Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate BPHYT_RS22535 BPHYT_RS22535 methionine ABC transporter ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__BFirm:BPHYT_RS22535 Length = 386 Score = 267 bits (682), Expect = 4e-76 Identities = 168/351 (47%), Positives = 211/351 (60%), Gaps = 21/351 (5%) Query: 4 FHDVHKTYRVA-GREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRI 62 F +V K + A G AL LN+ G++FG+IG SGAGKSTLLRL+N LE+PS G + Sbjct: 34 FDNVGKVFADARGVSTAALANVTLNVARGEVFGIIGRSGAGKSTLLRLVNGLEKPSSGAV 93 Query: 63 LVEGEDVTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDARV 122 V G V LD GL R+R+GM+FQHFNLLS+KTV +NIA+PL++AG +A +D +V Sbjct: 94 RVNGVSVGELDERGLVALRRRIGMVFQHFNLLSAKTVRENIALPLKIAG-VPKAAIDKKV 152 Query: 123 SELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQ 182 LL VGLS YPA LSGGQKQRVGIARAL P ILLCDEATSALDP+TT ++L Sbjct: 153 DALLELVGLSAKRDAYPASLSGGQKQRVGIARALVTDPDILLCDEATSALDPETTQAILA 212 Query: 183 LLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTR--- 239 LL +IN+ L LTIVLITHEM VIR VCD VAV++ G +VE G V VF PQH TR Sbjct: 213 LLRDINQRLNLTIVLITHEMQVIREVCDTVAVIERGEVVETGAVWRVFGDPQHDATRALL 272 Query: 240 RFVFEAERVDEDER----HDDFAHVPGLILRLTFRGEATYAPLLGTVARQTGVD---YSI 292 R + +D +R +D ++L + F G P LG +A VD S Sbjct: 273 RTLVHDLPIDLAKRIKPLNDIGQADAQILLDVRFTGVDAREPDLGGLASALSVDGGHVSF 332 Query: 293 LSGRIDRIKDTPYGQLTL---------ALVGGDLEAAMSQLNAADVHVEVL 334 + G IDRI+ G+L + + V + A + HVEVL Sbjct: 333 VHGGIDRIQGHAQGRLVVSAQVRADDGSTVQKQIAALLDSARRYANHVEVL 383 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: 350 Number of extensions: 16 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: 386 Length adjustment: 29 Effective length of query: 306 Effective length of database: 357 Effective search space: 109242 Effective search space used: 109242 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