Alignments for a candidate for leuC in Methylomonas methanica MC09

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Methylomonas methanica MC09

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_013820589.1 METME_RS20185 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_000214665.1:WP_013820589.1
          Length = 469

 Score =  596 bits (1537), Expect = e-175
 Identities = 294/461 (63%), Positives = 355/461 (77%), Gaps = 1/461 (0%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           KTLY+KL+D HVV+  ++ + L+YIDR L+HEVTSPQAF+GLR  GR   +  +  A  D
Sbjct: 4   KTLYDKLWDDHVVHTEDDGSCLIYIDRQLLHEVTSPQAFEGLRLSGRQPWRIARNLAVAD 63

Query: 63  HNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPGM 122
           HN+ T  +       ++R+Q++ L  NCKEFG+  + ++   QGIVHV+GPEQG TLPGM
Sbjct: 64  HNIPTTDRAKGIADPVSRLQVETLESNCKEFGITEFHMSDIRQGIVHVVGPEQGATLPGM 123

Query: 123 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAKD 182
           T+VCGDSHT+THGA  ALAFGIGTSEVEH LATQ L Q +AK M I+V GKA PG+TAKD
Sbjct: 124 TVVCGDSHTSTHGASAALAFGIGTSEVEHALATQCLVQKKAKNMLIKVNGKAGPGVTAKD 183

Query: 183 IVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFNY 242
           IVLA+IGK G+AGGTG+ +EF GEA+R LSMEGRMT+CNMAIE GA+AGL+A DETT  Y
Sbjct: 184 IVLAVIGKIGTAGGTGYTIEFGGEAVRALSMEGRMTICNMAIEAGARAGLIACDETTIEY 243

Query: 243 VKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVND 302
            +GR +APKG D++ AV YW+ L +D  A FD V+   A EI PQV+WGT+P  V+ V+ 
Sbjct: 244 YQGRPYAPKGDDWNMAVRYWQKLHSDSDAKFDKVIEFNAAEIKPQVSWGTSPEMVLPVDA 303

Query: 303 NIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEIA 362
           N+PDPA   DPV+R   E+AL YMGL+ G  +T++ +DKVFIGSCTNSRIEDLRAAA + 
Sbjct: 304 NVPDPAQETDPVKRQGIERALQYMGLQAGQKITDIKLDKVFIGSCTNSRIEDLRAAAAVI 363

Query: 363 KGRKVAPGV-QALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPG 421
           KGRK A  V Q L+VPGSG +K QAEAEGLDKIF  A FEWR PGCSMCLAMN DRL  G
Sbjct: 364 KGRKKADSVKQVLIVPGSGLIKQQAEAEGLDKIFTAANFEWREPGCSMCLAMNADRLEAG 423

Query: 422 ERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADI 462
           E CASTSNRNFEGRQG GGRTHLVSPAMAAAAA+ GHF ++
Sbjct: 424 EHCASTSNRNFEGRQGYGGRTHLVSPAMAAAAAIAGHFVNV 464


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: 743
Number of extensions: 29
Number of successful extensions: 2
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: 469
Length adjustment: 33
Effective length of query: 433
Effective length of database: 436
Effective search space:   188788
Effective search space used:   188788
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_013820589.1 METME_RS20185 (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.4398.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-241  787.7   1.0     2e-241  787.4   1.0    1.0  1  lcl|NCBI__GCF_000214665.1:WP_013820589.1  METME_RS20185 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000214665.1:WP_013820589.1  METME_RS20185 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  787.4   1.0    2e-241    2e-241       2     464 ..       3     465 ..       2     467 .. 0.99

  Alignments for each domain:
  == domain 1  score: 787.4 bits;  conditional E-value: 2e-241
                                 TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr 70 
                                                ktly+kl+d hvv+ +++++ l+yidr l+hevtspqafeglr  gr+  r+ + la  dhni+t+ r
  lcl|NCBI__GCF_000214665.1:WP_013820589.1   3 GKTLYDKLWDDHVVHTEDDGSCLIYIDRQLLHEVTSPQAFEGLRLSGRQPWRIARNLAVADHNIPTTDR 71 
                                               59******************************************************************* PP

                                 TIGR00170  71 dveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafga 139
                                                  i + +++lqv++le n+kefg+  f +s+ +qgivhvvgpe+g tlpg+t+vcgdsht+thga  a
  lcl|NCBI__GCF_000214665.1:WP_013820589.1  72 AKGIADPVSRLQVETLESNCKEFGITEFHMSDIRQGIVHVVGPEQGATLPGMTVVCGDSHTSTHGASAA 140
                                               ********************************************************************* PP

                                 TIGR00170 140 lafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageai 208
                                               lafgigtseveh latq l+q++ak++ i+v+gk+ +g+takdi+la+igkig+aggtgy +ef gea+
  lcl|NCBI__GCF_000214665.1:WP_013820589.1 141 LAFGIGTSEVEHALATQCLVQKKAKNMLIKVNGKAGPGVTAKDIVLAVIGKIGTAGGTGYTIEFGGEAV 209
                                               ********************************************************************* PP

                                 TIGR00170 209 rdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvv 277
                                               r+lsme+rmt+cnmaieaga+aglia dett+ey ++r+yapkg++++ av yw+ l++d +akfdkv+
  lcl|NCBI__GCF_000214665.1:WP_013820589.1 210 RALSMEGRMTICNMAIEAGARAGLIACDETTIEYYQGRPYAPKGDDWNMAVRYWQKLHSDSDAKFDKVI 278
                                               ********************************************************************* PP

                                 TIGR00170 278 tleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigs 346
                                                ++a +i pqv+wgt+p++vl+v+ +vpdp++ +dpv+++++e+al+y+gl++g+k++dik+dkvfigs
  lcl|NCBI__GCF_000214665.1:WP_013820589.1 279 EFNAAEIKPQVSWGTSPEMVLPVDANVPDPAQETDPVKRQGIERALQYMGLQAGQKITDIKLDKVFIGS 347
                                               ********************************************************************* PP

                                 TIGR00170 347 ctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmn 415
                                               ctnsriedlraaa+v+kg+k+ad+vk++l+vpgsgl+k+qae+egldkif +a fewre+gcs+cl+mn
  lcl|NCBI__GCF_000214665.1:WP_013820589.1 348 CTNSRIEDLRAAAAVIKGRKKADSVKQVLIVPGSGLIKQQAEAEGLDKIFTAANFEWREPGCSMCLAMN 416
                                               ********************************************************************* PP

                                 TIGR00170 416 ndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdir 464
                                                d+l+++e castsnrnfegrqg g+rthlvspamaaaaa+ag+fv++ 
  lcl|NCBI__GCF_000214665.1:WP_013820589.1 417 ADRLEAGEHCASTSNRNFEGRQGYGGRTHLVSPAMAAAAAIAGHFVNVT 465
                                               **********************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (469 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.55
//
[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