Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate SMc01740 SMc01740 L-lactate dehydrogenase (cytochrome) protein
Query= BRENDA::W1QKE8 (558 letters) >FitnessBrowser__Smeli:SMc01740 Length = 364 Score = 182 bits (462), Expect = 2e-50 Identities = 121/360 (33%), Positives = 185/360 (51%), Gaps = 25/360 (6%) Query: 169 PNVNEVMNLHDFEYIAKKILPKGAWAYYSSGADDEVSMRENHYAYQRIYFRPRVLVDVSK 228 P++ + +L + A+ LPK W GA+ E +++ N A I F+PRVL +VS Sbjct: 11 PHLGDFESLQEIIQKAQGALPKEKWDSLVGGAETETTLKRNRLAIDSIAFKPRVLRNVSV 70 Query: 229 VDTSTTLLGTPTSVPFYVSATALAKLGHPDGECSIARGAGKEGVIQMISTLASNSLEEIA 288 VD S G +P +++ T L P G ++A GA GV M+S+ LE +A Sbjct: 71 VDLSIEHFGRRLRLPIFLAPTGPLNLFGPGGGAAVASGAQVFGVAHMLSS-GCTPLESVA 129 Query: 289 AARVPGATQWFQLYVNEDRNVAFEMVKKAEKLGIKAIFVTVDAPSLGNREKDARVKFEGE 348 A P A + QLYV D + V +A G AI +TVD+ L R++D + Sbjct: 130 EA-APSALRMAQLYVRGDDASVHKYVGRALASGCAAICLTVDSAVLARRDRDIANRH--- 185 Query: 349 SDVQKSNEVVRSQGASRALSSFIDTRLTWDDVKKIKQSTKLPVLIKGVQRLEDVVQAVDD 408 R+ G + L W VK IK S +P+++KG+ +ED AVD Sbjct: 186 ----------RTAGLGKWPGQAYQAGLDWRTVKLIKDSYDIPLVLKGIATVEDARIAVDH 235 Query: 409 GFDGVVLSNHGGRQLDTAPPPVELLAEVVPELKRRNKLRPDFEIFIDGGVRRGTDILKAL 468 G D + +SNHGGRQLD +++L E++ + + K + +DGG RGTDI+KAL Sbjct: 236 GVDWIYVSNHGGRQLDHGRGTMDVLPEIIDAVGGQAK------VMVDGGFCRGTDIIKAL 289 Query: 469 ALGGQNVRVGVGLGRPFLYANSSYGENGVRKAIQLLKDELEMDMRLLGVRNLRELDETFV 528 A+G VGLGR YA ++ GE + + ++L++DE+ M LLGV + +LD +++ Sbjct: 290 AIGANL----VGLGRMQCYALAAGGEAAIIRMLELIEDEMLRSMALLGVPTIGDLDRSYL 345 Lambda K H 0.317 0.135 0.393 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: 462 Number of extensions: 22 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: 558 Length of database: 364 Length adjustment: 33 Effective length of query: 525 Effective length of database: 331 Effective search space: 173775 Effective search space used: 173775 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 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