Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate H281DRAFT_03532 H281DRAFT_03532 altronate hydrolase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >FitnessBrowser__Burk376:H281DRAFT_03532 Length = 441 Score = 802 bits (2071), Expect = 0.0 Identities = 398/432 (92%), Positives = 410/432 (94%), Gaps = 4/432 (0%) Query: 4 AAQQPTLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLDAFDDP----SAE 59 +AQQP L+GY R DGRKGIRNVVAVAYLVECAHHVAREIVT+FREPLDAF D SA Sbjct: 10 SAQQPMLQGYPRSDGRKGIRNVVAVAYLVECAHHVAREIVTEFREPLDAFGDTFADGSAG 69 Query: 60 REPPVHLIGFPGCYPNGYAEKMLERLTTHPNVGAVLFVSLGCESMNKHYLVDVVRASGRP 119 REPPVHLIGFPGCYPN YAEKMLERLTTHPNVGAVLFVSLGCESMNKHYLVDVVRASGRP Sbjct: 70 REPPVHLIGFPGCYPNEYAEKMLERLTTHPNVGAVLFVSLGCESMNKHYLVDVVRASGRP 129 Query: 120 VEVLTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGTSGITA 179 VEVLTIQEKGGTRSTIQYGVDW+RGAR+QLAAQ+KVPMALSELVIGTICGGSDGTSGITA Sbjct: 130 VEVLTIQEKGGTRSTIQYGVDWVRGARKQLAAQEKVPMALSELVIGTICGGSDGTSGITA 189 Query: 180 NPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVAKAARYYSIL 239 NPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARP LGD IVACVAKAARYYSIL Sbjct: 190 NPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPELGDAIVACVAKAARYYSIL 249 Query: 240 GHGSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLYLLDVVPDGEPR 299 GHGSFAVGNADGGLTTQEEKSLGAYAKSGASPI GI+KPGDIPPTGGLYLLDVVPDGEPR Sbjct: 250 GHGSFAVGNADGGLTTQEEKSLGAYAKSGASPIAGIVKPGDIPPTGGLYLLDVVPDGEPR 309 Query: 300 FGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPATYRNLSGDMDVD 359 FGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIK+CANPATYRNL+GDMDVD Sbjct: 310 FGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKICANPATYRNLAGDMDVD 369 Query: 360 AGRILEGRGTLDEVGREVFEQTVAVSRGAASKSETLGHQEFILTYKTFEPVGPACLPSSA 419 AGRILEGRGTLDEVGREVFEQTVAVS+GA SKSE LGHQEFILTYKTFEPVGPACLPS+ Sbjct: 370 AGRILEGRGTLDEVGREVFEQTVAVSQGAPSKSEMLGHQEFILTYKTFEPVGPACLPSNT 429 Query: 420 AAQHRVVAIEPH 431 A RVV + PH Sbjct: 430 VAPRRVVTVAPH 441 Lambda K H 0.318 0.137 0.408 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: 879 Number of extensions: 29 Number of successful extensions: 2 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: 431 Length of database: 441 Length adjustment: 32 Effective length of query: 399 Effective length of database: 409 Effective search space: 163191 Effective search space used: 163191 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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