Align Aspartate-proton symporter; L-aspartate transporter (characterized)
to candidate BPHYT_RS17540 BPHYT_RS17540 amino acid:proton symporter
Query= SwissProt::O07002 (520 letters) >FitnessBrowser__BFirm:BPHYT_RS17540 Length = 531 Score = 379 bits (974), Expect = e-109 Identities = 200/522 (38%), Positives = 308/522 (59%), Gaps = 15/522 (2%) Query: 4 QGNFQKSMSLFDLILIGMGAIFGSAWLFAVSNVASKAGPSGAFSWILGGAIILLIGLVYA 63 + + Q+++ F L+L G+G+I GS WLF A AGP+ +W++G +IL I L YA Sbjct: 2 KSSIQRNIGPFALMLTGLGSIIGSGWLFGAWKAAKIAGPAAVCAWVIGAVVILAIALTYA 61 Query: 64 ELGAALPRTGGIIRYPVYSHGHLVGYLISFVTIVAYTSLISIEVTAVRQYVAYW-FP--- 119 ELGA P +GG++RY YSHG LVG++ ++ +A S+I IE A QY++ W +P Sbjct: 62 ELGAMFPESGGMVRYARYSHGALVGFISAWANWIAIVSVIPIEAEASIQYMSTWPYPWAH 121 Query: 120 GLTIKGSDSPTISGWILQFALLCLFFLLNYWSVKTFAKANFIISIFKYIVPITIIIVLIF 179 L + GS T +G +L AL+ ++F+LNYW VK FA+AN I+IFK+++P I+ L+F Sbjct: 122 ALFVDGS--LTTNGLLLSAALVIIYFMLNYWGVKLFARANSAITIFKFLIPGATILGLMF 179 Query: 180 H-FQPENLS-VQGFAPFGFTGIQAAISTGGVMFAYLGLHPIVSVAGEVQNPKRNIPIALI 237 F EN FAP+G++ + A+ST G++FA+ G +++AGE +NP +++P A+I Sbjct: 180 AGFHKENFGEASTFAPYGWSAVLTAVSTSGIVFAFNGFQSPINLAGEARNPAKSVPFAVI 239 Query: 238 ICIIVSTIIYTVLQVTFIGAIPTETLKHGWPAIGREFSLPFKDIAVMLGLGWLATLVILD 297 I+++ +IY +LQ+ +IGA+ + GW F+ PF ++A+ L L WLA L+ +D Sbjct: 240 GSILLALVIYVLLQIAYIGAVNPSDVMKGWSHFN--FASPFAELAIALNLNWLAILLYVD 297 Query: 298 AILSPGGNGNIFMNTTSRLVYAWARNGTLFGIFSKVNKDTGTPRASLWLSFALSIFWTLP 357 A +SP G G +M TTSR++YA RN T+ +F V+ G PR ++W + +S + Sbjct: 298 AFVSPSGTGTTYMATTSRMIYAMERNNTMPKMFGNVHPFYGVPRQAMWFNLLVSFIFLFF 357 Query: 358 FPSWNALVNVCSVALILSYAIAPISSAALRVNAKDLNRPFYLKGMSIIGPLSFIFTAFIV 417 F W++L V SVA ++SY PIS ALR A DL RP ++ GM II P +F+ + I+ Sbjct: 358 FRGWSSLAAVISVATVISYLTGPISLMALRRAATDLERPLHIPGMKIIAPFAFVCASLIL 417 Query: 418 YWSGWKTVSWLLGSQLVMFLIYLCFSKYTPKEDVSLAQQLKSAWWLIGFYIMMLIFSYIG 477 YW+ W ++ +V +Y F + LK+AWWL+ + +M I S IG Sbjct: 418 YWAKWPLTGEIILLMVVALPVYFYFQ--AKSGFAGWGRDLKAAWWLVAYLPVMAILSLIG 475 Query: 478 S--FGHGLGIISNPVDLILVAIGSLAIYYWAKYTGLPKAAID 517 S FG G +I D+++V SL YYW +G +D Sbjct: 476 SKQFG-GHDLIPYGWDMVVVIAFSLVFYYWGVTSGYRSEYLD 516 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: 978 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: 520 Length of database: 531 Length adjustment: 35 Effective length of query: 485 Effective length of database: 496 Effective search space: 240560 Effective search space used: 240560 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