Align L-lactate dehydrogenase (EC 1.1.1.27) (characterized)
to candidate Echvi_2076 Echvi_2076 malate dehydrogenase, NAD-dependent
Query= BRENDA::Q27797 (326 letters) >FitnessBrowser__Cola:Echvi_2076 Length = 312 Score = 258 bits (659), Expect = 1e-73 Identities = 142/320 (44%), Positives = 210/320 (65%), Gaps = 16/320 (5%) Query: 10 KIAMIGSGMIGGTMGYLCVLRELAD-VVLFDVVTGMPEGKALDDSQATSI-ADTNVSVTS 67 K+ ++G+G +G T + RE+A+ +VL D+ G+ EGKALD Q I A + +V S Sbjct: 3 KVTVVGAGNVGATCADVLAYREIAEEIVLVDIKEGVAEGKALDIWQKAPINAYDSRTVGS 62 Query: 68 ANQYEKIAGSDVVIITAGLTKVPGKSDKEWSRNDLLPFNAKIIREVAQGVKKYCPLAFVI 127 N Y K AGSDVV+IT+GL + PG + R+DL+ NA I++ V + V K+ P A +I Sbjct: 63 TNDYTKTAGSDVVVITSGLPRKPGMT-----RDDLIETNAGIVKSVTENVVKHSPDAIII 117 Query: 128 VVTNPLDCMVKCFHEASGLPKNMVCGMANVLDSARFRRFIADQLEISPRDIQATVIGTHG 187 +V+NPLD M H S +P+ V GMA +LD+AR+R F+A+ L++SP++IQA ++G HG Sbjct: 118 IVSNPLDVMTYQAHITSKMPRTKVMGMAGILDTARYRAFLAEALDVSPKEIQAILMGGHG 177 Query: 188 DHMLPLARYVTVSGFPLREFIKKGKMTEAKLAEIVERTKKAGGEIVRLLGQGSAYYAPAL 247 D M+PL RY TV+G P+ E I+K KL I+ERTK GGE+V+L+G SA+YAP Sbjct: 178 DTMVPLPRYTTVAGIPVTELIEKD-----KLDAIIERTKFGGGELVKLMGT-SAWYAPGS 231 Query: 248 SAITMAQAFLKDEKRVLPCSVYCQGEYGLHDMFIGLPAVIGGGGIEQVIELELTHEEQ-- 305 +A M +A LK+++RV P V GEYG+ D ++G+P ++G GIE+VIEL+L +E+ Sbjct: 232 AAAQMVEAILKNQRRVFPVCVKLDGEYGIDDCYLGVPVILGKNGIEKVIELDLNEDEKAL 291 Query: 306 -ECFRKSVDDVVELNKSLAA 324 E RK V +V+ + S+ + Sbjct: 292 LETSRKHVKEVMAVLDSVGS 311 Lambda K H 0.320 0.137 0.395 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: 233 Number of extensions: 12 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 326 Length of database: 312 Length adjustment: 28 Effective length of query: 298 Effective length of database: 284 Effective search space: 84632 Effective search space used: 84632 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 (21.8 bits) S2: 48 (23.1 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