Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate 14152 b0007 predicted transporter (NCBI)
Query= TCDB::W0WFC6 (449 letters) >FitnessBrowser__Keio:14152 Length = 476 Score = 259 bits (663), Expect = 1e-73 Identities = 164/449 (36%), Positives = 245/449 (54%), Gaps = 21/449 (4%) Query: 11 LNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQ-GRSKDDE---SSGEISP 66 +N V+WG +M+ L+ G G + F V FR + Q G+S + G ++ Sbjct: 8 INSVLWGSVMIYLLFGAGCWFTFRTGF-------VQFRYIRQFGKSLKNSIHPQPGGLTS 60 Query: 67 FQALMTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKD 126 FQ+L T LAA VG+GN+AGVA AI GGPGA+FWMW A +GMAT F+E LA Y+E+D Sbjct: 61 FQSLCTSLAARVGSGNLAGVALAITAGGPGAVFWMWVAAFIGMATSFAECSLAQLYKERD 120 Query: 127 ERNEHVGGPMYAIKNGLGKRWAWLGAAFALFGGLAGFGIGNMVQVNSMADALEVSFGVPD 186 + GGP + + GLG R W+G FA+F +A I + VQ N++A AL SF P Sbjct: 121 VNGQFRGGPAWYMARGLGMR--WMGVLFAVFLLIAYGIIFSGVQANAVARALSFSFDFPP 178 Query: 187 WVTGVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAFQLIF 246 VTG+ + T L I G+ + ++ + VP M + +++ S+++ V++ +P IF Sbjct: 179 LVTGIILAVFTLLAITRGLHGVARLMQGFVPLMAIIWVLTSLVICVMNIGQLPHVIWSIF 238 Query: 247 THAFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGT---AGIAQAAGTTHSAVRSGL 303 AF A GG AG + AI G R +FSNEAG+G+ A A A+ H A + G+ Sbjct: 239 ESAFGWQEAAGGAAGYTLSQAITNGFQRSMFSNEAGMGSTPNAAAAAASWPPHPAAQ-GI 297 Query: 304 IGMLGTFIDTLIICSLTGLAIITSGVWTS--GASGAALSSAAFEAAMPGVGHYILSLALV 361 + M+G FIDTL+IC+ + + I+ +G T+ G L A M G ++L ++ Sbjct: 298 VQMIGIFIDTLVICTASAMLILLAGNGTTYMPLEGIQLIQKAMRVLMGSWGAEFVTLVVI 357 Query: 362 VFAYTTILGWSYYGERCWEYLA--GTRAILPFRIVWTLAIPFGAMTQLDFAWLVADTLNA 419 +FA+++I+ Y E +L +AI RI + G + L W +AD + A Sbjct: 358 LFAFSSIVANYIYAENNLFFLRLNNPKAIWCLRICTFATVIGGTLLSLPLMWQLADIIMA 417 Query: 420 LMAIPNLIALLLLSPVVFRLTREYFAKAR 448 MAI NL A+LLLSPVV + +Y + + Sbjct: 418 CMAITNLTAILLLSPVVHTIASDYLRQRK 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: 547 Number of extensions: 21 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: 476 Length adjustment: 33 Effective length of query: 416 Effective length of database: 443 Effective search space: 184288 Effective search space used: 184288 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