GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PA5503 in Pseudomonas litoralis 2SM5

Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate WP_090275879.1 BLU11_RS18455 methionine ABC transporter ATP-binding protein

Query= TCDB::Q9HT70
         (335 letters)



>NCBI__GCF_900105005.1:WP_090275879.1
          Length = 334

 Score =  517 bits (1331), Expect = e-151
 Identities = 265/335 (79%), Positives = 292/335 (87%), Gaps = 2/335 (0%)

Query: 1   MIEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGG 60
           MIEF  V+K YRV GR+IPAL  T L I+AGQ++G+IGHSGAGKSTLLRLINRLEEPS G
Sbjct: 1   MIEFQQVNKAYRVGGRDIPALHATDLTIEAGQVYGIIGHSGAGKSTLLRLINRLEEPSNG 60

Query: 61  RILVEGEDVTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDA 120
           RI+V GED TAL+AEGLRRFRQRVGMIFQHFNLLSS TVADN+A+PLRLAG  +R ++ A
Sbjct: 61  RIMVAGEDTTALNAEGLRRFRQRVGMIFQHFNLLSSATVADNVALPLRLAGSANRQQIAA 120

Query: 121 RVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASV 180
           RV+ LL RVGLSDHA KYPAQLSGGQKQRVGIARALA  PSILLCDEATSALDP TT  V
Sbjct: 121 RVASLLDRVGLSDHASKYPAQLSGGQKQRVGIARALATEPSILLCDEATSALDPHTTGQV 180

Query: 181 LQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRR 240
           LQLL+EINREL LTIVLITHEMDVIRRVCDQVAVMDGG IVEQG VADVFLHPQHPTTR 
Sbjct: 181 LQLLSEINRELNLTIVLITHEMDVIRRVCDQVAVMDGGRIVEQGTVADVFLHPQHPTTRS 240

Query: 241 FVFEAERVDEDERHDDFAHVPGLILRLTFRGEATYAPLLGTVARQTGVDYSILSGRIDRI 300
           FVF +E    +++ DDF HV G ILRLTF+GE+T+APLLG VAR+TGVDYSIL+GRIDRI
Sbjct: 241 FVFGSE--SAEDQADDFGHVSGQILRLTFQGESTFAPLLGQVARETGVDYSILAGRIDRI 298

Query: 301 KDTPYGQLTLALVGGDLEAAMSQLNAADVHVEVLR 335
           +D PYGQLTLAL+GGDL AA  +L AADVHVEVLR
Sbjct: 299 RDLPYGQLTLALIGGDLSAARERLAAADVHVEVLR 333


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: 466
Number of extensions: 8
Number of successful extensions: 2
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: 334
Length adjustment: 28
Effective length of query: 307
Effective length of database: 306
Effective search space:    93942
Effective search space used:    93942
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: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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