Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate Ac3H11_2555 Glutamine ABC transporter, periplasmic glutamine-binding protein (TC 3.A.1.3.2)
Query= reanno::pseudo3_N2E3:AO353_03055 (258 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2555 Length = 249 Score = 109 bits (273), Expect = 5e-29 Identities = 80/253 (31%), Positives = 129/253 (50%), Gaps = 15/253 (5%) Query: 2 KKLVLLGALALSVLSLPTFADEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEEM 61 + L+L A + + A + L++G +A +PP +G GFD ++ A+ + M Sbjct: 5 RNLLLASLAAAAFCTTGAQAQDNVLRVGTDATFPPMEF-VENGKRTGFDIELVEAIAKTM 63 Query: 62 KVKCVWVEQEFDGLIPALKVRKIDAILSSMSITDDRKKSVDFTNKYYNTPARLVMKAGTQ 121 + WV+ +F GLIP L ++ D +S++ ITD+RKK VDFT+ YY +++KA + Sbjct: 64 GKQVEWVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYAGGLVVMVKADNK 123 Query: 122 VSDNLAELKGKKIGVQRGSIH-NRFAEEVLKPLGAEIKPYGSQNEIYLDVAAGRLDGTVA 180 + LA+L GKK+ VQ G+ + E+ K E++ E++ V GR D V Sbjct: 124 AINKLADLDGKKVSVQVGTKSVSYLTEKFPKVQRVEVE---KNQEMFNLVDIGRADAAV- 179 Query: 181 DATLLDDGFLKTDSGKGFAFVGPAFTDEKYFGDGIGIAVRKGDKAELDK-INAAIVAIRA 239 T F + G + T E+Y G+A+RK D EL K +N AI ++A Sbjct: 180 --TGKPAAFQYVRTRPGLRVLDEQLTTEEY-----GMALRK-DTPELTKAVNGAITKLKA 231 Query: 240 NGKYKQIQDKYFN 252 +G Y I K+F+ Sbjct: 232 DGTYAAIVKKWFS 244 Lambda K H 0.318 0.138 0.395 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: 167 Number of extensions: 9 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: 258 Length of database: 249 Length adjustment: 24 Effective length of query: 234 Effective length of database: 225 Effective search space: 52650 Effective search space used: 52650 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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