Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate Ac3H11_3200 Amino acid ABC transporter permease protein
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3200 Length = 604 Score = 184 bits (468), Expect = 4e-51 Identities = 112/250 (44%), Positives = 143/250 (57%), Gaps = 14/250 (5%) Query: 2 IEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGR 61 + H V K Y + L+ L + G + ++G SG+GKSTLLR IN LE GG Sbjct: 356 VTIHGVSKRYGA----LEVLKDVTLTVLPGSVTVILGPSGSGKSTLLRSINHLERVDGGF 411 Query: 62 ILVEGE------DVTALDAEG---LRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGG 112 I ++GE D AL G + + R VGM+FQ+FNL TV +NI Sbjct: 412 IAIDGELIGYRQDADALYELGENDILKRRVDVGMVFQNFNLFPHLTVLENIVEAPVTVRK 471 Query: 113 FSRAEVDARVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSAL 172 +RAE +A ELLARVGLSD A YP QLSGGQ+QRV IARALA +P +LL DE TSAL Sbjct: 472 LARAEAEALALELLARVGLSDKAHSYPRQLSGGQQQRVAIARALALKPKVLLFDEPTSAL 531 Query: 173 DPQTTASVLQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLH 232 DP+ VL ++ E+ R T+V++THE+ R V D V M+ G +VE G A VF Sbjct: 532 DPELVGEVLDVIKELAR-TGTTLVIVTHEIGFAREVADTVVFMEQGRVVETGTPAKVFSQ 590 Query: 233 PQHPTTRRFV 242 P HP T F+ Sbjct: 591 PDHPRTAAFL 600 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: 430 Number of extensions: 24 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: 604 Length adjustment: 33 Effective length of query: 302 Effective length of database: 571 Effective search space: 172442 Effective search space used: 172442 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: 51 (24.3 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