Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate BWI76_RS15030 BWI76_RS15030 ABC transporter
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__Koxy:BWI76_RS15030 Length = 263 Score = 268 bits (685), Expect = 1e-76 Identities = 136/233 (58%), Positives = 175/233 (75%), Gaps = 3/233 (1%) Query: 1 MIEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGG 60 MIE + KTY GR PAL L + G ++G++G SGAGKSTL+R +N LE P+ G Sbjct: 1 MIEIAGLSKTYAGTGR--PALNDVSLQVPKGAVYGILGRSGAGKSTLIRCLNLLERPTSG 58 Query: 61 RILVEGEDVTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDA 120 RI+V G D+T +D LR +R R GMIFQHFNLL +++VADNIA+PL +A +A A Sbjct: 59 RIIVNGNDITRMDKTALREYRLRTGMIFQHFNLLHARSVADNIAVPLEIAK-VPKAARQA 117 Query: 121 RVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASV 180 RV+ELL VGL+D A +P+QLSGGQKQRVGIARALA RP +LLCDEATSALDP+TTASV Sbjct: 118 RVAELLELVGLADKAAAFPSQLSGGQKQRVGIARALAARPDVLLCDEATSALDPETTASV 177 Query: 181 LQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHP 233 L LLA+IN++L LTIVLITHE+DV++ +CD A+++ G I+E G +AD+ + P Sbjct: 178 LSLLADINQQLNLTIVLITHELDVVKTLCDHAALLEHGEIIESGRIADLLVAP 230 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: 271 Number of extensions: 10 Number of successful extensions: 2 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: 263 Length adjustment: 26 Effective length of query: 309 Effective length of database: 237 Effective search space: 73233 Effective search space used: 73233 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: 48 (23.1 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