Align Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized)
to candidate BWI76_RS10375 BWI76_RS10375 polar amino acid ABC transporter inner membrane subunit
Query= TCDB::Q9I403 (248 letters) >FitnessBrowser__Koxy:BWI76_RS10375 Length = 221 Score = 114 bits (284), Expect = 2e-30 Identities = 69/222 (31%), Positives = 120/222 (54%), Gaps = 20/222 (9%) Query: 1 MNYNWDWGVFFKSTGIGSETYLDWYIAGLGWTIAIALVGWIIALALGSLLGVMRTVPNRL 60 M+Y WD+ + +++ + + GLG T+ + L+ I+ LG +GV+R R Sbjct: 1 MHYQWDFSLVWQNLPV--------LLKGLGVTLELWLLAGIVGTLLGLAVGVVRARGPRF 52 Query: 61 VSGIATAYVEIFRNVPLLVQLFIWYFLVPDLLPEGLQTWFKQDLNPTTSAYLSVVVCLGL 120 + +A+VE+FRN P+L+QL +Y+ P L+ G+Q S + + + L L Sbjct: 53 FYPLTSAFVEVFRNTPVLIQLIWFYYAFPVLV--GIQF----------STFGAAALALTL 100 Query: 121 FTAARVCEQVRTGIQALPYGQTSAARAMGFRLPQIYRHVLLPQAFRIIIPPLTSEFLNIF 180 +TAA E R G+Q++ GQ A+A+G + R ++LPQ FR ++P LT+ + + Sbjct: 101 YTAAYSTEIFRAGLQSIERGQWEGAKALGMPPGVMLRRIILPQVFRRMLPALTNRMIELA 160 Query: 181 KNSSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTL 222 K +S+AS++ + EL+ Q + + E FT+ L+YF L Sbjct: 161 KVTSLASILTVNELMYQGRLLSSTWYRPVEIFTVVALLYFVL 202 Score = 22.3 bits (46), Expect = 0.008 Identities = 20/54 (37%), Positives = 25/54 (46%), Gaps = 5/54 (9%) Query: 36 ALVGWIIALALGSLLGVMRTV-----PNRLVSGIATAYVEIFRNVPLLVQLFIW 84 AL +I LA + L + TV RL+S VEIF V LL + IW Sbjct: 151 ALTNRMIELAKVTSLASILTVNELMYQGRLLSSTWYRPVEIFTVVALLYFVLIW 204 Lambda K H 0.327 0.141 0.433 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: 181 Number of extensions: 14 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 248 Length of database: 221 Length adjustment: 23 Effective length of query: 225 Effective length of database: 198 Effective search space: 44550 Effective search space used: 44550 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: 46 (22.3 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