Gaps = 35/120 (29%)
Query: 180 IPHG--VLLVGPPGTGKTLLARAVAGEANVP----FFTISGSDFVELFVGVGASRVRDMF 233
I G V L+GP G GKT + R VAG P F I G D V + + RD+
Sbjct: 29 IKQGTMVTLLGPSGCGKTTVLRLVAGLEK-PTEGQIF-IDGED-----VTHRSIQQRDI- 80
Query: 234 EQAKNNSPCIVFVDEIDAVGRHRGIG---------LGGGNDEREQTLNQLL--VEMDGFE 282
C+VF + A+ H +G LG +ER+Q + + L V++ GFE
Sbjct: 81 --------CMVF--QSYALFPHMSLGENVGYGLKMLGVPKEERKQRVKEALELVDLAGFE 130
>gnl|CDD|184926 PRK14962, PRK14962, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 472
Score = 34.0 bits (78), Expect = 0.12
Identities = 19/61 (31%), Positives = 26/61 (42%), Gaps = 11/61 (18%)
Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEA 205
TF +V G D K+ + + I H + GP GTGKT +AR +A
Sbjct: 12 TFSEVVGQDHVKKLIINAL-----------KKNSISHAYIFAGPRGTGKTTVARILAKSL 60
Query: 206 N 206
N
Sbjct: 61 N 61
>gnl|CDD|163222 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system.
Length = 852
Score = 33.8 bits (78), Expect = 0.15
Identities = 27/59 (45%), Positives = 32/59 (54%), Gaps = 16/59 (27%)
Query: 167 LCDPQKFKRLGGRIPHGV-LLVGPPGTGKTLLARAVA-----GEANVPFFTISGSDFVE 219
L DP+K P GV LLVGP G GKT A A+A GE N+ TI+ S+F E
Sbjct: 589 LEDPRK--------PLGVFLLVGPSGVGKTETALALAELLYGGEQNL--ITINMSEFQE 637
>gnl|CDD|179010 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 33.7 bits (78), Expect = 0.15
Identities = 14/28 (50%), Positives = 16/28 (57%)
Query: 178 GRIPHGVLLVGPPGTGKTLLARAVAGEA 205
G P VL+ GPPGTGKT + V E
Sbjct: 52 GSRPLNVLIYGPPGTGKTTTVKKVFEEL 79
Score = 29.4 bits (67), Expect = 2.8
Identities = 20/77 (25%), Positives = 29/77 (37%), Gaps = 9/77 (11%)
Query: 336 LAPNVI----LKTIARGTPGFSGADLR---NLVNEAALMAARRNRRLVTMQEFEDAKDKI 388
P V+ L IA T D R +L+ A L+A R R VT ++ A +K
Sbjct: 224 FYPGVVDDEVLDLIADLT-AREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKS 282
Query: 389 LMGAERRS-TAMTEEEK 404
+ + EK
Sbjct: 283 EIVHLSEVLRTLPLHEK 299
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 33.3 bits (77), Expect = 0.19
Identities = 13/29 (44%), Positives = 19/29 (65%), Gaps = 1/29 (3%)
Query: 174 KRLGGRIPHGVLLVGPPGTGKTLLARAVA 202
+RL R G+L+ G PG GK+ A+A+A
Sbjct: 251 ERLEER-AEGILIAGAPGAGKSTFAQALA 278
>gnl|CDD|184917 PRK14953, PRK14953, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 486
Score = 33.3 bits (76), Expect = 0.22
Identities = 19/61 (31%), Positives = 26/61 (42%), Gaps = 11/61 (18%)
Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEA 205
FK+V G + L+ V R+ H + GP GTGKT +AR +A
Sbjct: 14 FFKEVIGQEIVVRILKNAVKL-----------QRVSHAYIFAGPRGTGKTTIARILAKVL 62
Query: 206 N 206
N
Sbjct: 63 N 63
>gnl|CDD|150034 pfam09217, EcoRII-N, Restriction endonuclease EcoRII, N-terminal.
The N-terminal effector-binding domain of the
Restriction Endonuclease EcoRII has a DNA recognition
fold, allowing for binding to 5'-CCWGG sequences. It
assumes a structure composed of an eight-stranded
beta-sheet with the strands in the order of b2, b5, b4,
b3, b7, b6, b1 and b8. They are mostly antiparallel to
each other except that b3 is parallel to b7.
Alternatively, it may also be viewed as consisting of
two mini beta-sheets of four antiparallel beta-strands,
sheet I from beta-strands b2, b5, b4, b3 and sheet II
from strands b7, b6, b1, b8, folded into an open mixed
beta-barrel with a novel topology. Sheet I has a simple
Greek key motif while sheet II does not.
Length = 156
Score = 32.9 bits (75), Expect = 0.25
Identities = 33/174 (18%), Positives = 55/174 (31%), Gaps = 32/174 (18%)
Query: 27 SYSQFIKDVDAGRVRKISVIGTHITGFYVNGESSFQTYMPLVGSKLLDKLQSKDIEISSR 86
+Y+ FIK + A G H GFY+ + + + +K + + S
Sbjct: 6 NYAVFIKRLSANDTGAT---GGHQAGFYIPKGFAEDLFPDINHTKEENPSVMLKAKWQSH 62
Query: 87 PVNDGSPGLLSYLGSWFPLVLVVLVWMFLMRQIQGGGARGA---MGFGKSKAKLLSGNVG 143
V D + Y GG R FG N G
Sbjct: 63 SVTDSEARAIYYNQRLR------------------GGTRNEARITRFGGGFPLQDPDNTG 104
Query: 144 SVTFKDVAGVDEAKEDLQEIVDFLCDPQK-----FKRLGGRIPHGVLLVGPPGT 192
++ +A + D + ++C + +G +P G L+VGP G
Sbjct: 105 ALAV--LAFLPHQGGDCLLVHAWVCSTDEEEDLFEAEIGEVLP-GSLVVGPAGE 155
>gnl|CDD|183099 PRK11361, PRK11361, acetoacetate metabolism regulatory protein
AtoC; Provisional.
Length = 457
Score = 32.9 bits (75), Expect = 0.28
Identities = 41/149 (27%), Positives = 61/149 (40%), Gaps = 42/149 (28%)
Query: 184 VLLVGPPGTGKTLLARAV---AGEANVPFFTISGSDFVE-------------LFVGVGAS 227
VL+ G GTGK L+ARA+ + A PF ++ + E F G
Sbjct: 169 VLISGESGTGKELIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGHEKGAFTGAQTL 228
Query: 228 RVRDMFEQAKNNSPCIVFVDEIDAVGRHRGIGLGGGNDEREQTLNQLLVEMDGFESSEG- 286
R + +FE+A + + +DEI + L ERE FE G
Sbjct: 229 R-QGLFERANEGT---LLLDEIGEMPLVLQAKLLRILQERE------------FERIGGH 272
Query: 287 ------VILIAATNRPDVLDAALLRPGRF 309
+ +IAATNR D+ A+++ G F
Sbjct: 273 QTIKVDIRIIAATNR-DL--QAMVKEGTF 298
>gnl|CDD|184929 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 576
Score = 32.8 bits (75), Expect = 0.28
Identities = 19/57 (33%), Positives = 24/57 (42%), Gaps = 11/57 (19%)
Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVA 202
TF D+ G + LQ +D GR+ H L G G GKT AR +A
Sbjct: 14 TFSDLTGQEHVSRTLQNAID-----------TGRVAHAFLFTGARGVGKTSTARILA 59
>gnl|CDD|163066 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.
Length = 615
Score = 32.9 bits (75), Expect = 0.29
Identities = 15/33 (45%), Positives = 18/33 (54%), Gaps = 4/33 (12%)
Query: 181 PHGVLLVGPPGTGKTLLARAVAGEA----NVPF 209
P ++L GPPG GKT AR EA + PF
Sbjct: 175 PQHIILYGPPGVGKTTAARLALEEAKKLKHTPF 207
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 32.6 bits (74), Expect = 0.36
Identities = 18/55 (32%), Positives = 31/55 (56%), Gaps = 6/55 (10%)
Query: 148 KDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVA 202
D G++ K+ I+++L + ++ G I + LVGPPG GKT L +++A
Sbjct: 322 TDHYGLERVKD---RILEYLAVQSRVNKIKGPI---LCLVGPPGVGKTSLGQSIA 370
>gnl|CDD|180523 PRK06305, PRK06305, DNA polymerase III subunits gamma and tau;
Validated.
Length = 451
Score = 32.4 bits (74), Expect = 0.36
Identities = 21/63 (33%), Positives = 26/63 (41%), Gaps = 11/63 (17%)
Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEA 205
TF ++ G D +V L + +F R H L G GTGKT LAR A
Sbjct: 15 TFSEILGQDA-------VVAVLKNALRFNRAA----HAYLFSGIRGTGKTTLARIFAKAL 63
Query: 206 NVP 208
N
Sbjct: 64 NCQ 66
>gnl|CDD|162029 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
Members of this family from Pyrococcus horikoshii and
Pyrococcus abyssi each contain a predicted intein.
