Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate GFF139 Psest_0139 ABC-type histidine transport system, ATPase component
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__psRCH2:GFF139 Length = 257 Score = 172 bits (437), Expect = 6e-48 Identities = 99/251 (39%), Positives = 142/251 (56%), Gaps = 15/251 (5%) Query: 2 IEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGR 61 +E ++HK Y ++ L+ L + G + ++G SG+GKST LR IN LE P G Sbjct: 8 LEIRNLHKRYG----DLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHEGE 63 Query: 62 ILVEGE----------DVTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAG 111 ILV GE D+ A D + L R R +G +FQ+FNL T+ DNI R Sbjct: 64 ILVAGEQLKLKRDKQGDLVAADGKQLNRIRSELGFVFQNFNLWPHMTILDNIIEAPRRVL 123 Query: 112 GFSRAEVDARVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSA 171 G S+AE LLA+VG++D YP QLSGGQ+QR IAR LA +P ++L DE TSA Sbjct: 124 GQSKAEATEVAEALLAKVGIADKRHVYPNQLSGGQQQRAAIARTLAMQPKVILFDEPTSA 183 Query: 172 LDPQTTASVLQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFL 231 LDP+ VL ++ + E + T++L+THEM+ ++V +V + G + EQG VF Sbjct: 184 LDPEMVQEVLAVIRSLAEEGR-TMLLVTHEMNFAKQVSSEVVFLHQGLVEEQGTPEQVFD 242 Query: 232 HPQHPTTRRFV 242 +PQ ++F+ Sbjct: 243 NPQSARCKQFM 253 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: 204 Number of extensions: 9 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: 257 Length adjustment: 26 Effective length of query: 309 Effective length of database: 231 Effective search space: 71379 Effective search space used: 71379 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