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 Ac3H11_1002 ABC transporter ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1002 Length = 356 Score = 217 bits (552), Expect = 5e-61 Identities = 129/321 (40%), Positives = 192/321 (59%), Gaps = 29/321 (9%) Query: 11 KRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLYIDDKLMN 70 KRY + K +V+ NL I + +GPSGCGKSTTLRMIAG E +T G++ ++++ + Sbjct: 20 KRYASGKP-AVDAINLRIASGSYCCLLGPSGCGKSTTLRMIAGHESVTSGDILLENRNIT 78 Query: 71 DASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEILGLTEFLE 130 D R AM+FQ++AL+PH+S +N+AF LK++ K + + + E + L E Sbjct: 79 DLPAAARGTAMMFQSFALFPHLSALDNVAFSLKMKGVPKAERQAKARDLLERVALGHLAE 138 Query: 131 RKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHRRIGATTI 190 RKPA+LSGGQ+QRVA+ RA++ +V L+DEPLS LD LR+ MRAE+ + + +G T I Sbjct: 139 RKPAELSGGQQQRVALARALITQPRVLLLDEPLSALDPFLRIQMRAELRRWQKELGLTFI 198 Query: 191 YVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVAGFIGSPA 250 +VTH Q EAM LAD +V+M+ G IEQ+G+P E+YN PA++FVA F+G Sbjct: 199 HVTHSQEEAMALADTMVVMNH----------GVIEQVGSPHEVYNRPASEFVARFMG--G 246 Query: 251 MNFFEVTVEKERLVNQDGLSLA-----LPQGQEKIL---EEKGYLGKKVTLGIRPEDISS 302 N + T E + V D L +A LP G +++L + Y G V LG++ + ++ Sbjct: 247 HNVID-TPEGKVGVRTDHLQIAPASAELPWGAQRMLAVVTDVEYQGTYVLLGLQKQGVAL 305 Query: 303 DQIVHETFPNASVTADILVSE 323 NA+ ++VSE Sbjct: 306 S-------ANATAAYSVMVSE 319 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: 262 Number of extensions: 8 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: 356 Length adjustment: 30 Effective length of query: 347 Effective length of database: 326 Effective search space: 113122 Effective search space used: 113122 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 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