GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Magnetospirillum magneticum AMB-1

Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate WP_011385957.1 AMB_RS18215 acyl-CoA dehydrogenase

Query= metacyc::MONOMER-11693
         (386 letters)



>NCBI__GCF_000009985.1:WP_011385957.1
          Length = 378

 Score =  270 bits (691), Expect = 4e-77
 Identities = 151/377 (40%), Positives = 228/377 (60%), Gaps = 5/377 (1%)

Query: 6   TPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYGGMGGD 65
           T E + +R     FA + +AP    +   H FP + + EMG +G  G+  P E+ G G D
Sbjct: 4   TEEQQLIRDMARSFAREKLAPNAARWDREHLFPTDAIAEMGELGFLGMVVPSEWDGAGTD 63

Query: 66  YLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEILGAFGL 125
           Y++  +A+ E+A     ++  +    S+G MPI  +GT+AQK E+L  +  GE LG F L
Sbjct: 64  YVSYAMAVMEIAAGCGPLSTIMSVHNSVGCMPILTYGTEAQKDEFLRPMARGEKLGCFCL 123

Query: 126 TEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKPDGKPL 185
           TEP+ GSDA + RT AR D   + +V++G K FI+   T   G V +         GK  
Sbjct: 124 TEPEAGSDAASIRTRARRDG--DHYVLSGAKQFIS---TAKNGQVAIVFAVTDPQAGKRG 178

Query: 186 ISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQFLRILD 245
           IS+ +VP+ TPGFTV     K+G + SDT +L+F D+RVPA+  LGE+G G    L  L+
Sbjct: 179 ISAFVVPTDTPGFTVVRVEDKLGQHLSDTCQLAFEDMRVPASRRLGEEGDGLKIALANLE 238

Query: 246 EGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMARVGWR 305
            GR+ I+A + G+A+  +D ++ YA ER  FG+ I  +QA+ F++ADM  +  +A     
Sbjct: 239 GGRLGIAAQSVGMARSALDHALAYAKERKQFGKPIFEHQAVAFRLADMATRVEVAEQMVL 298

Query: 306 DAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRDSKILE 365
            AAS   AG P  KEA++AKL++S +A     +A QIHGGYG++ ++PV R++RD ++ +
Sbjct: 299 HAASLRDAGLPCLKEASMAKLFASEMAERVCSDAIQIHGGYGYLADFPVERIYRDVRVCQ 358

Query: 366 IGEGTSEVQRMLIAREL 382
           I EGTS++QR++I+R L
Sbjct: 359 IYEGTSDIQRLVISRAL 375


Lambda     K      H
   0.318    0.136    0.402 

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: 355
Number of extensions: 17
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 386
Length of database: 378
Length adjustment: 30
Effective length of query: 356
Effective length of database: 348
Effective search space:   123888
Effective search space used:   123888
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: 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