Align Inositol transport system permease protein (characterized)
to candidate Ac3H11_3036 Fructose ABC transporter, permease component FrcC
Query= reanno::WCS417:GFF2333 (340 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3036 Length = 319 Score = 185 bits (469), Expect = 2e-51 Identities = 107/311 (34%), Positives = 172/311 (55%), Gaps = 20/311 (6%) Query: 33 IGLVFELFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGIDLSSGSVLAL 92 I L+ + + + FL ++Q L++ QV ++ ++AIG T VI+T GIDLS G V+AL Sbjct: 18 IALILACAFFATQSERFL-SAQNFALILQQVMVVAVIAIGQTLVILTAGIDLSCGMVMAL 76 Query: 93 SAMIAASLAQTSDFSRAVFPSLTDLPVWIPVAMGLGVGLLAGAINGSIIAVTGIPPFIAT 152 ++ +A S V +A G+ V +L G ING ++ +PPFI T Sbjct: 77 GGIVMTKMAADYGLSAPV-----------AIACGMAVTMLFGLINGLLVTKIKLPPFIVT 125 Query: 153 LGMMVSARGLARYYTEGQPVSMLSDSYTAIGHG--------AMPVIIFLVVAVIFHIALR 204 LG + A + Y+ Q ++ + TA+G+ ++ L + ++ ALR Sbjct: 126 LGTLNIAFAATQLYSGAQTITDIPAGMTALGNTFQLGQTAIVWGAVLMLALYLVTWFALR 185 Query: 205 YTKYGKYTYAIGGNMQAARTSGINVKRHLIIVYSIAGLLAGLAGVVASARAATGQAGMGM 264 T G++ YA+G + +A R +GI + L+ VY +AGL G+A +++ AR G G Sbjct: 186 ETAPGRHVYAVGNSPEATRLTGIATDKVLLGVYVLAGLFYGIASLLSVARTGAGDPNAGQ 245 Query: 265 SYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQDIIKGLIIV 324 + LDAI+A V+GGTSL GG G I GT++GALI+GV +G T +GV + Q ++ G++++ Sbjct: 246 TENLDAISAVVLGGTSLFGGRGVILGTLVGALIVGVFRNGLTLMGVSSVYQILVTGILVI 305 Query: 325 VAVVIDQYRNK 335 +AV DQ K Sbjct: 306 LAVATDQLSRK 316 Lambda K H 0.325 0.140 0.394 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: 220 Number of extensions: 12 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: 340 Length of database: 319 Length adjustment: 28 Effective length of query: 312 Effective length of database: 291 Effective search space: 90792 Effective search space used: 90792 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