GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaH in Dyella japonica UNC79MFTsu3.2

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate N515DRAFT_0416 N515DRAFT_0416 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxybutyryl-CoA epimerase

Query= BRENDA::P34439
         (298 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_0416 N515DRAFT_0416
           3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase /
           3-hydroxybutyryl-CoA epimerase
          Length = 686

 Score =  177 bits (448), Expect = 8e-49
 Identities = 122/292 (41%), Positives = 160/292 (54%), Gaps = 23/292 (7%)

Query: 11  IRNVAIVGSGQMGSGIAQVTASSGFNVMLADVNKK----ALDRAMKAISQSVTHLSKKQK 66
           I +V +VG+G MG  IA   A  GF V L D   K    ALDRA +A+ +      KK K
Sbjct: 308 IEHVHVVGAGVMGGDIAAWAAFKGFQVTLQDREMKFIQPALDRA-RALYE------KKLK 360

Query: 67  GTDKEKSDFVTLTMSRIKTCNNVSTAVADADLIIEAAIENIDLKRGIFAQIEQSCKKDSI 126
             +K     V  T  R++  +     VA ADL IEA  EN + K+ ++A IE   + D I
Sbjct: 361 TPEK-----VEETARRLRA-DVEGKGVAAADLAIEAIFENAEAKQALYASIEPQFQADEI 414

Query: 127 LTTNTSSFLLEDVAKGLQDKTRFGGLHFFNPVPVMKLLEVIRSDDTSDETYATLIKFGTA 186
           L TNTSS  L+++ +GL+   RF GLHFFNPV  M L+EV+R D    E     + F  A
Sbjct: 415 LATNTSSIPLDELRRGLKAPQRFLGLHFFNPVAQMPLVEVVRHDGLDPEVEKRALAFCKA 474

Query: 187 VGKTTVACKDSPGFIVNRLLIPYFFEAARMYERGDASMTDIDEAMKLGAGHPMGPFELAD 246
           +GK  VA K +PGF+VNR+L+PY  EA R+Y  G        EA K G   PMGP ELAD
Sbjct: 475 IGKLPVAVKGTPGFLVNRILMPYLLEAIRLYNEGVPGPVLDKEAKKFGM--PMGPIELAD 532

Query: 247 YIGLDTVKFVMDGWAAKYPEVQLFEASPLVDKLVAEGKLGRKTGDGFYSYKK 298
            +GLD    V    A   P + L E  P ++  +A GK G+K G GFY +++
Sbjct: 533 TVGLDVCASVGKELA---PFLGL-ELPPGIEDKLAAGKRGKKDGQGFYVWQE 580


Lambda     K      H
   0.318    0.133    0.376 

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: 422
Number of extensions: 17
Number of successful extensions: 4
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: 298
Length of database: 686
Length adjustment: 33
Effective length of query: 265
Effective length of database: 653
Effective search space:   173045
Effective search space used:   173045
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: 51 (24.3 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