Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate WP_043460616.1 H537_RS0130090 altronate dehydratase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >NCBI__GCF_000430725.1:WP_043460616.1 Length = 511 Score = 205 bits (522), Expect = 2e-57 Identities = 143/415 (34%), Positives = 209/415 (50%), Gaps = 38/415 (9%) Query: 9 TLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFR---------EPLDAFDDPSAE 59 T EG +R DGR RN + + V C+ VAR I F+ +PL AF + Sbjct: 105 TFEGIVRADGRVATRNYIGILSSVNCSATVARAIADHFKGHPRLPADAQPLAAFPNVDGV 164 Query: 60 REPPVHLIGFPGCYPN--GYAEKMLERL----TTHPNVGAVLFVSLGCESMNKHYLV--D 111 V L GC + G A K+L R HPN A+L + LGCE+ L+ + Sbjct: 165 ----VALTHGLGCATDSEGEALKLLRRTLGGYARHPNFAALLVIGLGCETNQIAGLMAQE 220 Query: 112 VVRASGRPVEVLTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGS 171 + AS + + V IQ+ GGT ++ +GV + + ++ P+ S L +G CGGS Sbjct: 221 GLEASTK-LHVFNIQDSGGTAQSVAHGVALVESLLPEANRARRQPVPASHLTVGLQCGGS 279 Query: 172 DGTSGITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVAK 231 DG SGI+ANPA+G A D L+ G + I ET E+ G E + RA P + ++ V Sbjct: 280 DGYSGISANPALGAAVDRLVTHGGSAILSETPEIYGGEHLLTRRAVSPEVAGRLIERVRW 339 Query: 232 AARYYS---ILGHGSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLY 288 RY + + + + GN GGLTT EKSLGA AKSG + +V +++ GL Sbjct: 340 WERYTARNDMQMDNNPSAGNKAGGLTTILEKSLGAIAKSGTTALVDVLEYAQPATARGLL 399 Query: 289 LLDVVPDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPAT 348 +D G+ +S + +A GA++I FTTGRGS G A +P +K N A Sbjct: 400 YMDTP-------GYDPVSATGQ----VAGGANLICFTTGRGSAYGCAPAPSLKFSTNTAL 448 Query: 349 YRNLSGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGAASKSE--TLGHQEFI 401 + D+D++ G I++G T+DEVG +F Q +A + G +KSE G EF+ Sbjct: 449 WNRQRDDIDLNCGGIVDGEATVDEVGEAIFRQMLATASGQKTKSEGHGYGQHEFV 503 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: 640 Number of extensions: 40 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: 431 Length of database: 511 Length adjustment: 33 Effective length of query: 398 Effective length of database: 478 Effective search space: 190244 Effective search space used: 190244 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 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