GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapX in Phaeobacter inhibens BS107

Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate GFF2092 PGA1_c21250 aspartate aminotransferase AatA

Query= SwissProt::P16524
         (393 letters)



>FitnessBrowser__Phaeo:GFF2092
          Length = 400

 Score =  209 bits (531), Expect = 1e-58
 Identities = 134/373 (35%), Positives = 204/373 (54%), Gaps = 20/373 (5%)

Query: 23  LVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKA 82
           L A   DVI L+ G+PDF TP ++K AA +AI    T YT   G  EL+QAV     +  
Sbjct: 26  LRAAGRDVIGLSAGEPDFDTPDNIKEAAIRAIQAGKTKYTAPDGIAELKQAVCDKFARDN 85

Query: 83  DFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDT 142
              Y   +++ + TG  Q +  A    L+PGDEV++P P +  Y  ++ L G  P+ V++
Sbjct: 86  GLEY-TPAQVSVGTGGKQILYNALMATLNPGDEVVIPAPYWVSYPDMVRLAGGTPICVES 144

Query: 143 TSH-GFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIA-ALLKGRNVFVLSD 200
           +   GFK+T   +E A+TP TK  V   PSNPTG      ELK++   LL+  +V+V++D
Sbjct: 145 SLETGFKITPDQLEAAITPKTKWFVFNSPSNPTGAGYHPNELKALTDVLLRHPHVWVMTD 204

Query: 201 EIYSELTYDRPHY----SIATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKV 256
           ++Y  L +D   +     I   L D+T+  NG+SK+++MTGWRIG+   PK +   + K+
Sbjct: 205 DMYEHLVFDDFTFCTPAQIEPKLYDRTLTCNGVSKAYAMTGWRIGYAAGPKPLIDAMRKI 264

Query: 257 HQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSM-GLDVVKPSGAF 315
              + S   +ISQ AA+EA+    D  L     +++R D V   L  + G+    P GAF
Sbjct: 265 QSQSTSNPCTISQWAAVEALNGTQDYILPNTAVFRRRRDLVISMLSQIEGVACPVPDGAF 324

Query: 316 YIFPSIKS-FGMTSFD---------FSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSM 365
           Y++PSI    G TS           F+ ALLE+A VA+V G+++        R+S+A + 
Sbjct: 325 YVYPSIAGLIGRTSAGGVAITDDEAFAKALLEEADVAVVHGAAYGL--SPNFRISYAAAD 382

Query: 366 DTLREGLDRLELF 378
           +TL E   R+++F
Sbjct: 383 ETLTEACRRIQVF 395


Lambda     K      H
   0.319    0.135    0.388 

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: 353
Number of extensions: 23
Number of successful extensions: 7
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: 393
Length of database: 400
Length adjustment: 31
Effective length of query: 362
Effective length of database: 369
Effective search space:   133578
Effective search space used:   133578
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