Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate AZOBR_RS29790 AZOBR_RS29790 3-ketoacyl-ACP reductase
Query= uniprot:B2T9V3 (247 letters) >FitnessBrowser__azobra:AZOBR_RS29790 Length = 250 Score = 140 bits (353), Expect = 2e-38 Identities = 98/259 (37%), Positives = 134/259 (51%), Gaps = 27/259 (10%) Query: 1 MTQRLAGKTALITAAGQGIGLATAELFAREGARVIATDIRIDGLAGKPVE---------- 50 MT+RL GK ALIT A QG+GLA AE F REG RV D I+G A K V Sbjct: 1 MTKRLDGKVALITGAAQGLGLAMAETFVREGGRVAVVD--INGDAAKAVAERLGESAIGI 58 Query: 51 ----ARKLDVRDDAAIKALAAEIGAVDVLFNCAGFVHAGNILE-CSEEDWDFAFDLNVKA 105 R DV + I A + G +D+L N AG HA E +EE++D F LNVK+ Sbjct: 59 AANVTRMADV--EMTIAATVEKFGRLDILVNNAGSTHANGPFENVTEEEFDRVFALNVKS 116 Query: 106 MYRMIRAFLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITR 165 +Y +A + M + G I+N+ S A ++ P Y+A+K AV +TKS+A + Sbjct: 117 IYLYSKAVVATMRAQKSGVILNLGSTA-GLRPRPGLVWYNATKGAVHNITKSLALELAPD 175 Query: 166 GVRCNAICPGTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALY 225 +R A+ P +P L A G +A + P+GR+G+P ++A ALY Sbjct: 176 NIRVCALAPVATETPLL-------ATFMGGDTPEKRARMMGIVPLGRLGQPTDVANAALY 228 Query: 226 LGSDESSFTTGHAHVIDGG 244 L SDE++F TG IDGG Sbjct: 229 LASDEAAFLTGVVLEIDGG 247 Lambda K H 0.320 0.133 0.381 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: 152 Number of extensions: 11 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: 247 Length of database: 250 Length adjustment: 24 Effective length of query: 223 Effective length of database: 226 Effective search space: 50398 Effective search space used: 50398 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: 46 (22.3 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