Align L-rhamnose isomerase (EC 5.3.1.14) (characterized)
to candidate 353290 BT3764 L-rhamnose isomerase (NCBI ptt file)
Query= BRENDA::P32170 (419 letters) >FitnessBrowser__Btheta:353290 Length = 418 Score = 475 bits (1222), Expect = e-138 Identities = 225/415 (54%), Positives = 303/415 (73%), Gaps = 4/415 (0%) Query: 5 LEQAWELAKQRFAAVGIDVEEALRQLDRLPVSMHCWQGDDVSGFENPEGSLTGGIQATGN 64 +++A+E+A +R+AAVG+D E+ L+ + +S+HCWQ DDV+GFE G+L+GGIQATGN Sbjct: 7 IQKAYEIAVERYAAVGVDTEKVLKTMQDFHLSLHCWQADDVTGFEVQAGALSGGIQATGN 66 Query: 65 YPGKARNASELRADLEQAMRLIPGPKRLNLHAIYLE-SDTPVSRDQIKPEHFKNWVEWAK 123 YPGKARN ELRAD+ +A IPG RLNLH IY + V RDQ++PEHFK+W+EW K Sbjct: 67 YPGKARNIDELRADILKAASYIPGTHRLNLHEIYGDFQGKVVDRDQVEPEHFKSWIEWGK 126 Query: 124 ANQLGLDFNPSCFSHPLSADGFTLSHADDSIRQFWIDHCKASRRVSAYFGEQLGTPSVMN 183 + + LDFN + FSHP S D +LS+ D+ IRQFWI+H K R V+ G+ G P +MN Sbjct: 127 EHNMKLDFNSTSFSHPKSGD-LSLSNPDEGIRQFWIEHTKRCRAVAEEMGKAQGDPCIMN 185 Query: 184 IWIPDGMKDITVDRLAPRQRLLAALDEVISEKLNPAHHIDAVESKLFGIGAESYTVGSNE 243 +W+ DG KDITV+R+ R L +LD++ + + D +ESK+FGIG ESYTVGSN+ Sbjct: 186 LWVHDGSKDITVNRMKYRALLKDSLDQIFATEYKNMK--DCIESKVFGIGLESYTVGSND 243 Query: 244 FYMGYATSRQTALCLDAGHFHPTEVISDKISAAMLYVPQLLLHVSRPVRWDSDHVVLLDD 303 FY+GY SR + LD GHFHPTE ++DK+S+ +LYVP+L+LHVSRPVRWDSDHV ++DD Sbjct: 244 FYIGYGASRNKMVTLDTGHFHPTESVADKVSSLLLYVPELMLHVSRPVRWDSDHVTIMDD 303 Query: 304 ETQAIASEIVRHDLFDRVHIGLDFFDASINRIAAWVIGTRNMKKALLRALLEPTAELRKL 363 T + SEIVR +RVH GLD+FDASINRI A+VIG+R +K + RALLEP A+LR+ Sbjct: 304 PTMELFSEIVRCGALERVHYGLDYFDASINRIGAYVIGSRAAQKCMTRALLEPIAKLREY 363 Query: 364 EAAGDYTARLALLEEQKSLPWQAVWEMYCQRHDTPAGSEWLESVRAYEKEILSRR 418 EA G RLALLEE+K+LPW AVW+M+C +++ P G +++ + YE E+ S+R Sbjct: 364 EANGQGFQRLALLEEEKALPWNAVWDMFCLKNNVPVGEDFIAEIEKYEAEVTSKR 418 Lambda K H 0.319 0.134 0.410 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: 526 Number of extensions: 20 Number of successful extensions: 4 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: 419 Length of database: 418 Length adjustment: 32 Effective length of query: 387 Effective length of database: 386 Effective search space: 149382 Effective search space used: 149382 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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