Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate AO356_24000 AO356_24000 hydroxyacid dehydrogenase
Query= reanno::Smeli:SMc00832 (479 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_24000 Length = 474 Score = 171 bits (432), Expect = 7e-47 Identities = 134/445 (30%), Positives = 212/445 (47%), Gaps = 19/445 (4%) Query: 43 PFETDAFIAYRRMPLAVVLPETTEHVAAVLKYCSRYGIPIVPRGAGTSLSGGAIPQED-- 100 P+ TD Y +A V P +TE VAAV++ C+ P+V +G T L GGA P Sbjct: 26 PYLTDKQGRYVGQVIAAVHPASTEEVAAVVRACAATDTPVVVQGGNTGLIGGATPDSSGR 85 Query: 101 AIVVGLSKMSRTLDIDLFNRTATVQAGVTNLNISDAVSADGFFYAPDPSSQLACTIGGNI 160 A+++ L +M+R +D N T TV+AG + D G + ++ +CT+GGN+ Sbjct: 86 AMLLLLDRMNRVRAVDTDNDTLTVEAGCILQTVQDVAREAGRLFPLSLGAEGSCTLGGNL 145 Query: 161 GMNSGGAHCLKYGVTTNNLLGVKMVLFDGTVIE-LGGKALDAPGYDLLGLVCGSEGQLGI 219 G N+GG L+YG T LG+++V G V + L G D GYDL L GSEG LGI Sbjct: 146 GTNAGGTAVLRYGNTRELTLGLEVVTARGEVWDGLRGLRKDNTGYDLRDLFIGSEGTLGI 205 Query: 220 VTEATVRLIAKPEGARPVLFGFASSESAGSCVADI-IGSGIIPVAIEFMDRPAIEIC--- 275 +T AT++L P+ L F S E A + ++ G G A E + + + Sbjct: 206 ITAATLKLFPLPKAQATALLAFDSLEQAVALLSHARAGFGASLTAFELLSAECLALLREQ 265 Query: 276 -----EAFAQAGYPLDVEALLIVEVEGSEAEMDATLAGII-EIARRHGVMTIRESQSALE 329 FA A P ALL + SE+ ++ E +H + ++S ++ Sbjct: 266 FPDGPRPFASARQPW--FALLELSDNHSESHAREVFEQVLGEAFEQHLLADALIAESLVQ 323 Query: 330 AALIWKGRKSAFGATGRIADYICMDGTVPLSQLSHVLRRTGEIVAGY--GLRVANVFHAG 387 + W+ R++ A R + D +VP+SQ+ + T ++ G+R H G Sbjct: 324 SQAFWQLRENMSDAQKRAGRNMKHDISVPISQVVAFVAHTDALLQEQFPGVRHYTFGHLG 383 Query: 388 DGNMHPLILYNINDPEEAARAE-AAGNDILKLCVEA-GGCLTGEHGVGIEKRDLMLHQYS 445 DGN+H + + ++ +A AA + ++ A GG ++ EHG+G K + + S Sbjct: 384 DGNLHYNVAHPLDSTVDAHMGHYAALSRLVHDSAHAHGGSISAEHGIGQRKVNELGRYKS 443 Query: 446 RADLGQQMAARAAFDPQWLMNPSKV 470 +L + A DP+ L+NP KV Sbjct: 444 TVELDLMHRIKQALDPRNLLNPGKV 468 Lambda K H 0.320 0.138 0.404 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: 534 Number of extensions: 22 Number of successful extensions: 6 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: 479 Length of database: 474 Length adjustment: 33 Effective length of query: 446 Effective length of database: 441 Effective search space: 196686 Effective search space used: 196686 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: 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