Align Inositol transport system sugar-binding protein (characterized)
to candidate WP_004118879.1 RHSP_RS15695 ABC transporter substrate-binding protein
Query= reanno::WCS417:GFF2331 (309 letters) >NCBI__GCF_000359745.1:WP_004118879.1 Length = 320 Score = 112 bits (279), Expect = 2e-29 Identities = 89/293 (30%), Positives = 146/293 (49%), Gaps = 18/293 (6%) Query: 8 TALALSMLLASGV---ASAADLKIGVSMSAFDDTFLTYLREDMDKQAKSYPKGDGVQLQF 64 TAL + + A+ + ASA L +G S + + R K K G+ L+F Sbjct: 5 TALISATIFAACMFTSASAKQLVVGFSQIGSESGW----RAAETTLTKQEAKKRGIDLKF 60 Query: 65 EDARADVVKQLSQVENFISQKVDAIIVNPVDTASTANIIKAATAAKIPLVFVNRRPDSQT 124 DA+ Q+ + +FI+Q VDAI++ PV ++K A AKIP++ ++R + Sbjct: 61 ADAQQKQENQIKAIRSFIAQGVDAILLAPVVETGWDAVLKEAKEAKIPVILLDRTVNGPK 120 Query: 125 LAPGVAAVTSDDVEAGKLQMQYIAEKLGGKG-NIVILLGDLANNSTTNRTKGVKEVLTKY 183 + AVTSD V GK+ ++ + +G K NIV L G ++ R KG +E + + Sbjct: 121 -DLYLTAVTSDLVHEGKVAGDWLVKTVGDKKCNIVELQGTTGSSPAIARKKGFEEAVKGH 179 Query: 184 PGIKIEQEQTGIWLRDRGMTLVNDWL---TQGRDFQAVLSNNDEMAIGAAMALKSAG--- 237 +KI + QTG + R +G ++ +L G++ A+ ++ND+MA+GA A+K AG Sbjct: 180 DNLKIVRSQTGDFTRAKGKEVMESFLKAENGGKNICALYAHNDDMAVGAIQAIKEAGLKP 239 Query: 238 KKGVLIAGVDGTPDGLNAITKGD--MTVSAFQDAKGQADKSVETARKMAKNEP 288 K +L +D PD A+ G+ TV + G A +++ K K EP Sbjct: 240 GKDILTVSIDSVPDLFKAMAAGEANATVELTPNMAGPAFDALDAYLK-TKKEP 291 Lambda K H 0.314 0.131 0.357 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: 218 Number of extensions: 10 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: 309 Length of database: 320 Length adjustment: 27 Effective length of query: 282 Effective length of database: 293 Effective search space: 82626 Effective search space used: 82626 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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