Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate BPHYT_RS14820 BPHYT_RS14820 methionine ABC transporter ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__BFirm:BPHYT_RS14820 Length = 344 Score = 300 bits (768), Expect = 4e-86 Identities = 171/351 (48%), Positives = 223/351 (63%), Gaps = 28/351 (7%) Query: 1 MIEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGG 60 MIE ++ + + + AL L+I AG++FG+IG SGAGKSTL+R +N L PS G Sbjct: 1 MIEIRNISQRFAGPRGWVEALHNVNLSIPAGEVFGIIGRSGAGKSTLVRTLNLLTRPSEG 60 Query: 61 RILVEGEDVTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDA 120 I+V G D+T L A LR R+ +GMIFQHFNLLSS+TV +N+A+PL LAG R E++A Sbjct: 61 NIVVNGRDLTTLPAAQLREARREIGMIFQHFNLLSSRTVYENVALPLELAG-MKRDEIEA 119 Query: 121 RVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASV 180 V LL VGLS +YPAQ+SGGQKQRVGIARALA +P +LL DEATSALDP+TT ++ Sbjct: 120 NVLPLLELVGLSAQKDRYPAQISGGQKQRVGIARALASKPKVLLSDEATSALDPETTRAI 179 Query: 181 LQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRR 240 L LL INREL LTIVLITH+MDVI++VCD+VAV+D G +VE+G V DVFL P H TR Sbjct: 180 LDLLKRINRELNLTIVLITHQMDVIKQVCDRVAVLDAGRVVEEGKVIDVFLQPHHEVTRA 239 Query: 241 FVFE--------------AERVDEDERHDDFAHVPGLILRLTFRGEATYAPLLGTVARQT 286 + + AER+ H +LRL F G P+L R+ Sbjct: 240 LIGDVIAQELPPAMKARVAERLKTGSGH---------LLRLAFTGSGVDQPILSETIRRY 290 Query: 287 GVDYSILSGRIDRIKDTPYGQLTLALVGGD---LEAAMSQLNAADVHVEVL 334 +D++IL G+ID I+ +G L + L GG+ + A++ L V VE L Sbjct: 291 ELDFNILHGQIDEIQGQAFGSLAV-LAGGEPAKVAQALTYLREQGVVVEEL 340 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: 312 Number of extensions: 12 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: 344 Length adjustment: 28 Effective length of query: 307 Effective length of database: 316 Effective search space: 97012 Effective search space used: 97012 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