GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Escherichia coli BW25113

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate 1936874 b2870 hypothetical protein (NCBI)

Query= BRENDA::O93656
         (317 letters)



>FitnessBrowser__Keio:1936874
          Length = 396

 Score =  100 bits (248), Expect = 8e-26
 Identities = 92/346 (26%), Positives = 152/346 (43%), Gaps = 58/346 (16%)

Query: 5   LKGRDLLCLQDYTPEEIWTILETAKMLKIWQKIGKPHRLLEGKTLAMIFQKPSTRTRVSF 64
           L  +D L   + TP+E+  +L+ A  LK  +      ++        +F+  STRTR S+
Sbjct: 19  LHEKDFLLTWEQTPDELKQVLDVAAALKALRAENISTKVFNSGLGISVFRDNSTRTRFSY 78

Query: 65  EVAMAHLGGHALYLNAQDLQLRRGETIADTARVLSRYVDAIMAR---------VYDHK-- 113
             A+  LG     L+    Q+  GET+ +TA ++S   DAI  R          Y  +  
Sbjct: 79  ASALNLLGLAQQDLDEGKSQIAHGETVRETANMISFCADAIGIRDDMYLGAGNAYMREVG 138

Query: 114 -DVEDLAKYASVP----VINGLSDFSHPCQALADYMTIWEKKGTI---KGVKVVYV---- 161
             ++D  K   +P    ++N   D  HP Q++AD   + E  G++   KG K+       
Sbjct: 139 AALDDGYKQGVLPQRPALVNLQCDIDHPTQSMADLAWLREHFGSLENLKGKKIAMTWAYS 198

Query: 162 ---GDGNNVAHSLMIAGTKLGADVVVATPEGYEPDEKVIKWAEQNAAESGGSFELLHDPV 218
              G   +V   ++   T+ G DV +A PEGY+    V++ A+ NA  SGGSF  +    
Sbjct: 199 PSYGKPLSVPQGIIGLMTRFGMDVTLAHPEGYDLIPDVVEVAKNNAKASGGSFRQVTSME 258

Query: 219 KAVKDADVIYTDVWASMGQEAEAEERRKIFR----------------------PFQVNKD 256
           +A KDAD++Y   WA        EER ++ R                       +   ++
Sbjct: 259 EAFKDADIVYPKSWAPY---KVMEERTELLRANDHEGLKALEKQCLAQNAQHKDWHCTEE 315

Query: 257 LVKHAKP-DYMFMHCLPAH------RGEEVTDDVIDSPNSVVWDEA 295
           +++  +  + ++MHCLPA       +  EVT+ V +      + EA
Sbjct: 316 MMELTRDGEALYMHCLPADISGVSCKEGEVTEGVFEKYRIATYKEA 361


Lambda     K      H
   0.319    0.134    0.400 

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: 288
Number of extensions: 20
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 317
Length of database: 396
Length adjustment: 29
Effective length of query: 288
Effective length of database: 367
Effective search space:   105696
Effective search space used:   105696
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 (21.7 bits)
S2: 49 (23.5 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:

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