Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate GFF851 Psest_0865 ABC-type maltose transport systems, permease component
Query= uniprot:C8WUQ9 (301 letters) >FitnessBrowser__psRCH2:GFF851 Length = 296 Score = 174 bits (440), Expect = 3e-48 Identities = 97/288 (33%), Positives = 155/288 (53%), Gaps = 25/288 (8%) Query: 35 LWVSRIVIWCVIVMVLLPMWFVVIASFNPSNSYISFSLFPSNASLANYKALFQGGQFWT- 93 LW + + + +L P+ V+ SF N + + SLFP N +L ++ G +T Sbjct: 13 LWATHAALLAFVAAILFPLLMVISISFREGN-FATGSLFPENPTLEHWSLAL--GIPYTH 69 Query: 94 --------------WVRNSLVVGVVVAMAQSFITAMSAFAFSKLRFYGRKYGLMTLLLLQ 139 W+ NS+ + V ++ ++ SA+AF+++RF G+ L ++L+ Q Sbjct: 70 ADGSVTQPPFPVLLWLWNSVKIAFVSSILILLLSTTSAYAFARMRFGGKAPILKSMLIFQ 129 Query: 140 MFPNILAIAAFYTALAKLNM------IDMLGSYILVMLGTSAFNIWLLKGYMDSVPKELD 193 MFP +L++ A Y +L ++ G+ I+ LG A +IW +KGY +S+ L+ Sbjct: 130 MFPPVLSLVAIYALFDQLGQHVSWLGVNSHGAVIVASLGGMALHIWTIKGYFESIDASLE 189 Query: 194 EAAVIDGATTWQRFIHVTLPLSTPMMVVIFFLTLVGIFSEYMFAGTILQSPWNYTLGVGM 253 EAA++DGATTWQ F H+ LP+S P++ V+F L + +EY A +L TL VG Sbjct: 190 EAAIVDGATTWQAFFHILLPMSVPILAVVFILAFITSVTEYPIASVLLMDVDKLTLSVGA 249 Query: 254 YNLISGQFAKNWGEFAAAALLSAVPLAIVFAVAQRYLTKGLVAGSVKG 301 + Q WG+FAAAA+LS +P+ VF Q+++ GL AG VKG Sbjct: 250 QQYLYPQ-NYLWGDFAAAAVLSGLPITAVFLYCQKWIVGGLTAGGVKG 296 Lambda K H 0.328 0.136 0.417 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: 261 Number of extensions: 21 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: 301 Length of database: 296 Length adjustment: 27 Effective length of query: 274 Effective length of database: 269 Effective search space: 73706 Effective search space used: 73706 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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