Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate BWI76_RS06705 BWI76_RS06705 binding-protein-dependent transport system inner membrane protein
Query= uniprot:C8WUQ9 (301 letters) >FitnessBrowser__Koxy:BWI76_RS06705 Length = 283 Score = 198 bits (503), Expect = 1e-55 Identities = 98/272 (36%), Positives = 164/272 (60%), Gaps = 6/272 (2%) Query: 36 WVSRIVIWCVIV----MVLLPMWFVVIASFNPSNSYISFSLFPSNASLANYKALFQGG-Q 90 W+ + W V++ M++ P+ + V AS N NS +S S+ P N S +Y LF G Sbjct: 12 WIRLSLTWLVVIFVSTMIIYPLVWTVGASLNAGNSLLSTSIIPENLSFQHYADLFNGNVN 71 Query: 91 FWTWVRNSLVVGVVVAMAQSFITAMSAFAFSKLRFYGRKYGLMTLLLLQMFPNILAIAAF 150 + TW NS+ + + + + +A+AFS+ RF GR+ GLM LLLQM P A+ A Sbjct: 72 YLTWYWNSMKISFMTMVLTLISVSFTAYAFSRFRFKGRQNGLMLFLLLQMIPQFSALIAI 131 Query: 151 YTALAKLNMIDMLGSYILVMLGTSA-FNIWLLKGYMDSVPKELDEAAVIDGATTWQRFIH 209 + L +I+ + +L+ +G N WL+KGY+D++PK+LDE+A +DGA++++ F Sbjct: 132 FVLSQLLGLINSHLALVLIYVGGMIPMNTWLMKGYLDAIPKDLDESARMDGASSFRIFFE 191 Query: 210 VTLPLSTPMMVVIFFLTLVGIFSEYMFAGTILQSPWNYTLGVGMYNLISGQFAKNWGEFA 269 + +PLS P++ V+ + G +++ + TIL++P YTL +G+YNL++ + ++ +A Sbjct: 192 IIMPLSKPILAVVALFSFTGPLGDFILSSTILRTPDKYTLPIGLYNLVAQKMGASYTTYA 251 Query: 270 AAALLSAVPLAIVFAVAQRYLTKGLVAGSVKG 301 A A+L AVP+AI++ Q+Y GL +GS KG Sbjct: 252 AGAVLIAVPVAILYLALQKYFVSGLTSGSTKG 283 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: 264 Number of extensions: 17 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 301 Length of database: 283 Length adjustment: 26 Effective length of query: 275 Effective length of database: 257 Effective search space: 70675 Effective search space used: 70675 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