Align Sodium/proton-dependent alanine carrier protein (characterized)
to candidate WP_057687364.1 ABB28_RS15975 alanine:cation symporter family protein
Query= SwissProt::P30145 (445 letters) >NCBI__GCF_001431535.1:WP_057687364.1 Length = 501 Score = 447 bits (1151), Expect = e-130 Identities = 235/453 (51%), Positives = 304/453 (67%), Gaps = 22/453 (4%) Query: 1 MIRLVTMGKSSEAGVSSFQALTMSLSGRIGVGNVAGTATGIAYGGPGAVFWMWVITFIGA 60 M RL G+ S+AGVSSFQAL MS++GR+G+GN+AG AT IA+GGPGA+FWMWV+ F+GA Sbjct: 43 MCRLTVAGEKSDAGVSSFQALAMSMAGRMGIGNIAGVATAIAFGGPGAIFWMWVMGFLGA 102 Query: 61 ATAYVESTWRKFIKRNKTDNTVAVRRST-LKKALAGNGLRCSRA-AIILSMAVLMPGIQA 118 +T+YVE T + K + + ++KA+ + A A I++ LMPG+QA Sbjct: 103 STSYVECTLAQIYKTKDAEGRYRGGPAYYIEKAMGLKWYAMAFALATIVAAGFLMPGVQA 162 Query: 119 NSIADSFSNA--------------FGIP-----KLVTGIFVIAVLGFTIFGGVKRIAKTA 159 N+IADS NA FG+ KL G+ V +L IFGGVKRIA A Sbjct: 163 NAIADSIINACRGGALCGPLDGQAFGMDQVQALKLGIGVVVAVLLAVVIFGGVKRIANFA 222 Query: 160 EIVVPFMAVGYLFVAIAIIAANIEKVPDVFGLIFKSAFGADQVFGGILGSAVMWGVKRGL 219 EIVVPFMA G++ +AI I+ N ++VP +F IF SAFG FG ++G AV WGVKRG+ Sbjct: 223 EIVVPFMAAGFIIMAIVIMIMNADQVPVMFNTIFSSAFGTHAAFGAMIGLAVEWGVKRGI 282 Query: 220 YANEAGQGTGAHPAAAAEVSHPAKQGLVQAFSIYLDVFLVVTATALMILFTGQYNVINEK 279 YANEAGQGTG H AAA+EVSHPAKQG VQAF+IY D +V TATA +IL +G YNV + Sbjct: 283 YANEAGQGTGPHAAAASEVSHPAKQGYVQAFAIYFDTMMVCTATAFLILASGTYNVYSPV 342 Query: 280 TG-ETIVEHLKGVEPGAGYTQAAVDTLFPGFGSAFIAIALFFFAFTTMYAYYYIAETNLA 338 G E I + LKG+ GAGY QA V+ + PG+G++F+AIA+FFFAFTT+ AYYY+AETNL Sbjct: 343 AGAEPIFQGLKGIAEGAGYAQAGVEAVLPGWGASFVAIAIFFFAFTTIMAYYYMAETNLT 402 Query: 339 YLVRSEKRGTAFFALKLVFLAATFYGTVKTATTAWAMGDIGLGIMVWLNLIAILLLFKPA 398 YL + KR L+L + +G A AWA+GDIG+G+M WLN++AIL++ KPA Sbjct: 403 YLNNNAKRPLTVLLLRLGIIGMVIFGAFHNAQLAWALGDIGVGLMAWLNIVAILIVQKPA 462 Query: 399 YMALKDYEEQLKQGKDPEFNASKYGIKNAKFWE 431 +AL+DYE Q K G DP F+ GIKNA FW+ Sbjct: 463 MIALRDYERQKKLGLDPTFDPVALGIKNADFWQ 495 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: 648 Number of extensions: 29 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: 445 Length of database: 501 Length adjustment: 33 Effective length of query: 412 Effective length of database: 468 Effective search space: 192816 Effective search space used: 192816 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