Align Triokinase/FMN cyclase; Bifunctional ATP-dependent dihydroxyacetone kinase/FAD-AMP lyase (cyclizing); EC 2.7.1.28; EC 2.7.1.29; EC 4.6.1.15 (characterized)
to candidate BPHYT_RS32475 BPHYT_RS32475 dihydroxyacetone kinase
Query= SwissProt::F1RKQ4 (579 letters) >FitnessBrowser__BFirm:BPHYT_RS32475 Length = 567 Score = 462 bits (1188), Expect = e-134 Identities = 278/581 (47%), Positives = 358/581 (61%), Gaps = 27/581 (4%) Query: 4 KKLVNSVAGCADDALAGLVACNPSLQLLQGHRVALRSDLDSL--KGRVALLSGGGSGHEP 61 KKL+N V+ D L GL A NP+L LLQG + +R+D ++ +G VAL+SGGGSGHEP Sbjct: 2 KKLINEVSAVVPDMLDGLAALNPNLSLLQGGTIVVRADAEAAAARGEVALISGGGSGHEP 61 Query: 62 AHAGFIGKGMLTGVIAGAVFTSPAVGSILAAIRAVAQAGTVGTLLIVKNYTGDRLNFGLA 121 AH G++G GML+ +AG VFTSP+ ++L AIRAVA G G LLIVKNYTGDR NFGLA Sbjct: 62 AHGGYVGSGMLSAAVAGEVFTSPSTDAVLDAIRAVA--GAAGALLIVKNYTGDRFNFGLA 119 Query: 122 REQARAEGIPVEMVVVGDDSAFTVL-KKAGRRGLCGTVLIHKVAGALAEAGVGLEEITNR 180 E ARAEGIP EMV+V DD A T AGRRGL GTVLIHK+AGA A AG L E+ Sbjct: 120 AEIARAEGIPTEMVIVADDVALTASGDHAGRRGLAGTVLIHKIAGAAAAAGRPLGEVAQI 179 Query: 181 VSVVAKAMGTLGVSLSSCSVPGS-RPTFELSADEVELGLGIHGEAGVLRIKMATADEIVA 239 VA ++GT+GV+L++C+VP + +P FEL+ E+E GLGIHGE GV R + AD IV Sbjct: 180 ARDVAASLGTMGVALTACTVPAAGKPGFELADGEIEWGLGIHGEPGVERGALEPADAIVE 239 Query: 240 HMLNHMTDSSNVSHVPVQSGSSVVLMVNNLGGLSYLELGIIADAAVRFLEGRGVKIARAL 299 +L + V + +Q+G V L+VNNLGG EL I+A +A+R+L RG+++ RA Sbjct: 240 KLLAKI-----VGDLSLQTGERVALLVNNLGGTPSSELSIVAGSALRYLAKRGIEVERAW 294 Query: 300 VGTFMSALEMPGVSLTLLLVDEPLLKLIDAETTAAAWP----NVAKVSVTGRKRSRAAPA 355 GTF+SALEM GVSLTLL VD+ L +DA T +AWP VA+VSV R APA Sbjct: 295 AGTFLSALEMAGVSLTLLRVDDERLAWLDAATHTSAWPALSGRVARVSV------RPAPA 348 Query: 356 EPPEAPDATAAGGATSKQMVRVLERVCTTLLGLEDQLNALDRAAGDGDCGTTHSRAARAI 415 EP A AT + AT + RV+E VC LL E L +D+ GDGD G + SR ARAI Sbjct: 349 EPERASGATLSREATLR---RVIEAVCACLLEAEPTLTDMDQRVGDGDLGISLSRGARAI 405 Query: 416 QGWLKESPPPASPAQLLSKLSLLLLEKMGGSSGALYGLFLTAAAQPLKAK--TDLAAWSA 473 L + P +PA +L +S L +GG+SG LY + L AA L+ + W+ Sbjct: 406 LHELDDYPAETTPAAVLRSMSATLRRVVGGTSGPLYAVMLVRAAVALEQSGGSTPKEWAV 465 Query: 474 AMDAGLEAMQKYGKAAPGDRTMLDSLWAAGQELQAWKSPGANLLPVLTKALLENAEAAAE 533 A AG++ + + G A PGDRTM+D+L A LQ+ + L +A ++ A A Sbjct: 466 AFSAGVDGLMELGGAHPGDRTMVDALKPAADALQS-ALARQDALDAALQAAVDAVSAGAS 524 Query: 534 ATKNMEAGAGRASYISSARLDQPDPGAVAAAAILRAILEVL 574 T +M GR+SY+ L DPGA A A L AI E L Sbjct: 525 QTASMHPRRGRSSYVGDRALGHVDPGAHAVALWLAAIREAL 565 Lambda K H 0.315 0.131 0.367 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: 854 Number of extensions: 43 Number of successful extensions: 9 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: 579 Length of database: 567 Length adjustment: 36 Effective length of query: 543 Effective length of database: 531 Effective search space: 288333 Effective search space used: 288333 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