GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Trichormus variabilis ATCC 29413

Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_011316915.1 AVA_RS00085 aspartate aminotransferase

Query= curated2:B8CX89
         (389 letters)



>NCBI__GCF_000204075.1:WP_011316915.1
          Length = 403

 Score =  416 bits (1069), Expect = e-121
 Identities = 184/386 (47%), Positives = 272/386 (70%)

Query: 4   ADRIKNLPPYLFAEIDKMIARAKKEGVDVISFGIGDPDQPTPDNIINKMIEAVKDPSTHS 63
           ADRI+ LPPY+FA +D++ A+A+++G+D+I  G+G+PD  TP  +++  I+A+++P+ H 
Sbjct: 9   ADRIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQNPANHG 68

Query: 64  YPSYEGMYEYRKTVADWYKNNYGRELDPDKEVVSLIGSKEGIAHLPFCYINPGDIALVPD 123
           YP +EG   +R+ + +WY   YG  LDPD E + L+GSKEG++HL   Y+NPGD+ LVP 
Sbjct: 69  YPPFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPS 128

Query: 124 PGYPVYKTSVLLAGGKPVQVPLVEENNFLPDLKAIDEDIARKAKLFFINYPNNPTGAIAP 183
           P YP +    ++AGG    + L  EN++L DL AI E++ARKAK+ + NYP+NPTGA AP
Sbjct: 129 PAYPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAP 188

Query: 184 EEFYEELIDFADKYDIIIAHDAAYSEIGLDGYNPPSFMQFEGAKKVGIEFNSLSKPFNMT 243
            EF+EE++ FA KY+I++ HD  Y+E+  DGY P S ++  GAK +G+EF++LSK +NM 
Sbjct: 189 REFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMA 248

Query: 244 GWRVGWAVGRSDVIESLGRIKTNIDSGIFEAIQYAGIEALTGPEDNIEKMTELYSKRRDL 303
           GWRVG+ VG   VI+ L  +KTN+D GIF A+Q A   AL  P+  + ++ + Y  RRD 
Sbjct: 249 GWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDF 308

Query: 304 LVEGLRELGWEVPVNKATFYIWAKVPEGYNSTEFSTHVFEKTGIFFTPGNGYGEFGEGYV 363
           L++GL ELGW+VP  KAT Y+W K P G  ST+F+ ++ ++TG+  TPGN +G  GEGYV
Sbjct: 309 LIQGLGELGWDVPKTKATMYLWVKCPVGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGYV 368

Query: 364 RIALTVTEERIKEALERLKNSDIKFK 389
           RI+L    +R+ EAL R+K + I+++
Sbjct: 369 RISLIADCDRLGEALGRIKQAGIRYR 394


Lambda     K      H
   0.316    0.139    0.414 

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: 544
Number of extensions: 22
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: 389
Length of database: 403
Length adjustment: 31
Effective length of query: 358
Effective length of database: 372
Effective search space:   133176
Effective search space used:   133176
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 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 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