Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate 8500099 DvMF_0862 ABC transporter related (RefSeq)
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__Miya:8500099 Length = 248 Score = 190 bits (483), Expect = 3e-53 Identities = 106/227 (46%), Positives = 146/227 (64%), Gaps = 4/227 (1%) Query: 17 EIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGEDVTALDAEG 76 E+ AL L++ G+ + G SG+GKSTLLR INRLE G I+V+G+DV + D + Sbjct: 21 ELTALNDVSLDVMPGEKVVICGPSGSGKSTLLRSINRLETVDKGTIIVDGQDVNSPDND- 79 Query: 77 LRRFRQRVGMIFQHFNLLSSKTVADNIAM-PLRLAGGFSRAEVDARVSELLARVGLSDHA 135 + + RQ +GM+FQ FNL KTV N+ M P+RL RAE ++R ELL +VG+SD A Sbjct: 80 INKIRQELGMVFQSFNLFPHKTVLQNLTMAPMRLRKT-PRAEAESRALELLKKVGISDKA 138 Query: 136 RKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEINRELKLTI 195 +PA LSGGQ+QRV IARALA P I+L DE TSALDP+ VL ++ + RE +T+ Sbjct: 139 NVFPAMLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMIGEVLDVMVTLARE-GMTM 197 Query: 196 VLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRFV 242 V +THEM R V D++ MD G ++E+ D F P+HP ++F+ Sbjct: 198 VCVTHEMGFAREVADRIIFMDHGQVLEENAPQDFFGAPKHPRLQKFL 244 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: 212 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: 248 Length adjustment: 26 Effective length of query: 309 Effective length of database: 222 Effective search space: 68598 Effective search space used: 68598 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: 47 (22.7 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