Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate WP_057506835.1 ABB28_RS00975 sugar ABC transporter permease
Query= uniprot:A3DHA3 (284 letters) >NCBI__GCF_001431535.1:WP_057506835.1 Length = 293 Score = 157 bits (396), Expect = 3e-43 Identities = 92/285 (32%), Positives = 158/285 (55%), Gaps = 13/285 (4%) Query: 3 HKEALAGYLFSSPYLAGFLIFFAIPSAMSV--------YYCFTRGVGSFEFAGLDNFKSV 54 ++ +LAG++F++P + +FF +P A ++ Y G + F GL N+ + Sbjct: 2 NRSSLAGWIFAAPAVIVLGVFFGLPVASALALSVTDFDLYSLADGA-NLRFVGLGNYIDL 60 Query: 55 IASNSYRLAVKNTLIFNSVSVPVIMIVSLLLAMLLNK-ALRGARYFRMFFVLPLVIPVAS 113 + + + ++ NT F + VP+ + VSL A+LLN A R FR P+V + + Sbjct: 61 LQTPMFWKSLWNTTYFVVIGVPLSIAVSLGAAILLNAPAARFKALFRTALFAPVVTTLVA 120 Query: 114 IILVWQITFN-EFGVLNNLLNHFGIAGVEWLNSK-WSIAVLVLLYVWKNCGYNIILFTAG 171 + ++W+ F+ +G++N L H GI+ ++WL W++ ++L VWKN GYN+++F AG Sbjct: 121 VAVIWRYLFHTSYGLVNYGLGHIGISPIDWLGDPDWAMPTIMLFAVWKNFGYNMVIFLAG 180 Query: 172 LNSIPKDYYDAASIDGAGGFKCFTSITLPLLVPTIFFVFIISIINSFKVFREAYLLCGNY 231 L +IP D Y+AA IDGA +K F ITLP+L P + V +I++ F++F E Y++ Sbjct: 181 LQAIPHDLYEAARIDGASRWKQFLHITLPMLGPVLLVVGVITVSGYFQLFAEPYVMTRGD 240 Query: 232 PPLNMYMLQHFM-NNNFNNLNYQRLSTASLLMELFIVAIVFLMYK 275 P + + +FM F N R S + L+ L I+A+ +M + Sbjct: 241 PLQSTVSVLYFMFEEGFKWWNLGRASAVAFLLFLIILAVTSVMLR 285 Lambda K H 0.331 0.144 0.444 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: 236 Number of extensions: 17 Number of successful extensions: 5 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: 284 Length of database: 293 Length adjustment: 26 Effective length of query: 258 Effective length of database: 267 Effective search space: 68886 Effective search space used: 68886 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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