Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate Echvi_3653 Echvi_3653 ABC-type sulfate/molybdate transport systems, ATPase component
Query= SwissProt::Q9YGA6 (372 letters) >FitnessBrowser__Cola:Echvi_3653 Length = 290 Score = 160 bits (404), Expect = 5e-44 Identities = 101/268 (37%), Positives = 151/268 (56%), Gaps = 8/268 (2%) Query: 21 EMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIGDKLVADPEKGIFVPPKD 80 ++ L + GEF+ L GPSG GKT+TLRMI+GL P +G + + + D G V P Sbjct: 20 DIKLTISQGEFITLFGPSGSGKTSTLRMISGLLTPDKGHLSVNGEQWFDASFGKNVSPGR 79 Query: 81 RDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVREVAELLGLTELLNRKPREL 140 R + +FQ Y+L+P+MTV +NIAF LK K + E+ E +GL L + P+ L Sbjct: 80 RKLGYLFQDYSLFPNMTVKENIAFALKNAKDKAY-----LMELLESMGLLHLQDTLPKHL 134 Query: 141 SGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKKLQRQLGVTTIYVTHDQ 200 SGGQ+QRVAL RA+ KP + L+DEPLS LD +R +++ + + R+ +TTI V+HD Sbjct: 135 SGGQQQRVALARALALKPDILLLDEPLSALDPSMREKLQEYILAIHRKYALTTILVSHDA 194 Query: 201 VEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIGSPPMNFLDAIVTEDGFVDF 260 E + + DRI ++ G + + +P E + + F G M+ L+ V V Sbjct: 195 GEIIKLSDRIIELDHGKVLRQCTPKEFFGTGLTSAKFQFQGE-IMDILEDDVVHIVHVKT 253 Query: 261 GEFRLKLLPDQFEVLGELGYVGREVIFG 288 G +K++ D E ELG VG +V+ G Sbjct: 254 GNDLVKVVCDMDET-KELG-VGDKVLVG 279 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: 261 Number of extensions: 7 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: 372 Length of database: 290 Length adjustment: 28 Effective length of query: 344 Effective length of database: 262 Effective search space: 90128 Effective search space used: 90128 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