Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate YP_004141351.1 Mesci_2149 FMN-dependent alpha-hydroxy acid dehydrogenase
Query= reanno::Smeli:SM_b20850 (378 letters) >NCBI__GCF_000185905.1:YP_004141351.1 Length = 382 Score = 243 bits (621), Expect = 5e-69 Identities = 130/366 (35%), Positives = 202/366 (55%) Query: 9 DLKALARRRVPKLFFDYADSGAWTEGTYRANEEDFAGIKLRQRVLVDMSDRSLETTMIGQ 68 D + +A++R+P F+Y D A E TYR N E F L VL +S+ + T++GQ Sbjct: 12 DFRRMAQQRLPGPIFNYIDGAADDEVTYRRNTESFETCDLVPNVLRGVSEVDMSVTVMGQ 71 Query: 69 KVSMPVALAPTGLTGMQHADGEMLAAQAAEAFGVPFTLSTMSICSIEDVASVTTKPFWFQ 128 K++MP +PT L + H GE A+AA +G F +S++ S+E+ S+++ P +Q Sbjct: 72 KLAMPFYCSPTALQRLFHHQGERAVAKAAAKYGTMFGVSSLGTVSLEEARSISSGPQVYQ 131 Query: 129 LYVMREREFVLDLIDRAKAAKCSALVMTLDLQILGQRHKDLRNGLSAPPRLTPKHLWMMA 188 Y R+R ++ RAKA +++T+D G R +D R G + P +L + A Sbjct: 132 FYFHRDRGLNRAMMQRAKAVGVEVMMLTVDSITGGNRERDKRTGFAIPFKLNLTGMAQFA 191 Query: 189 TRPGWCMKMLGTNRRTFRNIVGHAKSVADLSSLQAWTNEQFDPQLSWKDVEWIKERWGGP 248 +P W + + H S+ + E DP ++W DV + + W GP Sbjct: 192 LKPAWAINYFTHEGFKLPQLDEHVDMGGGTMSISRYFTEMLDPSMTWDDVAEMVKLWSGP 251 Query: 249 LILKGILDPEDAKMAAKTGADAIIVSNHGGRQLDGAHSSISMLPRIVEAVGDQIEVHLDG 308 LKG++ EDAK A G I++SNHGGRQLDG+ ++ L IV+AVGD+I+V +DG Sbjct: 252 FCLKGVMSVEDAKRAVDIGCSGIVLSNHGGRQLDGSRAAFDQLAEIVDAVGDRIDVIMDG 311 Query: 309 GIRSGQDVLKAIALGAKGTYIGRPFLYGLGALGKEGVTLALDIIRKEMDTTMALCGKRRI 368 G++ G VLKA++LGAK +GR +L+ L A G+ GV AL+ +R E++ M L G I Sbjct: 312 GVQRGTHVLKALSLGAKAVGVGRYYLFPLAAAGQPGVERALEQMRVEIERGMKLMGCSSI 371 Query: 369 TEVGRD 374 ++ R+ Sbjct: 372 EQLSRN 377 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: 354 Number of extensions: 17 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: 378 Length of database: 382 Length adjustment: 30 Effective length of query: 348 Effective length of database: 352 Effective search space: 122496 Effective search space used: 122496 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