Alignments for a candidate for leuC in Methanothermobacter thermautotrophicus str. Delta H

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Methanothermobacter thermautotrophicus str. Delta H

Align 3-isopropylmalate dehydratase (EC 4.2.1.33); homoaconitate hydratase (EC 4.2.1.36) (characterized)
to candidate WP_010876998.1 MTH_RS06630 homoaconitase large subunit

Query= BRENDA::P81291
         (424 letters)



>NCBI__GCF_000008645.1:WP_010876998.1
          Length = 419

 Score =  553 bits (1424), Expect = e-162
 Identities = 271/424 (63%), Positives = 330/424 (77%), Gaps = 6/424 (1%)

Query: 1   MGMTIVEKILAKASGKKEVSPGDIVMANIDVAMVHDITGPLTVNTLKEYGIEKVWNPEKI 60
           M MT+ EKILA+ASGK  V  G+IVMA+IDVAM HD+TGPL+V + +  G ++VW+PEKI
Sbjct: 1   MSMTVSEKILARASGKDRVEAGEIVMADIDVAMTHDLTGPLSVESFRAIGEDRVWDPEKI 60

Query: 61  VILFDHQVPADSIKAAENHILMRKFVKEQGIKYFYDIREGVCHQVLPEKGHVAPGEVVVG 120
           V++FDHQVPADSI+AA+NH++MR FV+EQGI+ FYD+REGVCHQVLPEKGHV PGEVVVG
Sbjct: 61  VVIFDHQVPADSIEAAQNHMIMRDFVEEQGIRNFYDVREGVCHQVLPEKGHVVPGEVVVG 120

Query: 121 ADSHTCTHGAFGAFATGIGSTDMAHVFATGKLWFKVPETIYFNITGDLQPYVTSKDVILS 180
            DSHTCTHGA GAFATGIGSTDMA VFATGKLWF+VPET+ F++ G L+ +V +KDVIL+
Sbjct: 121 TDSHTCTHGALGAFATGIGSTDMAMVFATGKLWFRVPETLRFDVRGKLREHVYAKDVILN 180

Query: 181 IIGEVGVDGATYKACQFGGETVKKMSIASRMTMTNMAIEMGGKTGIIEPDEKTIQYVKEA 240
           IIG VG DGATY AC+F GETV +MS++ RM ++NMAIEMGGKTGI+EPDEKT+ YV+  
Sbjct: 181 IIGRVGADGATYMACEFAGETVAEMSVSDRMVLSNMAIEMGGKTGIVEPDEKTLNYVRRR 240

Query: 241 MKKHGTERPFEVIKGDEDAEFAEVYEIEADKIEPVFACPHNVDNVKQAREVAGKPIDQVF 300
             K     P+ V K D DA    V E++   +EP  ACPHNVDNVK   EV G  IDQVF
Sbjct: 241 SGK-----PWRVFKTDPDAPSLSVMEVDVSDLEPQVACPHNVDNVKPVTEVEGTEIDQVF 295

Query: 301 IGSCTNGRLEDLRMAIKIIEKHGGIADDVRVVVTPASREEYLKALKEGIIEKFLKYGCVV 360
           +GSCTNGRL DLR A  I+ K+  ++D VR++V PASRE Y +AL EG+IE F+  G +V
Sbjct: 296 LGSCTNGRLSDLRDAAAIL-KNRKVSDSVRMLVIPASREVYRRALDEGLIEIFVDAGALV 354

Query: 361 TNPSCSACMGSLYGVLGPGEVCVSTSNRNFRGRQGSLEAEIYLASPITAAACAVKGELVD 420
            NP C  C+G   G++GPGEV +STSNRNFRGRQGS EAE+YL+S   AAA AVKG +  
Sbjct: 355 CNPCCGPCLGGHVGLVGPGEVSLSTSNRNFRGRQGSPEAEVYLSSAAVAAASAVKGSITH 414

