Align tryptophan permease (characterized)
to candidate 14258 b0112 aromatic amino acid transporter (NCBI)
Query= CharProtDB::CH_091156 (592 letters) >FitnessBrowser__Keio:14258 Length = 457 Score = 229 bits (583), Expect = 2e-64 Identities = 135/398 (33%), Positives = 213/398 (53%), Gaps = 9/398 (2%) Query: 69 LDGSFDTSNLKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQII 128 ++G LKR LK RH+ +IA+GG+IGTGLF+GS I GP G+++G+AIAG Sbjct: 2 MEGQQHGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGP-GIILGYAIAGFIAF 60 Query: 129 GTIHGLGEITVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQY 188 + LGE+ V PV G+F+++ ++ F Y + + V E+ A +Q+ Sbjct: 61 LIMRQLGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQF 120 Query: 189 WNSSIDPVIWVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIILCVVLICGGGP 248 W I + A+F+ VI +INL V+ FGE EF F+ IK I V II L+ G Sbjct: 121 WYPEIPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSGNG 180 Query: 249 DHEFIGAKYWHDPGCLANGFPGVLSVLVVASYSLGGIEMTCLASGETD--PKGLPSAIKQ 306 + + W G L +GF G++ ++ + +S GG+E+ + + E D + +P A Q Sbjct: 181 GPQATVSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQ 240 Query: 307 VFWRILFFFLISLTLVGFLVPYTNQNLLGGSSVDNSPFVIAIKLHHIKALPSIVNAVILI 366 V +RIL F++ SL ++ L+P+T + D SPFV+ + + +N V+L Sbjct: 241 VIYRILIFYIGSLAVLLSLMPWTR------VTADTSPFVLIFHELGDTFVANALNIVVLT 294 Query: 367 SVLSVGNSCIFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLVKSGS 426 + LSV NSC++ +SR L +A QG P +D+ G P+ I+ ++L L L+ + Sbjct: 295 AALSVYNSCVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLA 354 Query: 427 MSEVFNWLMAIAGLATCIVWLSINLSHIRFRLAMKAQG 464 F LMA+ A I W I+L+H++FR A + QG Sbjct: 355 PESAFGLLMALVVSALVINWAMISLAHMKFRRAKQEQG 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: 734 Number of extensions: 45 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: 457 Length adjustment: 35 Effective length of query: 557 Effective length of database: 422 Effective search space: 235054 Effective search space used: 235054 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