Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate CA265_RS10520 CA265_RS10520 ABC transporter ATP-binding protein
Query= SwissProt::Q9YGA6 (372 letters) >lcl|FitnessBrowser__Pedo557:CA265_RS10520 CA265_RS10520 ABC transporter ATP-binding protein Length = 568 Score = 135 bits (339), Expect = 4e-36 Identities = 84/242 (34%), Positives = 140/242 (57%), Gaps = 10/242 (4%) Query: 12 VFGEVT----AVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIGDKLV 67 +FG+ T AV +++ EV GE + L+G SGCGKTT R I L +P+ G+I + + Sbjct: 325 LFGKTTDYVKAVDQLNFEVFPGETLGLVGESGCGKTTLGRTILRLIQPTSGEIIFNGENI 384 Query: 68 ADPEKGIFVPPKDRDIAMVFQS-YA-LYPHMTVYDNIAFPLKLRKVPRQEID--QRVREV 123 K + +DI ++FQ YA L P +++ +I PL++ K+ R + + Q+V E+ Sbjct: 385 THIGKTALRKLR-KDIQIIFQDPYASLNPKLSIGQSILEPLQVHKLYRNDSERKQKVLEL 443 Query: 124 AELLGLTEL-LNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAEL 182 + +GL E NR P E SGGQRQRV + RA+ +P+ + DE +S LD ++ ++ + Sbjct: 444 LDKVGLKEEHFNRYPHEFSGGQRQRVVIARALALQPKFIICDESVSALDVSVQAQVLNLI 503 Query: 183 KKLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIGS 242 K LQ + G+T I+++HD + DRI VMN+G +++ G P++++ P + I + Sbjct: 504 KDLQSEFGLTYIFISHDLAVVKHISDRILVMNKGKIEEEGFPEQIFYAPKAAYTQKLIEA 563 Query: 243 PP 244 P Sbjct: 564 IP 565 Score = 86.3 bits (212), Expect = 2e-21 Identities = 61/237 (25%), Positives = 115/237 (48%), Gaps = 10/237 (4%) Query: 18 AVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSR----GQIYIGDKLVADPEKG 73 AV+++S +VK G + ++G SG GK+ T I L + G+I D + + Sbjct: 22 AVKQISFKVKKGTVLGIVGESGSGKSVTSFSIMRLHDERAAKITGEIDFEDISLLNLSSN 81 Query: 74 IFVPPKDRDIAMVFQS--YALYPHMTVYDNIAFPLKL-RKVPRQEIDQRVREVAELLGLT 130 + I+M+FQ +L P T +A + L RKV + E + + + L Sbjct: 82 EIRQIRGNQISMIFQEPMTSLNPVFTCGYQVAEAIMLHRKVDQAEAKKHTIALFNEVQLP 141 Query: 131 ---ELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKKLQR 187 ++ P ++SGGQ+QRV + A+ P++ + DEP + LD ++ + L KL++ Sbjct: 142 RPEKIFESYPHQISGGQKQRVMIAMALSCDPKLLIADEPTTALDVTVQKTILQLLLKLKQ 201 Query: 188 QLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIGSPP 244 + + I+++HD + D +AVM +G + + G +++ P + + G + P Sbjct: 202 ERNMAMIFISHDLGVVNEIADEVAVMYKGEIVEQGPAKSIFENPQHPYTKGLLACRP 258 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: 442 Number of extensions: 19 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 372 Length of database: 568 Length adjustment: 33 Effective length of query: 339 Effective length of database: 535 Effective search space: 181365 Effective search space used: 181365 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: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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