Length = 608
Score = 32.1 bits (73), Expect = 0.51
Identities = 12/19 (63%), Positives = 17/19 (89%)
Query: 184 VLLVGPPGTGKTLLARAVA 202
VLL+G PG GK++LA+A+A
Sbjct: 40 VLLIGEPGVGKSMLAKAMA 58
>gnl|CDD|162545 TIGR01818, ntrC, nitrogen regulation protein NR(I). This model
represents NtrC, a DNA-binding response regulator that
is phosphorylated by NtrB and interacts with sigma-54.
NtrC usually controls the expression of glutamine
synthase, GlnA, and may be called GlnL, GlnG, etc.
Length = 463
Score = 31.6 bits (72), Expect = 0.60
Identities = 34/97 (35%), Positives = 47/97 (48%), Gaps = 21/97 (21%)
Query: 171 QKFKRLGGRIPHG---VLLVGPPGTGKTLLARAVAGE---ANVPFFTISGS----DFV-- 218
Q+ R GR+ VL+ G GTGK L+ARA+ AN PF ++ + D +
Sbjct: 144 QEVFRAIGRLSRSDITVLINGESGTGKELVARALHRHSPRANGPFIALNMAAIPKDLIES 203
Query: 219 ELF-----VGVGASRVRD-MFEQAKNNSPCIVFVDEI 249
ELF GA+ R FEQA + +F+DEI
Sbjct: 204 ELFGHEKGAFTGANTRRQGRFEQADGGT---LFLDEI 237
>gnl|CDD|148176 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 = 31.9 bits (73), Expect = 0.62
Identities = 16/42 (38%), Positives = 18/42 (42%), Gaps = 1/42 (2%)
Query: 181 PHGVLLVGPPGTGKTLLARAVAGE-ANVPFFTISGSDFVELF 221
P VLL G PG GKT LARA+ E I +
Sbjct: 12 PVAVLLGGQPGAGKTELARALLEELGGGNVVRIDPDELRTYH 53
>gnl|CDD|184916 PRK14952, PRK14952, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 584
Score = 31.8 bits (72), Expect = 0.64
Identities = 22/61 (36%), Positives = 26/61 (42%), Gaps = 11/61 (18%)
Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEA 205
TF +V G + E L +D GRI H L GP G GKT AR +A
Sbjct: 11 TFAEVVGQEHVTEPLSSALD-----------AGRINHAYLFSGPRGCGKTSSARILARSL 59
Query: 206 N 206
N
Sbjct: 60 N 60
>gnl|CDD|152572 pfam12137, RapA_C, RNA polymerase recycling family C-terminal.
This domain is found in bacteria. This domain is about
360 amino acids in length. This domain is found
associated with pfam00271, pfam00176. The function of
this domain is not known, but structurally it forms an
alpha-beta fold in nature with a central beta-sheet
flanked by helices and loops, the beta-sheet being
mainly antiparallel and flanked by four alpha helices,
among which the two longer helices exhibit a coiled-coil
arrangement.
Length = 362
Score = 31.7 bits (73), Expect = 0.64
Identities = 29/109 (26%), Positives = 53/109 (48%), Gaps = 21/109 (19%)
Query: 497 RVMVTQFGFSNLLGKVSYEEGQQEALLSHPVSRPRSISEETAQKIDKEVFRLIEEAYQKA 556
R+++ + G +NL +VS+E ++ PV+R TA+K+ K + IE+ QKA
Sbjct: 238 RLLLDKNG-NNLSAQVSFESLNKQL---SPVNR------HTARKLVKALRPQIEQLLQKA 287
Query: 557 KSIIQEKNDNFVAIAEALLEYETLSGKEIASL---------IRGEKISR 596
+ + +E+ + I +A + + E+A L IR E+I
Sbjct: 288 EKLAEEQLEEI--IEQAKQQMQQQLSAELARLKALKAVNPNIRDEEIEA 334
>gnl|CDD|181656 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau;
Validated.
Length = 598
Score = 31.4 bits (72), Expect = 0.66
Identities = 13/27 (48%), Positives = 15/27 (55%), Gaps = 4/27 (14%)
Query: 178 GRIPHGVLLVGPPGTGKT----LLARA 200
GRI +L G G GKT +LARA
Sbjct: 43 GRIAQAFMLTGVRGVGKTTTARILARA 69
>gnl|CDD|134335 PRK00625, PRK00625, shikimate kinase; Provisional.
Length = 173
Score = 31.3 bits (71), Expect = 0.72
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 184 VLLVGPPGTGKTLLARAVAGEANVPFFTI 212
+ L G P GKT +A+A ++PFF
Sbjct: 3 IFLCGLPTVGKTSFGKALAKFLSLPFFDT 31
>gnl|CDD|184928 PRK14964, PRK14964, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 491
Score = 31.3 bits (71), Expect = 0.72
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 178 GRIPHGVLLVGPPGTGKTLLARAVA 202
+IP +LLVG G GKT AR ++
Sbjct: 32 NKIPQSILLVGASGVGKTTCARIIS 56
>gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 484
Score = 31.5 bits (71), Expect = 0.74
Identities = 21/60 (35%), Positives = 26/60 (43%), Gaps = 11/60 (18%)
Query: 147 FKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEAN 206
F+DV D A LQ K G+I H + GP G GKT +AR +A N
Sbjct: 17 FRDVIHQDLAIGALQ---------NALK--SGKIGHAYIFFGPRGVGKTTIARILAKRLN 65
>gnl|CDD|168322 PRK05973, PRK05973, replicative DNA helicase; Provisional.
Length = 237
Score = 31.5 bits (72), Expect = 0.76
Identities = 23/71 (32%), Positives = 33/71 (46%), Gaps = 11/71 (15%)
Query: 175 RLGGRIPHG--VLLVGPPGTGKTLLARAVAGEA-----NVPFFTI--SGSDFVELF--VG 223
L ++ G VLL PG GKTLL +A EA FFT+ + D + +G
Sbjct: 56 ELFSQLKPGDLVLLGARPGHGKTLLGLELAVEAMKSGRTGVFFTLEYTEQDVRDRLRALG 115
Query: 224 VGASRVRDMFE 234
++ D+FE
Sbjct: 116 ADRAQFADLFE 126
>gnl|CDD|130041 TIGR00968, 3a0106s01, sulfate ABC transporter, ATP-binding protein.
Length = 237
Score = 31.3 bits (71), Expect = 0.81
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 169 DPQKFKRLGGRIPHG--VLLVGPPGTGKTLLARAVAG 203
Q + +P G V L+GP G+GK+ L R +AG
Sbjct: 12 SFQALDDVNLEVPTGSLVALLGPSGSGKSTLLRIIAG 48
>gnl|CDD|169554 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau;
Validated.
Length = 709
Score = 31.2 bits (70), Expect = 0.82
Identities = 21/61 (34%), Positives = 28/61 (45%), Gaps = 11/61 (18%)
Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEA 205
TF D+ G + + LQ +D GR+ H LL G G GKT +AR +A
Sbjct: 14 TFADLVGQEHVVKALQNALD-----------EGRLHHAYLLTGTRGVGKTTIARILAKSL 62
Query: 206 N 206
N
Sbjct: 63 N 63
>gnl|CDD|163293 TIGR03498, FliI_clade3, flagellar protein export ATPase FliI.
Members of this protein family are the FliI protein of
bacterial flagellum systems. This protein acts to drive
protein export for flagellar biosynthesis. The most
closely related family is the YscN family of bacterial
type III secretion systems. This model represents one
(of three) segment of the FliI family tree. These have
been modeled separately in order to exclude the type III
secretion ATPases more effectively.
Length = 418
Score = 31.1 bits (71), Expect = 0.89
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 10/57 (17%)
Query: 341 ILKTIARGTPGFSGADLRNLVNEAALMAARRNRRLVTMQEFEDAKDKILMGAERRST 397
+L +++R P + R LV RR R L + +E+ +D I +GA R+ +
Sbjct: 333 VLASVSRLAPRVWSPEERKLV--------RRLRAL--LARYEETEDLIRLGAYRKGS 379
>gnl|CDD|182778 PRK10851, PRK10851, sulfate/thiosulfate transporter subunit;
Provisional.
Length = 353
Score = 31.2 bits (71), Expect = 0.92
Identities = 15/26 (57%), Positives = 18/26 (69%), Gaps = 2/26 (7%)
Query: 180 IPHG--VLLVGPPGTGKTLLARAVAG 203
IP G V L+GP G+GKT L R +AG
Sbjct: 25 IPSGQMVALLGPSGSGKTTLLRIIAG 50
>gnl|CDD|181459 PRK08533, PRK08533, flagellar accessory protein FlaH; Reviewed.
