Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate 3608008 Dshi_1416 ABC transporter related (RefSeq)
Query= SwissProt::Q9YGA6 (372 letters) >FitnessBrowser__Dino:3608008 Length = 347 Score = 342 bits (876), Expect = 1e-98 Identities = 191/368 (51%), Positives = 238/368 (64%), Gaps = 24/368 (6%) Query: 1 MAGVRLVDVWKVFGEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQI 60 MA +RL V K +G V + L + D EF++LLGPSGCGKTTT+RMIAGLEEPS G+I Sbjct: 1 MAEIRLNHVQKRWGSFVGVEDFHLTIPDREFLVLLGPSGCGKTTTMRMIAGLEEPSSGEI 60 Query: 61 YIGDKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRV 120 +IGD++V + PKDRD+AMVFQSY LYP+M VY+NI FPLK+RKVP E + RV Sbjct: 61 WIGDRMVNA------LDPKDRDVAMVFQSYGLYPNMNVYENIRFPLKVRKVPEVEHEARV 114 Query: 121 REVAELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRA 180 + ++ L + L+RKP LSGGQRQRVAL RAIVR+P VFLMDEPLSNLDAKLRV RA Sbjct: 115 MRASAMVELDDFLHRKPAALSGGQRQRVALARAIVREPNVFLMDEPLSNLDAKLRVSTRA 174 Query: 181 ELKKLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFI 240 ++K L +L VTTIYVTHDQ+EAMT+ DR+ VM+ GV+QQVG+P E+YD+PANTFVA FI Sbjct: 175 QIKNLSHELQVTTIYVTHDQIEAMTLADRVVVMSAGVVQQVGTPMEIYDRPANTFVASFI 234 Query: 241 GSPPMNFLDAIVTEDGFVDFGEFRLKLLPDQFEVLGELGYVGREVIFGIRPEDLYDAMFA 300 GSP MN ++ VT+ F D+ + G G GR V G R ED A Sbjct: 235 GSPAMNLMEGAVTDGTFHG----------DRVAIAGLSGAAGR-VTLGFRAED------A 277 Query: 301 QVRVPGENLVRAVVEIVENLGSERIVHLRVGGVTFVGSFRSESRVREGVEVDVVFDMKKI 360 QV V + + A V +E LG +V ++ GG E R G V + Sbjct: 278 QV-VDSDGQIAAPVYSMELLGDATMVTVKAGGTLVAVKAPKEFRAEIGAPVQIRIPTGIC 336 Query: 361 HIFDKTTG 368 H+FD TG Sbjct: 337 HLFDAQTG 344 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: 397 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: 372 Length of database: 347 Length adjustment: 29 Effective length of query: 343 Effective length of database: 318 Effective search space: 109074 Effective search space used: 109074 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