Align ABC transporter permease (characterized, see rationale)
to candidate AO356_29015 AO356_29015 ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_29015 Length = 293 Score = 158 bits (399), Expect = 2e-43 Identities = 93/308 (30%), Positives = 168/308 (54%), Gaps = 16/308 (5%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60 M+ L+ +I GL+ G++Y+L+A+G+ ++Y + NFA G +L+ ALT S QG Sbjct: 1 MNFFLETLIGGLLAGTLYSLVAIGFVLIYKASGVFNFAQGAMLLFAALTFVSL--REQGL 58 Query: 61 MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAM 120 + + LL T++ VV A L IE++ RPL + ++ + +G+S +++ LA Sbjct: 59 -----SFALALLLTVLVMVVGALL---IERLVLRPLVNRSQITLFMATLGLSFIIEGLAQ 110 Query: 121 IIWKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRAT 180 + + + P +G I+ ++ GV+A+ +A L L N T +G A+RA Sbjct: 111 GLMGAQVRALDLGIEDVPLFVGEIMISQFDLIAAGVSALTVAVLALLFNKTRIGVALRAV 170 Query: 181 AENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAV 240 A++ R A +G+ + + + + V+ +AG+++ + G Q ++ L LKA + Sbjct: 171 ADDTRAALSLGINLNRIWQIVWAVAGVVGLVAGLLWGARQG-VQFSLS-LVVLKALPVLI 228 Query: 241 FGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL 300 GG ++ GA+VGG+++G E + YIG L GG + T FA+ + +I L +RP+GL Sbjct: 229 IGGFTSIGGAIVGGLIVGAAENLAEAYIGPLIGGGI----TPWFAYFLALIFLYIRPAGL 284 Query: 301 LGERVADR 308 G+R+ +R Sbjct: 285 FGDRIIER 292 Lambda K H 0.327 0.142 0.419 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: 198 Number of extensions: 11 Number of successful extensions: 3 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: 309 Length of database: 293 Length adjustment: 27 Effective length of query: 282 Effective length of database: 266 Effective search space: 75012 Effective search space used: 75012 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: 48 (23.1 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