GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argI 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)



>FitnessBrowser__Keio:18270
          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 Aug 03 2021. The underlying query database was built on Aug 03 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