Align D-serine/D-alanine/glycine transporter (characterized)
to candidate BPHYT_RS21680 BPHYT_RS21680 amino acid permease-associated protein
Query= SwissProt::P0AAE0 (470 letters) >FitnessBrowser__BFirm:BPHYT_RS21680 Length = 476 Score = 280 bits (715), Expect = 1e-79 Identities = 156/448 (34%), Positives = 248/448 (55%), Gaps = 13/448 (2%) Query: 19 LRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGELL 78 L+ L RH+ +IA+GG IG GLF+GSG + AGP+ + ++I G ++ VMR +GE+ Sbjct: 10 LKAGLKQRHMTMIALGGVIGAGLFVGSGVVVQQAGPAAVLSFLITGALVVLVMRMLGEMA 69 Query: 79 LSNLEYKSFSDFA------SDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPD 132 + SF ++A G AG+ TGW YW+ WV+ + VA QFW PD Sbjct: 70 CAMPAVGSFYEYARLAFGGKRASGNLAGFLTGWMYWYFWVIVVAVEAVAGAKLVQFWLPD 129 Query: 133 LSDWVASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTG 192 + W SL ++V L NL +V +GE EFWFA IK+ AI+ + +G + V + + Sbjct: 130 VPAWAISLVLLVTLTATNLVSVGSYGEFEFWFASIKVAAIMVFLFLGGMYVLGLWPAAKH 189 Query: 193 VEASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSI 252 V A L + GG PKG+ +G A + G E+V AAE ++P K++ +A NS+ Sbjct: 190 VTAVLPTLLSHGGLMPKGIGPVLSGAVAATGFYFGAEIVTIAAAEAQEPAKAVAKATNSV 249 Query: 253 PIRIIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSAN 312 R+++FYV ++++++++ PW+S +P+V +G+PAAASV+N +VLT+ S+ N Sbjct: 250 ITRVLVFYVGSILLVVALVPWNS-PKMATPYVSALDAMGIPAAASVMNAIVLTAVLSALN 308 Query: 313 SGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAF 372 SG+++ SRM+F L + G AP A AK+++R VP + + + VVM YV+P + AF Sbjct: 309 SGLYAASRMIFALTRHGDAPAALAKVNRRGVPVRAILIGTVFGYASVVMSYVSPDTVFAF 368 Query: 373 TMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFVVVL 432 + + + +F++V I L R +R EK +M + WV + V ++V Sbjct: 369 LVNSYGTVAIFVYVLIAISQLKLRARIER-DAPEKLRVRMWCYPYLTWVAIIGMVGILVA 427 Query: 433 LTLEDDTRQALLVTPLWFIALGLGWLFI 460 + + RQ PLWF LG L + Sbjct: 428 MAFIPEQRQ-----PLWFGVASLGVLLL 450 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: 603 Number of extensions: 28 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: 476 Length adjustment: 33 Effective length of query: 437 Effective length of database: 443 Effective search space: 193591 Effective search space used: 193591 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