Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 6939439 Sama_3531 molybdenum ABC transporter, ATP-binding protein (RefSeq)
Query= uniprot:A0A165KQ08 (355 letters) >FitnessBrowser__SB2B:6939439 Length = 370 Score = 156 bits (394), Expect = 9e-43 Identities = 91/221 (41%), Positives = 127/221 (57%), Gaps = 8/221 (3%) Query: 26 KVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGEIRIGGK------NVVGMPPRD 79 + D GEFL +VGPSG GK+TLL +IAGL +P G IR G + + P++ Sbjct: 20 EADFSCRAGEFLAVVGPSGGGKTTLLRMIAGLAKPENGSIRCGKRIWFDSDEGIHCSPQN 79 Query: 80 RDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEVAAMLQISHLLDRRPSQL 139 R I V Q + L+P LS NI AL+ +P ER+ R + + L DR PSQL Sbjct: 80 RHIGFVPQHFGLFPKLSALGNIMAALD--HLPSQERRPRALAALEKVNLHGLTDRLPSQL 137 Query: 140 SGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIKRLHQASGITSVYVTHDQ 199 SGGQ+QRVA+ RALAR+P++ L DEP S +D + R + E+ RL I + VTHD Sbjct: 138 SGGQKQRVALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKAELNIPVIMVTHDL 197 Query: 200 VEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIG 240 EA+ L + ++ G + Q GTP ++++RP N VA +G Sbjct: 198 NEALLLADSMLLISQGHMLQHGTPQDVFSRPRNEAVARQMG 238 Lambda K H 0.318 0.135 0.388 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: 284 Number of extensions: 9 Number of successful extensions: 2 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: 355 Length of database: 370 Length adjustment: 29 Effective length of query: 326 Effective length of database: 341 Effective search space: 111166 Effective search space used: 111166 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 (21.7 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