Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate 6938708 Sama_2811 glycerate dehydrogenase (RefSeq)
Query= BRENDA::Q9I530 (329 letters) >FitnessBrowser__SB2B:6938708 Length = 317 Score = 147 bits (370), Expect = 4e-40 Identities = 96/264 (36%), Positives = 142/264 (53%), Gaps = 25/264 (9%) Query: 72 VALRSAGYNHVDLAAAEALGLPVVHVPAYSPHAVAEHAVGLILTLNRRLHRAYNRTREGD 131 + + + G N VD+AAA+ LG+ V +VP Y P AVA+ +L R+ ++ +G Sbjct: 70 IGVLATGTNVVDVAAAKRLGIAVTNVPGYGPDAVAQMGFAHVLHHMSRVSAHHDAVTQGQ 129 Query: 132 FSLHGLTGF--------DLHGKRVGVIGTGQIGETFARIMAGFGCELLAYDPYPNPRIQA 183 +S G F L GK +G++G G I ARI FG +LL + P Sbjct: 130 WS--GQADFCFTLGQLESLSGKTLGLVGFGDIARQMARIGMAFGMKLLVHSR-SKPTDLP 186 Query: 184 LGGRYLALDALLAESDIVSLHCPLTADTRHLIDAQRLATMKPGAMLINTGRGALVNAAAL 243 G +++ALD L AESD++SLHCPLT DTR +++ + LA MK GA+LINT RG LV+ AL Sbjct: 187 EGAKFVALDTLFAESDVLSLHCPLTDDTRDMVNRESLALMKQGALLINTARGGLVDEVAL 246 Query: 244 IEALKSGQLGYLGLDVYEEEADIFFEDRSDQPLQDDVLARLLSFPNVVVTAHQAFLTREA 303 +AL +G++ G+DV E P ++ LL N+ +T H A+ T +A Sbjct: 247 ADALNAGRV-RAGVDVLSTE----------PPAPNN---PLLHAANISITPHNAWATVKA 292 Query: 304 LAAIADTTLDNIAAWQDGTPRNRV 327 + D ++N+ A+ G NRV Sbjct: 293 RQKLLDIAVENLRAFSRGESVNRV 316 Lambda K H 0.323 0.137 0.402 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: 266 Number of extensions: 20 Number of successful extensions: 5 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: 317 Length adjustment: 28 Effective length of query: 301 Effective length of database: 289 Effective search space: 86989 Effective search space used: 86989 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 48 (23.1 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