Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate H281DRAFT_01668 H281DRAFT_01668 gamma-aminobutyrate:proton symporter, AAT family
Query= uniprot:A0A2Z5MFR8 (461 letters) >FitnessBrowser__Burk376:H281DRAFT_01668 Length = 459 Score = 289 bits (739), Expect = 2e-82 Identities = 150/446 (33%), Positives = 249/446 (55%), Gaps = 2/446 (0%) Query: 5 LQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQ 64 +Q LK+ LK RHI +IALGG IG GLF+GS S++ AGP+ IL Y IGGV+ ++M Sbjct: 1 MQDYSLKKSLKQRHITMIALGGVIGAGLFVGSGSIIATAGPAAILSYLIGGVMVTLVMFM 60 Query: 65 LGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGV 124 LGEM ++ P +GSFS +A Y G++ GF GW YW ++ E +G +H + P + Sbjct: 61 LGEMASRNPDSGSFSTYANSYLGEWAGFAVGWLYWFKSMITITVEAILLGAILHDFLPWL 120 Query: 125 PTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGG-PQA 183 P AL + A N +V+A+GE E+W + KV +I ++ G +L G P Sbjct: 121 PVPAGALFMLIALMATNAYSVRAFGEAEYWLSFAKVATIIVFMVLGASILFGLQPGIPAP 180 Query: 184 SISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYR 243 + NL HGGF P+G + + + V++FS GG E+ + A E++ P K++ +A+ VI R Sbjct: 181 GLLNLTDHGGFMPNGISPVISGVMVVIFSLGGSEIAAVAAGESENPSKNVIRAIKSVILR 240 Query: 244 ILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGV 303 +++FY+ S+++L+ PW + A SP+V +FS G T A + +V+ + +SV NS + Sbjct: 241 VMVFYVGSVSILILCMPWTDKANLKSPYVSLFSMAGFTGAAVAMKIVLFVSFMSVMNSFL 300 Query: 304 YANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLMA 363 ++NSRML+ L+++G+AP + + +GVP A+ L + + + +++L + +L Sbjct: 301 FSNSRMLFSLSQRGHAPAMFGRTNAKGVPMNALVLCLVVCVSILGIHFLSGGDLFLMLAK 360 Query: 364 LVVAALVLNWALISLTHLKSRR-AMVAAGETLVFKSFWFPVSNWICLAFMALILVILAMT 422 A +++ W I + H RR + F+++++PVSNW+ L + +L A Sbjct: 361 SSGAFVMIVWIFIIVAHFAMRRQTKHEQRDPASFRAWFYPVSNWVALLALVAVLGSQAFN 420 Query: 423 PGLSVSVLLVPLWLVVMWAGYAFKRR 448 P + + A Y +RR Sbjct: 421 PESRFQFWFAVSTALAIVAWYYVRRR 446 Lambda K H 0.327 0.140 0.440 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: 480 Number of extensions: 25 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: 461 Length of database: 459 Length adjustment: 33 Effective length of query: 428 Effective length of database: 426 Effective search space: 182328 Effective search space used: 182328 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