GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Algoriphagus aquaeductus T4

Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_111393848.1 CLV31_RS15640 acyl-CoA dehydrogenase

Query= reanno::pseudo5_N2C3_1:AO356_26355
         (375 letters)



>NCBI__GCF_003253485.1:WP_111393848.1
          Length = 401

 Score =  226 bits (576), Expect = 8e-64
 Identities = 133/375 (35%), Positives = 198/375 (52%), Gaps = 7/375 (1%)

Query: 2   LPTEEQTQIRDMARQFAQERLKPFAAEWDREHRFPREAIAEMAELGFFGMLVPEQWGGCD 61
           L TEEQ  IR   R F ++ + P+  +W ++  FP E + +  E+G FG  +P ++G   
Sbjct: 26  LLTEEQKLIRSSIRDFVKKEISPYIEDWAQKAHFPYEIVKKFGEVGAFGPQLPVEYGCGG 85

Query: 62  TGYLAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAF 121
             Y++Y + ++EI  GD    +  SV  S+   PI KFG +EQ+ K+L  LASG +LG F
Sbjct: 86  LDYISYGLIMQEIERGDSGMRSTASVQGSLVMYPIYKFGTEEQRLKYLPRLASGELLGCF 145

Query: 122 ALTEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISA 181
            LTEP  GS+ S + T  +  GDHY+LNG K +I++   A + +V+A  +       I  
Sbjct: 146 GLTEPDHGSNPSGMVTNFKDMGDHYLLNGAKMWISNSPKADIAVVWAKNEEGR----IQG 201

Query: 182 FIVPTDSPGYSVARVEDKLGQHASDTCQILFEEVKVPVGNRL-GEEGEGYKIALANLEGG 240
            IV     G+S     +K    AS T +++F+ VKVP  N L G+ G G    +  L+  
Sbjct: 202 LIVERGMEGFSTPETHNKWSLRASCTGELVFDNVKVPKENLLPGKTGLG--APMMCLDSA 259

Query: 241 RVGIAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYA 300
           R GIA  A+G A   +E+AR YA ER  FGKPI   Q    +LA+M T+I  A+ +    
Sbjct: 260 RFGIAWGAIGAAMDCYESARRYAAERIQFGKPIGGFQLTQKKLAEMLTEITKAQLLAWKV 319

Query: 301 AALRDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIY 360
             + + G+   V  SMAK    EMA  +   A Q  GG G   ++P+ R   ++     Y
Sbjct: 320 GKMMNEGKAKTVHISMAKRNNVEMALNIAREARQIHGGMGITGEYPIMRHMMNLESVITY 379

Query: 361 EGTSDIQRMVISRNL 375
           EGT DI  +++   +
Sbjct: 380 EGTHDIHLLILGNEI 394


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: 321
Number of extensions: 12
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: 375
Length of database: 401
Length adjustment: 30
Effective length of query: 345
Effective length of database: 371
Effective search space:   127995
Effective search space used:   127995
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