Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate WP_139134956.1 BEN30_RS09695 transporter substrate-binding domain-containing protein
Query= reanno::acidovorax_3H11:Ac3H11_2555 (249 letters) >NCBI__GCF_001746755.1:WP_139134956.1 Length = 244 Score = 107 bits (266), Expect = 3e-28 Identities = 72/241 (29%), Positives = 121/241 (50%), Gaps = 6/241 (2%) Query: 7 LLLASLAAAAFCTTGAQAQDNVLRVGTDATFPPMEFVE-NGKRTGFDIELVEAIAKTMGK 65 + +A+L+ A T A A D LR+GT+ +PP V+ NG+ GFD+++ +A+ +M Sbjct: 1 MAIATLSVIALTAT-AYAADK-LRIGTEGAYPPFNLVDSNGELQGFDVDIAKALCASMKA 58 Query: 66 QVEWVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYAGGLVVMVKADNKAI 125 + +V D+ G+IP L ++FD V+++ IT+ER+K VDF++ YY L + K Sbjct: 59 ECTFVKQDWDGMIPALNKRKFDAIVASMSITEERQKAVDFSERYYTNKLQFVGKKGMDVD 118 Query: 126 NKLADLDGKKVSVQVGTKSVSYLTEKFPKVQRVEVEKNQEMFNLVDIGRADAAVTGKPAA 185 A L GK + Q T S +L + + + + + GR DA + Sbjct: 119 ISAAGLKGKVIGAQRATISGQWLEQNRADADIKLYDTQENAYLDLASGRLDAILADAFVN 178 Query: 186 FQYVRTRPGLRVL---DEQLTTEEYGMALRKDTPELTKAVNGAITKLKADGTYAAIVKKW 242 ++++ + G D + G+A+RK +L +N AI + ADGTY I K+ Sbjct: 179 YEWLNSDAGNAFEAKGDPVFDGDLIGIAIRKGEDDLRIKLNKAIKDIVADGTYGKINAKY 238 Query: 243 F 243 F Sbjct: 239 F 239 Lambda K H 0.317 0.133 0.369 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: 174 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: 249 Length of database: 244 Length adjustment: 24 Effective length of query: 225 Effective length of database: 220 Effective search space: 49500 Effective search space used: 49500 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: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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