Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate HSERO_RS07850 HSERO_RS07850 methionine ABC transporter ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__HerbieS:HSERO_RS07850 Length = 336 Score = 346 bits (888), Expect = e-100 Identities = 185/341 (54%), Positives = 235/341 (68%), Gaps = 13/341 (3%) Query: 1 MIEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGG 60 +I +HKTYR R+I AL+ L+I G++FG+IG SGAGKSTL+R +N LE P G Sbjct: 1 VIRIEQLHKTYRAGQRDIIALRDINLDIAQGEVFGIIGRSGAGKSTLIRTLNVLERPDSG 60 Query: 61 RILVEGEDVTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDA 120 R+L++GED+T L E L RQRVGM+FQHFNLL++KTVA NI PL++ G +SR E A Sbjct: 61 RVLIDGEDITGLGHEALLGLRQRVGMVFQHFNLLNAKTVAQNIDWPLKITGRYSREERAA 120 Query: 121 RVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASV 180 RV ELL VGL H +YP+QLSGGQKQRVGIARALA P +LLCDEATSALDP+TT S+ Sbjct: 121 RVDELLQLVGLDAHRDQYPSQLSGGQKQRVGIARALANHPRLLLCDEATSALDPETTQSI 180 Query: 181 LQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRR 240 L+LL EINR+L LTIVLITHEM+VIR +CD+VAV+DGGA+ EQG V D+FL PQH TR Sbjct: 181 LRLLLEINRKLGLTIVLITHEMEVIRSICDRVAVLDGGAVAEQGRVVDIFLRPQHAVTRS 240 Query: 241 FVFEAERVDEDE----RHDDFAHVPGLILRLTFRGEATYAPLLGTVARQTGVDYSILSGR 296 + ++ D E R D G ++RLT+ G+ P+L + T +I+ G Sbjct: 241 LLTQSHAWDAGESLYQRRPD-----GKLVRLTYAGDIAAQPILSQLTAATSALATIVRGT 295 Query: 297 IDRIKDTPYGQLTLALVGGDLEA---AMSQLNAADVHVEVL 334 + RIKDTPYGQL L GD +A + +L +D+ EVL Sbjct: 296 VSRIKDTPYGQL-LVEFSGDADALAQVLDRLQTSDIEHEVL 335 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: 352 Number of extensions: 13 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: 336 Length adjustment: 28 Effective length of query: 307 Effective length of database: 308 Effective search space: 94556 Effective search space used: 94556 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