Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate RR42_RS00275 RR42_RS00275 galactarate dehydratase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >FitnessBrowser__Cup4G11:RR42_RS00275 Length = 522 Score = 207 bits (527), Expect = 6e-58 Identities = 146/416 (35%), Positives = 208/416 (50%), Gaps = 34/416 (8%) Query: 4 AAQQPTLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLDAFDDPSAEREPP 63 AAQ T +G R DG RN + + V C+ VAR I FR + P A P Sbjct: 115 AAQPATFDGIKRADGGVATRNYIGILTSVNCSATVARAIADHFRRDIH----PQALAAYP 170 Query: 64 -----VHLIGFPGCY--PNGYAEKMLERL----TTHPNVGAVLFVSLGCESMNKHYLVDV 112 V L GC P G +L+R HPN +VL + LGCE+ L+ Sbjct: 171 NVDGVVALTHGVGCAVDPQGEGLAVLQRTLGGYACHPNFASVLVIGLGCETNQISALLAT 230 Query: 113 VR-ASGRPVEVLTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGS 171 A ++ TIQ+ GGT TI +G++ I+ + A ++ P+ LV+G CGGS Sbjct: 231 QGLAHSDRLQTFTIQDTGGTTKTIAHGIELIKAMLPKANAVERQPVPAHHLVVGLQCGGS 290 Query: 172 DGTSGITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACV-- 229 DG SGI+ANP +G A D L+ G T I ET E+ G E + RA P +G ++VA + Sbjct: 291 DGYSGISANPVLGAAVDLLVRNGGTAILSETPEIYGAEHLLTRRAQTPEIGRKLVARIRW 350 Query: 230 --AKAARYYSILGHGSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGL 287 A R+ + + + A GN GGLTT EKSLG AK G++ + + + GL Sbjct: 351 WEAYCERHGASMDNNPSA-GNKAGGLTTVLEKSLGGIAKGGSTNLAEVYEYAQPVRVRGL 409 Query: 288 YLLDVVPDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPA 347 +D G+ IS + +A GA++I FTTGRGS G A SP +K+ N A Sbjct: 410 VFMDTP-------GYDPISATGQ----VAGGANLICFTTGRGSAYGCAPSPSVKLATNTA 458 Query: 348 TYRNLSGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGAASKSET--LGHQEFI 401 ++ S DMD++ G +L+G T+ E+G +FE + + G S+SE G EF+ Sbjct: 459 LWQRQSDDMDLNCGTVLDGSATIAELGAALFELMLDTASGKRSRSELHGYGQNEFV 514 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: 660 Number of extensions: 41 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: 522 Length adjustment: 33 Effective length of query: 398 Effective length of database: 489 Effective search space: 194622 Effective search space used: 194622 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