Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__Caulo:CCNA_01670 Length = 339 Score = 188 bits (478), Expect = 2e-52 Identities = 120/316 (37%), Positives = 172/316 (54%), Gaps = 18/316 (5%) Query: 4 LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63 + + VEK +G L+ ++L+I GEL+ +GPSG GK+TLLR IAGLE G + D Sbjct: 3 IAIRSVEKQFGRYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVLFD 62 Query: 64 GTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIA----KKSQAEIDAAVEAAAE 119 G V A R + VFQ YAL+ HMTV +N++F L + K S+AEI VE + Sbjct: 63 GQDVTYASAAARRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIARRVEELLK 122 Query: 120 KLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQL 179 ++L R P LSGGQRQRVA+ R++ P V L DEP LDA +R + R E+ ++ Sbjct: 123 LVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSLRRELRRV 182 Query: 180 KEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPK 239 +A +T ++VTHDQ EA+ LA R+ +L G I Q+G+P ++++ PE FV F+G + Sbjct: 183 HDATGVTT-IFVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAPETAFVCGFVG--E 239 Query: 240 MNLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEAAPGGDYVF 299 N G++ G G +T A+ D A VRP D G + + Sbjct: 240 ANRFDGQVSG-GRFKAGALTVPASALKD---------GAATAYVRPHDFALDEAGFEVLI 289 Query: 300 EGKVAITEALGEVTLL 315 E + + AL VT L Sbjct: 290 E-RAQVQGALTAVTAL 304 Lambda K H 0.316 0.135 0.379 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: 333 Number of extensions: 12 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: 373 Length of database: 339 Length adjustment: 29 Effective length of query: 344 Effective length of database: 310 Effective search space: 106640 Effective search space used: 106640 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: 41 (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