Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate 350014 BT0486 altronate hydrolase (NCBI ptt file)
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >FitnessBrowser__Btheta:350014 Length = 496 Score = 160 bits (405), Expect = 8e-44 Identities = 122/410 (29%), Positives = 190/410 (46%), Gaps = 38/410 (9%) Query: 9 TLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLDAFDDPSAEREPPVHLIG 68 T +GY R +G G+RN + + V C + + ++ R E + ++ Sbjct: 109 TFKGYRRKNGDVGVRNEIWIIPTVGCVNGIIGQLAEGLRR--------ETEGKGVDAIVA 160 Query: 69 FP---GCYPNG----YAEKMLERLTTHPNVGAVLFVSLGCESMNKHYLVDVVRASGRPVE 121 FP GC G +K+L + HPN GAVL V LGCE+ + + + Sbjct: 161 FPHNYGCSQLGDDHENTKKILRDMVLHPNAGAVLIVGLGCENNQPDVFREFLGDYDQDRV 220 Query: 122 VLTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGTSGITANP 181 + +K G + G+D +R + + ++ + LSEL +G CGGSDG SGITANP Sbjct: 221 KFMVTQKVGDE--YEEGMDILRDLYAKASKDERTEVPLSELRVGLKCGGSDGFSGITANP 278 Query: 182 AVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVAKAARYYSILGH 241 +G D LI G T + E E+ G E + R L ++ V + Y+ L H Sbjct: 279 LLGMFSDFLIAQGGTSVLTEVPEMFGAETILMNRCENKDLFEQTVHLINDFKEYF--LSH 336 Query: 242 G-----SFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLYLLDVVPDG 296 G + + GN GG++T EEK+LG K G S + G++ G+ GL LL Sbjct: 337 GEPVGENPSPGNKAGGISTLEEKALGCTQKCGKSYVSGVMPYGERLQKKGLNLLSAPG-- 394 Query: 297 EPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPATYRNLSGDM 356 +D L A G H++LFTTGRG+ G+ + P +K+ N +N G + Sbjct: 395 ---------NDLVAATTLAASGCHMVLFTTGRGTPFGTFV-PTMKISTNSTLAKNKPGWI 444 Query: 357 DVDAGRILEGRGTLDEVGREVFEQTVAVSRGAASKSETLGHQEFILTYKT 406 D +AG I+E +++ E + V+ G +E G++E I +KT Sbjct: 445 DFNAGVIVENE-PMEKTCERFIEYVIKVASGEFVNNEKKGYRE-IAIFKT 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: 575 Number of extensions: 35 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: 496 Length adjustment: 33 Effective length of query: 398 Effective length of database: 463 Effective search space: 184274 Effective search space used: 184274 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