Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate 209326 DVU0390 glycolate oxidase, subunit GlcD, putative
Query= reanno::Smeli:SMc00832 (479 letters) >MicrobesOnline__882:209326 Length = 460 Score = 260 bits (664), Expect = 8e-74 Identities = 153/435 (35%), Positives = 228/435 (52%), Gaps = 11/435 (2%) Query: 43 PFETDAFIAYRRMPLAVVLPETTEHVAAVLKYCSRYGIPIVPRGAGTSLSGGAIPQEDAI 102 P++ DA R P VVLPE+ + A+++ + + P++PRG GT L+GG + + Sbjct: 32 PYDRDAS-ELRATPDMVVLPESVGQIQALMRLATEHRFPVIPRGGGTGLAGGCLALMGGV 90 Query: 103 VVGLSKMSRTLDIDLFNRTATVQAGVTNLNISDAVSADGFFYAPDPSSQLACTIGGNIGM 162 V+ + +M+R ID N A V AG + DA +A FY PDP+ T+GGN+ Sbjct: 91 VLSVERMNRVRAIDTRNLVAEVDAGCITQTLRDAAAAANLFYPPDPAGMDRSTVGGNVAT 150 Query: 163 NSGGAHCLKYGVTTNNLLGVKMVLFDGTVIELGGKA-LDAPGYDLLGLVCGSEGQLGIVT 221 N+GG C+KYGVT + +LGV+ VL DG ++ G + GYD+ L+CGSEG LG++T Sbjct: 151 NAGGPACVKYGVTRDYVLGVEAVLPDGELLRAGVRTRKGVVGYDMAHLLCGSEGTLGVIT 210 Query: 222 EATVRLIAKPEGARPVLFGFASSESAGSCVADIIGSGIIPVAIEFMDRPAIEICEAFAQA 281 T++LI P + FA SA VA ++G+G +P AIEFMD + + Sbjct: 211 GLTMKLIPLPAATVGMAVAFADMPSAMRAVAAVLGAGHLPSAIEFMDHRCLALVGEMLPF 270 Query: 282 GYPLDVEALLIVEVEGSEAEMDATLAGIIEIARRHGVMTIRESQSALEAALIWKGRKSAF 341 P +LLI+E++G A ++ L + I R G + + + E A IW R+ Sbjct: 271 PVPGARPSLLIIELDGQRATIEPQLDAVAAICREQGATQVLPAPTDAERATIWGVRRQ-- 328 Query: 342 GATGRIAD----YICMDGTVPLSQLSHVLRRTGEIVAGYGLRVANVFHAGDGNMHPLILY 397 + RI D Y+ D VPL ++ ++ YGL + HAGDGN+H + Sbjct: 329 -VSLRIHDYAGLYLSEDVAVPLVAIADLVAELPAFEERYGLEIFAFGHAGDGNIHLNVTS 387 Query: 398 NINDPEEAARAEAAGNDILKLCVEAGGCLTGEHGVGIEKRDLMLHQYSRADLGQQMAARA 457 + D E RAE + + VE GG ++GEHG+G K+ L+ + S + Q R Sbjct: 388 SSTDNRE--RAEEGVVALARRVVELGGTISGEHGIGEAKKHLVPLELSARSIALQKGIRG 445 Query: 458 AFDPQWLMNPSKVFP 472 FDP +MNP KVFP Sbjct: 446 VFDPLGIMNPGKVFP 460 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: 664 Number of extensions: 36 Number of successful extensions: 4 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: 460 Length adjustment: 33 Effective length of query: 446 Effective length of database: 427 Effective search space: 190442 Effective search space used: 190442 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