GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Ruegeria conchae TW15

Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate WP_010441027.1 G7G_RS0110000 acyl-CoA dehydrogenase

Query= reanno::pseudo3_N2E3:AO353_25680
         (375 letters)



>NCBI__GCF_000192475.1:WP_010441027.1
          Length = 385

 Score =  223 bits (567), Expect = 9e-63
 Identities = 129/375 (34%), Positives = 210/375 (56%), Gaps = 6/375 (1%)

Query: 4   TDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTG 63
           TDE    ++ A +F  + L P   +W  +    ++   +  + G     + E++GG   G
Sbjct: 12  TDEHRMFAEMAGRFMDDALVPNTEKWAEDGVVDRDFWLQAGQTGLMAGSIAEEYGGVGGG 71

Query: 64  YLAYAMAL-EEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFA 122
               ++ L E+ A GD      +    S+    I  +G++DQK ++L  LASG M+GA A
Sbjct: 72  MGFDSVTLYEQTARGDAGWGYGIQ---SIVTHYITTYGSEDQKHKWLPKLASGEMIGALA 128

Query: 123 LTEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAF 182
           +TEP  GSD  ++KT A  +G+ Y L G K FIT+GQ+A +VIV A TD S G +G+S  
Sbjct: 129 MTEPGTGSDVQAVKTTAEKDGNSYRLKGSKIFITNGQSADLVIVAAKTDKSLGAKGVSLI 188

Query: 183 IVPTD-SPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLG-EEGEGYKIALANLEGG 240
            V T+ + G++  R  +KLG   +DT ++ FEDV+VP+ N LG EEG+G+   +  L   
Sbjct: 189 AVETEGTEGFRRGRNLEKLGMKGNDTAELFFEDVKVPMTNLLGPEEGQGFYQLMKQLPWE 248

Query: 241 RVGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYA 300
           R+ I   ++G    A      Y +ER++FG+ +++ Q   F+LA+  T+  V R  V+  
Sbjct: 249 RLTIGIMALGAIDFAISETVKYVQERKAFGQRVMDFQNTRFKLAECKTKAEVLRSFVNDC 308

Query: 301 AALRDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIY 360
               ++G+     ASM K + SE+  ++    LQ  GGYG++ ++P+ R+Y D RV  IY
Sbjct: 309 IGKLEAGELDAATASMVKYWGSEVQNEIMHECLQLFGGYGFMMEYPIARLYADARVQMIY 368

Query: 361 EGTSDIQRMVISRNL 375
            GT+++ + +I+R+L
Sbjct: 369 GGTNEVMKELIARSL 383


Lambda     K      H
   0.319    0.134    0.389 

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: 317
Number of extensions: 15
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: 385
Length adjustment: 30
Effective length of query: 345
Effective length of database: 355
Effective search space:   122475
Effective search space used:   122475
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