Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate SMa0404 SMa0404 FMN-dependent dehydrogenase
Query= reanno::Smeli:SM_b20850 (378 letters) >FitnessBrowser__Smeli:SMa0404 Length = 381 Score = 292 bits (747), Expect = 1e-83 Identities = 152/361 (42%), Positives = 213/361 (59%) Query: 4 ILEIRDLKALARRRVPKLFFDYADSGAWTEGTYRANEEDFAGIKLRQRVLVDMSDRSLET 63 ++ I D + LARRR PK+FFDY D G++ E T RAN DF+ + LRQ VLV+ + L T Sbjct: 3 LVNIDDFRDLARRRRPKIFFDYIDGGSFEEETMRANRSDFSRLTLRQNVLVEPQPQDLAT 62 Query: 64 TMIGQKVSMPVALAPTGLTGMQHADGEMLAAQAAEAFGVPFTLSTMSICSIEDVASVTTK 123 +G++ +P L P G G+ GE+ A +AA A G+PF LST SI S+ D+ VT Sbjct: 63 AYLGKRHPLPFMLGPVGFLGLYSGKGEVKAVRAAHAAGIPFCLSTFSIASLADLRIVTDG 122 Query: 124 PFWFQLYVMREREFVLDLIDRAKAAKCSALVMTLDLQILGQRHKDLRNGLSAPPRLTPKH 183 P FQLYV+ +R + + A+ A L +T+D I G R +D+RNG + R+TP Sbjct: 123 PLHFQLYVLEDRSLCEEFLRAAEYAGVDTLFVTVDTAITGIRERDVRNGFRSLTRVTPDL 182 Query: 184 LWMMATRPGWCMKMLGTNRRTFRNIVGHAKSVADLSSLQAWTNEQFDPQLSWKDVEWIKE 243 +A +P W +++ + R + + A + + D LSWKD+ W++E Sbjct: 183 FARLALKPRWLAEVVLAGMPSVRAVEHRPEFGRGALEQAANLSRRIDKTLSWKDIAWLRE 242 Query: 244 RWGGPLILKGILDPEDAKMAAKTGADAIIVSNHGGRQLDGAHSSISMLPRIVEAVGDQIE 303 RW G L++KG+L P DA A G D ++VSNHGGRQLDGA S+I LP I VG Sbjct: 243 RWAGKLVIKGVLTPADAVRARDLGCDGVVVSNHGGRQLDGAPSTIRALPSIRATVGTDFC 302 Query: 304 VHLDGGIRSGQDVLKAIALGAKGTYIGRPFLYGLGALGKEGVTLALDIIRKEMDTTMALC 363 + LDGGIR G DV+KAIALGA G +GR + YGL A G+ GV + I+ +E+ ++AL Sbjct: 303 LMLDGGIRRGADVIKAIALGADGVMLGRAYAYGLSAAGQAGVAEVIAILEREISISLALM 362 Query: 364 G 364 G Sbjct: 363 G 363 Lambda K H 0.321 0.136 0.406 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: 388 Number of extensions: 15 Number of successful extensions: 2 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: 378 Length of database: 381 Length adjustment: 30 Effective length of query: 348 Effective length of database: 351 Effective search space: 122148 Effective search space used: 122148 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 (21.9 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