Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate Pf6N2E2_4172 Methionine ABC transporter ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4172 Length = 289 Score = 479 bits (1232), Expect = e-140 Identities = 239/289 (82%), Positives = 269/289 (93%) Query: 47 LLRLINRLEEPSGGRILVEGEDVTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMP 106 LLRLINRLE+ +GG+I+V+GE+VTALDA GLRRFRQ+VGMIFQHFNLL+SKTVADN+A+P Sbjct: 1 LLRLINRLEDSTGGKIIVDGEEVTALDASGLRRFRQQVGMIFQHFNLLASKTVADNVALP 60 Query: 107 LRLAGGFSRAEVDARVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCD 166 L LAG SR+E+D RV+ELLARVGLSDHARKYPAQLSGGQKQRVGIARALA +P ILLCD Sbjct: 61 LTLAGELSRSEIDQRVAELLARVGLSDHARKYPAQLSGGQKQRVGIARALATKPKILLCD 120 Query: 167 EATSALDPQTTASVLQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDV 226 EATSALDPQTTASVLQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMD G IVEQG V Sbjct: 121 EATSALDPQTTASVLQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDAGVIVEQGPV 180 Query: 227 ADVFLHPQHPTTRRFVFEAERVDEDERHDDFAHVPGLILRLTFRGEATYAPLLGTVARQT 286 A+VFLHP+HPTT+RFV E E++DE E+ DDFAHVPG I+RLTF+G+ATYAPLLGTVAR+T Sbjct: 181 AEVFLHPKHPTTKRFVQEDEQIDESEQRDDFAHVPGRIVRLTFQGDATYAPLLGTVARET 240 Query: 287 GVDYSILSGRIDRIKDTPYGQLTLALVGGDLEAAMSQLNAADVHVEVLR 335 GVDYSIL+GRIDRIKDTPYGQLTLA+ GGD+EAA ++ AADVH+EVLR Sbjct: 241 GVDYSILAGRIDRIKDTPYGQLTLAITGGDMEAAFARFTAADVHMEVLR 289 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: 404 Number of extensions: 9 Number of successful extensions: 1 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: 289 Length adjustment: 27 Effective length of query: 308 Effective length of database: 262 Effective search space: 80696 Effective search space used: 80696 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