Align Aspartate-proton symporter; L-aspartate transporter (characterized)
to candidate N515DRAFT_4366 N515DRAFT_4366 Amino acid transporter
Query= SwissProt::O07002 (520 letters) >FitnessBrowser__Dyella79:N515DRAFT_4366 Length = 554 Score = 350 bits (899), Expect = e-101 Identities = 193/525 (36%), Positives = 299/525 (56%), Gaps = 21/525 (4%) Query: 1 MSKQGNFQKSMSLFDLILIGMGAIFGSAWLFAVSNVASKAGPSGAFSWILGGAIILLIGL 60 MS ++ + F L+L G+G+I GS WLF A AGP ++W+LG AII+ I L Sbjct: 1 MSSSSPIRRDVGPFALMLTGLGSIIGSGWLFGAWRAAGLAGPGAIWAWVLGAAIIMTIAL 60 Query: 61 VYAELGAALPRTGGIIRYPVYSHGHLVGYLISFVTIVAYTSLISIEVTAVRQYVAYWFPG 120 YAELGA P +GG++RY YSHG LVG++ ++ +A S+I +E A QY+A W P Sbjct: 61 TYAELGAMFPESGGMVRYSHYSHGSLVGFIGAWANWIAIVSVIPVEAEASVQYMASW-PW 119 Query: 121 LTIK--------GSDSPTISGWILQFALLCLFFLLNYWSVKTFAKANFIISIFKYIVPIT 172 + G + G + L+ ++FLLN+WSVK FA++N I+IFK IVP Sbjct: 120 KWAQDLYMHMPDGHGELSEPGLGIAAVLVIVYFLLNFWSVKLFARSNTAITIFKLIVPAA 179 Query: 173 IIIVLI---FHFQPENLSVQGFA-PFGFTGIQAAISTGGVMFAYLGLHPIVSVAGEVQNP 228 I LI FH + ++ V G A + A++T G++F++ G V++AGE NP Sbjct: 180 TGIALIASGFHSENFSVGVHGDAHAIDLAAVLTAVATAGIVFSFNGFQSPVNLAGEAHNP 239 Query: 229 KRNIPIALIICIIVSTIIYTVLQVTFIGAIPTETL-KHGWPAIGREFSLPFKDIAVMLGL 287 ++IP A+I I+++TI+Y +LQ+ ++G++P + L K GW I +F PF ++A+++ L Sbjct: 240 GKSIPFAVIGSIVLATIVYVILQLAYLGSVPPDLLAKAGWHGI--DFRSPFAELAIIVNL 297 Query: 288 GWLATLVILDAILSPGGNGNIFMNTTSRLVYAWARNGTLFGIFSKVNKDTGTPRASLWLS 347 WLA L+ +DA +SP G G + TT+R++Y RNGTL I +++ G PR ++W + Sbjct: 298 HWLAMLLYVDAFISPSGTGITYTATTARMIYGMERNGTLPKILGRIHPKWGIPRPAMWFN 357 Query: 348 FALSIFWTLPFPSWNALVNVCSVALILSYAIAPISSAALRVNAKDLNRPFYLKGMSIIGP 407 A+S + F W L V SVA I+SY P+S+ LR A +L+RP + G+ I+ Sbjct: 358 LAVSYLFLFKFRGWGTLAAVISVATIISYLTGPVSAMTLRRTAPNLHRPLRIAGLPILAG 417 Query: 408 LSFIFTAFIVYWSGWKTVSWLLGSQLVMFLIYLCFSKYTPKEDVSLAQQLKSAWWLIGFY 467 ++FI ++YW+ W ++ +V +Y + D +QLK AWWLI + Sbjct: 418 IAFIMATELLYWAKWPLTGEIILLMVVALPVYFFYQFKAGWHD--FGRQLKGAWWLIFYL 475 Query: 468 IMMLIFSYIGS--FGHGLGIISNPVDLILVAIGSLAIYYWAKYTG 510 + + S+ GS FG G G +S +DL +VA+ L Y W +G Sbjct: 476 PTLALVSWAGSTMFG-GKGYLSYGMDLAVVAVVGLVFYLWGVKSG 519 Lambda K H 0.328 0.143 0.451 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: 986 Number of extensions: 59 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: 520 Length of database: 554 Length adjustment: 35 Effective length of query: 485 Effective length of database: 519 Effective search space: 251715 Effective search space used: 251715 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: 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