Alignments for a candidate for ilvD in Methylosarcina fibrata AML-C10

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Methylosarcina fibrata AML-C10

Align Dihydroxy-acid dehydratase, mitochondrial; DAD; EC 4.2.1.9 (characterized)
to candidate WP_020562313.1 A3OW_RS0104905 dihydroxy-acid dehydratase

Query= SwissProt::P39522
         (585 letters)



>NCBI__GCF_000372865.1:WP_020562313.1
          Length = 565

 Score =  613 bits (1580), Expect = e-180
 Identities = 305/563 (54%), Positives = 404/563 (71%), Gaps = 8/563 (1%)

Query: 22  KLNKYSYIITEPKGQGASQAMLYATGFKKEDFKKPQVGVGSCWWSGNPCNMHLLDLNNRC 81
           K   YS  + +   +  S+AML+A GF  EDFKKPQ+G+ S W    PCNMH+  L +  
Sbjct: 8   KTRTYSSQVVDGMERAPSRAMLHAVGFTNEDFKKPQIGIASTWSMVTPCNMHINKLADNA 67

Query: 82  SQSIEKAGLKAMQFNTIGVSDGISMGTKGMRYSLQSREIIADSFETIMMAQHYDANIAIP 141
           ++ +++ G KA+ FNTI +SDGISMGT+GM+YSL SRE+IADS ET++  Q +D  +AI 
Sbjct: 68  ARGVDQTGGKAVIFNTITISDGISMGTEGMKYSLVSREVIADSIETVVGCQGFDGIVAIG 127

Query: 142 SCDKNMPGVMMAMGRHNRPSIMVYGGTILPGHPTCGSSKISKNIDIVSAFQSYGEYISKQ 201
            CDKNMPG M+A+ R NRP+I VYGGTILPG   C   K    +D+VS F++ G   + +
Sbjct: 128 GCDKNMPGCMIALSRLNRPAIFVYGGTILPG---CHKDK---KLDVVSVFEAVGARANNK 181

Query: 202 FTEEEREDVVEHACPGPGSCGGMYTANTMASAAEVLGLTIPNSSSFPAVSKEKLAECDNI 261
             + E   +   A PG GSCGGMYTANTMASA E LG+++PNSS+  AVS++K  +C+  
Sbjct: 182 IDDAELAAIEAKAIPGAGSCGGMYTANTMASAIEALGMSLPNSSAQAAVSEDKRLDCERA 241

Query: 262 GEYIKKTMELGILPRDILTKEAFENAITYVVATGGSTNAVLHLVAVAHSAGVKLSPDDFQ 321
           G  + + ++ GI PRDI+TKEAFENAIT V+A GGSTNAVLHL+A+A++AGV L+ DDF 
Sbjct: 242 GAAVLELLKKGIKPRDIMTKEAFENAITVVIALGGSTNAVLHLLAMANAAGVDLTLDDFT 301

Query: 322 RISDTTPLIGDFKPSGKYVMADLINVGGTQSVIKYLYENNMLHGNTMTVTGDTLAERAKK 381
           RI    P++ D KPSG+Y MA+LI +GG Q ++K L +  +LHG+ +TVTG TLAE    
Sbjct: 302 RIGKNVPMVADLKPSGRYQMAELIEIGGIQPLMKELLDRGLLHGHCLTVTGKTLAENLAD 361

Query: 382 APSLPEGQEIIKPLSHPIKANGHLQILYGSLAPGGAVGKITGKEGTYFKGRARVFEEEGA 441
               PEGQ++I PL  PIK + HL +LYG+LA  GAV KITGKEG  F G+A+VF+ E  
Sbjct: 362 VKPYPEGQDMIHPLDQPIKKDSHLVVLYGNLAAEGAVAKITGKEGLVFTGKAKVFDAEEQ 421

Query: 442 FIEALERGEIKKGEKTVVVIRYEGPRGAPGMPEMLKPSSALMGYGLGKDVALLTDGRFSG 501
            ++A+  G+I KG+  V+VIRYEGP+G PGM EML P+SA+MG GLGK+VAL+TDGRFSG
Sbjct: 422 ALQAILNGDIVKGD--VIVIRYEGPKGGPGMREMLSPTSAVMGKGLGKEVALITDGRFSG 479

Query: 502 GSHGFLIGHIVPEAAEGGPIGLVRDGDEIIIDADNNKIDLLVSDKEMAQRKQSWVAPPPR 561
           G+HGF++GHI PEA  GG + +V++GDEI IDA+  ++ L V++ E+A+R   W  P PR
Sbjct: 480 GTHGFVVGHITPEAYTGGALAIVQNGDEITIDAETRQLTLHVNEHEIARRFDKWKQPAPR 539

