Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate RR42_RS26650 RR42_RS26650 galactarate dehydratase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >FitnessBrowser__Cup4G11:RR42_RS26650 Length = 507 Score = 209 bits (533), Expect = 1e-58 Identities = 139/408 (34%), Positives = 203/408 (49%), Gaps = 36/408 (8%) Query: 5 AQQPTLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFR-EPLDAFDDPSAEREPP 63 A++ T G++R DGR G RN + + V C+ V R I F E + A+ + Sbjct: 105 AERATFMGFVRPDGRVGTRNFIGILSSVNCSATVIRHIADHFTPERMAAYPNVDGVAA-- 162 Query: 64 VHLIGFPGCYPNGYAE------KMLERLTTHPNVGAVLFVSLGCESMNKHYLVDVVR-AS 116 GC + +E + L HPN+ VL V LGCE L++ Sbjct: 163 --FAQSSGCGMSSPSEHFDVLRRTLAGYARHPNLAGVLIVGLGCERNQVAGLMESQGLVP 220 Query: 117 GRPVEVLTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGTSG 176 G V + +Q+ GGT +TIQ G+ I + P+ S L IG CGGSDG SG Sbjct: 221 GSHVRTMVMQDSGGTAATIQAGIRAIEAMLPGANTATRQPVPASHLKIGLECGGSDGFSG 280 Query: 177 ITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVA------ 230 I+ANPA+G A D L+ G T I ET E+ G E+ + RA P +G +++ +A Sbjct: 281 ISANPALGAAMDILVRHGGTAILSETPEIHGVEYMLTRRAVTPEVGQKLLDRLAWWERYT 340 Query: 231 --KAARYYSILGHGSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLY 288 + A++ ++GH GN GGL EKSLG+ K G +P+ + + + G Sbjct: 341 AGQNAQFNGVVGH-----GNQQGGLANIFEKSLGSAMKGGTTPLQAVYEYAEPIEQSGFV 395 Query: 289 LLDVVPDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPAT 348 +D P A G+ IA GA++I FTTGRGS+ GS +P IK+ +N Sbjct: 396 FMD----------SPGYDPVAATGQ-IASGANLICFTTGRGSMFGSKPAPTIKLASNTPM 444 Query: 349 YRNLSGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGAASKSETLG 396 Y L GDMD++ G +L+G T+DE+G+ +FE + + G +KSE LG Sbjct: 445 YTRLEGDMDINCGLVLDGELTVDEMGQRIFEHILEAASGHPTKSEALG 492 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: 589 Number of extensions: 36 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: 507 Length adjustment: 33 Effective length of query: 398 Effective length of database: 474 Effective search space: 188652 Effective search space used: 188652 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