Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate HSERO_RS22255 HSERO_RS22255 3-phosphoglycerate dehydrogenase
Query= BRENDA::F8A9V0 (325 letters) >FitnessBrowser__HerbieS:HSERO_RS22255 Length = 308 Score = 169 bits (427), Expect = 1e-46 Identities = 106/267 (39%), Positives = 148/267 (55%), Gaps = 25/267 (9%) Query: 47 VSLFVSDKADGPVLEALHSYGVGLLALRSAGYDHIDIETAKRLGIKVVNVPAYSPHAIAD 106 VS V D A P+L + +G G+ D ID + A++ GI V + A+A+ Sbjct: 60 VSARVMDAA--PILRVISKHGTGI--------DSIDSQAAQQRGIAVKAAAGANAPAVAE 109 Query: 107 HTLAIMLALIRRLHRAHDKVRLGDFDLDGLMGFDLNGKVAGVIGLGKIGRLVATRLKAFG 166 HT A+++A + + ++R G +D +L G+ G++GLG IGR VA A G Sbjct: 110 HTWALIMACAKNVVGLDQRMREGHWDKSTHKSLELQGRTLGLVGLGAIGRRVAAVAAALG 169 Query: 167 CKVLGYDPYIQ--PEIVENVDLDTLITQADIISIHCPLTRENFHMFNEETFKRMKPGAIL 224 VL +DPY + P+ V+ VDLDTL Q+D++S+HCPLT EN HM N ++ RMK GAIL Sbjct: 170 MPVLAHDPYAKEAPQGVQLVDLDTLFAQSDVVSLHCPLTAENKHMINAQSLARMKDGAIL 229 Query: 225 VNTARGGLIDTKALLEALKSGKLGGAALDVYEYERGLFFKNHQKEGIKDPYLAQLLGLAN 284 VNTARGGLID +AL+ AL SGKL A LD +E KE P+ Q +G N Sbjct: 230 VNTARGGLIDEQALIAALDSGKLRAAGLDSFE-----------KEPFTAPHPLQRVG--N 276 Query: 285 VVLTGHQAFLTREAVKNIEETTVENIL 311 VL+ H +T +A + N+L Sbjct: 277 AVLSPHIGGVTSDAYIAMGTGAASNVL 303 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: 236 Number of extensions: 11 Number of successful extensions: 2 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: 308 Length adjustment: 27 Effective length of query: 298 Effective length of database: 281 Effective search space: 83738 Effective search space used: 83738 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 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