Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate WP_026608078.1 METAC_RS0117865 alpha-hydroxy-acid oxidizing protein
Query= reanno::WCS417:GFF3737 (376 letters) >NCBI__GCF_000427445.1:WP_026608078.1 Length = 376 Score = 569 bits (1466), Expect = e-167 Identities = 280/375 (74%), Positives = 317/375 (84%) Query: 1 MIISSASDYRAAAKRKLPRFLFDYIDGGAYAEHTLRANSSDLAEISLRQRILRNVDNLSL 60 MI+SSASDYR AA+R LP FLFDYIDGGA AE TL+AN +DLAE+ LRQR+L+NV +LSL Sbjct: 1 MIVSSASDYREAARRGLPSFLFDYIDGGANAEQTLKANMADLAEVILRQRVLKNVSDLSL 60 Query: 61 KTTLFGQELDMPVILSPVGLTGMYARRGEVQAAKAAANKGIPFCLSTVSVCPIEEVASQS 120 T FGQ +P+IL PVGL GM ARRGEVQ AKAAA KG+PF LSTVSVC +EEVASQ Sbjct: 61 ATEWFGQPSALPLILGPVGLAGMLARRGEVQVAKAAAKKGVPFVLSTVSVCSLEEVASQC 120 Query: 121 AQAIWFQLYVLKDRGFMRNALERAQAAGVTTLVFTVDMPTPGARYRDAHSGMSGPFAAQR 180 + IWFQLYVLKDRGFMRN LERA+AAGV LVFTVDM PGARYRDAHSGMSGPFAAQR Sbjct: 121 PRPIWFQLYVLKDRGFMRNVLERAEAAGVKNLVFTVDMAVPGARYRDAHSGMSGPFAAQR 180 Query: 181 RMLQAVTKPQWAFDVGLMGRPHDLGNISKYLGKPTHLEDYIGWLANNFDASISWKDLEWI 240 R+LQA+TKP WAFDVGL GRPHDLGN+S Y G+ L DY+GW+ NFD SI W DLEWI Sbjct: 181 RILQAITKPAWAFDVGLRGRPHDLGNVSSYFGEAIALSDYMGWIGKNFDPSICWADLEWI 240 Query: 241 REFWKGPMIIKGILDPQDAKDAVSFGADGIVVSNHGGRQLDGVLSTAKALPPIADAVGDD 300 R+FWKGPMIIKGILD +DA+DA+ FGA+GIVVSNHGGRQLDG LSTAKALPPI DAVG D Sbjct: 241 RDFWKGPMIIKGILDSEDARDAIRFGANGIVVSNHGGRQLDGALSTAKALPPIVDAVGSD 300 Query: 301 LTVLVDSGIRSGLDVVRMLALGAKACLLGRATAYALAADGQHGVENLLDIFAKEMRVAMT 360 L VL DSG+RSGLDVVRMLALGAK +LGR A+ALAA+GQ GVEN+LDIFA E+R+AMT Sbjct: 301 LVVLADSGVRSGLDVVRMLALGAKGVMLGRVPAFALAANGQAGVENVLDIFANEIRIAMT 360 Query: 361 LTGVTSIAQIDRSTL 375 L GV S++QI+++ L Sbjct: 361 LIGVPSVSQINKTVL 375 Lambda K H 0.321 0.136 0.401 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: 490 Number of extensions: 14 Number of successful extensions: 1 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: 376 Length of database: 376 Length adjustment: 30 Effective length of query: 346 Effective length of database: 346 Effective search space: 119716 Effective search space used: 119716 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 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