GapMind for Amino acid biosynthesis

 

Aligments for a candidate for dapC in Magnetospirillum magneticum AMB-1

Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate WP_043742980.1 AMB_RS00085 aspartate aminotransferase

Query= BRENDA::Q9ZEX3
         (397 letters)



>lcl|NCBI__GCF_000009985.1:WP_043742980.1 AMB_RS00085 aspartate
           aminotransferase
          Length = 399

 Score =  251 bits (642), Expect = 2e-71
 Identities = 158/398 (39%), Positives = 213/398 (53%), Gaps = 18/398 (4%)

Query: 1   MNPRLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLS 60
           ++ RLD L  YPF +L  LL    +P   +    +SIGEP+H  PA V + +AAN +   
Sbjct: 7   LDARLDGLPDYPFARLAKLLGAPARPDSTV----MSIGEPQHRPPALVAEVLAANTSSWG 62

Query: 61  VYPSTKGEPALRQAISQWLSRRYSIPAP--DPESEVLPVLGSREALFAFAQTVIDPSAG- 117
            YP   G   LRQA++ W  RRY +P    DPE  +LPV G+REAL+  AQTV     G 
Sbjct: 63  KYPPANGPAELRQAVADWAGRRYDLPQGLIDPEKAILPVAGTREALYLIAQTVCGDREGQ 122

Query: 118 -ALVVCPNPFYQIYEGAALLAGATPYYVNA--DPARDFGLRTGRVPDEVWRRTQLVFVCS 174
             LV+ PNPFYQ+Y GAA++AGA P +V     PA      T  +P ++  RT L +VCS
Sbjct: 123 RPLVLMPNPFYQVYAGAAVMAGAEPVFVPGANGPASQPDFST--LPADLLDRTALAYVCS 180

Query: 175 PGNPAGNVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRY 234
           P NP G+V            +  HGFV+A  ECYSEI+  +  PP G L+    LG +  
Sbjct: 181 PANPQGSVADAALLERQVRTARDHGFVLAVDECYSEIW--DKVPPPGVLKTCAALG-EGL 237

Query: 235 TNLVAFSSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAW-SMR 293
            N++ F+SLSKRS+VPG+RSG V GD  ++  F   R+Y G+A    ++AA+ A W    
Sbjct: 238 ANVLMFNSLSKRSSVPGLRSGVVVGDERVIHAFARLRSYGGAATPLPIAAAAAALWRDEA 297

Query: 294 RMCRKTAQYRAKFEAVLPILQNVLDVRAPQASFYLWAGTPGSDTAFARELYGRTGVTVLP 353
            +      YRAK +    +L        P   F+LW    G   A A +L+    + VLP
Sbjct: 298 HVTESNDLYRAKLDVAERVLGGRFGFYRPPGGFFLWLDV-GDGEAAAVKLWQEGNIRVLP 356

Query: 354 GSLLARE-AHNANPGQGRIRIALVAPLDQCVQAAERIA 390
           G+ LA E +   NPG   IR+ALV  L     A  R+A
Sbjct: 357 GAYLAAEDSEEGNPGSRFIRVALVHDLAGTEAALTRLA 394


Lambda     K      H
   0.321    0.135    0.412 

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: 551
Number of extensions: 34
Number of successful extensions: 9
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: 397
Length of database: 399
Length adjustment: 31
Effective length of query: 366
Effective length of database: 368
Effective search space:   134688
Effective search space used:   134688
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 preprint 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