Align S-adenosylmethionine permease GAP4; SAM permease; Amino-acid permease GAP4 (characterized)
to candidate BPHYT_RS07280 BPHYT_RS07280 amino acid permease
Query= SwissProt::Q59WB3 (607 letters) >FitnessBrowser__BFirm:BPHYT_RS07280 Length = 466 Score = 213 bits (541), Expect = 2e-59 Identities = 135/410 (32%), Positives = 215/410 (52%), Gaps = 20/410 (4%) Query: 72 MNLEEQGIDTSQLTPVERTIIASAKHPLARRLKARHLQMIAIGGSIGTGLFVGSGYALAN 131 M E++G DT I + L R L L MIAIGG+IGTGLF+GSG+A+ Sbjct: 1 MTQEQRGFDT----------IVEREKGLQRGLSTGQLSMIAIGGAIGTGLFLGSGFAIGF 50 Query: 132 GGPGAVLIGYVIVGYALLTVVNALGELSVQFPVSGSFNAFFSRFLEPSFGGTFGILYAAS 191 GP +VL+ Y I L ++ L E++V P SGSF A+ ++ P G Y +S Sbjct: 51 AGP-SVLVSYAIGALIALLLMGCLAEMTVAHPTSGSFGAYAEHYIAPWAGFLVRYAYWSS 109 Query: 192 WCISLPSELIAAAMTIQYWNTEVNPAVWVAVFWVVIVVINLFGVKGYGEMEYFLSIIKVL 251 ++ +E+ A A+ ++YW V W+ F ++ IN VK +G +EY S++K++ Sbjct: 110 IVFAVGTEVTAIAVYMKYWFPAVPGWYWIVGFSAALIGINSVSVKVFGAVEYVFSMLKIV 169 Query: 252 AVVGFIILGICITCGVGDQGYIG-GKYWHNPGAFNHGLKGVTSVFISAAFSFGGIELVAL 310 A+VGFI+LG + G IG Y + G F G+ G+ I + FS+ IE++A+ Sbjct: 170 AIVGFILLGAYVVFGAPADSTIGFANYTSHGGFFPKGVWGMWVAVIVSIFSYLSIEMIAV 229 Query: 311 AASETANPRISLPAAVKSTFWRIFIFYILTAIIIGCLVPYTNDDLLNGTGIAASPFVIAV 370 AA E +P+ ++ A ++T +R+ FY+LT ++ +VP+ N G SPFV + Sbjct: 230 AAGEARDPQKAITRAFRATMFRLVFFYLLTLALMLAIVPW------NAAGTDESPFVRVM 283 Query: 371 SQGGIRVVPHIMNAVVVIAVISVGNSSVYGCSRTLASLAVQGLLPKSMGYIDRGGRPLIA 430 + + ++N V+++A +S NS +Y +R + SL+ G P+ +G ++ G P+ A Sbjct: 284 AATHVPGAAGVINFVILVAALSAMNSQLYITTRMMFSLSRAGYAPRKLGALNGKGVPVAA 343 Query: 431 I-LFTSAIGLLGFLVVVDNEGDVFTWFFSICSLSSFFTWGAINVVHLRWR 479 + L T I L L VV + F S+ + FTW I V H +R Sbjct: 344 LWLSTIGIALATVLNVVYPDAS-FVLMMSVSMFGAMFTWLMIFVTHFFFR 392 Lambda K H 0.324 0.140 0.432 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: 752 Number of extensions: 37 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: 607 Length of database: 466 Length adjustment: 35 Effective length of query: 572 Effective length of database: 431 Effective search space: 246532 Effective search space used: 246532 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 52 (24.6 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