Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate Dsui_0414 Dsui_0414 oligopeptide/dipeptide ABC transporter, ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__PS:Dsui_0414 Length = 352 Score = 155 bits (393), Expect = 1e-42 Identities = 95/240 (39%), Positives = 139/240 (57%), Gaps = 7/240 (2%) Query: 18 IPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGEDVTALDAEGL 77 + A+ ++ G+ G++G SG GKST RL+ RL G ++ +GE V L Sbjct: 45 VHAVDGVNFSVPKGKTLGIVGESGCGKSTTARLVARLMPADAGELIFDGEGVEEFRGLRL 104 Query: 78 RRFRQRVGMIFQH-FNLLSSK-TVADNIAMPLRLAGGFSRAEVDARVSELLARVGL--SD 133 + FR+ + M+FQ F L+ + T+A+ IA R+ G +RA+ AR ELL RVGL S Sbjct: 105 KEFRRNLQMVFQDSFASLNPRLTIAETIAYGPRVHG-IARADHQAR--ELLDRVGLDPSH 161 Query: 134 HARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEINRELKL 193 A +YP +LSGGQ+QRV IARALA P +++ DEA +ALD A VL LL E+ E +L Sbjct: 162 FAGRYPHELSGGQRQRVNIARALAFDPRLVILDEAVAALDKSVQAQVLNLLQELKAERQL 221 Query: 194 TIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRFVFEAERVDEDER 253 T + I+H++ V+ + D V VM G ++E G V ++ P HP TR + +D + R Sbjct: 222 TYLFISHDLHVVHYLSDYVMVMYLGQVIESGPVERIYGQPAHPYTRALLSAVPSMDPEHR 281 Lambda K H 0.322 0.138 0.393 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: 319 Number of extensions: 17 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: 335 Length of database: 352 Length adjustment: 29 Effective length of query: 306 Effective length of database: 323 Effective search space: 98838 Effective search space used: 98838 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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