GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Lentibacillus jeotgali Grbi

Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (characterized)
to candidate WP_010529652.1 ON01_RS03640 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme

Query= SwissProt::Q2RK33
         (390 letters)



>NCBI__GCF_000224785.1:WP_010529652.1
          Length = 392

 Score =  372 bits (956), Expect = e-108
 Identities = 178/379 (46%), Positives = 250/379 (65%)

Query: 6   RIRELPPYLFARIEKKIAEARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPENHRYP 65
           ++  LPPYLF+ I++   + +E GVD+I LGIG PD+PTP  ++DKL  E+  P NHRY 
Sbjct: 7   KVSNLPPYLFSEIQQMKKKLQEDGVDVIDLGIGAPDLPTPDFIVDKLAEESKIPANHRYS 66

Query: 66  TSEGLLAFRQAVADWYQRLYGVDLDPRREVVTLIGSKEGIAHISLCYVDPGDINLVPDPG 125
              G   FR+AVA +Y++ Y VDLD   EV+ +IGSKEGIA++    ++PGD+ LVPDPG
Sbjct: 67  AYSGSKEFREAVAHFYKKQYDVDLDTETEVLAVIGSKEGIANLMHATINPGDMVLVPDPG 126

Query: 126 YPVYNIGTLLAGGESYFMPLTAANGFLPDLGAIPSDVARRAKLMFINYPNNPTGAVADLK 185
           YPVY     LAGG+S  +PL   NG+ P    +  +   +AKLM +NYP NPT A A+  
Sbjct: 127 YPVYETAVHLAGGKSAALPLDDTNGYAPLYDHVDQESINQAKLMLLNYPGNPTAATANYD 186

Query: 186 FFQEVVEFARSYDLIVCHDAAYSEITYDGYRAPSFLQAPGAKEVGIEFNSVSKPYNMTGW 245
            F + V  +R+  L++ +DAAY  IT+ GY+APS LQ P AKE+ +EF S+SK +NMTGW
Sbjct: 187 TFLKAVALSRANQLLLVNDAAYDMITFKGYKAPSVLQVPDAKELAVEFGSLSKSFNMTGW 246

Query: 246 RLGWACGRADVIEALARIKSNIDSGAFQAVQYAGIAALTGPQEGLAEVRRVYQERRDIIV 305
           R+G+  G  +VI ALA  KSNID+  F  +Q A  AAL      + +   +YQ+R + + 
Sbjct: 247 RIGYVVGNREVISALATFKSNIDTSQFLPIQKAAAAALRSDFSAVKKHNTIYQQRMEKLY 306

Query: 306 EGFNSLGWHLEKPKATFYVWAPVPRGYTSASFAEMVLEKAGVIITPGNGYGNYGEGYFRI 365
           + F  LG   +KP  T ++WA VP G+TS SFA  +L + GVI+TPGN +G+ GEGYFR+
Sbjct: 307 KAFKKLGIKADKPNGTIFLWAKVPDGFTSMSFANKLLHEGGVIVTPGNAFGSRGEGYFRV 366

Query: 366 ALTISKERMQEAIERLRRV 384
           ALT++ ER+ + I R+ ++
Sbjct: 367 ALTVTSERLDDVIVRMSQL 385


Lambda     K      H
   0.320    0.139    0.421 

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: 452
Number of extensions: 15
Number of successful extensions: 1
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: 390
Length of database: 392
Length adjustment: 31
Effective length of query: 359
Effective length of database: 361
Effective search space:   129599
Effective search space used:   129599
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 26 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