Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate 354002 BT4476 amino acid carrier protein (NCBI ptt file)
Query= TCDB::W0WFC6 (449 letters) >FitnessBrowser__Btheta:354002 Length = 462 Score = 272 bits (696), Expect = 1e-77 Identities = 160/446 (35%), Positives = 253/446 (56%), Gaps = 11/446 (2%) Query: 7 WVVDLNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSGEISP 66 ++ ++N ++W ++++++LG ++ + +F+ L LL + K + +S Sbjct: 3 FINEINDILWTYILIIMLLGCAVWFSIRTRFVQFRMLREMIILLSESAGKGKQGEKHVSS 62 Query: 67 FQALMTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKD 126 FQA +A+ VGTGN+AGVATAI +GGPGA+FWMW AL+G ++ F E LA Y+ + Sbjct: 63 FQAFAITIASRVGTGNLAGVATAIAIGGPGAVFWMWVIALLGASSAFIESTLAQLYKIRG 122 Query: 127 ERNEHVGGPMYAIKNGLGKRWAWLGAAFALFGGLA-GFGIGNMVQVNSMADALEVSFGVP 185 ++ VGGP Y +K GL + W+G FA+ + GF N VQ N++ A E +FG Sbjct: 123 -KDSFVGGPAYYMKKGL--KQPWMGILFAVLISITFGFAF-NSVQSNTICAAAEHAFGFN 178 Query: 186 DWVTGVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAFQLI 245 V G +T ++I GGIRRI V+ +VP M +GY+ ++++++++ +P LI Sbjct: 179 HTVLGGVLTALTLVIIFGGIRRIAHVSSIIVPVMALGYVGLALVIVLLNITHLPEVISLI 238 Query: 246 FTHAFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGTTHSAVRSGLIG 305 +HAF A GG G A+M G+ RG+FSNEAG+G+A A A V+ GLI Sbjct: 239 ISHAFGWEQALGGGVGMALMQ----GIKRGLFSNEAGMGSAPNAAATANVTHPVKQGLIQ 294 Query: 306 MLGTFIDTLIICSLTGLAIITSGVWTSGAS-GAALSSAAFEAAMPGVGHYILSLALVVFA 364 L F DTL+ C+ T I+ SG G+S G L+ A + G +++AL FA Sbjct: 295 TLAVFTDTLLNCTCTAFIILFSGAPLDGSSNGVQLTQQALTNEIGASGSIFVAVALFFFA 354 Query: 365 YTTILGWSYYGERCWEYLAGTRAIL-PFRIVWTLAIPFGAMTQLDFAWLVADTLNALMAI 423 +++ILG YYGE ++ + +L +RI+ + + FG++ LD W +AD ALMA+ Sbjct: 355 FSSILGNYYYGEANIRFITAKKWVLHTYRILVSGMVLFGSVATLDLVWSLADITMALMAV 414 Query: 424 PNLIALLLLSPVVFRLTREYFAKARS 449 NLIA++ L RL +Y A+ ++ Sbjct: 415 CNLIAIIFLGKYAIRLLSDYRAQKKA 440 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: 496 Number of extensions: 28 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: 462 Length adjustment: 33 Effective length of query: 416 Effective length of database: 429 Effective search space: 178464 Effective search space used: 178464 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 17 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