GapMind for catabolism of small carbon sources

 

Alignments 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_011385957.1 AMB_RS18215 acyl-CoA dehydrogenase

Query= BRENDA::Q39QF5
         (380 letters)



>NCBI__GCF_000009985.1:WP_011385957.1
          Length = 378

 Score =  256 bits (654), Expect = 7e-73
 Identities = 153/375 (40%), Positives = 215/375 (57%), Gaps = 5/375 (1%)

Query: 5   TEEQKLTLDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEMG 64
           TEEQ+L  DM R  A  ++AP A   D + LFP  A     +LG L  ++P+ + G    
Sbjct: 4   TEEQQLIRDMARSFAREKLAPNAARWDREHLFPTDAIAEMGELGFLGMVVPSEWDGAGTD 63

Query: 65  VLTLALILEELGRVCASTALLL-IAQTDGMLPIIHGGSPELKERYLRRFA-GESTLLTAL 122
            ++ A+ + E+   C   + ++ +  + G +PI+  G+   K+ +LR  A GE   L   
Sbjct: 64  YVSYAMAVMEIAAGCGPLSTIMSVHNSVGCMPILTYGTEAQKDEFLRPMARGEK--LGCF 121

Query: 123 AATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGISA 182
             TEP AGSD  +++TRA R GD YV++G K FI+      V +V+A TDP+ G +GISA
Sbjct: 122 CLTEPEAGSDAASIRTRARRDGDHYVLSGAKQFISTAKNGQVAIVFAVTDPQAGKRGISA 181

Query: 183 FVVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTNR 242
           FVV   TPG    R E K+G   S   +L FE+M VPA   +G EG G    +  L   R
Sbjct: 182 FVVPTDTPGFTVVRVEDKLGQHLSDTCQLAFEDMRVPASRRLGEEGDGLKIALANLEGGR 241

Query: 243 VFCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAA 302
           +  AAQ+VG+A+ ALD A+ + ++R QFGKPI     V F +ADMAT VE +  +   AA
Sbjct: 242 LGIAAQSVGMARSALDHALAYAKERKQFGKPIFEHQAVAFRLADMATRVEVAEQMVLHAA 301

Query: 303 ELLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQIY 362
            L D G    +   SMAK  AS+ A RV +DA+Q+ GG GY+ +  VER+ RD ++ QIY
Sbjct: 302 SLRDAG-LPCLKEASMAKLFASEMAERVCSDAIQIHGGYGYLADFPVERIYRDVRVCQIY 360

Query: 363 TGTNQITRMVTGRAL 377
            GT+ I R+V  RAL
Sbjct: 361 EGTSDIQRLVISRAL 375


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: 315
Number of extensions: 16
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: 380
Length of database: 378
Length adjustment: 30
Effective length of query: 350
Effective length of database: 348
Effective search space:   121800
Effective search space used:   121800
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 (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