Align Sodium/proton-dependent alanine carrier protein (characterized)
to candidate WP_057687367.1 ABB28_RS15990 alanine:cation symporter family protein
Query= SwissProt::P30145 (445 letters) >NCBI__GCF_001431535.1:WP_057687367.1 Length = 489 Score = 404 bits (1038), Expect = e-117 Identities = 199/437 (45%), Positives = 285/437 (65%), Gaps = 7/437 (1%) Query: 1 MIRLVTMGKSSEAGVSSFQALTMSLSGRIGVGNVAGTATGIAYGGPGAVFWMWVITFIGA 60 M+RL+ ++SE+G+S FQAL +SLS R+GVGN+AG A IA+GGPGA+FWMWV+ F GA Sbjct: 45 MLRLMFKHRASESGLSPFQALNISLSSRVGVGNIAGVAMAIAFGGPGAIFWMWVVAFFGA 104 Query: 61 ATAYVESTWRKFIKRNKTDNTVAVRRST-LKKALAGNGLRCSRAAIILSMAVLMPGIQAN 119 ++A+VEST + K+ + ++K L A ++ A ++ G Q+N Sbjct: 105 SSAFVESTLAQIYKQRDAQGQYRGGPAYYMEKGLGQRWYAVIFAICTVAAAAMLAGTQSN 164 Query: 120 SIADSFSNAFGIPKLVTGIFVIAVLGFTIFGGVKRIAKTAEIVVPFMAVGYLFVAIAIIA 179 +IA + A+ +P + + V+ +L IFGGV+RIA + +VP MA YL VA+ ++ Sbjct: 165 AIASALHEAWDLPVHASAVGVVLLLALIIFGGVRRIAAVTQWIVPLMATAYLLVALVVML 224 Query: 180 ANIEKVPDVFGLIFKSAFGADQVFGGILGSAVMWGVKRGLYANEAGQGTGAHPAAAAEVS 239 + E++P+V LI +SAFG D FG ++G A+ WGV+RG+ +NEAG G+GAHPAAAAEVS Sbjct: 225 LSYERIPEVLSLIMRSAFGLDATFGAMIGVAIQWGVRRGVLSNEAGMGSGAHPAAAAEVS 284 Query: 240 HPAKQGLVQAFSIYLDVFLVVTATALMILFTGQYNVINEKT------GETIVEHLKGVEP 293 HP KQGLVQAFS+Y+D +V +ATA +IL TG YNV + ++++L G+E Sbjct: 285 HPVKQGLVQAFSVYIDTMVVCSATAFLILSTGMYNVYDPAVNGVPDQARMLLDNLPGMEA 344 Query: 294 GAGYTQAAVDTLFPGFGSAFIAIALFFFAFTTMYAYYYIAETNLAYLVRSEKRGTAFFAL 353 G + Q AV++ PGFG +F+A+A+ FAFTT+ A YY+ +TN++YL R + Sbjct: 345 GPRFVQHAVESALPGFGKSFVALAILPFAFTTILALYYMGDTNVSYLCRDKPAAWIVNVF 404 Query: 354 KLVFLAATFYGTVKTATTAWAMGDIGLGIMVWLNLIAILLLFKPAYMALKDYEEQLKQGK 413 +++FLA Y + +AT AW +GDIG+G+M WLN+IAILLL KPA AL+DYE K G Sbjct: 405 RVLFLALAAYSAINSATLAWTLGDIGVGMMSWLNIIAILLLHKPALAALRDYETSRKAGI 464 Query: 414 DPEFNASKYGIKNAKFW 430 DP F + GIK A W Sbjct: 465 DPVFEPDRLGIKGASLW 481 Lambda K H 0.324 0.137 0.407 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: 610 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: 445 Length of database: 489 Length adjustment: 33 Effective length of query: 412 Effective length of database: 456 Effective search space: 187872 Effective search space used: 187872 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 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