Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate RR42_RS16445 RR42_RS16445 hypothetical protein
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__Cup4G11:RR42_RS16445 Length = 252 Score = 177 bits (450), Expect = 2e-49 Identities = 106/252 (42%), Positives = 145/252 (57%), Gaps = 15/252 (5%) Query: 1 MIEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGG 60 MI+ D++K + + AL L +Q G++ LIG SG+GKSTLLR IN LE P+ G Sbjct: 1 MIDVRDLYKHFDA----VKALNGVNLEVQRGEVVCLIGPSGSGKSTLLRSINYLERPTRG 56 Query: 61 RILVEGEDVTALDAEG----------LRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLA 110 I ++G+ V ++ G L R R VGM+FQ F L +V +N+ + + Sbjct: 57 DISIDGQTVGHVNQAGKKARPMSGRELARVRSEVGMVFQMFYLWPHLSVLENVTLGMVEV 116 Query: 111 GGFSRAEVDARVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATS 170 G A+ R +LLA+VGLS YP QLSGGQ+QRV IARALA P I+L DE TS Sbjct: 117 RGVRLADAAQRGRQLLAKVGLSGKYDAYPEQLSGGQRQRVAIARALAMDPKIILFDEPTS 176 Query: 171 ALDPQTTASVLQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVF 230 ALDP+ VLQ + + E +T+++ THEM RRV D+V MD G +VE G D+F Sbjct: 177 ALDPERVGEVLQTMETVAAE-GMTMIVATHEMGFARRVADRVVFMDEGRVVEAGSPGDIF 235 Query: 231 LHPQHPTTRRFV 242 PQ ++F+ Sbjct: 236 DRPQSARLKQFL 247 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: 236 Number of extensions: 9 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: 252 Length adjustment: 26 Effective length of query: 309 Effective length of database: 226 Effective search space: 69834 Effective search space used: 69834 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