Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate GFF927 PGA1_c09430 l-lactate dehydrogenase IldD
Query= reanno::WCS417:GFF3737 (376 letters) >FitnessBrowser__Phaeo:GFF927 Length = 401 Score = 236 bits (602), Expect = 8e-67 Identities = 139/370 (37%), Positives = 203/370 (54%), Gaps = 10/370 (2%) Query: 7 SDYRAAAKRKLPRFLFDYIDGGAYAEHTLRANSSDLAEISLRQRILRNVDNLSLKTTLFG 66 SD R A+R+LPRF+++Y+D G E T N + L ++ IL L G Sbjct: 14 SDLRQRARRRLPRFVWEYLDSGTGTEATKARNRAALDQLGFAPSILHGPQTPDLSRRFLG 73 Query: 67 QELDMPVILSPVGLTGMYARRGEVQAAKAAANKGIPFCLSTVSVCPIEEVASQSAQAIWF 126 + +P ++PVG++G+ E A+ AA +G+P+CLSTV+ E++ A WF Sbjct: 74 IDRPLPFGVAPVGMSGLIWPDAERLLARCAAAQGLPYCLSTVASQSPEDLVDDLGAAPWF 133 Query: 127 QLYVLKDRGFMRNALERAQAAGVTTLVFTVDMPTPGARYRDAHSGMSGPFAAQRRML-QA 185 QLY KD R+ L RA+AAG LV TVD+P R R SG++ P R+L Q Sbjct: 134 QLYPPKDPDIRRDLLARAKAAGFAGLVLTVDVPVASRRERQTRSGLTQPPRLTPRLLAQV 193 Query: 186 VTKPQWAFDVGLMGRPHDLGNISKYL---GKPTHLEDYIGWLANNFDASISWKDLEWIRE 242 +P WA + G PH + + Y+ G ++G+L S W ++W+R+ Sbjct: 194 AMRPAWAVGMARRGLPH-MKTLDTYVSGAGASLSSTAHVGYLLR---TSPDWDYVQWLRD 249 Query: 243 FWKGPMIIKGILDPQDAKDAVSFGADGIVVSNHGGRQLDGVLSTAKALPPIADAVGDDLT 302 W GP+IIKG++ +DA + GAD + VSNH GRQ D ST +ALP I A L Sbjct: 250 HWDGPLIIKGVMRAEDAAPLEAIGADALWVSNHAGRQFDAAPSTIEALPGIRAAT--RLP 307 Query: 303 VLVDSGIRSGLDVVRMLALGAKACLLGRATAYALAADGQHGVENLLDIFAKEMRVAMTLT 362 ++ DSGI SGLD++R LALGA +LGRA +ALAA G G ++L+DI K++ M Sbjct: 308 LIFDSGIESGLDILRALALGADYVMLGRAFHFALAALGSRGPDHLVDILRKDLDANMGQL 367 Query: 363 GVTSIAQIDR 372 G+ +++ + R Sbjct: 368 GLETLSALPR 377 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: 388 Number of extensions: 23 Number of successful extensions: 4 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: 401 Length adjustment: 30 Effective length of query: 346 Effective length of database: 371 Effective search space: 128366 Effective search space used: 128366 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