Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate AZOBR_RS05725 AZOBR_RS05725 FAD-binding protein
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__azobra:AZOBR_RS05725 Length = 495 Score = 229 bits (584), Expect = 2e-64 Identities = 145/455 (31%), Positives = 234/455 (51%), Gaps = 7/455 (1%) Query: 11 IAAIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNIP 70 IAA++ ++P E V + D L + P V++ ++ E+VS++++ E + Sbjct: 18 IAALRAIVPGEGVIADESELRAYECDGLTAYRQLPMVVVLPSTVEQVSRVLRTCKEMGVK 77 Query: 71 VVVRGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEEND 130 VV RG+GT L G +PL G++L N IL++D N V +PGV + +S V Sbjct: 78 VVPRGAGTSLSGGALPLADGVLLGMGKFNRILDIDFANRCVVTQPGVTNLGISTAVAHEG 137 Query: 131 LFYPPDPGEKSA-TIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIVKN 189 +Y PDP + A TI GNI+ N+GG+ +KYG+T + V GL +VL +G ++ LGGK + + Sbjct: 138 FYYAPDPSSQIACTIGGNIAENSGGVHCLKYGLTTNNVLGLEMVLMDGTVLRLGGKHL-D 196 Query: 190 SSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKSKAI 249 + GY L +V GSEG L V+T+ +++L P ++LI F V II + I Sbjct: 197 AGGYDLMGVVTGSEGLLGVVTEVTVRILKKPATARAVLIGFPTSEQGGDCVAAIIAAGII 256 Query: 250 PTAIEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCLAEGA 309 P +E M++ I AEDF+ +P A +++ DG E V+ + VA + ++G Sbjct: 257 PGGMEMMDKPAIHAAEDFVHAGYP-LDVEALLIVELDGPAAE-VDHLIDQVAEIARSKGC 314 Query: 310 KDVYIVDTVERKDSVWSARGAFLEAIKASTTEMDECDVVVPRNRIAEFIEFTHDLAKEMD 369 + + E + S W+ R A A+ + + D +PR + + +++ Sbjct: 315 CYSRVSTSEEERLSFWAGRKAAFPAVGRISPDYYCMDGTIPRKALPLVLHRMQEMSDRYA 374 Query: 370 VRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAM-DRMYAKALTFEGLVSGEHGIGYA 428 +R+ + HAGDGNLH + D E + AEA + + + G+++GEHG+G Sbjct: 375 LRVANVFHAGDGNLHPLILYD--ANKPGELERAEAFGNDILRLCVEVGGVLTGEHGVGVE 432 Query: 429 KRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKV 463 KR + + F L IK FDP LLNP KV Sbjct: 433 KRDLMTDQFDEVDLDQQQRIKCAFDPDGLLNPGKV 467 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: 553 Number of extensions: 31 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: 495 Length adjustment: 34 Effective length of query: 432 Effective length of database: 461 Effective search space: 199152 Effective search space used: 199152 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