Align Trehalose permease IIC protein (characterized, see rationale)
to candidate GFF4503 PS417_23050 trehalose permease IIC protein
Query= uniprot:A0A1N7UR85 (480 letters) >FitnessBrowser__WCS417:GFF4503 Length = 480 Score = 929 bits (2402), Expect = 0.0 Identities = 480/480 (100%), Positives = 480/480 (100%) Query: 1 MSHDYSTIAREILENLGGSDNLEQAAHCVTRLRLALKDPSLVNSSALNQVDLVKGSFFTG 60 MSHDYSTIAREILENLGGSDNLEQAAHCVTRLRLALKDPSLVNSSALNQVDLVKGSFFTG Sbjct: 1 MSHDYSTIAREILENLGGSDNLEQAAHCVTRLRLALKDPSLVNSSALNQVDLVKGSFFTG 60 Query: 61 GLFQVVIGPGEVEKVYAALREQTGLAAATIADVKKKGADKTNAMQRLVRVFSDVFMPILP 120 GLFQVVIGPGEVEKVYAALREQTGLAAATIADVKKKGADKTNAMQRLVRVFSDVFMPILP Sbjct: 61 GLFQVVIGPGEVEKVYAALREQTGLAAATIADVKKKGADKTNAMQRLVRVFSDVFMPILP 120 Query: 121 ALIIAGLLMGVNNLMGAQGMFIEGKTLLEAYPNLDGLWSLINLMANTSFVFLPALVGWSA 180 ALIIAGLLMGVNNLMGAQGMFIEGKTLLEAYPNLDGLWSLINLMANTSFVFLPALVGWSA Sbjct: 121 ALIIAGLLMGVNNLMGAQGMFIEGKTLLEAYPNLDGLWSLINLMANTSFVFLPALVGWSA 180 Query: 181 AKRFGGSEILGIVLGLMLVHPDLLNAWNYGKAVAGLDGQSLPYFDIFGWFKIEKVGYQGQ 240 AKRFGGSEILGIVLGLMLVHPDLLNAWNYGKAVAGLDGQSLPYFDIFGWFKIEKVGYQGQ Sbjct: 181 AKRFGGSEILGIVLGLMLVHPDLLNAWNYGKAVAGLDGQSLPYFDIFGWFKIEKVGYQGQ 240 Query: 241 ILPILMAAYVMSVIEKGLRARVPNAIQLLVVPITTIVVTGVLALAIIGPVTRHLGILITE 300 ILPILMAAYVMSVIEKGLRARVPNAIQLLVVPITTIVVTGVLALAIIGPVTRHLGILITE Sbjct: 241 ILPILMAAYVMSVIEKGLRARVPNAIQLLVVPITTIVVTGVLALAIIGPVTRHLGILITE 300 Query: 301 GVVTLFDLAPMVGGAIFGLLYAPLVITGMHHMFLAVDLQLISTQGGTFIWPMIVMSNLAQ 360 GVVTLFDLAPMVGGAIFGLLYAPLVITGMHHMFLAVDLQLISTQGGTFIWPMIVMSNLAQ Sbjct: 301 GVVTLFDLAPMVGGAIFGLLYAPLVITGMHHMFLAVDLQLISTQGGTFIWPMIVMSNLAQ 360 Query: 361 GSAALAVFYTTRNARDKSMASTSAISAYFGITEPAMFGVNLRFKFPFYAALVGSALGSIF 420 GSAALAVFYTTRNARDKSMASTSAISAYFGITEPAMFGVNLRFKFPFYAALVGSALGSIF Sbjct: 361 GSAALAVFYTTRNARDKSMASTSAISAYFGITEPAMFGVNLRFKFPFYAALVGSALGSIF 420 Query: 421 LALNKVQASAIGVGGLPGFISIVPQSIAVFVIGMVIAMVVPFVLTCGLSMKIVRPGYRVA 480 LALNKVQASAIGVGGLPGFISIVPQSIAVFVIGMVIAMVVPFVLTCGLSMKIVRPGYRVA Sbjct: 421 LALNKVQASAIGVGGLPGFISIVPQSIAVFVIGMVIAMVVPFVLTCGLSMKIVRPGYRVA 480 Lambda K H 0.325 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: 940 Number of extensions: 30 Number of successful extensions: 1 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: 480 Length of database: 480 Length adjustment: 34 Effective length of query: 446 Effective length of database: 446 Effective search space: 198916 Effective search space used: 198916 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: 51 (24.3 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