GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Desulfacinum infernum DSM 9756

Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_073037063.1 BUB04_RS03730 acyl-CoA dehydrogenase

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



>NCBI__GCF_900129305.1:WP_073037063.1
          Length = 382

 Score =  355 bits (912), Expect = e-103
 Identities = 178/373 (47%), Positives = 255/373 (68%), Gaps = 1/373 (0%)

Query: 4   TEEQTQIRDMARQFAEERLKPFAAEWDREHRFPREAIDEMAELGFFGMLVPEQWGGCDTG 63
           TEEQ  I+DMAR+FAE  + P AAE DR H+ P E + +M ELG  G+ +P ++GG    
Sbjct: 6   TEEQRMIQDMARKFAEREIAPVAAELDRTHKHPEEIVKKMGELGLMGITIPPEYGGAGMD 65

Query: 64  YLAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFAL 123
           Y++Y + + EI+    +C  IMSV NS+   P+  +G +EQK +FLTP+ASG  LG + L
Sbjct: 66  YVSYVLAMIEISKACASCGVIMSVCNSLYNFPVYTYGTEEQKQQFLTPVASGEYLGCYGL 125

Query: 124 TEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183
           TE  AGSD + ++T A L+G+ +V+NG K+FIT+G  A   ++ AVTD   G +GIS+F+
Sbjct: 126 TEAGAGSDPAKMRTTAVLDGNEWVINGEKKFITNGNVARYCVLAAVTDKEKGYKGISSFL 185

Query: 184 VPT-DSPGYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLGEEGEGYKIALANLEGGRV 242
           V   ++PG+ V RVE+KLG +AS T +++FED ++P  N LG+EGEG+K  L  L+GGR+
Sbjct: 186 VDLHNTPGFKVGRVEEKLGINASGTAELIFEDARIPKENLLGKEGEGFKQMLTTLDGGRI 245

Query: 243 GIAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAA 302
           GIA+QA+G+ RA  E A +YA+ R  FG+PI   QA+ ++LAD+ATQ+  A  +   AA 
Sbjct: 246 GIASQAIGIGRAVLEEAIEYAKTREQFGRPIASFQAIQWKLADIATQLDAAELLTLRAAW 305

Query: 303 LRDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYEG 362
           L  +G+    EA+MAKLFAS+ A       +Q LGGYGY  ++P+ER  RD ++ QIYEG
Sbjct: 306 LEQNGRGYEKEAAMAKLFASDTAMWAAVEGVQILGGYGYCKEYPMERHMRDAKITQIYEG 365

Query: 363 TSDIQRMVISRNL 375
           T++I R+VISRN+
Sbjct: 366 TNEIMRLVISRNI 378


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: 382
Number of extensions: 15
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: 375
Length of database: 382
Length adjustment: 30
Effective length of query: 345
Effective length of database: 352
Effective search space:   121440
Effective search space used:   121440
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 Apr 09 2024. 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