Align L-arabinonolactonase (characterized, see rationale)
to candidate WP_038204663.1 Q392_RS08560 SMP-30/gluconolactonase/LRE family protein
Query= uniprot:A0A1I2AUG6 (300 letters) >NCBI__GCF_000745855.1:WP_038204663.1 Length = 295 Score = 161 bits (408), Expect = 1e-44 Identities = 114/294 (38%), Positives = 139/294 (47%), Gaps = 10/294 (3%) Query: 4 RVVHHPANTLGEGILWCEREQALYWTDIQAATLWRHRPADGATRSWEMPERLGCLALCEA 63 R + + LGE W E QAL W D A LWR P GA +P +G +A C Sbjct: 6 RRIGETKDQLGESPCWLEDAQALCWIDALAGHLWRLHPGSGALERHHLPAPVGSVAPCGG 65 Query: 64 DGWLLLGLATRLAFFRPEDDLLLPLVSVEPDLP-TRLNDGACDRQGRFVFGTLHEPAAGE 122 D +++ L A + L L ++ D P R NDG CD G FV GT+H A Sbjct: 66 DA-VVVALRNSFARYDFATRSLRELGTIPVDDPQVRFNDGKCDPAGHFVAGTMHMARAPG 124 Query: 123 TRQPIGAFYRLNADLTLERLNLPGIGISNSVAFSPDGRTMYFCDSPSRVIQCCDYGDRCG 182 R G YRL AD G N FSPDG T Y DS RVI DY D G Sbjct: 125 ERVR-GGLYRLRADDGRIEQIADDNGFVNGPCFSPDGGTFYVGDSLERVIWAYDY-DPDG 182 Query: 183 ---EPRVFARVDDERGEPDGSAVDAQGCLWNAQWGLGRVVRYAPDGRVDRIVEVPATQPT 239 R+F + PDG+ VDAQG LW R+ R APDGR++R++E P T PT Sbjct: 183 PLRNKRLFLATGEFDCGPDGATVDAQGFLWTVLARAARIARVAPDGRIERLIEAPPTYPT 242 Query: 240 RPAFGDSPLDTLYITSARDGLSSAALATQPLAGALF-AADAGASGLPEPRFRGA 292 FG + LD LY+TS S+ QP G LF D A+GL R+RGA Sbjct: 243 SLCFGGARLDRLYLTSI--SRSARLEGRQPQDGGLFLIEDLPAAGLAPQRYRGA 294 Lambda K H 0.321 0.139 0.451 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: 357 Number of extensions: 21 Number of successful extensions: 4 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: 300 Length of database: 295 Length adjustment: 26 Effective length of query: 274 Effective length of database: 269 Effective search space: 73706 Effective search space used: 73706 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 24 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