Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate WP_085770992.1 B1812_RS07210 alpha-hydroxy-acid oxidizing protein
Query= reanno::WCS417:GFF3737 (376 letters) >NCBI__GCF_002117405.1:WP_085770992.1 Length = 382 Score = 514 bits (1325), Expect = e-150 Identities = 246/375 (65%), Positives = 302/375 (80%) Query: 1 MIISSASDYRAAAKRKLPRFLFDYIDGGAYAEHTLRANSSDLAEISLRQRILRNVDNLSL 60 MIIS DYR AA+R+LPRFLFDYIDGGA AE TL AN +DLA++ L+QR+L +V+NLSL Sbjct: 1 MIISRIEDYREAARRRLPRFLFDYIDGGAGAEQTLAANIADLAQVRLKQRVLAHVENLSL 60 Query: 61 KTTLFGQELDMPVILSPVGLTGMYARRGEVQAAKAAANKGIPFCLSTVSVCPIEEVASQS 120 +T FG+ + +PV+L PVGLTGM+ RRGE A+AAA G+P+ STVSVC IEE+A+QS Sbjct: 61 ETEWFGRRVSLPVVLGPVGLTGMFWRRGEAAVARAAAAAGVPYAPSTVSVCAIEEIAAQS 120 Query: 121 AQAIWFQLYVLKDRGFMRNALERAQAAGVTTLVFTVDMPTPGARYRDAHSGMSGPFAAQR 180 A +WFQLYVLKDRGFMR+ LERAQ GVTTLVFTVD+P G R+RDAHSG++GPF +R Sbjct: 121 AAPLWFQLYVLKDRGFMRSVLERAQEVGVTTLVFTVDLPVIGTRWRDAHSGLAGPFKTER 180 Query: 181 RMLQAVTKPQWAFDVGLMGRPHDLGNISKYLGKPTHLEDYIGWLANNFDASISWKDLEWI 240 ++ QA+ KP WA+DVG+ GRPHDLGNIS YLG+ T LEDY+GW+ N D SI W DLEW+ Sbjct: 181 QLFQALGKPAWAWDVGVCGRPHDLGNISHYLGRRTGLEDYLGWINANMDPSIGWSDLEWL 240 Query: 241 REFWKGPMIIKGILDPQDAKDAVSFGADGIVVSNHGGRQLDGVLSTAKALPPIADAVGDD 300 R FWKGP+IIKG+L P+DA+DA GA+ IVVSNHGGRQLDG STA+ALP I DA+GDD Sbjct: 241 RNFWKGPLIIKGVLTPEDARDAARLGAEAIVVSNHGGRQLDGAASTARALPKIRDAIGDD 300 Query: 301 LTVLVDSGIRSGLDVVRMLALGAKACLLGRATAYALAADGQHGVENLLDIFAKEMRVAMT 360 L + DSG+RSG+DV+RMLALGAK LGRA +ALAA G+ GV +L++ A+EMRVAMT Sbjct: 301 LLIFADSGVRSGVDVLRMLALGAKGVFLGRAQVFALAARGEQGVREMLEMIAQEMRVAMT 360 Query: 361 LTGVTSIAQIDRSTL 375 LTGV+S+ +ID S L Sbjct: 361 LTGVSSVEEIDASIL 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: 469 Number of extensions: 9 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: 382 Length adjustment: 30 Effective length of query: 346 Effective length of database: 352 Effective search space: 121792 Effective search space used: 121792 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