Alignments for a candidate for leuC in Desulfacinum infernum DSM 9756

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Desulfacinum infernum DSM 9756

Align 3-isopropylmalate dehydratase (EC 4.2.1.33); homoaconitate hydratase (EC 4.2.1.36) (characterized)
to candidate WP_073038272.1 BUB04_RS06990 3-isopropylmalate dehydratase large subunit

Query= BRENDA::P81291
         (424 letters)



>NCBI__GCF_900129305.1:WP_073038272.1
          Length = 424

 Score =  375 bits (963), Expect = e-108
 Identities = 186/422 (44%), Positives = 271/422 (64%), Gaps = 7/422 (1%)

Query: 3   MTIVEKILAKASGKKEVSPGDIVMANIDVAMVHDITGPLTVNTLKEYGIEKVWNPEKIVI 62
           M  +EKILA+ASGK  V  G+IV   +D+A V+D+  P T+++  E G  +V +P++I  
Sbjct: 1   MHAIEKILARASGKDSVRAGEIVNCRVDLAEVNDLY-PQTIHSFYEMGGRRVHSPDRITF 59

Query: 63  LFDHQVPADSIKAAENHILMRKFVKEQGIKYFYDIREGVCHQVLPEKGHVAPGEVVVGAD 122
           + DH  PA SI+ AEN   MR+F +EQGI+  +D+  GVCHQV+ + G V PG V++  D
Sbjct: 60  ILDHYAPASSIQQAENQKFMREFCREQGIELLFDVNSGVCHQVMVDHGLVYPGMVLIATD 119

Query: 123 SHTCTHGAFGAFATGIGSTDMAHVFATGKLWFKVPETIYFNITGDLQPYVTSKDVILSII 182
           SHT THGA GAF TG+G+TD+A + ATG LW +VPE +  ++TG L   V +KDVIL II
Sbjct: 120 SHTTTHGALGAFGTGVGATDLAVILATGHLWLRVPEILRIHLTGRLSVGVYAKDVILHII 179

Query: 183 GEVGVDGATYKACQFGGETVKKMSIASRMTMTNMAIEMGGKTGIIEPDEKTIQYVKEAMK 242
           G +G D A YKA +F G  VK++S++ RM + NM  EMG K   I+PD+ T+ ++K  +K
Sbjct: 180 GRLGADYAIYKAVEFTGPVVKELSVSERMALCNMTTEMGAKCAYIQPDQVTLGFLKGKVK 239

Query: 243 KHGTERPFEVIKGDEDAEFAEVYEIEADKIEPVFACPHNVDNVKQAREVAGKPIDQVFIG 302
                R  E ++ D D ++AE    +   I P  A P +VDNV+   E+ G P+ Q ++G
Sbjct: 240 -----RNLEPVETDPDFQYAEELFFDVSAIPPQLAVPSSVDNVRPLSELVGTPVHQAYLG 294

Query: 303 SCTNGRLEDLRMAIKIIEKHGGIADDVRVVVTPASREEYLKALKEGIIEKFLKYGCVVTN 362
           SCT GR EDL +A +I+ K   +  D R+VV PASR+ +L+AL+ G +   ++ G     
Sbjct: 295 SCTGGRAEDLAVAARIL-KGRRVHKDTRLVVVPASRDVFLEALQRGDVAALVEAGATFVT 353

Query: 363 PSCSACMGSLYGVLGPGEVCVSTSNRNFRGRQGSLEAEIYLASPITAAACAVKGELVDPR 422
           P C+AC+G+  G+L  GEVC++++NRNF GR G  ++ +YL SP   AA A+ G + DP 
Sbjct: 354 PGCAACLGTHEGILAAGEVCIASTNRNFPGRMGHTQSAVYLGSPAAVAAAALNGRITDPC 413

Query: 423 DL 424
           ++
Sbjct: 414 EI 415


Lambda     K      H
   0.318    0.136    0.400 

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: 506
Number of extensions: 16
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: 424
Length of database: 424
Length adjustment: 32
Effective length of query: 392
Effective length of database: 392
Effective search space:   153664
Effective search space used:   153664
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_073038272.1 BUB04_RS06990 (3-isopropylmalate dehydratase large subunit)
to HMM TIGR02086 (3-isopropylmalate dehydratase, large subunit)

