Align triokinase (EC 2.7.1.28); glycerone kinase (EC 2.7.1.29); FAD-AMP lyase (cyclizing) (EC 4.6.1.15) (characterized)
to candidate SM_b20767 SM_b20767 dihydroxyacetone kinase
Query= BRENDA::Q3LXA3 (575 letters) >FitnessBrowser__Smeli:SM_b20767 Length = 572 Score = 263 bits (672), Expect = 1e-74 Identities = 185/562 (32%), Positives = 286/562 (50%), Gaps = 21/562 (3%) Query: 14 ADDALAGLVAC-NPNLQLLQGHRVALRSDLDSLKGRVALLSGGGSGHEPAHAGFIGKGML 72 A ALAG A N++L++G V KG+VA++ GGGSGH PA AG++G G+ Sbjct: 12 ATTALAGFAAIYQRNVRLVKGGVVR---STKVPKGKVAVVVGGGSGHYPAFAGYVGPGLA 68 Query: 73 TGVIAGAVFTSPAVGSILAAIRAVAQAGTVGTLLIVKNYTGDRLNFGLAREQARAEGIPV 132 +AG VF SP+ ++ R Q G G LL NY GD LNFG+A E+ R+EGI V Sbjct: 69 DAAVAGDVFASPSTAAVARVCRHADQGG--GVLLGFGNYAGDVLNFGVAAERLRSEGIDV 126 Query: 133 EMVVIGDDSAFTVLK-KAGRRGLCGTVLIHKVAGALAEAGVGLEEIAKQVNVVAKAMGTL 191 ++ + DD A + A RRG+ G +++ K+AGA AEAG L+E+ + + Sbjct: 127 RILPVTDDVASAPAETSAKRRGIAGDLVVFKIAGAAAEAGKSLDEVERLARHANDRTVSF 186 Query: 192 GVSLSSCSVPGSK-PTFELSADEVELGLGIHGEAGVRRIKMATADEIVKLMLDHMTNTTN 250 GV+ C++PG+ P F + ++ LGLGIHGE GV +ATA ++ KL+ + Sbjct: 187 GVAFGGCTLPGAAGPLFTVPKGQMALGLGIHGEPGVSEETIATASDLAKLLTGKL----- 241 Query: 251 ASHVPVQPGSS--VVMMVNNLGGLSFLELGIIADATVRSLEGRGVKIARALVGTFMSALE 308 + +P S V ++N LG + EL ++ A R L G++I G F+++L+ Sbjct: 242 ---LAERPEGSRKVAAVLNGLGSTKYEELFVLWTAVARQLNDAGLEIVDPECGEFVTSLD 298 Query: 309 MPGISLTLLLVDEPLLKLIDAETTAAAWPNVAAVSITGRKRSRVAPAEPQEAPDSTAAGG 368 M G SLTLL +DE L L A T A ++ V PQ ++ A Sbjct: 299 MQGCSLTLLWLDEELEALWRAPTDAPVLRKGVIIAAEPATDEIVDADGPQSFGPASDASK 358 Query: 369 SASKRMALVLERVCSTLLGLEEHLNALDRAAGDGDCGTTHSRAARAIQEWLKEG-PPPAS 427 + K +A ++ + L EE L +D AGDGD G R + A + + A Sbjct: 359 ESGKCIARLIGNIAEALKEAEEELGRIDAFAGDGDHGQGMRRGSAAAFDAAQTAVVAGAG 418 Query: 428 PAQLLSKLSVLLLEKMGGSSGALYGLFLTAAAQPL--KAKTSLPAWSAAMDAGLEAMQKY 485 A +L+ ++ GG+SGA++GL L + + L + K S A L+ + + Sbjct: 419 AASVLAAAGDAWADRAGGTSGAIWGLALRSWSNALSDEEKVSDAAIVKGSRLALDGVTRL 478 Query: 486 GKAAPGDRTMLDSLWAAGQELQAWKSPGADLLQVLTKAVKSAEAAAEATKNMEAGAGRAS 545 G+A GD+T++D+L + L+ + G L++ A K+A+ AA+AT + GRA Sbjct: 479 GRARVGDKTLVDALVPFVETLERESAAGRPLVEAWDAAAKAAQEAADATSALTPKLGRAR 538 Query: 546 YISSARLEQPDPGAVAAAAILR 567 ++ + PD GAV+ A + R Sbjct: 539 PLAEKSIGHPDAGAVSLALVAR 560 Lambda K H 0.315 0.130 0.365 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 780 Number of extensions: 43 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 575 Length of database: 572 Length adjustment: 36 Effective length of query: 539 Effective length of database: 536 Effective search space: 288904 Effective search space used: 288904 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 (21.6 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory