Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate GFF2276 PGA1_c23080 ribose transport system permease protein RbsC
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__Phaeo:GFF2276 Length = 324 Score = 183 bits (465), Expect = 4e-51 Identities = 106/305 (34%), Positives = 176/305 (57%), Gaps = 4/305 (1%) Query: 22 LDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSV 81 L + G+ + F L + ++ F+T N+ +++R ++I G++A+G+T+V+++ +DLSV Sbjct: 13 LAKQGILIAFALFIIGFTIANPKFLTLDNFENVVRSSAILGVMALGVTFVVISGNLDLSV 72 Query: 82 GSILAFAGLCSAMVATQGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGMLSI 141 GS+++F+ + + G A+ A LG + GF+V L + + TLGMLS Sbjct: 73 GSMMSFSTIV-VLDLHDKLGPTLAIPAMFAMTLCLGALIGFLVGYLKLNSLIVTLGMLSA 131 Query: 142 ARGMTFILNDGS--PITDLPDAYLAL-GIGKIGPIGVPIIIFAVVALIFWMVLRYTTYGR 198 G+T + G I D + A+ G G I I PI+IF +A + ++L T +GR Sbjct: 132 IHGLTLTYSGGKNMDIADKEGTWFAIFGQGNILGIQTPILIFIALAALLGIILAKTPFGR 191 Query: 199 YVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYELDA 258 VYAVGGN +A SGI +V+F Y++S L AG++ ++R+ + G EL+ Sbjct: 192 KVYAVGGNGTAATFSGIRRARVVFLCYIMSALCVATAGLIQASRSMGSQNTVGQGLELEV 251 Query: 259 IAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLIIVFAVLID 318 +AAV++GG SL GG+G+I T+ G L++G I NGL L+G+ Q V +II+ AV +D Sbjct: 252 LAAVILGGASLLGGSGTIFKTVIGVLILGFIQNGLLLVGLDFSVQYVVTWIIIILAVWLD 311 Query: 319 VWRKK 323 + K+ Sbjct: 312 IAAKR 316 Lambda K H 0.326 0.141 0.412 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: 254 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: 325 Length of database: 324 Length adjustment: 28 Effective length of query: 297 Effective length of database: 296 Effective search space: 87912 Effective search space used: 87912 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 (21.6 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