Query: 421 PRDL 424
           P  L
Sbjct: 415 PGSL 418


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: 616
Number of extensions: 28
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: 424
Length of database: 419
Length adjustment: 32
Effective length of query: 392
Effective length of database: 387
Effective search space:   151704
Effective search space used:   151704
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_010876998.1 MTH_RS06630 (homoaconitase 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.1782635.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.6e-187  608.0   1.7   4.2e-187  607.8   1.7    1.0  1  NCBI__GCF_000008645.1:WP_010876998.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000008645.1:WP_010876998.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  607.8   1.7  4.2e-187  4.2e-187       1     409 [.       3     415 ..       3     417 .. 0.99

  Alignments for each domain:
  == domain 1  score: 607.8 bits;  conditional E-value: 4.2e-187
                             TIGR02086   1 ktlaekilsekvGke.vkaGeivevkvDlvmvhDgtgplvikalrelg.akvekkekivlvfDhvvPaptvea 71 
                                           +t+ ekil++++Gk+ v+aGeiv++ +D++m+hD tgpl ++++r +g ++v+++ekiv++fDh+vPa ++ea
  NCBI__GCF_000008645.1:WP_010876998.1   3 MTVSEKILARASGKDrVEAGEIVMADIDVAMTHDLTGPLSVESFRAIGeDRVWDPEKIVVIFDHQVPADSIEA 75 
                                           799***********98********************************99*********************** PP

                             TIGR02086  72 aelqkeirefakelgikv.fdvgeGichqvlvekgyakpgkvvvgaDshtttsGalgafatGlGatDvalala 143
                                           a+ +  +r+f+ e+gi++ +dv eG+chqvl ekg++ pg+vvvg+Dsht+t+GalgafatG+G+tD+a+++a
  NCBI__GCF_000008645.1:WP_010876998.1  76 AQNHMIMRDFVEEQGIRNfYDVREGVCHQVLPEKGHVVPGEVVVGTDSHTCTHGALGAFATGIGSTDMAMVFA 148
                                           ******************99***************************************************** PP

                             TIGR02086 144 tGktWlkvPesikveleGkleekvtakDvileivkelgadgatykaieftgeeiealsldeRltlsnlaveag 216
                                           tGk+W++vPe+++ +++Gkl+e+v+akDvil+i++++gadgaty+a ef ge++ ++s+++R+ lsn+a+e+g
  NCBI__GCF_000008645.1:WP_010876998.1 149 TGKLWFRVPETLRFDVRGKLREHVYAKDVILNIIGRVGADGATYMACEFAGETVAEMSVSDRMVLSNMAIEMG 221
                                           ************************************************************************* PP

                             TIGR02086 217 akaglvepdeetleylkkrrge.frilkadedakyeeeieidlseleplvavPhsvdnvkeveevegteidqv 288
                                           +k+g+vepde+tl+y+++r+g+ +r++k+d+da     +e+d+s+lep+va+Ph+vdnvk+v+evegteidqv
  NCBI__GCF_000008645.1:WP_010876998.1 222 GKTGIVEPDEKTLNYVRRRSGKpWRVFKTDPDAPSLSVMEVDVSDLEPQVACPHNVDNVKPVTEVEGTEIDQV 294
                                           *********************99************************************************** PP

                             TIGR02086 289 fiGsCtnGRledlkiaaeilegrevhkdvrlivvPasrkvyekaleeGlietlveaGaiiltpgCGPClGahl 361
                                           f+GsCtnGRl+dl+ aa il++r+v  +vr++v+Pasr+vy++al+eGlie++v+aGa++++p CGPClG h+
  NCBI__GCF_000008645.1:WP_010876998.1 295 FLGSCTNGRLSDLRDAAAILKNRKVSDSVRMLVIPASREVYRRALDEGLIEIFVDAGALVCNPCCGPCLGGHV 367
                                           ************************************************************************* PP

                             TIGR02086 362 GvladgevivsttnRnfkGRmGspkaeiYLasPavaavsaveGeitdp 409
                                           G +++gev++st+nRnf+GR Gsp+ae+YL+s avaa+sav+G it+p
  NCBI__GCF_000008645.1:WP_010876998.1 368 GLVGPGEVSLSTSNRNFRGRQGSPEAEVYLSSAAVAAASAVKGSITHP 415
                                           **********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (411 nodes)
Target sequences:                          1  (419 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.31
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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