Align Sugar ABC transporter permease (characterized, see rationale)
to candidate SM_b21150 SM_b21150 sugar uptake ABC transporter permease
Query= uniprot:A0A161ZE72 (280 letters) >FitnessBrowser__Smeli:SM_b21150 Length = 285 Score = 182 bits (461), Expect = 9e-51 Identities = 105/271 (38%), Positives = 154/271 (56%), Gaps = 6/271 (2%) Query: 13 LGFWCLIGVLLLYAVFPFYYAIVTSLKPSSALFEVSY--WIENPDFSNYAAV-LNQASFL 69 +G + I V L + + PF + SLKP LF Y W EN F Y + ++ F Sbjct: 16 VGIYGGIFVFLTFILAPFVEGFLVSLKPLGRLFSSPYRFWPENGSFEAYRTMWVSVPGFA 75 Query: 70 RAIGNSLVVALCVVTLALFLSLTAAYALGRVKFRGRGTVLMMVLGVSMFPQVAVLSGLFE 129 R I NS +++ V + L L + AAYA R KFRG G +L L V+MF +L LF Sbjct: 76 RYIFNSFFISIIVTAVVLALVVPAAYAFARFKFRGSGALLAAFLAVNMFSGAVLLIPLFR 135 Query: 130 VIRALGLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASPWVTLTRVL 189 ++R+ G+ NT +A+I+ F +P +W+L T+M ++P EL+EAA +DGAS + TL RV+ Sbjct: 136 LMRSFGVLNTYFAMIVPGVAFLIPSAIWLLRTYMMRIPRELDEAAFVDGASHFYTLRRVI 195 Query: 190 LPLLWPALVTTGLLAFIAAW-NEFLFALTFTLTDTQRTVPVAIALISGGSPHELPWGLLM 248 LP+ P + + FI ++ +F+FALTF +P+ + L + E+ W LM Sbjct: 196 LPIAMPGITVVAITTFIGSYAQQFIFALTF--NSKSEYMPLPVGLFAYFGRQEVVWNELM 253 Query: 249 AASVVVTVPLVILVLIFQRRIVSGLTAGALK 279 AAS V P VI++ QR +VSGLTAGA+K Sbjct: 254 AASFVGIAPAVIVIFFLQRYLVSGLTAGAVK 284 Lambda K H 0.329 0.141 0.433 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: 202 Number of extensions: 11 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: 280 Length of database: 285 Length adjustment: 26 Effective length of query: 254 Effective length of database: 259 Effective search space: 65786 Effective search space used: 65786 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: 47 (22.7 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