Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate Pf6N2E2_524 Inositol transport system permease protein
Query= uniprot:D8IZC8 (344 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_524 Length = 340 Score = 209 bits (531), Expect = 1e-58 Identities = 134/324 (41%), Positives = 199/324 (61%), Gaps = 28/324 (8%) Query: 35 LPVLVVLYLLFYGLTLYLSGDG-----TSNFASAENTMNILRQVAINLVLAAGMTFVILT 89 LP + ++L+ G+ L G S +++ + ++ QV+I +LA G+T VI+T Sbjct: 20 LPTELSIFLVLIGIGLVFEMFGWIMRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIIT 79 Query: 90 AGIDLSVGSVLAVSAVLGMQV------------SLGAAPGWAIPMF--IFSGLVMGMVNG 135 GIDLS GSVLA+SA++ + SL P W IP+ + GL+ G +NG Sbjct: 80 TGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVW-IPVVAGLGVGLLAGAING 138 Query: 136 AMVALLNINAFVVTLGTMTAFRGAAYLLADGTTV-LNNDIPSFEWIGNGDFLHVPWLIWV 194 +++A+ I F+ TLG M + RG A +G V + +D S+ IG+G +P +I++ Sbjct: 139 SIIAITGIPPFIATLGMMVSARGLARYYTEGQPVSMLSD--SYTAIGHGA---MPVIIFL 193 Query: 195 AVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMS 254 VAV+ + LR T G + YAIGGN+QAAR +GI V L+ VYSI+GL +GLAG ++ Sbjct: 194 VVAVIF--HIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIVYSIAGLLAGLAGVVA 251 Query: 255 ASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILGLS 314 ++R G YELDAIAA V+GGTSL GGVG I GTV+GALI+GVM +G T +G+ Sbjct: 252 SARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVD 311 Query: 315 SFWQYVAKGAVIVLAVILDKWRQK 338 ++ Q + KG +IV+AV++D++R K Sbjct: 312 AYIQDIIKGLIIVVAVVIDQYRNK 335 Lambda K H 0.324 0.138 0.417 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: 323 Number of extensions: 16 Number of successful extensions: 4 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: 344 Length of database: 340 Length adjustment: 29 Effective length of query: 315 Effective length of database: 311 Effective search space: 97965 Effective search space used: 97965 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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