Length = 230
Score = 31.2 bits (71), Expect = 0.98
Identities = 15/31 (48%), Positives = 22/31 (70%), Gaps = 2/31 (6%)
Query: 174 KRLGGRIPHG--VLLVGPPGTGKTLLARAVA 202
KRLGG IP G +L+ G TGK++L++ +A
Sbjct: 15 KRLGGGIPAGSLILIEGDESTGKSILSQRLA 45
>gnl|CDD|182917 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
Provisional.
Length = 758
Score = 31.0 bits (70), Expect = 0.99
Identities = 28/89 (31%), Positives = 40/89 (44%), Gaps = 17/89 (19%)
Query: 185 LLVGPPGTGKTLLARAVAG---EANVPFF----TISGSDFVELFVGVG-----ASRVRDM 232
LLVG G GKT +A +A + +VP TI D L G R + +
Sbjct: 211 LLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKAL 270
Query: 233 FEQAKNNSPCIVFVDEIDAVGRHRGIGLG 261
+Q + ++ I+F+DEI H IG G
Sbjct: 271 LKQLEQDTNSILFIDEI-----HTIIGAG 294
>gnl|CDD|180959 PRK07399, PRK07399, DNA polymerase III subunit delta'; Validated.
Length = 314
Score = 31.0 bits (71), Expect = 1.0
Identities = 14/54 (25%), Positives = 18/54 (33%), Gaps = 11/54 (20%)
Query: 147 FKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARA 200
F ++ G A E L + RI L GP G G+ L A
Sbjct: 3 FANLIGQPLAIELLTAAIK-----------QNRIAPAYLFAGPEGVGRKLAALC 45
>gnl|CDD|178887 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 30.9 bits (71), Expect = 1.0
Identities = 8/27 (29%), Positives = 14/27 (51%)
Query: 184 VLLVGPPGTGKTLLARAVAGEANVPFF 210
++L+G G GK+ + R +A F
Sbjct: 7 IVLIGFMGAGKSTIGRLLAKRLGYDFI 33
>gnl|CDD|184934 PRK14970, PRK14970, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 367
Score = 31.0 bits (70), Expect = 1.1
Identities = 29/104 (27%), Positives = 42/104 (40%), Gaps = 25/104 (24%)
Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEA 205
TF DV G I + L + + L +L GP G GKT AR +A +
Sbjct: 15 TFDDVVG-------QSHITNTLLNAIENNHLA----QALLFCGPRGVGKTTCARILARKI 63
Query: 206 NVPFFTISGSDFVELFVGVGASRVRDMFEQAKNNSPCIVFVDEI 249
N P + DF + + ++ + A NNS VD+I
Sbjct: 64 NQPGYDDPNEDF--------SFNIFEL-DAASNNS-----VDDI 93
>gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional.
Length = 259
Score = 30.8 bits (70), Expect = 1.2
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 184 VLLVGPPGTGKTLLARAV---AGEANVPFFTISGSDFV-ELFVGVGASRVRDMFEQAKNN 239
++L+GP G GKT LA A+ A A + + +D + +L R + ++
Sbjct: 105 IVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTTAADLLLQLSTAQRQGRYKTTLQRGVMA 164
Query: 240 SPCIVFVDEI 249
P ++ +DEI
Sbjct: 165 -PRLLIIDEI 173
>gnl|CDD|162744 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 = 30.9 bits (70), Expect = 1.2
Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 5/54 (9%)
Query: 184 VLLVGPPGTGKTLLARAVAGEANVPFFTISGSDFVELFVGVGASRVRDMFEQAK 237
+ + GPPG+GKT +A+ +A + ++ IS D +F + A D+ E
Sbjct: 3 ITISGPPGSGKTTVAKILAEKLSLKL--ISAGD---IFRELAAKMGLDLIEFLN 51
>gnl|CDD|128474 smart00177, ARF, ARF-like small GTPases; ARF, ADP-ribosylation
factor. Ras homologues involved in vesicular transport.
Activator of phospholipase D isoforms. Unlike Ras
proteins they lack cysteine residues at their C-termini
and therefore are unlikely to be prenylated. ARFs are
N-terminally myristoylated. Contains ATP/GTP-binding
motif (P-loop).
Length = 175
Score = 30.7 bits (69), Expect = 1.3
Identities = 40/142 (28%), Positives = 63/142 (44%), Gaps = 25/142 (17%)
Query: 173 FKRLGGRIPHGVLLVGPPGTGK-TLLARAVAGEA---------NVPFFTISGSDFVELFV 222
F +L G +L+VG GK T+L + GE+ NV T F V
Sbjct: 5 FSKLFGNKEMRILMVGLDAAGKTTILYKLKLGESVTTIPTIGFNVETVTYKNISFTVWDV 64
Query: 223 GVGASRVRDMFEQAKNNSPCIVFVDEIDAVGRHRGIGLGGGNDEREQTLNQLLVEMDGFE 282
G G ++R ++ N+ ++FV +D+ R R DE + L+++L E E
Sbjct: 65 G-GQDKIRPLWRHYYTNTQGLIFV--VDSNDRDR-------IDEAREELHRMLNED---E 111
Query: 283 SSEGVILIAATNR--PDVLDAA 302
+ VIL+ A + PD + AA
Sbjct: 112 LRDAVILVFANKQDLPDAMKAA 133
>gnl|CDD|181551 PRK08769, PRK08769, DNA polymerase III subunit delta'; Validated.
Length = 319
Score = 30.3 bits (68), Expect = 1.4
Identities = 13/25 (52%), Positives = 18/25 (72%)
Query: 178 GRIPHGVLLVGPPGTGKTLLARAVA 202
GR+ HG+L+ GP G GK +A A+A
Sbjct: 23 GRLGHGLLICGPEGLGKRAVALALA 47
>gnl|CDD|129002 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 = 30.3 bits (69), Expect = 1.5
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 10/56 (17%)
Query: 148 KDVAGVDEAKEDLQEIVDFLCDPQKFKRLG--GRIPHGVLLVGPPGTGKTLLARAV 201
D G++EA ++ V++ + L +I + L+GP G GK+ L +
Sbjct: 51 HDFFGMEEA---IERFVNYFKSAAQ--GLEERKQI---LYLLGPVGGGKSSLVECL 98
>gnl|CDD|183530 PRK12444, PRK12444, threonyl-tRNA synthetase; Reviewed.
Length = 639
Score = 30.5 bits (69), Expect = 1.6
Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 13/75 (17%)
Query: 530 PRSISEETAQKIDKEVFRLIEE---------AYQKAKSIIQEKNDNF-VAIAEALLEYET 579
P S++ E +KI+KE+ ++I E + ++A + QE ND + + EA+ E+
Sbjct: 113 PSSVNVEDLRKIEKEMKKIINENIKIERVEVSREEAAKLFQEMNDRLKLELLEAIPSGES 172
Query: 580 LS---GKEIASLIRG 591
++ E L RG
Sbjct: 173 ITLYKQGEFVDLCRG 187
>gnl|CDD|180131 PRK05563, PRK05563, DNA polymerase III subunits gamma and tau;
Validated.
Length = 559
Score = 30.2 bits (69), Expect = 1.6
Identities = 14/28 (50%), Positives = 17/28 (60%), Gaps = 4/28 (14%)
Query: 178 GRIPHGVLLVGPPGTGKT----LLARAV 201
G+I H L GP GTGKT + A+AV
Sbjct: 35 GKISHAYLFSGPRGTGKTSAAKIFAKAV 62
>gnl|CDD|181541 PRK08727, PRK08727, hypothetical protein; Validated.
Length = 233
Score = 30.2 bits (68), Expect = 1.6
Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 7/73 (9%)
Query: 184 VLLVGPPGTGKTLLARAVAGEANVPFFTISGSDFVELFVGVGASRVRDMFEQAKNNSPCI 243
+ L GP GTGKT LA A+ A +G L + A R+RD E + S +
Sbjct: 44 LYLSGPAGTGKTHLALALCAAAEQ-----AGRSSAYLPLQAAAGRLRDALEALEGRS--L 96
Query: 244 VFVDEIDAVGRHR 256
V +D ++++ R
Sbjct: 97 VALDGLESIAGQR 109
>gnl|CDD|178685 PLN03140, PLN03140, ABC transporter G family member; Provisional.
