Align L-arabinolactonase (EC 3.1.1.15) (characterized)
to candidate BPHYT_RS24170 BPHYT_RS24170 gluconolactonase
Query= reanno::ANA3:7024914 (300 letters) >FitnessBrowser__BFirm:BPHYT_RS24170 Length = 309 Score = 159 bits (403), Expect = 6e-44 Identities = 101/295 (34%), Positives = 148/295 (50%), Gaps = 20/295 (6%) Query: 19 LGEGVLWDDLHQSIWWTDILSSVIYRFHLASRSLETFPMPHRVGSFGLTAKPTTLIVAFD 78 +GE +W Q+++W DI + I R + S + +P +V + T L + Sbjct: 22 VGESPVWRAAEQALYWVDIPAQKIVRLRIDSGERSEWLLPEKVACIAFDHRGTVL-AGCE 80 Query: 79 IGIAIYDIEDQSLTW---------LAQPESHFAGNRFNDGRIDRQGRFWAGTMVEQRDTL 129 G+ + + + LA P+ RFNDGR DRQGRFWAGTMV+ Sbjct: 81 TGLFALTLTESAANGEAVQVTGRKLAAPDFACDDMRFNDGRCDRQGRFWAGTMVQDMAAA 140 Query: 130 QQTAALYCLDEKGHCHQHLT-NLEISNGLCWSVDGRTLYHADSP--KHQIYQYDFDIEQG 186 + ALY DE+G + L NGL WS DG T+Y +DS + QI+ +D+DIE G Sbjct: 141 KPAGALYRFDERGMLSAPVVEELITQNGLAWSPDGATMYLSDSHPLRRQIWAFDYDIESG 200 Query: 187 LLSRKRLFASTSHHI-FPDGSDVDAAGYLWNAQWGGGQVVRYRPDGEVDLILKLPVTHPT 245 +R+FA + H PDG+ VDA G W G ++R+ P+G++D + +P P Sbjct: 201 EPRNRRVFADLNQHAGRPDGAAVDADGCYWICANDAGLLLRFTPEGKLDRQIAVPAIKPA 260 Query: 246 SIAFGGEKRDLLIVTSAKHSLDASQLDQEPQAGDVFIYPLQGIYGVNSPRFCGQL 300 AFGG + D L VTS + + +AS+ D G +F GI G+ P F G+L Sbjct: 261 MCAFGGRELDTLFVTSIRPAANASEHD-----GHLFAV-RPGITGLPEPEFAGEL 309 Lambda K H 0.322 0.139 0.441 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: 284 Number of extensions: 16 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: 300 Length of database: 309 Length adjustment: 27 Effective length of query: 273 Effective length of database: 282 Effective search space: 76986 Effective search space used: 76986 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: 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