Align GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized)
to candidate WP_017597638.1 D471_RS0105135 amino acid permease
Query= SwissProt::P46349 (469 letters) >NCBI__GCF_000341125.1:WP_017597638.1 Length = 452 Score = 398 bits (1023), Expect = e-115 Identities = 202/434 (46%), Positives = 288/434 (66%), Gaps = 4/434 (0%) Query: 17 MTMISIAGVIGAGLFVGSGSVIHSTGPGAVVSYALAGLLVIFIMRMLGEMSAVNPTSGSF 76 M +I+I G +GAGLF+GSG+VIH+ GP AV SYALAG LV +R LGEM P G+F Sbjct: 1 MALIAIGGSVGAGLFIGSGAVIHTAGPAAVFSYALAGALVFLTLRALGEMVVSVPAGGAF 60 Query: 77 SQYAHDAIGPWAGFTIGWLYWFFWVIVIAIEAIAGAGIIQYWFHDIPLWLTSLILTIVLT 136 S YA A GP AGFTIGW+YW+ + +++A E++AGA I+ W + +P WL +L++ + +T Sbjct: 61 SDYARLAFGPRAGFTIGWIYWWLYAVLVAAESVAGASILGQWVN-LPQWLLALLVLLSMT 119 Query: 137 LTNVYSVKSFGEFEYWFSLIKVVTIIAFLIVGFAFIFGFAPGSEPVGFSNLTGKGGFFPE 196 + N+ SV+ F E E +FSL+KV TI+AFL++G + G GS +NL GGF P Sbjct: 120 VANLISVRVFAETESFFSLVKVGTIVAFLLIGGLWALGLWSGSGGSHVANLWEHGGFAPN 179 Query: 197 GISSVLLGIVVVIFSFMGTEIVAIAAGETSNPIESVTKATRSVVWRIIVFYVGSIAIVVA 256 G +VL VVV+F+F G EI+ IAAGE+ P V A +V+WRI +FY+ SI +VV Sbjct: 180 GWVAVLAATVVVLFAFGGVEIITIAAGESDEPERGVASAITNVLWRIGLFYLASIVVVVM 239 Query: 257 LLPWNSANILESPFVAVLEHIGVPAAAQIMNFIVLTAVLSCLNSGLYTTSRMLYSLAERN 316 ++PWN+ ++ SPFV V+E +GVP AA IM +VL AVLS LN+ +YTTSRML++L+ + Sbjct: 240 VVPWNTTDLERSPFVVVMETVGVPGAAVIMEVVVLVAVLSVLNAAMYTTSRMLFALSRQG 299 Query: 317 EAPRRFMKLSKKGVPVQAIVAGTFFSYIAVVMNYFSPDTVFLFLVNSSGAIALLVYLVIA 376 +APR + +K+GVP +AIV GT Y+AVV Y P VF FLV S GAI L++++ I Sbjct: 300 DAPRALSRTTKRGVPARAIVLGTVVGYVAVVAEYLLPGKVFGFLVASIGAILLVLFVTIC 359 Query: 377 VSQLKMRKKLEKTNPEALKIKMWLFPFLTYLTIIAICGILVSMAFIDSMRDELLLTGVIT 436 SQL + +++ + PE L ++MW FP+LT++ + + I V+MA I R L + Sbjct: 360 ASQLVVGRRVRRRAPERLTLRMWGFPYLTWVVLAGLIAIAVAMAAIPDQRQALFAS---L 416 Query: 437 GIVLISYLVFRKRK 450 G V+++ + F RK Sbjct: 417 GSVVVAVVAFEVRK 430 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: 629 Number of extensions: 28 Number of successful extensions: 2 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: 452 Length adjustment: 33 Effective length of query: 436 Effective length of database: 419 Effective search space: 182684 Effective search space used: 182684 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 24 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