Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein
Query= SwissProt::Q9YGA6 (372 letters) >NCBI__GCF_900129305.1:WP_073037934.1 Length = 365 Score = 298 bits (764), Expect = 1e-85 Identities = 173/371 (46%), Positives = 230/371 (61%), Gaps = 31/371 (8%) Query: 4 VRLVDVWKVFGEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIG 63 + + DV K +G V AVR +S V++G+ +++LGPSGCGKTT LR+IAGLE + G I+I Sbjct: 3 IEIRDVRKDYGRVQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIHIA 62 Query: 64 DKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVREV 123 V +PP R+I+MVFQSYAL+PH+ V +NI F LK+RKVP EI++R++ V Sbjct: 63 GTDVTH------LPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRV 116 Query: 124 AELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELK 183 +LLGL+ L+ KP ELSGG +QRVALGRAI+ + V LMDEPLSNLDAKLR MR E+ Sbjct: 117 VDLLGLSGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREIC 176 Query: 184 KLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIGSP 243 LQR+LG+T IYVTHDQVEAMTM DRI +M G + Q SP+ Y++PANTFVA FIG+P Sbjct: 177 SLQRRLGITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTP 236 Query: 244 PMNFLDAIVTEDGFVDFGEFRLKLLPDQFEVLGELGYVGRE---VIFGIRPEDLYDAMFA 300 PMN + T+ G E G L + G + +FGIRPE+L A Sbjct: 237 PMNIVPLCPTQGGAA-------------LEPGGRLLFPGMDPDRYLFGIRPENLRLAESG 283 Query: 301 QVRVPGENLVRAVVEIVENLGSERIVHLRVGGVTFVGSFRSESRVREGVEVDVVFDMKKI 360 Q A+V E LGS+ V + G + R +REG V + +D + Sbjct: 284 Q---------PAMVTGREYLGSDTFVSCEIHGQEVIVRTRGRRNIREGTVVHLTWDPGDV 334 Query: 361 HIFDKTTGKAI 371 ++FD T + + Sbjct: 335 NLFDARTQERV 345 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: 403 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: 372 Length of database: 365 Length adjustment: 30 Effective length of query: 342 Effective length of database: 335 Effective search space: 114570 Effective search space used: 114570 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 Apr 09 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