Align GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized)
to candidate BPHYT_RS21680 BPHYT_RS21680 amino acid permease-associated protein
Query= SwissProt::P46349 (469 letters) >FitnessBrowser__BFirm:BPHYT_RS21680 Length = 476 Score = 465 bits (1197), Expect = e-135 Identities = 231/451 (51%), Positives = 314/451 (69%), Gaps = 10/451 (2%) Query: 8 LKKELKTRHMTMISIAGVIGAGLFVGSGSVIHSTGPGAVVSYALAGLLVIFIMRMLGEMS 67 LK LK RHMTMI++ GVIGAGLFVGSG V+ GP AV+S+ + G LV+ +MRMLGEM+ Sbjct: 10 LKAGLKQRHMTMIALGGVIGAGLFVGSGVVVQQAGPAAVLSFLITGALVVLVMRMLGEMA 69 Query: 68 AVNPTSGSFSQYAHDAIGP------WAGFTIGWLYWFFWVIVIAIEAIAGAGIIQYWFHD 121 P GSF +YA A G AGF GW+YW+FWVIV+A+EA+AGA ++Q+W D Sbjct: 70 CAMPAVGSFYEYARLAFGGKRASGNLAGFLTGWMYWYFWVIVVAVEAVAGAKLVQFWLPD 129 Query: 122 IPLWLTSLILTIVLTLTNVYSVKSFGEFEYWFSLIKVVTIIAFLIVGFAFIFGFAPGSEP 181 +P W SL+L + LT TN+ SV S+GEFE+WF+ IKV I+ FL +G ++ G P ++ Sbjct: 130 VPAWAISLVLLVTLTATNLVSVGSYGEFEFWFASIKVAAIMVFLFLGGMYVLGLWPAAKH 189 Query: 182 VG--FSNLTGKGGFFPEGISSVLLGIVVVIFSFMGTEIVAIAAGETSNPIESVTKATRSV 239 V L GG P+GI VL G V + G EIV IAA E P ++V KAT SV Sbjct: 190 VTAVLPTLLSHGGLMPKGIGPVLSGAVAATGFYFGAEIVTIAAAEAQEPAKAVAKATNSV 249 Query: 240 VWRIIVFYVGSIAIVVALLPWNSANILESPFVAVLEHIGVPAAAQIMNFIVLTAVLSCLN 299 + R++VFYVGSI +VVAL+PWNS + +P+V+ L+ +G+PAAA +MN IVLTAVLS LN Sbjct: 250 ITRVLVFYVGSILLVVALVPWNSPK-MATPYVSALDAMGIPAAASVMNAIVLTAVLSALN 308 Query: 300 SGLYTTSRMLYSLAERNEAPRRFMKLSKKGVPVQAIVAGTFFSYIAVVMNYFSPDTVFLF 359 SGLY SRM+++L +AP K++++GVPV+AI+ GT F Y +VVM+Y SPDTVF F Sbjct: 309 SGLYAASRMIFALTRHGDAPAALAKVNRRGVPVRAILIGTVFGYASVVMSYVSPDTVFAF 368 Query: 360 LVNSSGAIALLVYLVIAVSQLKMRKKLEKTNPEALKIKMWLFPFLTYLTIIAICGILVSM 419 LVNS G +A+ VY++IA+SQLK+R ++E+ PE L+++MW +P+LT++ II + GILV+M Sbjct: 369 LVNSYGTVAIFVYVLIAISQLKLRARIERDAPEKLRVRMWCYPYLTWVAIIGMVGILVAM 428 Query: 420 AFIDSMRDELLLTGVITGIVLISYLVFRKRK 450 AFI R L G++L++YL+ R RK Sbjct: 429 AFIPEQRQPLWFGVASLGVLLLAYLL-RVRK 458 Lambda K H 0.326 0.140 0.417 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: 649 Number of extensions: 24 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: 469 Length of database: 476 Length adjustment: 33 Effective length of query: 436 Effective length of database: 443 Effective search space: 193148 Effective search space used: 193148 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: 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