GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argI in Marinobacter adhaerens HP15

Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate GFF3565 HP15_3507 aspartate carbamoyltransferase

Query= curated2:O27495
         (301 letters)



>FitnessBrowser__Marino:GFF3565
          Length = 327

 Score =  112 bits (281), Expect = 9e-30
 Identities = 95/318 (29%), Positives = 148/318 (46%), Gaps = 34/318 (10%)

Query: 1   MKHLLSVCDMDNVV--DLLDLADDYKEGKIRE----KILRGKTLAMIFEKSSTRTRVSFE 54
           ++H L++  +D  +  D+LD AD + E   R      +LRG+T+  +F +SSTRTR +FE
Sbjct: 9   LRHFLTLDGLDRALLTDILDTADSFIEVGERTIKKVPLLRGRTVVNLFFESSTRTRSTFE 68

Query: 55  VGAFQMGAQPLYLSASDLQLGRGEPIADTARTLSRYVDGIMIRAISHSDVVELAGEASVP 114
           + A ++ A  L L  S     +GE ++DT   L      + +   S S       E+  P
Sbjct: 69  LAAKRLSADVLNLDISTSATSKGESLSDTLLNLEAMASDMFVVRHSQSGAPHFIAESVTP 128

Query: 115 ---VIN-GLTDLEHPCQALADMQTIREKLGGFDG-RLVFVGD--GNNVCHSLLLITATLG 167
              +IN G     HP QA+ DM TIR+  G F+G ++  VGD   + V  S +     LG
Sbjct: 129 GVAIINAGDGRHAHPTQAMLDMLTIRQHKGRFEGLKVAIVGDVLHSRVARSQIRALNELG 188

Query: 168 MDMDVACPPGYEPDPGIREMAGKIADETGSRIRVIHDPSEAVRGADVVYTDVWVSMGYED 227
            +      PG         +  K  +  G  +   +D +  ++  DVV     + +  + 
Sbjct: 189 AEEVRVIAPG--------TLLPKDVESLGCTVE--YDMTRGMKDLDVV-----IMLRLQK 233

Query: 228 EAED------RLEVFRPYQVNMELMELAAPEAIFMHCLPAVRGQETTAEVIDGPHSVVWD 281
           E  +        E +R Y +N + + LA PE I MH  P  RG E  + V DGP SV+ +
Sbjct: 234 ERMEGALLPSEREFYRLYGLNQQKLALAHPECIVMHPGPINRGVEIESAVADGPQSVILN 293

Query: 282 QAENRLHAQKAIMHWLMG 299
           Q  N +  + A+M   MG
Sbjct: 294 QVTNGIAIRMAVMSMAMG 311


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: 219
Number of extensions: 10
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: 301
Length of database: 327
Length adjustment: 27
Effective length of query: 274
Effective length of database: 300
Effective search space:    82200
Effective search space used:    82200
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