Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate SMc03159 SMc03159 ABC transporter ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__Smeli:SMc03159 Length = 358 Score = 282 bits (722), Expect = 8e-81 Identities = 160/326 (49%), Positives = 209/326 (64%), Gaps = 9/326 (2%) Query: 2 IEFHDVHKTYRVAGRE--IPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSG 59 + F V K + +G AL L + G I G+IG SGAGKSTL+RL+N LE+PS Sbjct: 14 VVFDAVSKRFPASGGNTAFTALDNVSLAVARGSITGIIGRSGAGKSTLIRLVNGLEKPSS 73 Query: 60 GRILVEGEDVTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVD 119 G++ V+G DV ALD GLR R+ VGMIFQHFNLLSS+TV N+A+PL +AG R ++ Sbjct: 74 GKVFVDGVDVGALDEAGLRDLRRSVGMIFQHFNLLSSRTVFGNVALPLEIAG-MDRRAIE 132 Query: 120 ARVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTAS 179 RV LL VGL+D +YPA+LSGGQKQR+GIARALA P +LL DEATSALDP+TT S Sbjct: 133 QRVRPLLELVGLADKHGRYPAELSGGQKQRIGIARALATEPKLLLSDEATSALDPETTQS 192 Query: 180 VLQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTR 239 +L+LL IN EL LT++LITHEM+V++ V VAV+D G IVE+G DVF H +H TTR Sbjct: 193 ILELLRRINAELGLTVLLITHEMEVVKAVTSDVAVIDKGEIVERGHTFDVFTHSRHETTR 252 Query: 240 RFV--FEAERVDEDERH---DDFAHVPGLILRLTFRGEATYAPLLGTVARQTGVDYSILS 294 + ++ E A +++RLTF G A PL+ + + G + +I++ Sbjct: 253 ALLSGLAGSKLPEAVARGLKPAAASGDRVVVRLTFFGAAAERPLISQLIQSVGAEVNIIA 312 Query: 295 GRIDRIKDTPYGQLTLALVGGDLEAA 320 G ID I PYG L +A G D E + Sbjct: 313 GTIDEIGGKPYGSLVVA-YGADAETS 337 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: 16 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: 335 Length of database: 358 Length adjustment: 29 Effective length of query: 306 Effective length of database: 329 Effective search space: 100674 Effective search space used: 100674 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