Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate GFF3910 PGA1_65p00130 putative amino-acid ABC transporter, ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__Phaeo:GFF3910 Length = 251 Score = 175 bits (443), Expect = 1e-48 Identities = 98/219 (44%), Positives = 133/219 (60%), Gaps = 3/219 (1%) Query: 26 LNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGEDVTALDAEG--LRRFRQR 83 L IQ G+ +IG SG GKSTLLR +N L+ P G + + DV A A + R+R Sbjct: 30 LTIQPGERIVIIGPSGTGKSTLLRCLNFLDAPDAGLVRIGDLDVDAARASKAEILALRRR 89 Query: 84 VGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDARVSELLARVGLSDHARKYPAQLS 143 +FQ++ L ++KT A+NI L RAE +AR E+LA GL+D A YPA LS Sbjct: 90 TAFVFQNYALFANKTAAENIMEALITVQKQPRAEAEARAREILAETGLADKADAYPASLS 149 Query: 144 GGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEINRELKLTIVLITHEMD 203 GGQ+QRVGI RA+A ++L DE TSALDP+ VL L+ ++ E + T++++THEM Sbjct: 150 GGQQQRVGIGRAMALGAELMLFDEPTSALDPEWVGEVLALMHKVAEE-RQTMLIVTHEMQ 208 Query: 204 VIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRFV 242 R + D+V M+GG IVEQG +F PQ P TR F+ Sbjct: 209 FAREIADRVVFMEGGRIVEQGPPTQIFDAPQDPRTRAFL 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: 215 Number of extensions: 10 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: 251 Length adjustment: 26 Effective length of query: 309 Effective length of database: 225 Effective search space: 69525 Effective search space used: 69525 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