GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Thiomicrorhabdus arctica DSM 13458

Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (characterized)
to candidate WP_026329593.1 F612_RS0102765 alanine transaminase

Query= SwissProt::Q2RK33
         (390 letters)



>NCBI__GCF_000381085.1:WP_026329593.1
          Length = 398

 Score =  342 bits (877), Expect = 1e-98
 Identities = 160/386 (41%), Positives = 247/386 (63%), Gaps = 3/386 (0%)

Query: 5   RRIRELPPYLFARIEKKIAEARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPENHRY 64
           +RI  LPPY+F  + +  AEAR RG DII  G+G+PD  TP H++DKL+        HRY
Sbjct: 6   QRINRLPPYVFNIVGELKAEARRRGEDIIDFGMGNPDQDTPKHIVDKLIEVVQREGTHRY 65

Query: 65  PTSEGLLAFRQAVADWYQRLYGVDLDPRREVVTLIGSKEGIAHISLCYVDPGDINLVPDP 124
             S+G+   R+A+ +WY+  + V+LD   E V  IGSKEG+AH+++  VD GD  LVP+P
Sbjct: 66  SVSQGIPRLRKAICNWYKTKFDVELDYATEAVVTIGSKEGLAHLAMATVDKGDTVLVPNP 125

Query: 125 GYPVYNIGTLLAGGESYFMPLTAANGFLPDLGAIPSDVARRAKLMFINYPNNPTGAVADL 184
            YP++  G ++AG +   + +T    F  +L     +   + K++ +N+P NPT    +L
Sbjct: 126 AYPIHPFGFVIAGADVRHVKMTPDVDFFEELEKAIKESWPKPKMLILNFPGNPTTQTVEL 185

Query: 185 KFFQEVVEFARSYDLIVCHDAAYSEITYDGYRAPSFLQAPGAKEVGIEFNSVSKPYNMTG 244
           +FF+ V+  A+ +++ V HD AY++I +DGY APS LQ  GAK++ +EF ++SK YNM G
Sbjct: 186 EFFERVIAIAKEHNIWVIHDLAYADIVFDGYIAPSILQVEGAKDIAVEFYTLSKSYNMPG 245

Query: 245 WRLGWACGRADVIEALARIKSNIDSGAFQAVQYAGIAALTGPQEGLAEVRRVYQERRDII 304
           WR+G+  G   ++ AL RIKS +D G F  +Q A IAAL GPQE + E+  +Y+ RRD++
Sbjct: 246 WRVGFMVGNPTLVNALKRIKSYLDYGTFTPIQVAAIAALEGPQECVQEICDMYKLRRDVL 305

Query: 305 VEGFNSLGWHLEKPKATFYVWAPVPRGYT---SASFAEMVLEKAGVIITPGNGYGNYGEG 361
            EG N++GW +  PKAT ++WAP+P+ Y    S  F++ +L +A V ++PG G+G+YG+ 
Sbjct: 306 CEGLNTIGWPVVPPKATMFIWAPIPKEYKAMGSIEFSKKLLTEAKVAVSPGIGFGDYGDD 365

Query: 362 YFRIALTISKERMQEAIERLRRVLGK 387
           + R  L  ++ R ++AI  +R +  K
Sbjct: 366 HVRFGLIENEHRTRQAIRGIRDMFRK 391


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: 440
Number of extensions: 19
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: 398
Length adjustment: 31
Effective length of query: 359
Effective length of database: 367
Effective search space:   131753
Effective search space used:   131753
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 Apr 10 2024. The underlying query database was built on Apr 09 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