Align Amino acid permease-associated region (characterized, see rationale)
to candidate N515DRAFT_4366 N515DRAFT_4366 Amino acid transporter
Query= uniprot:B2SZ32 (555 letters) >FitnessBrowser__Dyella79:N515DRAFT_4366 Length = 554 Score = 704 bits (1816), Expect = 0.0 Identities = 338/518 (65%), Positives = 418/518 (80%), Gaps = 8/518 (1%) Query: 27 SSIQRNIGPFALMLTGLGSIIGSGWLFGAWKAAKIAGPAAVCAWVIGAVVILAIALTYAE 86 S I+R++GPFALMLTGLGSIIGSGWLFGAW+AA +AGP A+ AWV+GA +I+ IALTYAE Sbjct: 5 SPIRRDVGPFALMLTGLGSIIGSGWLFGAWRAAGLAGPGAIWAWVLGAAIIMTIALTYAE 64 Query: 87 LGAMFPESGGMVRYARYSHGALVGFISAWANWIAIVSVIPIEAEASIQYMSTWPYPWAHA 146 LGAMFPESGGMVRY+ YSHG+LVGFI AWANWIAIVSVIP+EAEAS+QYM++WP+ WA Sbjct: 65 LGAMFPESGGMVRYSHYSHGSLVGFIGAWANWIAIVSVIPVEAEASVQYMASWPWKWAQD 124 Query: 147 LFVD-----GSLTTNGLLLSAALVIIYFMLNYWGVKLFARANSAITIFKFLIPGATILGL 201 L++ G L+ GL ++A LVI+YF+LN+W VKLFAR+N+AITIFK ++P AT + L Sbjct: 125 LYMHMPDGHGELSEPGLGIAAVLVIVYFLLNFWSVKLFARSNTAITIFKLIVPAATGIAL 184 Query: 202 MFAGFHKENF--GEASTFAPYGWSAVLTAVSTSGIVFAFNGFQSPINLAGEARNPAKSVP 259 + +GFH ENF G +AVLTAV+T+GIVF+FNGFQSP+NLAGEA NP KS+P Sbjct: 185 IASGFHSENFSVGVHGDAHAIDLAAVLTAVATAGIVFSFNGFQSPVNLAGEAHNPGKSIP 244 Query: 260 FAVIGSILLALVIYVLLQIAYIGAVNPSDVMK-GWSHFNFASPFAELAIALNLNWLAILL 318 FAVIGSI+LA ++YV+LQ+AY+G+V P + K GW +F SPFAELAI +NL+WLA+LL Sbjct: 245 FAVIGSIVLATIVYVILQLAYLGSVPPDLLAKAGWHGIDFRSPFAELAIIVNLHWLAMLL 304 Query: 319 YVDAFVSPSGTGTTYMATTSRMIYAMERNNTMPKMFGNVHPFYGVPRQAMWFNLLVSFIF 378 YVDAF+SPSGTG TY ATT+RMIY MERN T+PK+ G +HP +G+PR AMWFNL VS++F Sbjct: 305 YVDAFISPSGTGITYTATTARMIYGMERNGTLPKILGRIHPKWGIPRPAMWFNLAVSYLF 364 Query: 379 LFFFRGWSSLAAVISVATVISYLTGPISLMALRRAATDLERPLHIPGMKIIAPFAFVCAS 438 LF FRGW +LAAVISVAT+ISYLTGP+S M LRR A +L RPL I G+ I+A AF+ A+ Sbjct: 365 LFKFRGWGTLAAVISVATIISYLTGPVSAMTLRRTAPNLHRPLRIAGLPILAGIAFIMAT 424 Query: 439 LILYWAKWPLTGEIILLMVVALPVYFYFQAKSGFAGWGRDLKAAWWLVAYLPVMAILSLI 498 +LYWAKWPLTGEIILLMVVALPVYF++Q K+G+ +GR LK AWWL+ YLP +A++S Sbjct: 425 ELLYWAKWPLTGEIILLMVVALPVYFFYQFKAGWHDFGRQLKGAWWLIFYLPTLALVSWA 484 Query: 499 GSKQFGGHDLIPYGWDMVVVIAFSLVFYYWGVTSGYRS 536 GS FGG + YG D+ VV LVFY WGV SG+R+ Sbjct: 485 GSTMFGGKGYLSYGMDLAVVAVVGLVFYLWGVKSGWRT 522 Lambda K H 0.326 0.139 0.445 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: 1274 Number of extensions: 64 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: 555 Length of database: 554 Length adjustment: 36 Effective length of query: 519 Effective length of database: 518 Effective search space: 268842 Effective search space used: 268842 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 (21.7 bits) S2: 53 (25.0 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