GapMind for Amino acid biosynthesis

 

Aligments for a candidate for argD in Sinorhizobium meliloti 1021

Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate SM_b20277 SM_b20277 hypothetical protein

Query= curated2:Q9JTX9
         (397 letters)



>lcl|FitnessBrowser__Smeli:SM_b20277 SM_b20277 hypothetical protein
          Length = 447

 Score =  209 bits (532), Expect = 1e-58
 Identities = 146/414 (35%), Positives = 212/414 (51%), Gaps = 47/414 (11%)

Query: 18  RASGSRVWDTEGREYIDFSGGIAVNALGHCHPALVDALNAQMHKLWHI-SNIYTTRPAQE 76
           R  G R++D EGR YID SGG AV+ LGH HP ++ AL+AQ+ ++ +  +  +TT  A+ 
Sbjct: 18  RGEGIRLFDAEGRAYIDASGGAAVSCLGHAHPDVLAALHAQLDRIAYAHTGFFTTEAAER 77

Query: 77  LAQKLVANS--FADKVFFCNSGSEANEAALKLARKYARDRFGGGKSEIVACINSFHGRTL 134
           LA +LVA++    D V+  + GSEA EAALK+AR+Y  ++    +  I+A   S+HG TL
Sbjct: 78  LADRLVADAPDGLDHVYLVSGGSEAVEAALKMARQYFVEKGEPQRRHIIARRQSYHGNTL 137

Query: 135 FTVSVGGQPKYSKDYAPLPQGITHVP-------------FNDIAA-----LEAAV----G 172
             ++ GG       + PL     H+                D AA     LEA +     
Sbjct: 138 GALAAGGNEWRRAQFRPLLVETHHIDPCFAYRLQQAGESDTDYAARAAGQLEAKILELGA 197

Query: 173 EQTCAVIIEPIQGES-GILPATAEYLQTARRLCDRHNALLILDEVQTGMGHTGRLFAYEH 231
           +Q  A + E + G + G +P  A+YL+  R +CD++  LLILDEV  GMG TG L A E 
Sbjct: 198 DQVIAFVAETVVGATAGAVPPVADYLKRVRAICDKYGVLLILDEVMCGMGRTGTLHACEQ 257

Query: 232 YGVVPDILSSAKALGCGF-PIGAMLATETIAAAFQPGT----HGSTFGGNPMACAVGSRA 286
            GVVPD+++ AK LG G+ P+GA+L +  I  AF  G+    HG T+ G+PMA A G   
Sbjct: 258 DGVVPDLMTIAKGLGGGYQPVGAVLLSSAIFQAFSEGSGFFQHGHTYMGHPMAAAAGLAV 317

Query: 287 FDIINAPETLHNVRSQGQKLQTALLDLGRKTGLFSQVRGMGLLLGCVLDAPYRGRA---- 342
            ++I     L NV S G  L+  L++          +RG GL     L A    ++    
Sbjct: 318 QEVIRRDGLLENVVSMGDYLERCLVERLGNHHHVGDIRGRGLFRAVELVADRATKSPFDP 377

Query: 343 -----SEITAAALKHGVMILVAG-------ADVLRFAPSLLLNDEDTAEGLRRL 384
                + I   A+  G+M+   G        D +  AP  +LN ED  + + RL
Sbjct: 378 GLKLNARIKKEAMARGLMVYPMGGTIDGQRGDHVLLAPPFILNREDVGQIVERL 431


Lambda     K      H
   0.321    0.136    0.406 

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: 457
Number of extensions: 22
Number of successful extensions: 6
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: 397
Length of database: 447
Length adjustment: 32
Effective length of query: 365
Effective length of database: 415
Effective search space:   151475
Effective search space used:   151475
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 (21.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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