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.757.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.59
//
[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:

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:

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:

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:

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