# 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/TIGR02086.hmm
# target sequence database:        /tmp/gapView.536.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02086  [M=411]
Accession:   TIGR02086
Description: IPMI_arch: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.7e-159  514.7   0.2   8.7e-159  514.5   0.2    1.0  1  lcl|NCBI__GCF_900129305.1:WP_073038272.1  BUB04_RS06990 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900129305.1:WP_073038272.1  BUB04_RS06990 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  514.5   0.2  8.7e-159  8.7e-159       3     409 ..       3     412 ..       1     414 [. 0.98

  Alignments for each domain:
  == domain 1  score: 514.5 bits;  conditional E-value: 8.7e-159
                                 TIGR02086   3 laekilsekvGke.vkaGeivevkvDlvmvhDgtgplvikalrelg.akvekkekivlvfDhvvPaptv 69 
                                                +ekil++++Gk+ v+aGeiv  +vDl+ v+D   p++i+++ e+g  +v+++++i+ ++Dh +Pa+++
  lcl|NCBI__GCF_900129305.1:WP_073038272.1   3 AIEKILARASGKDsVRAGEIVNCRVDLAEVNDLY-PQTIHSFYEMGgRRVHSPDRITFILDHYAPASSI 70 
                                               579*********98******************85.7888999999989********************* PP

                                 TIGR02086  70 eaaelqkeirefakelgikv.fdvgeGichqvlvekgyakpgkvvvgaDshtttsGalgafatGlGatD 137
                                               + ae qk +ref +e+gi+  fdv++G+chqv+v++g++ pg+v++++Dshttt+Galgaf+tG+GatD
  lcl|NCBI__GCF_900129305.1:WP_073038272.1  71 QQAENQKFMREFCREQGIELlFDVNSGVCHQVMVDHGLVYPGMVLIATDSHTTTHGALGAFGTGVGATD 139
                                               ********************9************************************************ PP

                                 TIGR02086 138 valalatGktWlkvPesikveleGkleekvtakDvileivkelgadgatykaieftgeeiealsldeRl 206
                                               +a++latG++Wl+vPe ++++l+G+l+  v+akDvil+i+++lgad+a yka+eftg ++++ls++eR+
  lcl|NCBI__GCF_900129305.1:WP_073038272.1 140 LAVILATGHLWLRVPEILRIHLTGRLSVGVYAKDVILHIIGRLGADYAIYKAVEFTGPVVKELSVSERM 208
                                               ********************************************************************* PP

                                 TIGR02086 207 tlsnlaveagakaglvepdeetleylkkrrge.frilkadedakyeeeieidlseleplvavPhsvdnv 274
                                               +l+n+++e+gak ++++pd+ tl +lk ++++  + +++d+d +y+ee+ +d+s+++p+ avP svdnv
  lcl|NCBI__GCF_900129305.1:WP_073038272.1 209 ALCNMTTEMGAKCAYIQPDQVTLGFLKGKVKRnLEPVETDPDFQYAEELFFDVSAIPPQLAVPSSVDNV 277
                                               ***************************9988868899******************************** PP

                                 TIGR02086 275 keveevegteidqvfiGsCtnGRledlkiaaeilegrevhkdvrlivvPasrkvyekaleeGlietlve 343
                                               ++++e  gt + q+++GsCt GR edl +aa+il+gr+vhkd rl+vvPasr+v+ +al++G +  lve
  lcl|NCBI__GCF_900129305.1:WP_073038272.1 278 RPLSELVGTPVHQAYLGSCTGGRAEDLAVAARILKGRRVHKDTRLVVVPASRDVFLEALQRGDVAALVE 346
                                               ********************************************************************* PP

                                 TIGR02086 344 aGaiiltpgCGPClGahlGvladgevivsttnRnfkGRmGspkaeiYLasPavaavsaveGeitdp 409
                                               aGa+ +tpgC  ClG+h G+la gev+++ tnRnf GRmG++++ +YL sPa +a++a++G+itdp
  lcl|NCBI__GCF_900129305.1:WP_073038272.1 347 AGATFVTPGCAACLGTHEGILAAGEVCIASTNRNFPGRMGHTQSAVYLGSPAAVAAAALNGRITDP 412
                                               *****************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (411 nodes)
Target sequences:                          1  (424 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: 7.87
//
[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