Align L-alanine and D-alanine permease (characterized)
to candidate H281DRAFT_01668 H281DRAFT_01668 gamma-aminobutyrate:proton symporter, AAT family
Query= reanno::pseudo5_N2C3_1:AO356_17670 (473 letters) >FitnessBrowser__Burk376:H281DRAFT_01668 Length = 459 Score = 317 bits (813), Expect = 4e-91 Identities = 164/445 (36%), Positives = 257/445 (57%), Gaps = 1/445 (0%) Query: 18 LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77 LK+ L +RHI ++ALG IG GLF+GS I AGPA +LSY+IGG+ + ++M LGEMA Sbjct: 6 LKKSLKQRHITMIALGGVIGAGLFVGSGSIIATAGPAAILSYLIGGVMVTLVMFMLGEMA 65 Query: 78 VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPRWIW 137 NP +GSFS YA YLG AGF GW YWF ++T E + + + P +P Sbjct: 66 SRNPDSGSFSTYANSYLGEWAGFAVGWLYWFKSMITITVEAILLGAILHDFLPWLPVPAG 125 Query: 138 ALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALGISN 197 AL L+++ + N +V+AFGE E+W + K+ TII ++ G I+ FG A G+ N Sbjct: 126 ALFMLIALMATNAYSVRAFGEAEYWLSFAKVATIIVFMVLGASIL-FGLQPGIPAPGLLN 184 Query: 198 LWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRILLF 257 L HGGFMPNG+S V+ + +V+F+ G E+ + AGE++NP K + AI SV R+++F Sbjct: 185 LTDHGGFMPNGISPVISGVMVVIFSLGGSEIAAVAAGESENPSKNVIRAIKSVILRVMVF 244 Query: 258 YVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTG 317 YVG++ +++ PW + SP+V F G AA + V+ + +S N +FS Sbjct: 245 YVGSVSILILCMPWTDKANLKSPYVSLFSMAGFTGAAVAMKIVLFVSFMSVMNSFLFSNS 304 Query: 318 RMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNYLVPEKVFVWVTSIATF 377 RML+SL+Q G APA F +T+ GVP AL+L + + + +++L +F+ + + Sbjct: 305 RMLFSLSQRGHAPAMFGRTNAKGVPMNALVLCLVVCVSILGIHFLSGGDLFLMLAKSSGA 364 Query: 378 GAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAFLVLVVGLMAYFPDTR 437 + W+ I++A R+ +R +R W YPVS+++AL LV V+G A+ P++R Sbjct: 365 FVMIVWIFIIVAHFAMRRQTKHEQRDPASFRAWFYPVSNWVALLALVAVLGSQAFNPESR 424 Query: 438 VALYVGPAFLVLLTVLFYTFKLQPT 462 + + + + +Y + P+ Sbjct: 425 FQFWFAVSTALAIVAWYYVRRRHPS 449 Lambda K H 0.328 0.142 0.444 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: 584 Number of extensions: 31 Number of successful extensions: 4 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: 473 Length of database: 459 Length adjustment: 33 Effective length of query: 440 Effective length of database: 426 Effective search space: 187440 Effective search space used: 187440 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