Align GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized)
to candidate AO353_12005 AO353_12005 GABA permease
Query= SwissProt::P46349 (469 letters) >FitnessBrowser__pseudo3_N2E3:AO353_12005 Length = 463 Score = 471 bits (1212), Expect = e-137 Identities = 239/456 (52%), Positives = 327/456 (71%), Gaps = 3/456 (0%) Query: 3 QSQSGLKKELKTRHMTMISIAGVIGAGLFVGSGSVIHSTGPGAVVSYALAGLLVIFIMRM 62 QS +GL++ LK RH+TM+SIAGVIGAGLFVGSG I + GP +++YA AG+LV+ +MRM Sbjct: 5 QSSNGLEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPAVLLAYAAAGMLVVLVMRM 64 Query: 63 LGEMSAVNPTSGSFSQYAHDAIGPWAGFTIGWLYWFFWVIVIAIEAIAGAGIIQYWFHDI 122 LGEM+ +P +GSFS YA AIG WAGFTIGWLYW+FWV+VI +EA A A I+ WF ++ Sbjct: 65 LGEMAVASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHAWFPNV 124 Query: 123 PLWLTSLILTIVLTLTNVYSVKSFGEFEYWFSLIKVVTIIAFLIVGFAFIFGFAPGSEPV 182 +W +LI+T++LT+TN++SVK++GEFE+WF+LIKV+ II F+++G IFGF PGS+ Sbjct: 125 AIWAFTLIITLLLTVTNLFSVKNYGEFEFWFALIKVLAIIGFIVLGVMAIFGFLPGSQVS 184 Query: 183 GFSNLTGKGGFFPEGISSVLLGIVVVIFSFMGTEIVAIAAGETSNPIESVTKATRSVVWR 242 G S+L GF P G+ +VL I+ +FSFMGTEIV IAA E+ NP + ++KAT SV+WR Sbjct: 185 GVSHLFDTQGFLPNGMGAVLGAILTTMFSFMGTEIVTIAAAESKNPGQQISKATNSVIWR 244 Query: 243 IIVFYVGSIAIVVALLPWNSANILE-SPFVAVLEHIGVPAAAQIMNFIVLTAVLSCLNSG 301 I +FY+ SI IVVAL+PWN + + VLE +G+P A I++ +VL AV SCLNS Sbjct: 245 IGLFYLVSIFIVVALVPWNDPVLASVGSYQTVLERMGIPNAKLIVDLVVLVAVTSCLNSA 304 Query: 302 LYTTSRMLYSLAERNEAPRRFMKLSKKGVPVQAIVAGTFFSYIAVVMNYFSPDTVFLFLV 361 LYT SRM++SL +R +AP + +K G P A++ T +++AV NY +P VF FL+ Sbjct: 305 LYTASRMMFSLGKRGDAPAVSQRTNKSGTPYWAVMLSTCAAFLAVFANYVAPAAVFEFLL 364 Query: 362 NSSGAIALLVYLVIAVSQLKMRKKLEKTNPEALKIKMWLFPFLTYLTIIAICGILVSMAF 421 SSGAIALLVYLVIA+SQL+MRK+ E + MWLFP LTY I+ I L M F Sbjct: 365 ASSGAIALLVYLVIAISQLRMRKQ-RMARGEKIAFSMWLFPGLTYAVIVFIVAALTIMLF 423 Query: 422 IDSMRDELLLTGVITGIVLISYL-VFRKRKVSEKAA 456 D+ R E+L TG+++ +V+ + L V R+RK+ ++ A Sbjct: 424 QDAHRVEILATGLLSLLVVAAGLFVARRRKLEQRGA 459 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: 658 Number of extensions: 24 Number of successful extensions: 3 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: 463 Length adjustment: 33 Effective length of query: 436 Effective length of database: 430 Effective search space: 187480 Effective search space used: 187480 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