Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__Dyella79:N515DRAFT_1562 Length = 384 Score = 176 bits (445), Expect = 1e-48 Identities = 100/232 (43%), Positives = 142/232 (61%), Gaps = 8/232 (3%) Query: 20 ALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGEDVTALDAEGLRR 79 AL L+I G+ L+G SG+GKS+LLR++ L++P G +L +G D+ AL A+ Sbjct: 17 ALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDVLRDGTDLLALPAQ---- 72 Query: 80 FRQRVGMIFQHFNLLSSKTVADNIAMPLRL---AGGFSRAEVDARVSELLARVGLSDHAR 136 R+ +G++FQH+ L TVADNIA LR+ A SR ++ ARV +LL RV L + R Sbjct: 73 -RRDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAARVEDLLRRVQLEELGR 131 Query: 137 KYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEINRELKLTIV 196 +YP QLSGGQ+QRV +ARALA PS+LL DE ALD Q ++ L ++ R L LT V Sbjct: 132 RYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRVWLRDLQRSLGLTTV 191 Query: 197 LITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRFVFEAERV 248 L+TH+ D + D+V VM+ G I + G ++++ P P FV A R+ Sbjct: 192 LVTHDQDEALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHGFVGRANRI 243 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: 361 Number of extensions: 22 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: 384 Length adjustment: 29 Effective length of query: 306 Effective length of database: 355 Effective search space: 108630 Effective search space used: 108630 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