GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Rhodococcus qingshengii djl-6-2

Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate WP_050654861.1 C1M55_RS10170 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= uniprot:Q88CC3
         (496 letters)



>NCBI__GCF_002893965.1:WP_050654861.1
          Length = 501

 Score =  205 bits (522), Expect = 3e-57
 Identities = 136/441 (30%), Positives = 218/441 (49%), Gaps = 11/441 (2%)

Query: 22  PVHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLREHKA 81
           PV  P  G     + L    +  A ID A +AF AWR     RR +++  F E+L   K 
Sbjct: 27  PVTNPATGQITGRLALANLEDARAVIDAAAAAFPAWRDTSLARRTQVLFSFRELLNARKG 86

Query: 82  DLGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETWHPLG 141
           +L E+++ E GK+  + LGE+    ++ +FA G+   L G    +      +     PLG
Sbjct: 87  ELAEIITAEHGKVLSDALGEISRGQEVVEFACGIPHLLKGGYTENASTKVDVYSIRQPLG 146

Query: 142 VVGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFGDAPA 201
            VG+IS FNFP  V  W   +A+ AGN+V+ KPSEK P  A+    L+ +A       P 
Sbjct: 147 PVGIISPFNFPAMVPMWFFPVAIAAGNTVILKPSEKDPTAAIWLAELWAEA-----GLPP 201

Query: 202 GLAQLVIGGREAGEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILELGG-NNAMI 260
           G+  ++ G + A + ++++  V  +S  GST + + V     A  G+ +  LGG  N  I
Sbjct: 202 GVFNVLQGDKLAVDELLENKAVKAISFVGSTPIAQYVYATGTAN-GKRVQALGGAKNHAI 260

Query: 261 LAPSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKVRIGDPRK 320
           + P ADLDLA   ++ +  G+AG+RC  +  L+    I DE+VA++      +  GD  K
Sbjct: 261 VLPDADLDLAADAMVNAGFGSAGERCMAISALVAVGDIADELVAKIVERTTPLVTGDGTK 320

Query: 321 DNLVGPLIDKQSFDAMQGALAKARDEGGQ-VFGGERQLADQYPNAYYVSPAIAE-MPAQS 378
           ++ +GPL+ K   D +   +     +G   V  G    AD  P+ +++ P + + +    
Sbjct: 321 NSDMGPLVTKAHRDKVASYVDAGEKDGATIVVDGRTVQADGGPDGFWLGPTLIDHVTTDM 380

Query: 379 DVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERFQSASGSDCGIA 438
            +   E F P+L V+  D +++AL L N  P G  + IFT D   A RFQ+    + G+ 
Sbjct: 381 SIYTDEIFGPVLSVVRVDTYDQALELINNNPYGNGTAIFTNDGGAARRFQNE--VEVGMI 438

Query: 439 NVNIGTSGAEIGGAFGGEKET 459
            +N+         +FGG K +
Sbjct: 439 GINVPIPVPMAYYSFGGWKNS 459


Lambda     K      H
   0.318    0.135    0.396 

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: 548
Number of extensions: 29
Number of successful extensions: 5
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: 496
Length of database: 501
Length adjustment: 34
Effective length of query: 462
Effective length of database: 467
Effective search space:   215754
Effective search space used:   215754
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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