Align L-lactate dehydrogenase (EC 1.1.1.27) (characterized)
to candidate WP_011461218.1 DHAF_RS08965 malate dehydrogenase
Query= BRENDA::Q27797 (326 letters) >NCBI__GCF_000021925.1:WP_011461218.1 Length = 320 Score = 243 bits (619), Expect = 6e-69 Identities = 124/308 (40%), Positives = 194/308 (62%), Gaps = 12/308 (3%) Query: 10 KIAMIGSGMIGGTMGYLCVLRELADVVLFDVVTGM--PEGKALDDSQATSIADTNVSVTS 67 KI++IGSG G T ++ ++ L D+VL D +GKALD +A + ++V VT Sbjct: 3 KISVIGSGFTGTTTAFMLAMKGLGDIVLLDTQANENPTKGKALDIMEAGPLTRSSVRVTG 62 Query: 68 ANQYEKIAGSDVVIITAGLTKVPGKSDKEWSRNDLLPFNAKIIREVAQGVKKYCPLAFVI 127 + Y+ SDVV+ITAG+ + PG S RN+L NA I+ V + V ++ P + +I Sbjct: 63 TSDYQDTLDSDVVVITAGIARKPGMS-----RNELCDINAGIVTHVVRQVVQHSPNSTLI 117 Query: 128 VVTNPLDCMVKCFHEASGLPKNMVCGMANVLDSARFRRFIADQLEISPRDIQATVIGTHG 187 +++NP+D M + SG +N + G + VLDSARFR F+A +L++S D+ V+G HG Sbjct: 118 ILSNPVDIMTYVAFKESGFKRNRIIGQSGVLDSARFRYFVASELKVSAEDVTGFVLGVHG 177 Query: 188 DHMLPLARYVTVSGFPLREFIKKGKMTEAKLAEIVERTKKAGGEIVRLLGQGSAYYAPAL 247 D M+PL RY +V G P+++ + EA++ +I+ERT++AG EIV LLG GSAYYAPA Sbjct: 178 DDMVPLVRYCSVHGIPIQQLLP-----EAEIEKIMERTRQAGSEIVNLLGNGSAYYAPAA 232 Query: 248 SAITMAQAFLKDEKRVLPCSVYCQGEYGLHDMFIGLPAVIGGGGIEQVIELELTHEEQEC 307 + M ++ L D+ RV+PC V+ +GE G D+ + +PAVIG G+E+++ ++L EE++ Sbjct: 233 ALTEMIESILLDKHRVMPCIVHLEGELGYQDLVLNVPAVIGRQGVEKILPIDLLPEEEDL 292 Query: 308 FRKSVDDV 315 +SV + Sbjct: 293 IERSVASI 300 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: 235 Number of extensions: 12 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: 326 Length of database: 320 Length adjustment: 28 Effective length of query: 298 Effective length of database: 292 Effective search space: 87016 Effective search space used: 87016 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 24 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