Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate SMc02776 SMc02776 altronate hydrolase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >FitnessBrowser__Smeli:SMc02776 Length = 501 Score = 210 bits (534), Expect = 9e-59 Identities = 147/409 (35%), Positives = 206/409 (50%), Gaps = 37/409 (9%) Query: 9 TLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFR-------EPLDAFDDPSAERE 61 T GY R DGR RN + + V C+ V R I + E +D F Sbjct: 106 TFLGYRRADGRAATRNYIGIVASVNCSTTVCRAIADEANRRILPKYEGIDGF-------V 158 Query: 62 PPVHLIGFPGCYPNGYAEKMLERLTT----HPNVGAVLFVSLGCESMNKHYLVDVVRASG 117 P VH G G G K L R H N G VL V LGCE +N+ L A G Sbjct: 159 PIVHDQGC-GMSSTGDGMKNLHRTLAGYARHANFGGVLMVGLGCE-VNQLTLYGQSGA-G 215 Query: 118 RPVEVLTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGTSGI 177 IQE GG+R +++ + + +++AA ++VP+ +SE+++G CGGSDG SGI Sbjct: 216 AEKRHFNIQEAGGSRRSVERALGILDEIAKEVAAARRVPIPVSEIIVGLQCGGSDGLSGI 275 Query: 178 TANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVAKAARYYS 237 TANPA+G A D L AG T I ET E+ G E +++RA + ++ +A Y + Sbjct: 276 TANPALGAAVDILAAAGGTAILSETSEIYGAEHLLRSRAVNETVAVKLDGLIAWWEDYVA 335 Query: 238 ILG---HGSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLYLLDVVP 294 + G + + GN GGLTT EKSLGA AK G SP+ + + GL +D Sbjct: 336 MHGASLDNNPSPGNKRGGLTTILEKSLGAVAKGGRSPLTAVYNYAERVTEPGLVFMDTP- 394 Query: 295 DGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPATYRNLSG 354 G+ +S + +A GA+VI FTTGRGS G +P IK+ +N A YR + Sbjct: 395 ------GYDPVSATGQ----VAGGANVIAFTTGRGSCFGCRPAPSIKLTSNTALYRAMEE 444 Query: 355 DMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGAASKSETLGH--QEFI 401 DMD+D G I G T+ ++GR +FE + + G +KSE G+ EF+ Sbjct: 445 DMDIDCGVIASGETTIADLGRGIFELIIETASGRKTKSELFGYGDNEFV 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: 632 Number of extensions: 33 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: 501 Length adjustment: 33 Effective length of query: 398 Effective length of database: 468 Effective search space: 186264 Effective search space used: 186264 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