GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Amycolatopsis halophila YIM 93223

Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate WP_034273245.1 AMYHA_RS19255 acyl-CoA dehydrogenase family protein

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



>NCBI__GCF_000504245.1:WP_034273245.1
          Length = 386

 Score =  516 bits (1330), Expect = e-151
 Identities = 269/385 (69%), Positives = 303/385 (78%), Gaps = 3/385 (0%)

Query: 1   MDHRLTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYG 60
           +D RL  E + LR TV +FA   V+P IGD+YER EFPY +V  MG+MGLFGLPFPEE G
Sbjct: 2   IDLRLDDEHDALRATVADFARSEVSPVIGDYYERGEFPYPLVATMGKMGLFGLPFPEELG 61

Query: 61  GMGGDYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEIL 120
           GMGGDYLAL IALEELARVDSSVAI L AGVSLGAMP++ FGT  Q+  WLP LC GE L
Sbjct: 62  GMGGDYLALCIALEELARVDSSVAIALSAGVSLGAMPLYRFGTVEQRERWLPSLCRGEAL 121

Query: 121 GAFGLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKP 180
            AFGLTEPDGG+DAGATRT A LD    +WVINGTKCFITNSGTDIT +VTVTAVTG   
Sbjct: 122 AAFGLTEPDGGTDAGATRTRAELDGG--DWVINGTKCFITNSGTDITSVVTVTAVTGGHA 179

Query: 181 DGKPL-ISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQ 239
                 IS+I+VPSGTPGF V   YSKVGW ASDT ELSF D RVP +NLLG++GRG AQ
Sbjct: 180 GTSGAEISTILVPSGTPGFDVGPSYSKVGWCASDTHELSFTDCRVPESNLLGQRGRGMAQ 239

Query: 240 FLRILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHM 299
           FL ILDE RIAISA+  GLAQGCVDE V+YA +R AFG  IG+ QAIQF IADM  + H 
Sbjct: 240 FLSILDESRIAISAVGVGLAQGCVDECVRYASQREAFGAPIGSRQAIQFTIADMATRVHT 299

Query: 300 ARVGWRDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWR 359
           AR+ +  A ++L+ GEPFK+EAA+AKL SS  A+DNAR+ATQI GGYGFMNE PV R +R
Sbjct: 300 ARLAYYAAVAKLLRGEPFKQEAAMAKLVSSNAAMDNARDATQIFGGYGFMNESPVGRFYR 359

Query: 360 DSKILEIGEGTSEVQRMLIARELGL 384
           D+KILEIGEGTSEVQRMLIAR LGL
Sbjct: 360 DAKILEIGEGTSEVQRMLIARHLGL 384


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: 538
Number of extensions: 16
Number of successful extensions: 3
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: 386
Length of database: 386
Length adjustment: 30
Effective length of query: 356
Effective length of database: 356
Effective search space:   126736
Effective search space used:   126736
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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