Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate GFF2246 PGA1_c22780 glycine betaine transport ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__Phaeo:GFF2246 Length = 352 Score = 187 bits (476), Expect = 3e-52 Identities = 103/233 (44%), Positives = 143/233 (61%), Gaps = 2/233 (0%) Query: 16 REIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGEDVTALDAE 75 + + L +++QAG+I ++G SG+GKSTL+R +NRL EP+ G I+V+GEDV L + Sbjct: 40 KHVLGLNNINVDMQAGEITVVMGLSGSGKSTLIRHLNRLIEPTAGEIIVQGEDVMQLSED 99 Query: 76 GLRRFRQ-RVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDARVSELLARVGLSDH 134 GLR RQ ++ M+FQ F LL KTV N MPL + G A D ++ L RVGLS Sbjct: 100 GLRHARQEKMSMVFQKFALLPHKTVLKNAGMPLSVRGE-DEATCDREAAKWLERVGLSGF 158 Query: 135 ARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEINRELKLT 194 YPAQLSGG +QRVGIARAL I+L DEA SALDP + LL E+ +EL T Sbjct: 159 ENHYPAQLSGGMQQRVGIARALTANTPIMLMDEAFSALDPLIRTDMQDLLLELQKELHKT 218 Query: 195 IVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRFVFEAER 247 I+ ITH++D ++ D + ++ G +V+QG+ + L+P P FV + R Sbjct: 219 IIFITHDLDEALKLADHLVILKDGFVVQQGEPQHILLNPNDPYIEDFVSDINR 271 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: 319 Number of extensions: 8 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: 352 Length adjustment: 29 Effective length of query: 306 Effective length of database: 323 Effective search space: 98838 Effective search space used: 98838 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