GapMind for catabolism of small carbon sources

 

Aligments for a candidate for arcB in Escherichia coli BW25113

Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate 18270 b4245 aspartate carbamoyltransferase catalytic subunit (NCBI)

Query= curated2:A1ATU5
         (305 letters)



>lcl|FitnessBrowser__Keio:18270 b4245 aspartate carbamoyltransferase
           catalytic subunit (NCBI)
          Length = 311

 Score = 91.7 bits (226), Expect = 2e-23
 Identities = 98/323 (30%), Positives = 149/323 (46%), Gaps = 48/323 (14%)

Query: 3   RHFLSLHDYTKEELDRLLALAIELKQEQKQGGEHHLLKGKTLAMIFDKSSTRTRISFEVG 62
           +H +S++D ++++L+ +LA A +LK   +      LLK K +A  F ++STRTR+SFE  
Sbjct: 8   KHIISINDLSRDDLNLVLATAAKLKANPQP----ELLKHKVIASCFFEASTRTRLSFETS 63

Query: 63  IYQLGGH--GLFISTGTSQMGRGEPLKDTARVLSRYCDGIMIRTFGQEIVDELAA--YAT 118
           +++LG    G   S  TS   +GE L DT  V+S Y D I++R   QE    LA      
Sbjct: 64  MHRLGASVVGFSDSANTSLGKKGETLADTISVISTYVDAIVMR-HPQEGAARLATEFSGN 122

Query: 119 VPVIN-GLTDLFHPCQIMADVMTVMEHKGGYAGLKFAWVGDGNNMANTWIEAAAIFGFD- 176
           VPV+N G     HP Q + D+ T+ E +G    L  A VGD            A+  FD 
Sbjct: 123 VPVLNAGDGSNQHPTQTLLDLFTIQETQGRLDNLHVAMVGDLKYGRTVHSLTQALAKFDG 182

Query: 177 --------LALACPQGYEP--DAKVMAWAAERAPGRVTLTAD-------PKEAVSGAHVI 219
                    ALA PQ      D K +AW+   +   V    D        KE +  +   
Sbjct: 183 NRFYFIAPDALAMPQYILDMLDEKGIAWSLHSSIEEVMAEVDILYMTRVQKERLDPSEYA 242

Query: 220 NTDVWASMGMEAEQKVREQAFGGFCLDDALAGLAHPDHIVLHCLPAHRGEEISDSVIEGS 279
           N  V A   + A             L +A A +      VLH LP  R +EI+  V +  
Sbjct: 243 N--VKAQFVLRASD-----------LHNAKANMK-----VLHPLP--RVDEIATDVDKTP 282

Query: 280 NSRVWDEAENRLHAQKAIMATLM 302
           ++  + +A N + A++A++A ++
Sbjct: 283 HAWYFQQAGNGIFARQALLALVL 305


Lambda     K      H
   0.320    0.135    0.409 

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: 203
Number of extensions: 13
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: 305
Length of database: 311
Length adjustment: 27
Effective length of query: 278
Effective length of database: 284
Effective search space:    78952
Effective search space used:    78952
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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