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

Query= SwissProt::P18335
         (406 letters)



>FitnessBrowser__MR1:200454
          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:

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