Align L-lactate dehydrogenase; EC 1.1.1.27 (uncharacterized)
to candidate BPHYT_RS27110 BPHYT_RS27110 dehydrogenase
Query= curated2:Q07251 (349 letters) >FitnessBrowser__BFirm:BPHYT_RS27110 Length = 367 Score = 212 bits (540), Expect = 1e-59 Identities = 123/326 (37%), Positives = 179/326 (54%), Gaps = 5/326 (1%) Query: 26 ADDVAEHLVESDRCGYISHGLSILPNYRTALDGHSVNPQGRAKCVLDQGTLMVFDGDGGF 85 A+ VA+HLV ++ G+ SHG+ ++P Y +L + A V D G ++ +G GF Sbjct: 37 AELVADHLVAANLTGHDSHGVGMIPRYVASLADGELQLNLHADVVKDAGAVLTVEGGRGF 96 Query: 86 GQHVGKSVMQAAIERVRQHGHCIVTLRRSHHLGRMGHYGEMAAAAGFVLLSFTNVINRAP 145 GQ V M+ IER ++ G C V LR +HH+GR+GH+ E A AG V F NV P Sbjct: 97 GQVVAFEAMEQGIERAKRLGICAVGLRGAHHIGRIGHWAEQCARAGLVSFHFVNVAG-DP 155 Query: 146 VVAPFGGRVARLTTNPLCFAGPMPNGRPPLVVDIATSAIAINKARVLAEKGEPAPEGSII 205 +VAPFGG R+ TNP C A P P G+PPLV+D ATS +A K RV +G+ G++I Sbjct: 156 LVAPFGGADRRIGTNPFCAAYPRP-GKPPLVLDFATSTVAYGKTRVAYNQGKQVQPGALI 214 Query: 206 GADGNPTTDASTMFGEHPGALLPFGGHKGYALGVVAELLAGVLSGGGTIQPDN-PRGGVA 264 +G T + M G+L PFGGHKG+ L + E+ G LSGG T Sbjct: 215 DHEGRATLEPKVMHEAPFGSLTPFGGHKGFGLAAMCEIFGGALSGGFTTHSTTLGTTNAI 274 Query: 265 TNNLFAVLLNPALDLGLDWQSAEVEAFVRYLHDTPPAPGVDRVQYPGEYEAANRAQ-ASD 323 N + +V+++PA D Q AE +AF+ ++ +P A G DR+ PGE E RAQ ++ Sbjct: 275 INCMLSVIIDPAAFDAPDAQ-AEADAFIDWVKASPLAAGADRIYEPGEPERVTRAQREAE 333 Query: 324 TLNINPAIWRNLERLAQSLNVAVPTA 349 + ++ A W + A ++ ++ A Sbjct: 334 GIPVDAATWAQILAAALAVGMSAEEA 359 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: 363 Number of extensions: 27 Number of successful extensions: 4 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: 367 Length adjustment: 29 Effective length of query: 320 Effective length of database: 338 Effective search space: 108160 Effective search space used: 108160 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