GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11885 in Herbaspirillum seropedicae SmR1

Align Rhizopine-binding protein (characterized, see rationale)
to candidate HSERO_RS05170 HSERO_RS05170 LacI family transcription regulator

Query= uniprot:A0A0N9WNI6
         (308 letters)



>FitnessBrowser__HerbieS:HSERO_RS05170
          Length = 324

 Score =  118 bits (295), Expect = 2e-31
 Identities = 90/299 (30%), Positives = 148/299 (49%), Gaps = 17/299 (5%)

Query: 13  SLMLASGAALADLRIGVSMSQFDDTWLTYLRESMDKQAKSMPDGVKLQFEDARSDVVKQL 72
           ++ L + AA   L +G S    +  W T    S+   AK    GV L+F DA+     Q+
Sbjct: 21  AMSLPAFAADKPLTMGFSQVGAESEWRTANTVSIKDAAKQA--GVNLKFADAQQKQENQV 78

Query: 73  SQVESFISQKVDAIVVNPVDTAATRKITEAAVKAGIPLVYVNRRPDDLKLPKGVITVASN 132
             + SFI+QKVD I  +PV  +    +   A  A IP++  +R  +       V  + S+
Sbjct: 79  KAIRSFIAQKVDVIAFSPVVESGWETVLREAKAAKIPVILTDRAVNVSDKSLYVTFIGSD 138

Query: 133 DLEAGQMQMQYLAEKMK----GKGDIVILLGDLANNSTTNRTKGVKEVLAKYPGIKIDQE 188
            +E G+   ++L EK K    G  +IV L G + +    +R  G +EV+   P +KI + 
Sbjct: 139 FVEEGRRAGRWLLEKAKSMPAGDINIVELQGTVGSAPAIDRKAGFEEVIKGEPRLKIIRS 198

Query: 189 QTGTWSRDKGMTLVNDWL-TQGRKFDAIVSNNDEMAIGAAMALKQAGVEKG-SVLIAGVD 246
           QTG ++R KG  ++  +L  +G+K + + ++ND+MAIGA  A+++AG++ G  ++I  +D
Sbjct: 199 QTGDFTRAKGKEVMEAFLKAEGKKINVLYAHNDDMAIGAIQAIEEAGMKPGKDIIIISID 258

Query: 247 GTPDGLRAVKKGDLAVSV-FQDANGQAVDSIDAAVKMAKNEPVEQAVWVPYRLITPENV 304
           G      A+  G L V+V      G  +  I   +K  K         VP R+ T E +
Sbjct: 259 GVKGAFEAMMAGKLNVTVECSPLLGPQLMQIAKDIKAGKE--------VPKRITTEEGI 309


Lambda     K      H
   0.315    0.130    0.360 

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: 219
Number of extensions: 13
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: 308
Length of database: 324
Length adjustment: 27
Effective length of query: 281
Effective length of database: 297
Effective search space:    83457
Effective search space used:    83457
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 48 (23.1 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