Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate Ac3H11_1767 L-lactate dehydrogenase (EC 1.1.2.3)
Query= BRENDA::Q8Z0C8 (365 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1767 Length = 419 Score = 219 bits (559), Expect = 8e-62 Identities = 139/376 (36%), Positives = 205/376 (54%), Gaps = 32/376 (8%) Query: 8 INLFEYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTS 67 ++L ++E A+ L + F Y A D +L++NR VF R+L DVSQ + Sbjct: 41 LSLHDFEDAARRRLPRPIFGYIAGAAEDNASLRDNREVFGEYAFTTRVLRDVSQRSQAVE 100 Query: 68 VLGQPLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKF 127 + G+ P IAPM L+ G+L A AA AG V+S S +EEVA + Sbjct: 101 LFGERYSSPFGIAPMGINALSTYRGDLVLACAAQRAGIVSVMSGTSLIPMEEVA----RE 156 Query: 128 SPSLQWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLP--PG 185 SP WFQ Y+ D+ AL++R AG++ L +TVD P+ RE + R F P PG Sbjct: 157 SPGT-WFQAYLPGDQARIDALIDRVERAGFRTLVVTVDIPISANRENNIRTGFSTPLRPG 215 Query: 186 LHLA-------------NLTTISGLNIPHAPGESGLFTYFAQQLNPA----------LTW 222 L LA + T+ +PH E+ T A ++ + L+W Sbjct: 216 LRLAWDGLVRPRWVAGTFVRTLLRHGMPHF--ENSFATRGAPIVSSSVLRDFSARDHLSW 273 Query: 223 DDLEWLQSLSPLPLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIV 282 + LE ++ PLV+KG+LR +DA +A GA +V+SNHGGRQLDGA++++ L +V Sbjct: 274 NHLEAIRRRWKGPLVVKGVLRVEDALQARNLGADGVVLSNHGGRQLDGAVSAMRVLEAVV 333 Query: 283 AAVNGKAEVLLDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKE 342 AAV VL+DGG RRG+D++KA+A+GA+ VL+GRP + AV G+AGV H I LL+ E Sbjct: 334 AAVGPAFPVLIDGGFRRGSDVLKAIALGARMVLVGRPFNYAAAVAGEAGVQHAIGLLRDE 393 Query: 343 LNVAMALIGCSQLQDI 358 ++ +A++G D+ Sbjct: 394 VDRNLAMLGARACTDL 409 Lambda K H 0.320 0.136 0.391 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: 355 Number of extensions: 17 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 365 Length of database: 419 Length adjustment: 31 Effective length of query: 334 Effective length of database: 388 Effective search space: 129592 Effective search space used: 129592 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 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