Alignments for a candidate for ilvD in Methylococcus capsulatus Bath

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Methylococcus capsulatus Bath

Align Dihydroxy-acid dehydratase, mitochondrial; DAD; EC 4.2.1.9 (characterized)
to candidate WP_010961325.1 MCA_RS10195 dihydroxy-acid dehydratase

Query= SwissProt::P39522
         (585 letters)



>NCBI__GCF_000008325.1:WP_010961325.1
          Length = 562

 Score =  601 bits (1549), Expect = e-176
 Identities = 300/559 (53%), Positives = 395/559 (70%), Gaps = 8/559 (1%)

Query: 26  YSYIITEPKGQGASQAMLYATGFKKEDFKKPQVGVGSCWWSGNPCNMHLLDLNNRCSQSI 85
           +S  + +   +  S+AML+A GF   DF KPQ+G+ S W    PCNMH+  L    ++ +
Sbjct: 9   HSSQVVDGMERAPSRAMLHAVGFADADFAKPQIGIASTWAMVTPCNMHINKLAEDAARGV 68

Query: 86  EKAGLKAMQFNTIGVSDGISMGTKGMRYSLQSREIIADSFETIMMAQHYDANIAIPSCDK 145
           +  G KA+ FNTI +SDGISMGT+GM+YSL SRE+IADS ET++  Q YD  +AI  CDK
Sbjct: 69  DGGGGKAVIFNTITISDGISMGTEGMKYSLVSREVIADSIETVVACQGYDGVVAIGGCDK 128

Query: 146 NMPGVMMAMGRHNRPSIMVYGGTILPGHPTCGSSKISKNIDIVSAFQSYGEYISKQFTEE 205
           NMPG ++A+ R NRP++ VYGGTILPG   C   K    +D+VS F++ G   + +  + 
Sbjct: 129 NMPGCLIALARLNRPAVFVYGGTILPG---CHDGK---KLDVVSVFEAVGARANHRIDDA 182

Query: 206 EREDVVEHACPGPGSCGGMYTANTMASAAEVLGLTIPNSSSFPAVSKEKLAECDNIGEYI 265
           E   +  +A PGPGSCGGMYTANTMASA E LG+++P SS+  A+S+ K  +C+  G  +
Sbjct: 183 ELHAIESNAIPGPGSCGGMYTANTMASAIEALGMSLPGSSAQVAISRAKELDCERAGAQV 242

Query: 266 KKTMELGILPRDILTKEAFENAITYVVATGGSTNAVLHLVAVAHSAGVKLSPDDFQRISD 325
            K ++LG+ PRDI+TK+AFENAIT V+A GGSTNAVLHL+A+A++ GV L  DDF RI  
Sbjct: 243 LKLLDLGLKPRDIMTKKAFENAITVVIALGGSTNAVLHLLAMANACGVDLKLDDFTRIGR 302

Query: 326 TTPLIGDFKPSGKYVMADLINVGGTQSVIKYLYENNMLHGNTMTVTGDTLAERAKKAPSL 385
             P++ D KPSG+Y MA+L+ +GG Q ++K L +  +LHG+ MTVTG TL E    AP  
Sbjct: 303 KVPMLADLKPSGRYSMAELVEIGGIQPLMKTLLDAGLLHGDCMTVTGKTLEENLADAPDY 362

Query: 386 PEGQEIIKPLSHPIKANGHLQILYGSLAPGGAVGKITGKEGTYFKGRARVFEEEGAFIEA 445
           P GQ++I+ L +PIK + HL IL G+LAP GAV KITGKEG  F G ARVF+ E A + A
Sbjct: 363 PAGQDMIRSLDNPIKKDSHLVILKGNLAPEGAVAKITGKEGLSFTGTARVFDCEEAALTA 422

Query: 446 LERGEIKKGEKTVVVIRYEGPRGAPGMPEMLKPSSALMGYGLGKDVALLTDGRFSGGSHG 505
           +  G I KG+  V+VIRYEGP+G PGM EML P+SA+MG GLGK+VAL+TDGRFSGG+HG
Sbjct: 423 ILDGTIVKGD--VIVIRYEGPKGGPGMREMLSPTSAVMGKGLGKEVALITDGRFSGGTHG 480

Query: 506 FLIGHIVPEAAEGGPIGLVRDGDEIIIDADNNKIDLLVSDKEMAQRKQSWVAPPPRYTRG 565
           F++GHI PEA  GGP+ +VRDGD I IDA+  ++ L V+D E+ +R   W  P PRYT+G
Sbjct: 481 FVVGHITPEAYTGGPLAIVRDGDTITIDAETRELSLHVTDDEIGRRLAQWTQPAPRYTKG 540

