Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate SMc00832 SMc00832 glycolate oxidase subunit protein
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__Smeli:SMc00832 Length = 479 Score = 213 bits (543), Expect = 9e-60 Identities = 142/456 (31%), Positives = 229/456 (50%), Gaps = 10/456 (2%) Query: 11 IAAIKELIPAERVFVGTEIG-EDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNI 69 +A + +L+P E + E G + F D + P ++ +TE V+ ++KY + I Sbjct: 22 VADLADLLP-EGGLISDERGLKPFETDAFIAYRRMPLAVVLPETTEHVAAVLKYCSRYGI 80 Query: 70 PVVVRGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEEN 129 P+V RG+GT L G +P I++ + M+ L++D N T TV+ GV + +S V + Sbjct: 81 PIVPRGAGTSLSGGAIPQEDAIVVGLSKMSRTLDIDLFNRTATVQAGVTNLNISDAVSAD 140 Query: 130 DLFYPPDPGEKSA-TIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIVK 188 FY PDP + A TI GNI N+GG +KYGVT + + G+ +VL +G +IELGGK + Sbjct: 141 GFFYAPDPSSQLACTIGGNIGMNSGGAHCLKYGVTTNNLLGVKMVLFDGTVIELGGKAL- 199 Query: 189 NSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKSKA 248 ++ GY L LV GSEG L ++T+A ++L+ P+ +L F + A V II S Sbjct: 200 DAPGYDLLGLVCGSEGQLGIVTEATVRLIAKPEGARPVLFGFASSESAGSCVADIIGSGI 259 Query: 249 IPTAIEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCLAEG 308 IP AIEFM+R I E F +P A +++ +G+ E ++A + + G Sbjct: 260 IPVAIEFMDRPAIEICEAFAQAGYP-LDVEALLIVEVEGSEAE-MDATLAGIIEIARRHG 317 Query: 309 AKDVYIVDTVERKDSVWSARGAFLEAIKASTTEMDECDVVVPRNRIAEFIEFTHDLAKEM 368 + + +W R + A + D VP ++++ + T ++ Sbjct: 318 VMTIRESQSALEAALIWKGRKSAFGA-TGRIADYICMDGTVPLSQLSHVLRRTGEIVAGY 376 Query: 369 DVRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAMDRMYAK-ALTFEGLVSGEHGIGY 427 +R+ + HAGDGN+H + + EA AEA K + G ++GEHG+G Sbjct: 377 GLRVANVFHAGDGNMHPLILYN--INDPEEAARAEAAGNDILKLCVEAGGCLTGEHGVGI 434 Query: 428 AKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKV 463 KR +L+ + L + FDP+ L+NP KV Sbjct: 435 EKRDLMLHQYSRADLGQQMAARAAFDPQWLMNPSKV 470 Lambda K H 0.318 0.136 0.388 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: 513 Number of extensions: 24 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: 466 Length of database: 479 Length adjustment: 33 Effective length of query: 433 Effective length of database: 446 Effective search space: 193118 Effective search space used: 193118 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 (21.7 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