Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate WP_046009929.1 OLEAN_RS15165 sodium:alanine symporter family protein
Query= TCDB::W0WFC6 (449 letters) >NCBI__GCF_000967895.1:WP_046009929.1 Length = 461 Score = 533 bits (1374), Expect = e-156 Identities = 266/443 (60%), Positives = 328/443 (74%), Gaps = 14/443 (3%) Query: 11 LNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSGEISPFQAL 70 +NG WGP ML+LI TGL+L LGLK P++ + GF LLW GR E G+IS F AL Sbjct: 8 INGWAWGPPMLLLIAITGLFLTLGLKAYPILNIKKGFSLLWSGRKAKGE--GDISGFNAL 65 Query: 71 MTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKDERNE 130 MT L+AT+GTGNIAGVATAI +GGPGALFWMW AL+GMATK+SE VLAVHYREKDE Sbjct: 66 MTSLSATIGTGNIAGVATAIAMGGPGALFWMWMIALIGMATKYSEAVLAVHYREKDENGN 125 Query: 131 HVGGPMYAIKNGLGKRWAWLGAAFALFGGLAGFGIGNMVQVNSMADALEVSFGVPDWVTG 190 VGGPMY IKNGLG W W+ AFA FG +AGFGIGN VQ NS+AD + SF V + TG Sbjct: 126 FVGGPMYYIKNGLGVNWKWMATAFAFFGMIAGFGIGNGVQANSVADVMHSSFQVSELTTG 185 Query: 191 VATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAFQLIFTHAF 250 + ++ LV+LGGI+RI VA LVPFM + YI+ +I+LV++ + IP AF I T+AF Sbjct: 186 IIMAILAALVLLGGIKRIATVAGKLVPFMAITYIIGGLILLVIYFDRIPAAFSTILTYAF 245 Query: 251 TPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGTTHSAVRSGLIGMLGTF 310 TP +A GGFAGA+V AIRFG+ARG+FSNEAGLG+A IA AA T++ V+ G I MLGTF Sbjct: 246 TPASAAGGFAGASVWMAIRFGIARGVFSNEAGLGSAPIAHAAAQTNNPVQQGTIAMLGTF 305 Query: 311 IDTLIICSLTGLAIITSGVWT-------SGASGAALSSAAFEAAMPGVGHY-----ILSL 358 IDTL+IC++TGL I+ SG W SGA L++AAF P +G + I++ Sbjct: 306 IDTLVICTITGLVIVASGAWQVIDPGTGKALSGANLTAAAFSQGFPSIGGFNFGEMIVTF 365 Query: 359 ALVVFAYTTILGWSYYGERCWEYLAGTRAILPFRIVWTLAIPFGAMTQLDFAWLVADTLN 418 L++FA+TT+LGWS+YGE+C EYL G ++I+ FRIVW LAIP GA +LD AWLVADTLN Sbjct: 366 GLIIFAFTTLLGWSFYGEKCAEYLFGVKSIIIFRIVWVLAIPIGATFELDLAWLVADTLN 425 Query: 419 ALMAIPNLIALLLLSPVVFRLTR 441 ALMA+PNL+ALLLLSPVVF+LT+ Sbjct: 426 ALMALPNLVALLLLSPVVFKLTK 448 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: 691 Number of extensions: 38 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: 449 Length of database: 461 Length adjustment: 33 Effective length of query: 416 Effective length of database: 428 Effective search space: 178048 Effective search space used: 178048 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