Align GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized)
to candidate 16753 b2663 gamma-aminobutyrate transporter (NCBI)
Query= SwissProt::P46349 (469 letters) >FitnessBrowser__Keio:16753 Length = 466 Score = 430 bits (1105), Expect = e-125 Identities = 219/442 (49%), Positives = 306/442 (69%), Gaps = 3/442 (0%) Query: 12 LKTRHMTMISIAGVIGAGLFVGSGSVIHSTGPGAVVSYALAGLLVIFIMRMLGEMSAVNP 71 LK+RH+TM+SIAGVIGA LFVGS I GP +++Y AGLLV+ IMRML EM+ P Sbjct: 14 LKSRHVTMLSIAGVIGASLFVGSSVAIAEAGPAVLLAYLFAGLLVVMIMRMLAEMAVATP 73 Query: 72 TSGSFSQYAHDAIGPWAGFTIGWLYWFFWVIVIAIEAIAGAGIIQYWFHDIPLWLTSLIL 131 +GSFS YA AIG WAG+TIGWLYW+FWV+VI +EA A I+ W IP+WL SL++ Sbjct: 74 DTGSFSTYADKAIGRWAGYTIGWLYWWFWVLVIPLEANIAAMILHSWVPGIPIWLFSLVI 133 Query: 132 TIVLTLTNVYSVKSFGEFEYWFSLIKVVTIIAFLIVGFAFIFGFAPGSEPVGFSNLTGKG 191 T+ LT +N+ SVK++GEFE+W +L KV+ I+AF+ +G I GF P +E G S L G Sbjct: 134 TLALTGSNLLSVKNYGEFEFWLALCKVIAILAFIFLGAVAISGFYPYAEVSGISRLWDSG 193 Query: 192 GFFPEGISSVLLGIVVVIFSFMGTEIVAIAAGETSNPIESVTKATRSVVWRIIVFYVGSI 251 GF P G +VL +++ +FSFMG EIV IAA E+ P + + +AT SV+WRI +FY+ SI Sbjct: 194 GFMPNGFGAVLSAMLITMFSFMGAEIVTIAAAESDTPEKHIVRATNSVIWRISIFYLCSI 253 Query: 252 AIVVALLPWNSANI-LESPFVAVLEHIGVPAAAQIMNFIVLTAVLSCLNSGLYTTSRMLY 310 +VVAL+PWN + + +VLE + +P A IM+ ++L +V SCLNS LYT SRMLY Sbjct: 254 FVVVALIPWNMPGLKAVGSYRSVLELLNIPHAKLIMDCVILLSVTSCLNSALYTASRMLY 313 Query: 311 SLAERNEAPRRFMKLSKKGVPVQAIVAGTFFSYIAVVMNYFSPDTVFLFLVNSSGAIALL 370 SL+ R +AP K+++ P A++ T +++ VV+NY++P VF FL++SSGAIALL Sbjct: 314 SLSRRGDAPAVMGKINRSKTPYVAVLLSTGAAFLTVVVNYYAPAKVFKFLIDSSGAIALL 373 Query: 371 VYLVIAVSQLKMRKKLEKTNPEALKIKMWLFPFLTYLTIIAICGILVSMAFIDSMRDELL 430 VYLVIAVSQL+MRK L E ++++MWL+P+LT+L I I +LV M F + + E++ Sbjct: 374 VYLVIAVSQLRMRKILRAEGSE-IRLRMWLYPWLTWLVIGFITFVLVVMLFRPAQQLEVI 432 Query: 431 LTGVIT-GIVLISYLVFRKRKV 451 TG++ GI+ ++ R +K+ Sbjct: 433 STGLLAIGIICTVPIMARWKKL 454 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: 611 Number of extensions: 25 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: 466 Length adjustment: 33 Effective length of query: 436 Effective length of database: 433 Effective search space: 188788 Effective search space used: 188788 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