GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Miya:8501200
          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.

Links

Downloads

Related tools

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