Align Amino acid transporter (characterized, see rationale)
to candidate WP_102938052.1 B1812_RS04230 amino acid permease
Query= uniprot:A0A0H3C3Q5 (483 letters) >NCBI__GCF_002117405.1:WP_102938052.1 Length = 481 Score = 326 bits (835), Expect = 1e-93 Identities = 180/479 (37%), Positives = 280/479 (58%), Gaps = 23/479 (4%) Query: 9 SFWTRRKAIDTITAGH-ADSHQLKKTLSWPHLVALGVGAIVGTGIYTLTG-VGAGLAGPG 66 S + RK+I + A + A+ + LK+ L W L+A+G+G I+G GI+ LTG A AGPG Sbjct: 7 SVYFSRKSIHLVIAENDAEENGLKRALGWASLMAMGIGGIIGAGIFVLTGQAAADYAGPG 66 Query: 67 VILSFLIAGAVCACAALCYAELSTMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVC 126 V +SFL++G C ALCYAEL+ +IPA+GS YTY+Y +GE AW +GW+L+LEY Sbjct: 67 VTISFLLSGLACTFVALCYAELAALIPAAGSTYTYTYVTLGEIFAWIIGWNLVLEYAAGA 126 Query: 127 AAVAVGWSAHAHGLFKMIGF--PDAL----------LAGPHQGGLINMPAVFISMAVAGL 174 A VAVGW+ + + + + +G P+AL + G H G+ N+PA I + + L Sbjct: 127 ATVAVGWAGYFNRVMQGLGIHLPEALTSAYFANAHSIGGTH--GVFNVPAAAIILLLTAL 184 Query: 175 LALGTRESATVNMVLVFVKIIALIVFVVLCLPAFNLAHFTPFMPNGFQAHVPEGAAADAA 234 L GT ES+ N ++V +K++ ++V + + + A++TP +P G + Sbjct: 185 LMRGTSESSFFNNIIVVIKVMVVLVVIFVGAAHVDAANWTPLIPENTDHFGHFGWS---- 240 Query: 235 KVGVMAAASLIFFAFYGFDAVSTAAEETKNPKRDLTIGIVGSMAVCTAIYMIVAAVSIGA 294 GV+ AS++FFA+ GFD VSTAA+E P+RD+ IGI+GS+ +CT +Y+ VAAV+ G Sbjct: 241 --GVVRGASVVFFAYIGFDGVSTAAQEAHTPQRDVPIGILGSLVICTILYVAVAAVATGV 298 Query: 295 SRTEVFSKSEAPLVFILESLNHGKIAQLVALAAVIALPTVILAFMYGQSRIFFVMARDGL 354 + + P+ +++ ++ +V L A+ L T IL ++GQ+RIF+ MA+DGL Sbjct: 299 VSYKELGVPD-PMALVMDRTGVAWLSWVVKLGAIAGLTTAILLLLFGQTRIFYAMAQDGL 357 Query: 355 LPRALSKVNAKTGTPVMMTLLTGVLAAVISGLLSLKDIAELANAGTLWAFIAVGASVILL 414 LP+ + V+ TP + L GV A+ +GL + + E+ + GTL AF V +V+ L Sbjct: 358 LPKVFAAVHPVWRTPAVSQALVGVFVALAAGLFPINILDEMVSIGTLAAFALVCGAVLHL 417 Query: 415 RLREPNRPRVFSTPLWPIVAPAGILGCLYLFLSLPGKTQLYFLYAHLIGAVVYLAYGMR 473 R +P+ R F P P + GI CL L ++LP +T L + IG +Y YG++ Sbjct: 418 RRSQPDMHRPFRAPGIPAMPLLGIASCLALMVALPLETWLRLIVWTAIGMAIYFFYGVK 476 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: 708 Number of extensions: 42 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: 481 Length adjustment: 34 Effective length of query: 449 Effective length of database: 447 Effective search space: 200703 Effective search space used: 200703 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