Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate CCNA_01462 CCNA_01462 lactate 2-monooxygenase
Query= reanno::Smeli:SM_b20850 (378 letters) >FitnessBrowser__Caulo:CCNA_01462 Length = 391 Score = 186 bits (472), Expect = 1e-51 Identities = 124/363 (34%), Positives = 186/363 (51%), Gaps = 19/363 (5%) Query: 5 LEIRDLKALARRRVPKLFFDYADSGAWTEGTYRANEEDFAGIKLRQRVLVDMSDRSLETT 64 ++ + L+A A + Y G E T R N + F + R++VD S R L Sbjct: 25 VDFKTLEARATAAMSPDLLSYVQGGCGDEFTQRRNADAFHDWGVVPRMMVDASKRDLSIE 84 Query: 65 MIGQKVSMPVALAPTGLTGM--QHADGEMLAAQAAEAFGVPFTLSTMSICSIEDV-ASVT 121 + G K+ P+ ++P G+ GM Q G++ A AA+ GVP ST++ IE V A++ Sbjct: 85 LFGLKLPTPLFMSPIGVIGMCAQDGHGDIATAVAAQRTGVPVMASTLANDPIEKVGAALG 144 Query: 122 TKPFWFQLYVMREREFVLDLIDRAKAAKCSALVMTLDLQILGQRHKDLRNGLSAPPRLTP 181 +FQLY ++R+ LI RA+ A ALV+TLD + G R +DL + P+L Sbjct: 145 DGVGFFQLYTPKDRDLAESLIRRAETAGFKALVVTLDTWVTGWRPRDLNDANF--PQLRG 202 Query: 182 KHLWMMATRPGWCMKMLGTNRRTFRNIVGHAKSVADLSSLQAWTNEQFDPQLSWKDVEWI 241 L T P F I+G + ++++ W F L+W+D+ W+ Sbjct: 203 HVLQNYFTDP------------RFLEILGKPVAEDPATAIRTWGG-LFGKTLTWEDLAWL 249 Query: 242 KERWGGPLILKGILDPEDAKMAAKTGADAIIVSNHGGRQLDGAHSSISMLPRIVEAVGDQ 301 + P++LKGI P+DA+ A G D + SNHGGRQ +G ++I +L +V A G+ Sbjct: 250 RSATKLPIVLKGICHPDDARRAVDLGVDGVFCSNHGGRQANGGIAAIDLLEDVVTASGN- 308 Query: 302 IEVHLDGGIRSGQDVLKAIALGAKGTYIGRPFLYGLGALGKEGVTLALDIIRKEMDTTMA 361 V D G+RSG D KA+A+GA+ IGRP+ YGL G +GV L I E+D MA Sbjct: 309 TPVLFDSGVRSGSDAAKALAMGARAVGIGRPYAYGLAIGGVDGVVHVLRSILAELDLLMA 368 Query: 362 LCG 364 + G Sbjct: 369 VDG 371 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: 375 Number of extensions: 21 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: 378 Length of database: 391 Length adjustment: 30 Effective length of query: 348 Effective length of database: 361 Effective search space: 125628 Effective search space used: 125628 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