Align Inositol transport system ATP-binding protein (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__Caulo:CCNA_01670 Length = 339 Score = 117 bits (293), Expect = 3e-31 Identities = 79/223 (35%), Positives = 124/223 (55%), Gaps = 16/223 (7%) Query: 8 IRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFE 67 I ++ +EK FG AL V +++ GE LLG +G+GK+T ++T++G+ P G +LF+ Sbjct: 3 IAIRSVEKQFGRYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVLFD 62 Query: 68 GQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRI 127 GQ + +A A A + V Q A+ M+V++N G + +RK G K + A R+ Sbjct: 63 GQDVTYA---SAAARRVGFVFQQYALFKHMTVAKNIAFGLD-VRK-GKDKPSKAEIARRV 117 Query: 128 TMEEMRKM----GINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQ 183 EE+ K+ G+ R P Q LSGG+RQ VA++RA+ VL+LDEP AL Sbjct: 118 --EELLKLVELEGLGGRYPSQ----LSGGQRQRVALSRALAVQPSVLLLDEPFGALDATV 171 Query: 184 TANVLATIDKVR-KQGVAVVFITHNVRHALAVGDRFTVLNRGK 225 ++ + +V GV +F+TH+ AL + DR +LN G+ Sbjct: 172 RKSLRRELRRVHDATGVTTIFVTHDQEEALELADRVAILNNGR 214 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: 199 Number of extensions: 11 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: 339 Length adjustment: 26 Effective length of query: 235 Effective length of database: 313 Effective search space: 73555 Effective search space used: 73555 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