Align tryptophan permease (characterized)
to candidate GFF1065 PS417_05405 D-alanine/D-serine/glycine permease
Query= CharProtDB::CH_091156 (592 letters) >FitnessBrowser__WCS417:GFF1065 Length = 472 Score = 199 bits (507), Expect = 2e-55 Identities = 132/387 (34%), Positives = 195/387 (50%), Gaps = 11/387 (2%) Query: 78 LKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQIIGTIHGLGEI 137 LKR L RH+ ++A+G IG GLF+GS KAI GP +++ + I G I+ + LGE+ Sbjct: 18 LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGP-AIMLSYIIGGLAILVIMRALGEM 76 Query: 138 TVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQYWNSSIDPVI 197 V PV G+F+ Y +L P F+ Y W EI A A+ + W I Sbjct: 77 AVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGVWFPDTPRWI 136 Query: 198 WVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIILCVVLIC-GGGPDHEFIG-A 255 W + SINL V+ FGE EF F+ IK +T+ +I V +I G G D +G + Sbjct: 137 WALAALISMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALGIS 196 Query: 256 KYWHDPGCLANGFPGVLSVLVVASYSLGGIEMTCLASGE--TDPKGLPSAIKQVFWRILF 313 W G + NG GVL L + ++ G+EM L +GE K +PSAI VFWRIL Sbjct: 197 NLWAHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPSAIGSVFWRILL 256 Query: 314 FFLISLTLVGFLVPYTNQNLLGGSSVDNSPFVIAIKLHHIKALPSIVNAVILISVLSVGN 373 F++ +L ++ + P+ N +G SPFV+ + IK I+N V++ + LS N Sbjct: 257 FYVGALFVILSIYPW---NEIG---TQGSPFVMTFERLGIKTAAGIINFVVITAALSSCN 310 Query: 374 SCIFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLVKSGSMSEVFNW 433 IF++ R L S+A G P F G P ++ + LL L+ +VF W Sbjct: 311 GGIFSTGRMLYSLAQNGQAPATFAKTSSNGVPRKALLLSIFALLLGVLLNYLVPEKVFVW 370 Query: 434 LMAIAGLATCIVWLSINLSHIRFRLAM 460 + +IA WL I L+ ++FR ++ Sbjct: 371 VTSIATFGAIWTWLMILLAQLKFRKSL 397 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: 755 Number of extensions: 44 Number of successful extensions: 5 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: 472 Length adjustment: 35 Effective length of query: 557 Effective length of database: 437 Effective search space: 243409 Effective search space used: 243409 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