Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate WP_057687364.1 ABB28_RS15975 alanine:cation symporter family protein
Query= TCDB::W0WFC6 (449 letters) >NCBI__GCF_001431535.1:WP_057687364.1 Length = 501 Score = 242 bits (618), Expect = 2e-68 Identities = 153/473 (32%), Positives = 234/473 (49%), Gaps = 51/473 (10%) Query: 11 LNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSGEISPFQAL 70 +N ++W ++ + L GLY + +FM + RL G ++S +S FQAL Sbjct: 8 INSIIWSKALIFMCLAAGLYFSVRTRFMQIRGFFEMCRLTVAG----EKSDAGVSSFQAL 63 Query: 71 MTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKDERNE 130 +A +G GNIAGVATAI GGPGA+FWMW +G +T + E LA Y+ KD Sbjct: 64 AMSMAGRMGIGNIAGVATAIAFGGPGAIFWMWVMGFLGASTSYVECTLAQIYKTKDAEGR 123 Query: 131 HVGGPMYAIKNGLGKRWAWLGAAFALFGGLAGFGIGNMVQVNSMADAL------------ 178 + GGP Y I+ +G + W AFAL +A + VQ N++AD++ Sbjct: 124 YRGGPAYYIEKAMGLK--WYAMAFALATIVAAGFLMPGVQANAIADSIINACRGGALCGP 181 Query: 179 --EVSFGVPDWV------TGVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIV 230 +FG+ D V GV ++ +VI GG++RI AE +VPFM G+I+ ++++ Sbjct: 182 LDGQAFGM-DQVQALKLGIGVVVAVLLAVVIFGGVKRIANFAEIVVPFMAAGFIIMAIVI 240 Query: 231 LVVHAEAIPGAFQLIFTHAFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQ 290 ++++A+ +P F IF+ AF AA G G AV +GV RGI++NEAG GT A Sbjct: 241 MIMNADQVPVMFNTIFSSAFGTHAAFGAMIGLAV----EWGVKRGIYANEAGQGTGPHAA 296 Query: 291 AAGTTHSAVRSGLIGMLGTFIDTLIICSLTGLAIITSGVWT----------------SGA 334 AA + G + + DT+++C+ T I+ SG + A Sbjct: 297 AASEVSHPAKQGYVQAFAIYFDTMMVCTATAFLILASGTYNVYSPVAGAEPIFQGLKGIA 356 Query: 335 SGAALSSAAFEAAMPGVGHYILSLALVVFAYTTILGWSYYGERCWEYLAGTR----AILP 390 GA + A EA +PG G +++A+ FA+TTI+ + Y E YL +L Sbjct: 357 EGAGYAQAGVEAVLPGWGASFVAIAIFFFAFTTIMAYYYMAETNLTYLNNNAKRPLTVLL 416 Query: 391 FRIVWTLAIPFGAMTQLDFAWLVADTLNALMAIPNLIALLLLSPVVFRLTREY 443 R+ + FGA AW + D LMA N++A+L++ R+Y Sbjct: 417 LRLGIIGMVIFGAFHNAQLAWALGDIGVGLMAWLNIVAILIVQKPAMIALRDY 469 Lambda K H 0.326 0.140 0.437 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: 561 Number of extensions: 38 Number of successful extensions: 6 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: 449 Length of database: 501 Length adjustment: 33 Effective length of query: 416 Effective length of database: 468 Effective search space: 194688 Effective search space used: 194688 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