Align D-lactate dehydrogenase; EC 1.1.1.28 (characterized)
to candidate Echvi_3161 Echvi_3161 Lactate dehydrogenase and related dehydrogenases
Query= CharProtDB::CH_091799 (329 letters) >FitnessBrowser__Cola:Echvi_3161 Length = 331 Score = 329 bits (844), Expect = 5e-95 Identities = 169/329 (51%), Positives = 227/329 (68%), Gaps = 2/329 (0%) Query: 1 MKLAVYSTKQYDKKYLQQVNESFGFELEFFDFLLTEKTAKTANGCEAVCIFVNDDGSRPV 60 MK +YST ++DK ++ N+ +L F +F LT++TA A G +A+ +F NDD S V Sbjct: 1 MKTTIYSTHKFDKPSIENANKG-KHQLNFLEFRLTKETALLAEGSKAIALFSNDDASSEV 59 Query: 61 LEELKKHGVKYIALRCAGFNNVDLDAAKELGLKVVRVPAYDPEAVAEHAIGMMMTLNRRI 120 L+ L K G+K+IALR AGFN+VDL+ A EL +KV RVPAY P A+AEH + +++ LNRR+ Sbjct: 60 LDILHKLGIKFIALRSAGFNHVDLEKAAELNIKVARVPAYSPYAIAEHTMALILALNRRL 119 Query: 121 HRAYQRTRDANFSLEGLTGFTMYGKTAGVIGTGKIGVAMLRILKGFGMRLLAFDPYPSAA 180 +A+ R R+ NFSL GLTGF + GKT GVIGTGKIG +++IL GFG +LA D S Sbjct: 120 IKAHNRVREQNFSLNGLTGFDLNGKTVGVIGTGKIGSVLVKILHGFGCNILAQDIEESKD 179 Query: 181 ALE-LGVEYVDLPTLFSESDVISLHCPLTPENYHLLNEAAFEQMKNGVMIVNTSRGALID 239 ++ G+ Y D TL +D+ISLH PL HL+N+ MK+GVM++NTSRG L+D Sbjct: 180 LIDKYGLIYSDCATLCKHADIISLHVPLKASTKHLINKEHIALMKSGVMLINTSRGGLVD 239 Query: 240 SQAAIEALKNQKIGSLGMDVYENERDLFFEDKSNDVIQDDVFRRLSACHNVLFTGHQAFL 299 ++A IE LK +KIG LG+DVYE E LFFED S+D++QDDV RL +NVL T HQAFL Sbjct: 240 TKAVIEGLKTKKIGYLGLDVYEEEEGLFFEDHSDDILQDDVIARLMTFNNVLITSHQAFL 299 Query: 300 TAEALTSISQTTLQNLSNLEKGETCPNEL 328 T ALT+I++TT+ NL EK + NE+ Sbjct: 300 TKTALTNIAETTIYNLDCFEKQKPSGNEI 328 Lambda K H 0.320 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: 284 Number of extensions: 6 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: 329 Length of database: 331 Length adjustment: 28 Effective length of query: 301 Effective length of database: 303 Effective search space: 91203 Effective search space used: 91203 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: 49 (23.5 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