Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate N515DRAFT_3653 N515DRAFT_3653 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= uniprot:A0A2Z5MFR8 (461 letters) >FitnessBrowser__Dyella79:N515DRAFT_3653 Length = 453 Score = 388 bits (997), Expect = e-112 Identities = 192/436 (44%), Positives = 281/436 (64%), Gaps = 6/436 (1%) Query: 10 LKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQLGEMV 69 L+R L RHI +ALG AIG GLFLGSA+ + AGPS++ Y GG + F+IMR LGEM Sbjct: 5 LQRRLTPRHITFMALGMAIGAGLFLGSANAINLAGPSVLFAYLFGGAMIFIIMRALGEMA 64 Query: 70 AQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVPTWVS 129 +PVAGSFS +A++Y G F G+L+GWNYW+L V V MAE TAVG Y+ W+P +P W+ Sbjct: 65 VHDPVAGSFSTYAHRYLGPFAGYLTGWNYWILMVGVGMAESTAVGIYMRQWFPELPQWIW 124 Query: 130 ALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYL--LVSGHGGPQASISN 187 A I +NL VK YGE EFWF +IKVV V+ MIL G + L G+GG ++N Sbjct: 125 VFGSVAMIGGLNLMAVKVYGEMEFWFTLIKVVTVVLMILGGAGMIWLGWGNGGQPVGLAN 184 Query: 188 LWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYRILIF 247 LWSHGG+FPHGF G+ L V++F+FGG+E IG+ A EA +P+++IP+AVN V++RILIF Sbjct: 185 LWSHGGWFPHGFTGMVLALPVVVFAFGGIETIGMAAGEAAQPERTIPRAVNSVLWRILIF 244 Query: 248 YICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGVYANS 307 Y+ +L V++++YPW+++ GSPFV F ++G A ++N VV+TAALS +NS ++ S Sbjct: 245 YVGALFVIMAIYPWDQLGTQGSPFVTTFGKLGIPQAAGLINFVVITAALSGFNSTTFSGS 304 Query: 308 RMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLMALVVA 367 RMLY L+ + AP L +V GVP A+ ++ V++NYL+P ++M+++ Sbjct: 305 RMLYSLSTKAQAPAFLGQVSEHGVPVRAVLVTLACLVFGVVLNYLLPERIFAMMMSILAF 364 Query: 368 ALVLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALILVILAMTPGLSV 427 V W ++ + H RR A F +P+++ +CL F+A +L +L + V Sbjct: 365 NTVWTWMMVLIAHYSFRRRHGAT----AFPLRAWPLTSVVCLLFLAFVLFMLGYSADTRV 420 Query: 428 SVLLVPLWLVVMWAGY 443 ++ + W+V++ Y Sbjct: 421 ALYVGAGWVVLLSLAY 436 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: 601 Number of extensions: 34 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: 453 Length adjustment: 33 Effective length of query: 428 Effective length of database: 420 Effective search space: 179760 Effective search space used: 179760 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