Align L-lactate dehydrogenase; EC 1.1.1.27 (uncharacterized)
to candidate BWI76_RS16775 BWI76_RS16775 malate/lactate/ureidoglycolate dehydrogenase
Query= curated2:Q07251 (349 letters) >FitnessBrowser__Koxy:BWI76_RS16775 Length = 360 Score = 218 bits (555), Expect = 2e-61 Identities = 130/351 (37%), Positives = 189/351 (53%), Gaps = 9/351 (2%) Query: 2 KISLTSARQLARDILAAQQVPADIADDVAEHLVESDRCGYISHGLSILPNY-RTALDGHS 60 + T Q + + A +A+HL+ ++ G+ SHG+ ++P+Y R+ G+ Sbjct: 6 RFQATDLHQFVKTLFTHMGSSPTEASLIADHLIAANLAGHDSHGVGMIPSYVRSHAQGY- 64 Query: 61 VNPQGRAKCVLDQGTLMVFDGDGGFGQHVGKSVMQAAIERVRQHGHCIVTLRRSHHLGRM 120 + A + D G ++ DG+GGFGQ V MQ IE+ +QHG V LR +HH+GR+ Sbjct: 65 LQLNRHASVMKDAGAVVTLDGNGGFGQVVAHEAMQIGIEKAKQHGLAAVALRNAHHIGRI 124 Query: 121 GHYGEMAAAAGFVLLSFTNVINRAPVVAPFGGRVARLTTNPLCFAGPMPNGRPPLVVDIA 180 G++ E AAAG + + F NV+ +VAPF G+ +R TNPLC P G PPL++D A Sbjct: 125 GYWAEQCAAAGMISIHFVNVVGNV-MVAPFRGKDSRFGTNPLCVVFPRV-GHPPLLLDYA 182 Query: 181 TSAIAINKARVLAEKGEPAPEGSIIGADGNPTTDASTMFGEHPGALLPFGGHKGYALGVV 240 TSAIA K RV KG P P GS+I A G PTTD + M GALL F HKGYAL + Sbjct: 183 TSAIAFGKTRVAWHKGVPVPAGSLIDARGVPTTDPAVMQTSPLGALLTFAEHKGYALATL 242 Query: 241 AELLAGVLSGGGTIQPDNPRGGVAT--NNLFAVLLNPALDLGLDWQSAEVEAFVRYLHDT 298 E + G +SGG T + +G V N + ++L+P D Q E EAF+ + + Sbjct: 243 CEAIGGAVSGGKTSHQETLQGSVDAIFNCMTTIILSPEAFDAPDMQ-RETEAFIDWCKQS 301 Query: 299 PPAPGVDRVQYPGEYEAANRAQ-ASDTLNINPAIWRNLERLAQSLNVAVPT 348 P P + PGE+E ANR Q + + ++ W+ + A+ + V T Sbjct: 302 PHEPDAP-ILAPGEWEEANRRQRLAQGIPLDAGSWQAICAAAEEVGVPADT 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: 346 Number of extensions: 20 Number of successful extensions: 5 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: 360 Length adjustment: 29 Effective length of query: 320 Effective length of database: 331 Effective search space: 105920 Effective search space used: 105920 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