Alignments for a candidate for leuC in Desulfovibrio gracilis DSM 16080

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Desulfovibrio gracilis DSM 16080

Align isopropylmalate/citramalate isomerase large subunit LeuC (EC 4.2.1.33; EC 4.2.1.35) (characterized)
to candidate WP_078716441.1 B5D49_RS04295 3-isopropylmalate dehydratase large subunit

Query= reanno::DvH:208495
         (419 letters)



>NCBI__GCF_900167125.1:WP_078716441.1
          Length = 418

 Score =  630 bits (1625), Expect = 0.0
 Identities = 315/417 (75%), Positives = 350/417 (83%), Gaps = 1/417 (0%)

Query: 1   MAHTLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSFRAMGAKRVFDKDRV 60
           M  TLA+KI+Q+HT E   +AG IVRCRV MVLANDITAPLAIKSF+AMGA RVFD+D+V
Sbjct: 1   MPKTLAEKIIQQHTQEP-AEAGNIVRCRVDMVLANDITAPLAIKSFKAMGADRVFDRDKV 59

Query: 61  ALVMDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVV 120
           ALV DHFTP KDI++A+QVK  REFA  MGVTHYYEGG+ GVEHALLPELG+VGPGDVVV
Sbjct: 60  ALVCDHFTPNKDIDSAEQVKTVREFAEAMGVTHYYEGGNVGVEHALLPELGIVGPGDVVV 119

Query: 121 GADSHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLIL 180
           GADSHTCTYGGLGAFATG+GSTD+A AMALGETWFKVPPTIR   +GT   +VGAKD +L
Sbjct: 120 GADSHTCTYGGLGAFATGMGSTDIAAAMALGETWFKVPPTIRVEISGTPQPHVGAKDYML 179

Query: 181 TLIGAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYCTT 240
            LIG IGV GALY+ALEF G A+EAL VEGRMTMANMAIEAGGKAGLFA D KT+ Y   
Sbjct: 180 RLIGEIGVAGALYKALEFGGPAVEALSVEGRMTMANMAIEAGGKAGLFAVDDKTIAYARR 239

Query: 241 AGRTGDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKDVTVQQVVIGSC 300
           AGR+G+ A + D+ A YER +   + GM+P +ACPHLPDNV  V EV  + V Q VIGSC
Sbjct: 240 AGRSGNQAMTPDSDAGYERVVVIRLDGMSPQIACPHLPDNVHSVDEVAGLRVDQAVIGSC 299

Query: 301 TNGRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIVGPATC 360
           TNGRI D+REAAAVL+G+KVS  VRCIVLPATP IW+QAL+EGLIE FMEAGC+VGPATC
Sbjct: 300 TNGRIEDMREAAAVLKGKKVSSRVRCIVLPATPAIWKQALKEGLIEVFMEAGCVVGPATC 359

Query: 361 GPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVTGVITDPS 417
           GPCLGGHMGILA GERAIATTNRNFKGRMGSLESEVYLS PA AAASAV G I  PS
Sbjct: 360 GPCLGGHMGILAGGERAIATTNRNFKGRMGSLESEVYLSNPAVAAASAVVGEIVHPS 416


Lambda     K      H
   0.320    0.136    0.401 

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: 653
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: 419
Length of database: 418
Length adjustment: 32
Effective length of query: 387
Effective length of database: 386
Effective search space:   149382
Effective search space used:   149382
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate WP_078716441.1 B5D49_RS04295 (3-isopropylmalate dehydratase large subunit)
to HMM TIGR02083 (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/TIGR02083.hmm
# target sequence database:        /tmp/gapView.14829.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02083  [M=419]
Accession:   TIGR02083
Description: LEU2: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.5e-193  627.5   1.6   6.4e-193  627.3   1.6    1.0  1  lcl|NCBI__GCF_900167125.1:WP_078716441.1  B5D49_RS04295 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900167125.1:WP_078716441.1  B5D49_RS04295 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  627.3   1.6  6.4e-193  6.4e-193       2     419 .]       4     418 .]       3     418 .] 0.99

