Alignments for a candidate for leuC in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Desulfovibrio vulgaris Hildenborough

Align isopropylmalate/citramalate isomerase large subunit LeuC (EC 4.2.1.33; EC 4.2.1.35) (characterized)
to candidate 208495 DVU2982 3-isopropylmalate dehydratase, large subunit, putative

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



>MicrobesOnline__882:208495
          Length = 419

 Score =  832 bits (2150), Expect = 0.0
 Identities = 419/419 (100%), Positives = 419/419 (100%)

Query: 1   MAHTLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSFRAMGAKRVFDKDRV 60
           MAHTLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSFRAMGAKRVFDKDRV
Sbjct: 1   MAHTLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSFRAMGAKRVFDKDRV 60

Query: 61  ALVMDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVV 120
           ALVMDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVV
Sbjct: 61  ALVMDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVV 120

Query: 121 GADSHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLIL 180
           GADSHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLIL
Sbjct: 121 GADSHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLIL 180

Query: 181 TLIGAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYCTT 240
           TLIGAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYCTT
Sbjct: 181 TLIGAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYCTT 240

Query: 241 AGRTGDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKDVTVQQVVIGSC 300
           AGRTGDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKDVTVQQVVIGSC
Sbjct: 241 AGRTGDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKDVTVQQVVIGSC 300

Query: 301 TNGRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIVGPATC 360
           TNGRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIVGPATC
Sbjct: 301 TNGRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIVGPATC 360

Query: 361 GPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVTGVITDPSTL 419
           GPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVTGVITDPSTL
Sbjct: 361 GPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVTGVITDPSTL 419


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: 825
Number of extensions: 22
Number of successful extensions: 1
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: 419
Length adjustment: 32
Effective length of query: 387
Effective length of database: 387
Effective search space:   149769
Effective search space used:   149769
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 208495 DVU2982 (3-isopropylmalate dehydratase, large subunit, putative)
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.23575.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.5e-159  516.3   1.2   2.9e-159  516.1   1.2    1.0  1  lcl|MicrobesOnline__882:208495  DVU2982 3-isopropylmalate dehydr


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:208495  DVU2982 3-isopropylmalate dehydratase, large subunit, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  516.1   1.2  2.9e-159  2.9e-159       2     410 ..       4     417 ..       3     418 .. 0.98

  Alignments for each domain:
  == domain 1  score: 516.1 bits;  conditional E-value: 2.9e-159
                       TIGR02086   2 tlaekilsekvGke.vkaGeivevkvDlvmvhDgtgplvikalrelg.akvekkekivlvfDhvvPaptveaaelqkei 78 
                                     tla+kil +++ +    aG+iv  +v +v+++D t+pl+ik++r +g ++v++k+++ lv+Dh +P +++eaa+  k +
  lcl|MicrobesOnline__882:208495   4 TLAQKILQRHTDEAiTDAGQIVRCRVSMVLANDITAPLAIKSFRAMGaKRVFDKDRVALVMDHFTPQKDIEAAQQVKLT 82 
                                     9***********994579*****************************899***************************** PP

                       TIGR02086  79 refakelgikv.fdv.geGichqvlvekgyakpgkvvvgaDshtttsGalgafatGlGatDvalalatGktWlkvPesi 155
                                     refa+e+g+++ ++  + G+ h +l e g++ pg+vvvgaDsht+t+G+lgafatGlG+tDva a+a+G+tW+kvP +i
  lcl|MicrobesOnline__882:208495  83 REFAREMGVTHyYEGgDCGVEHALLPELGLVGPGDVVVGADSHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTI 161
                                     ***********7665156************************************************************* PP

                       TIGR02086 156 kveleGkleekvtakDvileivkelgadgatykaieftgeeiealsldeRltlsnlaveagakaglvepdeetleylkk 234
                                     + +++G l  +v akD+il++++ +g dga y+a+ef g  ieal++++R+t++n+a+eag+kagl+ +d +tl y  +
  lcl|MicrobesOnline__882:208495 162 RATFTGTLPAYVGAKDLILTLIGAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYCTT 240
                                     *****************************************************************************99 PP

                       TIGR02086 235 rrge.frilkadedakyeeeieidlseleplvavPhsvdnvkeveevegteidqvfiGsCtnGRledlkiaaeilegre 312
                                       ++    ++ad +a ye e+ +d++ ++p+va+Ph +dnvk+v+ev+ ++++qv iGsCtnGR+ dl++aa +l+gr+
  lcl|MicrobesOnline__882:208495 241 AGRTgDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKDVTVQQVVIGSCTNGRIGDLREAAAVLRGRK 319
                                     9888777899********************************************************************* PP

                       TIGR02086 313 vhkdvrlivvPasrkvyekaleeGlietlveaGaiiltpgCGPClGahlGvladgevivsttnRnfkGRmGspkaeiYL 391
                                     v +dvr+iv Pa   ++++al+eGliet++eaG+i+ + +CGPClG h+G+ladge+ ++ttnRnfkGRmGs ++e+YL
  lcl|MicrobesOnline__882:208495 320 VSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIVGPATCGPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYL 398
                                     ******************************************************************************* PP

                       TIGR02086 392 asPavaavsaveGeitdpe 410
                                     ++Pa+aa+sav+G+itdp 
  lcl|MicrobesOnline__882:208495 399 SGPATAAASAVTGVITDPS 417
                                     *****************96 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.29
//
[ok]

This GapMind analysis is from Apr 09 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