Align GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized)
to candidate WP_058929813.1 AU252_RS05225 amino acid permease
Query= SwissProt::P46349 (469 letters) >NCBI__GCF_001484605.1:WP_058929813.1 Length = 470 Score = 369 bits (947), Expect = e-106 Identities = 195/455 (42%), Positives = 285/455 (62%), Gaps = 4/455 (0%) Query: 4 SQSGLKKELKTRHMTMISIAGVIGAGLFVGSGSVIHSTGPGAVVSYALAGLLVIFIMRML 63 S L LK R +TM+ + IGAGLF+GSG+ I + GP ++SY +AG L+I +M L Sbjct: 8 SGRALGAALKPRQLTMMGLGSAIGAGLFIGSGAGIQAAGPAVLISYLVAGTLIILVMWAL 67 Query: 64 GEMSAVNPTSGSFSQYAHDAIGPWAGFTIGWLYWFFWVIVIAIEAIAGAGIIQYWFHDIP 123 GEM+A NP SG+FS Y A GP AG T+GWL+W V+VIA EA+ AG++ F +P Sbjct: 68 GEMAAANPDSGAFSVYTAKAYGPVAGATVGWLWWLQLVVVIAAEALGAAGLLSTIFPALP 127 Query: 124 LWLTSLILTIVLTLTNVYSVKSFGEFEYWFSLIKVVTIIAFLIVGFAFIFGFAPGSEPVG 183 +WL + + +VLT N+ SVK+FGEFE+WF+L+KV I+ FL+VG A +FG+ PG + G Sbjct: 128 VWLMAFVFIVVLTAVNLTSVKNFGEFEFWFALLKVAAIVGFLLVGAALLFGWLPGVQSPG 187 Query: 184 FSNLTGKGGFFPEGISSVLLGIVVVIFSFMGTEIVAIAAGETSNPIESVTKATRSVVWRI 243 +N TG GF P+G + + + VV F+F GTEIV++AA ET+ P SV A R+V+WRI Sbjct: 188 LANFTG-DGFAPDGFAGIATALFVVAFAFGGTEIVSVAAAETAEPARSVRTAVRTVLWRI 246 Query: 244 IVFYVGSIAIVVALLPWNSANILESPFVAVLEHIGVPAAAQIMNFIVLTAVLSCLNSGLY 303 +VFY+G+I ++ A++P SA L+SPF AVLE G+P AA + + + A+LS LN+ LY Sbjct: 247 LVFYIGAIFVIAAVVPVGSAG-LKSPFAAVLEAAGMPGAATAITLVAVAALLSALNANLY 305 Query: 304 TTSRMLYSLAERNEAPRRFMKLSKKGVPVQAIVAGTFFSYIAVVMNYFSPDTVFLFLVNS 363 SRM YSLA+R EAPR +SK VPV A++A F + VV+ P+ V L+N Sbjct: 306 GASRMAYSLADRGEAPRLLASVSKARVPVVAVLASVAFGVVTVVLELAFPEKVLPVLLNI 365 Query: 364 SGAIALLVYLVIAVSQLKMRKKLEKTNPEALKIKMWLFPFLTYLTIIAICGILVSMAFID 423 G+ LLV+ ++QL +R + + E L ++M FP+LT ++ + I + Sbjct: 366 VGSTCLLVWTSALLAQLALRLRANREGTE-LPLRMPGFPWLTCFGLLILAAIFTVGFIGE 424 Query: 424 SMRDELLLTGVITGIVLI-SYLVFRKRKVSEKAAA 457 R +LL T + ++ + ++L R KV+ + A Sbjct: 425 DSRPQLLSTFALVALLAVANWLHHRSGKVAGRVEA 459 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: 621 Number of extensions: 30 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: 470 Length adjustment: 33 Effective length of query: 436 Effective length of database: 437 Effective search space: 190532 Effective search space used: 190532 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 Apr 09 2024. 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