Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate AO353_24520 AO353_24520 short-chain dehydrogenase
Query= reanno::pseudo5_N2C3_1:AO356_20240 (272 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24520 Length = 249 Score = 122 bits (307), Expect = 6e-33 Identities = 90/251 (35%), Positives = 132/251 (52%), Gaps = 12/251 (4%) Query: 19 LKDKVVLLTGAA--QGIGEAIVAAFASQQARLVISDIQAQKVEAVAAHWRERGADVHALQ 76 L+ KV ++TGAA +GIG A FA Q AR+VI D+ AA E + A Sbjct: 3 LQGKVAIITGAASARGIGRATATTFAQQGARVVILDLDESAARDAAASLGEGHLGIGANV 62 Query: 77 ADVSKQQDLQAMARRAVELHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYG 136 AD + Q QA+A+ +E GRID+L+N AG+ L++ D+ + + L G Sbjct: 63 AD--ELQVRQAVAK-IIEHFGRIDILINNAGITQPLKTLDIRPSDYDKVLDVSLRGTLLM 119 Query: 137 CKAVLPQMIEQGVGSIINIASVHSSH--IIPGCFPYPVAKHGLLGLTRALGIEYAPKGVR 194 +AV+P M +Q GSI+ ++SV + I G Y AK G+LGL +A+ E P VR Sbjct: 120 SQAVIPTMRQQSSGSIVCMSSVSAQRGGGIFGGPHYSAAKAGVLGLAKAMARELGPDKVR 179 Query: 195 VNAIAPGYIETQLNVDYWNGFADPHAERQRALDLHPPRRVGQPIEVAMTAVFLASDEAPF 254 VN+IAPG I T + G R +D P R+G+ +VA A+FLASD + + Sbjct: 180 VNSIAPGLIHTDI-----TGGLMQDERRHAIIDGIPLGRLGEAQDVANAALFLASDLSSY 234 Query: 255 INASCITIDGG 265 + + ++GG Sbjct: 235 LTGITLDVNGG 245 Lambda K H 0.321 0.137 0.419 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: 143 Number of extensions: 11 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: 272 Length of database: 249 Length adjustment: 24 Effective length of query: 248 Effective length of database: 225 Effective search space: 55800 Effective search space used: 55800 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 (21.9 bits) S2: 47 (22.7 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