  Alignments for each domain:
  == domain 1  score: 627.3 bits;  conditional E-value: 6.4e-193
                                 TIGR02083   2 tlaekiladkagkeevkpgelilakldlvlgndvttplaikafkelgvkkvfdkdkvalvldhftpnkd 70 
                                               tlaeki+ +++  e  ++g+++  ++d+vl+nd+t+plaik+fk +g+++vfd+dkvalv dhftpnkd
  lcl|NCBI__GCF_900167125.1:WP_078716441.1   4 TLAEKIIQQHTQ-EPAEAGNIVRCRVDMVLANDITAPLAIKSFKAMGADRVFDRDKVALVCDHFTPNKD 71 
                                               89*****99975.569***************************************************** PP

                                 TIGR02083  71 ikaaeqvklirefakekeiekyfeigelgvehallpekglvvsgdliigadshtctygalgafatgvgs 139
                                               i +aeqvk +refa   ++ +y+e g++gvehallpe g+v +gd+++gadshtctyg lgafatg+gs
  lcl|NCBI__GCF_900167125.1:WP_078716441.1  72 IDSAEQVKTVREFAEAMGVTHYYEGGNVGVEHALLPELGIVGPGDVVVGADSHTCTYGGLGAFATGMGS 140
                                               ********************************************************************* PP

                                 TIGR02083 140 tdlavamatgkawfkvpeaikfvlkgklkdyvsakdlilkiigkigvdgalykslefsgeglkelsvdd 208
                                               td+a+ama g++wfkvp +i++ + g  +++v akd +l++ig+igv galyk+lef+g++++ lsv++
  lcl|NCBI__GCF_900167125.1:WP_078716441.1 141 TDIAAAMALGETWFKVPPTIRVEISGTPQPHVGAKDYMLRLIGEIGVAGALYKALEFGGPAVEALSVEG 209
                                               ********************************************************************* PP

                                 TIGR02083 209 rltianmaieagaktgifevdektieyvkgrakrelkiykadedakyervieidlselepqvafphlpe 277
                                               r+t+anmaieag+k+g+f vd+kti+y++  ++   +    d da yerv+ i l+ + pq+a phlp+
  lcl|NCBI__GCF_900167125.1:WP_078716441.1 210 RMTMANMAIEAGGKAGLFAVDDKTIAYARRAGRSGNQAMTPDSDAGYERVVVIRLDGMSPQIACPHLPD 278
                                               *****************************9999999********************************* PP

                                 TIGR02083 278 ntkeideaekeeikidqvvigsctngrledlrlaaeilkgkkvakevrliilpasqkvylealkeglle 346
                                               n +++de++   +++dq+vigsctngr+ed+r aa +lkgkkv+  vr+i+lpa++ ++++alkegl+e
  lcl|NCBI__GCF_900167125.1:WP_078716441.1 279 NVHSVDEVA--GLRVDQAVIGSCTNGRIEDMREAAAVLKGKKVSSRVRCIVLPATPAIWKQALKEGLIE 345
                                               ********9..99******************************************************** PP

                                 TIGR02083 347 ifieagavvstptcgpclgghmgilaegeravsttnrnfvgrmghpksevylaspavaaasaikgkias 415
                                               +f+eag+vv++ tcgpclgghmgila gera++ttnrnf grmg  +sevyl+ pavaaasa+ g+i++
  lcl|NCBI__GCF_900167125.1:WP_078716441.1 346 VFMEAGCVVGPATCGPCLGGHMGILAGGERAIATTNRNFKGRMGSLESEVYLSNPAVAAASAVVGEIVH 414
                                               ********************************************************************* PP

                                 TIGR02083 416 peev 419
                                               p ++
  lcl|NCBI__GCF_900167125.1:WP_078716441.1 415 PSHI 418
                                               9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (419 nodes)
Target sequences:                          1  (418 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: 11.90
//
[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