GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17590 in Pseudomonas fluorescens FW300-N2E3

Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate AO353_28165 AO353_28165 ABC transporter substrate-binding protein

Query= uniprot:A0A1N7UK26
         (258 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_28165
          Length = 259

 Score =  229 bits (585), Expect = 3e-65
 Identities = 120/258 (46%), Positives = 171/258 (66%), Gaps = 4/258 (1%)

Query: 4   LRSL-FAALLLPLCATAHAQEWKEIRFGVFPEYPPFESVAADGSLQGFDIELGNAICAKL 62
           LR+L +  +L  L  T  +Q  + I+FGV P YPPFE    DGSL GFDI+LGNA+CA+L
Sbjct: 3   LRTLQYTVMLFGLIITPLSQAQQVIKFGVDPSYPPFEQKQPDGSLSGFDIDLGNALCAEL 62

Query: 63  EVKCTWVHNEFDGMIPALRARKFDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRKSAD 122
            VKC WV   FDGM+PAL+A+KFDAI+S+ + T AR + +DFS +++ +P+S++ RK+A 
Sbjct: 63  SVKCIWVEQNFDGMVPALKAKKFDAILSAFSATEARRQQVDFSHKIYTAPSSLVARKNAG 122

Query: 123 FGDTPESLMGKQVGVLQGSLQEAYARAHLAKLGAQIKAYQSQDQNYADLQNGRLDATLTD 182
              T  SL GK VGV+QGSLQE++A++     G +I +YQ+QDQ ++DL NGRL+A    
Sbjct: 123 LLPTAASLKGKSVGVVQGSLQESFAKSEWGSQGVEILSYQTQDQVFSDLINGRLEAAFQA 182

Query: 183 KLEAQLNFLSKPEGSDFK-TGPAFKDPTLPLD-IAMGLRKNDQALRALINKGIAAVQADG 240
            ++A +  L KP+G  F   G    D  +  D +A+G+RKN+  LR  +N  IA ++  G
Sbjct: 183 SVQADIGLLQKPQGQGFAFAGDPITDKRIIGDGVAIGVRKNEPDLREQLNTAIAGIRQSG 242

Query: 241 TYAQIQKKYFGDQDIYHE 258
            Y +I K+YF + DIY E
Sbjct: 243 QYDRIAKQYF-NFDIYGE 259


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: 201
Number of extensions: 9
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: 258
Length of database: 259
Length adjustment: 24
Effective length of query: 234
Effective length of database: 235
Effective search space:    54990
Effective search space used:    54990
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