Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate AO356_29455 AO356_29455 amino acid transporter
Query= uniprot:A0A2Z5MFR8 (461 letters) >lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_29455 AO356_29455 amino acid transporter Length = 484 Score = 311 bits (796), Expect = 4e-89 Identities = 158/446 (35%), Positives = 256/446 (57%), Gaps = 7/446 (1%) Query: 6 QQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQL 65 +Q L+R L NRHIQL+A+GGAIGTGLF+GS ++ +G S+IL Y I G+ + +MR + Sbjct: 10 EQPALQRTLSNRHIQLMAMGGAIGTGLFMGSGKIIALSGTSIILIYMIIGLFVYFVMRAM 69 Query: 66 GEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVP 125 GEM+ +F+ FA Y G F GW+YW+ + + + + VG + YW+P VP Sbjct: 70 GEMLLSNLNFKTFADFAGAYLGPRAAFFLGWSYWLSWSVAVIGDAVVVGGFFQYWFPDVP 129 Query: 126 TWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGGPQ--- 182 W+ A+ + A+N+ V+ +GE EFWFAIIK++AV+ +I L+ S P Sbjct: 130 AWIPAIGMLMTLFALNVLTVRLFGEIEFWFAIIKIIAVVTLIGVSLVLIASSFVSPSGVT 189 Query: 183 ASISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIY 242 AS+++L FP+G G F + +FSF G ELIG AAE P+K++PKA+N + Sbjct: 190 ASLNHLLDKQAAFPNGLFGFFAGFQMAIFSFAGTELIGTAAAETRNPEKTLPKAINSIPL 249 Query: 243 RILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSG 302 RI++FY+ +LA ++++ W +V+ SPFV +F G A ++N VVLT+A S NSG Sbjct: 250 RIILFYVLALACIIAVTSWQQVSPSKSPFVELFLVAGFPAAAGIVNFVVLTSAASSANSG 309 Query: 303 VYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLM 362 V+++SRML+GLA Q NAP ++ VP +++ + L V++ +++P + Sbjct: 310 VFSSSRMLFGLANQDNAPGIFRRLSGNSVPLLSLAFTTLLMLVGVLLLFIVPEVMTAFTI 369 Query: 363 ALVVAAL--VLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALILVILA 420 V+A+ + W+ I +++ R+ +K W LAF+ +L +LA Sbjct: 370 VSTVSAILVIFTWSTILASYIAYRKKRPELHAKSAYKMPGGVPMAWFSLAFLGFVLCLLA 429 Query: 421 MTPGLSVSVLLVPLWLVVMWAGYAFK 446 + P +++L++P W + W A++ Sbjct: 430 LRPDTRIALLVMPGWFI--WLAIAYQ 453 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: 515 Number of extensions: 26 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: 461 Length of database: 484 Length adjustment: 33 Effective length of query: 428 Effective length of database: 451 Effective search space: 193028 Effective search space used: 193028 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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