Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate AO353_16120 AO353_16120 D-alanine/D-serine/glycine permease
Query= uniprot:A0A2Z5MFR8 (461 letters) >FitnessBrowser__pseudo3_N2E3:AO353_16120 Length = 472 Score = 399 bits (1025), Expect = e-115 Identities = 201/451 (44%), Positives = 288/451 (63%), Gaps = 5/451 (1%) Query: 10 LKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQLGEMV 69 LKR L RHI+L+ALG IG GLFLGSA ++ AGP+++L Y IGG+ +IMR LGEM Sbjct: 18 LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77 Query: 70 AQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVPTWVS 129 PVAGSFS +A Y G GFL+GWNYW L+++ +AE+TAV Y+ W+P VP W+ Sbjct: 78 VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPEVPRWIW 137 Query: 130 ALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHG--GPQASISN 187 AL + +INL VKA+GE EFWFA+IK+V +I M++ G ++ G G G ISN Sbjct: 138 ALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVVGGVGVIAFGFGNDGVALGISN 197 Query: 188 LWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYRILIF 247 LWSHGGF P+G G+ L ++MF++ G+E+IG+TA EA PQK+IP A+ V +RIL+F Sbjct: 198 LWSHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRILLF 257 Query: 248 YICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGVYANS 307 Y+ +L V+LS+YPWNE+ GSPFVM F ++G A ++N VV+TAALS N G+++ Sbjct: 258 YVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTG 317 Query: 308 RMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLMALVVA 367 RMLY LA+ G AP K GVP A+ LS A V++NYL+P + + A+ Sbjct: 318 RMLYSLAQNGQAPAGFAKTS-NGVPRRALLLSIGALLLGVLLNYLVPEKVFVWVTAIATF 376 Query: 368 ALVLNWALISLTHLKSRRAMVAAGE-TLVFKSFWFPVSNWICLAFMALILVILAMTPGLS 426 + W +I L LK R+ + A L ++ + +PVS+++ LAF+ +++ ++A P Sbjct: 377 GAIWTWVMILLAQLKFRKGLSPAERAALKYRMWLYPVSSYLALAFLVMVVGLMAYFPDTR 436 Query: 427 VSVLLVPLWLVVMWA-GYAFKRRRAAAHVAA 456 V++ + P +LV++ Y FK + AA Sbjct: 437 VALYVGPAFLVLLTVLFYVFKLQPTGVPQAA 467 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: 567 Number of extensions: 30 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: 472 Length adjustment: 33 Effective length of query: 428 Effective length of database: 439 Effective search space: 187892 Effective search space used: 187892 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