Align tryptophan permease (characterized)
to candidate N515DRAFT_3653 N515DRAFT_3653 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= CharProtDB::CH_091156 (592 letters) >FitnessBrowser__Dyella79:N515DRAFT_3653 Length = 453 Score = 177 bits (450), Expect = 6e-49 Identities = 116/387 (29%), Positives = 189/387 (48%), Gaps = 11/387 (2%) Query: 75 TSNLKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQIIGTIHGL 134 T +L+R L PRH+ +A+G +IG GLF+GS AI GP V+ + G+ I + L Sbjct: 2 TQHLQRRLTPRHITFMALGMAIGAGLFLGSANAINLAGP-SVLFAYLFGGAMIFIIMRAL 60 Query: 135 GEITVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQYWNSSID 194 GE+ V PV G+F+ Y R+L P ++ Y + V E A + ++ W + Sbjct: 61 GEMAVHDPVAGSFSTYAHRYLGPFAGYLTGWNYWILMVGVGMAESTAVGIYMRQWFPELP 120 Query: 195 PVIWVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIILCVVLI-CGGGPDHEFI 253 IWV A+I +NL V+ +GE EF F+ IK +TV I+ +I G G + + Sbjct: 121 QWIWVFGSVAMIGGLNLMAVKVYGEMEFWFTLIKVVTVVLMILGGAGMIWLGWGNGGQPV 180 Query: 254 G-AKYWHDPGCLANGFPGVLSVLVVASYSLGGIEMTCLASGET--DPKGLPSAIKQVFWR 310 G A W G +GF G++ L V ++ GGIE +A+GE + +P A+ V WR Sbjct: 181 GLANLWSHGGWFPHGFTGMVLALPVVVFAFGGIETIGMAAGEAAQPERTIPRAVNSVLWR 240 Query: 311 ILFFFLISLTLVGFLVPYTNQNLLGGSSVDNSPFVIAIKLHHIKALPSIVNAVILISVLS 370 IL F++ +L ++ + P+ G SPFV I ++N V++ + LS Sbjct: 241 ILIFYVGALFVIMAIYPWDQLGTQG------SPFVTTFGKLGIPQAAGLINFVVITAALS 294 Query: 371 VGNSCIFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLVKSGSMSEV 430 NS F+ SR L S++ + P + G + G P+ ++ + ++ + Sbjct: 295 GFNSTTFSGSRMLYSLSTKAQAPAFLGQVSEHGVPVRAVLVTLACLVFGVVLNYLLPERI 354 Query: 431 FNWLMAIAGLATCIVWLSINLSHIRFR 457 F +M+I T W+ + ++H FR Sbjct: 355 FAMMMSILAFNTVWTWMMVLIAHYSFR 381 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: 749 Number of extensions: 47 Number of successful extensions: 6 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: 453 Length adjustment: 35 Effective length of query: 557 Effective length of database: 418 Effective search space: 232826 Effective search space used: 232826 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