Length = 1470
Score = 30.2 bits (68), Expect = 1.6
Identities = 15/30 (50%), Positives = 21/30 (70%), Gaps = 1/30 (3%)
Query: 185 LLVGPPGTGKTLLARAVAGEANVPFFTISG 214
LL+GPP +GKT L A+AG+ + P +SG
Sbjct: 195 LLLGPPSSGKTTLLLALAGKLD-PSLKVSG 223
>gnl|CDD|116881 pfam08298, 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 = 358
Score = 30.1 bits (68), Expect = 1.8
Identities = 24/92 (26%), Positives = 40/92 (43%), Gaps = 10/92 (10%)
Query: 147 FKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVL-LVGPPGTGKTLLARAV-AGE 204
F D G++E ++ IV++ + G +L L+GP G GK+ LA +
Sbjct: 57 FADFFGMEET---IERIVNYF----RHAAQGLEERKQILYLLGPVGGGKSSLAERLKKLL 109
Query: 205 ANVPFFTISGSDFVELFVG-VGASRVRDMFEQ 235
VP + + GS E + +RD+ E
Sbjct: 110 ELVPIYALKGSPVFESPLHLFNPHHLRDILED 141
>gnl|CDD|179771 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 30.2 bits (69), Expect = 1.9
Identities = 11/30 (36%), Positives = 18/30 (60%), Gaps = 2/30 (6%)
Query: 188 GPPGTGKTLLARAVAGEANVPFFTISGSDF 217
GPPG+GKT +AR +A + + +S +
Sbjct: 7 GPPGSGKTTVARLLAEKLGLKH--VSAGEI 34
>gnl|CDD|163593 TIGR03881, KaiC_arch_4, KaiC domain protein, PAE1156 family.
Members of this protein family are archaeal
single-domain KaiC_related proteins, homologous to the
Cyanobacterial circadian clock cycle protein KaiC, an
autokinase/autophosphorylase that has two copies of the
domain.
Length = 229
Score = 30.1 bits (68), Expect = 2.1
Identities = 14/26 (53%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 174 KRLGGRIPHG--VLLVGPPGTGKTLL 197
K L G IP G V + G PGTGKT+
Sbjct: 11 KLLEGGIPRGFFVAVTGEPGTGKTIF 36
>gnl|CDD|182930 PRK11054, helD, DNA helicase IV; Provisional.
Length = 684
Score = 29.9 bits (68), Expect = 2.1
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 268 EQTLNQLLVEMDGFESSEGVILIAATN---RPDVLDAALLR 305
E L LL ++ G+ + IL+ A RP +LD A R
Sbjct: 543 EDQLEALLDKLSGYAKPDERILLLARYHHLRPALLDKAATR 583
>gnl|CDD|131585 TIGR02533, type_II_gspE, general secretory pathway protein E. This
family describes GspE, the E protein of the type II
secretion system, also called the main terminal branch
of the general secretion pathway. This model separates
GspE from the PilB protein of type IV pilin
biosynthesis.
Length = 486
Score = 29.7 bits (67), Expect = 2.3
Identities = 18/39 (46%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 171 QKFKRLGGRIPHGVLLV-GPPGTGKTLLARAVAGEANVP 208
+F+RL R PHG++LV GP G+GKT A N P
Sbjct: 232 SRFERLIRR-PHGIILVTGPTGSGKTTTLYAALSRLNTP 269
>gnl|CDD|150789 pfam10156, Med17, Subunit 17 of Mediator complex. This Mediator
complex subunit was formerly known as Srb4 in yeasts or
Trap80 in Drosophila and human. The Med17 subunit is
located within the head domain and is essential for cell
viability to the extent that a mutant strain of
cerevisiae lacking it shows all RNA polymerase
II-dependent transcription ceasing at non-permissive
temperatures.
Length = 454
Score = 29.6 bits (67), Expect = 2.4
Identities = 9/34 (26%), Positives = 15/34 (44%), Gaps = 4/34 (11%)
Query: 378 MQEFEDAKDKILMGAERRSTAMTEEEKKITAYHE 411
++ +A D +L AER + +E T Y
Sbjct: 176 LKSLNEAADLLLKAAERLEKEVAKE----TKYWS 205
>gnl|CDD|181256 PRK08154, PRK08154, anaerobic benzoate catabolism transcriptional
regulator; Reviewed.
Length = 309
Score = 29.5 bits (67), Expect = 2.4
Identities = 16/78 (20%), Positives = 28/78 (35%), Gaps = 14/78 (17%)
Query: 150 VAGVDEAKEDLQEIVDFL-----CDPQKFKRLGGRIP---------HGVLLVGPPGTGKT 195
+ VD + D I + L + + + + L+G G GK+
Sbjct: 88 LGDVDTSSPDWLLIRELLEQASPAQLARVRDALSGMLGAGRRAARRRRIALIGLRGAGKS 147
Query: 196 LLARAVAGEANVPFFTIS 213
L R +A VPF ++
Sbjct: 148 TLGRMLAARLGVPFVELN 165
>gnl|CDD|181175 PRK07940, PRK07940, DNA polymerase III subunit delta'; Validated.
Length = 394
Score = 29.5 bits (67), Expect = 2.5
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 2/56 (3%)
Query: 147 FKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVA 202
+ D+ G + +L+ G + H L GPPG+G+++ ARA A
Sbjct: 4 WDDLVGQEAVVAELRAAA--RAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFA 57
>gnl|CDD|181538 PRK08699, PRK08699, DNA polymerase III subunit delta'; Validated.
Length = 325
Score = 29.8 bits (67), Expect = 2.5
Identities = 11/24 (45%), Positives = 12/24 (50%)
Query: 179 RIPHGVLLVGPPGTGKTLLARAVA 202
R P+ L G G GKT AR A
Sbjct: 19 RRPNAWLFAGKKGIGKTAFARFAA 42
>gnl|CDD|180644 PRK06647, PRK06647, DNA polymerase III subunits gamma and tau;
Validated.
Length = 563
Score = 29.7 bits (67), Expect = 2.6
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 178 GRIPHGVLLVGPPGTGKTLLARAVA 202
+I + + GP G GKT ARA A
Sbjct: 35 NKIANAYIFSGPRGVGKTSSARAFA 59
>gnl|CDD|180719 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 29.5 bits (67), Expect = 2.8
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 185 LLVGPPGTGKTLLARAVAGE 204
L G GTGKT L+ +A E
Sbjct: 187 LFYGNTGTGKTFLSNCIAKE 206
>gnl|CDD|180132 PRK05564, PRK05564, DNA polymerase III subunit delta'; Validated.
Length = 313
Score = 29.6 bits (67), Expect = 2.8
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 178 GRIPHGVLLVGPPGTGKTLLARAVA 202
R H ++VG G GK+LLA+ +A
Sbjct: 23 NRFSHAHIIVGEDGIGKSLLAKEIA 47
>gnl|CDD|180790 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau;
Validated.
Length = 830
Score = 29.4 bits (66), Expect = 2.9
Identities = 14/30 (46%), Positives = 16/30 (53%)
Query: 177 GGRIPHGVLLVGPPGTGKTLLARAVAGEAN 206
GGR+ H L G G GKT L+R A N
Sbjct: 34 GGRLHHAYLFTGTRGVGKTTLSRIFAKALN 63
>gnl|CDD|140006 PRK13949, PRK13949, shikimate kinase; Provisional.
Length = 169
Score = 29.3 bits (66), Expect = 3.0
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 184 VLLVGPPGTGKTLLARAVAGEANVPF 209
+ LVG G GKT L +A+A E + F
Sbjct: 4 IFLVGYMGAGKTTLGKALARELGLSF 29
>gnl|CDD|163585 TIGR03873, F420-0_ABC_ATP, proposed F420-0 ABC transporter,
ATP-binding protein. This small clade of ABC-type
transporter ATP-binding protein components is found as a
three gene cassette along with a periplasmic
substrate-binding protein (TIGR03868) and a permease
(TIGR03869). The organisms containing this cassette are
all Actinobacteria and all contain numerous genes
requiring the coenzyme F420. This model was defined
based on five such organisms, four of which are lacking
all F420 biosynthetic capability save the final
side-chain polyglutamate attachment step (via the gene
cofE: TIGR01916). In Jonesia denitrificans DSM 20603 and
marine actinobacterium PHSC20C1 this cassette is in an
apparent operon with the cofE gene and, in PHSC20C1,
also with a F420-dependent glucose-6-phosphate
dehydrogenase (TIGR03554). Based on these observations
we propose that this ATP-binding protein is a component
of an F420-0 (that is, F420 lacking only the
polyglutamate tail) transporter.
Length = 256
Score = 29.4 bits (66), Expect = 3.0
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 11/40 (27%)
Query: 175 RLGGRI---------PHGVL--LVGPPGTGKTLLARAVAG 203
GGR+ P G L L+GP G+GK+ L R +AG
Sbjct: 10 SAGGRLIVDGVDVTAPPGSLTGLLGPNGSGKSTLLRLLAG 49
>gnl|CDD|182758 PRK10820, PRK10820, DNA-binding transcriptional regulator TyrR;
Provisional.
