Align L-alanine and D-alanine permease (characterized)
to candidate BWI76_RS01140 BWI76_RS01140 amino acid permease
Query= reanno::WCS417:GFF1065 (472 letters) >FitnessBrowser__Koxy:BWI76_RS01140 Length = 461 Score = 475 bits (1222), Expect = e-138 Identities = 232/450 (51%), Positives = 323/450 (71%), Gaps = 3/450 (0%) Query: 12 TAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMR 71 T + L+R L RHI L+ALG IGVGLF+G+A ++ AGP+++L+YII GL + IMR Sbjct: 2 TEKKAELQRGLEARHIELIALGGTIGVGLFMGAASTLKWAGPSVLLAYIIAGLFVFFIMR 61 Query: 72 ALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGVWFPD 131 ++GEM PV GSF+ YA Y+ P G+LT W+YWF+W+ ++EITA+ VY+ WFP+ Sbjct: 62 SMGEMLFLEPVTGSFAVYAHRYMSPFFGYLTAWSYWFMWMAVGISEITAIGVYVQFWFPE 121 Query: 132 TPRWIWALAALISMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGV 191 +WI AL A+ + NL AV+ +GE EFWFA+IK+ TII M++ G+G+I FGFGN G Sbjct: 122 MAQWIPALIAVGLVALANLAAVRLYGEIEFWFAMIKVTTIIVMIVVGLGVIFFGFGNGGH 181 Query: 192 ALGISNLWAHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPSAIGSVF 251 A+G NL HGGF G +G L +L +V+ +Y GVE+IG+TAGEAKNPQ T+ SA+G V Sbjct: 182 AIGFGNLTEHGGFFAGGWKGFLTALCIVVASYQGVELIGITAGEAKNPQVTLRSAVGKVL 241 Query: 252 WRILLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNG 311 WRIL+FYVGA+FVI++I+PW++IG+ GSPFV+TF ++GI AAGIINFVV+TAALS CN Sbjct: 242 WRILIFYVGAIFVIVTIFPWDQIGSNGSPFVLTFAKIGITAAAGIINFVVLTAALSGCNS 301 Query: 312 GIFSTGRMLYSLAQNGQAPATFAKTSSNGVPRKALLLSIFALLLGVLLNYLV--PEKVFV 369 G++S GRMLY+LA+N Q PA AK S NGVP + LSI LL+G LNY++ P++VFV Sbjct: 302 GMYSCGRMLYALARNRQLPAAIAKVSRNGVPSAGVALSILILLVGSCLNYIIPNPQRVFV 361 Query: 370 WVTSIATFGAIWTWLMILLAQLKFRKSLSPAEQAGLKYRMWLYPVSSYLALAFLLLVVGL 429 +V S + + W +IL++QL+FR A A +R L+P ++YL +AFL+ V+ Sbjct: 362 YVYSASVLPGMVPWFVILISQLRFRLVHKEA-MASHPFRSLLFPWANYLTMAFLVCVLIG 420 Query: 430 MAYFPDTRIALYVGPVFLVLLTVLFYVFKL 459 M + DTR++L+VG +FL +T+++ VF L Sbjct: 421 MGFNDDTRMSLFVGIIFLAAVTLIYKVFGL 450 Lambda K H 0.328 0.142 0.447 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: 696 Number of extensions: 34 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: 472 Length of database: 461 Length adjustment: 33 Effective length of query: 439 Effective length of database: 428 Effective search space: 187892 Effective search space used: 187892 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (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