GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvE in Escherichia coli BW25113

Align Probable aspartate aminotransferase; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate 16397 b2290 aspartate aminotransferase (NCBI)

Query= curated2:P63499
         (429 letters)



>FitnessBrowser__Keio:16397
          Length = 405

 Score =  523 bits (1348), Expect = e-153
 Identities = 239/400 (59%), Positives = 319/400 (79%), Gaps = 1/400 (0%)

Query: 30  QSAKLQDVLYEIRGPVHQHAARLEAEGHRILKLNIGNPAPFGFEAPDVIMRDIIQALPYA 89
           +S+KL++V Y+IRGPV + A RLE EG+++LKLNIGNPAPFGF+APD I+ D+I+ LP A
Sbjct: 6   KSSKLENVCYDIRGPVLKEAKRLEEEGNKVLKLNIGNPAPFGFDAPDEILVDVIRNLPTA 65

Query: 90  QGYSDSQGILSARRAVVTRYELVPGFPRFDVDDVYLGNGVSELITMTLQALLDNGDQVLI 149
           QGY DS+G+ SAR+A++  Y+   G     V+D+Y+GNGVSELI   +QALL++GD++L+
Sbjct: 66  QGYCDSKGLYSARKAIMQHYQ-ARGMRDVTVEDIYIGNGVSELIVQAMQALLNSGDEMLV 124

Query: 150 PSPDYPLWTASTSLAGGTPVHYLCDETQGWQPDIADLESKITERTKALVVINPNNPTGAV 209
           P+PDYPLWTA+ SL+ G  VHYLCDE+  W PD+ D+ +KIT RT+ +V+INPNNPTGAV
Sbjct: 125 PAPDYPLWTAAVSLSSGKAVHYLCDESSDWFPDLDDIRAKITPRTRGIVIINPNNPTGAV 184

Query: 210 YSCEILTQMVDLARKHQLLLLADEIYDKILYDDAKHISLASIAPDMLCLTFNGLSKAYRV 269
           YS E+L ++V++AR+H L++ ADEIYDKILYDDA+H S+A +APD+L +TFNGLSK YRV
Sbjct: 185 YSKELLMEIVEIARQHNLIIFADEIYDKILYDDAEHHSIAPLAPDLLTITFNGLSKTYRV 244

Query: 270 AGYRAGWLAITGPKEHASSFIEGIGLLANMRLCPNVPAQHAIQVALGGHQSIEDLVLPGG 329
           AG+R GW+ + GPK+HA  +IEG+ +LA+MRLC NVPAQHAIQ ALGG+QSI + + PGG
Sbjct: 245 AGFRQGWMVLNGPKKHAKGYIEGLEMLASMRLCANVPAQHAIQTALGGYQSISEFITPGG 304

Query: 330 RLLEQRDIAWTKLNEIPGVSCVKPAGALYAFPRLDPEVYDIDDDEQLVLDLLLSEKILVT 389
           RL EQR+ AW  +N+IPGVSCVKP GALY FP++D + ++I DD+++VLD LL EK+L+ 
Sbjct: 305 RLYEQRNRAWELINDIPGVSCVKPRGALYMFPKIDAKRFNIHDDQKMVLDFLLQEKVLLV 364

Query: 390 QGTGFNWPAPDHLRLVTLPWSRDLAAAIERLGNFLVSYRQ 429
           QGT FNWP PDH R+VTLP   D+  ++ +   FL  Y Q
Sbjct: 365 QGTAFNWPWPDHFRIVTLPRVDDIELSLSKFARFLSGYHQ 404


Lambda     K      H
   0.320    0.138    0.419 

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: 604
Number of extensions: 19
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: 429
Length of database: 405
Length adjustment: 31
Effective length of query: 398
Effective length of database: 374
Effective search space:   148852
Effective search space used:   148852
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 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 paper from 2022 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