Alignments for a candidate for DAPtransferase in Lentibacillus jeotgali Grbi

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_029329002.1 ON01_RS05560 LL-diaminopimelate aminotransferase

Query= SwissProt::Q6LX26
         (416 letters)



>NCBI__GCF_000224785.1:WP_029329002.1
          Length = 412

 Score =  469 bits (1206), Expect = e-137
 Identities = 226/412 (54%), Positives = 297/412 (72%), Gaps = 5/412 (1%)

Query: 4   YIQNLFAERIGGKSFGKEDVIYKFEKIKRAKQAAKLKYPDMELIDMGVGEPDEMADESVV 63
           YIQ LFAERIGG  FG +   +KFEKIK+AK+ A   +P+ ELIDMGVGEPD MA +  V
Sbjct: 6   YIQKLFAERIGGSDFGVKTSDFKFEKIKKAKREAINAHPETELIDMGVGEPDSMAAQPFV 65

Query: 64  EVLCEEAKKHVNRGYSDNGVQALKDEIPIYLEKIFGVKDLDPVNEVVHSIGSKPALAYIT 123
             L EE++K  NR YSDNG+   K     Y+  +F V DL P  E+ H+IG K AL+ + 
Sbjct: 66  NTLAEESQKPENRFYSDNGIDEFKQAATAYMRNVFNVSDLHPETEINHAIGVKSALSILP 125

Query: 124 SVFINPGDVTLMTVPGYPVTATHTKWYGGSVETLPLLEKNNFLPELDAISKEVRENAKIL 183
             FINPGD+T+M  P YPV  THT++ GG V  LP+   N+FLPELD++S +V E AK+L
Sbjct: 126 KAFINPGDITIMPTPNYPVLGTHTEYLGGEVVYLPIHADNSFLPELDSLSDDVLEKAKLL 185

Query: 184 YLNYPNNPTGAQATKKFYKEAVDFAFENDLIVIQDAAYAALTYGDKPLSFLSVKDAKEVG 243
           YLNYPNNPTGA AT++F++E V FA  ++LIVI DAAYA+L + +KPLSFLSV  AK+VG
Sbjct: 186 YLNYPNNPTGAVATREFFEEVVAFAKRHELIVIHDAAYASLVFDEKPLSFLSVPGAKDVG 245

Query: 244 VEIHSFSKAYNMTGWRLAFVAGNELIVRGFAAVKDNYDSGQFIPIQKAGIHCLRHPEITE 303
           +E+HS SK++NMTGWR+ FVAGN  ++  F  +KDN DSGQFIPIQKA  H L HPEITE
Sbjct: 246 IELHSLSKSFNMTGWRIGFVAGNAKLISAFKTIKDNSDSGQFIPIQKAASHALAHPEITE 305

Query: 304 KTRAKYERRLSKMVKILKEAGFNAKMPGGTFYLYVKAPIGTKDGAKFANAEEFSQFMIKE 363
           +T AKY RR+  +VK+L+E GF  + P G+F+LY + P   + G  F +AEEFS ++IK 
Sbjct: 306 QTAAKYSRRMDILVKVLREQGFQVEKPEGSFFLYTRIPKAVEGGPGFQSAEEFSHYLIKN 365

Query: 364 KLISTVPWDDAGNFVRMAACFEAFKDGEISIEEEDRILNEVKRRLTEVEFVF 415
            LISTVPWDDAG++VR++  F+A +     + EE+R+L E+ +RL+ V+F+F
Sbjct: 366 LLISTVPWDDAGSYVRLSVTFQAER-----VTEEERVLGEIGKRLSTVKFIF 412


Lambda     K      H
   0.317    0.136    0.391 

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: 538
Number of extensions: 13
Number of successful extensions: 2
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: 416
Length of database: 412
Length adjustment: 31
Effective length of query: 385
Effective length of database: 381
Effective search space:   146685
Effective search space used:   146685
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the original 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

GapMind for Amino acid biosynthesis