GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Rhodobacter viridis JA737

Align isobutyryl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_110806794.1 C8J30_RS15730 acyl-CoA/acyl-ACP dehydrogenase

Query= reanno::pseudo3_N2E3:AO353_25670
         (383 letters)



>NCBI__GCF_003217355.1:WP_110806794.1
          Length = 547

 Score =  218 bits (554), Expect = 4e-61
 Identities = 140/385 (36%), Positives = 198/385 (51%), Gaps = 14/385 (3%)

Query: 6   LTEEQVMIRDMARDFARGEIAPHAQAWE-KAGWIDDALVAKMGELGLLGMVVPEEWGGTY 64
           L EE  MIR+    +A   + P+A  W  K   I   ++ ++ +LG+ G+ +PEE+GG  
Sbjct: 163 LDEELEMIREQFHRYAEERVIPNAHEWHLKDELIPMEIIEELADLGVFGLTIPEEYGGLG 222

Query: 65  VDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGTEEQKQTWLADLASGQAIGCF 124
           +   +  +  EE+S G    G+L    + +    +L  GTEEQKQ WL  LASGQ +   
Sbjct: 223 LSKASMVVVTEELSRGYIGVGSL-GTRSEIAAELILCGGTEEQKQKWLPGLASGQILSTA 281

Query: 125 CLTEPQAGSEAHNLRTRAELRDGQWVINGAKQFVSNGRRAKLAIVFAVTDPDLGK-KGLS 183
             TEP  GS+  +LRTRA      WVI G K ++++ +R  +  + A T+PD    +GLS
Sbjct: 282 VFTEPNTGSDLGSLRTRAVKEGDDWVITGNKTWITHAQRTHVMTLLARTEPDTTDWRGLS 341

Query: 184 AFLV---------PTDTPGFIVDRSEHKMGIRASDTCAVTLNNCTIPEANLLG-ERGKGL 233
            FL          P  TPG      E  +G R      +  +   +   NLLG E G+G 
Sbjct: 342 MFLAEKTPGTDENPFPTPGMTGGEIE-VLGYRGMKEYELGFDGFRVKGENLLGGETGRGF 400

Query: 234 AIALSNLEGGRIGIAAQALGIARAAFEAALAYARDRVQFDKPIIEHQSVANMLADMHTRL 293
              +   E  RI  AA+A+G+A+AA E  + YA DR QF K +IE   V   LA M   +
Sbjct: 401 KQLMETFESARIQTAARAVGVAQAACEIGMRYAIDRKQFGKSLIEFPRVGGKLAMMAVEI 460

Query: 294 NAARLLILHAARLRSAGKPCLSEASQAKLFASEMAEKVCSSAIQIHGGYGYLEDYPVERY 353
             AR L   +A  +  G  C  EA  AKL  + +A     +A+QIHGG G+  +Y + R 
Sbjct: 461 MIARQLTYFSAWEKDHGHRCDVEAGMAKLLGARVAWAASDNALQIHGGNGFALEYTISRI 520

Query: 354 YRDARITQIYEGSSEIQRMVIAREL 378
             DARI  I+EG++EIQ  VIAR L
Sbjct: 521 LCDARILNIFEGAAEIQAQVIARRL 545


Lambda     K      H
   0.319    0.134    0.394 

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: 425
Number of extensions: 22
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: 383
Length of database: 547
Length adjustment: 33
Effective length of query: 350
Effective length of database: 514
Effective search space:   179900
Effective search space used:   179900
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: 51 (24.3 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