GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Ch1CoA in Magnetospirillum magneticum AMB-1

Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate WP_011384980.1 AMB_RS13080 acyl-CoA dehydrogenase

Query= BRENDA::Q39QF5
         (380 letters)



>lcl|NCBI__GCF_000009985.1:WP_011384980.1 AMB_RS13080 acyl-CoA
           dehydrogenase
          Length = 383

 Score =  221 bits (563), Expect = 3e-62
 Identities = 139/372 (37%), Positives = 199/372 (53%), Gaps = 9/372 (2%)

Query: 12  LDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEMGVLTLALI 71
           LD +       + P    + E    P         LGL    +P  YGG  + +    L 
Sbjct: 12  LDTLSRFVRERLVPNEERIAEDDALPAEIIAEMKDLGLFGLSIPEEYGGLGLTMEEEVLC 71

Query: 72  LEELGRVCASTALLLIAQTD---GMLPIIHGGSPELKERYLRRFAGESTLLTALAATEPA 128
             E+G+   S A   I  T+   G   II  G+ E K++YL R A    L+ + A TEP 
Sbjct: 72  AFEIGQT--SPAFRSIFGTNNGIGSQGIIIDGTEEQKQKYLPRLA-TGELIASFALTEPN 128

Query: 129 AGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPE-KGSKGISAFVVEK 187
           AGSD  +++T A + GD Y++NG K FITN   A +  + A TDP  KG+ GISAF+VE 
Sbjct: 129 AGSDAASLRTTARKDGDHYIVNGTKRFITNAPEASIFTLMARTDPNNKGAGGISAFIVEA 188

Query: 188 GTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGA-EGTGFANLMQTLSTNRVFCA 246
            +PGL  G+ + KMG +G+   ++ FE++ VPA NIIG  EG GF   M+ L   R+  +
Sbjct: 189 DSPGLSLGKIDKKMGQKGAHTCDVIFEDVRVPAANIIGGIEGQGFKTAMKVLDRGRLHIS 248

Query: 247 AQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAAELLD 306
           A  VG+++  +  +V++  +RVQFGKPI     VQ M+AD  T   A+R +   AA   D
Sbjct: 249 ATCVGVSERLIRDSVKYAAERVQFGKPIGEFQLVQAMLADSRTEAYAARCMVLDAARKKD 308

Query: 307 DGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQIYTGTN 366
            G   +    +  K  AS+   R+   AVQV GG+GY+ + G+ER  RD +L +IY GT 
Sbjct: 309 QGINVST-EAACCKMFASEAVGRIADRAVQVHGGAGYISDYGIERFYRDVRLFRIYEGTT 367

Query: 367 QITRMVTGRALL 378
           QI ++V  R +L
Sbjct: 368 QIQQLVIARNML 379


Lambda     K      H
   0.319    0.134    0.371 

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: 329
Number of extensions: 17
Number of successful extensions: 5
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: 380
Length of database: 383
Length adjustment: 30
Effective length of query: 350
Effective length of database: 353
Effective search space:   123550
Effective search space used:   123550
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 (21.7 bits)
S2: 50 (23.9 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, 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