Align ABC transporter for L-Arginine, periplasmic substrate-binding component (characterized)
to candidate 16034 b1920 cystine transporter subunit (NCBI)
Query= reanno::BFirm:BPHYT_RS07735 (264 letters) >FitnessBrowser__Keio:16034 Length = 266 Score = 111 bits (278), Expect = 1e-29 Identities = 75/229 (32%), Positives = 117/229 (51%), Gaps = 12/229 (5%) Query: 35 GVEASYAPFESKSPSGELQGFDIDVGNAVCAKLKAKCVWVENSFDGLIPALQARKFNAIN 94 G+E +Y PF + G+L GF+++ + L + +DG++ +L +++ + + Sbjct: 46 GLEGTYPPFSFQGDDGKLTGFEVEFAQQLAKHLGVEASLKPTKWDGMLASLDSKRIDVVI 105 Query: 95 SDMTITDQRRQAVDFTDPIYTIPN-QMIAKKGS-GLLPTPASLKGKHVGVLQGTIQETYA 152 + +TI+D+R++ DF+ P YTI Q + KKG+ G + T LKGK VGV GT E + Sbjct: 106 NQVTISDERKKKYDFSTP-YTISGIQALVKKGNEGTIKTADDLKGKKVGVGLGTNYEEW- 163 Query: 153 KARWAPAGVDVVPYQTQDQIYADLASGRLDAAFQDAEAASKGFLKKPQGAGFEFAGPAVT 212 R GVDV Y Y DL GR+DA D A+ +KK AVT Sbjct: 164 -LRQNVQGVDVRTYDDDPTKYQDLRVGRIDAILVD-RLAALDLVKKTNDT------LAVT 215 Query: 213 DEKLLGAGVGFGVRKGDKALKDALNQALKELKADGTIDRFAAKYFDVKV 261 E G +RKG++ L A+N A+ E++ DGT+ + K+F V Sbjct: 216 GEAFSRQESGVALRKGNEDLLKAVNDAIAEMQKDGTLQALSEKWFGADV 264 Lambda K H 0.317 0.133 0.383 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: 216 Number of extensions: 19 Number of successful extensions: 4 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: 264 Length of database: 266 Length adjustment: 25 Effective length of query: 239 Effective length of database: 241 Effective search space: 57599 Effective search space used: 57599 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