Align Inositol transport system ATP-binding protein (characterized)
to candidate 7026050 Shewana3_3192 sulfate ABC transporter, ATPase subunit (RefSeq)
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__ANA3:7026050 Length = 376 Score = 89.4 bits (220), Expect = 1e-22 Identities = 70/221 (31%), Positives = 117/221 (52%), Gaps = 14/221 (6%) Query: 8 IRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFE 67 IR+ I K FG AL+ +++D+ GE LLG +G+GK+T ++ ++G+ G I F Sbjct: 3 IRLTNISKKFGQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGQIHFG 62 Query: 68 GQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPI-RKIGPLKLFDHDYANR 126 + + RD + V Q+ A+ M+V+ N G E I +K P K + R Sbjct: 63 NRDVTQVHVRD---RRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSKA---EIQKR 116 Query: 127 IT-MEEMRKMG-INLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQT 184 ++ + EM ++G + R P+Q LSGG++Q +A+ARA+ +VL+LDEP AL + Sbjct: 117 VSHLLEMVQLGHLAQRYPEQ----LSGGQKQRIALARALATQPEVLLLDEPFGALDAKVR 172 Query: 185 ANVLATIDKVRKQ-GVAVVFITHNVRHALAVGDRFTVLNRG 224 + + + + VF+TH+ AL + DR V++ G Sbjct: 173 KELRRWLRSLHDELKFTSVFVTHDQDEALELSDRVVVMSNG 213 Lambda K H 0.321 0.137 0.395 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: 242 Number of extensions: 10 Number of successful extensions: 3 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: 261 Length of database: 376 Length adjustment: 27 Effective length of query: 234 Effective length of database: 349 Effective search space: 81666 Effective search space used: 81666 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 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