Align L-alanine and D-alanine permease (characterized)
to candidate 14258 b0112 aromatic amino acid transporter (NCBI)
Query= reanno::pseudo5_N2C3_1:AO356_17670 (473 letters) >FitnessBrowser__Keio:14258 Length = 457 Score = 395 bits (1016), Expect = e-114 Identities = 195/444 (43%), Positives = 280/444 (63%), Gaps = 4/444 (0%) Query: 15 GGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALG 74 G LKR L RHI+L+ALG IG GLFLGSA I+ AGP I+L Y I G +IMR LG Sbjct: 8 GEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMRQLG 67 Query: 75 EMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPR 134 EM V PVAGSFS +A Y G AGF +GWNYW L+++ +AE+TAV Y+ W+P++P Sbjct: 68 EMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPEIPT 127 Query: 135 WIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALG 194 W+ A V + +INL VK FGE EFWFA+IK++ ++AM+I G G + F GN G Sbjct: 128 WVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFG-GWLLFS-GNGGPQAT 185 Query: 195 ISNLWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRI 254 +SNLW GGF+P+G +G++M + ++MF++ G+E++G+TA EA NP+++IP A V +RI Sbjct: 186 VSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIYRI 245 Query: 255 LLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIF 314 L+FY+G+L V+LS+ PW + SPFV+ F LG A +N VV+TAALS N ++ Sbjct: 246 LIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYNSCVY 305 Query: 315 STGRMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNYLVPEKVFVWVTSI 374 RML+ LAQ G AP A GVP +L+S L VL+NYL PE F + ++ Sbjct: 306 CNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGLLMAL 365 Query: 375 ATFGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAFLVLVVGLMAYFP 434 + W MI LA +KFR++ + ++ LYP+ +++ L F+ V+ +M P Sbjct: 366 VVSALVINWAMISLAHMKFRRA-KQEQGVVTRFPALLYPLGNWICLLFMAAVLVIMLMTP 424 Query: 435 DTRVALYVGPAFLVLLTVLFYTFK 458 +++Y+ P +L++L + Y FK Sbjct: 425 GMAISVYLIPVWLIVLGI-GYLFK 447 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: 636 Number of extensions: 28 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: 457 Length adjustment: 33 Effective length of query: 440 Effective length of database: 424 Effective search space: 186560 Effective search space used: 186560 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