GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PA5503 in Escherichia coli BW25113

Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate 17341 b3271 predicted amino-acid transporter subunit (NCBI)

Query= TCDB::Q9HT70
         (335 letters)



>FitnessBrowser__Keio:17341
          Length = 252

 Score =  171 bits (433), Expect = 2e-47
 Identities = 99/242 (40%), Positives = 137/242 (56%), Gaps = 6/242 (2%)

Query: 1   MIEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGG 60
           MI   +V+K Y     +   L+   L +Q G+   L G SG+GKST +R IN LEE   G
Sbjct: 12  MITLENVNKWYG----QFHVLKNINLTVQPGERIVLCGPSGSGKSTTIRCINHLEEHQQG 67

Query: 61  RILVEGEDVTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDA 120
           RI+V+G ++   D   + R RQ VGM+FQHFNL    TV  N  +         + E + 
Sbjct: 68  RIVVDGIELNE-DIRNIERVRQEVGMVFQHFNLFPHLTVLQNCTLAPIWVRKMPKKEAED 126

Query: 121 RVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASV 180
                L RV +++HA K+P Q+SGGQ+QRV IAR+L  +P I+L DE TSALDP+    V
Sbjct: 127 LAVHYLERVRIAEHAHKFPGQISGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMVKEV 186

Query: 181 LQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRR 240
           L  +  +  +  +T++ +THEM   R V D+V  MD G IVEQ    + F HP+   TR 
Sbjct: 187 LDTMIGL-AQSGMTMLCVTHEMGFARTVADRVIFMDRGEIVEQAAPDEFFAHPKSERTRA 245

Query: 241 FV 242
           F+
Sbjct: 246 FL 247


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: 203
Number of extensions: 7
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: 252
Length adjustment: 26
Effective length of query: 309
Effective length of database: 226
Effective search space:    69834
Effective search space used:    69834
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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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