Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate 17201 b3128 (D)-galactarate dehydrogenase (NCBI)
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >FitnessBrowser__Keio:17201 Length = 523 Score = 144 bits (364), Expect = 5e-39 Identities = 122/413 (29%), Positives = 184/413 (44%), Gaps = 47/413 (11%) Query: 9 TLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLDAFDDPSAEREPPVH-LI 67 T EGY DG G +N++ + V C V +V L + P V ++ Sbjct: 119 TFEGYRNADGSVGTKNLLGITTSVHCVAGVVDYVVKIIERDL-------LPKYPNVDGVV 171 Query: 68 GFPGCYPNGYAE---------KMLERLTTHPNVGA-VLFVSLGCESMNKHYLV----DVV 113 G Y G A + + ++ +PN G V+ + LGCE + L+ DV Sbjct: 172 GLNHLYGCGVAINAPAAVVPIRTIHNISLNPNFGGEVMVIGLGCEKLQPERLLTGTDDVQ 231 Query: 114 RASGRPVEVLTIQEKG--GTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGS 171 ++++Q++ G +S ++ + ++L +Q+ SELV+G CGGS Sbjct: 232 AIPVESASIVSLQDEKHVGFQSMVEDILQIAERHLQKLNQRQRETCPASELVVGMQCGGS 291 Query: 172 DGTSGITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVAK 231 D SG+TANPAVG A D L+ GAT +F E E+ + RA +G + + + Sbjct: 292 DAFSGVTANPAVGYASDLLVRCGATVMFSEVTEVRDAIHLLTPRAVNEEVGKRL---LEE 348 Query: 232 AARYYSILGHGSF------AVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTG 285 Y + L G + GN GGL EK+LG+ AKSG S IV ++ PG P Sbjct: 349 MEWYDNYLNMGKTDRSANPSPGNKKGGLANVVEKALGSIAKSGKSAIVEVLSPGQRPTKR 408 Query: 286 GLYLLDVVPDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCAN 345 GL + SD + +A G V +FTTGRG+ G PVIK+ Sbjct: 409 GLI-----------YAATPASDFVCGTQQVASGITVQVFTTGRGTPYGLMAVPVIKMATR 457 Query: 346 PATYRNLSGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGAASKSETLGHQ 398 MD++AG I G T++EVG ++F + V+ G K +T Q Sbjct: 458 TELANRWFDLMDINAGTIATGEETIEEVGWKLFHFILDVASG---KKKTFSDQ 507 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: 613 Number of extensions: 33 Number of successful extensions: 4 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: 523 Length adjustment: 33 Effective length of query: 398 Effective length of database: 490 Effective search space: 195020 Effective search space used: 195020 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