Align tryptophan permease (characterized)
to candidate BPHYT_RS07280 BPHYT_RS07280 amino acid permease
Query= CharProtDB::CH_091156 (592 letters) >FitnessBrowser__BFirm:BPHYT_RS07280 Length = 466 Score = 193 bits (490), Expect = 1e-53 Identities = 121/392 (30%), Positives = 199/392 (50%), Gaps = 14/392 (3%) Query: 73 FDT-----SNLKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQI 127 FDT L+R L L MIAIGG+IGTGLF+GSG AI GP V++ +AI Sbjct: 8 FDTIVEREKGLQRGLSTGQLSMIAIGGAIGTGLFLGSGFAIGFAGP-SVLVSYAIGALIA 66 Query: 128 IGTIHGLGEITVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQ 187 + + L E+TV P G+F Y ++ P F+V Y F + E+ A A+ ++ Sbjct: 67 LLLMGCLAEMTVAHPTSGSFGAYAEHYIAPWAGFLVRYAYWSSIVFAVGTEVTAIAVYMK 126 Query: 188 YWNSSIDPVIWVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIILCVVLICGGG 247 YW ++ W+ F A ++ IN V+ FG E+ FS +K + + GFI+L ++ G Sbjct: 127 YWFPAVPGWYWIVGFSAALIGINSVSVKVFGAVEYVFSMLKIVAIVGFILLGAYVVFGAP 186 Query: 248 PDHEFIGAKYWHDPGCLANGFPGVLSVLVVASYSLGGIEMTCLASGET-DP-KGLPSAIK 305 D A Y G G G+ ++V+ +S IEM +A+GE DP K + A + Sbjct: 187 ADSTIGFANYTSHGGFFPKGVWGMWVAVIVSIFSYLSIEMIAVAAGEARDPQKAITRAFR 246 Query: 306 QVFWRILFFFLISLTLVGFLVPYTNQNLLGGSSVDNSPFVIAIKLHHIKALPSIVNAVIL 365 +R++FF+L++L L+ +VP+ + D SPFV + H+ ++N VIL Sbjct: 247 ATMFRLVFFYLLTLALMLAIVPW------NAAGTDESPFVRVMAATHVPGAAGVINFVIL 300 Query: 366 ISVLSVGNSCIFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLVKSG 425 ++ LS NS ++ ++R + S++ G P G ++ G P+ + +++ LA ++ Sbjct: 301 VAALSAMNSQLYITTRMMFSLSRAGYAPRKLGALNGKGVPVAALWLSTIGIALATVLNVV 360 Query: 426 SMSEVFNWLMAIAGLATCIVWLSINLSHIRFR 457 F +M+++ WL I ++H FR Sbjct: 361 YPDASFVLMMSVSMFGAMFTWLMIFVTHFFFR 392 Lambda K H 0.326 0.141 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: 770 Number of extensions: 46 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: 592 Length of database: 466 Length adjustment: 35 Effective length of query: 557 Effective length of database: 431 Effective search space: 240067 Effective search space used: 240067 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 (21.6 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