GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argI in Paraburkholderia bryophila 376MFSha3.1

Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate H281DRAFT_04817 H281DRAFT_04817 aspartate carbamoyltransferase

Query= curated2:O27495
         (301 letters)



>FitnessBrowser__Burk376:H281DRAFT_04817
          Length = 341

 Score =  104 bits (259), Expect = 3e-27
 Identities = 95/319 (29%), Positives = 149/319 (46%), Gaps = 34/319 (10%)

Query: 1   MKHLLSVCDMDNVV--DLLDLADDYKEGKIRE----KILRGKTLAMIFEKSSTRTRVSFE 54
           +KHLLS+  +   +   +LD A  +     RE     +LRGK++  +F ++STRTR +FE
Sbjct: 36  LKHLLSIEGLPKAIVNHILDTASQFVSVTDREVKKVPLLRGKSVFNLFFENSTRTRTTFE 95

Query: 55  VGAFQMGAQPLYLSASDLQLGRGEPIADTARTLS-RYVDGIMIRAISHSDVVELAGEAS- 112
           + A ++ A  L L+ +     +GE + DT   LS  + D  ++R  S      +A   + 
Sbjct: 96  IAATRLSADVLNLNINASSTSKGESLLDTINNLSAMHADMFVVRHASSGAPYLIAQHCAP 155

Query: 113 -VPVIN-GLTDLEHPCQALADMQTIREKLGGFDG-RLVFVGD--GNNVCHSLLLITATLG 167
            V VIN G     HP Q L DM TIR     F   R+  VGD   + V  S +    TLG
Sbjct: 156 HVHVINAGDGRHAHPTQGLLDMYTIRHYKKDFTNLRVAIVGDILHSRVARSDIHALTTLG 215

Query: 168 MDMDVACPPGYEPDPGIREMAGKIADETGSRIRVIHDPSEAVRGADVVYTDVWVSMGYED 227
           +    A  P      G+ +M           +RV H+  E ++  DV+     + +  ++
Sbjct: 216 VPEVRAIGPRTLLPGGLEQMG----------VRVFHNLDEGLKDVDVI-----IMLRLQN 260

Query: 228 E------AEDRLEVFRPYQVNMELMELAAPEAIFMHCLPAVRGQETTAEVIDGPHSVVWD 281
           E           E F+ + +  E + LA P+AI MH  P  RG E  ++V DGP SV+ +
Sbjct: 261 ERMSGALLPSAQEYFKSWGLTPERLALAKPDAIVMHPGPMNRGVEIDSQVADGPQSVILN 320

Query: 282 QAENRLHAQKAIMHWLMGD 300
           Q    +  + A+M  + G+
Sbjct: 321 QVTFGIAVRMAVMGIVAGN 339


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: 208
Number of extensions: 14
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: 341
Length adjustment: 28
Effective length of query: 273
Effective length of database: 313
Effective search space:    85449
Effective search space used:    85449
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