Align GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized)
to candidate WP_084931869.1 HA51_RS03435 amino acid permease
Query= SwissProt::P46349 (469 letters) >NCBI__GCF_002095475.1:WP_084931869.1 Length = 474 Score = 404 bits (1039), Expect = e-117 Identities = 212/454 (46%), Positives = 291/454 (64%), Gaps = 9/454 (1%) Query: 12 LKTRHMTMISIAGVIGAGLFVGSGSVIHSTGPGAVVSYALAGLLVIFIMRMLGEMSAVNP 71 LKTRH++M+++ GVIGAGLFVGS +VI STGPGA ++Y + G++V IMRMLGEM+A P Sbjct: 15 LKTRHISMLALGGVIGAGLFVGSSAVIASTGPGAFITYLITGIMVALIMRMLGEMAAARP 74 Query: 72 TSGSFSQYAHDAIGPWAGFTIGWLYWFFWVIVIAIEAIAGAGIIQYWFHDIPLWLTSLIL 131 GSF +YA A G AGF GWLYW+FWVIV+ EA+ G II W ++P+WL SL L Sbjct: 75 LKGSFVEYARLAFGNAAGFATGWLYWYFWVIVVGFEAVVGGQIIHGWTPELPVWLISLGL 134 Query: 132 TIVLTLTNVYSVKSFGEFEYWFSLIKVVTIIAFLIVGFAFIFGFAPGSEPVGFSNLTGKG 191 I++T N+ SV+SFGE EYWF+ IKVV I+ FL+V A++ P S FSNLT +G Sbjct: 135 MILMTSLNLLSVRSFGEAEYWFAGIKVVAIVIFLLVAGAYVLHLFPHS-TANFSNLTSQG 193 Query: 192 GFFPEGISSVLLGIVVVIFSFMGTEIVAIAAGETSNPIESVTKATRSVVWRIIVFYVGSI 251 GFFP G ++ G+V VIFS G E+ IAA E+ +P E++ KA +V+ RI+VF+V + Sbjct: 194 GFFPHGAGTLFTGVVTVIFSMTGVEVATIAAAESEHPAENIRKAVNTVMVRILVFFVLAT 253 Query: 252 AIVVALLPWNSANILESPFVAVLEHIGVPAAAQIMNFIVLTAVLSCLNSGLYTTSRMLYS 311 ++V PW +S FV + IG+P + ++ ++L AVLS LN+GLYT+SR+L Sbjct: 254 FLIVVAQPWTDVVPGKSAFVTTFDKIGIPGSGTMLTIVILVAVLSVLNAGLYTSSRLLAV 313 Query: 312 LAERNEAPRRFMKLSKKGVPVQAIVAGTFFSYIAVVMNYFSPDTVFLFLVNSSGAIALLV 371 L+ EAP + SK+GVP A++ T Y AVV+ PDTVFLFL+NSSGA+ L V Sbjct: 314 LSSNGEAPAWMAQRSKRGVPSLAVITSTLVGYAAVVIAALWPDTVFLFLLNSSGAVFLFV 373 Query: 372 YLVIAVSQLKMRKKLEKTNPEALKIKMWLFPFLTYLTIIAICGILVSMAFIDSMRDELLL 431 YL+I +SQLK+RK E + LK +MW P++ L ++ +LVSMA R LL Sbjct: 374 YLMICLSQLKLRKTWE--HEGTLKFRMWGHPWIPLLVTASVIAVLVSMAVDADKRLSLLQ 431 Query: 432 TGVITGIVLISYLVF------RKRKVSEKAAANP 459 + + ++L SY V +R+ E A P Sbjct: 432 SILALMVILTSYAVLLFARSRSQRRTREIRAGRP 465 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: 593 Number of extensions: 26 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: 474 Length adjustment: 33 Effective length of query: 436 Effective length of database: 441 Effective search space: 192276 Effective search space used: 192276 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