Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate BPHYT_RS35665 BPHYT_RS35665 ABC transporter permease
Query= uniprot:C8WUR0 (321 letters) >FitnessBrowser__BFirm:BPHYT_RS35665 Length = 296 Score = 131 bits (329), Expect = 2e-35 Identities = 90/295 (30%), Positives = 151/295 (51%), Gaps = 18/295 (6%) Query: 28 LSPALVTICVLSILPIFYTIYISFTNFNQMHFLSYQFVGLKNYEELLNPHDPLSNLFLPT 87 ++P+LV + PIF ++ S ++ + F GL+N+ + + DP FL Sbjct: 16 IAPSLVLALFIISYPIFNIVWQSLHEVSRFGAIR-DFTGLQNFYTIFS--DPA---FLAA 69 Query: 88 FIWTLVYALCTTALAYLVGLFLAVLLNNKHMRERTLYRTLLIVPWAVPNLISMLAWQGLL 147 TLV+ +C L+ + +A++LN + R + RT++++PW+V ++ + W+ Sbjct: 70 ARRTLVWTICVVGGTVLISVPVALVLN-QDFYGRGVARTIVMLPWSVSLTMTAVVWRWAF 128 Query: 148 NDQYGQINALLH--GVFGLPRIPWLTSALWARIAVIMVNVWAGFPYMMTVCLGALQSIPT 205 ND YG +N L G+ P I WL + A I V + P+ +T+ LG L S+P Sbjct: 129 NDDYGMVNVTLQRLGLISGP-IHWLATPELAFPVEIAVGILVSVPFTVTILLGGLSSVPG 187 Query: 206 DQYEAAEIDGANWWQVFRYVTMPSVWRISLPLLIPSFSYNFNNFNASYLLTGGGPPNSNN 265 D YEAA +DGA+ WQ FR +TMP + ++ + Y FN+F +++T GGP NS Sbjct: 188 DIYEAARMDGASAWQQFRKLTMPLLRPFINMTILLNVIYVFNSFPIIWVMTQGGPDNS-- 245 Query: 266 PFLGQTDILATAAYKMTLTFNRYDLGATISVLLFILVALISWVQMRYTGAFKEVD 320 T IL T Y++ R A +S+++ +++ + S +R A KE D Sbjct: 246 -----THILVTYLYELGFRLGRPGEAAAVSLIMLVMLFIFSIAYLRLQPA-KEGD 294 Lambda K H 0.327 0.140 0.451 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: 358 Number of extensions: 19 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: 321 Length of database: 296 Length adjustment: 27 Effective length of query: 294 Effective length of database: 269 Effective search space: 79086 Effective search space used: 79086 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 (21.7 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