Align L-rhamnonate dehydratase (EC 4.2.1.90) (characterized)
to candidate AZOBR_RS26635 AZOBR_RS26635 mandelate racemase
Query= metacyc::MONOMER-16232 (397 letters) >FitnessBrowser__azobra:AZOBR_RS26635 Length = 393 Score = 147 bits (370), Expect = 7e-40 Identities = 113/361 (31%), Positives = 175/361 (48%), Gaps = 44/361 (12%) Query: 61 TLVVEIEAEDGTVGFAVTTGG-----EPAAYIVEKHLARFLEGRAPTDYEKIWDQMYFST 115 +L+V I +DG VG+ GG EP + LA L GR ++++ +Y Sbjct: 32 SLLVRITTDDGLVGWG--EGGQYGPAEPPESCIIDVLAPRLIGRRADQPVRVFEDLYSFC 89 Query: 116 QYYGRKGLVVNAISGVDLALWDLLGKLRQEPVYHLLGGAVRDELQFYATGA-RPD----- 169 + +G+KG + A+S +D+ALWDL GK PV+ L+GGA RD++ Y TG PD Sbjct: 90 RDFGQKGTYIEALSAIDIALWDLWGKSLNRPVHALMGGAFRDKVAAYGTGCYYPDYFRDT 149 Query: 170 ------------KAKEFGFIGGKMPLHHGPAEGVEGLKKNIAELADMRSKVGDDFWLMWD 217 + +E G K+ + G+ + ++I +A +R +G D +M D Sbjct: 150 PRMMAALAEEAQRYREAGLPAIKIKI------GLLPIAQDIERVALVRDVLGPDTLIMVD 203 Query: 218 CWMALDVDYATRLAIAAHDFGLKWIEEAISPDDYWGYQQLKRNVPKGMLVTTGEHEATRW 277 A + A R+ A F ++W EE + P+D GY++++ ++ + + GE E TR+ Sbjct: 204 ANHAYNTAGAIRIGRALERFDVRWFEEPVPPEDRQGYRRVRDSI--DVPIAGGECEYTRY 261 Query: 278 GFRMLMEMDCCDIIQPDVGWCGGVTELLKISALADAHGKMVVPH--GSSVYSYHFVITRH 335 GFR L+ C DI QPD+ GG TE KI AL AHG M VPH GS + + Sbjct: 262 GFRELLAGGCIDIAQPDLCCAGGFTEWQKILALTTAHGVMTVPHIWGSGIALAAALQALA 321 Query: 336 NSPFAEFLMMHPGPTEVVPMF-----HPQLLGEPVPDNGRMKVSALDKP---GFGVDLNP 387 +P + + P + PM H L + + DN + L P G GV+++P Sbjct: 322 TAPLVPYTALGV-PLQNEPMVEFDRTHNPLRDDLLIDNFTLVDGCLALPGGAGLGVEVDP 380 Query: 388 D 388 D Sbjct: 381 D 381 Lambda K H 0.322 0.140 0.451 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: 468 Number of extensions: 21 Number of successful extensions: 3 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: 397 Length of database: 393 Length adjustment: 31 Effective length of query: 366 Effective length of database: 362 Effective search space: 132492 Effective search space used: 132492 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 (21.9 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