Alignments for a candidate for leuC in Halomonas desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Halomonas desiderata SP1

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_086508765.1 BZY95_RS04400 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_002151265.1:WP_086508765.1
          Length = 481

 Score =  582 bits (1499), Expect = e-170
 Identities = 294/469 (62%), Positives = 354/469 (75%), Gaps = 8/469 (1%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           +TLY+KL+  H+V E ++ T L+YIDR L+HEVTSPQAF+GLR  GR   +     AT D
Sbjct: 4   QTLYDKLWSQHLVKERDDGTALIYIDRQLLHEVTSPQAFEGLRLAGRKPWRLDANLATPD 63

Query: 63  HNVSTQTKDINACGE------MARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQG 116
           HNV T  K+  A G       ++ IQ+Q L  NC EFG+E + +N P QGIVHV+GPEQG
Sbjct: 64  HNVPTTLKE-RAEGNAGIKDPVSLIQVQTLDDNCVEFGIEEFKINDPRQGIVHVVGPEQG 122

Query: 117 VTLPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAP 176
            TLPGMT+VCGDSHTATHGAF ALA GIGTSEVEHVLATQ L   + K M++ V+GK   
Sbjct: 123 ATLPGMTVVCGDSHTATHGAFAALAHGIGTSEVEHVLATQCLLAQKMKNMQVRVEGKLGT 182

Query: 177 GITAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPD 236
           G+TAKD+VLAIIGK G+AGGTG+ +EF G AIRDLSMEGRMT+CNMAIE GA+ GL+A D
Sbjct: 183 GVTAKDVVLAIIGKIGTAGGTGYAIEFAGSAIRDLSMEGRMTVCNMAIEAGARVGLIAVD 242

Query: 237 ETTFNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQ 296
           +TT  Y+  R  AP+G+ +  AVA W+ L +D  A FD VVTL A EI PQV+WGT+P  
Sbjct: 243 DTTIEYLAERPFAPRGEQWQAAVADWRNLVSDADARFDKVVTLDAAEIEPQVSWGTSPEM 302

Query: 297 VISVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLR 356
           V  ++  +PDPA   D   +    +AL YMGL P   +TE+ +DKVFIGSCTNSRIEDLR
Sbjct: 303 VTGISGEVPDPAEQNDDTVKRGYTRALEYMGLAPKQKITEIKLDKVFIGSCTNSRIEDLR 362

Query: 357 AAAEIAKGRKVAPGVQ-ALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNN 415
            AA++A+G+KVA  ++ A+VVPGSG VK QAEAEGLDK+FIEAGFEWR PGCSMCLAMN 
Sbjct: 363 EAAKVARGKKVADSIKLAMVVPGSGLVKRQAEAEGLDKVFIEAGFEWREPGCSMCLAMNA 422

Query: 416 DRLNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRN 464
           D+L  GE CASTSNRNFEGRQG GGRTHLVSPAMAAAAA+ GHF D+R+
Sbjct: 423 DKLGAGEHCASTSNRNFEGRQGYGGRTHLVSPAMAAAAAIAGHFVDVRS 471


Lambda     K      H
   0.317    0.134    0.396 

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: 711
Number of extensions: 29
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: 466
Length of database: 481
Length adjustment: 33
Effective length of query: 433
Effective length of database: 448
Effective search space:   193984
Effective search space used:   193984
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_086508765.1 BZY95_RS04400 (3-isopropylmalate dehydratase large subunit)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

# 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/TIGR00170.hmm
# target sequence database:        /tmp/gapView.19421.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00170  [M=466]
Accession:   TIGR00170
Description: leuC: 3-isopropylmalate dehydratase, large subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.1e-236  769.1   0.6   8.7e-236  768.8   0.6    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086508765.1  BZY95_RS04400 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086508765.1  BZY95_RS04400 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  768.8   0.6  8.7e-236  8.7e-236       3     466 .]       4     472 ..       2     472 .. 0.99

  Alignments for each domain:
  == domain 1  score: 768.8 bits;  conditional E-value: 8.7e-236
                                 TIGR00170   3 ktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr. 70 
                                               +tly+kl+ +h+vke +++t l+yidr l+hevtspqafeglr agrk  r d  lat dhn++t+ + 
  lcl|NCBI__GCF_002151265.1:WP_086508765.1   4 QTLYDKLWSQHLVKERDDGTALIYIDRQLLHEVTSPQAFEGLRLAGRKPWRLDANLATPDHNVPTTLKe 72 
                                               8****************************************************************9997 PP

                                 TIGR00170  71 ....dveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathg 135
                                                   +  ik+ ++ +qv++l+ n+ efg++ f +++ +qgivhvvgpe+g tlpg+t+vcgdshtathg
  lcl|NCBI__GCF_002151265.1:WP_086508765.1  73 raegNAGIKDPVSLIQVQTLDDNCVEFGIEEFKINDPRQGIVHVVGPEQGATLPGMTVVCGDSHTATHG 141
                                               78888899************************************************************* PP

                                 TIGR00170 136 afgalafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefa 204
                                               af ala gigtsevehvlatq l  ++ k+++++vegkl +g+takd++laiigkig+aggtgy +efa
  lcl|NCBI__GCF_002151265.1:WP_086508765.1 142 AFAALAHGIGTSEVEHVLATQCLLAQKMKNMQVRVEGKLGTGVTAKDVVLAIIGKIGTAGGTGYAIEFA 210
                                               ********************************************************************* PP

                                 TIGR00170 205 geairdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakf 273
                                               g airdlsme+rmtvcnmaieaga+ glia d+tt+ey+ +r++ap+g++++ ava w+ l +d +a+f
  lcl|NCBI__GCF_002151265.1:WP_086508765.1 211 GSAIRDLSMEGRMTVCNMAIEAGARVGLIAVDDTTIEYLAERPFAPRGEQWQAAVADWRNLVSDADARF 279
                                               ********************************************************************* PP

                                 TIGR00170 274 dkvvtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkv 342
                                               dkvvtl+a +i pqv+wgt+p++v  +++evpdp++  d+  k++  +al+y+gl p++k+++ik+dkv
  lcl|NCBI__GCF_002151265.1:WP_086508765.1 280 DKVVTLDAAEIEPQVSWGTSPEMVTGISGEVPDPAEQNDDTVKRGYTRALEYMGLAPKQKITEIKLDKV 348
                                               ********************************************************************* PP

                                 TIGR00170 343 figsctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslc 411
                                               figsctnsriedlr+aa+v++gkkvad++kla+vvpgsglvk+qae+egldk+f+eagfewre+gcs+c
  lcl|NCBI__GCF_002151265.1:WP_086508765.1 349 FIGSCTNSRIEDLREAAKVARGKKVADSIKLAMVVPGSGLVKRQAEAEGLDKVFIEAGFEWREPGCSMC 417
                                               ********************************************************************* PP

                                 TIGR00170 412 lgmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdirel 466
                                               l+mn d+l+++e castsnrnfegrqg g+rthlvspamaaaaa+ag+fvd+r +
  lcl|NCBI__GCF_002151265.1:WP_086508765.1 418 LAMNADKLGAGEHCASTSNRNFEGRQGYGGRTHLVSPAMAAAAAIAGHFVDVRSF 472
                                               *****************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (481 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 9.58
//
[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