GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaZ1 in Shewanella loihica PV-4

Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate 5209192 Shew_1670 enoyl-CoA hydratase (RefSeq)

Query= uniprot:A0A2Z5MCI7
         (262 letters)



>lcl|FitnessBrowser__PV4:5209192 Shew_1670 enoyl-CoA hydratase
           (RefSeq)
          Length = 257

 Score =  116 bits (291), Expect = 4e-31
 Identities = 79/248 (31%), Positives = 127/248 (51%), Gaps = 5/248 (2%)

Query: 16  TLVLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITG-ADNFFCAGGNLNRLLE 74
           T VLT++NP A N    D  A   + +  +  +  I A+V+TG  + FF AG +L    +
Sbjct: 12  TAVLTMNNPPA-NTWTADSLALLKQKVTELNANKEIYALVLTGEGEKFFSAGADLKLFAD 70

Query: 75  NRAKDPSVQAQSIDLLAEWISALRLSSKPVIAAVDGAAAGAGFSLALACDLIVAADDAKF 134
               + +  A+      E +S  R  S   IAA++G A G G  +ALACD+ +A   A  
Sbjct: 71  GDKGNAATMAKHFGEAFEALSGFRGVS---IAAINGYAMGGGLEVALACDIRIAEAQAVM 127

Query: 135 VMSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKPGTARD 194
            +  A VGL P  GG+  L   +    A  +++ G+ +GA +   +G++ ++   G A D
Sbjct: 128 ALPEATVGLLPCAGGTQNLTAMVGEGWAKRMILCGERVGADKALSIGLIEEVVDKGAALD 187

Query: 195 AAVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEGISAFL 254
            A+A A+++   SP+SV   K L+ +    P ++ L  ER+ FV      +  EG++AFL
Sbjct: 188 TAMALAEKVANQSPSSVTVCKQLIQSGRAMPRTQALPLERELFVGLFDTEDQAEGVNAFL 247

Query: 255 EKRAPVYK 262
           EKR   +K
Sbjct: 248 EKRKANWK 255


Lambda     K      H
   0.317    0.132    0.377 

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: 111
Number of extensions: 3
Number of successful extensions: 1
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: 262
Length of database: 257
Length adjustment: 24
Effective length of query: 238
Effective length of database: 233
Effective search space:    55454
Effective search space used:    55454
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 (21.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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