Aligments for a candidate for ilvH in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Aligments for a candidate for ilvH in Desulfovibrio vulgaris Miyazaki F

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate 8501200 DvMF_1934 sulfoacetaldehyde acetyltransferase (RefSeq)

Query= BRENDA::P00893
         (574 letters)



>lcl|FitnessBrowser__Miya:8501200 DvMF_1934 sulfoacetaldehyde
           acetyltransferase (RefSeq)
          Length = 580

 Score =  268 bits (684), Expect = 6e-76
 Identities = 178/571 (31%), Positives = 285/571 (49%), Gaps = 29/571 (5%)

Query: 1   MEMLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADG 60
           M  ++ +E +   L+ +GV  V G  G A +D+ D L    GID + VRHEQ A HM D 
Sbjct: 1   MPKMTPSEAMAEVLVQEGVTHVSGILGSAFMDLLD-LFPAAGIDFISVRHEQTAGHMEDA 59

Query: 61  LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVG 120
             R TG  GV +  +GPG TN +T +ATA M   P+VVLS    +  +G+D FQECD   
Sbjct: 60  FTRMTGRAGVCIGQNGPGITNYVTAVATANMAHTPMVVLSPSAGSISVGWDGFQECDTWN 119

Query: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180
           + +P+ K S  V   +    +L+ AF +A + R GPV+VD+P+D          + P   
Sbjct: 120 LFKPITKASLRVPHPKRAADILRTAFRIAYAER-GPVLVDIPRDYFYGELDEDILAP--- 175

Query: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240
           S     P   G+  Q + A++ L AAK+PV+  G G + +G  + +K   E LN PV C+
Sbjct: 176 SQYRVAPGGIGNPEQFREAVEVLKAAKRPVIVSGRGVVDSGALETVKALAEHLNAPVACT 235

Query: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVR---FDDRTTNNLAKYCPN 297
            +   AFP  H    G +G  G+  A   +  ADVI AVG R   F      ++  +   
Sbjct: 236 YLHNDAFPCDHPLWTGPIGYMGSKAAMRILQQADVILAVGTRLSYFGTLPQYDINYFPKT 295

Query: 298 ATVLHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLD---------EIR 348
           A ++ IDI+P  I+KT    + +  DA+    ++L  + +   +   D         E+ 
Sbjct: 296 AKIVQIDINPRHIAKTHPVAVGLCADAKDAAVELLARVREAMPNPRRDDAVYAMVKAELE 355

Query: 349 DWWQQIEQWRARQCLKYDTHSEKIKPQAVIETLWR-LTKGDAYVTSDVGQHQMFAALYYP 407
           DW+++I        ++   H     P+  ++ + R +T+ +A  T+D+G     A  Y  
Sbjct: 356 DWYKEIAAIADEPVMEGRMH-----PRKALDVVGRFVTEHNAIATTDIGNTSSTANSYLR 410

Query: 408 FDKPRRWINSGGLGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELP 467
           F   +R + +   G  GF   A LG ++A PE+TVV + GDG+  M++ E+ TA+QY LP
Sbjct: 411 FRNAKRSVATLTFGNTGFAYQAGLGAQLACPEDTVVAIVGDGAWGMSLFEVPTAVQYNLP 470

Query: 468 VLVVNLNNRYLGMVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESK 527
           V+    NN      K+ Q   Y+ R   + + S   +  +AEA G  G +++     ++ 
Sbjct: 471 VIATVYNNGAWCAEKKNQVDFYNNRFVGADIWS-NSYAAIAEAMGATGYKVN----TQAD 525

Query: 528 LSEALEQVRNNRL-VFVDVTVDGSEHVYPMQ 557
           L++AL+  R +R    +++  DG+    P +
Sbjct: 526 LADALDAARKSRKPSVIEIMTDGTRLAPPFR 556


Lambda     K      H
   0.319    0.135    0.403 

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: 729
Number of extensions: 33
Number of successful extensions: 5
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: 574
Length of database: 580
Length adjustment: 36
Effective length of query: 538
Effective length of database: 544
Effective search space:   292672
Effective search space used:   292672
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 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:

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, 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

GapMind for Amino acid biosynthesis