Align L-lactate dehydrogenase (EC 1.1.1.27) (characterized)
to candidate WP_013418327.1 RVAN_RS03215 malate dehydrogenase
Query= BRENDA::Q8I8U5 (330 letters) >NCBI__GCF_000166055.1:WP_013418327.1 Length = 323 Score = 340 bits (873), Expect = 2e-98 Identities = 167/314 (53%), Positives = 227/314 (72%), Gaps = 5/314 (1%) Query: 9 RPKIAMVGSGMIGGTMAFLCSLRELGDVVLFDVVPNMPMGKAMDISHNSSVVDTGITVYG 68 R KIA++GSGMIGGT+A L L+ELGDVV+FD+ +P GKA+D++ ++ V + G Sbjct: 3 RAKIALIGSGMIGGTLAHLIGLKELGDVVMFDIAEGLPQGKALDLAESAPVDGFNVGFQG 62 Query: 69 SNSYECLKGADVVIITAGITKIPGKSDKEWSRMDLLPVNIKIMREVGAAIKSYCPNAFVI 128 N Y +KGADVVI+TAG+ + G S R DLL +N+K+M +VGA IK Y P+AFVI Sbjct: 63 VNDYADIKGADVVIVTAGVPRKAGMS-----RDDLLEINLKVMEQVGAGIKKYAPDAFVI 117 Query: 129 NITNPLDVMVAALQESSGLPHHRICGMAGMLDSSRFRRMIADKLEVSPRDVQGMVIGVHG 188 ITNPLD MV ALQ +G+P +++ GMAG+LD SRFR +A + +VS DV V+G HG Sbjct: 118 CITNPLDAMVWALQRVTGMPKNQVVGMAGVLDGSRFRYFLAREFDVSVEDVTAFVLGGHG 177 Query: 189 DHMVPLSRYATVNGIPLSEFVKKGWIKQEEVDDIVQKTKVAGGEIVRLLGQGSAYYAPGA 248 D MVPL+RY TV GIPL + +K WI E +++IVQ+T+ G E+V+LL GSAYYAP A Sbjct: 178 DTMVPLTRYTTVAGIPLPDLIKMNWITHERLNEIVQRTRDGGAEVVKLLKTGSAYYAPAA 237 Query: 249 SAIQMAESYLKDRKRVMVCSCYLQGQYGVQNHYLGVPCVIGGRGVEKIIELELTAQERQE 308 SAI+MAESYLKD+KRV+ C+ YL G+YGV+ Y+GVP VIG +G+E++IE++L ER + Sbjct: 238 SAIEMAESYLKDKKRVLPCAAYLTGEYGVKGLYIGVPTVIGAKGMERVIEIDLNTHERLD 297 Query: 309 LQGSIDEVKEMQKA 322 S++ VK + +A Sbjct: 298 FNRSVEAVKNLVEA 311 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: 335 Number of extensions: 18 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: 330 Length of database: 323 Length adjustment: 28 Effective length of query: 302 Effective length of database: 295 Effective search space: 89090 Effective search space used: 89090 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: 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