Query: 562 YTRGTLSKYAKLVSNASNGCVLD 584
           YTRG L+KYAKLVS+AS G V D
Sbjct: 540 YTRGVLAKYAKLVSSASKGAVTD 562


Lambda     K      H
   0.315    0.134    0.390 

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: 980
Number of extensions: 52
Number of successful extensions: 3
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: 585
Length of database: 565
Length adjustment: 36
Effective length of query: 549
Effective length of database: 529
Effective search space:   290421
Effective search space used:   290421
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate WP_020562313.1 A3OW_RS0104905 (dihydroxy-acid dehydratase)
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00110.hmm
# target sequence database:        /tmp/gapView.14982.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00110  [M=543]
Accession:   TIGR00110
Description: ilvD: dihydroxy-acid dehydratase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-239  782.5   9.3   1.2e-239  782.3   9.3    1.0  1  lcl|NCBI__GCF_000372865.1:WP_020562313.1  A3OW_RS0104905 dihydroxy-acid de


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000372865.1:WP_020562313.1  A3OW_RS0104905 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  782.3   9.3  1.2e-239  1.2e-239       1     542 [.      24     562 ..      24     563 .. 1.00

  Alignments for each domain:
  == domain 1  score: 782.3 bits;  conditional E-value: 1.2e-239
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               ++ra+l+a+G+++ed++kP+i+++++++ ++P+++h+++la+ ++++++++Gg+a+ fnti++sDGi+m
  lcl|NCBI__GCF_000372865.1:WP_020562313.1  24 PSRAMLHAVGFTNEDFKKPQIGIASTWSMVTPCNMHINKLADNAARGVDQTGGKAVIFNTITISDGISM 92 
                                               589****************************************************************** PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               g+eGmkysL+sre+iaDs+etvv  + +D++v+i+ CDk++PG ++a  rln+Pai+v+GG++ +g  k
  lcl|NCBI__GCF_000372865.1:WP_020562313.1  93 GTEGMKYSLVSREVIADSIETVVGCQGFDGIVAIGGCDKNMPGCMIALSRLNRPAIFVYGGTILPGCHK 161
                                               *******************************************************************99 PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                 +k+d+v+vfeavg+ a++k++++el +ie  a P+agsC+G++tan+ma++ ealG+slP+ss+ +a
  lcl|NCBI__GCF_000372865.1:WP_020562313.1 162 -DKKLDVVSVFEAVGARANNKIDDAELAAIEAKAIPGAGSCGGMYTANTMASAIEALGMSLPNSSAQAA 229
                                               .8******************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276
                                               +s++k+  ++++g+ + el+kk ikPrdi+tkeafenait+++alGGstn+vLhlla+a+ agv+l+ld
  lcl|NCBI__GCF_000372865.1:WP_020562313.1 230 VSEDKRLDCERAGAAVLELLKKGIKPRDIMTKEAFENAITVVIALGGSTNAVLHLLAMANAAGVDLTLD 298
                                               ********************************************************************* PP

                                 TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345
                                               df r+ ++vP++a+lkPsg++ +++l + GG++ ++kel  +gllh ++ltvtGktlae+l++vk  ++
  lcl|NCBI__GCF_000372865.1:WP_020562313.1 299 DFTRIGKNVPMVADLKPSGRYQMAELIEIGGIQPLMKELLDRGLLHGHCLTVTGKTLAENLADVKPYPE 367
                                               ********************************************************************* PP

                                 TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414
                                               +qd+i++ld+p+kk+++l vL+Gnla eGav+ki+g+e   l+f+G+akvf+ ee+al+ail+g++ +G
  lcl|NCBI__GCF_000372865.1:WP_020562313.1 368 GQDMIHPLDQPIKKDSHLVVLYGNLAAEGAVAKITGKEG--LVFTGKAKVFDAEEQALQAILNGDIVKG 434
                                               ***************************************..9*************************** PP

                                 TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483
                                               dv+viryeGPkGgPGmremL Ptsa++g GLgk+vaLitDGrfsGgt+G+++Gh++Pea++gGa+a+v+
  lcl|NCBI__GCF_000372865.1:WP_020562313.1 435 DVIVIRYEGPKGGPGMREMLSPTSAVMGKGLGKEVALITDGRFSGGTHGFVVGHITPEAYTGGALAIVQ 503
                                               ********************************************************************* PP

                                 TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                               +GD+i+iD+e r+l l+v+e+e+a+r +k+k++ +r+++g+Lakyaklvssa+kGav+d
  lcl|NCBI__GCF_000372865.1:WP_020562313.1 504 NGDEITIDAETRQLTLHVNEHEIARRFDKWKQPAPRYTRGVLAKYAKLVSSASKGAVTD 562
                                               *********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (565 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 9.39
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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