Align L-lactate dehydrogenase (EC 1.1.1.27) (characterized)
to candidate WP_093395901.1 BM091_RS11400 malate dehydrogenase
Query= BRENDA::Q9GT92 (321 letters) >NCBI__GCF_900114975.1:WP_093395901.1 Length = 311 Score = 300 bits (768), Expect = 3e-86 Identities = 149/312 (47%), Positives = 214/312 (68%), Gaps = 5/312 (1%) Query: 2 IERRKIAVIGSGQIGGNIAYIVGKDNLADVVLFDIAEGIPQGKALDITHSMVMFGSTSKV 61 I+R+KI ++G+G +G A+ L D+ L DI EG+PQGKALD+ + + G +++ Sbjct: 3 IKRKKITIVGAGFVGATAAHWAAIKELGDICLVDIIEGMPQGKALDLLEASPVEGFDARI 62 Query: 62 IGTNDYADISGSDVVIITASIPGRPKDDRSELLFGNARILDSVAEGVKKYCPNAFVICIT 121 IGTNDYAD + SD+VIITA +P +P R +LLF NA I+ +V E + KY PNAF+I ++ Sbjct: 63 IGTNDYADTADSDLVIITAGLPRKPGMSRDDLLFKNAEIVKNVTEQIAKYSPNAFLIVVS 122 Query: 122 NPLDVMVSHFQKVSGLPHNKVCGMAGVLDSSRFRTFIAQHFGVNASDVSANVIGGHGDGM 181 NPLD MV KVSG P N+V GMAGVLD++RFRTFIA GV+ DV+A V+GGHGD M Sbjct: 123 NPLDAMVYVAHKVSGFPVNRVMGMAGVLDAARFRTFIAMELGVSVEDVTAFVLGGHGDTM 182 Query: 182 VPVTSSVSVGGVPLSSFIKQGLITQEQIDEIVCHTRIAWKEVADNLKTGTAYFAPAAAAV 241 VP+ +V G+PL L+ E+I+ +V TR E+ + LKTG+A+FAP+A+A+ Sbjct: 183 VPLPRYSTVAGIPLPE-----LLPPERIEALVERTRNGGAEIVNLLKTGSAFFAPSASAI 237 Query: 242 KMAEAYLKDRKAVVPCSAFCSNHYGVKGIYMGVPTIIGKNGVEDILELDLTPLKQKLLGE 301 KMAE+ LKD+K ++PC+A+C Y V G ++GVP ++G NGVE ++E+ LTP ++ + Sbjct: 238 KMAESILKDKKRILPCAAYCDKEYDVGGYFVGVPVLLGGNGVEKVIEIKLTPEEKAAFQK 297 Query: 302 SINEVNTISKVL 313 S+ V ++ K L Sbjct: 298 SVEAVKSLVKKL 309 Lambda K H 0.319 0.136 0.394 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: 243 Number of extensions: 9 Number of successful extensions: 2 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: 321 Length of database: 311 Length adjustment: 27 Effective length of query: 294 Effective length of database: 284 Effective search space: 83496 Effective search space used: 83496 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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