GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Pseudomonas putida KT2440

Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate PP_0283 PP_0283 Arginine/ornithine transport ATP-binding protein AotP

Query= reanno::pseudo3_N2E3:AO353_21725
         (265 letters)



>FitnessBrowser__Putida:PP_0283
          Length = 257

 Score =  254 bits (650), Expect = 1e-72
 Identities = 129/250 (51%), Positives = 178/250 (71%), Gaps = 1/250 (0%)

Query: 16  LEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQILLD 75
           LEIR+LHK+YG  E+LKG+ LT + G+V++++GSSGSGK+TLLRC+N+LE    G+IL+ 
Sbjct: 8   LEIRNLHKRYGEQEILKGISLTARDGDVISILGSSGSGKSTLLRCINLLENPHQGEILVA 67

Query: 76  GESIGYHEV-NGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLHK 134
           GE++      NG  +    + I + R+  G  FQ FNL+PH++ L N+     +V    K
Sbjct: 68  GEALKLKAAKNGDLIAADNRQINRVRSEIGFVFQNFNLWPHMSILDNIIEAPRRVLGQSK 127

Query: 135 DEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPE 194
            EA+  AE  L +VG+ ++R  YP QLSGGQQQR AIAR +AM P ++LFDE TSALDPE
Sbjct: 128 AEAIEAAEALLNKVGIYDKRHSYPAQLSGGQQQRAAIARTLAMKPKVILFDEPTSALDPE 187

Query: 195 LVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQSP 254
           +V EVL+VI+ LAE+G TMLLVTHEM FA  VS ++VF++QG +EEQG P+++FE P S 
Sbjct: 188 MVQEVLNVIRALAEEGRTMLLVTHEMSFARHVSSEVVFLHQGLVEEQGSPQQVFENPTSA 247

Query: 255 RLAEFLKNTR 264
           R  +F+ + R
Sbjct: 248 RCKQFMSSHR 257


Lambda     K      H
   0.319    0.135    0.379 

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: 189
Number of extensions: 7
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: 265
Length of database: 257
Length adjustment: 25
Effective length of query: 240
Effective length of database: 232
Effective search space:    55680
Effective search space used:    55680
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 (21.8 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