Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein
Query= uniprot:A0A165KQ08 (355 letters) >FitnessBrowser__Dyella79:N515DRAFT_1562 Length = 384 Score = 221 bits (562), Expect = 3e-62 Identities = 124/308 (40%), Positives = 187/308 (60%), Gaps = 13/308 (4%) Query: 4 SLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEG 63 SL I + +R+G + L + +A GEF+ L+GPSG GKS+LL I+AGLD+P G Sbjct: 2 SLSIRQLTRRYG----AFAALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRG 57 Query: 64 EIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMR-KMPKPERQK---RI 119 ++ G +++ +P + RDI +VFQ YAL+P ++VADNI F L +R + +P R+ R+ Sbjct: 58 DVLRDGTDLLALPAQRRDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAARV 117 Query: 120 DEVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRA 179 +++ +Q+ L R P+QLSGGQRQRVA+ RALA +P L L DEP LDA++R +R Sbjct: 118 EDLLRRVQLEELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRV 177 Query: 180 EIKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFI 239 ++ L ++ G+T+V VTHDQ EA+ L R+ VM G ++Q+G P EIY PA +V F+ Sbjct: 178 WLRDLQRSLGLTTVLVTHDQDEALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHGFV 237 Query: 240 GSPTMNLLRGAVTGGQFGIQGAAL-NLAPPPSSANEVLLGVRPEHLVM--QETAPWRGRV 296 G N +RG V + + G + P + E+ +RPEHL + + W GR+ Sbjct: 238 G--RANRIRGHVERDRLHLGGHSFQGELPGDLAGREIEAWLRPEHLALASRGLGGWTGRL 295 Query: 297 SVVEPTGP 304 ++ GP Sbjct: 296 QHLDLAGP 303 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: 365 Number of extensions: 15 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: 384 Length adjustment: 30 Effective length of query: 325 Effective length of database: 354 Effective search space: 115050 Effective search space used: 115050 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