Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate 14258 b0112 aromatic amino acid transporter (NCBI)
Query= TCDB::P40812 (497 letters) >FitnessBrowser__Keio:14258 Length = 457 Score = 331 bits (849), Expect = 3e-95 Identities = 170/446 (38%), Positives = 271/446 (60%), Gaps = 10/446 (2%) Query: 22 HEEGYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILRAL 81 H E + + NR +Q+IA+GGAIGTGLFLG+ + +Q AGP + L Y I G +F I+R L Sbjct: 7 HGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMRQL 66 Query: 82 GELVLHRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGD 141 GE+V+ P +GSF +A ++ G A + +GW Y++ + + + ++TAV Y+ +W + + Sbjct: 67 GEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFW--YPE 124 Query: 142 VPQWVFALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVG--TIFLGTGQPLE 199 +P WV A ++ +N+ VK F EMEFWFA+IKV+A+V ++ G +F G G P Sbjct: 125 IPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSGNGGP-- 182 Query: 200 GNATGFHLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINS 259 AT +L D GGF PHG ++++ ++F+F +ELVG A E +P++ +PKA N Sbjct: 183 -QATVSNL-WDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQ 240 Query: 260 VIWRIGLFYVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSL 319 VI+RI +FY+GS+ +L+ L+PW A SPFV F +LG ++ + +NIVVLTAALS Sbjct: 241 VIYRILIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVY 300 Query: 320 NSGLYCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVFE 379 NS +YC R+L ++ G+APK +A + ++ VP IL + +V + V +NYL P F Sbjct: 301 NSCVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFG 360 Query: 380 IVLNFASLGIIASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLLSVLVL 439 +++ ++ +WA I + M+ R+A K+ + F P +W+ LLF+ +VLV+ Sbjct: 361 LLMALVVSALVINWAMISLAHMKFRRA-KQEQGVVTRFPALLYPLGNWICLLFMAAVLVI 419 Query: 440 MAFDYPNGTYTIASLPLIAILLVAGW 465 M P ++ +P+ I+L G+ Sbjct: 420 MLMT-PGMAISVYLIPVWLIVLGIGY 444 Lambda K H 0.328 0.140 0.434 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: 592 Number of extensions: 31 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: 497 Length of database: 457 Length adjustment: 33 Effective length of query: 464 Effective length of database: 424 Effective search space: 196736 Effective search space used: 196736 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