Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate PfGW456L13_876 Glutamate transport ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_876 Length = 245 Score = 172 bits (436), Expect = 8e-48 Identities = 96/223 (43%), Positives = 138/223 (61%), Gaps = 2/223 (0%) Query: 26 LNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGEDVTALDAEGLRRFRQRVG 85 L+I+ GQ+ +IG SG+GKSTLLR +N LE + G I V+GE + A A+ LR RQ+VG Sbjct: 24 LSIEEGQVVAIIGRSGSGKSTLLRTLNGLESINDGVIEVDGEYLDAARAD-LRSLRQKVG 82 Query: 86 MIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDARVSELLARVGLSDHARKYPAQLSGG 145 M+FQ FNL TV +N+ + ++ +A+ ++L RVGL + +P +LSGG Sbjct: 83 MVFQQFNLFPHLTVGENVMLAPQVVQKVPKAKAAELARQMLERVGLGEKFDAFPDRLSGG 142 Query: 146 QKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEINRELKLTIVLITHEMDVI 205 Q+QRV IARALA P +LLCDE TSALDP+ VL ++ ++ RE +T++++THEM Sbjct: 143 QQQRVAIARALAMSPKVLLCDEITSALDPELVNEVLSVVRQLARE-GMTLIMVTHEMRFA 201 Query: 206 RRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRFVFEAERV 248 R V D++ M G + E GD +F +PQ F+ E V Sbjct: 202 REVGDKLVFMHQGKVHEVGDPKVLFANPQTAELANFIGTVEAV 244 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: 206 Number of extensions: 6 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: 245 Length adjustment: 26 Effective length of query: 309 Effective length of database: 219 Effective search space: 67671 Effective search space used: 67671 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 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