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_034270170.1 AMYHA_RS09585 acyl-CoA dehydrogenase family protein

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



>NCBI__GCF_000504245.1:WP_034270170.1
          Length = 383

 Score =  563 bits (1451), Expect = e-165
 Identities = 288/384 (75%), Positives = 322/384 (83%), Gaps = 2/384 (0%)

Query: 1   MDHRLTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYG 60
           +D RL    E LR+TVE FA   VAP IGDFYER EFPY IV +MG MGLFGLPFPE+Y 
Sbjct: 2   IDLRLDDTYETLRKTVENFAQREVAPVIGDFYEREEFPYGIVAQMGEMGLFGLPFPEKYD 61

Query: 61  GMGGDYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEIL 120
           GMGGDY AL +ALEELARVDSSVAITLEAGVSLGAMPI+ FGTD QK +WLP +C GE L
Sbjct: 62  GMGGDYFALCLALEELARVDSSVAITLEAGVSLGAMPIYRFGTDEQKEQWLPAMCRGETL 121

Query: 121 GAFGLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKP 180
           GAFGLTEP GGSDAGAT+TTA++D  +  WVING+K FITNSGTDIT LVTVTAVTG K 
Sbjct: 122 GAFGLTEPGGGSDAGATKTTAKIDGDS--WVINGSKSFITNSGTDITSLVTVTAVTGTKD 179

Query: 181 DGKPLISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQF 240
           +G   IS+IIVPSGTPGFTV   YSKVGWNASDT  LSF DVRVP  NL+G+QGRGYAQF
Sbjct: 180 NGGKEISAIIVPSGTPGFTVEKKYSKVGWNASDTHGLSFDDVRVPQENLVGQQGRGYAQF 239

Query: 241 LRILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMA 300
           L ILDEGRIAI+AL+TGLAQGCVDE ++YA ER AFGR IGA QAIQFK+ADME++ H A
Sbjct: 240 LSILDEGRIAIAALSTGLAQGCVDECLRYAREREAFGRPIGANQAIQFKLADMELRTHNA 299

Query: 301 RVGWRDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRD 360
           R+ +  AAS+++ GEPFKKEAAIAKL SS  A+DNAREATQI GGYGFMNE+PV R +RD
Sbjct: 300 RLAYYAAASKMLRGEPFKKEAAIAKLTSSNAAMDNAREATQIFGGYGFMNEFPVGRFYRD 359

Query: 361 SKILEIGEGTSEVQRMLIARELGL 384
           +KILE+GEGTSEVQRMLIARELGL
Sbjct: 360 AKILEVGEGTSEVQRMLIARELGL 383


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: 565
Number of extensions: 16
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: 386
Length of database: 383
Length adjustment: 30
Effective length of query: 356
Effective length of database: 353
Effective search space:   125668
Effective search space used:   125668
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.

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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