Align tryptophan permease (characterized)
to candidate BPHYT_RS15500 BPHYT_RS15500 aromatic amino acid transporter
Query= CharProtDB::CH_091156 (592 letters) >FitnessBrowser__BFirm:BPHYT_RS15500 Length = 461 Score = 216 bits (551), Expect = 1e-60 Identities = 141/435 (32%), Positives = 225/435 (51%), Gaps = 15/435 (3%) Query: 78 LKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQIIGTIHGLGEI 137 LKR LK RH+ +IA+GG+IGTGLF+GS + GP +++G+AI G + LGE+ Sbjct: 10 LKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGP-SMILGYAIGGIIAFMIMRQLGEM 68 Query: 138 TVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQYWNSSIDPVI 197 + PV G+F+++ ++ F+ Y + + V E+ A + YW + + Sbjct: 69 VAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYIHYWWPGVPTWV 128 Query: 198 WVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIILCVVLICGGGPDHEFIGAKY 257 + +A+I +INL V+ +GE EF F+ IK + V G I+ L+ G + Sbjct: 129 SALVCFALINAINLANVKAYGETEFWFAIIKVVAVIGMIVFGGYLLISGHGGPQASITNL 188 Query: 258 WHDPGCLANGFPGVLSVLVVASYSLGGIEMTCLASGETD--PKGLPSAIKQVFWRILFFF 315 W G +GF G+ +L V +S GG+E+ + + E D K +P A+ QV +RIL F+ Sbjct: 189 WSHGGFFPHGFHGLFMMLAVIMFSFGGLELIGITAAEADQPQKSIPKAVNQVIYRILIFY 248 Query: 316 LISLTLVGFLVPYTNQNLLGGSSVDNSPFVIAIKLHHIKALPSIVNAVILISVLSVGNSC 375 + SLT++ L P+ N+ GG SPFV+ +++N V+L + LSV NS Sbjct: 249 ICSLTVLLSLYPW-NEVAAGG-----SPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSG 302 Query: 376 IFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLVKSGSMSEVFNWLM 435 ++A+SR L +A QG P +DR G P + I ++L +V +E LM Sbjct: 303 VYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLM 362 Query: 436 AIAGLATCIVWLSINLSHIRFRLAMKAQGKSLDELEFVSAVGIW-GSAYSALINCLILIA 494 A+ A + W I+L+H++ R AM A G++L F V W A+ ALI L+++A Sbjct: 363 ALVVAALVLNWALISLTHLKSRKAMVAAGETLVFKSFWFPVSNWICLAFMALI--LVILA 420 Query: 495 Q---FYCSLWPIGGW 506 S+W + W Sbjct: 421 MTPGLSVSVWLVPAW 435 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: 756 Number of extensions: 43 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: 461 Length adjustment: 35 Effective length of query: 557 Effective length of database: 426 Effective search space: 237282 Effective search space used: 237282 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