Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate RR42_RS07805 RR42_RS07805 ABC transporter substrate-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2555 (249 letters) >FitnessBrowser__Cup4G11:RR42_RS07805 Length = 251 Score = 104 bits (260), Expect = 1e-27 Identities = 80/245 (32%), Positives = 118/245 (48%), Gaps = 10/245 (4%) Query: 7 LLLASLAAA-AFCTTGAQAQDNVLRVGTDATFPPMEF--VENGKRTGFDIELVEAIAKTM 63 + L SLAAA +F A AQ V+++G T P F V+ G I++ A++K + Sbjct: 4 IALKSLAAALSFALVSAYAQQPVIKIGATPTAVPFNFLNVKTNALEGVMIDVARAVSKEL 63 Query: 64 GKQVEWVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSY--YAGGLVVMVKAD 121 G E I F LIP L +++ DM SA T R VDF+++ Y L+V + D Sbjct: 64 GVTPEISGIPFATLIPSLQTRKIDMISSAFAKTPARAVAVDFSETVLTYKEALLVPIN-D 122 Query: 122 NKAINKLADLDGKKVSVQVGTKSVSYLTEKFPKVQRVEVEKNQEMFNLVDIGRADAAVTG 181 KA DL GK V VQ+GT V L + + ++ + +GR DA Sbjct: 123 TKAYRNYDDLKGKVVGVQMGTSYVEPLKAVQGFKELKMYDTMADLVRDIGLGRVDAGFGD 182 Query: 182 KPAAFQYVRTRPG--LRVLD--EQLTTEEYGMALRKDTPELTKAVNGAITKLKADGTYAA 237 P VRT +R++D + L + +A+RK E+ VN A+ K+K +G A Sbjct: 183 GPVVAYQVRTSASKQVRLVDTYQSLLATDIALAVRKGDTEMLARVNAAVAKIKQNGELAD 242 Query: 238 IVKKW 242 I+KKW Sbjct: 243 ILKKW 247 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: 111 Number of extensions: 4 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: 251 Length adjustment: 24 Effective length of query: 225 Effective length of database: 227 Effective search space: 51075 Effective search space used: 51075 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 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