Alignments for a candidate for leuC in Dechloromonas agitata is5

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Dechloromonas agitata is5

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_027456324.1 K420_RS0100520 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_000519045.1:WP_027456324.1
          Length = 468

 Score =  597 bits (1539), Expect = e-175
 Identities = 301/467 (64%), Positives = 357/467 (76%), Gaps = 2/467 (0%)

Query: 1   MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60
           M+KTLY+KL++ HVV +  + T LLYIDRHLVHEVTSPQAF+GL+  GR   +     AT
Sbjct: 1   MSKTLYDKLWENHVVRQEADGTALLYIDRHLVHEVTSPQAFEGLKLAGRKPWRVSSIVAT 60

Query: 61  MDHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELY-DLNHPYQGIVHVMGPEQGVTL 119
            DHN  T   +      ++R Q++ L  N +E G   Y        GI+HV+GPE G TL
Sbjct: 61  PDHNTPTDHWEEGIKDPISRQQVETLDANIREVGALAYFPFKDQRMGILHVVGPENGATL 120

Query: 120 PGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGIT 179
           PGMT+VCGDSHT+THGAF  +A GIGTSEVEHVLATQ L Q ++KTM I V+GK   G+T
Sbjct: 121 PGMTVVCGDSHTSTHGAFACMAHGIGTSEVEHVLATQCLLQKKSKTMLIAVEGKLGKGVT 180

Query: 180 AKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETT 239
           AKD+ LAIIG  G+AGGTG+ +E+ G AIR LSMEGRMTLCNMAIE GA+ G VA D+TT
Sbjct: 181 AKDVALAIIGAIGTAGGTGYAIEYGGSAIRSLSMEGRMTLCNMAIEGGARLGFVAVDDTT 240

Query: 240 FNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVIS 299
            NY+KGR  +P G+++D AVAYW+TL +D GA FD VVTL+AE+I PQVTWGT+P  V+ 
Sbjct: 241 INYLKGRPFSPTGENWDKAVAYWRTLHSDPGAQFDRVVTLKAEDIRPQVTWGTSPEMVVP 300

Query: 300 VNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAA 359
           V+  +PDPA  ADPV+R   E+AL YMGL P  P+ ++AIDKVFIGSCTNSRIEDLR AA
Sbjct: 301 VDAVVPDPAREADPVKREGMERALQYMGLNPNTPIKDIAIDKVFIGSCTNSRIEDLREAA 360

Query: 360 EIAKGRKVAPGVQ-ALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRL 418
            + KGR++A  V+ AL VPGSG VK QAEAEGLDKIF+ AGFEWR PGCSMCLAMN DRL
Sbjct: 361 AVLKGRRIAANVKLALAVPGSGLVKRQAEAEGLDKIFVAAGFEWREPGCSMCLAMNADRL 420

Query: 419 NPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
            PGERCASTSNRNFEGRQG GGRTHLVSPAMAAAAAV GHFAD+R +
Sbjct: 421 EPGERCASTSNRNFEGRQGPGGRTHLVSPAMAAAAAVAGHFADVREV 467


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: 770
Number of extensions: 21
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: 468
Length adjustment: 33
Effective length of query: 433
Effective length of database: 435
Effective search space:   188355
Effective search space used:   188355
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_027456324.1 K420_RS0100520 (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.28313.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.1e-237  773.6   0.0   3.5e-237  773.4   0.0    1.0  1  lcl|NCBI__GCF_000519045.1:WP_027456324.1  K420_RS0100520 3-isopropylmalate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000519045.1:WP_027456324.1  K420_RS0100520 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  773.4   0.0  3.5e-237  3.5e-237       1     466 []       1     467 [.       1     467 [. 0.99

  Alignments for each domain:
  == domain 1  score: 773.4 bits;  conditional E-value: 3.5e-237
                                 TIGR00170   1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistes 69 
                                               m+ktly+kl+++hvv+++ ++t llyidrhlvhevtspqafegl+ agrk  rv++ +at dhn +t+ 
  lcl|NCBI__GCF_000519045.1:WP_027456324.1   1 MSKTLYDKLWENHVVRQEADGTALLYIDRHLVHEVTSPQAFEGLKLAGRKPWRVSSIVATPDHNTPTDH 69 
                                               79******************************************************************* PP

                                 TIGR00170  70 rdveikeekaklqvkeleknvkefg.vklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgaf 137
                                                +  ik+  ++ qv++l+ n++e+g + +f +++++ gi+hvvgpe+g tlpg+t+vcgdsht+thgaf
  lcl|NCBI__GCF_000519045.1:WP_027456324.1  70 WEEGIKDPISRQQVETLDANIREVGaLAYFPFKDQRMGILHVVGPENGATLPGMTVVCGDSHTSTHGAF 138
                                               ************************95689**************************************** PP

                                 TIGR00170 138 galafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefage 206
                                                ++a gigtsevehvlatq l q+++kt+ i vegkl kg+takd+ laiig ig+aggtgy +e+ g 
  lcl|NCBI__GCF_000519045.1:WP_027456324.1 139 ACMAHGIGTSEVEHVLATQCLLQKKSKTMLIAVEGKLGKGVTAKDVALAIIGAIGTAGGTGYAIEYGGS 207
                                               ********************************************************************* PP

                                 TIGR00170 207 airdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdk 275
                                               air+lsme+rmt+cnmaie ga+ g++a d+tt++y+k+r+++p g++++kavayw+tl++d+ga+fd+
  lcl|NCBI__GCF_000519045.1:WP_027456324.1 208 AIRSLSMEGRMTLCNMAIEGGARLGFVAVDDTTINYLKGRPFSPTGENWDKAVAYWRTLHSDPGAQFDR 276
                                               ********************************************************************* PP

                                 TIGR00170 276 vvtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfi 344
                                               vvtl+a+di pqvtwgt+p++v++v+  vpdp+  adpv+++++e+al+y+gl+p+t++kdi++dkvfi
  lcl|NCBI__GCF_000519045.1:WP_027456324.1 277 VVTLKAEDIRPQVTWGTSPEMVVPVDAVVPDPAREADPVKREGMERALQYMGLNPNTPIKDIAIDKVFI 345
                                               ********************************************************************* PP

                                 TIGR00170 345 gsctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclg 413
                                               gsctnsriedlr+aa+v+kg+++a nvklal vpgsglvk+qae+egldkif++agfewre+gcs+cl+
  lcl|NCBI__GCF_000519045.1:WP_027456324.1 346 GSCTNSRIEDLREAAAVLKGRRIAANVKLALAVPGSGLVKRQAEAEGLDKIFVAAGFEWREPGCSMCLA 414
                                               ********************************************************************* PP

                                 TIGR00170 414 mnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdirel 466
                                               mn d+l+++ercastsnrnfegrqg g+rthlvspamaaaaavag+f+d+re+
  lcl|NCBI__GCF_000519045.1:WP_027456324.1 415 MNADRLEPGERCASTSNRNFEGRQGPGGRTHLVSPAMAAAAAVAGHFADVREV 467
                                               ***************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (468 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.02
//
[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