GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bch in Pseudomonas fluorescens FW300-N2E2

Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate Pf6N2E2_1922 Enoyl-CoA hydratase (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)

Query= reanno::psRCH2:GFF2391
         (364 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1922
          Length = 703

 Score = 78.6 bits (192), Expect = 5e-19
 Identities = 63/185 (34%), Positives = 88/185 (47%), Gaps = 13/185 (7%)

Query: 12  VRNHVGHLTLNRPAGLNAVTLEMVRLLQQQLSAWAADPQIHAVVLRANGEKAFCAGGDIR 71
           V   V  +T+N P  +NA+T EM   +   ++   ADP + A+VL   G+  F AG DIR
Sbjct: 11  VEGVVAVITVNNPP-VNALTPEMRGSIIDAVTHANADPAVAAIVLMGGGQN-FIAGADIR 68

Query: 72  SLYDSFQRGDTEHETFFEEEYALDQYIHAYPKPLLALMDGFVLGGGMGLVQGASLRVVTE 131
                 Q G     T      ALD    A  KP +A + G+ LGGG+        R+   
Sbjct: 69  ------QFGKARTITTSMSAAALD----ASAKPTVAAIHGYALGGGLEHALACHYRIALP 118

Query: 132 RVRMGMPEVGIGYFPDVGGSYFLSRLPG-ELGTYMGVTGLQIRAADALHVGLADWCVSHD 190
             ++G+PEV +G  P  GG+  L RL G  + T + V+   I A +AL +GL    V   
Sbjct: 119 TAKLGLPEVALGLIPGGGGTQRLPRLVGAAVATDLLVSSRHIHAPEALQIGLISQIVPGT 178

Query: 191 QIAEL 195
           Q  EL
Sbjct: 179 QNQEL 183


Lambda     K      H
   0.321    0.136    0.412 

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: 577
Number of extensions: 33
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: 364
Length of database: 703
Length adjustment: 34
Effective length of query: 330
Effective length of database: 669
Effective search space:   220770
Effective search space used:   220770
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 (21.9 bits)
S2: 52 (24.6 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