Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate Echvi_2719 Echvi_2719 amino acid carrier protein
Query= TCDB::W0WFC6 (449 letters) >FitnessBrowser__Cola:Echvi_2719 Length = 695 Score = 263 bits (673), Expect = 1e-74 Identities = 168/440 (38%), Positives = 247/440 (56%), Gaps = 27/440 (6%) Query: 29 LYLMLGLKFMPLVRLGV----GFRL---LWQGRSKDDESSGEISPFQALMTCLAATVGTG 81 ++L++G F ++G GFR L G+ + ++ G+IS FQA T +ATVG G Sbjct: 248 IWLVVGAAFFTF-KMGFINIRGFRHAIGLATGKYDEPDAPGKISHFQAFATATSATVGLG 306 Query: 82 NIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKDERNEHVGGPMYAIKN 141 NIAGVA AI LGGPGA FW+ +GM++KF+E L + YR + + GGPM +K+ Sbjct: 307 NIAGVAIAISLGGPGATFWIIIAGFLGMSSKFTECTLGLKYRHIAKDGKIFGGPMNYLKH 366 Query: 142 GLGKR-----WAWLGAAFALFGGLAGFGIGNMVQVNSMADALEVSFGVPD----WVTGVA 192 GL +R L A FA+F FG GNM Q N L F V + WV GV Sbjct: 367 GLERRNMKNLGKVLAAVFAIFCVAFSFGGGNMFQANQSYKILATQFPVLEGFGFWV-GVI 425 Query: 193 TMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAFQLIFTHAFTP 252 ++ G+VI+GGI I KV E +VPFM YI +++V+ V+ I AF I+ AF Sbjct: 426 LAILVGVVIIGGIESIAKVTEKIVPFMAGLYIFGALVVIFVNIGNIGQAFNAIWDGAFNA 485 Query: 253 IAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGTTHSAVRSGLIGMLGTFID 312 A GGF G V+ G RG+FSNEAG G+A IA +A T++ G +G+L F+D Sbjct: 486 TAMKGGFIGVLVV-----GFQRGVFSNEAGTGSAAIAHSAVKTNNPPSEGFVGLLEPFVD 540 Query: 313 TLIICSLTGLAIITSGVW-TSGASGAALSSAAFEAAMPGVGHYILSLALVVFAYTTILGW 371 T+++C+LT L II +G G G L+S AF A++ Y+L++A+++FA+++++ W Sbjct: 541 TIVVCTLTALVIIFTGKHEAQGMGGVELTSQAF-ASVISWFPYLLAIAVLLFAFSSMVSW 599 Query: 372 SYYGERCWEYLAG--TRAILPFRIVWTLAIPFGAMTQLDFAWLVADTLNALMAIPNLIAL 429 SYYG R W YL G R+ L +++V+ + + GA L +D + M+ PN+I L Sbjct: 600 SYYGLRSWTYLFGKSKRSELAYKLVFVVFVVIGASISLGAVLDFSDMMILSMSFPNIIGL 659 Query: 430 LLLSPVVFRLTREYFAKARS 449 ++S V Y K ++ Sbjct: 660 YIMSGEVRNDMNSYLKKLKN 679 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: 681 Number of extensions: 35 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: 695 Length adjustment: 36 Effective length of query: 413 Effective length of database: 659 Effective search space: 272167 Effective search space used: 272167 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: 53 (25.0 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