GapMind for Amino acid biosynthesis

 

Aligments 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 (characterized)
to candidate 200454 SO1276 4-aminobutyrate aminotransferase (NCBI ptt file)

Query= SwissProt::P18335
         (406 letters)



>lcl|FitnessBrowser__MR1:200454 SO1276 4-aminobutyrate
           aminotransferase (NCBI ptt file)
          Length = 425

 Score =  218 bits (556), Expect = 2e-61
 Identities = 136/394 (34%), Positives = 202/394 (51%), Gaps = 41/394 (10%)

Query: 30  KGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHIS-NVFTNEPALR 88
           + + + +WD +G+E++DFAGGIAV   GH HP +  A+  Q E   H    V   E  ++
Sbjct: 30  RAENASVWDVEGREFIDFAGGIAVLNTGHLHPKVKAAVAAQLEDFSHTCFMVLGYESYIQ 89

Query: 89  LGRKL---IEATFAERVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRS 145
           +  KL   +   FA++     SG+EA E A K+AR Y        +  +IAF + +HGR+
Sbjct: 90  VCEKLNQLVPGDFAKKTALFTSGSEAVENAVKVARAYTK------RAGVIAFTSGYHGRT 143

Query: 146 LFTVSVGGQ-PKYSDGFGPKPADIIHVPFNDLHAVKAVMDDHT----------------- 187
           +  +++ G+   YS G G   A++    F    A+  V DD                   
Sbjct: 144 MAALALTGKVAPYSKGMGLMSANVFRAEFPC--ALHGVSDDDAMASIERIFKNDAEPSDI 201

Query: 188 CAVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYGVT 247
            A+++EP+QGEGG  A +P F+Q LR LCD+   +L+ DEVQ G GRTG  FA    GV+
Sbjct: 202 AAIILEPVQGEGGFYAVSPAFMQRLRALCDREGIMLIADEVQTGAGRTGTFFAMEQMGVS 261

Query: 248 PDILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIINTPEV 307
            DI T AK++ GGFP+S +   A++  A  PG  G TYGGNPLACA A A  ++    ++
Sbjct: 262 ADITTFAKSIAGGFPLSGITGRAQVMDAIGPGGLGGTYGGNPLACAAALAVLEVFEEEKL 321

Query: 308 LEGIQAKRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAEL------KPQYKGRARDFLYAG 361
           LE   A   R    L  +  ++   +D+RG+G +   EL       PQY       L   
Sbjct: 322 LERANAIGDRIKSALNTMQVEHPQIADVRGLGAMNAIELMEDGKPAPQY---CAQILAEA 378

Query: 362 AEAGVMVLNAGP--DVMRFAPSLVVEDADIDEGM 393
              G+++L+ G   +V+R    L V D  +D G+
Sbjct: 379 RNRGLILLSCGTYGNVLRILVPLTVSDTQLDAGL 412


Lambda     K      H
   0.322    0.138    0.415 

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: 460
Number of extensions: 18
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: 425
Length adjustment: 31
Effective length of query: 375
Effective length of database: 394
Effective search space:   147750
Effective search space used:   147750
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