GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Acidovorax sp. GW101-3H11

Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate Ac3H11_3978 Aspartate carbamoyltransferase (EC 2.1.3.2)

Query= curated2:O27495
         (301 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3978
          Length = 320

 Score = 99.0 bits (245), Expect = 1e-25
 Identities = 96/318 (30%), Positives = 143/318 (44%), Gaps = 36/318 (11%)

Query: 3   HLLSVCDM--DNVVDLLDLADDYKEGKIRE----KILRGKTLAMIFEKSSTRTRVSFEVG 56
           HLLS+  +  D V  +LD A ++     RE     +LRGK++  +F ++STRTR +FE+ 
Sbjct: 17  HLLSIEGLPRDIVTHILDTAANFVSVNDREVKKVPLLRGKSVFNLFFENSTRTRTTFEIA 76

Query: 57  AFQMGAQPLYLSASDLQLGRGEPIADTARTLSRYVDGIMIRAISHSDVVELAGEASVP-- 114
           A ++ A  L L  +     +GE + DT   LS     + +   S S    L  +   P  
Sbjct: 77  AKRLSADVLNLDIARSSASKGESLLDTIANLSAMAADLFVVRHSESGAPYLIAQHVAPHV 136

Query: 115 -VIN-GLTDLEHPCQALADMQTIREKLGGFDGRLV-FVGD--GNNVCHSLLLITATLG-M 168
            VIN G     HP Q L DM TIR     F    V  VGD   + V  S +    TLG  
Sbjct: 137 HVINAGDGRHAHPTQGLLDMYTIRHYKKDFSNLTVAIVGDVLHSRVARSDIHGLTTLGCA 196

Query: 169 DMDVACPPGYEPDPGIREMAGKIADETGSRIRVIHDPSEAVRGADVVYTDVWVSMGYEDE 228
           ++ V  P    P           +D     +RV H   E ++ ADVV     + +  ++E
Sbjct: 197 EVRVVGPRTLVP-----------SDMAQMGVRVCHTLEEGIKDADVV-----IMLRLQNE 240

Query: 229 ------AEDRLEVFRPYQVNMELMELAAPEAIFMHCLPAVRGQETTAEVIDGPHSVVWDQ 282
                      E F+ + +  E ++LA P+AI MH  P  RG E  + V+DG  SV+  Q
Sbjct: 241 RMSGALLPSSQEYFKSFGLTQEKLQLAKPDAIVMHPGPINRGVEIDSAVVDGKQSVILPQ 300

Query: 283 AENRLHAQKAIMHWLMGD 300
               +  + A+M  + G+
Sbjct: 301 VTFGIAVRMAVMSIVAGN 318


Lambda     K      H
   0.320    0.137    0.405 

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: 206
Number of extensions: 10
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: 301
Length of database: 320
Length adjustment: 27
Effective length of query: 274
Effective length of database: 293
Effective search space:    80282
Effective search space used:    80282
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:

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