Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_011842348.1 RSPH17029_RS17190 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= uniprot:A8LLL2 (373 letters) >NCBI__GCF_000015985.1:WP_011842348.1 Length = 359 Score = 309 bits (792), Expect = 7e-89 Identities = 168/315 (53%), Positives = 215/315 (68%), Gaps = 7/315 (2%) Query: 1 MADLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL 60 MA + L + K YG ++ + ++L+++ GE + FVGPSGCGKST+LRMIAGLE I+GG + Sbjct: 1 MARISLQKIVKRYGGMEAIHGVDLEVEDGEFVAFVGPSGCGKSTMLRMIAGLEDISGGHM 60 Query: 61 EIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEK 120 I +VND+ P R +AMVFQ YALYPHMTVR+N+ F LK+ + I VE AA Sbjct: 61 RIGDRLVNDIEPKGRDVAMVFQDYALYPHMTVRDNIGFGLKMRGEPAETIRKKVEEAARI 120 Query: 121 LQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLK 180 LQL LDR P LSGGQRQRVA+GR+IVR PKV+LFDEPLSNLDA LRV R +I +L Sbjct: 121 LQLEDLLDRRPGQLSGGQRQRVAMGRAIVRKPKVFLFDEPLSNLDAKLRVEMRTQIKRL- 179 Query: 181 EAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKM 240 M +T +YVTHDQVEAMTLA R+VVL G I Q G PLELYE+P FVA+FIGSP+M Sbjct: 180 HRMLRTTTIYVTHDQVEAMTLADRVVVLRKGSIIQHGRPLELYERPSCRFVAEFIGSPQM 239 Query: 241 NLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEAAP-GGDYVF 299 N+LPG++ + T +E+ G +S P +G +++VG+RPE + AP D+V Sbjct: 240 NILPGRVASSDRGTVIEVGGGAIPLSHLPVP---VGTSLDVGLRPEHLEPCAPEEADFVA 296 Query: 300 EGKVAITEALGEVTL 314 E V + E LG TL Sbjct: 297 E--VDVLEELGSDTL 309 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: 414 Number of extensions: 16 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: 359 Length adjustment: 30 Effective length of query: 343 Effective length of database: 329 Effective search space: 112847 Effective search space used: 112847 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 Apr 10 2024. 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