Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate WP_005816838.1 DHAF_RS12190 amino acid permease
Query= TCDB::P40812 (497 letters) >NCBI__GCF_000021925.1:WP_005816838.1 Length = 462 Score = 378 bits (970), Expect = e-109 Identities = 188/452 (41%), Positives = 295/452 (65%), Gaps = 9/452 (1%) Query: 22 HEEGYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILRAL 81 H H+ + NR +QMIA+GGAIGTGLF G+ +Q+ GPA+ + YL+ G FFI+RAL Sbjct: 7 HHVELHRGLKNRHIQMIALGGAIGTGLFYGSATTIQLVGPAIIVSYLLGGTAIFFIVRAL 66 Query: 82 GELVLHRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGD 141 GE+ + +P +G+F +A ++LG+ + +GW Y+ N+ + ++T V +Y+++W + + Sbjct: 67 GEMCVDQPVAGAFSYFAYKYLGDFPGFFSGWNYWFNYIAVSMAELTVVGVYINFW--YPN 124 Query: 142 VPQWVFALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGT--IFLGTGQPLE 199 VPQWV AL L I+ +N+I V+ F E EFWFALIKV+AI+ + G IF G G E Sbjct: 125 VPQWVTALAFLVIITLINLINVEAFGEFEFWFALIKVVAILAMIAFGLVMIFFGLG---E 181 Query: 200 GNATGFHLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINS 259 A GF + +GGF P+G+ L+ + V+F+F +EL+G A E DP++ +PKAIN Sbjct: 182 QGAVGFSNLWTHGGFLPNGVWGLLLSLVIVMFSFGGVELIGITAAEADDPKRSIPKAINQ 241 Query: 260 VIWRIGLFYVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSL 319 V+WRI +FY+G++ +L++L PW+ SPFV FS +G+P I+N VVLTAALS Sbjct: 242 VVWRILIFYIGALTILMILYPWDQIGTSGSPFVEIFSAIGIPAAAHILNFVVLTAALSVY 301 Query: 320 NSGLYCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVFE 379 NSG+Y GR+L +++ G+APKF+ K+SR +P G+ A+ V ++ V LN+LVP +VF Sbjct: 302 NSGIYSNGRMLHGLALQGNAPKFLTKVSRNGIPINGVFASSAVTLIAVILNFLVPGKVFL 361 Query: 380 IVLNFASLGIIASWAFIMVCQMRLRQA-IKEGKAADVSFKLPGAPFTSWLTLLFLLSVLV 438 +++ A++ I +WA I+V Q+R R+ ++G+ + FK+P P ++++ L FL V+V Sbjct: 362 YLISIATIAGIFNWAMILVTQLRFRKVEAEKGREDQLQFKMPLYPISNYIALAFLAMVVV 421 Query: 439 LMAFDYPNGTYTIASLPLIAILLVAGWFGVRR 470 LMA+ P+ Y++ P+ I+L G+ +RR Sbjct: 422 LMAY-IPDMVYSLYIGPIWIIILYIGYKFLRR 452 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: 675 Number of extensions: 40 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: 497 Length of database: 462 Length adjustment: 34 Effective length of query: 463 Effective length of database: 428 Effective search space: 198164 Effective search space used: 198164 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 24 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