Align tryptophan permease (characterized)
to candidate H281DRAFT_04042 H281DRAFT_04042 aromatic amino acid:proton symporter, AAT family
Query= CharProtDB::CH_091156 (592 letters) >FitnessBrowser__Burk376:H281DRAFT_04042 Length = 506 Score = 215 bits (547), Expect = 4e-60 Identities = 140/429 (32%), Positives = 223/429 (51%), Gaps = 12/429 (2%) Query: 69 LDGSFDTSNLKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQII 128 LD + LKR LK RH+ +IA+GG+IGTGLF+GS + GP +++G+AI G Sbjct: 46 LDNALQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGP-SMILGYAIGGVIAF 104 Query: 129 GTIHGLGEITVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQY 188 + LGE+ + PV G+F+++ ++ F+ Y + + V E+ A V Y Sbjct: 105 MIMRQLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHY 164 Query: 189 WNSSIDPVIWVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIILCVVLICGGGP 248 W + + + +A I +INL V+ +GE EF F+ IK + V G I+ L+ G Sbjct: 165 WWPGVPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHG 224 Query: 249 DHEFIGAKYWHDPGCLANGFPGVLSVLVVASYSLGGIEMTCLASGETD--PKGLPSAIKQ 306 + + W G +GF G+ ++L V +S GG+E+ + + E D K +P A+ Q Sbjct: 225 GPQASISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQ 284 Query: 307 VFWRILFFFLISLTLVGFLVPYTNQNLLGGSSVDNSPFVIAIKLHHIKALPSIVNAVILI 366 V +RIL F++ SL ++ L P+ N+ GG SPFV+ +++N V+L Sbjct: 285 VIYRILIFYICSLAVLLSLYPW-NEVAAGG-----SPFVMIFSQIGSTLTANVLNVVVLT 338 Query: 367 SVLSVGNSCIFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLVKSGS 426 + LSV NS ++A+SR L +A QG P +DR G P + I ++L +V Sbjct: 339 AALSVYNSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLI 398 Query: 427 MSEVFNWLMAIAGLATCIVWLSINLSHIRFRLAMKAQGKSLDELEFVSAVGIW-GSAYSA 485 +E LMA+ A + W I+L+H++ R AM A G++L F V W A+ A Sbjct: 399 PAEALGLLMALVVAALVLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMA 458 Query: 486 LINCLILIA 494 LI L+++A Sbjct: 459 LI--LVILA 465 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: 795 Number of extensions: 44 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: 506 Length adjustment: 36 Effective length of query: 556 Effective length of database: 470 Effective search space: 261320 Effective search space used: 261320 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: 53 (25.0 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