Align GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized)
to candidate PP_0284 PP_0284 gamma-aminobutyrate permease
Query= SwissProt::P46349 (469 letters) >FitnessBrowser__Putida:PP_0284 Length = 461 Score = 457 bits (1176), Expect = e-133 Identities = 237/455 (52%), Positives = 320/455 (70%), Gaps = 3/455 (0%) Query: 4 SQSGLKKELKTRHMTMISIAGVIGAGLFVGSGSVIHSTGPGAVVSYALAGLLVIFIMRML 63 + + L + LK RH+TM+SIAGVIGAGLFVGSG I + GP +++YA AG LV+ +MRML Sbjct: 5 NSNDLAQGLKQRHVTMLSIAGVIGAGLFVGSGHAIAAAGPAVLLAYAAAGTLVVLVMRML 64 Query: 64 GEMSAVNPTSGSFSQYAHDAIGPWAGFTIGWLYWFFWVIVIAIEAIAGAGIIQYWFHDIP 123 GEM+ +P +GSFS YA AIG WAGFTIGWLYW+FWV+VI +EA A A I+ WF + Sbjct: 65 GEMAVASPDTGSFSTYADRAIGRWAGFTIGWLYWWFWVLVIPLEANAAAAILHAWFPAVD 124 Query: 124 LWLTSLILTIVLTLTNVYSVKSFGEFEYWFSLIKVVTIIAFLIVGFAFIFGFAPGSEPVG 183 LW SLI+T+ LTLTN+ SVK++GEFE+WF+L+KV+ II F+ VG A +FGF P S+ G Sbjct: 125 LWAFSLIITLALTLTNLCSVKNYGEFEFWFALLKVLAIIGFIAVGCAALFGFVPSSQVSG 184 Query: 184 FSNLTGKGGFFPEGISSVLLGIVVVIFSFMGTEIVAIAAGETSNPIESVTKATRSVVWRI 243 S+L GF P G+ +VL ++ +FSFMGTEIV IAA E+ +P + +++AT SV+WRI Sbjct: 185 TSHLFDTQGFMPNGLGAVLAAMLTTMFSFMGTEIVTIAAAESKDPGKQISRATNSVIWRI 244 Query: 244 IVFYVGSIAIVVALLPWNSANILES-PFVAVLEHIGVPAAAQIMNFIVLTAVLSCLNSGL 302 +FY+ SI +VVAL+PWN + E+ + VL IGVP A I++ +VL AV SCLNS L Sbjct: 245 CLFYLVSIFLVVALVPWNDPALAETGSYQTVLSRIGVPNAKLIVDIVVLIAVTSCLNSAL 304 Query: 303 YTTSRMLYSLAERNEAPRRFMKLSKKGVPVQAIVAGTFFSYIAVVMNYFSPDTVFLFLVN 362 YT+SRML+SL++R +AP + +K P A++ T +++ V N+ +P VF FL+ Sbjct: 305 YTSSRMLFSLSKRGDAPAIAQRTTKAATPHVAVLLSTAAAFLCVFANFVAPAQVFEFLLA 364 Query: 363 SSGAIALLVYLVIAVSQLKMRKKLEKTNPEALKIKMWLFPFLTYLTIIAICGILVSMAFI 422 SSGAIALLVYLVIAVSQL+MR + E E + KMWLFP LT+ TI I ILV MA Sbjct: 365 SSGAIALLVYLVIAVSQLRMRAQRE-ARGEKITFKMWLFPGLTWATIAFIVAILVVMALR 423 Query: 423 DSMRDELLLTGVIT-GIVLISYLVFRKRKVSEKAA 456 + R E++ T +++ G+V LV RKR+ + +AA Sbjct: 424 EDHRAEIIATALLSIGVVAAGLLVHRKREAAGRAA 458 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: 592 Number of extensions: 23 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: 461 Length adjustment: 33 Effective length of query: 436 Effective length of database: 428 Effective search space: 186608 Effective search space used: 186608 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