Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate Pf1N1B4_4976 D-serine/D-alanine/glycine transporter
Query= uniprot:A0A2Z5MFR8 (461 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4976 Length = 473 Score = 318 bits (815), Expect = 2e-91 Identities = 165/462 (35%), Positives = 264/462 (57%), Gaps = 8/462 (1%) Query: 6 QQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQL 65 +Q L+R L NRHIQL+A+GGAIGTGLF+GS ++ +G S+IL Y I G+ + +MR + Sbjct: 10 EQAVLQRTLSNRHIQLMAMGGAIGTGLFMGSGKIIALSGTSIILIYMIIGLFVYFVMRAM 69 Query: 66 GEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVP 125 GE++ SF+ FA Y G F GW+YW+ + + + + VG + YW+P VP Sbjct: 70 GELLLSNLNFKSFADFAGAYLGPRAAFFLGWSYWLSWSVAVVGDAVVVGGFFQYWFPDVP 129 Query: 126 TWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGGP---Q 182 W+ A+ + A+N+ VK +GE EFWFAIIK++AV+ +I L+ S P Sbjct: 130 AWIPAIGMMLTLFALNVLTVKLFGEVEFWFAIIKIIAVVALISVSVLLIASSFVSPTGVT 189 Query: 183 ASISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIY 242 AS+++L FP+G G F + +FSF G ELIG AAE P+K++PKA+N + Sbjct: 190 ASLTHLLDKQAAFPNGLFGFFAGFQMAIFSFAGTELIGTAAAETRSPEKTLPKAINSIPL 249 Query: 243 RILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSG 302 RI++FY+ SL ++++ W +V+ SPFV +F G A ++N VVLT+A S NSG Sbjct: 250 RIILFYVLSLVCIIAVTSWQQVSPNKSPFVELFLIAGFPAAAGIVNFVVLTSAASSANSG 309 Query: 303 VYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLM 362 V+++SRML+GLA+ GNAP ++ + VP +++ + V++ ++IP + Sbjct: 310 VFSSSRMLFGLADLGNAPGIFRRLSKNSVPLISLAFTTFLMLLGVLLLFIIPEVMTAFTI 369 Query: 363 ALVVAAL--VLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALILVILA 420 V+A+ + W+ I +++ R+A +K W LAF+A +L +LA Sbjct: 370 VSTVSAILVIFTWSTILASYIAYRKARPDLHAQSRYKMPGGVPMAWFSLAFLAFVLCLLA 429 Query: 421 MTPGLSVSVLLVPLWLVVMWAGYA---FKRRRAAAHVAARVV 459 + P +++ ++P W + + Y FK R A+H A ++ Sbjct: 430 LRPDTRLALCVMPAWFIWLAIAYQFSHFKSRNQASHAAGSLL 471 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: 498 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: 461 Length of database: 473 Length adjustment: 33 Effective length of query: 428 Effective length of database: 440 Effective search space: 188320 Effective search space used: 188320 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