GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PA5503 in Pseudomonas fluorescens GW456-L13

Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate PfGW456L13_876 Glutamate transport ATP-binding protein

Query= TCDB::Q9HT70
         (335 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_876
          Length = 245

 Score =  172 bits (436), Expect = 8e-48
 Identities = 96/223 (43%), Positives = 138/223 (61%), Gaps = 2/223 (0%)

Query: 26  LNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGEDVTALDAEGLRRFRQRVG 85
           L+I+ GQ+  +IG SG+GKSTLLR +N LE  + G I V+GE + A  A+ LR  RQ+VG
Sbjct: 24  LSIEEGQVVAIIGRSGSGKSTLLRTLNGLESINDGVIEVDGEYLDAARAD-LRSLRQKVG 82

Query: 86  MIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDARVSELLARVGLSDHARKYPAQLSGG 145
           M+FQ FNL    TV +N+ +  ++     +A+      ++L RVGL +    +P +LSGG
Sbjct: 83  MVFQQFNLFPHLTVGENVMLAPQVVQKVPKAKAAELARQMLERVGLGEKFDAFPDRLSGG 142

Query: 146 QKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEINRELKLTIVLITHEMDVI 205
           Q+QRV IARALA  P +LLCDE TSALDP+    VL ++ ++ RE  +T++++THEM   
Sbjct: 143 QQQRVAIARALAMSPKVLLCDEITSALDPELVNEVLSVVRQLARE-GMTLIMVTHEMRFA 201

Query: 206 RRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRFVFEAERV 248
           R V D++  M  G + E GD   +F +PQ      F+   E V
Sbjct: 202 REVGDKLVFMHQGKVHEVGDPKVLFANPQTAELANFIGTVEAV 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: 206
Number of extensions: 6
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: 245
Length adjustment: 26
Effective length of query: 309
Effective length of database: 219
Effective search space:    67671
Effective search space used:    67671
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.

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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