Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate 206150 DVU0724 sodium/alanine symporter family protein
Query= TCDB::W0WFC6 (449 letters) >MicrobesOnline__882:206150 Length = 468 Score = 434 bits (1115), Expect = e-126 Identities = 228/437 (52%), Positives = 294/437 (67%), Gaps = 6/437 (1%) Query: 11 LNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSGEISPFQAL 70 +N VWGP +L L++GTG+YL + L + +VRL + R ++ GR + G++S F AL Sbjct: 10 VNAFVWGPPLLALLVGTGIYLTIRLGLLQVVRLPLALRYVF-GRDDEHHEEGDVSSFAAL 68 Query: 71 MTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKDERNE 130 T LAAT+GTGNI GVATA+ GGPGALFWMW A GMATK++E +LAV YR D + Sbjct: 69 CTALAATIGTGNIVGVATAVAAGGPGALFWMWVAAFFGMATKYAEGLLAVKYRVTDANGQ 128 Query: 131 HVGGPMYAIKNGLGKRWAWLGAAFALFGGL-AGFGIGNMVQVNSMADALEVSFGVPDWVT 189 GGPMY ++ GLG R L AFAL G L A FGIG QVN++ DA +S G+P T Sbjct: 129 MSGGPMYYLERGLGSRM--LARAFALCGILVAFFGIGTFAQVNAIKDAASLSLGIPPLAT 186 Query: 190 GVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAFQLIFTHA 249 V LV LGG+R I +VAE +VPFM V YI+AS VLV+H + IP A +I A Sbjct: 187 AVVLTTTVALVTLGGLRSIARVAEKVVPFMAVFYIIASCAVLVMHLDRIPDAVMVILHSA 246 Query: 250 FTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGTTHSAVRSGLIGMLGT 309 F P AA GG AG V+ A+R GVARG+FSNE+GLG+A IA AA T S VR GLI M GT Sbjct: 247 FNPQAALGGAAGMTVLTAMRAGVARGVFSNESGLGSAPIAAAAARTKSCVRQGLISMTGT 306 Query: 310 FIDTLIICSLTGLAIITSGVWTS-GASGAALSSAAFEAAM-PGVGHYILSLALVVFAYTT 367 F DT++IC++TGL ++ +GVW +GAA+++AAF A + +G Y +L L++FA+TT Sbjct: 307 FFDTIVICTMTGLVLVVTGVWNDPQLAGAAMTNAAFAAGLESSLGQYAATLGLILFAFTT 366 Query: 368 ILGWSYYGERCWEYLAGTRAILPFRIVWTLAIPFGAMTQLDFAWLVADTLNALMAIPNLI 427 ILGW+YYGERC EYL G R ILP+R+V+ + GA L+ W++AD +N LMAIPNLI Sbjct: 367 ILGWNYYGERCTEYLFGVRGILPYRLVFIGLVAAGAFVHLELIWVLADIVNGLMAIPNLI 426 Query: 428 ALLLLSPVVFRLTREYF 444 LL LS V+ TR +F Sbjct: 427 GLLGLSGVIIAETRAFF 443 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: 576 Number of extensions: 28 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: 449 Length of database: 468 Length adjustment: 33 Effective length of query: 416 Effective length of database: 435 Effective search space: 180960 Effective search space used: 180960 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