Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate WP_011800998.1 PNAP_RS07975 galactarate dehydratase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >NCBI__GCF_000015505.1:WP_011800998.1 Length = 532 Score = 171 bits (434), Expect = 4e-47 Identities = 139/429 (32%), Positives = 206/429 (48%), Gaps = 60/429 (13%) Query: 1 MPVAAQQP---------TLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLD 51 +P+A +P T EGY DG G RN++A+ V+C V V + ++ L Sbjct: 98 LPIATVKPEPLPPLEGYTFEGYRNADGSVGSRNILAITTTVQCVAGVVEFAVKRIKDEL- 156 Query: 52 AFDDPSAEREPPVH-LIGFPGCYPNGYAE---------KMLERLTTHPNVGA-VLFVSLG 100 R P V ++G Y G A + L +T +PN G V+ VSLG Sbjct: 157 ------LPRFPNVDDVVGLEHSYGCGVAIDAPDAIIPIRTLRNITLNPNFGGEVMVVSLG 210 Query: 101 CES--------------MNKHYLVDVVRASGRPVEVLTIQEKG--GTRSTIQYGVDWIRG 144 CE M++ + DV + P++V+ +Q + G S I + Sbjct: 211 CEKLQPERLLPPGTIPIMDERNVADVGVTAEAPLDVVCLQSEQHVGFMSMIDSIMSAAEL 270 Query: 145 AREQLAAQQKVPMALSELVIGTICGGSDGTSGITANPAVGRAFDHLIDAGATCIFEETGE 204 E+L A+++ + SELV+G CGGSD SG+TANPAVG D L+ AGAT +F ET E Sbjct: 271 HLERLDARRRETVPASELVVGVQCGGSDAFSGVTANPAVGFCTDLLVRAGATVMFSETTE 330 Query: 205 LVGCEFHMKTRAARPALGDEIVACVAKAARYYSILGHG------SFAVGNADGGLTTQEE 258 + + RA P + + A + + A Y + L G + GN GGL+ E Sbjct: 331 VRDGIDQLTARATTPEVAE---AMIREMAWYDAYLEKGRVDRSANTTPGNKKGGLSNIVE 387 Query: 259 KSLGAYAKSGASPIVGIIKPGDIPPTGGLYLLDVVPDGEPRFGFPNISDNAEIGELIACG 318 K++G+ KSG++PI G++ PG+ GL L F SD +A G Sbjct: 388 KAMGSIVKSGSAPISGVLSPGEKVRQKGLKGL--------VFAATPASDFICGTLQLAAG 439 Query: 319 AHVILFTTGRGSVVGSAISPVIKVCANPATYRNLSGDMDVDAGRILEGRGTLDEVGREVF 378 ++ +FTTGRG+ G A PVIKV R MD++AGRI +G T+++VGRE+F Sbjct: 440 INLHVFTTGRGTPYGLAEVPVIKVATRTDLARRWHDLMDINAGRIADGDATIEDVGRELF 499 Query: 379 EQTVAVSRG 387 + + V+ G Sbjct: 500 QFMLDVASG 508 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: 43 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: 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