Align L-lactate dehydrogenase; L-LDH; EC 1.1.1.27 (characterized)
to candidate WP_013135367.1 ARNIT_RS07815 lactate dehydrogenase
Query= SwissProt::Q9EVR0 (318 letters) >NCBI__GCF_000092245.1:WP_013135367.1 Length = 329 Score = 254 bits (650), Expect = 2e-72 Identities = 130/317 (41%), Positives = 198/317 (62%), Gaps = 7/317 (2%) Query: 6 KIVVIGASNVGSAVANKIADFQLATEVVLIDLNEDKAWGEAKDSSHATSCIYSTNIKFHL 65 K+VVIGA +VGS V L ++ +ID+ + A+GEA D + AT+ Y NI Sbjct: 5 KLVVIGAGHVGSYVLADAMKIGLFGKIGVIDILNNVAFGEAIDQAQATAMTYMNNIDVTS 64 Query: 66 GDYEDCKDANIIVITAGPSIRPGET-----PDRLKLAGTNAKIMSSVMGEIVKRTKEAMI 120 G YE C+DA+IIV+ AGPS+ P + PDR +L N +++ VM I K TK+A+I Sbjct: 65 GGYEQCEDADIIVVAAGPSVIPDKNDSKSEPDRAQLTKINCEVIREVMTGITKYTKDAII 124 Query: 121 IMITNPLDVATYVVSTQFDYPRNLILGTGTMLETYRFRRILADKYQVDPKNINGYVLGEH 180 I+ITNPLD Y+ +FDYP+ + GTGTML++ R R+++AD Y +DPK++ GY++GEH Sbjct: 125 ILITNPLDTMVYIAENEFDYPKGRVFGTGTMLDSARLRKVVADMYNIDPKSVTGYMMGEH 184 Query: 181 GNAAFVAWSTTGCAGFPIDDLDEYFHRTEKLSH-EAVEQELVQVAYDVINKKGFTNTGIA 239 G AF S AG DL++YF + ++ EA+++E+V AY V+N KG+TN G+A Sbjct: 185 GKTAFPVLSRLNIAGISFTDLNKYFDEKDSITQAEAIQKEIVSAAYKVMNGKGWTNAGVA 244 Query: 240 MAACRFIKSVLYDEHTILPCSAVLEGEYGIK-DVALSIPRMVCADGIMRSFEVHLTDDEL 298 AA ++VL DE ++ P S L G+YG DVALS+P ++ +G+++ V L + E Sbjct: 245 QAAVTMAQAVLLDERSVYPTSTTLRGQYGHDGDVALSMPCIIGREGVIKQIAVSLNEWET 304 Query: 299 EKMHKAAQSVRSALDGA 315 +K+ ++ ++ A+ A Sbjct: 305 KKLQESIDYIKLAMKDA 321 Lambda K H 0.319 0.135 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: 258 Number of extensions: 7 Number of successful extensions: 4 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: 318 Length of database: 329 Length adjustment: 28 Effective length of query: 290 Effective length of database: 301 Effective search space: 87290 Effective search space used: 87290 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