Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate WP_053935921.1 WG78_RS01020 altronate dehydratase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >NCBI__GCF_001294205.1:WP_053935921.1 Length = 532 Score = 137 bits (344), Expect = 1e-36 Identities = 125/432 (28%), Positives = 181/432 (41%), Gaps = 50/432 (11%) Query: 6 QQPTLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPL--------------- 50 Q T EG +R DGR G N + LV C + + PL Sbjct: 107 QDATFEGVVRADGRVGTANYWLIFPLVFCENRNVEHLRNALEGPLGYATQDLAAYTLALL 166 Query: 51 -DAFDDPSAEREP-----PVHLIGFPGCYPNGYAE-----KMLERLTTHPNVGAVLFVSL 99 + P A P V +I G A+ K+L HPNV + SL Sbjct: 167 GEEMAAPRAVTRPFANVDGVRIITHAGGCGGTRADARSLCKVLAAYADHPNVAGITVFSL 226 Query: 100 GCESMNKHYLVDVVRASGRPVE---VLTIQEKGGTRSTIQYGV--DWIRGAREQLAAQQK 154 GC++ D ++A + ++ Q+K + + V D + G + A ++ Sbjct: 227 GCQNAQISMFQDALKARNPAFDKPCLIYEQQKWDSEDAMMKAVLQDTLNGLKAANAVTRQ 286 Query: 155 VPMALSELVIGTICGGSDGTSGITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKT 214 P+ LS L IG CGGSDG SG++ANPA+G D ++ G I E EL G E + Sbjct: 287 -PVPLSALKIGVKCGGSDGFSGLSANPAMGLVSDMVVAVGGGSILAEFPELCGVEASLIE 345 Query: 215 RAARPALGDEIVACVAKAARYYSILGHGSFAV----GNADGGLTTQEEKSLGAYAKSGAS 270 R + + +G SFA GN GL T KS GA K G S Sbjct: 346 RCQNDDDKRRFLGMMRDFEARAQAVG-TSFAANPSPGNIRDGLITDAIKSAGAAKKGGTS 404 Query: 271 PIVGIIKPGDIPPTGGLYLLDVVPDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGS 330 PIV ++ G+ GL LL P G D + ++A GA+V+LF+TG G+ Sbjct: 405 PIVSVLDYGEPAARPGLSLL-CTPGG----------DVESVTGIVASGANVVLFSTGLGT 453 Query: 331 VVGSAISPVIKVCANPATYRNLSGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGA-A 389 G+ I PV+K+ N L +D D G ++ G L EV +FE + + G Sbjct: 454 PTGNPIVPVLKIATNTRMATRLKDMIDFDCGPVISGT-PLPEVAEGLFEMVLQTAGGRYR 512 Query: 390 SKSETLGHQEFI 401 +K++ L +FI Sbjct: 513 AKADRLQQYDFI 524 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: 577 Number of extensions: 34 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 431 Length of database: 532 Length adjustment: 34 Effective length of query: 397 Effective length of database: 498 Effective search space: 197706 Effective search space used: 197706 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