Align L-alanine and D-alanine permease (characterized)
to candidate H281DRAFT_04042 H281DRAFT_04042 aromatic amino acid:proton symporter, AAT family
Query= reanno::pseudo5_N2C3_1:AO356_17670 (473 letters) >FitnessBrowser__Burk376:H281DRAFT_04042 Length = 506 Score = 405 bits (1040), Expect = e-117 Identities = 198/441 (44%), Positives = 287/441 (65%), Gaps = 4/441 (0%) Query: 18 LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77 LKR L RHI+L+ALG IG GLFLGSA ++ AGP+++L Y IGG+ +IMR LGEM Sbjct: 55 LKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQLGEMV 114 Query: 78 VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPRWIW 137 PVAGSFS +A Y G GFL+GWNYW L+++ +AE+TAV Y+ W+P VP W+ Sbjct: 115 AQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVPTWVS 174 Query: 138 ALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALGISN 197 AL + +INL VKA+GE EFWFA+IK+V +I M++ G ++ G G G ISN Sbjct: 175 ALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHG--GPQASISN 232 Query: 198 LWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRILLF 257 LW+HGGF P+G G+ L ++MF++ G+E+IG+TA EA PQK+IP A+ V +RIL+F Sbjct: 233 LWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYRILIF 292 Query: 258 YVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTG 317 Y+ +L V+LS+YPWNE+ GSPFVM F ++G A ++N VV+TAALS N G+++ Sbjct: 293 YICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGVYANS 352 Query: 318 RMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNYLVPEKVFVWVTSIATF 377 RMLY LA+ G AP K GVP A+ LS A V++NYL+P + + ++ Sbjct: 353 RMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLMALVVA 412 Query: 378 GAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAFLVLVVGLMAYFPDTR 437 + W +I L LK R+++ A+ L ++ + +PVS+++ LAF+ L++ ++A P Sbjct: 413 ALVLNWALISLTHLKSRRAMVAAGE-TLVFKSFWFPVSNWICLAFMALILVILAMTPGLS 471 Query: 438 VALYVGPAFLVLLTVLFYTFK 458 V++ + P +LV++ Y FK Sbjct: 472 VSVLLVPVWLVVMWA-GYAFK 491 Lambda K H 0.328 0.142 0.444 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: 694 Number of extensions: 30 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: 473 Length of database: 506 Length adjustment: 34 Effective length of query: 439 Effective length of database: 472 Effective search space: 207208 Effective search space used: 207208 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: 52 (24.6 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