Alignments for a candidate for leuC in Methanosarcina barkeri Fusaro

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Methanosarcina barkeri Fusaro

Align 3-isopropylmalate dehydratase (EC 4.2.1.33); homoaconitate hydratase (EC 4.2.1.36) (characterized)
to candidate WP_011306943.1 MBAR_RS10415 3-isopropylmalate dehydratase large subunit

Query= BRENDA::P81291
         (424 letters)



>NCBI__GCF_000195895.1:WP_011306943.1
          Length = 413

 Score =  433 bits (1113), Expect = e-126
 Identities = 221/419 (52%), Positives = 289/419 (68%), Gaps = 10/419 (2%)

Query: 4   TIVEKILAKASGKKEVSPGDIVMANIDVAMVHDITGPLTVNTLKEYGIEKVWNPEKIVIL 63
           TI EKI ++A+G  E    D V+A++D AM HD T  L VN  KE  ++KVW+P +IVI 
Sbjct: 3   TISEKIFSRATGA-EAKANDFVLADVDYAMAHDGTSVLAVNAFKEMEMKKVWDPSRIVIP 61

Query: 64  FDHQVPADSIKAAENHILMRKFVKEQGIKYFYDIREGVCHQVLPEKGHVAPGEVVVGADS 123
           FDH  PA++  +A     +R++VKEQGI  FY++ EG+CHQVLPE G   PG++VVGADS
Sbjct: 62  FDHIAPANNEISATLQKEIREWVKEQGIPNFYELGEGICHQVLPENGFALPGKLVVGADS 121

Query: 124 HTCTHGAFGAFATGIGSTDMAHVFATGKLWFKVPETIYFNITGDLQPYVTSKDVILSIIG 183
           H+CT+GAFGAFATG+G+TDMA +FATGKLWFKVPE+  F + G L   V +KD+ L +IG
Sbjct: 122 HSCTYGAFGAFATGVGATDMAEIFATGKLWFKVPESFRFTVEGRLGKGVYAKDLTLYLIG 181

Query: 184 EVGVDGATYKACQFGGETVKKMSIASRMTMTNMAIEMGGKTGIIEPDEKTIQYVKEAMKK 243
           + G+DGATYKA +F G+ + ++S++ RMT+ NMAIEMG KTGI+ PDEKT  ++     K
Sbjct: 182 KTGIDGATYKAVEFYGQAISELSVSGRMTLCNMAIEMGAKTGIVPPDEKTFAFL-----K 236

Query: 244 HGTERPFEVIKGDEDAEFAEVYEIEADKIEPVFACPHNVDNVKQAREVAGKPIDQVFIGS 303
           +    P++ +  D+DA + +     A+ IEP  ACPH VDNVK   EV G  IDQVFIG+
Sbjct: 237 NRAAAPYDPVYADQDAVYVKEPVYSAEDIEPQVACPHQVDNVKPVGEVEGTHIDQVFIGT 296

Query: 304 CTNGRLEDLRMAIKIIEKHGGIADDVRVVVTPASREEYLKALKEGIIEKFLKYGCVVTNP 363
           CTNGRLEDL +A  I++   G    VR +V PASR   L A++ G +E  LK G  +  P
Sbjct: 297 CTNGRLEDLEVAAAILK---GKKVAVRTIVIPASRTTLLAAIENGTMEILLKAGITLATP 353

Query: 364 SCSACMGSLYGVLGPGEVCVSTSNRNFRGRQGSLEAEIYLASPITAAACAVKGELVDPR 422
            C  C+G+  GVLG GEVC+ST+NRNF+GR G     IYLASP TAAA A+ GE+ DPR
Sbjct: 354 GCGPCLGAHQGVLGEGEVCLSTANRNFKGRMGK-SGFIYLASPATAAASALAGEITDPR 411


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: 529
Number of extensions: 27
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: 413
Length adjustment: 32
Effective length of query: 392
Effective length of database: 381
Effective search space:   149352
Effective search space used:   149352
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: 50 (23.9 bits)

