Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate 200449 SO1271 polyamine ABC transporter, ATP-binding protein (NCBI ptt file)
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__MR1:200449 Length = 378 Score = 150 bits (380), Expect = 4e-41 Identities = 83/244 (34%), Positives = 134/244 (54%), Gaps = 6/244 (2%) Query: 17 EIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGEDVTALDAEG 76 ++ A+ L I G+IF L+G SG+GKSTLLR++ E P+ GRI ++GED+T L Sbjct: 32 DVRAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTSGRIYLDGEDITDLPP-- 89 Query: 77 LRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDARVSELLARVGLSDHAR 136 + + + M+FQ + L TVA NIA L+ +AE++ RV E+L V + + + Sbjct: 90 ---YERPINMMFQSYALFPHMTVAQNIAFGLK-QDKLPKAEIEQRVQEMLKLVHMEQYGK 145 Query: 137 KYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEINRELKLTIV 196 + P QLSGGQ+QRV +AR+LA RP +LL DE ALD + + + EI + +T V Sbjct: 146 RKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVEILERVGVTCV 205 Query: 197 LITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRFVFEAERVDEDERHDD 256 ++TH+ + + ++++M G I + G D++ P F+ + D+ Sbjct: 206 MVTHDQEEAMTMAGRISIMSDGWIAQTGSPMDIYESPNSRMIAEFIGSVNLFSGEIEVDE 265 Query: 257 FAHV 260 H+ Sbjct: 266 VDHL 269 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: 293 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: 378 Length adjustment: 29 Effective length of query: 306 Effective length of database: 349 Effective search space: 106794 Effective search space used: 106794 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