Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate WP_090447142.1 BLS63_RS17895 maltose ABC transporter permease MalG
Query= uniprot:C8WUQ9 (301 letters) >NCBI__GCF_900100495.1:WP_090447142.1 Length = 296 Score = 172 bits (437), Expect = 6e-48 Identities = 98/286 (34%), Positives = 155/286 (54%), Gaps = 21/286 (7%) Query: 35 LWVSRIVIWCVIVMVLLPMWFVVIASFNPSNSYISFSLFPSNASLANYK-------ALFQ 87 LW++ + + I +++ P+ VV SF N + + SL P +L ++ L Sbjct: 13 LWLTHLGLLGFIGLIVFPLLMVVSISFREGN-FATGSLLPDQPTLEHWSLALGIPYTLAD 71 Query: 88 GG------QFWTWVRNSLVVGVVVAMAQSFITAMSAFAFSKLRFYGRKYGLMTLLLLQMF 141 G TW+ NSL + + + ++ SA+AF++LRF G+ L +L+ QMF Sbjct: 72 GSVVNPPFPVLTWLWNSLKIAFISSALILMLSTTSAYAFARLRFAGKGPILKGMLIFQMF 131 Query: 142 PNILAIAAFYTALAKLNM------IDMLGSYILVMLGTSAFNIWLLKGYMDSVPKELDEA 195 P +L++ A Y +L ++ G+ I+ LG A +IW +KGY +S+ L+EA Sbjct: 132 PPVLSLVAIYALFDQLGQYAGWLGVNSHGAVIVASLGGMALHIWTIKGYFESIDASLEEA 191 Query: 196 AVIDGATTWQRFIHVTLPLSTPMMVVIFFLTLVGIFSEYMFAGTILQSPWNYTLGVGMYN 255 A++DGATTWQ F+H+ LP+S P++ V+F L + +EY A +L TL VG Sbjct: 192 AIVDGATTWQAFVHILLPMSVPILAVVFILAFITSITEYPIASVLLMDVDKLTLSVGAQQ 251 Query: 256 LISGQFAKNWGEFAAAALLSAVPLAIVFAVAQRYLTKGLVAGSVKG 301 + Q WG+FAAAA+LS +P+ VF Q+++ GL AG VKG Sbjct: 252 YLYEQ-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: 260 Number of extensions: 17 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: 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 24 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