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 7026842 Shewana3_3971 cell division ATP-binding protein FtsE (RefSeq)

Query= TCDB::Q9HT70
         (335 letters)



>FitnessBrowser__ANA3:7026842
          Length = 233

 Score =  154 bits (388), Expect = 3e-42
 Identities = 90/239 (37%), Positives = 141/239 (58%), Gaps = 10/239 (4%)

Query: 1   MIEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGG 60
           MI+F  V K Y   G ++ AL+    ++Q G++  L GHSGAGKSTLL+LI  +E  + G
Sbjct: 1   MIDFQQVSKIY--PGGQM-ALEEVNFHLQKGEMAFLTGHSGAGKSTLLKLITVIERATTG 57

Query: 61  RILVEGEDVTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDA 120
           R+ + G D+  +  + +   R+ +GMIFQ+ +LL  ++V DN+A+PL +  GFS  E+  
Sbjct: 58  RVAINGHDIAKISPKHVPYLRRNIGMIFQNHHLLMDRSVFDNVALPL-VIEGFSHGEIRK 116

Query: 121 RVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASV 180
           RV+  L  VGL    R  P  LSGG++QRVGIARA+  +P +LL DE T  LDP+ +  +
Sbjct: 117 RVAGALDMVGLYGKERHNPIMLSGGEQQRVGIARAIVNKPPLLLADEPTGNLDPKLSMDI 176

Query: 181 LQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTR 239
           L+L    N +   ++++ TH++ +I R+  +   +  G ++   +     LH  H T R
Sbjct: 177 LRLFETFN-DAGTSVLIATHDLGLIARMKYRTFTLKQGRMLGAQE-----LHHGHATAR 229


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: 232
Number of extensions: 12
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: 233
Length adjustment: 26
Effective length of query: 309
Effective length of database: 207
Effective search space:    63963
Effective search space used:    63963
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