Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate SMc04263 SMc04263 amino acid carrier transmembrane protein
Query= TCDB::W0WFC6 (449 letters) >FitnessBrowser__Smeli:SMc04263 Length = 472 Score = 318 bits (814), Expect = 3e-91 Identities = 185/447 (41%), Positives = 261/447 (58%), Gaps = 16/447 (3%) Query: 11 LNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSGEISPFQAL 70 LN + WG +++ +L GLY + L F +V FR+L +G SKD + ISPFQAL Sbjct: 8 LNTIFWGYVLIYGLLAVGLYFTVRLGFPQIVHFSEMFRVLSRGGSKD---AAGISPFQAL 64 Query: 71 MTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKDERNE 130 M LA+ VGTGN+AGVA A++LGGPGA FWMW A VGMAT ++E LA Y+ ++E + Sbjct: 65 MVSLASRVGTGNLAGVAVALYLGGPGATFWMWIVAFVGMATAYAESALAQLYKIRNEDGQ 124 Query: 131 HVGGPMYAIKNGLGKRWA--WLGAAFALFGGLAGFGIGNMVQVNSMADALEVSFGVPDWV 188 + GGP + I GL WA A L GL + N VQ NS+ADA++ +FGVP Sbjct: 125 YRGGPAFYIARGLNAPWAATIFSACLILSFGL----VFNAVQANSIADAVQGAFGVPKLA 180 Query: 189 TGVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAFQLIFTH 248 GVA L++G+VI GGIR+I +VAE +VPFM Y++ +V VL+ +A A+PG I + Sbjct: 181 VGVAVALLSGVVIFGGIRQIARVAEIVVPFMAAAYLLTAVYVLIANASAVPGVLWTIISS 240 Query: 249 AFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGT--THSAVRSGLIGM 306 AF A GG G + AA+ GV RG+FSNEAG+G+A A T H G + Sbjct: 241 AFGFQEAAGGITG-GIAAAMLNGVKRGLFSNEAGMGSAPNIAAVATPVPHHPSSQGFVQS 299 Query: 307 LGTFIDTLIICSLTGLAIITSGVWT--SGASGAALSSAAFEAAMPGVGHYILSLALVVFA 364 LG FIDT++IC+ T + I+ SG SG +G L+ AA + G Y +++A+ FA Sbjct: 300 LGVFIDTILICTATSVMILLSGTLEPGSGVTGTQLTQAAMSTHIGSAGTYFIAIAIFFFA 359 Query: 365 YTTILGWSYYGERCWEYLAGTR--AILPFRIVWTLAIPFGAMTQLDFAWLVADTLNALMA 422 +T+I+G Y E YL G ++ R + +GA + + AD LMA Sbjct: 360 FTSIIGNYSYAENALTYLGGGNRLGLMIMRCATLAMVVWGAYESITTVFDAADASMGLMA 419 Query: 423 IPNLIALLLLSPVVFRLTREYFAKARS 449 NL+A+LLLS + +LT++YF + ++ Sbjct: 420 TINLVAILLLSGTIAKLTKDYFEQRKA 446 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: 559 Number of extensions: 42 Number of successful extensions: 7 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: 472 Length adjustment: 33 Effective length of query: 416 Effective length of database: 439 Effective search space: 182624 Effective search space used: 182624 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