Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate WP_090447139.1 BLS63_RS17880 maltose/maltodextrin ABC transporter ATP-binding protein MalK
Query= reanno::acidovorax_3H11:Ac3H11_792 (358 letters) >NCBI__GCF_900100495.1:WP_090447139.1 Length = 371 Score = 188 bits (477), Expect = 2e-52 Identities = 108/295 (36%), Positives = 175/295 (59%), Gaps = 10/295 (3%) Query: 27 LKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVLFDGRDVTRASPQERNIAQVF 86 + ++ EDG +GPSGCGK+T+L +++GL S G +L + V P ER++ VF Sbjct: 22 IDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDISSGDLLIGEQRVNDLPPMERSVGMVF 81 Query: 87 QFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRVGVIAEMLEMSGQLNQRAAGLAADAKQK 146 Q +Y MTVAEN+AF L+ KV +G I+++V ++ +L++ L ++ L+ +Q+ Sbjct: 82 QSYALYPHMTVAENMAFGLKLAKVDKGAIRRKVEEVSRILQLDQLLERKPKDLSGGQRQR 141 Query: 147 ISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQIHHELKLTLIYVTHDQVEALTF 206 +++GR +VR + LFDEPL+ +D L+ Q+R ++ ++H L+ T+IYVTHDQVEA+T Sbjct: 142 VAIGRTMVR-EPKVFLFDEPLSNLDAALRVQMRIEISRLHQRLRSTMIYVTHDQVEAMTM 200 Query: 207 ADQVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGMNFLPAHRDGENLSV------A 260 AD++VV+ G+ QVG L+ P + FV F+GSP MNFL G + Sbjct: 201 ADKIVVLNAGQIAQVGQPLELYHYPRNQFVAGFLGSPQMNFLKVKALGASSEAVEIEMPG 260 Query: 261 GHRLASPV-GRALPAG-ALQVGIRPEYLALAQPQQAGALPGTVVQVQDIGTYQML 313 G+R+ V G + AG L +G+RPE+ A+ Q A G + + +G + ++ Sbjct: 261 GYRMQVLVDGSEVQAGDELTLGVRPEHFVDAE-QADFAFYGQIGVAERLGDHNLI 314 Lambda K H 0.320 0.136 0.395 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: 290 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: 358 Length of database: 371 Length adjustment: 29 Effective length of query: 329 Effective length of database: 342 Effective search space: 112518 Effective search space used: 112518 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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