Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_086511012.1 BZY95_RS16625 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= uniprot:A0A165KQ08 (355 letters) >NCBI__GCF_002151265.1:WP_086511012.1 Length = 346 Score = 293 bits (749), Expect = 6e-84 Identities = 154/311 (49%), Positives = 198/311 (63%), Gaps = 19/311 (6%) Query: 23 VLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGEIRIGGKNVVGMPPRDRDI 82 V+ +++ + G F +LVGPSGCGKSTLL +IAGL+ T G I IGG++V P +R+I Sbjct: 19 VIPNLNLRIEDGSFTVLVGPSGCGKSTLLRMIAGLETVTRGAISIGGRDVTTAEPSERNI 78 Query: 83 AMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEVAAMLQISHLLDRRPSQLSGG 142 AMVFQSYALYP ++VA NI F + + K+P ER ++ E A +L + LL+R+P++LSGG Sbjct: 79 AMVFQSYALYPHMTVARNIDFGMRLAKVPTEERMAKVAEAARLLNLEELLERKPAELSGG 138 Query: 143 QRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIKRLHQASGITSVYVTHDQVEA 202 QRQRVA+GRA+ R P +FLFDEPLSNLDA LR MR E+ LHQ T +YVTHDQVEA Sbjct: 139 QRQRVAIGRAIVRNPGVFLFDEPLSNLDAALRNRMRVELAELHQRLDATMIYVTHDQVEA 198 Query: 203 MTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSPTMNLLRGAVTGGQFGIQGAA 262 MTL I VM G ++Q+GTP +Y RP +VA FIGSP MNL+ G V Sbjct: 199 MTLADCIVVMNAGQIEQVGTPMNLYQRPETLFVAGFIGSPKMNLIEGEVA---------- 248 Query: 263 LNLAPPPSSANEVLLGVRPEHL-VMQETAPWRGRVSVVEPTGPDTYVMVDT-AAGSVTLR 320 + LG+RPEHL V E WR RV VVE G D + VD+ A G +T+R Sbjct: 249 -------KAHGATTLGIRPEHLEVSHEAGEWRTRVRVVEMLGADAFAYVDSDATGPLTVR 301 Query: 321 TDAQTRVQPGE 331 V+ G+ Sbjct: 302 LPGDAEVRSGD 312 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: 341 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: 346 Length adjustment: 29 Effective length of query: 326 Effective length of database: 317 Effective search space: 103342 Effective search space used: 103342 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