GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PA5503 in Pseudomonas putida KT2440

Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate PP_2774 PP_2774 glycine betaine ABC transporter, ATPase/permease fusion protein

Query= TCDB::Q9HT70
         (335 letters)



>FitnessBrowser__Putida:PP_2774
          Length = 698

 Score =  173 bits (439), Expect = 1e-47
 Identities = 96/234 (41%), Positives = 145/234 (61%), Gaps = 3/234 (1%)

Query: 2   IEFHDVHKTYRVAGREIP-ALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGG 60
           +EF  V K Y  +  +   A++   L ++ G++  L+G SG+GKSTLLR +NRL EPS G
Sbjct: 35  LEFRAVTKRYEGSRSDSTNAVEQVNLAVRRGEVLCLMGTSGSGKSTLLRHVNRLIEPSSG 94

Query: 61  RILVEGEDVTALDAEGLRRFR-QRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVD 119
            +L++GE +++L    LR+ R QR+GM+FQHF LL  ++V DN+A+PL L G        
Sbjct: 95  EVLIDGEVLSSLTQPTLRQLRSQRIGMVFQHFGLLPHRSVLDNVALPLELRGEPESTRRT 154

Query: 120 ARVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTAS 179
           A + +L A VGL   + ++P +LSGG +QRVG+ARAL   P ILL DE  SALDP     
Sbjct: 155 AALRQLQA-VGLKAWSERFPHELSGGMQQRVGLARALVTNPDILLMDEPFSALDPTIRRD 213

Query: 180 VLQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHP 233
           +     ++ RE  +T +L+TH+     R+ D++AV+ GG +++ G   ++  HP
Sbjct: 214 LQGRFLQLVRERGITTLLVTHDPGEALRLADRIAVLRGGRLIQVGTPGELLEHP 267


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: 541
Number of extensions: 37
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: 698
Length adjustment: 34
Effective length of query: 301
Effective length of database: 664
Effective search space:   199864
Effective search space used:   199864
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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