GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PA5503 in Shewanella sp. ANA-3

Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate 7026050 Shewana3_3192 sulfate ABC transporter, ATPase subunit (RefSeq)

Query= TCDB::Q9HT70
         (335 letters)



>FitnessBrowser__ANA3:7026050
          Length = 376

 Score =  158 bits (399), Expect = 2e-43
 Identities = 94/231 (40%), Positives = 132/231 (57%), Gaps = 12/231 (5%)

Query: 17  EIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGEDVTALDAEG 76
           +  AL P  L+IQ G++ GL+G SG+GK+TLLR+I  LE    G+I     DVT +    
Sbjct: 14  QFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGQIHFGNRDVTQVHVRD 73

Query: 77  LRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGF---SRAEVDARVSELLARVGLSD 133
                +RVG +FQ++ L    TVADN+A  L +       S+AE+  RVS LL  V L  
Sbjct: 74  -----RRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSKAEIQKRVSHLLEMVQLGH 128

Query: 134 HARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEINRELKL 193
            A++YP QLSGGQKQR+ +ARALA +P +LL DE   ALD +    + + L  ++ ELK 
Sbjct: 129 LAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELRRWLRSLHDELKF 188

Query: 194 TIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRFVFE 244
           T V +TH+ D    + D+V VM  G I +     +++  P      RFVF+
Sbjct: 189 TSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQP----NSRFVFD 235


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: 287
Number of extensions: 12
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: 376
Length adjustment: 29
Effective length of query: 306
Effective length of database: 347
Effective search space:   106182
Effective search space used:   106182
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 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