Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate Synpcc7942_1680 Synpcc7942_1680 Sulphate transport system permease protein 1
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__SynE:Synpcc7942_1680 Length = 338 Score = 157 bits (397), Expect = 4e-43 Identities = 89/223 (39%), Positives = 133/223 (59%), Gaps = 6/223 (2%) Query: 20 ALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGEDVTALDAEGLRR 79 A++ L ++ G + L+G SG+GKSTLLRLI LE+P GRI + G D T E +R Sbjct: 17 AVKDVDLTVETGSLVALLGPSGSGKSTLLRLIAGLEQPDSGRIFLTGRDATN---ESVRD 73 Query: 80 FRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDARVSELLARVGLSDHARKYP 139 +++G +FQH+ L TV NIA L L ++ +V ARV ELL V L+ +YP Sbjct: 74 --RQIGFVFQHYALFKHLTVRKNIAFGLELRK-HTKEKVRARVEELLELVQLTGLGDRYP 130 Query: 140 AQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEINRELKLTIVLIT 199 +QLSGGQ+QRV +ARALA +P +LL DE ALD + + L +++ E+ +T V +T Sbjct: 131 SQLSGGQRQRVALARALAVQPQVLLLDEPFGALDAKVRKDLRSWLRKLHDEVHVTTVFVT 190 Query: 200 HEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRFV 242 H+ + V DQ+ VM+ G + + G A+++ +P P F+ Sbjct: 191 HDQEEAMEVADQIVVMNHGKVEQIGSPAEIYDNPATPFVMSFI 233 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: 274 Number of extensions: 17 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: 338 Length adjustment: 28 Effective length of query: 307 Effective length of database: 310 Effective search space: 95170 Effective search space used: 95170 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