Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate 3609758 Dshi_3141 ABC transporter related (RefSeq)
Query= SwissProt::Q9YGA6 (372 letters) >FitnessBrowser__Dino:3609758 Length = 352 Score = 346 bits (888), Expect = e-100 Identities = 185/371 (49%), Positives = 246/371 (66%), Gaps = 21/371 (5%) Query: 1 MAGVRLVDVWKVFGEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQI 60 MA V L D+ K +G+ V SL V+D EF++LLGPSGCGKTTT+RMIAGLE+P+ G+I Sbjct: 1 MAEVILKDLTKRWGDFVGVDNQSLHVRDEEFLVLLGPSGCGKTTTMRMIAGLEDPTDGEI 60 Query: 61 YIGDKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRV 120 +IGD++V D PKDRD+AMVFQ+Y LYPHMT+++NIA+PL++R V + EI RV Sbjct: 61 WIGDRMVNDDL------PKDRDVAMVFQNYGLYPHMTIFENIAYPLRVRGVDKAEIPPRV 114 Query: 121 REVAELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRA 180 + AE + LT+ L+RKP+ LSGGQRQRVAL RAIVRKP+VFLMDEPLSNLDAKLRV MRA Sbjct: 115 QRAAEQVELTKFLHRKPKALSGGQRQRVALARAIVRKPKVFLMDEPLSNLDAKLRVTMRA 174 Query: 181 ELKKLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFI 240 ELK L R+L +TT+YVTHDQ+EAMT+ DR+AVM GV+QQ+G+PDE+Y+ PAN FVAGFI Sbjct: 175 ELKHLSRELQITTVYVTHDQIEAMTLADRVAVMKHGVIQQLGTPDEIYNDPANLFVAGFI 234 Query: 241 GSPPMNFLDAIVTEDGFVDFGEFRLKLLPDQFEVLGELGYVGREVIFGIRPEDLYDAMFA 300 GSP MN ++ V + FV G RL +P I G+R +D+ Sbjct: 235 GSPAMNLINGSVEDGMFVTTGGTRLVKVPSPDRA---------RAILGVRADDM------ 279 Query: 301 QVRVPGENLVRAVVEIVENLGSERIVHLRVGGVTFVGSFRSESRVREGVEVDVVFDMKKI 360 QV G+ + + EN G ++ ++ G + R + V + + + Sbjct: 280 QVHEAGQGDIDVTIYAFENTGESTLLTVQWGKQRVIARGDRHLRKEQDDVVGISLNTDHL 339 Query: 361 HIFDKTTGKAI 371 ++FD T + I Sbjct: 340 YLFDPDTEERI 350 Lambda K H 0.323 0.142 0.406 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: 419 Number of extensions: 21 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: 372 Length of database: 352 Length adjustment: 29 Effective length of query: 343 Effective length of database: 323 Effective search space: 110789 Effective search space used: 110789 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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