Align GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized)
to candidate H281DRAFT_01668 H281DRAFT_01668 gamma-aminobutyrate:proton symporter, AAT family
Query= SwissProt::P46349 (469 letters) >FitnessBrowser__Burk376:H281DRAFT_01668 Length = 459 Score = 375 bits (964), Expect = e-108 Identities = 186/445 (41%), Positives = 282/445 (63%), Gaps = 1/445 (0%) Query: 8 LKKELKTRHMTMISIAGVIGAGLFVGSGSVIHSTGPGAVVSYALAGLLVIFIMRMLGEMS 67 LKK LK RH+TMI++ GVIGAGLFVGSGS+I + GP A++SY + G++V +M MLGEM+ Sbjct: 6 LKKSLKQRHITMIALGGVIGAGLFVGSGSIIATAGPAAILSYLIGGVMVTLVMFMLGEMA 65 Query: 68 AVNPTSGSFSQYAHDAIGPWAGFTIGWLYWFFWVIVIAIEAIAGAGIIQYWFHDIPLWLT 127 + NP SGSFS YA+ +G WAGF +GWLYWF +I I +EAI I+ + +P+ Sbjct: 66 SRNPDSGSFSTYANSYLGEWAGFAVGWLYWFKSMITITVEAILLGAILHDFLPWLPVPAG 125 Query: 128 SLILTIVLTLTNVYSVKSFGEFEYWFSLIKVVTIIAFLIVGFAFIFGFAPGSEPVGFSNL 187 +L + I L TN YSV++FGE EYW S KV TII F+++G + +FG PG G NL Sbjct: 126 ALFMLIALMATNAYSVRAFGEAEYWLSFAKVATIIVFMVLGASILFGLQPGIPAPGLLNL 185 Query: 188 TGKGGFFPEGISSVLLGIVVVIFSFMGTEIVAIAAGETSNPIESVTKATRSVVWRIIVFY 247 T GGF P GIS V+ G++VVIFS G+EI A+AAGE+ NP ++V +A +SV+ R++VFY Sbjct: 186 TDHGGFMPNGISPVISGVMVVIFSLGGSEIAAVAAGESENPSKNVIRAIKSVILRVMVFY 245 Query: 248 VGSIAIVVALLPWNSANILESPFVAVLEHIGVPAAAQIMNFIVLTAVLSCLNSGLYTTSR 307 VGS++I++ +PW L+SP+V++ G AA M ++ + +S +NS L++ SR Sbjct: 246 VGSVSILILCMPWTDKANLKSPYVSLFSMAGFTGAAVAMKIVLFVSFMSVMNSFLFSNSR 305 Query: 308 MLYSLAERNEAPRRFMKLSKKGVPVQAIVAGTFFSYIAVVMNYFSPDTVFLFLVNSSGAI 367 ML+SL++R AP F + + KGVP+ A+V + +++ S +FL L SSGA Sbjct: 306 MLFSLSQRGHAPAMFGRTNAKGVPMNALVLCLVVCVSILGIHFLSGGDLFLMLAKSSGAF 365 Query: 368 ALLVYLVIAVSQLKMRKKLEKTNPEALKIKMWLFPFLTYLTIIAICGILVSMAFIDSMRD 427 ++V++ I V+ MR++ + + + W +P ++ ++A+ +L S AF R Sbjct: 366 VMIVWIFIIVAHFAMRRQTKHEQRDPASFRAWFYPVSNWVALLALVAVLGSQAFNPESRF 425 Query: 428 ELLLTGVITGIVLISYLVFRKRKVS 452 + V T + ++++ R+R S Sbjct: 426 QFWF-AVSTALAIVAWYYVRRRHPS 449 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: 22 Number of successful extensions: 2 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: 459 Length adjustment: 33 Effective length of query: 436 Effective length of database: 426 Effective search space: 185736 Effective search space used: 185736 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