Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate H281DRAFT_02450 H281DRAFT_02450 glycine betaine/proline transport system ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__Burk376:H281DRAFT_02450 Length = 393 Score = 179 bits (453), Expect = 1e-49 Identities = 94/226 (41%), Positives = 145/226 (64%), Gaps = 2/226 (0%) Query: 17 EIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGEDVTALDAEG 76 +I + ++ G+IF L+G SG+GKSTL+RLINRL EPS G++L++G DV ++ Sbjct: 41 QIVGVHNVSFEVKEGEIFVLMGLSGSGKSTLIRLINRLVEPSAGKVLIDGRDVASVPRAE 100 Query: 77 LRRFRQR-VGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDARVSELLARVGLSDHA 135 L R++ + M+FQ F L+ +TV N A L +AG SR E +AR +L +VGL+ A Sbjct: 101 LTALRRKDMSMVFQSFALMPQRTVLSNAAFGLEVAG-VSRKEREARAMTVLEQVGLAPFA 159 Query: 136 RKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEINRELKLTI 195 K PAQLSGG +QRVG+ARALA PS+++ DEA SALDP + +L ++ RE + TI Sbjct: 160 AKLPAQLSGGMQQRVGLARALAVNPSLMIMDEAFSALDPLKRKEMQNVLLDLQREQQRTI 219 Query: 196 VLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRF 241 + ++H+++ R+ ++A+M+GG +V+ G ++ +P R F Sbjct: 220 LFVSHDLEEAMRIGTRIAIMEGGKVVQIGTPQEIITNPADDYVRAF 265 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: 316 Number of extensions: 14 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: 393 Length adjustment: 29 Effective length of query: 306 Effective length of database: 364 Effective search space: 111384 Effective search space used: 111384 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