Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >NCBI__GCF_900129305.1:WP_073037934.1 Length = 365 Score = 256 bits (654), Expect = 7e-73 Identities = 149/374 (39%), Positives = 217/374 (58%), Gaps = 30/374 (8%) Query: 4 LKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLY 63 +++ ++ K Y + +V + + + + +V +GPSGCGK+T LR+IAGLE +T G ++ Sbjct: 3 IEIRDVRKDYGRVQ--AVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIH 60 Query: 64 IDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEIL 123 I + P R+I+MVFQ+YAL+PH++V EN+ FGLK+RK D+I +R+ ++L Sbjct: 61 IAGTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRVVDLL 120 Query: 124 GLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHR 183 GL+ L+ KP +LSGG +QRVA+GRAI+ + V LMDEPLSNLDAKLR +MR EI + R Sbjct: 121 GLSGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSLQR 180 Query: 184 RIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVA 243 R+G T IYVTHDQ EAMT+ADRIV+M G+I Q +P+ Y PAN FVA Sbjct: 181 RLGITMIYVTHDQVEAMTMADRIVLMRD----------GQIVQDDSPENFYERPANTFVA 230 Query: 244 GFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPEDISSD 303 FIG+P MN + + + G L P G + GIRPE++ Sbjct: 231 RFIGTPPMNIVPLCPTQGGAALEPGGRLLFP----------GMDPDRYLFGIRPENLR-- 278 Query: 304 QIVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSHSPGEKVQLTFNIA 363 + E+ A VT E LGS++ + + E R R + G V LT++ Sbjct: 279 --LAESGQPAMVTG----REYLGSDTFVSCEIHGQEVIVRTRGRRNIREGTVVHLTWDPG 332 Query: 364 KGHFFDLETEKRIN 377 + FD T++R++ Sbjct: 333 DVNLFDARTQERVD 346 Lambda K H 0.318 0.135 0.379 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: 335 Number of extensions: 13 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: 377 Length of database: 365 Length adjustment: 30 Effective length of query: 347 Effective length of database: 335 Effective search space: 116245 Effective search space used: 116245 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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