Length = 520
Score = 29.3 bits (66), Expect = 3.3
Identities = 28/81 (34%), Positives = 33/81 (40%), Gaps = 20/81 (24%)
Query: 185 LLVGPPGTGKTLLARAV---AGEANVPFFTI---SGSDFV---ELFVGVGASRV------ 229
L+ G GTGK LLA A + PF + S D V ELF G
Sbjct: 231 LITGDTGTGKDLLAYACHLRSPRGKKPFLALNCASIPDDVVESELF-GHAPGAYPNALEG 289
Query: 230 -RDMFEQAKNNSPCIVFVDEI 249
+ FEQA S V +DEI
Sbjct: 290 KKGFFEQANGGS---VLLDEI 307
>gnl|CDD|162808 TIGR02329, propionate_PrpR, propionate catabolism operon regulatory
protein PrpR. At least five distinct pathways exists
for the catabolism of propionate by way of
propionyl-CoA. Members of this family represent the
transcriptional regulatory protein PrpR, whose gene is
found in most cases divergently transcribed from an
operon for the methylcitric acid cycle of propionate
catabolism. 2-methylcitric acid, a catabolite by this
pathway, is a coactivator of PrpR.
Length = 526
Score = 29.1 bits (65), Expect = 3.3
Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 175 RLGGRIPHGVLLVGPPGTGKTLLARA---VAGEANVPFFTISGSDFVE 219
RL R VL++G GTGK L+A+A ++G + PF I+ E
Sbjct: 229 RLYARSDATVLILGESGTGKELVAQAIHQLSGRRDFPFVAINCGAIAE 276
>gnl|CDD|169667 PRK09112, PRK09112, DNA polymerase III subunit delta'; Validated.
Length = 351
Score = 29.2 bits (66), Expect = 3.3
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 178 GRIPHGVLLVGPPGTGKTLLA 198
G++ H +L GP G GK LA
Sbjct: 42 GKLHHALLFEGPEGIGKATLA 62
>gnl|CDD|163196 TIGR03265, PhnT2, putative 2-aminoethylphosphonate ABC transporter,
ATP-binding protein. This ABC transporter ATP-binding
protein is found in a number of genomes in operon-like
contexts strongly suggesting a substrate specificity for
2-aminoethylphosphonate (2-AEP). The characterized
PhnSTUV system is absent in the genomes in which this
system is found. These genomes encode systems for the
catabolism of 2-AEP, making the need for a
2-AEP-specific transporter likely.
Length = 353
Score = 29.2 bits (66), Expect = 3.3
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 184 VLLVGPPGTGKTLLARAVAG 203
V L+GP G GKT L R +AG
Sbjct: 33 VCLLGPSGCGKTTLLRIIAG 52
>gnl|CDD|181743 PRK09270, PRK09270, nucleoside triphosphate hydrolase
domain-containing protein; Reviewed.
Length = 229
Score = 29.1 bits (66), Expect = 3.4
Identities = 10/30 (33%), Positives = 13/30 (43%), Gaps = 2/30 (6%)
Query: 173 FKRLGGRIPHGVLLVGPPGTGKTLLARAVA 202
R V + GPPG GK+ LA +
Sbjct: 27 QAEPQRRTI--VGIAGPPGAGKSTLAEFLE 54
>gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional.
Length = 254
Score = 29.1 bits (65), Expect = 3.4
Identities = 16/36 (44%), Positives = 19/36 (52%), Gaps = 5/36 (13%)
Query: 184 VLLVGPPGTGKTLLA-----RAVAGEANVPFFTISG 214
V+ +GPPGTGKT LA RA V F T +
Sbjct: 101 VVFLGPPGTGKTHLAIGLGIRACQAGHRVLFATAAQ 136
>gnl|CDD|163508 TIGR03796, NHPM_micro_ABC1, NHPM bacteriocin system ABC
transporter, peptidase/ATP-binding protein. This
protein describes an multidomain ABC transporter subunit
that is one of three protein families associated with
some regularity with a distinctive family of putative
bacteriocins. It includes a bacteriocin-processing
peptidase domain at the N-terminus. Model TIGR03793
describes a conserved propeptide region for this
bacteriocin family, unusual because it shows obvious
homology a region of the enzyme nitrile hydratase up to
the classic Gly-Gly cleavage motif. This family is
therefore predicted to be a subunit of a bacteriocin
processing and export system characteristic to this
system that we designate NHPM, Nitrile Hydratase
Propeptide Microcin.
Length = 710
Score = 29.1 bits (66), Expect = 3.7
Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 2/26 (7%)
Query: 180 IPHG--VLLVGPPGTGKTLLARAVAG 203
+ G V LVG G+GK+ +A+ VAG
Sbjct: 502 LQPGQRVALVGGSGSGKSTIAKLVAG 527
>gnl|CDD|182852 PRK10938, PRK10938, putative molybdenum transport ATP-binding
protein ModF; Provisional.
Length = 490
Score = 29.2 bits (66), Expect = 3.8
Identities = 12/18 (66%), Positives = 15/18 (83%)
Query: 187 VGPPGTGKTLLARAVAGE 204
VG G+GK+ LARA+AGE
Sbjct: 35 VGANGSGKSALARALAGE 52
>gnl|CDD|149505 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1 and Miro-2), are atypical Rho GTPases. They have
a unique domain organisation, with tandem GTP-binding
domains and two EF hand domains (pfam00036), that may
bind calcium. They are also larger than classical small
GTPases. It has been proposed that they are involved in
mitochondrial homeostasis and apoptosis.
Length = 118
Score = 28.9 bits (65), Expect = 3.8
Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 6/75 (8%)
Query: 184 VLLVGPPGTGKTLLARAVAGEANVPFFTIS------GSDFVELFVGVGASRVRDMFEQAK 237
V+++G G+GK+ L + G P D +E+ + D + +
Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGEFPPEIPEEIQGDTLAVDTLEVDGDTELLHIWDFGGREE 61
Query: 238 NNSPCIVFVDEIDAV 252
I+F+ DA+
Sbjct: 62 LKFEHIIFMKTADAI 76
>gnl|CDD|130283 TIGR01216, ATP_synt_epsi, ATP synthase, F1 epsilon subunit (delta
in mitochondria). This model describes one of the five
types of subunits in the F1 part of F1/F0 ATP synthases.
Members of this family are designated epsilon in
bacterial and chloroplast systems but designated delta
in mitochondria, where the counterpart of the bacterial
delta subunit is designated OSCP. In a few cases
(Propionigenium modestum, Acetobacterium woodii) scoring
above the trusted cutoff and designated here as
exceptions, Na+ replaces H+ for translocation.
Length = 130
Score = 28.8 bits (65), Expect = 4.1
Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 4/43 (9%)
Query: 536 ETAQKIDKEVFRLIEEAYQKAKSIIQEKNDNFVAIAEALLEYE 578
A ID+ E+A + A+ +++ D+ +AEALL+ +
Sbjct: 82 VFADDIDEAE---AEKALEAAEKLLESAEDDK-DLAEALLKLK 120
>gnl|CDD|179826 PRK04328, PRK04328, hypothetical protein; Provisional.
Length = 249
Score = 28.9 bits (65), Expect = 4.1
Identities = 13/26 (50%), Positives = 18/26 (69%), Gaps = 2/26 (7%)
Query: 176 LGGRIP--HGVLLVGPPGTGKTLLAR 199
L G IP + VLL G PGTGK++ ++
Sbjct: 16 LYGGIPERNVVLLSGGPGTGKSIFSQ 41
>gnl|CDD|184126 PRK13539, PRK13539, cytochrome c biogenesis protein CcmA;
Provisional.
Length = 207
Score = 28.7 bits (65), Expect = 4.3
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 184 VLLVGPPGTGKTLLARAVAG 203
++L GP G+GKT L R +AG
Sbjct: 31 LVLTGPNGSGKTTLLRLIAG 50
>gnl|CDD|184118 PRK13531, PRK13531, regulatory ATPase RavA; Provisional.
Length = 498
Score = 28.8 bits (65), Expect = 4.3
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 184 VLLVGPPGTGKTLLAR 199
V L+GPPG K+L+AR
Sbjct: 42 VFLLGPPGIAKSLIAR 57
>gnl|CDD|180615 PRK06547, PRK06547, hypothetical protein; Provisional.
Length = 172
Score = 28.9 bits (65), Expect = 4.3
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 176 LGGRIPHGVLLVGPPGTGKTLLARAVAGEA 205
GG + VL+ G G+GKT LA A+A
Sbjct: 11 CGGGMIT-VLIDGRSGSGKTTLAGALAART 39
>gnl|CDD|181214 PRK08058, PRK08058, DNA polymerase III subunit delta'; Validated.
Length = 329
Score = 28.7 bits (65), Expect = 4.4
Identities = 10/25 (40%), Positives = 12/25 (48%)
Query: 178 GRIPHGVLLVGPPGTGKTLLARAVA 202
R+ H L G GTGK A +A
Sbjct: 25 NRLSHAYLFEGAKGTGKKATALWLA 49
>gnl|CDD|183258 PRK11650, ugpC, glycerol-3-phosphate transporter ATP-binding
subunit; Provisional.
