Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate WP_072910078.1 BUB13_RS17610 amino acid ABC transporter ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >NCBI__GCF_900142125.1:WP_072910078.1 Length = 244 Score = 181 bits (460), Expect = 1e-50 Identities = 99/242 (40%), Positives = 148/242 (61%), Gaps = 2/242 (0%) Query: 1 MIEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGG 60 MI+ D+ K + G E+ A+ +I++G++ +IG SG+GKST LR +N LE + G Sbjct: 1 MIKTVDLKKIFTGRGTEVRAVDGVTTHIKSGEVVVVIGPSGSGKSTYLRCLNGLETLTDG 60 Query: 61 RILVEGEDVTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDA 120 I+++G D+ + L + R+ VGM+FQ FNL KTV DNI + ++ +R E + Sbjct: 61 HIMIDGIDLADKKTD-LNKVRREVGMVFQQFNLFPHKTVLDNIILAQQVVRKRNRKEAED 119 Query: 121 RVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASV 180 + +LL +VG++D YP LSGGQ+QRV IARALA P I+L DE TSALDP+ V Sbjct: 120 KARQLLKKVGIADKESVYPGHLSGGQQQRVAIARALAMDPKIMLFDEPTSALDPEMVGEV 179 Query: 181 LQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRR 240 L ++ ++ RE +T+V++THEM R V D+V MD G +VE+G F P+ + Sbjct: 180 LDVMKQLARE-GMTMVVVTHEMGFAREVADRVIFMDHGKLVEEGTPEHFFTEPREERAKD 238 Query: 241 FV 242 F+ Sbjct: 239 FL 240 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: 205 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: 335 Length of database: 244 Length adjustment: 26 Effective length of query: 309 Effective length of database: 218 Effective search space: 67362 Effective search space used: 67362 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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