Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate WP_038214882.1 Q392_RS25485 alpha-hydroxy-acid oxidizing protein
Query= reanno::acidovorax_3H11:Ac3H11_1623 (390 letters) >NCBI__GCF_000745855.1:WP_038214882.1 Length = 393 Score = 572 bits (1473), Expect = e-168 Identities = 275/383 (71%), Positives = 323/383 (84%), Gaps = 4/383 (1%) Query: 7 ITCIEDLRAIAQRRVPRMFYDYADSGSYTEGTYRANESDFQRIKLRQRVAVNMEGRSTRT 66 ITC+EDLRA+A+RRVPRMFYDY D GS+TE TY ANE+DF RIKLRQRVAVN+E RS +T Sbjct: 5 ITCVEDLRAMARRRVPRMFYDYVDGGSWTESTYAANEADFARIKLRQRVAVNLENRSLKT 64 Query: 67 TMVGQDVAMPVAIAPTGLTGMQHADGEILGAKAAKAFGIPFTLSTMSICSIEDIAEHTGR 126 M+GQ+VAMPVA+APTG TGM HADGEIL AKAA+AFG+PFTLSTMSICSIED+A H R Sbjct: 65 RMLGQEVAMPVALAPTGNTGMVHADGEILAAKAAEAFGVPFTLSTMSICSIEDVARHVER 124 Query: 127 HPFWFQVYVMRDRDFIERLIDRAKAANCSALQLTLDLQILGQRHKDIKNGLSAPPKPTIA 186 PFWFQ+Y+MRDR FI LIDRA+ ANCSAL LTLDLQ+ GQRHKD +NGL+ PPKPT Sbjct: 125 -PFWFQLYMMRDRAFIRSLIDRARQANCSALMLTLDLQVPGQRHKDRRNGLTTPPKPTFP 183 Query: 187 NLINLATKPRWCLGMLGTKRRSFGNIVGHAKGVGDLSSLSSWTAEQFDPQLNWGDVEWIK 246 NL++LAT+PRWC GML T RR+FGNIVGHA+GV +S+LS+W ++QFDP L+W DVEW+K Sbjct: 184 NLVDLATRPRWCAGMLRTPRRTFGNIVGHARGVDSISTLSTWASKQFDPTLSWQDVEWVK 243 Query: 247 KRWGGKLILKGIMDAEDARLAVNSGADALIVSNHGGRQLDGAPSSIAALPGIADAVAQMG 306 K WGGKLILKGI+D EDAR A +SGADAL+VSNHGGRQLDGAPS+I +LP I DA A Sbjct: 244 KLWGGKLILKGILDPEDARHAASSGADALVVSNHGGRQLDGAPSTIESLPAIVDAAASQ- 302 Query: 307 GGIEVWMDGGIRSGQDVLKARALGAQGTLIGRSFLYGLGAYGEAGVTRALQIIQKELDIT 366 +EVW+DGGIR+GQDVLKA ALGA T+IGR FLYGLGA G+AGV + L++I ELD+T Sbjct: 303 --MEVWLDGGIRTGQDVLKALALGASATMIGRPFLYGLGAAGQAGVRKCLELIASELDLT 360 Query: 367 MAFCGHTNINTVDRSILLPGTYP 389 MA CG T + +VDR ILLPGT+P Sbjct: 361 MALCGRTEVRSVDRGILLPGTFP 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: 543 Number of extensions: 21 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: 393 Length adjustment: 31 Effective length of query: 359 Effective length of database: 362 Effective search space: 129958 Effective search space used: 129958 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