Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_087506594.1 CBE68_RS13315 ABC transporter ATP-binding protein
Query= uniprot:A0A165KQ08 (355 letters) >NCBI__GCF_002165625.1:WP_087506594.1 Length = 350 Score = 194 bits (494), Expect = 2e-54 Identities = 119/288 (41%), Positives = 170/288 (59%), Gaps = 19/288 (6%) Query: 5 LDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGE 64 L++ + RF K +VL + ++ GE L+GPSGCGKSTLL +IAGL +P G Sbjct: 8 LELNQVRLRF----KQQQVLDCISLNQLTGEINCLLGPSGCGKSTLLKLIAGLIKPDSGT 63 Query: 65 IRIGGKNVVG----MPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRID 120 I + GK + + P R I MVFQ AL+P L+VA+NI F L + PK ++Q+R+ Sbjct: 64 ISMAGKELSSKRNVIAPEQRQIGMVFQDLALFPHLTVAENICFGLYQQ--PKQQQQQRLQ 121 Query: 121 EVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAE 180 ++ ++ ++ ++ PS LSGGQ+QRVA+ RALA +P+L L DEP S D+ L+ + E Sbjct: 122 QLLELIGLTAKAEQYPSALSGGQQQRVALARALAPKPKLLLLDEPFSGFDSHLKSTLVPE 181 Query: 181 IKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIG 240 ++++ + GITS+ VTHDQ EA L R+AVM G V Q TP +IY PA+ +VA FIG Sbjct: 182 LRQILKHEGITSLIVTHDQHEAFALADRVAVMNDGQVHQYDTPQQIYRCPASAFVARFIG 241 Query: 241 SPTMNLLRGAVTGGQFGIQGAALNLAPPPSSA----NEVLLGVRPEHL 284 S L+ G VT AL P PS +EV + +R E + Sbjct: 242 SG--QLIAGKVTATAI---ETALGTLPLPSKQLAGNSEVSVLIRAEDI 284 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: 271 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: 355 Length of database: 350 Length adjustment: 29 Effective length of query: 326 Effective length of database: 321 Effective search space: 104646 Effective search space used: 104646 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 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