Alignments for a candidate for leuC in Hydrogenovibrio halophilus DSM 15072

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Hydrogenovibrio halophilus DSM 15072

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_019895993.1 A377_RS0108985 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_000384235.1:WP_019895993.1
          Length = 480

 Score =  567 bits (1460), Expect = e-166
 Identities = 280/467 (59%), Positives = 351/467 (75%), Gaps = 4/467 (0%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           +TLY+KL+ +H + E  + T L+YIDR L+HEVTSPQAF+GLR  GR   +     AT D
Sbjct: 8   QTLYDKLWQSHRIREDADGTALIYIDRQLLHEVTSPQAFEGLRLAGRKPWRVDANVATCD 67

Query: 63  HNVSTQTKD---INACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTL 119
           HNV T + +    +    ++RIQ+Q L +N  EFG+  + +  P QGIVHV+GPE+G+TL
Sbjct: 68  HNVPTTSLEGGVSSIVDPVSRIQVQTLDRNAAEFGILEFPMGDPRQGIVHVVGPEEGITL 127

Query: 120 PGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGIT 179
           PGMT+VCGDSHTATHGA GALA G+GTSEVEHVLATQ L Q + K M ++V G+ APG+T
Sbjct: 128 PGMTLVCGDSHTATHGALGALAHGVGTSEVEHVLATQCLIQKKMKNMLVKVDGQLAPGVT 187

Query: 180 AKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETT 239
            KD++LA+IG+ G+AGG G+ +EF G+  RD+++EGRMT+CNMAIE GA+ GLVA D+ T
Sbjct: 188 PKDVILAVIGQIGTAGGNGYAIEFGGQVFRDMTVEGRMTVCNMAIEAGARVGLVAVDDKT 247

Query: 240 FNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVIS 299
             YVKGR +APKG+ ++ AV  W++L +DEGA FD VV +    I PQV+WGT+P  V  
Sbjct: 248 IEYVKGRPYAPKGELWEQAVESWQSLVSDEGAVFDKVVEIDGSAIEPQVSWGTSPEMVGP 307

Query: 300 VNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAA 359
           +N  +PDP   AD V+  S   AL YMGL PG P  ++ +D +FIGSCTNSRIEDLRAAA
Sbjct: 308 INGCVPDPDKQADSVKAESIRHALQYMGLTPGTPFVDIGVDYIFIGSCTNSRIEDLRAAA 367

Query: 360 EIAKGRKVAPGVQ-ALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRL 418
           E+ KGRKVA  V+ A+VVPGSG VK QAEAEGLD+IF++AGFEWR PGCSMCLAMN D+L
Sbjct: 368 EVVKGRKVADSVELAMVVPGSGLVKQQAEAEGLDRIFLDAGFEWRNPGCSMCLAMNADKL 427

Query: 419 NPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
             G+ CASTSNRNFEGRQG GGRTHLVSP MAAAAAV G F D+R +
Sbjct: 428 PAGKHCASTSNRNFEGRQGAGGRTHLVSPEMAAAAAVAGRFVDVRTM 474


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: 755
Number of extensions: 25
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_019895993.1 A377_RS0108985 (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.337211.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.4e-228  744.3   0.1   2.8e-228  744.1   0.1    1.0  1  NCBI__GCF_000384235.1:WP_019895993.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000384235.1:WP_019895993.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  744.1   0.1  2.8e-228  2.8e-228       2     465 ..       7     473 ..       6     474 .. 0.99

  Alignments for each domain:
  == domain 1  score: 744.1 bits;  conditional E-value: 2.8e-228
                             TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr...d 71 
                                           ++tly+kl+++h ++e+ ++t l+yidr l+hevtspqafeglr agrk  rvd  +at dhn++t+s     
  NCBI__GCF_000384235.1:WP_019895993.1   7 PQTLYDKLWQSHRIREDADGTALIYIDRQLLHEVTSPQAFEGLRLAGRKPWRVDANVATCDHNVPTTSLeggV 79 
                                           89****************************************************************9985544 PP

                             TIGR00170  72 veikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgi 144
                                             i++ ++++qv++l++n+ efg+  f + + +qgivhvvgpeeg+tlpg+t+vcgdshtathga+gala g+
  NCBI__GCF_000384235.1:WP_019895993.1  80 SSIVDPVSRIQVQTLDRNAAEFGILEFPMGDPRQGIVHVVGPEEGITLPGMTLVCGDSHTATHGALGALAHGV 152
                                           6899********************************************************************* PP

                             TIGR00170 145 gtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeerm 217
                                           gtsevehvlatq l+q++ k++ ++v+g+la+g+t kd+ila+ig+ig+agg gy +ef g+++rd+++e+rm
  NCBI__GCF_000384235.1:WP_019895993.1 153 GTSEVEHVLATQCLIQKKMKNMLVKVDGQLAPGVTPKDVILAVIGQIGTAGGNGYAIEFGGQVFRDMTVEGRM 225
                                           ************************************************************************* PP

                             TIGR00170 218 tvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtw 290
                                           tvcnmaieaga+ gl+a d+ t+eyvk+r+yapkg+ +e+av+ w++l +dega+fdkvv ++++ i pqv+w
  NCBI__GCF_000384235.1:WP_019895993.1 226 TVCNMAIEAGARVGLVAVDDKTIEYVKGRPYAPKGELWEQAVESWQSLVSDEGAVFDKVVEIDGSAIEPQVSW 298
                                           ************************************************************************* PP

                             TIGR00170 291 gtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvk 363
                                           gt+p++v ++n+ vpdp++ ad v+ +s+ +al+y+gl+pgt++ di vd +figsctnsriedlraaaevvk
  NCBI__GCF_000384235.1:WP_019895993.1 299 GTSPEMVGPINGCVPDPDKQADSVKAESIRHALQYMGLTPGTPFVDIGVDYIFIGSCTNSRIEDLRAAAEVVK 371
                                           ************************************************************************* PP

                             TIGR00170 364 gkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegr 436
                                           g+kvad+v+la+vvpgsglvk+qae+egld+ifl+agfewr++gcs+cl+mn d+l++++ castsnrnfegr
  NCBI__GCF_000384235.1:WP_019895993.1 372 GRKVADSVELAMVVPGSGLVKQQAEAEGLDRIFLDAGFEWRNPGCSMCLAMNADKLPAGKHCASTSNRNFEGR 444
                                           ************************************************************************* PP

                             TIGR00170 437 qgkgarthlvspamaaaaavagkfvdire 465
                                           qg+g+rthlvsp maaaaavag+fvd+r 
  NCBI__GCF_000384235.1:WP_019895993.1 445 QGAGGRTHLVSPEMAAAAAVAGRFVDVRT 473
                                           ***************************97 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 19.07
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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