Align L-lactate dehydrogenase; EC 1.1.1.27 (uncharacterized)
to candidate AZOBR_RS16020 AZOBR_RS16020 malate dehydrogenase
Query= curated2:Q07251 (349 letters) >FitnessBrowser__azobra:AZOBR_RS16020 Length = 356 Score = 245 bits (626), Expect = 1e-69 Identities = 132/322 (40%), Positives = 187/322 (58%), Gaps = 4/322 (1%) Query: 29 VAEHLVESDRCGYISHGLSILPNYRTALDGHSVNPQGRAKCVLDQGTLMVFDGDGGFGQH 88 VA +LV+SD G+ SHG+ + Y +L+ + P A+ V D+ +V DG+ G+GQ Sbjct: 31 VAANLVDSDATGHASHGVCQIAVYAKSLELGHLQPNRHARVVRDEAPFLVVDGEVGYGQV 90 Query: 89 VGKSVMQAAIERVRQHGHCIVTLRRSHHLGRMGHYGEMAAAAGFVLLSFTNVINRAPVVA 148 + + AI R + G C++ LR +HH+GR+G YGE AAG + + F NV++R P+ A Sbjct: 91 IAREATDLAIARAKAGGACVLALRNAHHIGRVGAYGEQCIAAGLIGVFFVNVVSR-PLAA 149 Query: 149 PFGGRVARLTTNPLCFAGPMPNGRPPLVVDIATSAIAINKARVLAEKGEPAPEGSIIGAD 208 P GG RL TNP+C A P G PP ++D ATSA+A NK RV A G+ +G +I Sbjct: 150 PHGGGRPRLGTNPICIAVPATPGHPPFLLDFATSAVAANKCRVAAASGKEVADGLLIDER 209 Query: 209 GNPTTDASTMFGEHPGALLPFGGHKGYALGVVAELLAGVLSGGGTIQPDNPRGGVATNNL 268 G PT D MF + GA+LPFGGHKGY L + E+LAG L+GG P+N R G NN+ Sbjct: 210 GAPTRDPGVMFRDPTGAILPFGGHKGYGLALACEILAGALAGGLPALPENLRPGRVVNNV 269 Query: 269 FAVLLNPA--LDLGLDWQSAEVEAFVRYLHDTPPAPGVDRVQYPGEYEAANRAQASDT-L 325 A L++PA D G A +A + ++ DTPP PG D V PG E +R A++ + Sbjct: 270 LAFLIDPARVSDAGSGGWQALTDAVLDHIQDTPPVPGGDGVLVPGGPERRSRVLAAERGI 329 Query: 326 NINPAIWRNLERLAQSLNVAVP 347 ++P R L + +L + VP Sbjct: 330 TLDPDTVRALHGIGGALGLDVP 351 Lambda K H 0.319 0.136 0.409 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: 448 Number of extensions: 31 Number of successful extensions: 3 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: 349 Length of database: 356 Length adjustment: 29 Effective length of query: 320 Effective length of database: 327 Effective search space: 104640 Effective search space used: 104640 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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