Query: 566 TLSKYAKLVSNASNGCVLD 584
            L+KYA+LVS AS G V D
Sbjct: 541 VLAKYARLVSPASEGAVTD 559


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: 1023
Number of extensions: 40
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: 562
Length adjustment: 36
Effective length of query: 549
Effective length of database: 526
Effective search space:   288774
Effective search space used:   288774
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_010961325.1 MCA_RS10195 (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.12145.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.6e-235  766.9   6.5   6.4e-235  766.7   6.5    1.0  1  lcl|NCBI__GCF_000008325.1:WP_010961325.1  MCA_RS10195 dihydroxy-acid dehyd


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008325.1:WP_010961325.1  MCA_RS10195 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  766.7   6.5  6.4e-235  6.4e-235       1     542 [.      21     559 ..      21     560 .. 1.00

  Alignments for each domain:
  == domain 1  score: 766.7 bits;  conditional E-value: 6.4e-235
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               ++ra+l+a+G+ d+d+ kP+i++++++  ++P+++h+++la+ ++++++  Gg+a+ fnti++sDGi+m
  lcl|NCBI__GCF_000008325.1:WP_010961325.1  21 PSRAMLHAVGFADADFAKPQIGIASTWAMVTPCNMHINKLAEDAARGVDGGGGKAVIFNTITISDGISM 89 
                                               589****************************************************************** PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               g+eGmkysL+sre+iaDs+etvv  + +D++v+i+ CDk++PG l+a +rln+Pa++v+GG++ +g   
  lcl|NCBI__GCF_000008325.1:WP_010961325.1  90 GTEGMKYSLVSREVIADSIETVVACQGYDGVVAIGGCDKNMPGCLIALARLNRPAVFVYGGTILPGCHD 158
                                               ******************************************************************999 PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                ++k+d+v+vfeavg+ a+ +++++el++ie +a P++gsC+G++tan+ma++ ealG+slPgss+  a
  lcl|NCBI__GCF_000008325.1:WP_010961325.1 159 -GKKLDVVSVFEAVGARANHRIDDAELHAIESNAIPGPGSCGGMYTANTMASAIEALGMSLPGSSAQVA 226
                                               .9******************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276
                                               +s  k+  ++++g+++ +l+   +kPrdi+tk+afenait+++alGGstn+vLhlla+a+  gv+l+ld
  lcl|NCBI__GCF_000008325.1:WP_010961325.1 227 ISRAKELDCERAGAQVLKLLDLGLKPRDIMTKKAFENAITVVIALGGSTNAVLHLLAMANACGVDLKLD 295
                                               ********************************************************************* PP

                                 TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345
                                               df r+ rkvP+la+lkPsg++ +++l + GG++ ++k+l  +gllh d++tvtGktl+e+l++++  ++
  lcl|NCBI__GCF_000008325.1:WP_010961325.1 296 DFTRIGRKVPMLADLKPSGRYSMAELVEIGGIQPLMKTLLDAGLLHGDCMTVTGKTLEENLADAPDYPA 364
                                               ********************************************************************* PP

                                 TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414
                                               +qd+irsldnp+kk+++l +LkGnla+eGav+ki+g+e   l f+G+a+vf+ ee+al ail+g + +G
  lcl|NCBI__GCF_000008325.1:WP_010961325.1 365 GQDMIRSLDNPIKKDSHLVILKGNLAPEGAVAKITGKEG--LSFTGTARVFDCEEAALTAILDGTIVKG 431
                                               ***************************************..9*************************** PP

                                 TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483
                                               dv+viryeGPkGgPGmremL Ptsa++g GLgk+vaLitDGrfsGgt+G+++Gh++Pea++gG++a+v+
  lcl|NCBI__GCF_000008325.1:WP_010961325.1 432 DVIVIRYEGPKGGPGMREMLSPTSAVMGKGLGKEVALITDGRFSGGTHGFVVGHITPEAYTGGPLAIVR 500
                                               ********************************************************************* PP

                                 TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                               dGD+i+iD+e r+l l+v ++e+ +r a+++++ +r++kg+Lakya+lvs a++Gav+d
  lcl|NCBI__GCF_000008325.1:WP_010961325.1 501 DGDTITIDAETRELSLHVTDDEIGRRLAQWTQPAPRYTKGVLAKYARLVSPASEGAVTD 559
                                               *********************************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (562 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: 8.48
//
[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