Align L-alanine and D-alanine permease (characterized)
to candidate BPHYT_RS07280 BPHYT_RS07280 amino acid permease
Query= reanno::WCS417:GFF1065 (472 letters) >FitnessBrowser__BFirm:BPHYT_RS07280 Length = 466 Score = 334 bits (857), Expect = 3e-96 Identities = 173/440 (39%), Positives = 265/440 (60%), Gaps = 5/440 (1%) Query: 18 LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77 L+R L + ++A+G IG GLFLGS AI AGP++++SY IG L L++M L EM Sbjct: 18 LQRGLSTGQLSMIAIGGAIGTGLFLGSGFAIGFAGPSVLVSYAIGALIALLLMGCLAEMT 77 Query: 78 VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGVWFPDTPRWIW 137 V +P +GSF YA+ Y+ P AGFL + YW + E+TA+AVYM WFP P W W Sbjct: 78 VAHPTSGSFGAYAEHYIAPWAGFLVRYAYWSSIVFAVGTEVTAIAVYMKYWFPAVPGWYW 137 Query: 138 ALAALISMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALGISN 197 + ++ IN ++VK FG E+ F+++KIV I+ ++ G ++ FG D +G +N Sbjct: 138 IVGFSAALIGINSVSVKVFGAVEYVFSMLKIVAIVGFILLGAYVV-FGAPADST-IGFAN 195 Query: 198 LWAHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPSAIGSVFWRILLF 257 +HGGF P GV G+ +++ + +F+YL +EMI + AGEA++PQK I A + +R++ F Sbjct: 196 YTSHGGFFPKGVWGMWVAVIVSIFSYLSIEMIAVAAGEARDPQKAITRAFRATMFRLVFF 255 Query: 258 YVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTG 317 Y+ L ++L+I PWN GT SPFV + AAG+INFV++ AALS+ N ++ T Sbjct: 256 YLLTLALMLAIVPWNAAGTDESPFVRVMAATHVPGAAGVINFVILVAALSAMNSQLYITT 315 Query: 318 RMLYSLAQNGQAPATFAKTSSNGVPRKALLLSIFALLLGVLLNYLVPEKVFVWVTSIATF 377 RM++SL++ G AP + GVP AL LS + L +LN + P+ FV + S++ F Sbjct: 316 RMMFSLSRAGYAPRKLGALNGKGVPVAALWLSTIGIALATVLNVVYPDASFVLMMSVSMF 375 Query: 378 GAIWTWLMILLAQLKFRKSLSPAEQAGLKYRMWLYPVSSYLALAFLLLVVGLMAYFPDTR 437 GA++TWLMI + FR + A L +RMW YP +S L ++ + + + R Sbjct: 376 GAMFTWLMIFVTHFFFRHR---HQGAPLAFRMWGYPGTSALGAGLMVSALVTTWFTREFR 432 Query: 438 IALYVGPVFLVLLTVLFYVF 457 + L +G F+V L V+++V+ Sbjct: 433 MTLVIGVPFIVSLLVVYFVW 452 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: 645 Number of extensions: 29 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: 472 Length of database: 466 Length adjustment: 33 Effective length of query: 439 Effective length of database: 433 Effective search space: 190087 Effective search space used: 190087 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