Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate Ac3H11_631 Methionine ABC transporter ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_631 Length = 351 Score = 297 bits (761), Expect = 2e-85 Identities = 165/348 (47%), Positives = 227/348 (65%), Gaps = 19/348 (5%) Query: 1 MIEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGG 60 MI+ + +TY+ + AL+ L IQ G++FG+IG SGAGKS+L+R+IN L P+ G Sbjct: 1 MIDLRGITQTYQGPQGPVEALRGIDLTIQPGEVFGIIGKSGAGKSSLVRVINLLNRPTTG 60 Query: 61 RILVEGEDVTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDA 120 +++V G D+T L+ LR R+ +GM+FQHFNLLSS+TV DN A+PL LAG S+ ++ Sbjct: 61 QVIVGGRDLTQLNDAQLREARREIGMVFQHFNLLSSRTVFDNAALPLELAG-MSKTDIRE 119 Query: 121 RVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASV 180 RV+ LL VGL A +YPAQ+SGGQKQRVGIARALA RP +LL DEATSALDP+TT S+ Sbjct: 120 RVNPLLELVGLDHLADRYPAQISGGQKQRVGIARALASRPKVLLSDEATSALDPETTRSI 179 Query: 181 LQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRR 240 L LL ++NREL LT+VLITH+M VI++V D VAV++ G IVEQG V DVF PQ T+ Sbjct: 180 LDLLRQVNRELGLTVVLITHQMQVIKQVADHVAVIEAGRIVEQGRVLDVFTRPQQAITKS 239 Query: 241 FVFEAERVDEDERHDDFAHV--------------PGLILRLTFRGEATYAPLLGTVARQT 286 + E + ++ HV G +LRL++ G++ Y P+L + R+ Sbjct: 240 LIDEI--LPQELPVSVLDHVRKLTRQLATTAPDHAGRLLRLSYSGDSAYQPILSQLIREF 297 Query: 287 GVDYSILSGRIDRIKDTPYGQLTLALVGGDLE--AAMSQLNAADVHVE 332 GVD SIL G++D I+D +G L + G ++ A+ L A V V+ Sbjct: 298 GVDMSILHGQVDEIQDETFGSLAVYASGEPMQVRGAVEHLRAGGVAVQ 345 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: 336 Number of extensions: 17 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: 351 Length adjustment: 29 Effective length of query: 306 Effective length of database: 322 Effective search space: 98532 Effective search space used: 98532 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