Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate Ac3H11_2838 L-lactate dehydrogenase (EC 1.1.2.3)
Query= BRENDA::W1QKE8 (558 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2838 Length = 381 Score = 220 bits (561), Expect = 7e-62 Identities = 139/368 (37%), Positives = 194/368 (52%), Gaps = 21/368 (5%) Query: 173 EVMNLHDFEYIAKKILPKGAWAYYSSGADDEVSMRENHYAYQRIYFRPRVLVDVSKVDTS 232 E+ NL D E A++ L AWAY+S GA DE+++R N A+ + PRVL ++ T Sbjct: 13 EIANLADHELQARQQLDDNAWAYFSGGAGDEITLRANRSAWDALPLWPRVLRPLAGGHTR 72 Query: 233 TTLLGTPTSVPFYVSATALAKLGHPDGECSIARGAGKEGVIQMISTLASNSLEEIAAARV 292 LLG + P ++ A +L H DGE ++A A G ++ST AS SLE IA A Sbjct: 73 VQLLGRTLAHPILLAPVAFQRLAHADGELAMAYAAAALGAGVVLSTQASVSLEAIAEAVQ 132 Query: 293 PGATQ---WFQLYVNEDRNVAFEMVKKAEKLGIKAIFVTVDAPSLGNREKDARVKFEGES 349 P + WFQLY+ DR +V++AE G +A+ +TVDAP+ G R+++ R F Sbjct: 133 PDPGRGPLWFQLYLQHDRGFTQALVQRAEAAGYEALVLTVDAPTSGVRDRERRAGFRLPP 192 Query: 350 DVQKSN--------EVVRSQGASRALSSFIDTRLTWDDVKKIKQSTKLPVLIKGVQRLED 401 V N G S + TWDDV ++ T+LPVL+KGV D Sbjct: 193 GVGPVNLAGLPPPPPPDLRPGQSALFDGLLHQAPTWDDVAWLQSITRLPVLLKGVLHPAD 252 Query: 402 VVQAVDDGFDGVVLSNHGGRQLDTAPPPVELLAEVVPELKRRNKLRPDFEIFIDGGVRRG 461 QAV G G+++SNHGGR LDTAP L VV + + +DGG+RRG Sbjct: 253 ARQAVAAGAAGLIVSNHGGRTLDTAPATATALPRVV------QAVGGAVPVLVDGGIRRG 306 Query: 462 TDILKALALGGQNVRVGVGLGRPFLYANSSYGENGVRKAIQLLKDELEMDMRLLGVRNLR 521 TD+LKA+ALG V V GRP ++ ++ G GV ++LL+DELE+ M L G L Sbjct: 307 TDVLKAMALGASAVLV----GRPAVWGLANAGATGVAHVLRLLRDELEVAMALTGCATLA 362 Query: 522 ELDETFVD 529 + +D Sbjct: 363 DATPALLD 370 Lambda K H 0.317 0.135 0.393 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: 529 Number of extensions: 29 Number of successful extensions: 5 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: 558 Length of database: 381 Length adjustment: 33 Effective length of query: 525 Effective length of database: 348 Effective search space: 182700 Effective search space used: 182700 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 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