Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate N515DRAFT_2630 N515DRAFT_2630 amino acid/polyamine/organocation transporter, APC superfamily
Query= uniprot:A0A2Z5MFR8 (461 letters) >FitnessBrowser__Dyella79:N515DRAFT_2630 Length = 454 Score = 437 bits (1125), Expect = e-127 Identities = 209/439 (47%), Positives = 302/439 (68%), Gaps = 3/439 (0%) Query: 8 DGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQLGE 67 D L+RGL+ RHI+L+ALG AIG GLFLGSA+ ++ AGP+++L Y +GGV F+IMR LGE Sbjct: 5 DSLQRGLQERHIRLMALGSAIGVGLFLGSANAIRLAGPAILLSYLLGGVAIFIIMRALGE 64 Query: 68 MVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVPTW 127 M Q PVAGSFS +A Y G PG+L+GWNYW ++++ +AE+TAVG Y+ W+P VP W Sbjct: 65 MAVQNPVAGSFSRYAQDYLGPLPGYLTGWNYWFMWLMTCIAEITAVGVYMGVWFPDVPQW 124 Query: 128 VSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHG--GPQASI 185 + AL + A+NLA VKAYGE EFWFA+IKVV ++ MI+ GG ++V G G G I Sbjct: 125 IWALAALVTMGAVNLAAVKAYGEFEFWFAMIKVVTIVLMIVGGGAMIVFGLGNQGVPTGI 184 Query: 186 SNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYRIL 245 SNLW+HGGF P+G G+ L ++MF++ G+E+IG+TA EAD P+KSIP A+N V +RIL Sbjct: 185 SNLWTHGGFMPNGAKGMLMALQMVMFAYLGVEMIGLTAGEADNPKKSIPDAINSVFWRIL 244 Query: 246 IFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGVYA 305 IFY+ +L V++S+YPWNE+ GSPFVM F ++G A ++N VVLTAALS N G+Y+ Sbjct: 245 IFYVGALFVIMSIYPWNELGTHGSPFVMTFERLGIKSAAGIINFVVLTAALSSCNGGIYS 304 Query: 306 NSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLMALV 365 RML+ LA+QG APR G+P A+ +S +A V++NYL+PA+ + + Sbjct: 305 TGRMLFNLAQQGQAPRTFAVTSPSGIPNRAVLVSLVALLFGVLLNYLVPAKVFVWVTSAA 364 Query: 366 VAALVLNWALISLTHLKSRRAMVAAGET-LVFKSFWFPVSNWICLAFMALILVILAMTPG 424 + W ++ +T +K RR + A + LVF+ +FP ++++ LAF+ L++ ++ P Sbjct: 365 TFGAIWTWGIVLITQMKYRRGLSEAQRSQLVFRMPFFPYASYLALAFLVLVVGLMGYFPD 424 Query: 425 LSVSVLLVPLWLVVMWAGY 443 V++++ PLWLV++ Y Sbjct: 425 TRVALIVGPLWLVLLTVLY 443 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: 556 Number of extensions: 27 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: 454 Length adjustment: 33 Effective length of query: 428 Effective length of database: 421 Effective search space: 180188 Effective search space used: 180188 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