Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate WP_015943466.1 DHAF_RS07420 methionine ABC transporter ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >NCBI__GCF_000021925.1:WP_015943466.1 Length = 340 Score = 303 bits (775), Expect = 5e-87 Identities = 163/339 (48%), Positives = 221/339 (65%), Gaps = 5/339 (1%) Query: 1 MIEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGG 60 MI ++ K Y ++ A++ L+I G I+G+IG SGAGKSTL+R INRLEEP+GG Sbjct: 1 MIRIENLTKVYTSRKEQVTAIEDISLHIPKGAIYGIIGLSGAGKSTLVRCINRLEEPTGG 60 Query: 61 RILVEGEDVTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDA 120 +I+++G+++TA+ A LR+ RQ++GMIFQHF+LL S+TV DNIA PL +AG F + E+ Sbjct: 61 KIIIDGQNLTAMSAAELRQARQKIGMIFQHFHLLQSRTVFDNIAFPLEIAG-FKKPEIAE 119 Query: 121 RVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASV 180 RV ELL VGL D A YP+QLSGGQKQRVGIARALA P +LLCDEATSALDPQTT S+ Sbjct: 120 RVKELLPLVGLEDKAHVYPSQLSGGQKQRVGIARALATNPKVLLCDEATSALDPQTTLSI 179 Query: 181 LQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRR 240 L LL +IN+ LTI++ITHEM V++ +C VAV+ I EQG V VF+ PQ + Sbjct: 180 LNLLKDINQRFGLTIIMITHEMKVVKEICTDVAVIHESKIAEQGPVESVFIQPQSSVAKE 239 Query: 241 FVFEA--ERVDEDERHDDFAHVPGLILRLTFRGEATYAPLLGTVARQTGVDYSILSGRID 298 F+ + ED + H I+R+ F G P++ + ++ V +IL G ID Sbjct: 240 FISTVFPNELPEDLLRELATHPNSQIVRIQFLGSRASDPIIADLMKECEVRANILYGSID 299 Query: 299 RIKDTPYGQLTLALVG--GDLEAAMSQLNAADVHVEVLR 335 ++ T +G LTL L G G L A L ++ VEV++ Sbjct: 300 HLRSTLFGTLTLELQGDPGQLALAHQYLAQRELKVEVIQ 338 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: 285 Number of extensions: 12 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: 340 Length adjustment: 28 Effective length of query: 307 Effective length of database: 312 Effective search space: 95784 Effective search space used: 95784 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 24 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