Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate Pf1N1B4_1702 Methionine ABC transporter ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1702 Length = 373 Score = 281 bits (719), Expect = 2e-80 Identities = 161/340 (47%), Positives = 213/340 (62%), Gaps = 8/340 (2%) Query: 2 IEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGR 61 + F + KTY + AL L IQ G++FG+IG SGAGKS+L+R INRLE+PS GR Sbjct: 31 VRFIGLGKTYNGQQGPVAALHGIDLAIQRGEVFGIIGRSGAGKSSLIRTINRLEQPSSGR 90 Query: 62 ILVEGEDVTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDAR 121 +L++ D+ D + L R+R+GMIFQHFNL+S+KTV N+ +PL++AG + + + + Sbjct: 91 VLIDQVDIGEFDEDRLVALRRRIGMIFQHFNLMSAKTVWQNVELPLKVAG-VPKEQRERK 149 Query: 122 VSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVL 181 V ELL VGL + YPAQLSGGQKQRVGIARAL P ILLCDEATSALDP+TT S+L Sbjct: 150 VRELLELVGLQGKHKSYPAQLSGGQKQRVGIARALVHDPEILLCDEATSALDPETTQSIL 209 Query: 182 QLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRF 241 LL EIN+ L LTIVLITHEM VIR +CD+V V++ G IVEQG V +VF +PQH ++ Sbjct: 210 GLLREINQRLGLTIVLITHEMAVIRDICDRVVVLEHGQIVEQGPVWEVFGNPQHEVSKTL 269 Query: 242 VFEAERVDEDERHDDFAHVP-----GLILRLTFRGEATYAPLLGTVARQTGVDYSILSGR 296 + + +E P ++LRL F G + P L + G +L G Sbjct: 270 LAPLQHALPEELQSRLRPQPQSSDAAVVLRLQFTGSTSEEPDLAALFSALGGRVRLLQGG 329 Query: 297 IDRIKDTPYGQLTLALVGGDLEAAMSQLNAAD--VHVEVL 334 ++RI+ GQL LA+ G L A + A + VEVL Sbjct: 330 VERIQGHALGQLLLAVTGSSLSAEELRQRAGNWAQQVEVL 369 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: 349 Number of extensions: 15 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: 373 Length adjustment: 29 Effective length of query: 306 Effective length of database: 344 Effective search space: 105264 Effective search space used: 105264 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