Align tryptophan permease (characterized)
to candidate GFF4632 PS417_23700 aromatic amino acid transporter
Query= CharProtDB::CH_091156 (592 letters) >FitnessBrowser__WCS417:GFF4632 Length = 467 Score = 201 bits (512), Expect = 4e-56 Identities = 131/402 (32%), Positives = 206/402 (51%), Gaps = 10/402 (2%) Query: 70 DGSFDTSNLKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQIIG 129 D + LKR LK RH+ +IA+GG+IGTGLF+GS + GP +++G+AIAG Sbjct: 3 DDMVNPVGLKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGP-SMILGYAIAGFIAFL 61 Query: 130 TIHGLGEITVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQYW 189 + LGE+ V PV G+F+++ ++ F+ Y + + V E+ A +Q+W Sbjct: 62 IMRQLGEMIVEEPVAGSFSHFAHKYWGGYAGFLAGWNYWVLYVLVGMAELTAVGKYIQFW 121 Query: 190 NSSIDPVIWVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIIL-CVVLICG-GG 247 I + +F+ + IN V+ FGE EF F+ IK + + G I+L C +L G GG Sbjct: 122 WPDIPTWVSALVFFVAVNLINTLNVKFFGETEFWFAIIKVVAIVGMIVLGCYLLFSGTGG 181 Query: 248 PDHEFIGAKYWHDPGCLANGFPGVLSVLVVASYSLGGIEMTCLASGETDP--KGLPSAIK 305 P + W G NG G+L + +S GG+E+ + + E K +P AI Sbjct: 182 PQASV--SNLWSHGGFFPNGGMGLLMSMAFIMFSFGGLELVGITAAEASEPRKVIPKAIN 239 Query: 306 QVFWRILFFFLISLTLVGFLVPYTN--QNL-LGGSSVDNSPFVIAIKLHHIKALPSIVNA 362 QV +RIL F++ +LT++ L P+ Q L G + SPFV L I+N Sbjct: 240 QVVYRILIFYVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFSLIGNDTAAHILNF 299 Query: 363 VILISVLSVGNSCIFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLV 422 V+L + LSV NS ++ +SR L +A QG P +++ G P+ + ++L +L +V Sbjct: 300 VVLTAALSVYNSGVYCNSRMLFGLAEQGDAPKSLMKLNKQGVPIRALAISALVTMLCVVV 359 Query: 423 KSGSMSEVFNWLMAIAGLATCIVWLSINLSHIRFRLAMKAQG 464 + L A+ + I W I+++HI+FR AM QG Sbjct: 360 NYVAPQSALELLFALVVASLMINWALISITHIKFRKAMGEQG 401 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: 728 Number of extensions: 41 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 592 Length of database: 467 Length adjustment: 35 Effective length of query: 557 Effective length of database: 432 Effective search space: 240624 Effective search space used: 240624 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