Align LacI family transcriptional regulator (characterized, see rationale)
to candidate SMc02324 SMc02324 periplasmic binding ABC transporter protein
Query= uniprot:A0A161ZH48 (318 letters) >FitnessBrowser__Smeli:SMc02324 Length = 329 Score = 105 bits (263), Expect = 1e-27 Identities = 77/252 (30%), Positives = 125/252 (49%), Gaps = 15/252 (5%) Query: 9 LLAVAMLAAASAALPVSSAFAETPEKPKVALVMKSLANEFFLTMEDGAKAYQKDHSGDFE 68 L ++ + AA + AL ++A AE K+ALV+K+L FF GA+ K+ GD E Sbjct: 4 LKSLMVTAAVAVALMANAAHAENK---KIALVVKALGIGFFEAANKGAQEAAKE-LGDVE 59 Query: 69 LISNGIKDETDTAGQTRIVEQMILSKVNALVIAPADSKAMVPVIKKAVDAGITVINIDNQ 128 +I G T GQ ++ +I KV+A+ ++ D+ A+VP +KKA+D GI VI+ D+ Sbjct: 60 IIYTG-PTSTTAEGQIEVINSLIAQKVDAIAVSANDTDALVPALKKAMDRGIKVISWDSG 118 Query: 129 L--DPAVVKSKNITVPFVGPDNRKGARLVGEYLAKQLKAGDEVGIIEGVSTTTNAQQRTA 186 + + ++ + P +G ++ + A L G +V ++ +T TN A Sbjct: 119 VAKEGRLMHLNPSSSPLIG-------NMIIKLAADNLPEGGDVAVLSASATATNQNTWIA 171 Query: 187 GFKDAM-EAAQIKVVSLQSGDWEIDKGGKVASSMLSEYPNIKALLAGNDSMAVGAVSAVR 245 K I VV+ GD DK + ++ +PN+KA++A V A AV Sbjct: 172 EMKKVQGNYKGINVVATVYGDDLADKSYRETQGLIQSHPNLKAIIAPTSVGIVAAAQAVT 231 Query: 246 AAGKAGKVQVVG 257 AGK G++ V G Sbjct: 232 DAGKIGQINVTG 243 Lambda K H 0.314 0.130 0.348 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: 203 Number of extensions: 16 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: 318 Length of database: 329 Length adjustment: 28 Effective length of query: 290 Effective length of database: 301 Effective search space: 87290 Effective search space used: 87290 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 48 (23.1 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