Align D-serine/D-alanine/glycine transporter (characterized)
to candidate 14258 b0112 aromatic amino acid transporter (NCBI)
Query= SwissProt::P0AAE0 (470 letters) >FitnessBrowser__Keio:14258 Length = 457 Score = 358 bits (919), Expect = e-103 Identities = 182/450 (40%), Positives = 278/450 (61%), Gaps = 5/450 (1%) Query: 17 QSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGE 76 + L+R L NRHIQLIA+GGAIGTGLF+GS I AGP II Y I GF+ F +MR +GE Sbjct: 9 EQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMRQLGE 68 Query: 77 LLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPDLSDW 136 +++ SFS FA G +AG+ +GW YW +V+ MA++ A+ Y QFW+P++ W Sbjct: 69 MVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPEIPTW 128 Query: 137 VASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGVEAS 196 V++ V++ +NL VK+FGEMEFWFA+IK++A+V++I+ G ++ F G +A+ Sbjct: 129 VSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLL---FSGNGGPQAT 185 Query: 197 FAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPIRI 256 ++LW+ GG+ P G +G I +F+F G+ELVG TAAE +PE+S+P+A N + RI Sbjct: 186 VSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIYRI 245 Query: 257 IMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSGVF 316 ++FY+ +L V++S+ PW+ V + SPFV +F +G A+ +N VVLT+A S NS V+ Sbjct: 246 LIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYNSCVY 305 Query: 317 STSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTMIT 376 SRMLFGLAQ+G APKA A + KR VP + S + V++ Y+ P M Sbjct: 306 CNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGLLMAL 365 Query: 377 TVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFVVVLLTLE 436 VSA++ W +I +++ +R+ + + + L L W+C+ F V+V++ + Sbjct: 366 VVSALVIN--WAMISLAHMKFRRAKQEQGVVTRFPALLYPLGNWICLLFMAAVLVIMLMT 423 Query: 437 DDTRQALLVTPLWFIALGLGWLFIGKKRAA 466 ++ + P+W I LG+G+LF K A Sbjct: 424 PGMAISVYLIPVWLIVLGIGYLFKEKTAKA 453 Lambda K H 0.329 0.141 0.440 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: 612 Number of extensions: 32 Number of successful extensions: 3 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: 470 Length of database: 457 Length adjustment: 33 Effective length of query: 437 Effective length of database: 424 Effective search space: 185288 Effective search space used: 185288 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 (21.8 bits) S2: 51 (24.3 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