Align candidate WP_011306943.1 MBAR_RS10415 (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.15258.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-177  576.7   0.1   1.3e-177  576.6   0.1    1.0  1  lcl|NCBI__GCF_000195895.1:WP_011306943.1  MBAR_RS10415 3-isopropylmalate d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000195895.1:WP_011306943.1  MBAR_RS10415 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  576.6   0.1  1.3e-177  1.3e-177       2     410 ..       3     411 ..       2     412 .. 0.99

  Alignments for each domain:
  == domain 1  score: 576.6 bits;  conditional E-value: 1.3e-177
                                 TIGR02086   2 tlaekilsekvGkevkaGeivevkvDlvmvhDgtgplvikalrelg.akvekkekivlvfDhvvPaptv 69 
                                               t+ eki+s+++G e ka + v++ vD +m+hDgt+ l+++a++e+  +kv+++++iv+ fDh +Pa++ 
  lcl|NCBI__GCF_000195895.1:WP_011306943.1   3 TISEKIFSRATGAEAKANDFVLADVDYAMAHDGTSVLAVNAFKEMEmKKVWDPSRIVIPFDHIAPANNE 71 
                                               799******************************************9999******************** PP

                                 TIGR02086  70 eaaelqkeirefakelgikv.fdvgeGichqvlvekgyakpgkvvvgaDshtttsGalgafatGlGatD 137
                                                +a lqkeire++ke+gi++ ++ geGichqvl e+g+a pgk+vvgaDsh++t+Ga+gafatG+GatD
  lcl|NCBI__GCF_000195895.1:WP_011306943.1  72 ISATLQKEIREWVKEQGIPNfYELGEGICHQVLPENGFALPGKLVVGADSHSCTYGAFGAFATGVGATD 140
                                               ********************99*********************************************** PP

                                 TIGR02086 138 valalatGktWlkvPesikveleGkleekvtakDvileivkelgadgatykaieftgeeiealsldeRl 206
                                               +a ++atGk+W+kvPes++ ++eG+l + v+akD+ l ++++ g dgatyka+ef g+ i++ls+++R+
  lcl|NCBI__GCF_000195895.1:WP_011306943.1 141 MAEIFATGKLWFKVPESFRFTVEGRLGKGVYAKDLTLYLIGKTGIDGATYKAVEFYGQAISELSVSGRM 209
                                               ********************************************************************* PP

                                 TIGR02086 207 tlsnlaveagakaglvepdeetleylkkrrge.frilkadedakyeeeieidlseleplvavPhsvdnv 274
                                               tl+n+a+e+gak+g+v+pde+t  +lk+r++  +  ++ad+da y++e    ++++ep+va+Ph+vdnv
  lcl|NCBI__GCF_000195895.1:WP_011306943.1 210 TLCNMAIEMGAKTGIVPPDEKTFAFLKNRAAApYDPVYADQDAVYVKEPVYSAEDIEPQVACPHQVDNV 278
                                               *****************************9998889********************************* PP

                                 TIGR02086 275 keveevegteidqvfiGsCtnGRledlkiaaeilegrevhkdvrlivvPasrkvyekaleeGlietlve 343
                                               k+v evegt+idqvfiG+CtnGRledl++aa il+g++  + vr+iv+Pasr+ +  a+e+G++e+l++
  lcl|NCBI__GCF_000195895.1:WP_011306943.1 279 KPVGEVEGTHIDQVFIGTCTNGRLEDLEVAAAILKGKK--VAVRTIVIPASRTTLLAAIENGTMEILLK 345
                                               **************************************..89*************************** PP

                                 TIGR02086 344 aGaiiltpgCGPClGahlGvladgevivsttnRnfkGRmGspkaeiYLasPavaavsaveGeitdpe 410
                                               aG++++tpgCGPClGah+Gvl++gev++st+nRnfkGRmG+    iYLasPa+aa+sa++Geitdp+
  lcl|NCBI__GCF_000195895.1:WP_011306943.1 346 AGITLATPGCGPCLGAHQGVLGEGEVCLSTANRNFKGRMGKS-GFIYLASPATAAASALAGEITDPR 411
                                               ****************************************75.78********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (411 nodes)
Target sequences:                          1  (413 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.54
//
[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