Length = 356
Score = 28.7 bits (65), Expect = 4.4
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 184 VLLVGPPGTGKTLLARAVAG 203
++LVGP G GK+ L R VAG
Sbjct: 33 IVLVGPSGCGKSTLLRMVAG 52
>gnl|CDD|177743 PLN00134, PLN00134, fumarate hydratase; Provisional.
Length = 458
Score = 28.9 bits (65), Expect = 4.4
Identities = 13/46 (28%), Positives = 25/46 (54%)
Query: 553 YQKAKSIIQEKNDNFVAIAEALLEYETLSGKEIASLIRGEKISRPS 598
Y KA ++ ++ + + EA L+ L+ +E L+ EK++ PS
Sbjct: 410 YDKAAAVAKKAHKEGTTLKEAALKLGVLTAEEFDELVVPEKMTGPS 455
>gnl|CDD|172992 PRK14526, PRK14526, adenylate kinase; Provisional.
Length = 211
Score = 28.7 bits (64), Expect = 4.5
Identities = 12/35 (34%), Positives = 22/35 (62%), Gaps = 2/35 (5%)
Query: 183 GVLLVGPPGTGKTLLARAVAGEANVPFFTISGSDF 217
++ +GPPG+GK +A+ ++ E N ++ IS D
Sbjct: 2 KLVFLGPPGSGKGTIAKILSNELN--YYHISTGDL 34
>gnl|CDD|179891 PRK04914, PRK04914, ATP-dependent helicase HepA; Validated.
Length = 956
Score = 28.7 bits (65), Expect = 4.6
Identities = 22/99 (22%), Positives = 40/99 (40%), Gaps = 20/99 (20%)
Query: 507 NLLGKVSYEEGQQEALLSHPVSRPRSISEETAQKIDKEVFRLIEEAYQKAKSIIQEKNDN 566
+L +V +E + V+R TA K+ K V + I + QKA++ + +
Sbjct: 841 DLSAQVEFESLNR---QLSAVNRH------TASKLVKAVQQDIHKLLQKAEAQAEAQARE 891
Query: 567 FVAIAEALLEYETLSGKEIASL---------IRGEKISR 596
I +A E + E++ L IR ++I
Sbjct: 892 L--IEQAKQEADEKLSAELSRLEALKAVNPNIRDDEIEA 928
>gnl|CDD|162095 TIGR00895, 2A0115, benzoate transport.
Length = 398
Score = 28.9 bits (65), Expect = 4.6
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 98 YLGSWFPLVLVVLVWMFL 115
Y+G PL+L++L+ FL
Sbjct: 175 YVGGIAPLLLLLLLMRFL 192
>gnl|CDD|180308 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau;
Validated.
Length = 605
Score = 28.7 bits (64), Expect = 4.7
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 179 RIPHGVLLVGPPGTGKTLLARAVAGEAN 206
++ H + GP G GKT +A+ A N
Sbjct: 36 KLTHAYIFSGPRGIGKTSIAKIFAKAIN 63
>gnl|CDD|183521 PRK12422, PRK12422, chromosomal replication initiation protein;
Provisional.
Length = 445
Score = 28.6 bits (64), Expect = 4.8
Identities = 40/140 (28%), Positives = 59/140 (42%), Gaps = 23/140 (16%)
Query: 184 VLLVGPPGTGKTLLARAVAG---EANVPFFTISGSDFVELFVGVGASRVRDM--FEQAKN 238
+ L GP G+GKT L +A E+ + F E V A R +M F Q
Sbjct: 144 IYLFGPEGSGKTHLMQAAVHALRESGGKILYVRSELFTEHL--VSAIRSGEMQRFRQFYR 201
Query: 239 NSPCIVFVDEIDAVGRHRGIGLGGGNDEREQTLNQLLVEMDGFESSEG-VILIAATNRPD 297
N +F+++I+ G G +E T N L +EG +I+I++T P
Sbjct: 202 NVD-ALFIEDIEVFS-----GKGATQEEFFHTFNSL--------HTEGKLIVISSTCAPQ 247
Query: 298 VLDAALLR-PGRFDRQITVP 316
L A R RF+ I +P
Sbjct: 248 DLKAMEERLISRFEWGIAIP 267
>gnl|CDD|163589 TIGR03877, thermo_KaiC_1, KaiC domain protein, Ph0284 family.
Members of this family contain a single copy of the KaiC
domain (pfam06745) that occurs in two copies of the
circadian clock protein kinase KaiC itself. Members
occur primarily in thermophilic archaea and in
Thermotoga.
Length = 237
Score = 28.6 bits (64), Expect = 5.0
Identities = 13/26 (50%), Positives = 18/26 (69%), Gaps = 2/26 (7%)
Query: 176 LGGRIP--HGVLLVGPPGTGKTLLAR 199
L G IP + VLL G PGTGK++ ++
Sbjct: 14 LHGGIPERNVVLLSGGPGTGKSIFSQ 39
>gnl|CDD|179011 PRK00413, thrS, threonyl-tRNA synthetase; Reviewed.
Length = 638
Score = 28.5 bits (65), Expect = 5.2
Identities = 15/65 (23%), Positives = 32/65 (49%), Gaps = 10/65 (15%)
Query: 527 VSRPRSISEETAQKIDKEVFRLIEEAY---------QKAKSIIQEKNDNF-VAIAEALLE 576
R R + E + I+KE+ +I+E Y ++A + +++ + + V + E + E
Sbjct: 106 FDRERPFTPEDLEAIEKEMKEIIKENYPIEREVVSREEAIELFKDRGEPYKVELIEEIPE 165
Query: 577 YETLS 581
E +S
Sbjct: 166 DEEIS 170
>gnl|CDD|162612 TIGR01932, hflC, HflC protein. HflK and HflC are paralogs encoded
by tandem genes in Proteobacteria, spirochetes, and some
other bacterial lineages. The HflKC complex is anchored
in the membrane and exposed to the periplasm. The
complex is not active as a protease, but rather binds to
and appears to modulate the ATP-dependent protease FtsH.
The overall function of HflKC is not fully
described.//Regulation of FtsH protease appears to be
negative (PubMed:8947034, PubMed:96367).
Length = 317
Score = 28.6 bits (64), Expect = 5.3
Identities = 24/89 (26%), Positives = 40/89 (44%), Gaps = 17/89 (19%)
Query: 508 LLGKVSYEEGQQEALLSHPVS-------RPRSISEETAQKI----DKEVFRLIEEAYQKA 556
+ K++Y + E++ + S RS EE A++I + EV +++ EAY+ A
Sbjct: 199 RIKKINYSDELSESIYNRMRSEREQIARMHRSQGEEKAEEILGKAEYEVRKILSEAYRTA 258
Query: 557 KSIIQEKNDNFVAIAEALLEYETLSGKEI 585
+ I E AEA Y GK+
Sbjct: 259 RIIKGE------GDAEAAKIYSDAYGKDP 281
>gnl|CDD|179408 PRK02292, PRK02292, V-type ATP synthase subunit E; Provisional.
Length = 188
Score = 28.4 bits (64), Expect = 5.4
Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 10/60 (16%)
Query: 528 SRPRSISEETAQKIDKEVFRLIEEAYQKAKSIIQEKNDNFVAIAEALLEYETLSGKEIAS 587
+R I E D+E +I EA A+ I+++ AEA E E L +E++S
Sbjct: 16 ARASEIRAEA----DEEAEEIIAEAEADAEEILED------REAEAEREIEQLREQELSS 65
>gnl|CDD|181800 PRK09362, PRK09362, phosphoribosylaminoimidazole-succinocarboxamide
synthase; Reviewed.
Length = 238
Score = 28.5 bits (65), Expect = 5.9
Identities = 11/34 (32%), Positives = 19/34 (55%), Gaps = 4/34 (11%)
Query: 536 ETAQKIDKEVFRL----IEEAYQKAKSIIQEKND 565
ET +K+DK+ FR + EAY++ + E +
Sbjct: 205 ETNEKLDKDRFRRDLGGVIEAYEEVLKRLGELLE 238
>gnl|CDD|130214 TIGR01144, ATP_synt_b, ATP synthase, F0 subunit b. This model
describes the F1/F0 ATP synthase b subunit in bacteria
only. Scoring just below the trusted cutoff are the
N-terminal domains of Mycobacterial b/delta fusion
proteins and a subunit from an archaeon, Methanosarcina
barkeri, in which the ATP synthase homolog differs in
architecture and is not experimentally confirmed. This
model helps resolve b from the related b' subunit.
Within the family is an example from a
sodium-translocating rather than proton-translocating
ATP synthase.
Length = 147
Score = 28.5 bits (64), Expect = 6.1
Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 1/56 (1%)
Query: 533 ISEETAQKIDKEVFRLIEEAYQKAKSIIQEKNDNFVAI-AEALLEYETLSGKEIAS 587
+++ A K+ +++EA +A+ II+ N I EA E K A
Sbjct: 40 RAKKEAALAQKKAQVILKEAKDEAQEIIENANKRGSEILEEAKAEAREEREKIKAQ 95
>gnl|CDD|163225 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.
