Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate SM_b20427 SM_b20427 amino acid ABC transporter ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__Smeli:SM_b20427 Length = 261 Score = 188 bits (477), Expect = 1e-52 Identities = 100/234 (42%), Positives = 140/234 (59%), Gaps = 9/234 (3%) Query: 18 IPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGEDVTALDAEG- 76 + L + + G+ LIG SG+GK+T+LR++ LE S G I V+GE + + G Sbjct: 18 LTVLDGLSMEVMPGEKLALIGPSGSGKTTILRILMTLETISDGFIQVDGEQLYHMKKAGS 77 Query: 77 --------LRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDARVSELLAR 128 L + R+++GM+FQHFNL K V DN+ + L G +RA+ + R ELL Sbjct: 78 LVPADERHLHKMREKIGMVFQHFNLFPHKCVLDNVTLAPMLTKGMARAQAEKRAMELLDM 137 Query: 129 VGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEIN 188 VGL+D A+ PAQLSGGQKQRV IARALA P I+L DE TSALDP+ VL ++ ++ Sbjct: 138 VGLADKAKSMPAQLSGGQKQRVAIARALALSPKIMLFDEVTSALDPELVEEVLNVMRKLA 197 Query: 189 RELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRFV 242 E +T++L+THEM D+V D G IVE+G D+F HP+ T+ F+ Sbjct: 198 SETDMTMLLVTHEMGFAHDFADRVLFFDRGKIVEEGKPEDIFRHPKQERTQTFL 251 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: 233 Number of extensions: 12 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: 261 Length adjustment: 26 Effective length of query: 309 Effective length of database: 235 Effective search space: 72615 Effective search space used: 72615 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: 48 (23.1 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