Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate PfGW456L13_322 Histidine ABC transporter, ATP-binding protein (TC 3.A.1)
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_322 Length = 276 Score = 172 bits (436), Expect = 9e-48 Identities = 96/218 (44%), Positives = 136/218 (62%), Gaps = 2/218 (0%) Query: 26 LNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGEDVTALDAEGLRRFRQR-V 84 L+I +G+IF ++G SG+GKSTL+R NRL +P+ G ILV+G D+ D E LR FR+R + Sbjct: 53 LSIGSGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGVDILQYDMEALREFRRRKI 112 Query: 85 GMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDARVSELLARVGLSDHARKYPAQLSG 144 M+FQ F LL K+V DN+A L++ G S+A R + VGL + KYP QLSG Sbjct: 113 SMVFQSFGLLPHKSVLDNVAYGLKIRGE-SKAMCAERALHWINTVGLKGYENKYPHQLSG 171 Query: 145 GQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEINRELKLTIVLITHEMDV 204 G +QRVG+ARALA I+L DEA SALDP A + L E+ + L TIV ITH++D Sbjct: 172 GMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFITHDLDE 231 Query: 205 IRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRFV 242 R+ +++A++ G +++ G ++ P RFV Sbjct: 232 AVRIGNRIAILKDGRLIQVGTPREILHSPADEYVDRFV 269 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: 217 Number of extensions: 10 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: 276 Length adjustment: 27 Effective length of query: 308 Effective length of database: 249 Effective search space: 76692 Effective search space used: 76692 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