Align glyoxylate reductase (EC 1.1.1.26); 4-hydroxybutyrate dehydrogenase (EC 1.1.1.61); glyoxylate reductase (NADP+) (EC 1.1.1.79) (characterized)
to candidate Synpcc7942_1857 Synpcc7942_1857 3-hydroxyacid dehydrogenase
Query= BRENDA::Q9LSV0 (289 letters) >FitnessBrowser__SynE:Synpcc7942_1857 Length = 288 Score = 150 bits (378), Expect = 4e-41 Identities = 89/285 (31%), Positives = 144/285 (50%), Gaps = 3/285 (1%) Query: 1 MEVGFLGLGIMGKAMSMNLLKNGFKVTVWNRTLSKCDELVEHGASVCESPAEVIKKCKYT 60 M G +G G++G A++ LL G +TVWNRT + LV GA++ +PA ++ C+ Sbjct: 1 MRCGLIGTGLLGTAIAERLLTVGQLLTVWNRTAERSQPLVALGATIAPTPAALLADCEVC 60 Query: 61 IAMLSDPCAALSVVFDKGGVLEQICEGKGYIDMSTVDAETSLKINEAITGKGGRFVEGPV 120 + +LSD A + + + + + GK I M T+ S I + I GG+++E PV Sbjct: 61 LLLLSDAEAIAATLLTEESRSQLV--GKTIIQMGTISPAESRAIADQIAAAGGQYLEAPV 118 Query: 121 SGSKKPAEDGQLIILAAGDKALFEESIPAFDVLGKRSFYLGQVGNGAKMKLIVNMIMGSM 180 GS A +G LI++ + A+FE+ L ++G +G A +KL +N ++GS+ Sbjct: 119 LGSLPEARNGTLIVMVGAEPAVFEQWRSLLCHLSPEPEWIGPIGTAATLKLALNQLIGSL 178 Query: 181 MNAFSEGLVLADKSGLSSDTLLDILDLGAMTNPMFKGKGPSMNKSSYP-PAFPLKHQQKD 239 +AF L L +SGL+ + + IL A+ P F K + Y P FP H KD Sbjct: 179 TSAFGGSLALLQRSGLAVEPFMAILRQSALYAPTFDKKLSRLLSHQYDNPNFPTTHLAKD 238 Query: 240 MRLALALGDENAVSMPVAAAANEAFKKARSLGLGDLDFSAVIEAV 284 +RL + ++ +KA + G GD D+SA+ EA+ Sbjct: 239 LRLFRETAADLGITTDAVEGVESIVQKAIAQGWGDQDYSALYEAI 283 Lambda K H 0.317 0.134 0.379 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: 144 Number of extensions: 5 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: 289 Length of database: 288 Length adjustment: 26 Effective length of query: 263 Effective length of database: 262 Effective search space: 68906 Effective search space used: 68906 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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