Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate Echvi_4032 Echvi_4032 amino acid carrier protein
Query= TCDB::W0WFC6 (449 letters) >FitnessBrowser__Cola:Echvi_4032 Length = 452 Score = 325 bits (832), Expect = 2e-93 Identities = 179/451 (39%), Positives = 259/451 (57%), Gaps = 18/451 (3%) Query: 8 VVDLNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSGEISPF 67 ++D + +WG +L L+LG G L L +P G +++ G+ D + G+I+ F Sbjct: 5 IIDFSNWIWGWPLLYLLLGGGTLLFLYSGLIPFRGFGHAMKVVG-GKYDDPNAKGDITSF 63 Query: 68 QALMTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKDE 127 QAL + +AATVG GNI+GVA AI GGPGA+FWMW +A VGMATK+ LA+ YR KD Sbjct: 64 QALSSAIAATVGLGNISGVALAIGTGGPGAIFWMWVSAFVGMATKYFTCTLAIMYRGKDS 123 Query: 128 RNEHVGGPMYAIKNGLGKRWAWLGAAFALFGGLAGFGIGNMVQVNSMADALEV----SFG 183 GGPMY I+ G+GK+W +L F + G + G+ + Q N + D + V FG Sbjct: 124 SGHIQGGPMYVIEEGMGKKWRFLSVIFCVAGIM---GLLAIFQANQLTDVIRVVLLKPFG 180 Query: 184 VPD-----WVTGVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAI 238 + W+ GV+ ML+ VILGGI+RI VA LVPFM Y ++ +++L + I Sbjct: 181 LDHGTTTRWILGVSMMLLVATVILGGIQRIAAVASKLVPFMVTLYFISVLVILFRFGDEI 240 Query: 239 PGAFQLIFTHAFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGTTHSA 298 +F I AFT A GG GA ++ G R FSNEAG+GTA + A Sbjct: 241 LPSFWFILEDAFTGKAVLGGSIGAVIIT----GARRAAFSNEAGIGTAPMVHGASKNEEP 296 Query: 299 VRSGLIGMLGTFIDTLIICSLTGLAIITSGVWTSG-ASGAALSSAAFEAAMPGVGHYILS 357 VR GLI MLG FIDT+++C+LT + I+ +GVW +G G ++ +AF++ +P VG Y L Sbjct: 297 VREGLIAMLGPFIDTIVVCTLTAMTIMVTGVWETGEKDGVLMTLSAFQSGIPVVGKYFLM 356 Query: 358 LALVVFAYTTILGWSYYGERCWEYLAGTRAILPFRIVWTLAIPFGAMTQLDFAWLVADTL 417 A++VFA +T+ +SYYG +C+ YL G + + L I GA+ L D + Sbjct: 357 AAVLVFALSTMFTYSYYGHKCFNYLFGADKANYYNYFYLLTIVGGAVVSLKVVMSFVDGM 416 Query: 418 NALMAIPNLIALLLLSPVVFRLTREYFAKAR 448 A+MA P +I+ + LSP V T++YF + + Sbjct: 417 YAVMAFPTMISAIYLSPKVRAATKDYFRRMK 447 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: 580 Number of extensions: 28 Number of successful extensions: 5 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: 452 Length adjustment: 33 Effective length of query: 416 Effective length of database: 419 Effective search space: 174304 Effective search space used: 174304 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