Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate 7024902 Shewana3_2076 inner membrane ABC transporter permease protein YjfF (RefSeq)
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__ANA3:7024902 Length = 320 Score = 145 bits (367), Expect = 1e-39 Identities = 96/308 (31%), Positives = 160/308 (51%), Gaps = 6/308 (1%) Query: 41 ASLLL-MILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTF 99 ASLLL M L +F F + ++L+ A + A+ T VII+ GIDLSVG ++ Sbjct: 13 ASLLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIAL 72 Query: 100 CAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLKGLS 159 V+ +++T + L + G L G + G +I K+ PFI TL M L +GL+ Sbjct: 73 SGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAGMFLARGLA 132 Query: 160 LVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASIILNKTVFGR 219 +S D + A+A+ S+ +L + + + ILF V I +++++ T FG Sbjct: 133 TTLSEESIAI--DHPFYDAVAEMSIALPGNGALDLSSLIFILFFVII--AVVMHYTRFGT 188 Query: 220 YTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELDA 279 +A+G N+ + L G+ + +++Y S + +AG++ S G ELDA Sbjct: 189 NVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGVELDA 248 Query: 280 IAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRI-MSVAQEWQTVVTGVIIILAVYL 338 IAAVVIGGT L+GG+G +LGT++G +M V+ + S++ W +V G+++ + L Sbjct: 249 IAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLFFFILL 308 Query: 339 DILRRRRR 346 L R+ Sbjct: 309 QKLLNGRK 316 Lambda K H 0.326 0.139 0.398 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: 272 Number of extensions: 13 Number of successful extensions: 2 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: 347 Length of database: 320 Length adjustment: 28 Effective length of query: 319 Effective length of database: 292 Effective search space: 93148 Effective search space used: 93148 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: 49 (23.5 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