Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate PP_3601 PP_3601 galactarate dehydratase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >FitnessBrowser__Putida:PP_3601 Length = 517 Score = 156 bits (394), Expect = 2e-42 Identities = 123/399 (30%), Positives = 188/399 (47%), Gaps = 41/399 (10%) Query: 9 TLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLDAFDDPSAEREPPVH-LI 67 T EGY DG G RN++ + V+C V V + R L + P V ++ Sbjct: 116 TFEGYRNADGTVGTRNILGITTTVQCVTGVLEHAVKRIRNEL-------LPKYPNVDDVV 168 Query: 68 GFPGCYPNGYAE---------KMLERLTTHPNVGA-VLFVSLGCESMNKHYLVDVVRASG 117 Y G A + + L +PN+G L +SLGCE + V+ + Sbjct: 169 AITHSYGCGVAINARDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQAS---QVMHDND 225 Query: 118 RPVEV-----LTIQEKG-GTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGS 171 V++ +Q+ G I+ +D ++L +++ + SEL++G CGGS Sbjct: 226 PSVDLSDPWLYRLQDASLGFVEMIEQIMDLAETRLKKLDQRRRETVPASELILGMQCGGS 285 Query: 172 DGTSGITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVAK 231 D SGITANPA+G A D L+ AGAT +F E E+ + + +RA + D +V + Sbjct: 286 DAFSGITANPALGYAADLLVRAGATVLFSEVTEVRDAIYMLTSRAENQDVADALVREMDW 345 Query: 232 AARYY---SILGHGSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLY 288 RY + + GN GGL+ EKSLG+ KSG+ I G++ PG+ GL Sbjct: 346 YDRYLQQGAADRSANTTPGNKKGGLSNIVEKSLGSIVKSGSGAIQGVLGPGERANRKGLI 405 Query: 289 LLDVVPDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPAT 348 F SD +A G ++ +FTTGRG+ G A++PV+KVC Sbjct: 406 -----------FCATPASDFVCGTLQLAAGMNLHVFTTGRGTPYGLAMAPVVKVCTRSEL 454 Query: 349 YRNLSGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRG 387 + +D+DAGRI GR T++E+G E+F + V+ G Sbjct: 455 AQRWPDLIDIDAGRIASGRSTIEELGWELFHYYLDVASG 493 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: 574 Number of extensions: 31 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: 517 Length adjustment: 33 Effective length of query: 398 Effective length of database: 484 Effective search space: 192632 Effective search space used: 192632 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