Length = 1169
Score = 28.5 bits (64), Expect = 6.1
Identities = 10/17 (58%), Positives = 14/17 (82%), Gaps = 1/17 (5%)
Query: 185 LLVGPPGTGKT-LLARA 200
L++GPPG+GKT LL +
Sbjct: 115 LVIGPPGSGKTTLLQNS 131
>gnl|CDD|132302 TIGR03258, PhnT, 2-aminoethylphosphonate ABC transport system,
ATP-binding component PhnT. This ATP-binding component
of an ABC transport system is found in Salmonella and
Burkholderia lineages in the vicinity of enzymes for the
breakdown of 2-aminoethylphosphonate.
Length = 362
Score = 28.4 bits (63), Expect = 6.4
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 186 LVGPPGTGKTLLARAVAG 203
L+G G GKT L RA+AG
Sbjct: 36 LIGKSGCGKTTLLRAIAG 53
>gnl|CDD|149899 pfam08975, 2H-phosphodiest, Domain of unknown function (DUF1868).
This group of 2H-phosphodiesterases comprises a single
family typified by the protein mlr3352 from M.loti.
Members are also present in various
alpha-proteobacteria, Synechocystis, Streptococcus and
Chilo iridescent virus. The presence of a member of this
predominantly bacterial group in a large eukaryotic DNA
virus represents a potential case of horizontal transfer
from a bacterial source into a virus. Several proteins
of bacterial origin have been noticed in the insect
viruses (L.M.Iyer, E.V.Koonin and L.Aravind, unpublished
observations and these appear to have been acquired from
endo-symbiotic or parasitic bacteria that share the same
host cells with the viruses. Presence of 2H proteins in
the proteomes of large DNA viruses (e.g. T4 57B protein
and the Fowl-pox virus FPV025) may point to some role
for these proteins in regulating the viral tRNA
metabolism. Each member of this family contains an
internal duplication, each of which contains an HXTX
motif that defines the family.
Length = 112
Score = 28.1 bits (63), Expect = 6.8
Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 5/41 (12%)
Query: 410 HEAGHAVVACHVPKADPLHKATIIPRGRALGMVMQLPEADR 450
G+ VV CH+ + P + A + R R + P AD+
Sbjct: 10 PFPGNTVV-CHLDQQSPGYAAVLDIRRRLKAL----PFADK 45
>gnl|CDD|185327 PRK15429, PRK15429, formate hydrogenlyase transcriptional activator
FhlA; Provisional.
Length = 686
Score = 28.3 bits (63), Expect = 6.8
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 184 VLLVGPPGTGKTLLARAV 201
VL++G GTGK L+ARA+
Sbjct: 402 VLILGETGTGKELIARAI 419
>gnl|CDD|184037 PRK13409, PRK13409, putative ATPase RIL; Provisional.
Length = 590
Score = 28.2 bits (64), Expect = 7.0
Identities = 15/30 (50%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 177 GGRIPHG-VL-LVGPPGTGKTLLARAVAGE 204
GG I G V+ +VGP G GKT A+ +AG
Sbjct: 359 GGEIYEGEVIGIVGPNGIGKTTFAKLLAGV 388
>gnl|CDD|162243 TIGR01189, ccmA, heme ABC exporter, ATP-binding protein CcmA. This
model describes the cyt c biogenesis protein encoded by
ccmA in bacteria. An exception is, an arabidopsis
protein. Quite likely this is encoded by an organelle.
Bacterial c-type cytocromes are located on the
periplasmic side of the cytoplasmic membrane. Several
gene products encoded in a locus designated as 'ccm' are
implicated in the transport and assembly of the
functional cytochrome C. This cluster includes genes:
ccmA;B;C;D;E;F;G and H. The posttranslational pathway
includes the transport of heme moiety, the secretion of
the apoprotein and the covalent attachment of the heme
with the apoprotein. The proteins ccmA and B represent
an ABC transporter; ccmC and D participate in heme
transfer to ccmE, which function as a periplasmic heme
chaperone. The presence of ccmF, G and H is suggested to
be obligatory for the final functional assembly of
cytochrome c.
Length = 198
Score = 28.1 bits (63), Expect = 7.1
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 182 HGVLLVGPPGTGKTLLARAVAG 203
+ + GP G GKT L R +AG
Sbjct: 27 EALQVTGPNGIGKTTLLRILAG 48
>gnl|CDD|162129 TIGR00954, 3a01203, Peroxysomal Fatty Acyl CoA Transporter (FAT)
Family protei.
Length = 659
Score = 28.2 bits (63), Expect = 7.2
Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 175 RLGGRIPHG--VLLVGPPGTGKTLLARAVAG 203
L +P G +L+ GP G GK+ L R +
Sbjct: 470 SLSFEVPSGNHLLICGPNGCGKSSLFRILGE 500
>gnl|CDD|162298 TIGR01313, therm_gnt_kin, carbohydrate kinase, thermoresistant
glucokinase family. This model represents a subfamily
of proteins that includes thermoresistant and
thermosensitve isozymes of gluconate kinase
(gluconokinase) in E. coli and other related proteins;
members of this family are often named by similarity to
the thermostable isozyme. These proteins show homology
to shikimate kinases and adenylate kinases but not to
gluconate kinases from the FGGY family of carbohydrate
kinases.
Length = 163
Score = 28.1 bits (63), Expect = 7.7
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 186 LVGPPGTGKTLLARAVAGEANVPFFTISGSDF 217
L+G G+GK+ +A A+A F I G D
Sbjct: 3 LMGVAGSGKSTIASALAHRLGAKF--IEGDDL 32
>gnl|CDD|184924 PRK14960, PRK14960, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 702
Score = 28.1 bits (62), Expect = 7.8
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 178 GRIPHGVLLVGPPGTGKTLLARAVA 202
GR+ H L G G GKT +AR +A
Sbjct: 34 GRLHHAYLFTGTRGVGKTTIARILA 58
>gnl|CDD|162555 TIGR01842, type_I_sec_PrtD, type I secretion system ABC
transporter, PrtD family. Type I protein secretion is a
system in some Gram-negative bacteria to export proteins
(often proteases) across both inner and outer membranes
to the extracellular medium. This is one of three
proteins of the type I secretion apparatus. Targeted
proteins are not cleaved at the N-terminus, but rather
carry signals located toward the extreme C-terminus to
direct type I secretion.
Length = 544
Score = 28.1 bits (63), Expect = 8.1
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 5/47 (10%)
Query: 162 EIVDFLCDPQKFKRLGG---RIPHG--VLLVGPPGTGKTLLARAVAG 203
E V + K L G R+ G + ++GP G+GK+ LAR + G
Sbjct: 320 ENVTIVPPGGKKPTLRGISFRLQAGEALAIIGPSGSGKSTLARLIVG 366
>gnl|CDD|180213 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 27.9 bits (63), Expect = 8.1
Identities = 12/26 (46%), Positives = 12/26 (46%), Gaps = 5/26 (19%)
Query: 184 VLLVGPPGTGKT-----LLARAVAGE 204
V LVGP G GKT L AR
Sbjct: 224 VALVGPTGVGKTTTLAKLAARYALLY 249
>gnl|CDD|162131 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein.
Length = 1394
Score = 27.8 bits (62), Expect = 8.2
Identities = 6/21 (28%), Positives = 13/21 (61%)
Query: 184 VLLVGPPGTGKTLLARAVAGE 204
+++G PG+G + L + +A
Sbjct: 90 TVVLGRPGSGCSTLLKTIASN 110
>gnl|CDD|131926 TIGR02880, cbbX_cfxQ, probable Rubsico expression protein CbbX.
Proteins in this family are now designated CbbX. Some
previously were CfxQ (carbon fixation Q). Its gene is
often found immmediately downstream of the Rubisco large
and small chain genes, and it is suggested to be
necessary for Rubisco expression. CbbX has been shown to
be necessary for photoautotrophic growth. This protein
belongs to the larger family of pfam00004, ATPase family
Associated with various cellular Activities. Within that
larger family, members of this family are most closely
related to the stage V sporulation protein K, or SpoVK,
in endospore-forming bacteria such as Bacillus subtilis.
