Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate GFF3356 HP15_3298 glycine betaine/L-proline ABC transporter, ATPase subunit
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__Marino:GFF3356 Length = 352 Score = 178 bits (451), Expect = 2e-49 Identities = 97/233 (41%), Positives = 146/233 (62%), Gaps = 2/233 (0%) Query: 16 REIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGEDVTALDAE 75 R + L+ ++I G+I ++G SG+GKSTL+R +NRL +P+ G I V+GED+ + E Sbjct: 41 RHVLGLRDINVDIHDGEITVIMGLSGSGKSTLIRHLNRLIDPTAGEIRVDGEDIMSYSEE 100 Query: 76 GLRRFR-QRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDARVSELLARVGLSDH 134 LR+ R +R+ M+FQ F LL KTV +N M + G ++ ++ +A + LARVGL + Sbjct: 101 QLRKLRRERMSMVFQKFALLPHKTVLENAGMAKDIRG-YTTSDFEADARKWLARVGLEGN 159 Query: 135 ARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEINRELKLT 194 +YP QLSGG +QRVGIARAL I+L DEA SALDP + + LL E+ EL+ T Sbjct: 160 EYQYPHQLSGGMQQRVGIARALVSDAPIMLMDEAFSALDPLIRSDMQDLLLELQEELQKT 219 Query: 195 IVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRFVFEAER 247 IV ITH++D ++ D + ++ G +V+QGD ++ L+P P F+ + R Sbjct: 220 IVFITHDLDEALKLADHLVILKDGEVVQQGDPQEILLNPGDPYIVDFISDINR 272 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: 275 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: 352 Length adjustment: 29 Effective length of query: 306 Effective length of database: 323 Effective search space: 98838 Effective search space used: 98838 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