Alignments for a candidate for ilvI in Desulfotalea psychrophila LSv54

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Desulfotalea psychrophila LSv54

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_011188115.1 DP_RS04400 sulfoacetaldehyde acetyltransferase

Query= BRENDA::P9WG41
         (618 letters)



>NCBI__GCF_000025945.1:WP_011188115.1
          Length = 598

 Score =  190 bits (483), Expect = 1e-52
 Identities = 145/556 (26%), Positives = 258/556 (46%), Gaps = 40/556 (7%)

Query: 37  QLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASGYA 96
           ++T  +A I  L+  G++  FGI G A++P+ D LF    +      HE  AG  A GY 
Sbjct: 5   KMTTEEAFITVLQMHGIEHAFGIIGSAMMPISD-LFPKAGITFWDCAHEGNAGMMADGYT 63

Query: 97  HVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISGIT 156
             +G++ + +A +GPG TN +TP+  A  +  P++ +T Q     +G   FQE +   + 
Sbjct: 64  RASGKMSMMVAQNGPGITNFITPVKTAYWNHTPLLLVTPQAANATMGQGGFQEVEQMAVF 123

Query: 157 MPITKHNFLVRSGDDIPRVLAEAFH---IAASGRPGAVLVDIPKDVLQGQCTFSWPPRME 213
             +  +   VR     PR +AE  +   + A        ++IP+D       ++    +E
Sbjct: 124 KDMVAYQEEVRD----PRRMAEVLNRVIMQAKRASAPAQINIPRDY------WTQVIEIE 173

Query: 214 LPGYKPNTKPHS--RQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVT 271
           LP      +P    + + +AA+L++ A+ PV+  G GVI G A +   ELAE    PV  
Sbjct: 174 LPAIVDFERPAGGEKALEKAAELLSKAKFPVILNGAGVILGGAIKDTIELAERLDAPVCC 233

Query: 272 TLMARGAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGK---LDSFAP 328
                 AFP SH    G  G +G+ A +  + ++D+++ALGTR +   T     +D +  
Sbjct: 234 GYQHNDAFPGSHPLAAGPLGYNGSKAGMELIAQADVVLALGTRLNPFSTLPGYGIDYWPQ 293

Query: 329 EAKVIHADIDPAEIGKNRHADVPIVGDVKAVITELIAML-----------RHHHIPGT-- 375
            A +I  DI+P  IG  +   V I+GD K V   ++  L           R  +I  T  
Sbjct: 294 NAAIIQVDINPDRIGLTKAVKVGIIGDAKKVARGILNRLTATAGDTDREIRKANIGKTKA 353

Query: 376 ---IEMADWWAYLNGVRKTYPLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQM 432
              +E+A+     +    ++      +    +SP      +  +   +A+  + +G +  
Sbjct: 354 EWSVELANLVHEEDDPGTSWNKRARDREPDKMSPREAWNAMKSVIPENAIISSDIGNNCA 413

Query: 433 WAAQFIRYEKPRSWLNSGGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELAT 492
               +  +E+ R +L  G  G  G+  PA  GAKIA P   V  + GDG F ++  E+ +
Sbjct: 414 IGNAYPTFEEGRKYLAPGMFGPCGYGFPAICGAKIAQPDVPVIGMAGDGAFGISMNEMVS 473

Query: 493 CA-VEGIPVKVALINNGNLGMVRQWQSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVG 551
           C   +  P+ + +  N   G  ++  +L+Y++ +  T+L  +      + K+A+A G +G
Sbjct: 474 CGRKDWPPITMIIFRNYQWGAEKRNTTLWYSDNFVGTELDPN----VSYAKIAQACGLIG 529

Query: 552 LRCEREEDVVDVINQA 567
           ++    +D+   + +A
Sbjct: 530 VQATCTDDLTAQLKEA 545


Lambda     K      H
   0.319    0.136    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: 830
Number of extensions: 51
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 618
Length of database: 598
Length adjustment: 37
Effective length of query: 581
Effective length of database: 561
Effective search space:   325941
Effective search space used:   325941
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: 53 (25.0 bits)

This GapMind analysis is from Jul 25 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 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 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