Length = 284
Score = 27.9 bits (62), Expect = 8.5
Identities = 54/228 (23%), Positives = 93/228 (40%), Gaps = 38/228 (16%)
Query: 188 GPPGTGKTLLARAVAGEANVPFF-------TISGSDFVELFVGVGASRVRDMFEQAKNNS 240
G PGTGKT +A +A + + +++ D V ++G A + +++ ++A
Sbjct: 65 GNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTRDDLVGQYIGHTAPKTKEILKRAMGG- 123
Query: 241 PCIVFVDEIDAVGRHRGIGLGGGNDERE---QTLNQLLVEMDGFESSEGVILIAATNRPD 297
++F+DE A +R ++ER+ + + LL M+ VIL +R D
Sbjct: 124 --VLFIDE--AYYLYR------PDNERDYGQEAIEILLQVMENQRDDLVVILAGYKDRMD 173
Query: 298 VLDAALLRPGRFDRQIT--VPNPDIVGREHI----LMVHSRNVPLAPN---VILKTIA-- 346
+ PG F ++ V PD E + LM+ + + IA
Sbjct: 174 SFFES--NPG-FSSRVAHHVDFPDYSEAELLVIAGLMLKEQQYRFSAEAEEAFADYIALR 230
Query: 347 RGTPGFSGA-DLRNLVNEAALMAARRNRRLVTMQEFEDAKDKILMGAE 393
R P F+ A +RN ++ A L A NR + D D + E
Sbjct: 231 RTQPHFANARSIRNAIDRARLRQA--NRLFCDLDRVLDKSDLETIDPE 276
>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
utilisation. Members of this family function in
ethanolamine and propanediol degradation pathways,
however the exact roles of these proteins is poorly
understood.
Length = 143
Score = 28.0 bits (63), Expect = 8.6
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 184 VLLVGPPGTGKTLLARAVAGE 204
++L+G G GKT L +A+ GE
Sbjct: 4 IMLIGRSGCGKTTLTQALNGE 24
>gnl|CDD|182441 PRK10416, PRK10416, signal recognition particle-docking protein
FtsY; Provisional.
Length = 318
Score = 27.8 bits (63), Expect = 8.6
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 145 VTFKDVAGVDEAKEDL-QEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKT 195
V K++ +E KE L +E+ + L +K + + P +L+VG G GKT
Sbjct: 77 VKRKNLKDPEELKELLKEELAEILEPVEKPLNIEEKKPFVILVVGVNGVGKT 128
>gnl|CDD|184919 PRK14955, PRK14955, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 397
Score = 27.9 bits (62), Expect = 8.7
Identities = 13/29 (44%), Positives = 15/29 (51%)
Query: 178 GRIPHGVLLVGPPGTGKTLLARAVAGEAN 206
GR+ HG + G G GKT AR A N
Sbjct: 35 GRVGHGYIFSGLRGVGKTTAARVFAKAVN 63
>gnl|CDD|169949 PRK09536, btuD, corrinoid ABC transporter ATPase; Reviewed.
Length = 402
Score = 27.9 bits (62), Expect = 8.8
Identities = 13/22 (59%), Positives = 14/22 (63%)
Query: 182 HGVLLVGPPGTGKTLLARAVAG 203
V LVGP G GKT L RA+ G
Sbjct: 30 SLVGLVGPNGAGKTTLLRAING 51
>gnl|CDD|181587 PRK08939, PRK08939, primosomal protein DnaI; Reviewed.
Length = 306
Score = 27.9 bits (63), Expect = 8.9
Identities = 18/63 (28%), Positives = 27/63 (42%), Gaps = 10/63 (15%)
Query: 145 VTFKDVAGVDEAKED-LQEIVDFLCD--PQKFKRLGGRIPHGVLLVGPPGTGKTLLARAV 201
+ D+ D + D L +DFL P + + G+ L G G GK+ L A+
Sbjct: 124 ASLADIDLDDRDRLDALMAALDFLEAYPPGEKVK-------GLYLYGDFGVGKSYLLAAI 176
Query: 202 AGE 204
A E
Sbjct: 177 ANE 179
>gnl|CDD|185081 PRK15127, PRK15127, multidrug efflux system protein AcrB;
Provisional.
Length = 1049
Score = 27.9 bits (62), Expect = 8.9
Identities = 47/197 (23%), Positives = 70/197 (35%), Gaps = 49/197 (24%)
Query: 35 VDAGRVRKISVIGT--------HITGFYVNGE-------SSFQTYMPLVGSKLLDKLQS- 78
+D GRV+K+ V+ I +YV S+F + GS L++
Sbjct: 763 IDRGRVKKVYVMSEAKYRMLPDDIGDWYVRAADGQMVPFSAFSSSRWEYGSPRLERYNGL 822
Query: 79 KDIEISSRPVNDGSPGLLSYLGSWFPLVLVVLVWMFLMRQIQGGGARGAMGF---GKSKA 135
+EI + S G M LM ++ G +G+ G S
Sbjct: 823 PSMEILGQAAPGKSTGEA----------------MELMEELASKLPTG-VGYDWTGMSYQ 865
Query: 136 KLLSGNVGSVTFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKT 195
+ LSGN + + IV FLC ++ IP V+LV P G
Sbjct: 866 ERLSGNQAPALYA-----------ISLIVVFLCLAALYESWS--IPFSVMLVVPLGVIGA 912
Query: 196 LLARAVAGEANVPFFTI 212
LLA G N +F +
Sbjct: 913 LLAATFRGLTNDVYFQV 929
>gnl|CDD|128763 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 27.8 bits (62), Expect = 9.0
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 182 HGVLLVGPPGTGKTLLA 198
V+L P G+GKTL A
Sbjct: 25 RDVILAAPTGSGKTLAA 41
>gnl|CDD|163070 TIGR02915, PEP_resp_reg, putative PEP-CTERM system response
regulator. Members of this protein family share
full-length homology with (but do not include) the
acetoacetate metabolism regulatory protein AtoC. These
proteins have a Fis family DNA binding sequence
(pfam02954), a response regulator receiver domain
(pfam00072), and sigma-54 interaction domain
(pfam00158).
Length = 445
Score = 27.8 bits (62), Expect = 9.1
Identities = 12/18 (66%), Positives = 15/18 (83%)
Query: 184 VLLVGPPGTGKTLLARAV 201
VLL+G GTGK +LARA+
Sbjct: 165 VLLLGESGTGKEVLARAL 182
>gnl|CDD|177488 PHA02774, PHA02774, E1; Provisional.
Length = 613
Score = 27.9 bits (63), Expect = 9.2
Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 5/39 (12%)
Query: 162 EIVDFLCDPQKFKRLGGRIP--HGVLLVGPPGTGKTLLA 198
E + FL K IP + +++ GPP TGK++
Sbjct: 416 EFISFLT---ALKDFLKGIPKKNCLVIYGPPDTGKSMFC 451
>gnl|CDD|179921 PRK05057, aroK, shikimate kinase I; Reviewed.
Length = 172
Score = 27.8 bits (62), Expect = 9.2
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 184 VLLVGPPGTGKTLLARAVAGEANVPFF 210
+ LVGP G GK+ + R +A + N+ F+
Sbjct: 7 IFLVGPMGAGKSTIGRQLAQQLNMEFY 33
>gnl|CDD|182710 PRK10765, PRK10765, nitroreductase A; Provisional.
Length = 240
Score = 27.6 bits (62), Expect = 9.5
Identities = 13/39 (33%), Positives = 17/39 (43%), Gaps = 5/39 (12%)
Query: 520 EALLSHPVSRPRSISEETAQKIDKEVFRLIEEAYQKAKS 558
E +LSH RSI T + I + I A + A S
Sbjct: 6 ELILSH-----RSIRHFTDEPISEAQREAIINAARAASS 39
>gnl|CDD|181235 PRK08118, PRK08118, topology modulation protein; Reviewed.
Length = 167
Score = 27.7 bits (62), Expect = 9.6
Identities = 10/27 (37%), Positives = 18/27 (66%)
Query: 184 VLLVGPPGTGKTLLARAVAGEANVPFF 210
++L+G G+GK+ LAR + + N+P
Sbjct: 4 IILIGSGGSGKSTLARQLGEKLNIPVH 30
>gnl|CDD|182893 PRK11000, PRK11000, maltose/maltodextrin transporter ATP-binding
protein; Provisional.
Length = 369
Score = 27.7 bits (62), Expect = 9.8
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 184 VLLVGPPGTGKTLLARAVAG 203
V+ VGP G GK+ L R +AG
Sbjct: 32 VVFVGPSGCGKSTLLRMIAG 51
>gnl|CDD|183622 PRK12608, PRK12608, transcription termination factor Rho;
Provisional.
Length = 380
Score = 27.7 bits (62), Expect = 9.9
Identities = 15/28 (53%), Positives = 17/28 (60%), Gaps = 6/28 (21%)
Query: 185 LLVGPPGTGKTLL----ARAVAGEANVP 208
L+V PP GKT+L A AVA AN P
Sbjct: 137 LIVAPPRAGKTVLLQQIAAAVA--ANHP 162
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.317 0.135 0.380
Gapped
Lambda K H
0.267 0.0669 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 10,736,177
Number of extensions: 739306
Number of successful extensions: 2285
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2259
Number of HSP's successfully gapped: 229
Length of query: 647
Length of database: 5,994,473
Length adjustment: 100
Effective length of query: 547
Effective length of database: 3,833,673
Effective search space: 2097019131
Effective search space used: 2097019131
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: 60 (27.0 bits)