Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate 5208275 Shew_0787 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding (RefSeq)
Query= BRENDA::A0A140N893 (329 letters) >FitnessBrowser__PV4:5208275 Length = 329 Score = 437 bits (1123), Expect = e-127 Identities = 201/328 (61%), Positives = 266/328 (81%) Query: 1 MKLAVYSTKQYDKKYLQQVNESFGFELEFFDFLLTEKTAKTANGCEAVCIFVNDDGSRPV 60 M++ +S K YD ++ + N++FG ++E+FD+ L ++ K A G E +C FVND V Sbjct: 1 MRIGFFSAKHYDMEHFNRTNQAFGAQIEYFDYRLCMQSVKLAYGFEVICAFVNDSLCEEV 60 Query: 61 LEELKKHGVKYIALRCAGFNNVDLDAAKELGLKVVRVPAYDPEAVAEHAIGMMMTLNRRI 120 L EL K+G K IA+RCAGFNNVDL+AAK LG++VV VPAY PE+VAEH + +M+TLNR++ Sbjct: 61 LVELAKNGTKIIAMRCAGFNNVDLEAAKRLGIRVVNVPAYSPESVAEHTVALMLTLNRKV 120 Query: 121 HRAYQRTRDANFSLEGLTGFTMYGKTAGVIGTGKIGVAMLRILKGFGMRLLAFDPYPSAA 180 H+AYQRTRDANFSLEGL GF M+G+T GVIGTGKIGVA ++IL GFG +++ +DPYP+ A Sbjct: 121 HKAYQRTRDANFSLEGLVGFNMHGRTVGVIGTGKIGVATIKILLGFGCKVVVYDPYPNQA 180 Query: 181 ALELGVEYVDLPTLFSESDVISLHCPLTPENYHLLNEAAFDQMKNGVMIVNTSRGALIDS 240 L++G+EY+ L L++ SD++SLHCPLT EN+HLLN+A+FD+MK GVM++NTSRG L+++ Sbjct: 181 VLDMGIEYLSLDELYAVSDILSLHCPLTKENHHLLNKASFDKMKPGVMVINTSRGGLLNA 240 Query: 241 QAAIEALKNQKIGSLGMDVYENERDLFFEDKSNDVIQDDVFRRLSACHNVLFTGHQAFLT 300 A+EALK +IGSLG+DVYENE++LFFEDKSN +IQDDVFRRLSACHNV+FTGHQAFLT Sbjct: 241 FDAMEALKTGQIGSLGLDVYENEKELFFEDKSNQIIQDDVFRRLSACHNVIFTGHQAFLT 300 Query: 301 AEALTSISQTTLQNLSNLEKGETCPNEL 328 EAL +I+ T+L N+ L GE CPN+L Sbjct: 301 EEALGAIAHTSLTNVRQLLDGEACPNQL 328 Lambda K H 0.320 0.136 0.389 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: 343 Number of extensions: 11 Number of successful extensions: 1 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: 329 Length adjustment: 28 Effective length of query: 301 Effective length of database: 301 Effective search space: 90601 Effective search space used: 90601 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