Align Amino acid transporter (characterized, see rationale)
to candidate WP_085770386.1 B1812_RS03615 amino acid permease
Query= uniprot:A0A0H3C3Q5 (483 letters) >NCBI__GCF_002117405.1:WP_085770386.1 Length = 488 Score = 315 bits (807), Expect = 2e-90 Identities = 180/472 (38%), Positives = 270/472 (57%), Gaps = 20/472 (4%) Query: 13 RRKAIDTITAGHADSHQLKKTLSWPHLVALGVGAIVGTGIYTLTGVGAGL-AGPGVILSF 71 R K+I+++ A + L++ L LV +G+G ++G GI+ LTGV A AGPGV LSF Sbjct: 8 RAKSIESLQAEALERGALRRALGLWQLVGIGLGGLIGVGIFVLTGVVAATQAGPGVALSF 67 Query: 72 LIAGAVCACAALCYAELSTMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVCAAVAV 131 LIAG AALCYAE ++M+P +GSAYTY+YA +GE AW +GW L+LEY LV A V++ Sbjct: 68 LIAGVASGAAALCYAEFASMLPVAGSAYTYAYAVLGELPAWIIGWDLLLEYALVVAVVSI 127 Query: 132 GWSAHAHGLFKMIGFPDALLA----GPHQGGLINMPAVFISMAVAGLLALGTRESATVNM 187 GWS + L + G A G G ++++ A+ + VA LL L A N Sbjct: 128 GWSGYLRALLALFGVAPPEWAAGAPGTGDGHILDLFAMLGAFGVALLLTLRVEWGARFNT 187 Query: 188 VLVFVKIIALIVFVVLCLPAFNLAHFTPFMPNGFQAHVPEGAAADAAKVGVMAAASLIFF 247 +V +KI A+IV ++ P N A++ PFMP GF GV+ A+++FF Sbjct: 188 AMVLLKIAAVIVVILAAAPHINPANWRPFMPFGFG--------------GVVEGAAVVFF 233 Query: 248 AFYGFDAVSTAAEETKNPKRDLTIGIVGSMAVCTAIYMIVAAVSIGASRTEVFSKSEAPL 307 A +G+D ++TA EE P+RDL ++ S+ V +Y++++ G +R + + AP+ Sbjct: 234 AVFGYDTLTTAGEEALEPQRDLPRAVLLSLVVSLTLYILMSLALTGIARYDTLDNA-APV 292 Query: 308 VFILESLNHGKIAQLVALAAVIALPTVILAFMYGQSRIFFVMARDGLLPRALSKVNAKTG 367 +L G +V+ AAV+ + +V+LAF+ G +RI+F M+RDGLLP ++ + + Sbjct: 293 ASAFAALGMGWATLVVSAAAVVGILSVMLAFLLGCARIWFAMSRDGLLPAWFARPHPQFA 352 Query: 368 TPVMMTLLTGVLAAVISGLLSLKDIAELANAGTLWAFIAVGASVILLRLREPNRPRVFST 427 TP TL+ G L A++S ++++AEL N GTL AF+ + +VI LR P+ PR F Sbjct: 353 TPYRPTLIAGGLCALVSAFFPIREVAELVNIGTLSAFVVICLAVIALRHTRPDVPRGFRA 412 Query: 428 PLWPIVAPAGILGCLYLFLSLPGKTQLYFLYAHLIGAVVYLAYGMRKSVLAQ 479 PL P + G+ L+L LP F+ +IG VY YG R S LA+ Sbjct: 413 PLSPYLPLIGVGFSLWLLSKLPAIAWERFVVWLIIGLAVYFLYGRRHSRLAK 464 Lambda K H 0.326 0.138 0.415 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: 661 Number of extensions: 37 Number of successful extensions: 7 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: 483 Length of database: 488 Length adjustment: 34 Effective length of query: 449 Effective length of database: 454 Effective search space: 203846 Effective search space used: 203846 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 Apr 09 2024. 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