Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate WP_082109398.1 AL072_RS27445 alpha-hydroxy-acid oxidizing protein
Query= reanno::acidovorax_3H11:Ac3H11_1623 (390 letters) >NCBI__GCF_001305595.1:WP_082109398.1 Length = 415 Score = 556 bits (1432), Expect = e-163 Identities = 267/380 (70%), Positives = 320/380 (84%), Gaps = 4/380 (1%) Query: 7 ITCIEDLRAIAQRRVPRMFYDYADSGSYTEGTYRANESDFQRIKLRQRVAVNMEGRSTRT 66 ITCIEDLR +A+RRVPRMFYDY D GS+TE TYRAN +D ++ RQR+ +++ GR+T + Sbjct: 8 ITCIEDLRILARRRVPRMFYDYVDCGSWTESTYRANTADLAALQFRQRIGMSIAGRTTES 67 Query: 67 TMVGQDVAMPVAIAPTGLTGMQHADGEILGAKAAKAFGIPFTLSTMSICSIEDIAEHTGR 126 ++G+ VAMPVA+APTGLTGMQHADGEIL A+AA+ FG+PFTLST+SICSIED+A +TG+ Sbjct: 68 RILGESVAMPVALAPTGLTGMQHADGEILAARAAERFGVPFTLSTVSICSIEDVAANTGK 127 Query: 127 HPFWFQVYVMRDRDFIERLIDRAKAANCSALQLTLDLQILGQRHKDIKNGLSAPPKPTIA 186 PFWFQ+YVMRDR F+ERLI RAKAANCSAL LTLDLQI GQRHKD+KNGLS PPKPT+ Sbjct: 128 -PFWFQLYVMRDRAFVERLIARAKAANCSALVLTLDLQIQGQRHKDLKNGLSTPPKPTLR 186 Query: 187 NLINLATKPRWCLGMLGTKRRSFGNIVGHAKGVGDLSSLSSWTAEQFDPQLNWGDVEWIK 246 NL++LATKP WCLGML TKRR+FGNIVGH GV D+SSL++W ++QFDP L W DV WIK Sbjct: 187 NLVDLATKPGWCLGMLRTKRRTFGNIVGHVSGVSDVSSLAAWVSQQFDPTLTWEDVRWIK 246 Query: 247 KRWGGKLILKGIMDAEDARLAVNSGADALIVSNHGGRQLDGAPSSIAALPGIADAVAQMG 306 K WGGKLI+KG++D EDARLAV +GADA++VSNHGGRQLDGAPSSIA LP IA+AV Q Sbjct: 247 KLWGGKLIVKGVLDVEDARLAVENGADAIVVSNHGGRQLDGAPSSIAMLPAIAEAVGQQ- 305 Query: 307 GGIEVWMDGGIRSGQDVLKARALGAQGTLIGRSFLYGLGAYGEAGVTRALQIIQKELDIT 366 EV D GIRSGQD+LKA ALGA+G ++GR+FLYGLGA GEAGVTR L+I+Q+ELD+T Sbjct: 306 --TEVLFDSGIRSGQDILKAAALGAKGVMVGRAFLYGLGAMGEAGVTRCLEILQRELDLT 363 Query: 367 MAFCGHTNINTVDRSILLPG 386 M CG T+I D SIL+ G Sbjct: 364 MGLCGLTDIGAADPSILING 383 Lambda K H 0.320 0.137 0.412 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: 560 Number of extensions: 24 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: 390 Length of database: 415 Length adjustment: 31 Effective length of query: 359 Effective length of database: 384 Effective search space: 137856 Effective search space used: 137856 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: 50 (23.9 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