Align GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized)
to candidate WP_058932055.1 AU252_RS18980 amino acid permease
Query= SwissProt::P46349 (469 letters) >NCBI__GCF_001484605.1:WP_058932055.1 Length = 459 Score = 344 bits (882), Expect = 4e-99 Identities = 186/432 (43%), Positives = 270/432 (62%), Gaps = 6/432 (1%) Query: 5 QSGLKKELKTRHMTMISIAGVIGAGLFVGSGSVIHSTGPGAVVSYALAGLLVIFIMRMLG 64 +S L +K R +TM+ + IGAGLF+GSG+ I + GP ++SY +AG L+I +M LG Sbjct: 11 ESHLGHTMKPRQLTMMGLGSAIGAGLFLGSGAGIQAAGPAVLISYLVAGTLIILVMWALG 70 Query: 65 EMSAVNPTSGSFSQYAHDAIGPWAGFTIGWLYWFFWVIVIAIEAIAGAGIIQYWFHDIPL 124 EM+A NPTSG+FS YA A+G AG T+GWL+W V+VIA EA+ AG++ + IP+ Sbjct: 71 EMAAANPTSGAFSVYAERALGKTAGATVGWLWWLQLVVVIAAEALGAAGLLFSVWPAIPV 130 Query: 125 WLTSLILTIVLTLTNVYSVKSFGEFEYWFSLIKVVTIIAFLIVGFAFIFGFAPGSEPVGF 184 W +L +V T N+ VK+FGEFE+WF+++KV I+AFL VG A + G P G Sbjct: 131 WALALTFMVVFTAINLTGVKNFGEFEFWFAILKVAAIVAFLAVGAALLLGLLPDVASPGL 190 Query: 185 SNLTGKGGFFPEGISSVLLGIVVVIFSFMGTEIVAIAAGETSNPIESVTKATRSVVWRII 244 +N+T F P G+ V + VVIF+F GTEIVA+AA ET +P SV KA R+V+WRI+ Sbjct: 191 ANIT--TDFAPAGLGGVATALFVVIFAFGGTEIVAVAAAETEDPEHSVGKAIRTVLWRIL 248 Query: 245 VFYVGSIAIVVALLPWNSANILESPFVAVLEHIGVPAAAQIMNFIVLTAVLSCLNSGLYT 304 VFY+GS+ ++ A+LP +S L SPF VL+ +P A + + + A+LS LN+ LY Sbjct: 249 VFYIGSVFVIAAVLPVSSEG-LASPFAGVLDAARIPGAGTAITLVAVVALLSALNANLYG 307 Query: 305 TSRMLYSLAERNEAPRRFMKLSKKGVPVQAIVAGTFFSYIAVVMNYFSPDTVFLFLVNSS 364 SRM+YSLAER EAPR +LS VP+ A+ F + A V+ PD + L Sbjct: 308 ASRMVYSLAERGEAPRFLARLSGASVPMLAVGVSVAFGFFATVLELLFPDRILPALFQLV 367 Query: 365 GAIALLVYLVIAVSQLKMRKKLEKTNPEALKIKMWLFPFLTYLTIIAICGILVSMAF-ID 423 G+ L+V+ VSQL +R++ ++ E L ++M FP LT ++ + G++ ++ F + Sbjct: 368 GSTCLVVWGTALVSQLILRRRADREGAE-LPLRMKGFPGLTICGLV-LLGLIFAIGFSAE 425 Query: 424 SMRDELLLTGVI 435 S R +LL T V+ Sbjct: 426 SSRGQLLSTFVL 437 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: 582 Number of extensions: 29 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 469 Length of database: 459 Length adjustment: 33 Effective length of query: 436 Effective length of database: 426 Effective search space: 185736 Effective search space used: 185736 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