GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapX in Sinorhizobium meliloti 1021

Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate SMc01578 SMc01578 aspartate aminotransferase

Query= SwissProt::P16524
         (393 letters)



>FitnessBrowser__Smeli:SMc01578
          Length = 400

 Score =  223 bits (569), Expect = 6e-63
 Identities = 144/378 (38%), Positives = 213/378 (56%), Gaps = 20/378 (5%)

Query: 18  RKFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLY 77
           +K   L A+  DVI L  G+PDF TP ++K AA  AID   T YTP +G  ELR+A+   
Sbjct: 21  QKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETKYTPVSGIPELREAIAKK 80

Query: 78  MKKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKP 137
            K++ + +Y A ++ I+ TG  Q +  AF   L+PGDEV++P P +  Y  ++ LCG  P
Sbjct: 81  FKRENNLDYTA-AQTIVGTGGKQILFNAFMATLNPGDEVVIPAPYWVSYPEMVALCGGTP 139

Query: 138 VIVDT-TSHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIA-ALLKGRNV 195
           V V T   + FKL A  ++ A+TP TK  V   PSNP+G   S EELK++   L+K  +V
Sbjct: 140 VFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSHEELKALTDVLMKHPHV 199

Query: 196 FVLSDEIYSELTYDRPHYS----IATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAK 251
           +VL+D++Y  LTY    ++    +   L ++T+ +NG+SK+++MTGWRIG+   P  + K
Sbjct: 200 WVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAMTGWRIGYAAGPLHLIK 259

Query: 252 HILKVHQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRL-VSMGLDVVK 310
            +  +     S A+SI+Q AA+EA+    D     +E ++ R D V   L  + G+    
Sbjct: 260 AMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRDLVVSMLNQAKGISCPT 319

Query: 311 PSGAFYIFPSIKS-FGMTS---------FDFSMALLEDAGVALVPGSSFSTYGEGYVRLS 360
           P GAFY++PS     G T+          DF   LLE  GVA+V GS+F   G  + R+S
Sbjct: 320 PEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAVVHGSAFG-LGPNF-RIS 377

Query: 361 FACSMDTLREGLDRLELF 378
           +A S   L E   R++ F
Sbjct: 378 YATSEALLEEACRRIQRF 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: 354
Number of extensions: 21
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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