GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Dyella japonica UNC79MFTsu3.2

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate N515DRAFT_3308 N515DRAFT_3308 acetylornithine/N-succinyldiaminopimelate aminotransferase

Query= BRENDA::O30508
         (406 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3308
          Length = 411

 Score =  368 bits (945), Expect = e-106
 Identities = 193/393 (49%), Positives = 258/393 (65%), Gaps = 3/393 (0%)

Query: 15  RYMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRI 74
           RY +P Y P   +   G+G+RVWD  GR+ +D   GIAV +LGH  P LV AL  QA+++
Sbjct: 16  RYWLPVYRPREVVLDHGKGARVWDTEGRDYVDLGAGIAVNALGHQDPDLVDALVTQARKL 75

Query: 75  WHVSNVFTNEPALRLARKLVDAT-FAERVFLANSGAEANEAAFKLARRYA-NDVYGPQKY 132
           WH SNVF  EP L LA +LV A+ FAERVFL NSG EANEAA KL R++A +    P++ 
Sbjct: 76  WHSSNVFYTEPPLHLAEELVQASGFAERVFLCNSGTEANEAAIKLVRKWAASKGRAPEQR 135

Query: 133 EIIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISD-KTCAVV 191
            I+    SFHGRTL  V    QPKY + + P   G  ++ +ND+  L+AA +     AV+
Sbjct: 136 VILTFRGSFHGRTLAAVTATAQPKYQENYEPLPGGFRYLDFNDVAGLEAAFAQGDVAAVM 195

Query: 192 LEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDIL 251
           LEP+QGEGGVLPA  A++  AR+LCD H ALLV DE+Q GMGR G LFA+   GV PDI+
Sbjct: 196 LEPVQGEGGVLPASPAFIRRARELCDTHEALLVLDEIQCGMGRTGTLFAHAQDGVTPDIV 255

Query: 252 SSAKSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGV 311
           + AK+LG GFPIGAML   ++A+ +  G HGTT+GGNP+A+AVA  AL  + + E++  V
Sbjct: 256 TLAKALGCGFPIGAMLAGPKVAEVMQYGAHGTTFGGNPMAAAVARVALRKLASAELMANV 315

Query: 312 KAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVLQA 371
             + +  +  L  I  E  +F E+RG GL++GA L + +KG+A +VL+ A    ++VLQA
Sbjct: 316 AKQAQALRDGLAAIDGELKLFAEVRGRGLMLGAVLAEAYKGRAGEVLDHAAAHGLLVLQA 375

Query: 372 SPDVVRFAPSLVIDDAEIDEGLERFERAVAKLV 404
            PDV+RF P L I DA++ EGL R   A+A  V
Sbjct: 376 GPDVLRFVPPLNITDADLAEGLARLRAALADFV 408


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: 484
Number of extensions: 21
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: 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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