GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Sphingomonas koreensis DSMZ 15582

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate Ga0059261_4131 Ga0059261_4131 Ornithine/acetylornithine aminotransferase

Query= BRENDA::O30508
         (406 letters)



>FitnessBrowser__Korea:Ga0059261_4131
          Length = 398

 Score =  289 bits (740), Expect = 9e-83
 Identities = 164/382 (42%), Positives = 221/382 (57%), Gaps = 10/382 (2%)

Query: 22  APAAFIPVRGEGSRVWDQSGRE-LIDFAGGIAVTSLGHAHPALVKALTEQAQRIWHVSNV 80
           AP AF   RGEG+ ++   G E  +D   G+A  +LGH HP LV AL  QA ++WH+SN+
Sbjct: 12  APIAFD--RGEGAWLYPVDGGEPYLDCVAGVATNALGHCHPVLVAALEAQAAKLWHISNM 69

Query: 81  FTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIAASNS 140
           F       LA +L  A+FA+ VF  NSG EA E A K+ARRY      PQ+  +I  S +
Sbjct: 70  FEMPGQNALAERLTTASFADTVFFTNSGTEAVECAIKVARRYHAARGEPQRQTVIGFSGA 129

Query: 141 FHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDK-TCAVVLEPIQGEG 199
           FHGRT   +N  G P + DGFG +  G  H   ++  AL  AI+D  T AVV+EP+QGEG
Sbjct: 130 FHGRTYGAMNAAGNPAHLDGFGDRLPGFVHFAVDNWPALALAIADSATAAVVVEPVQGEG 189

Query: 200 GVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHY-GVVPDILSSAKSLG 258
           G     + +L+  R  C  H  LL++DEVQ+GMGR G+LFA+  Y    PDI++ AK+LG
Sbjct: 190 GARAMTEPFLDKLRAACTAHGVLLIYDEVQTGMGRTGKLFAHQWYPDATPDIMALAKALG 249

Query: 259 GGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGVKAKHERF 318
            GFP+GA L T E A  +  G HGTT GGNPLA AVA AA D I  PE L   +   +  
Sbjct: 250 SGFPVGACLATAEAASGMVPGVHGTTAGGNPLAMAVAIAAFDEIAKPETLTHAREVAQHL 309

Query: 319 KSRLQKIGQEY-GIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVLQASPDVVR 377
           ++ L ++   + G+  EIRG GLL+G  L        R  + AA ++ ++V     + VR
Sbjct: 310 RAGLDRLAATHPGVISEIRGKGLLVGVRLVP----NNRAFMAAAREQRLLVAGGGDNCVR 365

Query: 378 FAPSLVIDDAEIDEGLERFERA 399
             P L +  AE D+ L+R + A
Sbjct: 366 LLPPLTLTVAEADQILDRLDTA 387


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: 421
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: 398
Length adjustment: 31
Effective length of query: 375
Effective length of database: 367
Effective search space:   137625
Effective search space used:   137625
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