Align Gluconolactonase (characterized, see rationale)
to candidate Ac3H11_2081 Gluconolactonase (EC 3.1.1.17)
Query= uniprot:A0A165IRV8 (316 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2081 Length = 316 Score = 167 bits (422), Expect = 4e-46 Identities = 111/299 (37%), Positives = 148/299 (49%), Gaps = 23/299 (7%) Query: 35 LGEGVLWSVREQAVYWVDILGRELHRWDPATGAHQRWTFDEEISAIAERAHAPGFIVTLR 94 LGE W E+++YW DI G+ +H W P +G H++W E A A ++ LR Sbjct: 13 LGESPFWHPTEKSLYWCDIQGQAVHAWHPESGRHRQWRMPSEPGCCAPAADGQ-LVIGLR 71 Query: 95 RGFALFDPA------TDMAPRYLHQPEP-DRAGNRFNDGKCDAQGRFWAGSMDFACEAPT 147 GF L D A T + L PE D A R NDG+CD GRFWAGS+ AP Sbjct: 72 NGFYLLDTAKGSTDPTALTCLALLPPEQHDTAVLRLNDGRCDTAGRFWAGSVITPRTAPN 131 Query: 148 GALYRYDSD-----GSCTRHDDGFAVT-NGPTWSGTGQGAAMFFNATIEGNTYRYDSDLA 201 AL+ +D G RH G T NG +S + ++++ T E ++D D+ Sbjct: 132 AALWCLQADAASATGYRVRHMAGDNFTANGLAFSPDDR--TLYWSNTPEHRIDQFDFDVD 189 Query: 202 TGTVSNKTLWKHW------LPEDGLPDGMTTDAQGRLWIAHWGGWCVTCHDPVTAAELGR 255 TG +SN+ W + P G PDG D +G W+A + G CV P L R Sbjct: 190 TGAISNRRPWVQFDRKVEGQPYGGRPDGAAVDVEGNYWVAMYEGACVLQLSPAGEV-LQR 248 Query: 256 VRLPVSQVTTCAFGGADLRTLFISSARVGLTPEQLAAEPLAGALFAVDTDSLGLPAHPF 314 + +PV T FGG DLRTLFI+SAR G E+ AE AG+LF+V GLP + F Sbjct: 249 IEVPVQCPTMVCFGGEDLRTLFITSARAGRPVEEREAEVPAGSLFSVRVTVAGLPVNFF 307 Lambda K H 0.321 0.137 0.457 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: 416 Number of extensions: 29 Number of successful extensions: 6 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: 316 Length of database: 316 Length adjustment: 27 Effective length of query: 289 Effective length of database: 289 Effective search space: 83521 Effective search space used: 83521 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 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