Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate H281DRAFT_00169 H281DRAFT_00169 carbohydrate ABC transporter ATP-binding protein, CUT1 family
Query= SwissProt::Q9YGA6 (372 letters) >FitnessBrowser__Burk376:H281DRAFT_00169 Length = 371 Score = 330 bits (846), Expect = 4e-95 Identities = 182/378 (48%), Positives = 248/378 (65%), Gaps = 15/378 (3%) Query: 1 MAGVRLVDVWKVFGE-VTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQ 59 MA + + DV+K + V ++ ++++++DG+F+IL+G SGCGK+T L MIAGLE ++G+ Sbjct: 1 MASLSIRDVYKTYPNGVPVLKGVNIDIEDGQFLILVGGSGCGKSTLLNMIAGLETVTKGE 60 Query: 60 IYIGDKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQR 119 I I K V + + PKDRDIAMVFQSYALYP MTV +NI+F L +RKVP+QE Q Sbjct: 61 IQIDGKTVNN------LSPKDRDIAMVFQSYALYPSMTVRENISFGLNIRKVPKQEQAQI 114 Query: 120 VREVAELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMR 179 V V+ L +T LL+RKP +LSGGQRQRVA+GRA+ R P +FL DEPLSNLDAKLR+ MR Sbjct: 115 VDRVSNTLQITHLLDRKPGQLSGGQRQRVAMGRALARDPVMFLFDEPLSNLDAKLRIEMR 174 Query: 180 AELKKLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGF 239 +E+K L ++LG T +YVTHDQ+EAMT+GDRIAVM G++QQ G+P E+YD P+N FVAGF Sbjct: 175 SEIKLLHQRLGTTIVYVTHDQIEAMTLGDRIAVMKDGIVQQFGAPQEIYDSPSNLFVAGF 234 Query: 240 IGSPPMNFLDAIVTEDGF-----VDFGEFRLKL-LPDQFEVLGELGYVGREVIFGIRPED 293 IG+PPMNF+ + E G +D G R L LP F+ +VGREVI G+RPE Sbjct: 235 IGAPPMNFIQGKLVEQGAGVGIELDTGVTRTALNLP--FDSAKVKSHVGREVILGLRPER 292 Query: 294 LYDAMFAQVRVPGENLVRAVVEIVENLGSERIVHLRVGGVTFVGSFRSESRVREGVEVDV 353 + DA A + V+++E G + +V +V G V S + + Sbjct: 293 ITDARGAHGDHARLQQIEVKVDVIEPTGPDTLVFAQVNGKRVVSRVHPASNPQPLTNTTL 352 Query: 354 VFDMKKIHIFDKTTGKAI 371 +FD K +FD + + I Sbjct: 353 LFDTSKAVLFDPSNEERI 370 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: 416 Number of extensions: 21 Number of successful extensions: 4 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: 371 Length adjustment: 30 Effective length of query: 342 Effective length of database: 341 Effective search space: 116622 Effective search space used: 116622 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 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