Alignments for a candidate for leuC in Thermithiobacillus tepidarius DSM 3134

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Thermithiobacillus tepidarius DSM 3134

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_051180794.1 G579_RS15645 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_000423825.1:WP_051180794.1
          Length = 480

 Score =  601 bits (1549), Expect = e-176
 Identities = 300/464 (64%), Positives = 361/464 (77%), Gaps = 2/464 (0%)

Query: 1   MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60
           + KTLY+K+++ HVV   E +  LLYIDR L+HEVTSPQAF+GLR  GR   +     A 
Sbjct: 2   LGKTLYDKIWEQHVV-ATEGDATLLYIDRQLIHEVTSPQAFEGLRVAGRKPWRVDANVAV 60

Query: 61  MDHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLP 120
            DHNV T  ++      ++R+Q++ L +NC EFG+E + +    QGIVHV+ PEQG+TLP
Sbjct: 61  PDHNVPTIGREQGIADPVSRLQVETLDRNCAEFGIEEFAMGDVRQGIVHVIAPEQGLTLP 120

Query: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITA 180
           GMT+VCGDSHTATHGA GALAFGIGTSEVEHVLATQ L   + K+M+I V+G+   G TA
Sbjct: 121 GMTVVCGDSHTATHGALGALAFGIGTSEVEHVLATQCLWTQKTKSMRIRVEGELPAGCTA 180

Query: 181 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTF 240
           KDIVLA+IGK G+AGGTG+ +EF G AI  LS+EGRMT+CNMAIE GA+AG+VA D+ T 
Sbjct: 181 KDIVLAVIGKIGTAGGTGYTIEFAGPAIEALSIEGRMTVCNMAIEAGARAGMVAVDDKTI 240

Query: 241 NYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISV 300
           +YVKGR  AP+G  ++ AVA W+ L++D  A FD  V L A EI PQVTWGT+P  V+ +
Sbjct: 241 DYVKGRPFAPQGALWEQAVAAWRELRSDPDAVFDREVVLDAAEIQPQVTWGTSPEMVVGI 300

Query: 301 NDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360
           ND +PDPA   DPV R + E+ALAYMGL+   P+T +AIDKVFIGSCTN+RIEDLRAAA 
Sbjct: 301 NDRVPDPAREPDPVRRHAMEQALAYMGLEANTPMTAIAIDKVFIGSCTNARIEDLRAAAA 360

Query: 361 IAKGRKVAPGV-QALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLN 419
           +AKG KVAP V QALVVPGSG VK QAEAEGLD+IF EAGFEWR PGCSMCLAMN DRL 
Sbjct: 361 VAKGHKVAPHVKQALVVPGSGLVKRQAEAEGLDRIFKEAGFEWRDPGCSMCLAMNADRLE 420

Query: 420 PGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463
           PGERCA+TSNRNFEGRQG+GGRTHLVSPA+AAAAA+ GHF D+R
Sbjct: 421 PGERCAATSNRNFEGRQGKGGRTHLVSPAVAAAAAIAGHFVDVR 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: 783
Number of extensions: 31
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: 480
Length adjustment: 33
Effective length of query: 433
Effective length of database: 447
Effective search space:   193551
Effective search space used:   193551
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_051180794.1 G579_RS15645 (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.30101.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.8e-239  779.0   0.3   7.9e-239  778.8   0.3    1.0  1  lcl|NCBI__GCF_000423825.1:WP_051180794.1  G579_RS15645 3-isopropylmalate d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000423825.1:WP_051180794.1  G579_RS15645 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  778.8   0.3  7.9e-239  7.9e-239       3     465 ..       4     465 ..       2     466 .. 0.99

  Alignments for each domain:
  == domain 1  score: 778.8 bits;  conditional E-value: 7.9e-239
                                 TIGR00170   3 ktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrd 71 
                                               ktly+k++++hvv  +e++++llyidr l+hevtspqafeglr+agrk  rvd  +a  dhn++t  r+
  lcl|NCBI__GCF_000423825.1:WP_051180794.1   4 KTLYDKIWEQHVVA-TEGDATLLYIDRQLIHEVTSPQAFEGLRVAGRKPWRVDANVAVPDHNVPTIGRE 71 
                                               9***********96.6999************************************************** PP

                                 TIGR00170  72 veikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgal 140
                                                 i + +++lqv++l++n+ efg++ f + +++qgivhv+ pe+gltlpg+t+vcgdshtathga+gal
  lcl|NCBI__GCF_000423825.1:WP_051180794.1  72 QGIADPVSRLQVETLDRNCAEFGIEEFAMGDVRQGIVHVIAPEQGLTLPGMTVVCGDSHTATHGALGAL 140
                                               ********************************************************************* PP

                                 TIGR00170 141 afgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageair 209
                                               afgigtsevehvlatq l+ +++k+++i+veg+l  g takdi+la+igkig+aggtgy +efag ai+
  lcl|NCBI__GCF_000423825.1:WP_051180794.1 141 AFGIGTSEVEHVLATQCLWTQKTKSMRIRVEGELPAGCTAKDIVLAVIGKIGTAGGTGYTIEFAGPAIE 209
                                               ********************************************************************* PP

                                 TIGR00170 210 dlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvt 278
                                               +ls+e+rmtvcnmaieaga+ag++a d+ t++yvk+r++ap+g+ +e+ava w+ l++d++a+fd++v+
  lcl|NCBI__GCF_000423825.1:WP_051180794.1 210 ALSIEGRMTVCNMAIEAGARAGMVAVDDKTIDYVKGRPFAPQGALWEQAVAAWRELRSDPDAVFDREVV 278
                                               ********************************************************************* PP

                                 TIGR00170 279 leakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsc 347
                                               l+a +i pqvtwgt+p++v+ +n+ vpdp+   dpv+++ +e+alay+gle++t+++ i++dkvfigsc
  lcl|NCBI__GCF_000423825.1:WP_051180794.1 279 LDAAEIQPQVTWGTSPEMVVGINDRVPDPAREPDPVRRHAMEQALAYMGLEANTPMTAIAIDKVFIGSC 347
                                               ********************************************************************* PP

                                 TIGR00170 348 tnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnn 416
                                               tn+riedlraaa+v+kg+kva+ vk+alvvpgsglvk+qae+egld+if eagfewr++gcs+cl+mn 
  lcl|NCBI__GCF_000423825.1:WP_051180794.1 348 TNARIEDLRAAAAVAKGHKVAPHVKQALVVPGSGLVKRQAEAEGLDRIFKEAGFEWRDPGCSMCLAMNA 416
                                               ********************************************************************* PP

                                 TIGR00170 417 dvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdire 465
                                               d+l+++erca+tsnrnfegrqgkg+rthlvspa+aaaaa+ag+fvd+r 
  lcl|NCBI__GCF_000423825.1:WP_051180794.1 417 DRLEPGERCAATSNRNFEGRQGKGGRTHLVSPAVAAAAAIAGHFVDVRA 465
                                               ***********************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (480 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: 9.56
//
[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