Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate GFF755 PGA1_c07690 (S)-mandelate dehydrogenase MdlB
Query= reanno::WCS417:GFF3737 (376 letters) >FitnessBrowser__Phaeo:GFF755 Length = 363 Score = 229 bits (585), Expect = 7e-65 Identities = 141/372 (37%), Positives = 200/372 (53%), Gaps = 21/372 (5%) Query: 3 ISSASDYRAAAKRKLPRFLFDYIDGGAYAEHTLRANSSDLAEISLRQRILRNVDNLSLKT 62 I SA D R A+R+LP +FDYIDG A E N + L I+LR RILR+V SL T Sbjct: 6 IHSAEDARRLARRRLPWMVFDYIDGAAGQETGAARNRAALDAITLRPRILRDVSQRSLAT 65 Query: 63 TLFGQELDMPVILSPVGLTGMYARRGEVQAAKAAANKGIPFCLSTVSVCPIEEVASQSAQ 122 ++FG E D P ++P+G+ + A ++ A+ AA+ +P +STV+ P+E + + Sbjct: 66 SIFGAETDRPFGIAPMGMCNLAAPGADLMLARLAAHHRVPHGVSTVASTPLEILLEAAEG 125 Query: 123 AIWFQLYVLKDRGFMRNALERAQAAGVTTLVFTVDMPTPGARYRDAHSGMSGPF-AAQRR 181 WFQLY D ERA+AAG TLV TVD+P G R R+ G PF R+ Sbjct: 126 YAWFQLYFSGDGTGTFKLAERARAAGYQTLVLTVDVPEVGRRPRELRHGFKMPFRIGPRQ 185 Query: 182 MLQAVTKPQWAFDVGLMGRPHDLGNISKYLGKPTHLEDYIGWLANNFD-----ASISWKD 236 + P+W+ L G+P + N +E Y +FD A +W Sbjct: 186 FIDFALHPRWSLATLLKGKP-VMANF--------EMEGY------DFDRTESRARATWDT 230 Query: 237 LEWIREFWKGPMIIKGILDPQDAKDAVSFGADGIVVSNHGGRQLDGVLSTAKALPPIADA 296 L +R+ W G +++KG+LD +DA+ VS GAD I +S+HG RQL+ + + L I Sbjct: 231 LARLRDLWPGKLVVKGVLDVEDARALVSAGADAIQISSHGARQLEAAPAPIEMLAKIRAD 290 Query: 297 VGDDLTVLVDSGIRSGLDVVRMLALGAKACLLGRATAYALAADGQHGVENLLDIFAKEMR 356 G V DSGIRSG DV++ + GA LGR YA+AA G+ G+E L D ++E+ Sbjct: 291 FGPTFPVFYDSGIRSGEDVLKAITTGADFVFLGRILQYAIAARGEAGLEQLWDALSEELS 350 Query: 357 VAMTLTGVTSIA 368 +AM TG S+A Sbjct: 351 IAMAQTGRVSLA 362 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: 295 Number of extensions: 9 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: 376 Length of database: 363 Length adjustment: 30 Effective length of query: 346 Effective length of database: 333 Effective search space: 115218 Effective search space used: 115218 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: 49 (23.5 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