Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 2 (characterized)
to candidate 206177 DVU0751 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= reanno::pseudo3_N2E3:AO353_16285 (248 letters) >MicrobesOnline__882:206177 Length = 596 Score = 157 bits (397), Expect = 5e-43 Identities = 89/239 (37%), Positives = 143/239 (59%), Gaps = 12/239 (5%) Query: 3 YNWDWGVFF-KSTGVGSETYLDWFITGLGWTIAIAIVAWIIALMLGSVLGVMRT---VPN 58 Y + W + F ++T G+ L+ + GLG T+ I++++ +AL LG+VLG+ R P Sbjct: 35 YQFQWDILFTRNTTYGTHLGLE-ILKGLGVTVRISLISSALALGLGTVLGIARLSLFAPL 93 Query: 59 RLVSGIATCYVELFRNVPLLVQLFIWYFLVPDLLPQNLQDWYKQDLNPTTSAYLSVVVCL 118 RL AT VE FRN PLLVQLF WYF P +LP+N+++ L + + L Sbjct: 94 RLT---ATAVVEFFRNTPLLVQLFFWYFAFPAILPENIREL----LFTGNFEFWCATIGL 146 Query: 119 GLFTAARVCEQVRTGIQALPRGQESAARAMGFKLPQIYWNVLLPQAYRIVIPPLTSEFLN 178 ++T+A + E +R G+Q++P+G AA + G Q+ ++LP A+R +IPPL SEFLN Sbjct: 147 SVYTSAFMAEVIRAGLQSIPKGLLEAAYSSGLNYVQVLRTIILPMAFRAIIPPLGSEFLN 206 Query: 179 VFKNSSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMSLMLLMRMVEKKV 237 KNSS+A ++G+ EL Q++Q + FEA + AT++Y +L++ + ++ V K+ Sbjct: 207 NMKNSSLAMVVGVAELTWQSQQVESLTFKGFEATSAATVLYLSLSLLISFILNGVNGKM 265 Score = 109 bits (273), Expect = 1e-28 Identities = 68/245 (27%), Positives = 120/245 (48%), Gaps = 21/245 (8%) Query: 3 YNWDWGVFFKSTGV--------GSETYLDWFITGLGWTIAIAIVAWIIALMLGSVLGVMR 54 YN++WGV + G L + GL +++ +A++A ++ +G V+G+ R Sbjct: 356 YNFNWGVIADNLRTLLIWHFPNGQSDELFMGLGGLAYSLLMAVIAISVSFFIGLVVGIGR 415 Query: 55 TVPNRLVSGIATCYVELFRNVPLLVQLFIWYFLVPDLLPQNLQDWYKQDLNPTTSAYLSV 114 T NR+ Y+EL R PL++ +F YF +P L N + + S Sbjct: 416 TSDNRICRIPCLLYIELIRGNPLIIVIFWIYFFIPVLF------------NTFFNVFWSA 463 Query: 115 VVCLGLFTAARVCEQVRTGIQALPRGQESAARAMGFKLPQIYWNVLLPQAYRIVIPPLTS 174 + L LFT A + E VR GIQ +P GQ AA + G Q ++LPQA + +IP + Sbjct: 464 TIALTLFTGAYLAEIVRAGIQNIPAGQVEAAYSTGLTFVQTMRRIILPQALKQMIPAIVG 523 Query: 175 EFLNVFKNSSVASLIGLMELLAQTKQ-TAEFSANLFEAFTLATLIYFTLNMSLMLLMRMV 233 +F+ +FK++S+A ++G++EL + E + +YF S+ + + Sbjct: 524 QFIAIFKDTSLAFVLGVLELTFVAQGINNRLMVYPMEIYGTVAFLYFICCWSMSVYAARL 583 Query: 234 EKKVA 238 E++++ Sbjct: 584 ERRLS 588 Lambda K H 0.326 0.139 0.432 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: 393 Number of extensions: 25 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