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_3674 Ga0059261_3674 adenosylmethionine-8-amino-7-oxononanoate transaminase

Query= reanno::Koxy:BWI76_RS11670
         (406 letters)



>FitnessBrowser__Korea:Ga0059261_3674
          Length = 415

 Score =  134 bits (336), Expect = 6e-36
 Identities = 100/300 (33%), Positives = 146/300 (48%), Gaps = 21/300 (7%)

Query: 29  EGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHT-GNGYTNEPVLRLA 87
           EG+ L    G+  ID      V   GH +PR+V A+ +QA K       G+T+EP   +A
Sbjct: 26  EGAVLHTADGRRVIDAISSWWVTTHGHGNPRIVAAIRDQAEKLDQLIFAGWTHEPAETVA 85

Query: 88  KQLIDATFA--DRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGRTLFT 145
           + L+       D VFF +SG+ + E A+K+A  +  +R G  +  I+  + ++HG T+  
Sbjct: 86  RDLVAMMPRPLDHVFFSDSGSTSVEVAIKMALGHFANR-GEPRHRIIVMQGSYHGDTIGG 144

Query: 146 VSAGGQPAYSQDFAPLPPQIQHAI-------YNDLDSAKALIDDNT--CAVIVEPMQ-GE 195
           +S G +  +++ +APL   +           Y  LD+ + L   +    A+IVEP+  G 
Sbjct: 145 MSVGARGVFNRSYAPLLFDVDTIPFPEGANEYRALDALEQLCAQSPLPAAMIVEPLVLGA 204

Query: 196 GGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLSTAKAL- 254
           GG+       LR +RE+C AH  L I DEV TG GRTG L A     V PDLL  +K L 
Sbjct: 205 GGMKMYPPGVLRAMREICAAHGVLFIADEVMTGWGRTGTLLACEQAAVVPDLLCLSKGLT 264

Query: 255 GGGFPIGALLA------SERCASVMTVGTHGTTYGGNPLACAVAGEVFATINTREVLNGV 308
           GG  P+   +A      S R      +  H ++Y  NP+ACA A    A      VL  V
Sbjct: 265 GGSLPLAVTMATPEIFESHRSKDRSKMFFHSSSYTANPIACAAAAANLAIWREEPVLERV 324


Lambda     K      H
   0.321    0.137    0.412 

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: 410
Number of extensions: 21
Number of successful extensions: 5
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: 415
Length adjustment: 31
Effective length of query: 375
Effective length of database: 384
Effective search space:   144000
Effective search space used:   144000
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: 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