Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate 206675 DVU1236 amino acid ABC transporter, ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >MicrobesOnline__882:206675 Length = 247 Score = 194 bits (494), Expect = 1e-54 Identities = 109/227 (48%), Positives = 148/227 (65%), Gaps = 4/227 (1%) Query: 17 EIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGEDVTALDAEG 76 E+ AL L++QAG+ +IG SG+GKSTLLR INRLE G I+V+G+D+ A D++ Sbjct: 20 ELTALHDVSLDVQAGEKVVIIGPSGSGKSTLLRSINRLENVDKGSIIVDGKDIRAEDSD- 78 Query: 77 LRRFRQRVGMIFQHFNLLSSKTVADNIAM-PLRLAGGFSRAEVDARVSELLARVGLSDHA 135 + RQ +GM+FQ FNL KTV N+ M P+RL R E ++R +LL +VG+SD A Sbjct: 79 INVIRQDLGMVFQSFNLFPHKTVLQNLTMAPMRLRK-VPRDEAESRALDLLKKVGISDKA 137 Query: 136 RKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEINRELKLTI 195 YPA LSGGQ+QRV IARALA P I+L DE TSALDP+ VL ++ + +E +T+ Sbjct: 138 NVYPAMLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMIGEVLDVMVTLAKE-GMTM 196 Query: 196 VLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRFV 242 V +THEM R V D++ MD G I+EQG F P+HP ++F+ Sbjct: 197 VCVTHEMGFAREVADRIIFMDHGQILEQGTPQHFFEAPEHPRLQKFL 243 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: 218 Number of extensions: 13 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: 247 Length adjustment: 26 Effective length of query: 309 Effective length of database: 221 Effective search space: 68289 Effective search space used: 68289 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