Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate AO353_28150 AO353_28150 arginine aminotransferase
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28150 Length = 667 Score = 183 bits (464), Expect = 1e-50 Identities = 111/252 (44%), Positives = 146/252 (57%), Gaps = 15/252 (5%) Query: 1 MIEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGG 60 MIE +HK + I L+ L + G + LIG SG+GKSTLLR IN LE P G Sbjct: 415 MIEVDGLHKRFG----NIEVLKGVSLTAREGDVISLIGASGSGKSTLLRCINMLEVPDQG 470 Query: 61 RILVEGEDVT----------ALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLA 110 RILV+GE + DA+ L R R +GM+FQ+FNL +TV +N+ Sbjct: 471 RILVDGESIQLNFDRPGAPLVSDAKQLVRIRSSLGMVFQNFNLWPHRTVLENLIEAPTQV 530 Query: 111 GGFSRAEVDARVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATS 170 SRAE R LL RVGL+ +YPA LSGGQ+QRV IARALA RP ++L DE TS Sbjct: 531 LRESRAEATERAEALLERVGLAAKRNEYPAFLSGGQQQRVAIARALAMRPKVMLFDEPTS 590 Query: 171 ALDPQTTASVLQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVF 230 ALDP+ VL+++ + E + T++L+THEM R V +VA + G I E G +VF Sbjct: 591 ALDPELVGEVLRVIRSLAEEGR-TMILVTHEMAFARDVSSKVAYLHQGLIEEAGSPDEVF 649 Query: 231 LHPQHPTTRRFV 242 +HP+ R+FV Sbjct: 650 VHPRSERCRQFV 661 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: 501 Number of extensions: 22 Number of successful extensions: 4 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: 667 Length adjustment: 33 Effective length of query: 302 Effective length of database: 634 Effective search space: 191468 Effective search space used: 191468 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