GapMind for Amino acid biosynthesis

 

Alignments 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:

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