Alignments for a candidate for leuC in Allochromatium vinosum DSM 180

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Allochromatium vinosum DSM 180

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_012970815.1 ALVIN_RS07970 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_000025485.1:WP_012970815.1
          Length = 467

 Score =  603 bits (1556), Expect = e-177
 Identities = 303/466 (65%), Positives = 362/466 (77%), Gaps = 1/466 (0%)

Query: 1   MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60
           +AKTLY+KL+D HVV   +  T LLYIDR L+HEVTSPQAF+GLR  GR   +     A 
Sbjct: 2   VAKTLYDKLWDEHVVRVDDTGTALLYIDRQLIHEVTSPQAFEGLRLAGRQPWRVSANLAV 61

Query: 61  MDHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLP 120
            DHNV T  +       ++R+Q++ L  NC+ FG+    +    QG+VHV+GPEQG TLP
Sbjct: 62  PDHNVPTTDRAAGIADPVSRLQVETLGTNCQTFGITELSMGDKRQGVVHVVGPEQGFTLP 121

Query: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITA 180
           G T+VCGDSHTATHGAFGALAFGIGTSEVEHVLATQTL Q ++K+M I V G+   G+TA
Sbjct: 122 GATVVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLIQRKSKSMLISVDGQLGAGVTA 181

Query: 181 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTF 240
           KDIVLAIIG+ G+AGGTG V+EF GEAIR LSMEGRMT+CNMAIE GA+AGL+  DE T 
Sbjct: 182 KDIVLAIIGEIGTAGGTGFVIEFGGEAIRALSMEGRMTVCNMAIEAGARAGLIGVDEKTV 241

Query: 241 NYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISV 300
           +Y++GR  AP+G+ F+ A A+W+TL +D GA FD V+ + A  + PQVTWGT+P  V  V
Sbjct: 242 DYMRGRPLAPEGELFERAAAHWRTLVSDAGAQFDRVLHIDAASLKPQVTWGTSPEMVQPV 301

Query: 301 NDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360
           +  +PDPA+ +DPV+     +AL YMGL  G P++E+  DKVFIGSCTNSRIEDLRAAAE
Sbjct: 302 DGRVPDPAAESDPVKANGIRRALDYMGLTAGTPISEIRPDKVFIGSCTNSRIEDLRAAAE 361

Query: 361 IAKGRKVAPGVQ-ALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLN 419
           IAKGRKVA  ++ A+VVPGSG VK QAEAEGLDKIF+ AGFEWR PGCSMCLAMN DRL 
Sbjct: 362 IAKGRKVADSIKLAMVVPGSGLVKEQAEAEGLDKIFVAAGFEWREPGCSMCLAMNADRLE 421

Query: 420 PGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
           PGERCASTSNRNFEGRQG+GGRTHLVSPAMAAAAAVTGHF D+R +
Sbjct: 422 PGERCASTSNRNFEGRQGQGGRTHLVSPAMAAAAAVTGHFVDVRTL 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: 750
Number of extensions: 22
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: 467
Length adjustment: 33
Effective length of query: 433
Effective length of database: 434
Effective search space:   187922
Effective search space used:   187922
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_012970815.1 ALVIN_RS07970 (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.30862.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-240  784.2   0.2   2.2e-240  784.0   0.2    1.0  1  lcl|NCBI__GCF_000025485.1:WP_012970815.1  ALVIN_RS07970 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025485.1:WP_012970815.1  ALVIN_RS07970 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  784.0   0.2  2.2e-240  2.2e-240       2     465 ..       3     466 ..       2     467 .] 1.00

  Alignments for each domain:
  == domain 1  score: 784.0 bits;  conditional E-value: 2.2e-240
                                 TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr 70 
                                               aktly+kl+d+hvv+ ++++t llyidr l+hevtspqafeglr agr+  rv+  la  dhn++t+ r
  lcl|NCBI__GCF_000025485.1:WP_012970815.1   3 AKTLYDKLWDEHVVRVDDTGTALLYIDRQLIHEVTSPQAFEGLRLAGRQPWRVSANLAVPDHNVPTTDR 71 
                                               89******************************************************************* PP

                                 TIGR00170  71 dveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafga 139
                                                  i + +++lqv++l  n++ fg+  + + +++qg+vhvvgpe+g+tlpg t+vcgdshtathgafga
  lcl|NCBI__GCF_000025485.1:WP_012970815.1  72 AAGIADPVSRLQVETLGTNCQTFGITELSMGDKRQGVVHVVGPEQGFTLPGATVVCGDSHTATHGAFGA 140
                                               ********************************************************************* PP

                                 TIGR00170 140 lafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageai 208
                                               lafgigtsevehvlatqtl+q ++k++ i v+g+l  g+takdi+laiig ig+aggtg+v+ef geai
  lcl|NCBI__GCF_000025485.1:WP_012970815.1 141 LAFGIGTSEVEHVLATQTLIQRKSKSMLISVDGQLGAGVTAKDIVLAIIGEIGTAGGTGFVIEFGGEAI 209
                                               ********************************************************************* PP

                                 TIGR00170 209 rdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvv 277
                                               r+lsme+rmtvcnmaieaga+agli  de t +y+++r++ap g+ fe a a+w+tl +d ga+fd+v+
  lcl|NCBI__GCF_000025485.1:WP_012970815.1 210 RALSMEGRMTVCNMAIEAGARAGLIGVDEKTVDYMRGRPLAPEGELFERAAAHWRTLVSDAGAQFDRVL 278
                                               ********************************************************************* PP

                                 TIGR00170 278 tleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigs 346
                                                ++a  + pqvtwgt+p++v +v++ vpdp+  +dpv+ +++ +al+y+gl++gt++ +i+ dkvfigs
  lcl|NCBI__GCF_000025485.1:WP_012970815.1 279 HIDAASLKPQVTWGTSPEMVQPVDGRVPDPAAESDPVKANGIRRALDYMGLTAGTPISEIRPDKVFIGS 347
                                               ********************************************************************* PP

                                 TIGR00170 347 ctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmn 415
                                               ctnsriedlraaae++kg+kvad++kla+vvpgsglvk+qae+egldkif++agfewre+gcs+cl+mn
  lcl|NCBI__GCF_000025485.1:WP_012970815.1 348 CTNSRIEDLRAAAEIAKGRKVADSIKLAMVVPGSGLVKEQAEAEGLDKIFVAAGFEWREPGCSMCLAMN 416
                                               ********************************************************************* PP

                                 TIGR00170 416 ndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdire 465
                                                d+l+++ercastsnrnfegrqg+g+rthlvspamaaaaav+g+fvd+r 
  lcl|NCBI__GCF_000025485.1:WP_012970815.1 417 ADRLEPGERCASTSNRNFEGRQGQGGRTHLVSPAMAAAAAVTGHFVDVRT 466
                                               ************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (467 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: 7.58
//
[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