Alignments for a candidate for leuC in Hydrogenovibrio marinus DSM 11271

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Hydrogenovibrio marinus DSM 11271

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_197942621.1 P166_RS0105925 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_000711315.1:WP_197942621.1
          Length = 473

 Score =  583 bits (1503), Expect = e-171
 Identities = 292/468 (62%), Positives = 352/468 (75%), Gaps = 3/468 (0%)

Query: 1   MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60
           M KTLY+KL+D HVV + E+ T L+YIDR L+HEVTSPQAF+GL+  GR   +     AT
Sbjct: 1   MGKTLYDKLWDGHVVRQEEDGTALIYIDRQLLHEVTSPQAFEGLKMSGRKPWRVDANVAT 60

Query: 61  MDHNVSTQ--TKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVT 118
            DHNV T   T   +    ++RIQ+Q L  N K FG+  + +    QGIVHV+GPE+GVT
Sbjct: 61  PDHNVPTTAYTSAEDIKDPISRIQVQTLDANTKYFGITEFGIGDVRQGIVHVVGPEEGVT 120

Query: 119 LPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGI 178
           LPGMT+VCGDSHTATHGA GALA G+GTSEVEHVLATQ L Q + K M ++V G+  PG+
Sbjct: 121 LPGMTLVCGDSHTATHGALGALAHGVGTSEVEHVLATQCLLQKKMKNMLVKVDGQLRPGV 180

Query: 179 TAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDET 238
           T KD++LAIIGK G+AGG GH +EF G+  +D+S+EGRMT+CNMAIE GA+ GLVA D+ 
Sbjct: 181 TPKDVILAIIGKIGTAGGNGHAIEFGGQVFKDMSVEGRMTVCNMAIEAGARVGLVAVDDK 240

Query: 239 TFNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVI 298
           T  YVKGR +APK +D+D AVA W  L +D  A FDTVV +   EI PQV+WGT+P  V 
Sbjct: 241 TIEYVKGRPYAPKAEDWDKAVAAWSNLHSDANAVFDTVVEMNGVEIEPQVSWGTSPEMVT 300

Query: 299 SVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAA 358
            VN  +P+P + ADPV+     +AL YMGL  G+ +T++ +D VFIGSCTNSRIED+RAA
Sbjct: 301 DVNGKVPNPDAEADPVKAGGIRRALEYMGLDAGMSITDIPVDYVFIGSCTNSRIEDIRAA 360

Query: 359 AEIAKGRKVAPGV-QALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDR 417
           A++ KGRKVA  V QAL+VPGSG VK QAE EGLDKIFIEAGFEWR PGCSMCLAMN DR
Sbjct: 361 AKVLKGRKVAASVEQALMVPGSGLVKKQAEEEGLDKIFIEAGFEWRNPGCSMCLAMNADR 420

Query: 418 LNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
           L  G+ CASTSNRNFEGRQG GGRTHLVSP MAAAAAV GHF D+R +
Sbjct: 421 LPSGKHCASTSNRNFEGRQGAGGRTHLVSPEMAAAAAVAGHFVDVRTM 468


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: 759
Number of extensions: 26
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: 473
Length adjustment: 33
Effective length of query: 433
Effective length of database: 440
Effective search space:   190520
Effective search space used:   190520
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_197942621.1 P166_RS0105925 (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.81713.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-231  754.4   1.7   2.3e-231  754.2   1.7    1.0  1  NCBI__GCF_000711315.1:WP_197942621.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000711315.1:WP_197942621.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  754.2   1.7  2.3e-231  2.3e-231       1     465 [.       1     467 [.       1     468 [. 0.99

  Alignments for each domain:
  == domain 1  score: 754.2 bits;  conditional E-value: 2.3e-231
                             TIGR00170   1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr..d 71 
                                           m ktly+kl+d hvv+++e++t l+yidr l+hevtspqafegl+  grk  rvd  +at dhn++t++    
  NCBI__GCF_000711315.1:WP_197942621.1   1 MGKTLYDKLWDGHVVRQEEDGTALIYIDRQLLHEVTSPQAFEGLKMSGRKPWRVDANVATPDHNVPTTAYtsA 73 
                                           789***************************************************************9876436 PP

                             TIGR00170  72 veikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgi 144
                                            +ik+  +++qv++l+ n+k fg+  f++ +++qgivhvvgpeeg+tlpg+t+vcgdshtathga+gala g+
  NCBI__GCF_000711315.1:WP_197942621.1  74 EDIKDPISRIQVQTLDANTKYFGITEFGIGDVRQGIVHVVGPEEGVTLPGMTLVCGDSHTATHGALGALAHGV 146
                                           6899********************************************************************* PP

                             TIGR00170 145 gtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeerm 217
                                           gtsevehvlatq l q++ k++ ++v+g+l +g+t kd+ilaiigkig+agg g+ +ef g++++d+s+e+rm
  NCBI__GCF_000711315.1:WP_197942621.1 147 GTSEVEHVLATQCLLQKKMKNMLVKVDGQLRPGVTPKDVILAIIGKIGTAGGNGHAIEFGGQVFKDMSVEGRM 219
                                           ************************************************************************* PP

                             TIGR00170 218 tvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtw 290
                                           tvcnmaieaga+ gl+a d+ t+eyvk+r+yapk ++++kava w  l++d +a+fd+vv +++++i pqv+w
  NCBI__GCF_000711315.1:WP_197942621.1 220 TVCNMAIEAGARVGLVAVDDKTIEYVKGRPYAPKAEDWDKAVAAWSNLHSDANAVFDTVVEMNGVEIEPQVSW 292
                                           ************************************************************************* PP

                             TIGR00170 291 gtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvk 363
                                           gt+p++v  vn++vp+p+  adpv+  ++ +al+y+gl++g++++di vd vfigsctnsried+raaa+v+k
  NCBI__GCF_000711315.1:WP_197942621.1 293 GTSPEMVTDVNGKVPNPDAEADPVKAGGIRRALEYMGLDAGMSITDIPVDYVFIGSCTNSRIEDIRAAAKVLK 365
                                           ************************************************************************* PP

                             TIGR00170 364 gkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegr 436
                                           g+kva +v++al+vpgsglvkkqae+egldkif+eagfewr++gcs+cl+mn d+l++++ castsnrnfegr
  NCBI__GCF_000711315.1:WP_197942621.1 366 GRKVAASVEQALMVPGSGLVKKQAEEEGLDKIFIEAGFEWRNPGCSMCLAMNADRLPSGKHCASTSNRNFEGR 438
                                           ************************************************************************* PP

                             TIGR00170 437 qgkgarthlvspamaaaaavagkfvdire 465
                                           qg+g+rthlvsp maaaaavag+fvd+r 
  NCBI__GCF_000711315.1:WP_197942621.1 439 QGAGGRTHLVSPEMAAAAAVAGHFVDVRT 467
                                           ***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (473 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 23.97
//
[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