GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Amycolatopsis halophila YIM 93223

Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_034275109.1 AMYHA_RS25070 acyl-CoA dehydrogenase family protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_1146
         (375 letters)



>NCBI__GCF_000504245.1:WP_034275109.1
          Length = 386

 Score =  269 bits (687), Expect = 1e-76
 Identities = 155/374 (41%), Positives = 229/374 (61%), Gaps = 5/374 (1%)

Query: 5   EEQTQIRDMARQFAEERLKPFAAEWDREHRFPREAIDEMAELGFFGMLVPEQWGGCDTGY 64
           EE  ++R   R  AE+ + P A E D   R+P EA++ + + GF  + +P+++GG     
Sbjct: 13  EEHEELRAAVRALAEKEIAPHAEEVDETERYPVEALEALNKAGFSAVHIPDEYGGQGADA 72

Query: 65  LAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFALT 124
           +A  + +EE+A    + S I +V N +G + ++  G++E K K L  +A GA   ++AL+
Sbjct: 73  IATDIVIEEVARVCASSSLIPAV-NKLGTMNVILGGSEELKHKVLGDVAGGAT-ASYALS 130

Query: 125 EPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGK--RGISAF 182
           E +AGSD +S++T+A  +GD++VLNG K +IT+   +    V AVTDP A     GISAF
Sbjct: 131 EREAGSDPASMRTKAIRDGDNWVLNGTKCWITNAGESSWYTVMAVTDPDAKNPAAGISAF 190

Query: 183 IVPTDSPGYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLGEEGEGYKIALANLEGGRV 242
            V  + PG+ V   E KLG   S T +I FE+  +P    +GE G+G K+A + L+  R 
Sbjct: 191 AVHAEDPGFVVGPKERKLGIKGSPTREIYFENCTIPGDRIIGEPGQGLKLAFSTLDHTRH 250

Query: 243 GIAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAA 302
            I AQA+G+A+ A +A  DY +ER  FGK I E Q V F LADMA ++  AR +V+ AAA
Sbjct: 251 SIGAQALGIAQGALDATIDYVKERQQFGKAIAEFQGVQFMLADMAMKVEAARHLVYSAAA 310

Query: 303 LRDSGQ-PALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYE 361
             + G       +S AK FAS++A +V + A+Q  GG GY  DFP+ER+ RD ++ QIYE
Sbjct: 311 KVERGDADKSFASSAAKTFASDVAMEVTTDAVQLFGGAGYTRDFPVERMMRDAKITQIYE 370

Query: 362 GTSDIQRMVISRNL 375
           GT+ IQRMV++R L
Sbjct: 371 GTNQIQRMVMARQL 384


Lambda     K      H
   0.320    0.134    0.388 

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: 351
Number of extensions: 18
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: 375
Length of database: 386
Length adjustment: 30
Effective length of query: 345
Effective length of database: 356
Effective search space:   122820
Effective search space used:   122820
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 (21.8 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