GapMind for Amino acid biosynthesis

 

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

Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (uncharacterized)
to candidate 201879 SO2741 adenosylmethionine--8-amino-7-oxononanoate aminotransferase (NCBI ptt file)

Query= curated2:Q7N9E5
         (403 letters)



>FitnessBrowser__MR1:201879
          Length = 461

 Score =  153 bits (387), Expect = 9e-42
 Identities = 125/418 (29%), Positives = 204/418 (48%), Gaps = 44/418 (10%)

Query: 18  PIYSPAQFIPVRG----QGSRVWDQHGKEYIDFAGGIAVVALGHCHPTLVDVLKQQGEKL 73
           P  S  + +PV G    QG  +    G++ ID          G+ HP ++  ++QQ  +L
Sbjct: 17  PYTSMTRALPVFGVHSAQGCELELVDGRKLIDGTSSWWACVHGYGHPAILTAMEQQLHQL 76

Query: 74  WHIS-NIFTNEPALILAQKLIDATFAE--RVFFANSGAEANEAAFKLARHYAIARHNPY- 129
            H+     T+EPA+ L +KL+  T     +VF  +SG+ A E A K+A  Y   +  P  
Sbjct: 77  SHVMFGGITHEPAIELCKKLLAMTCEPLTKVFLCDSGSIAVEVAIKMALQYWQGQDLPLA 136

Query: 130 ----KTKIIAFHQGFHGRTLFTVSV----GGQPKYADGFGPKPA--DIIHVPF------N 173
               K +I+   +G+HG T   +SV    GG          K    D    PF      +
Sbjct: 137 QKAQKQRILTVKKGYHGDTFAAMSVCDPEGGMHTMFGEAVIKQCFVDAPQTPFGESLHQD 196

Query: 174 DLDAVKAVIDDH---TCAVVLEPV-QGEGGVTAAAPAFIHGVRELCDKHQVLLVFDEVQS 229
           DL  ++ ++ +      AV++EP+ QG GG+   +  ++ G+R LCD++ VLL+ DE+ +
Sbjct: 197 DLAPMQRILREQHQDIAAVIIEPIMQGAGGMRFYSSEYLRGLRALCDEYNVLLILDEIAT 256

Query: 230 GMGRTGKLFSYMHYDVTPDIITTAKALGNGF-PISAMLTTVNIASVMTPG-----AHGTT 283
           G GRTGKLF+Y H D+TPDI+   KAL  G+  ++A L T N+A  ++        HG T
Sbjct: 257 GFGRTGKLFAYEHTDITPDILCLGKALTGGYISLAATLCTDNVAQGISQSPAGVFMHGPT 316

Query: 284 YGGNPLACAVANVAFDIINT---PAVLAGVEKRHNLMVNFLNDINQKYSIFGEIRGKGLL 340
           + GNPLACA A  + D+IN    PA +A +E++    +    DI         ++   +L
Sbjct: 317 FMGNPLACAAACASLDLINQQEWPAQVAAIEQQMQRELADAIDI-------PSVKAVRVL 369

Query: 341 IGAELKAPHQGKAKDILQLAAENGLMLLSAGGDVLRFTPSLIISEEEIAQGMERLEQV 398
               +   HQ      LQ    +  + +    +++   P  +IS  +++Q  + ++QV
Sbjct: 370 GAVGVLEMHQAVNTAALQQQFVDLGVWVRPFANLIYIMPPYVISSAQLSQLTQAMKQV 427


Lambda     K      H
   0.321    0.138    0.410 

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: 472
Number of extensions: 23
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: 403
Length of database: 461
Length adjustment: 32
Effective length of query: 371
Effective length of database: 429
Effective search space:   159159
Effective search space used:   159159
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: 51 (24.3 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