GapMind for Amino acid biosynthesis

 

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

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate H281DRAFT_06478 H281DRAFT_06478 succinylornithine aminotransferase apoenzyme

Query= BRENDA::O30508
         (406 letters)



>FitnessBrowser__Burk376:H281DRAFT_06478
          Length = 411

 Score =  506 bits (1303), Expect = e-148
 Identities = 239/397 (60%), Positives = 308/397 (77%)

Query: 8   VERADFDRYMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKAL 67
           V R  FD  MVP +APAAF+P RG GSRVWD  GR+ IDFAGGIAVT+LGHAHP L+K L
Sbjct: 6   VTRKTFDEVMVPVFAPAAFVPDRGLGSRVWDTQGRDYIDFAGGIAVTALGHAHPELLKVL 65

Query: 68  TEQAQRIWHVSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVY 127
            EQ  ++WH+ N +TNEP LRLAR+L + TFA+R F ANSGAEANEAA KLARR A + +
Sbjct: 66  HEQGSKLWHIGNGYTNEPVLRLARRLEELTFADRAFFANSGAEANEAALKLARRVAFERH 125

Query: 128 GPQKYEIIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDKT 187
           G  KYEII+ + SFHGRT FTV+VGGQPKYS+GFGP  +GI H+PYND++A + AI  KT
Sbjct: 126 GADKYEIISFTQSFHGRTFFTVSVGGQPKYSEGFGPVPQGIVHLPYNDIQAAQKAIGAKT 185

Query: 188 CAVVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVV 247
           CAV++EPIQGEGGV+PA  A+L+  R+ CD+H ALL+FDEVQ+G+GR G  +AY   GV 
Sbjct: 186 CAVIVEPIQGEGGVIPADPAFLKALREACDQHGALLIFDEVQTGVGRSGYFYAYQDTGVT 245

Query: 248 PDILSSAKSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEV 307
           PDIL++AK+LG GFPIGAMLTT E+A H  VG HGTTYGGNPL SA+AE  +++I+ P++
Sbjct: 246 PDILTTAKALGNGFPIGAMLTTNELAAHFKVGVHGTTYGGNPLGSAIAEKVVELISDPKL 305

Query: 308 LDGVKAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVM 367
           L+GV+ + E  K  L K+ + +G+FDE+RG GLLIGA LTD +KG+A+D + AA +  V+
Sbjct: 306 LEGVRTRSEVLKGHLAKLNERFGLFDEVRGKGLLIGAQLTDAYKGRAKDFVTAAGQHGVI 365

Query: 368 VLQASPDVVRFAPSLVIDDAEIDEGLERFERAVAKLV 404
           +L A PDV+RF PSL++   +++EG ER  +A+A +V
Sbjct: 366 MLMAGPDVLRFVPSLIMPLDDMNEGFERLAKAIADVV 402


Lambda     K      H
   0.318    0.135    0.394 

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: 554
Number of extensions: 16
Number of successful extensions: 1
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: 406
Length of database: 411
Length adjustment: 31
Effective length of query: 375
Effective length of database: 380
Effective search space:   142500
Effective search space used:   142500
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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