Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate N515DRAFT_1085 N515DRAFT_1085 D-methionine transport system ATP-binding protein
Query= SwissProt::Q9YGA6 (372 letters) >FitnessBrowser__Dyella79:N515DRAFT_1085 Length = 336 Score = 134 bits (338), Expect = 3e-36 Identities = 83/243 (34%), Positives = 136/243 (55%), Gaps = 8/243 (3%) Query: 4 VRLVDVWKVFG----EVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQ 59 +R VDV K + ++ A++ SL++ DGE ++G SG GK+T +R+I LE PS G Sbjct: 2 IRFVDVHKSYRVDGKDIPALQPFSLDIADGEVFGIIGHSGAGKSTLIRLINLLERPSGGS 61 Query: 60 IYI-GDKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLR-KVPRQEID 117 I I G ++ A + + + R I M+FQ + L TV DNIAFPL+L + +I Sbjct: 62 ILIDGTEMTALGDAALRA--QRRRIGMIFQHFNLLSSQTVADNIAFPLRLAGETDAGKIK 119 Query: 118 QRVREVAELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVR 177 RV E+ +GL ++ P +LSGGQ+QRV + RA+ +P + L DE S LD + Sbjct: 120 ARVDELLRRVGLEAHASKYPAQLSGGQKQRVGIARALANRPSILLCDEATSALDPQTTAS 179 Query: 178 MRAELKKLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVA 237 + L ++ R+L +T + +TH+ + DR+AV++ G + + G+ +V+ P + Sbjct: 180 VLELLAEINRELKLTIVLITHEMDVVRRVCDRVAVLDAGRIVEHGAVADVFLHPRHPTTR 239 Query: 238 GFI 240 F+ Sbjct: 240 RFV 242 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: 260 Number of extensions: 12 Number of successful extensions: 3 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: 336 Length adjustment: 29 Effective length of query: 343 Effective length of database: 307 Effective search space: 105301 Effective search space used: 105301 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