Align GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized)
to candidate BWI76_RS19685 BWI76_RS19685 lysine transporter
Query= SwissProt::P46349 (469 letters) >FitnessBrowser__Koxy:BWI76_RS19685 Length = 489 Score = 344 bits (882), Expect = 4e-99 Identities = 174/387 (44%), Positives = 251/387 (64%), Gaps = 9/387 (2%) Query: 7 GLKKELKTRHMTMISIAGVIGAGLFVGSGSVIHSTGPG-AVVSYALAGLLVIFIMRMLGE 65 GL++ELK RH+TMI+I G IG GLFV SG+ I GPG A++SY L GL+V F+M LGE Sbjct: 12 GLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYILIGLMVYFLMTSLGE 71 Query: 66 MSAVNPTSGSFSQYAHDAIGPWAGFTIGWLYWFFWVIVIAIEAIAGAGIIQYWFHDIPLW 125 ++A P SGSF+ Y + + GF +GW YW+ W + IA++ +A ++ YWF D P W Sbjct: 72 LAAFMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMTYWFPDAPGW 131 Query: 126 LTSLILTIVLTLTNVYSVKSFGEFEYWFSLIKVVTIIAFLIVGFAFIFGFAPGSEPVGFS 185 + S + ++ L N SVK FGE EYWFSLIKV T+I F+IVG IFG G++P G+S Sbjct: 132 VWSALFLGIMFLLNWISVKGFGEAEYWFSLIKVATVIIFIIVGVMMIFGIFKGAQPAGWS 191 Query: 186 NLTGKGGFFPEGISSVLLGIVVVIFSFMGTEIVAIAAGETSNPIESVTKATRSVVWRIIV 245 N F G ++++ ++V FSF GTE++ IAAGE+ NP +++ +A R V WRI++ Sbjct: 192 NWVIDDAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESENPEKNIPRAVRQVFWRILL 251 Query: 246 FYVGSIAIVVALLPWNSANILE--------SPFVAVLEHIGVPAAAQIMNFIVLTAVLSC 297 FYV +I I+ ++P+ ++L SPF V +H G+ +AA IMN ++LTAVLS Sbjct: 252 FYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAIMNAVILTAVLSA 311 Query: 298 LNSGLYTTSRMLYSLAERNEAPRRFMKLSKKGVPVQAIVAGTFFSYIAVVMNYFSPDTVF 357 NSG+Y ++RMLY+LA +APR F KLSK GVP A+ A T + + + + F TV+ Sbjct: 312 GNSGMYASTRMLYTLACDGKAPRIFSKLSKGGVPRNALYATTVIAGLCFLSSMFGNQTVY 371 Query: 358 LFLVNSSGAIALLVYLVIAVSQLKMRK 384 L+L+N+SG + +L IA+S + R+ Sbjct: 372 LWLLNTSGMTGFIAWLGIAISHYRFRR 398 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: 647 Number of extensions: 24 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: 489 Length adjustment: 34 Effective length of query: 435 Effective length of database: 455 Effective search space: 197925 Effective search space used: 197925 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