Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate 8499890 DvMF_0655 ABC transporter related (RefSeq)
Query= SwissProt::Q9YGA6 (372 letters) >FitnessBrowser__Miya:8499890 Length = 350 Score = 292 bits (747), Expect = 1e-83 Identities = 173/369 (46%), Positives = 230/369 (62%), Gaps = 25/369 (6%) Query: 1 MAGVRLVDVWKVFGEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQI 60 M+ ++L++V + +G+V AV ++S EV+ G ++LLGPSGCGK+TTLR+IAGLE + G+I Sbjct: 1 MSAIQLLNVSRHWGDVRAVDDVSFEVEQGTMLVLLGPSGCGKSTTLRLIAGLESVTSGRI 60 Query: 61 YIGDKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRV 120 IG++ V +PP R +AMVFQSYAL+PH+TV +NI F L +RKVP E ++R+ Sbjct: 61 MIGERDVTH------LPPAQRQLAMVFQSYALFPHLTVRENILFGLTVRKVPEAEREKRL 114 Query: 121 REVAELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRA 180 ++LGL+ LL RKP ELSGGQ+QRVALGRA+V + V LMDEPLSNLDAKLR MR Sbjct: 115 TRAVDILGLSALLQRKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRHEMRR 174 Query: 181 ELKKLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFI 240 E++ LQ+ LG+T +YVTHDQ EAM+M DRI +M G + Q +P E+Y +PA TF FI Sbjct: 175 EIRALQQTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPSELYSRPATTFAGNFI 234 Query: 241 GSPPMNFLDAIVTEDGFVDFGEFRLKLLPDQFEVLGELGYVGREVIFGIRPEDLYDAMFA 300 G+PPMN L + G V R V+ YV GIRPE Sbjct: 235 GTPPMN-LVRLDDARGSVCVAGSR----SGTVSVVDSADYV-----LGIRPE-------- 276 Query: 301 QVRVPGENLVRAVVEIVENLGSERIVHLRVGGVTFVGSFRSESRVREGVEVDVVFDMKKI 360 +R+ E RAVVE VE LGS ++ RVGG + G E+ + + I Sbjct: 277 HIRIVPEGW-RAVVESVEYLGSGSVLGCRVGGEELSVVVDGVPTIAVGAEIYLHCPDEHI 335 Query: 361 HIFDKTTGK 369 HIFD TG+ Sbjct: 336 HIFDAKTGE 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: 372 Number of extensions: 19 Number of successful extensions: 4 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: 350 Length adjustment: 29 Effective length of query: 343 Effective length of database: 321 Effective search space: 110103 Effective search space used: 110103 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