Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.110) (characterized)
to candidate AZOBR_RS05480 AZOBR_RS05480 protein fixA
Query= BRENDA::H6LBB0 (264 letters) >FitnessBrowser__azobra:AZOBR_RS05480 Length = 283 Score = 179 bits (453), Expect = 7e-50 Identities = 95/247 (38%), Positives = 148/247 (59%), Gaps = 9/247 (3%) Query: 1 MKILVCIKQVPGTSNVEVDPETGVLIRDGVESKLNPYDLFGLETAFRLKEQLGGTITTLS 60 M I+VCIKQVP ++ + + P T ++R GV + +NP+DLF LE A R+K+++G +T L+ Sbjct: 1 MHIVVCIKQVPDSAQIRIHPVTNTIMRQGVPAIINPFDLFSLEEALRIKDKVGARVTVLT 60 Query: 61 MGPMQSKEVLMESFYMGADEGCLLSDRKFGGADVVATSYTLAQGTKRLGD---FDLIICG 117 MGP ++ L ++ +GAD+ LL+DRKF G+D +ATSY L K+L + DL+ CG Sbjct: 61 MGPPMAETSLRKALSLGADDAVLLTDRKFAGSDTLATSYALTSAIKKLSEEEQVDLVFCG 120 Query: 118 KQTTDGDTAQVGPEMAEFLGIPHVTNVIKILAADE--KGLTLQMNMEESLEIQRVPYPCL 175 KQT DGDTAQVGP +A LG +T + KI + D+ + + + E +++ + PC+ Sbjct: 121 KQTVDGDTAQVGPGIATRLGFQQLTYITKIESIDQGAREIVVHRRSEGGVQVLKTALPCM 180 Query: 176 ITVDKDIYTPRLPSYKRKLDISKNPEIKILTL-KDMYDTNEKKYGLSGSPTQVERIFPPE 234 IT+ + T R + + D+ + + T KD E K GL GSPT V ++F P+ Sbjct: 181 ITMLEGTNTIR---FGKMDDMFRAARYGLKTWNKDTTGAEETKVGLKGSPTVVSKVFVPK 237 Query: 235 SNVEKTS 241 +K + Sbjct: 238 PRAQKAT 244 Lambda K H 0.316 0.137 0.386 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: 190 Number of extensions: 10 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: 264 Length of database: 283 Length adjustment: 25 Effective length of query: 239 Effective length of database: 258 Effective search space: 61662 Effective search space used: 61662 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: 42 (22.0 bits) S2: 47 (22.7 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