Align L-lactate dehydrogenase; EC 1.1.1.27 (uncharacterized)
to candidate RR42_RS29130 RR42_RS29130 dehydrogenase
Query= curated2:Q07251 (349 letters) >FitnessBrowser__Cup4G11:RR42_RS29130 Length = 364 Score = 228 bits (581), Expect = 2e-64 Identities = 133/348 (38%), Positives = 189/348 (54%), Gaps = 6/348 (1%) Query: 2 KISLTSARQLARDILAAQQVPADIADDVAEHLVESDRCGYISHGLSILPNYRTALDGHSV 61 +I + Q D+ A A A A+HLV ++ G+ SHG+ ++P Y + G + Sbjct: 5 RIPTPALHQWVVDLWRAAGSDAREARLTADHLVGANLSGHDSHGVGMIPKYVMSWQGEQL 64 Query: 62 NPQGRAKCVLDQGTLMVFDGDGGFGQHVGKSVMQAAIERVRQHGHCIVTLRRSHHLGRMG 121 R V + G ++ DG+ G GQ V + M AIER R+HG C++ LR SHHLGR+G Sbjct: 65 QLNQRVSVVHEAGGILSLDGNRGMGQAVTEEAMGLAIERAREHGVCVLGLRASHHLGRVG 124 Query: 122 HYGEMAAAAGFVLLSFTNVINRAPVVAPFGGRVARLTTNPLCFAGPMPNGRPPLVVDIAT 181 H+ E A AAG + + F NV+++ P+VAP GG AR TNP P+ G PLV+D AT Sbjct: 125 HWAEQATAAGMISIHFVNVLSK-PIVAPHGGYEARYGTNPFTIGVPVAGGE-PLVMDFAT 182 Query: 182 SAIAINKARVLAEKGEPAPEGSIIGADGNPTTDASTMF---GEHPGALLPFGGHKGYALG 238 SAIA+ K RV KG P G ++ +G+PT D + MF GE GAL PFG HKGY L Sbjct: 183 SAIALGKVRVANNKGVAVPPGCLLDTEGHPTDDPAVMFPPAGEAQGALRPFGEHKGYVLA 242 Query: 239 VVAELLAGVLSGGGTIQPDN-PRGGVATNNLFAVLLNPALDLGLDWQSAEVEAFVRYLHD 297 V+ ELL ++GG TI+P+ NN+ A++ +P EV+AFV +L Sbjct: 243 VMCELLGAAVTGGHTIRPETLTHEHAVWNNMLAIVFDPERLGSSTTFGHEVQAFVDWLRS 302 Query: 298 TPPAPGVDRVQYPGEYEAANRAQASDTLNINPAIWRNLERLAQSLNVA 345 + PG D + PGE E A R ++ + ++ L+ A + A Sbjct: 303 SHLQPGTDAILLPGEPERAWRRARAEFMPVDSGTLAQLDDAAARVQAA 350 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: 444 Number of extensions: 25 Number of successful extensions: 6 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: 364 Length adjustment: 29 Effective length of query: 320 Effective length of database: 335 Effective search space: 107200 Effective search space used: 107200 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