Alignments for a candidate for leuC in Halomonas desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Halomonas desiderata SP1

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_086508303.1 BZY95_RS01840 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_002151265.1:WP_086508303.1
          Length = 465

 Score =  504 bits (1297), Expect = e-147
 Identities = 250/466 (53%), Positives = 330/466 (70%), Gaps = 4/466 (0%)

Query: 1   MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60
           M  TL++K++DAH +   E+   LL+IDRH VHE  S  AF+ L      V +P  TF  
Sbjct: 3   MPTTLFDKVWDAHEILRGESGQSLLWIDRHFVHE-GSFHAFNKLHERELSVARPDLTFGI 61

Query: 61  MDHNVSTQTKDINACGEM-ARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTL 119
            DH V T T+ ++A G+   R  +++L  N +  G+ L+ L+ P QGIVHV+GPEQG+T 
Sbjct: 62  ADHYVPTLTRRLDAIGDAKVRGMIEQLADNTRHHGITLFGLDDPRQGIVHVLGPEQGLTQ 121

Query: 120 PGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGIT 179
           PG+ +VCGDSHT+THGAFG++AFGIG SEV HVLATQTL Q R K M++ V+G+ APGI+
Sbjct: 122 PGLLMVCGDSHTSTHGAFGSIAFGIGASEVAHVLATQTLWQSRPKKMRLTVEGELAPGIS 181

Query: 180 AKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETT 239
           AKDI L  I + G+ G  G+ +E+ G AIR LSME R+TLCN++IE GA+ G++APD TT
Sbjct: 182 AKDIALTWIARLGADGARGYAIEYAGSAIRSLSMEARLTLCNLSIEGGARCGMIAPDATT 241

Query: 240 FNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVIS 299
           F+Y++GR  AP+G  ++ A+AYW+TL++D+GA FD    L A EI+P VTWG +P + + 
Sbjct: 242 FDYLRGRPFAPRGAQWEQALAYWQTLKSDDGARFDREERLAAAEIAPTVTWGVSPEEALP 301

Query: 300 VNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAA 359
           ++  +PDPA   D  +      +L YMGL  G  LT++ ID+VFIGSCTN+R+EDLRAAA
Sbjct: 302 IDARVPDPADQRDAGKARQLRDSLDYMGLAAGQKLTDIVIDRVFIGSCTNARLEDLRAAA 361

Query: 360 EIAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLN 419
            + +GR+    V  +V PGS  VK QAEAEGLD +F EAG EWR  GCSMC+ MN D + 
Sbjct: 362 AVLRGRR--SKVPGIVSPGSTQVKRQAEAEGLDAVFREAGLEWRESGCSMCVGMNGDLVP 419

Query: 420 PGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
           PGERCAST+NRNF+GRQG G RTHL+SPAM AAAAV G  AD+R +
Sbjct: 420 PGERCASTTNRNFKGRQGPGARTHLMSPAMVAAAAVAGRLADVREL 465


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: 668
Number of extensions: 20
Number of successful extensions: 4
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: 465
Length adjustment: 33
Effective length of query: 433
Effective length of database: 432
Effective search space:   187056
Effective search space used:   187056
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_086508303.1 BZY95_RS01840 (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.18839.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.6e-200  651.4   0.0     4e-200  651.2   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086508303.1  BZY95_RS01840 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086508303.1  BZY95_RS01840 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  651.2   0.0    4e-200    4e-200       1     466 []       3     465 .]       3     465 .] 0.98

  Alignments for each domain:
  == domain 1  score: 651.2 bits;  conditional E-value: 4e-200
                                 TIGR00170   1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistes 69 
                                               m+ tl++k++dah + ++e++++ll+idrh+vhe  s  af+ l++++  v r+d t++  dh ++t +
  lcl|NCBI__GCF_002151265.1:WP_086508303.1   3 MPTTLFDKVWDAHEILRGESGQSLLWIDRHFVHE-GSFHAFNKLHERELSVARPDLTFGIADHYVPTLT 70 
                                               899*******************************.5899****************************** PP

                                 TIGR00170  70 rdveik.eekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgaf 137
                                               r +++  + k +  +++l  n+++ g+ lf+l++ +qgivhv+gpe+glt pg  +vcgdsht+thgaf
  lcl|NCBI__GCF_002151265.1:WP_086508303.1  71 RRLDAIgDAKVRGMIEQLADNTRHHGITLFGLDDPRQGIVHVLGPEQGLTQPGLLMVCGDSHTSTHGAF 139
                                               *987661567788999***************************************************** PP

                                 TIGR00170 138 galafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefage 206
                                               g++afgig+sev hvlatqtl+q+r+k+++++veg+la+gi+akdi l+ i ++g+ g  gy +e+ag 
  lcl|NCBI__GCF_002151265.1:WP_086508303.1 140 GSIAFGIGASEVAHVLATQTLWQSRPKKMRLTVEGELAPGISAKDIALTWIARLGADGARGYAIEYAGS 208
                                               ********************************************************************* PP

                                 TIGR00170 207 airdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdk 275
                                               air+lsme+r+t+cn++ie ga+ g+iapd ttf+y+++r++ap+g+++e+a+ayw+tlk+d+ga+fd+
  lcl|NCBI__GCF_002151265.1:WP_086508303.1 209 AIRSLSMEARLTLCNLSIEGGARCGMIAPDATTFDYLRGRPFAPRGAQWEQALAYWQTLKSDDGARFDR 277
                                               ********************************************************************* PP

                                 TIGR00170 276 vvtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfi 344
                                               +  l a +i+p+vtwg++p+++l+++  vpdp++  d  + ++   +l+y+gl +g+kl+di +d+vfi
  lcl|NCBI__GCF_002151265.1:WP_086508303.1 278 EERLAAAEIAPTVTWGVSPEEALPIDARVPDPADQRDAGKARQLRDSLDYMGLAAGQKLTDIVIDRVFI 346
                                               ********************************************************************* PP

                                 TIGR00170 345 gsctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclg 413
                                               gsctn+r+edlraaa+v++g++  ++v   +v pgs +vk+qae+egld +f eag+ewre+gcs+c+g
  lcl|NCBI__GCF_002151265.1:WP_086508303.1 347 GSCTNARLEDLRAAAAVLRGRR--SKVP-GIVSPGSTQVKRQAEAEGLDAVFREAGLEWRESGCSMCVG 412
                                               ********************98..5677.899************************************* PP

                                 TIGR00170 414 mnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdirel 466
                                               mn d ++++ercast+nrnf+grqg garthl+spam aaaavag+++d+rel
  lcl|NCBI__GCF_002151265.1:WP_086508303.1 413 MNGDLVPPGERCASTTNRNFKGRQGPGARTHLMSPAMVAAAAVAGRLADVREL 465
                                               ***************************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (465 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: 00:00:00.03
# Mc/sec: 6.95
//
[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