Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate Pf1N1B4_1107 D-galactarate dehydratase (EC 4.2.1.42)
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1107 Length = 517 Score = 149 bits (375), Expect = 3e-40 Identities = 126/416 (30%), Positives = 192/416 (46%), Gaps = 42/416 (10%) Query: 4 AAQQP----TLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLDAFDDPSAE 59 AAQ P T EGY DG G RN++ + V+C V V + ++ L Sbjct: 107 AAQAPLEGFTFEGYRNADGTVGTRNILGITTTVQCVTGVLDHAVKRIKDEL-------LP 159 Query: 60 REPPVH-LIGFPGCYPNGYAE---------KMLERLTTHPNVGA-VLFVSLGCESMNKHY 108 + P V ++ Y G A + + L +PN+G L +SLGCE + Sbjct: 160 KYPNVDDVVALTHSYGCGVAITATDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQAGQ 219 Query: 109 LVDVVRAS---GRPVEVLTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIG 165 ++ +S P G I+ + ++L +++ + SEL++G Sbjct: 220 VMHENDSSVDLSDPWLYRLQDSSHGFTEMIEQIMALAETRLKKLDLRRRETVPASELILG 279 Query: 166 TICGGSDGTSGITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEI 225 CGGSD SGITANPA+G A D L+ AGAT +F E E+ + + +RA + E+ Sbjct: 280 MQCGGSDAFSGITANPALGYASDLLLRAGATVMFSEVTEVRDAIYLLTSRAETEEVAQEL 339 Query: 226 VACVAKAARYYS---ILGHGSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIP 282 V + RY + + GN GGL+ EKSLG+ KSG+S I G++ PG+ Sbjct: 340 VREMDWYDRYLAKGEADRSANTTPGNKKGGLSNIVEKSLGSIVKSGSSAINGVLGPGERF 399 Query: 283 PTGGLYLLDVVPDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKV 342 GL F SD +A G ++ +FTTGRG+ G A++PV+KV Sbjct: 400 KRKGLI-----------FCATPASDFVCGTLQLAAGMNLHVFTTGRGTPYGLAMAPVVKV 448 Query: 343 CANPATYRNLSGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGAASKSETLGHQ 398 + +D+DAGRI GR +++E+G E+F + V+ G K +T Q Sbjct: 449 STRTELAQRWPDLIDIDAGRIATGRASIEELGWELFHYYLDVASG---KKQTWAEQ 501 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: 573 Number of extensions: 25 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