GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Shewanella oneidensis MR-1

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 199805 SO0617 acetylornithine aminotransferase (NCBI ptt file)

Query= BRENDA::O30508
         (406 letters)



>FitnessBrowser__MR1:199805
          Length = 405

 Score =  532 bits (1371), Expect = e-156
 Identities = 257/397 (64%), Positives = 321/397 (80%)

Query: 7   QVERADFDRYMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKA 66
           ++ RA FD  MVPNYAPAA IPVRGEGSRVWDQ G E IDFAGGIAV  LGH HPALV A
Sbjct: 6   KLNRAQFDAVMVPNYAPAAVIPVRGEGSRVWDQEGNEFIDFAGGIAVNCLGHCHPALVNA 65

Query: 67  LTEQAQRIWHVSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDV 126
           L  Q +++WH+SNV TNEPAL LA KLV++TFAERV+ ANSGAEANEAA KLARRYA + 
Sbjct: 66  LKTQGEKLWHLSNVMTNEPALELATKLVNSTFAERVYFANSGAEANEAALKLARRYALEK 125

Query: 127 YGPQKYEIIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDK 186
           +G +K EIIA   +FHGRT FTV+VGGQ  YSDGFGPK + ITH+P+ND+ AL+AA+SDK
Sbjct: 126 HGVEKDEIIAFDKAFHGRTFFTVSVGGQAAYSDGFGPKPQSITHLPFNDVAALEAAVSDK 185

Query: 187 TCAVVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGV 246
           TCA++LEP+QGEGG++ A  A+L+  R+L ++HNAL++FDEVQ+G+GR GEL+AYM   +
Sbjct: 186 TCAIMLEPLQGEGGIIDADPAFLKAVRELANKHNALVIFDEVQTGVGRTGELYAYMGTDI 245

Query: 247 VPDILSSAKSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPE 306
           VPDIL++AK+LGGGFPI AMLTT EIA+HL VGTHG+TYGGNPLA A+  A LDV+NTPE
Sbjct: 246 VPDILTTAKALGGGFPIAAMLTTTEIAEHLKVGTHGSTYGGNPLACAIGNAVLDVVNTPE 305

Query: 307 VLDGVKAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAV 366
           VL+GVK + +  +  L KI ++Y +F E+RG GLL+GA L ++++G++RD L A+  E +
Sbjct: 306 VLNGVKHREQLLRDGLNKINEKYHVFSEVRGKGLLLGAVLNEQYQGRSRDFLVASVAEGL 365

Query: 367 MVLQASPDVVRFAPSLVIDDAEIDEGLERFERAVAKL 403
           M L A  +VVRFAPSLVI +A+I EGL RFERAVA +
Sbjct: 366 MSLMAGANVVRFAPSLVIPEADIAEGLARFERAVASI 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: 528
Number of extensions: 12
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: 405
Length adjustment: 31
Effective length of query: 375
Effective length of database: 374
Effective search space:   140250
Effective search space used:   140250
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