Align GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized)
to candidate RR42_RS05070 RR42_RS05070 amino acid permease
Query= SwissProt::P46349 (469 letters) >FitnessBrowser__Cup4G11:RR42_RS05070 Length = 466 Score = 323 bits (827), Expect = 1e-92 Identities = 175/464 (37%), Positives = 268/464 (57%), Gaps = 7/464 (1%) Query: 1 MNQSQSGLKKELKTRHMTMISIAGVIGAGLFVGSGSVIHSTGPGAVVSYALAGLLVIFIM 60 M Q + GL + LK + MI+I G IG GLF+GSG I GPG ++SYA+ L+ + +M Sbjct: 1 MVQREQGLHRSLKPAQLAMIAIGGAIGTGLFMGSGFAIGFAGPGVLLSYAIGALVTLLLM 60 Query: 61 RMLGEMSAVNPTSGSFSQYAHDAIGPWAGFTIGWLYWFFWVIVIAIEAIAGAGIIQYWFH 120 L EM+ +PTSGSF YA + P AGF + + YW V+ + E A A + YWF Sbjct: 61 GCLAEMTVAHPTSGSFGAYAEHYVSPLAGFLVRYAYWASIVLAVGTEVTAVALYMGYWFP 120 Query: 121 DIPLWLTSLILTIVLTLTNVYSVKSFGEFEYWFSLIKVVTIIAFLIVGFAFIFGFAPGSE 180 +P W + + L L N+ V FG EY FS++K+V I+AF++V +FG APGS Sbjct: 121 QVPAWFWIVSFSAALILINLVGVGIFGAVEYLFSMVKIVAIVAFILVAAYIVFG-APGST 179 Query: 181 P-----VGFSNLTGKGGFFPEGISSVLLGIVVVIFSFMGTEIVAIAAGETSNPIESVTKA 235 GF + T GGF P G+ + + ++V IFS++ E++A+AAGE +P +V +A Sbjct: 180 GSGAAGAGFHHYTAHGGFLPNGLWGMWVAVIVSIFSYLSIEMIAVAAGEAQDPERAVLQA 239 Query: 236 TRSVVWRIIVFYVGSIAIVVALLPWNSANILESPFVAVLEHIGVPAAAQIMNFIVLTAVL 295 RS + R+ +FY+ ++A+++A++PWN A +SPFV V+E I VP AA I+NF+VL A L Sbjct: 240 FRSTMIRLGLFYLLTLALMLAIVPWNQAGAQKSPFVQVMEAIHVPGAAAIINFVVLIAAL 299 Query: 296 SCLNSGLYTTSRMLYSLAERNEAPRRFMKLSKKGVPVQAIVAGTFFSYIAVVMNYFSPDT 355 S +NS LY T+R ++SLA +APR F ++SK+G+PV+A++ + +A +N F P Sbjct: 300 SAMNSQLYITTRTMFSLARAGQAPRSFGEVSKRGIPVRALLLSSIGIALATGLNVFYPGN 359 Query: 356 VFLFLVNSSGAIALLVYLVIAVSQLKMRKKLEKTNPEALKIKMWLFPFLTYLTIIAICGI 415 FL ++ S AL + +I V+ + R++ L +M FP LT L + I Sbjct: 360 AFLLMMAISMFGALFTWFMIFVTHYRFRRQWAAAGNRPLAFRMRGFPLLTLLGAGMMLAI 419 Query: 416 LVSMAFIDSMRDELLLTGVITGIVLISYLV-FRKRKVSEKAAAN 458 +++ D+ R L+ + ++YL+ FR R AN Sbjct: 420 MLTTLLTDAFRMTLITGIPFLAALSVAYLLRFRHRAAPAPLPAN 463 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: 594 Number of extensions: 34 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: 469 Length of database: 466 Length adjustment: 33 Effective length of query: 436 Effective length of database: 433 Effective search space: 188788 Effective search space used: 188788 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