Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_075858559.1 cpu_RS03150 phosphoglycerate dehydrogenase
Query= BRENDA::F8A9V0 (325 letters) >NCBI__GCF_001950255.1:WP_075858559.1 Length = 525 Score = 172 bits (435), Expect = 2e-47 Identities = 104/298 (34%), Positives = 163/298 (54%), Gaps = 21/298 (7%) Query: 10 PYEEEFLGPILPSDWDVEMTPDFLDETTVEKAKGAQVVSLFVSDKADGPVLEALHSYGVG 69 P E+ L + + VE +E ++ + + K ++EA + + Sbjct: 8 PVSEKGLNILREEGFIVEEKTKLSEEELIKIISEFDALIVRSETKVTARIIEAAEN--LK 65 Query: 70 LLALRSAGYDHIDIETAKRLGIKVVNVPAYSPHAIADHTLAIMLALIRRLHRAHDKVRLG 129 ++ G D+ID+ A + GI VVN P + A A+HT A+M+AL+R + +AH ++ G Sbjct: 66 IIGRAGVGVDNIDLAAASKKGIIVVNSPEGNTIAAAEHTFALMMALLRNIPQAHAALKEG 125 Query: 130 DFDLDGLMGFDLNGKVAGVIGLGKIGRLVATRLKAFGCKVLGYDPYIQPEI-----VENV 184 + G++L GK G+IGLG+IG VA R+KAF KV+GYDP+I E + + Sbjct: 126 KWLRKEFTGYELRGKTVGIIGLGRIGTAVAKRVKAFETKVIGYDPFISEERAHMLGITLM 185 Query: 185 DLDTLITQADIISIHCPLTRENFHMFNEETFKRMKPGAILVNTARGGLIDTKALLEALKS 244 L+ L+ +ADI+++H PL E ++ N E K MK A ++N ARGG+ID +AL EALK+ Sbjct: 186 SLEELLQKADIVTMHLPLNNETRNLINRERLKLMKKSAFIINCARGGIIDEEALYEALKT 245 Query: 245 GKLGGAALDVYEYERGLFFKNHQKEGIKDPYLAQLLGLANVVLTGHQAFLTREAVKNI 302 G++ GAALDV+ KE + + + L L NV++T H T+EA N+ Sbjct: 246 GEIAGAALDVF-----------SKEPLTE---SPLFELPNVIVTPHLGASTKEAQVNV 289 Lambda K H 0.321 0.140 0.407 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: 392 Number of extensions: 19 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: 325 Length of database: 525 Length adjustment: 31 Effective length of query: 294 Effective length of database: 494 Effective search space: 145236 Effective search space used: 145236 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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