Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate WP_015798465.1 AFER_RS05335 alpha-hydroxy-acid oxidizing protein
Query= reanno::acidovorax_3H11:Ac3H11_1623 (390 letters) >NCBI__GCF_000023265.1:WP_015798465.1 Length = 458 Score = 264 bits (674), Expect = 4e-75 Identities = 138/385 (35%), Positives = 214/385 (55%), Gaps = 8/385 (2%) Query: 1 VPDLSKITCIEDLRAIAQRRVPRMFYDYADSGSYTEGTYRANESDFQRIKLRQRVAVNME 60 +P L + I+DLR +A+ R PR +DY D + E + NE F + R V ++ Sbjct: 42 LPTLDRAATIDDLRRLAKLRTPRPVFDYVDGAAEAERSMLRNEGSFADVVFRPHVLRDVS 101 Query: 61 GRSTRTTMVGQDVAMPVAIAPTGLTGMQHADGEILGAKAAKAFGIPFTLSTMSICSIEDI 120 T++G A+P APTG T M H DGE+ + A + GIP+ LST+ + E++ Sbjct: 102 SVDPTWTVLGSPSALPFGFAPTGFTRMMHTDGELAVGRVAASLGIPYGLSTVGTTTPEEL 161 Query: 121 AEHTGRHPFWFQVYVMRDRDFIERLIDRAKAANCSALQLTLDLQILGQRHKDIKNGLSAP 180 A WFQ+YV RDR ++RA+ A AL LT+D+ + G R +D++NGL+ P Sbjct: 162 AAELPHLRRWFQLYVWRDRGPTRAFVERAREAGFEALILTVDVPVAGARMRDVRNGLTLP 221 Query: 181 PKPTIANLINLATKPRWCLGMLGTKRRSFGNIVGHAKGVGDLSSLSSWTAEQFDPQLNWG 240 P P++ + A P W L F ++ +G + S+ FDP + + Sbjct: 222 PTPSLRTFLQGALHPAWSRDFLTKPPVRFASLETGFEG-----TAGSFIDRMFDPTVTFD 276 Query: 241 DVEWIKKRWGGKLILKGIMDAEDARLAVNSGADALIVSNHGGRQLDGAPSSIAALPGIAD 300 D+EW++ W GK+++KG+ +DA G DA++VSNHGGRQLD + +A LP + + Sbjct: 277 DIEWVRSLWSGKIVVKGVQRIDDAERLAAIGVDAIVVSNHGGRQLDRTLAPLALLPIVRE 336 Query: 301 AVAQMGGGIEVWMDGGIRSGQDVLKARALGAQGTLIGRSFLYGLGAYGEAGVTRALQIIQ 360 ++ G +EVW+DGG+R+G DV+ A LGAQ L+GR++LYGL A GE GV A +I+ Sbjct: 337 ---RLDGRVEVWVDGGVRAGSDVVAAIGLGAQFVLVGRAYLYGLMAGGERGVAVAGRILA 393 Query: 361 KELDITMAFCGHTNINTVDRSILLP 385 + TMA G + + ++ ++ P Sbjct: 394 DGVTRTMALLGIRSFDELESDMVAP 418 Lambda K H 0.320 0.137 0.412 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: 484 Number of extensions: 26 Number of successful extensions: 3 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: 390 Length of database: 458 Length adjustment: 32 Effective length of query: 358 Effective length of database: 426 Effective search space: 152508 Effective search space used: 152508 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