GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17590 in Pseudomonas putida KT2440

Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate PP_0282 PP_0282 L-arginine ABC transporter - periplasmic binding subunit

Query= uniprot:A0A1N7UK26
         (258 letters)



>FitnessBrowser__Putida:PP_0282
          Length = 250

 Score =  167 bits (423), Expect = 2e-46
 Identities = 95/246 (38%), Positives = 151/246 (61%), Gaps = 11/246 (4%)

Query: 7   LFAALLLPLCATAHAQEWKEIRFGVFPEYPPFESVAADGSLQGFDIELGNAICAKLEVKC 66
           L AA  L + A A A E  ++R G+   YPPF +  A G++ GFD ++G+A+CAK++V+C
Sbjct: 9   LAAAATLVMSANAMAAE--KLRMGIEAAYPPFNNKDASGNVVGFDKDIGDALCAKMKVEC 66

Query: 67  TWVHNEFDGMIPALRARKFDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRKSADFGDT 126
           + V +++DG+IPAL A+KFD ++SS+++T  R++ +DF++  + +    I  K+ DF   
Sbjct: 67  SVVTSDWDGIIPALNAKKFDFLVSSLSITDERKQAVDFTNPYYSNKLQFIAPKNVDFKTD 126

Query: 127 PESLMGKQVGVLQGSLQEAYARAHLAKLGAQIKAYQSQDQNYADLQNGRLDATLTDKLEA 186
            ESL GK +G  + +L   Y   +   +  +IK Y +Q+  Y DL +GR+D  L DK   
Sbjct: 127 KESLKGKVIGTQRATLAGTYLEDNYPDV--EIKLYDTQENAYLDLVSGRIDGILADKY-V 183

Query: 187 QLNFLSKPEGSDFKTGPAFK-DPTLPLD-IAMGLRKNDQALRALINKGIAAVQADGTYAQ 244
           Q  +L   +GS+F+    FK +P +  D I + +RK D  LR  +NK +A ++ADGTY +
Sbjct: 184 QYEWLKSKDGSNFE----FKGEPVMDSDKIGIAVRKGDTKLRDDLNKALAEIKADGTYKK 239

Query: 245 IQKKYF 250
           I  KYF
Sbjct: 240 INDKYF 245


Lambda     K      H
   0.319    0.135    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: 166
Number of extensions: 9
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: 258
Length of database: 250
Length adjustment: 24
Effective length of query: 234
Effective length of database: 226
Effective search space:    52884
Effective search space used:    52884
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