Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate 5210738 Shew_3166 extracellular solute-binding protein (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_2555 (249 letters) >FitnessBrowser__PV4:5210738 Length = 242 Score = 119 bits (297), Expect = 7e-32 Identities = 76/245 (31%), Positives = 127/245 (51%), Gaps = 12/245 (4%) Query: 3 LRRNLLLASLAAAAFCTTGAQAQDNVLRVGTDATFPPMEFV---ENGKRTGFDIELVEAI 59 + +++LLA A + + QD ++ VGT+A FPP E+V + GFDI+L + Sbjct: 1 MNKSILLAGFTALLLLSGCGKEQDYLV-VGTNAAFPPFEYVGGVSGDQVMGFDIDLARKV 59 Query: 60 AKTMGKQVEWVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYAGGLVVMVK 119 A+ GK ++ ++ F LI L + + DM S + IT ER+ VDF++ YY VV+V Sbjct: 60 AEDAGKTLKVENMKFDSLIVALNAGKIDMIASGMTITPERQASVDFSEPYYEATQVVLVN 119 Query: 120 ADNKAINKLADLDGKKVSVQVGTKSVSYLTEKFPK---VQRVEVEKNQEMFNLVDIGRAD 176 + +I+ LADL GK +VQ+G+ + + +K+ + E E+ N G+ D Sbjct: 120 KQDDSIHSLADLTGKHFAVQLGS-TADMMAKKYTQSVTAFNTGFEAIMELKN----GKVD 174 Query: 177 AAVTGKPAAFQYVRTRPGLRVLDEQLTTEEYGMALRKDTPELTKAVNGAITKLKADGTYA 236 + A Y+ P L+++ E YG A+ K PEL ++N + +K +G Y Sbjct: 175 LVLFDSEPAANYLAKNPELKLISLDFPPEFYGFAVAKSQPELLASINKTLATMKQNGEYD 234 Query: 237 AIVKK 241 A++ K Sbjct: 235 ALLAK 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: 141 Number of extensions: 5 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: 242 Length adjustment: 24 Effective length of query: 225 Effective length of database: 218 Effective search space: 49050 Effective search space used: 49050 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