Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate Ac3H11_2066 SN-glycerol-3-phosphate transport ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2066 Length = 355 Score = 267 bits (682), Expect = 4e-76 Identities = 153/327 (46%), Positives = 209/327 (63%), Gaps = 20/327 (6%) Query: 2 ADLKLTGVEKAYG----DVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITG 57 + L + G+ K +G V+VL +++ + GE ++ VGPSGCGKSTLL +IAGL++ T Sbjct: 3 SSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTE 62 Query: 58 GTLEIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAA 117 G + I G V +PP R IAMVFQSYALYP ++V +N+ FAL++ K + E ++ Sbjct: 63 GEIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEV 122 Query: 118 AEKLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIA 177 A LQ+ LDR P LSGGQRQRVA+GR++ R P+++LFDEPLSNLDA LRV R EI Sbjct: 123 AAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIK 182 Query: 178 QLKEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGS 237 +L +A T VYVTHDQVEAMTL +RI V+ GG + Q+G+P E+Y +P N +VA FIGS Sbjct: 183 RLHQA-SGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGS 241 Query: 238 PKMNLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMV--EAAPGG 295 P MNLL G + TG Q ++ G A++ P S V +GVRPE +V E AP Sbjct: 242 PTMNLLRGAV--TGGQFGIQ----GAALNLAPPPSS--ANEVLLGVRPEHLVMQETAP-- 291 Query: 296 DYVFEGKVAITEALGEVTLLYFEAPSG 322 + G+V++ E G T + + +G Sbjct: 292 ---WRGRVSVVEPTGPDTYVMVDTAAG 315 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: 359 Number of extensions: 15 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: 355 Length adjustment: 29 Effective length of query: 344 Effective length of database: 326 Effective search space: 112144 Effective search space used: 112144 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