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) >FitnessBrowser__Pedo557:CA265_RS10520 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:
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