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 206177 DVU0751 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= TCDB::Q9I403 (248 letters) >MicrobesOnline__882:206177 Length = 596 Score = 160 bits (406), Expect = 4e-44 Identities = 94/239 (39%), Positives = 142/239 (59%), Gaps = 12/239 (5%) Query: 3 YNWDWGVFF-KSTGIGSETYLDWYIAGLGWTIAIALVGWIIALALGSLLGVMRT---VPN 58 Y + W + F ++T G+ L+ + GLG T+ I+L+ +AL LG++LG+ R P Sbjct: 35 YQFQWDILFTRNTTYGTHLGLE-ILKGLGVTVRISLISSALALGLGTVLGIARLSLFAPL 93 Query: 59 RLVSGIATAYVEIFRNVPLLVQLFIWYFLVPDLLPEGLQTWFKQDLNPTTSAYLSVVVCL 118 RL ATA VE FRN PLLVQLF WYF P +LPE + ++ L + + L Sbjct: 94 RLT---ATAVVEFFRNTPLLVQLFFWYFAFPAILPENI----RELLFTGNFEFWCATIGL 146 Query: 119 GLFTAARVCEQVRTGIQALPYGQTSAARAMGFRLPQIYRHVLLPQAFRIIIPPLTSEFLN 178 ++T+A + E +R G+Q++P G AA + G Q+ R ++LP AFR IIPPL SEFLN Sbjct: 147 SVYTSAFMAEVIRAGLQSIPKGLLEAAYSSGLNYVQVLRTIILPMAFRAIIPPLGSEFLN 206 Query: 179 IFKNSSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMSLMLIMRLVERKV 237 KNSS+A ++G+ EL Q++Q + FEA + AT++Y +L++ + I+ V K+ Sbjct: 207 NMKNSSLAMVVGVAELTWQSQQVESLTFKGFEATSAATVLYLSLSLLISFILNGVNGKM 265 Score = 110 bits (276), Expect = 5e-29 Identities = 69/249 (27%), Positives = 122/249 (48%), Gaps = 29/249 (11%) Query: 3 YNWDWGVFFKSTGIGSETYLDWY------------IAGLGWTIAIALVGWIIALALGSLL 50 YN++WGV + T L W+ + GL +++ +A++ ++ +G ++ Sbjct: 356 YNFNWGVIADNL----RTLLIWHFPNGQSDELFMGLGGLAYSLLMAVIAISVSFFIGLVV 411 Query: 51 GVMRTVPNRLVSGIATAYVEIFRNVPLLVQLFIWYFLVPDLLPEGLQTWFKQDLNPTTSA 110 G+ RT NR+ Y+E+ R PL++ +F YF +P L N + Sbjct: 412 GIGRTSDNRICRIPCLLYIELIRGNPLIIVIFWIYFFIPVLF------------NTFFNV 459 Query: 111 YLSVVVCLGLFTAARVCEQVRTGIQALPYGQTSAARAMGFRLPQIYRHVLLPQAFRIIIP 170 + S + L LFT A + E VR GIQ +P GQ AA + G Q R ++LPQA + +IP Sbjct: 460 FWSATIALTLFTGAYLAEIVRAGIQNIPAGQVEAAYSTGLTFVQTMRRIILPQALKQMIP 519 Query: 171 PLTSEFLNIFKNSSVASLIGLMELLAQTKQ-TAEFSANLFEAFTLATLIYFTLNMSLMLI 229 + +F+ IFK++S+A ++G++EL + E + +YF S+ + Sbjct: 520 AIVGQFIAIFKDTSLAFVLGVLELTFVAQGINNRLMVYPMEIYGTVAFLYFICCWSMSVY 579 Query: 230 MRLVERKVA 238 +ER+++ Sbjct: 580 AARLERRLS 588 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: 420 Number of extensions: 29 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: 596 Length adjustment: 30 Effective length of query: 218 Effective length of database: 566 Effective search space: 123388 Effective search space used: 123388 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: 50 (23.9 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