Align L-lactate dehydrogenase [cytochrome]; EC 1.1.2.3 (characterized)
to candidate WP_013418570.1 RVAN_RS04465 alpha-hydroxy-acid oxidizing protein
Query= CharProtDB::CH_000618 (396 letters) >NCBI__GCF_000166055.1:WP_013418570.1 Length = 377 Score = 609 bits (1571), Expect = e-179 Identities = 298/376 (79%), Positives = 335/376 (89%) Query: 1 MIISAASDYRAAAQRILPPFLFHYMDGGAYSEYTLRRNVEDLSEVALRQRILKNMSDLSL 60 MIISA +DYR AA+R LP FLF Y+DGGAY+E+TLR NV DL+ +ALRQR+LKN++D SL Sbjct: 1 MIISATTDYREAARRRLPQFLFDYIDGGAYAEHTLRHNVSDLASIALRQRVLKNVADRSL 60 Query: 61 ETTLFNEKLSMPVALAPVGLCGMYARRGEVQAAKAADAHGIPFTLSTVSVCPIEEVAPAI 120 ET +F +KL+MPV LAPVGL GMYARRGEVQAA+AA + G+PFTLSTVSVCPIEEV Sbjct: 61 ETEIFGQKLAMPVTLAPVGLTGMYARRGEVQAARAAASRGVPFTLSTVSVCPIEEVQKKS 120 Query: 121 KRPMWFQLYVLRDRGFMRNALERAKAAGCSTLVFTVDMPTPGARYRDAHSGMSGPNAAMR 180 P+WFQLYVL+DRGFMRNALERA+AAG +TLVFTVDMP PGARYRDAHSGMSG NA R Sbjct: 121 PAPIWFQLYVLKDRGFMRNALERAQAAGITTLVFTVDMPVPGARYRDAHSGMSGKNAHFR 180 Query: 181 RYLQAVTHPQWAWDVGLNGRPHDLGNISAYLGKPTGLEDYIGWLGNNFDPSISWKDLEWI 240 R +QAVTHP W+WDVGL GRPHDLGNISAYLGKPTGL DYIGWLG+NFDPSISWKDLEWI Sbjct: 181 RMIQAVTHPGWSWDVGLRGRPHDLGNISAYLGKPTGLGDYIGWLGSNFDPSISWKDLEWI 240 Query: 241 RDFWDGPMVIKGILDPEDARDAVRFGADGIVVSNHGGRQLDGVLSSARALPAIADAVKGD 300 R+FW GPM+IKGILD EDARDAVRFGADGI+VSNHGGRQLDGVLSSARALPAIADAVKGD Sbjct: 241 REFWKGPMIIKGILDVEDARDAVRFGADGIIVSNHGGRQLDGVLSSARALPAIADAVKGD 300 Query: 301 IAILADSGIRNGLDVVRMIALGADTVLLGRAFLYALATAGQAGVANLLNLIEKEMKVAMT 360 I ILADSGIR+GLDVVRM+ALGAD ++GRA+ YALA AG+AGVANLL+L KEM+VAM Sbjct: 301 IKILADSGIRSGLDVVRMLALGADCTMIGRAYTYALAAAGEAGVANLLDLFAKEMRVAMA 360 Query: 361 LTGAKSISEITQDSLV 376 LTG +SI+EIT+DSLV Sbjct: 361 LTGVRSIAEITRDSLV 376 Lambda K H 0.320 0.136 0.407 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: 539 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: 396 Length of database: 377 Length adjustment: 30 Effective length of query: 366 Effective length of database: 347 Effective search space: 127002 Effective search space used: 127002 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 (21.8 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