Alignments for a candidate for leuC in Maridesulfovibrio zosterae DSM 11974

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Maridesulfovibrio zosterae DSM 11974

Align isopropylmalate/citramalate isomerase large subunit LeuC (EC 4.2.1.33; EC 4.2.1.35) (characterized)
to candidate WP_027722228.1 H589_RS0111935 3-isopropylmalate dehydratase large subunit

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



>NCBI__GCF_000425265.1:WP_027722228.1
          Length = 419

 Score =  640 bits (1650), Expect = 0.0
 Identities = 309/419 (73%), Positives = 352/419 (84%)

Query: 1   MAHTLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSFRAMGAKRVFDKDRV 60
           M  TLAQKILQ HTDE + +AGQIVRC VSMVLANDITAPLAIKSF+AMGA +VFDKD+V
Sbjct: 1   MPKTLAQKILQAHTDETVKEAGQIVRCNVSMVLANDITAPLAIKSFKAMGADQVFDKDKV 60

Query: 61  ALVMDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVV 120
           ALV DHFTP KDI++A+QVK+ REFA E  +THYYEGG+ GVEHALLPELGLVGP D+V+
Sbjct: 61  ALVCDHFTPNKDIDSAEQVKVVREFAHEKNITHYYEGGEVGVEHALLPELGLVGPSDIVI 120

Query: 121 GADSHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLIL 180
           GADSHTCTYGGLGAFATG+GSTD+AGAMALGETWFKVPP+I+    GT   YV AKD IL
Sbjct: 121 GADSHTCTYGGLGAFATGMGSTDIAGAMALGETWFKVPPSIKVEIEGTPGKYVSAKDYIL 180

Query: 181 TLIGAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYCTT 240
            LIG IGV GALY+ALEF G+ ++ + +EGRMT+ANMAIEAGGK GLF  D+KTL YC  
Sbjct: 181 NLIGTIGVSGALYKALEFSGSVVDDMSIEGRMTIANMAIEAGGKVGLFPVDSKTLEYCQA 240

Query: 241 AGRTGDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKDVTVQQVVIGSC 300
           AGRTGD    AD GAVYER +  DVTGM P +ACPHLPDNVKP+ EVK++ + Q VIGSC
Sbjct: 241 AGRTGDVELRADEGAVYERVVKIDVTGMKPQIACPHLPDNVKPIDEVKNMKIHQAVIGSC 300

Query: 301 TNGRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIVGPATC 360
           TNGRI DLR AA VL+GRK  ++VR IVLPATP IW+QAL+EGLIE FM++G IVGPATC
Sbjct: 301 TNGRISDLRIAAEVLKGRKADKNVRLIVLPATPSIWKQALKEGLIEIFMDSGAIVGPATC 360

Query: 361 GPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVTGVITDPSTL 419
           GPCLGGHMGILA GER+IATTNRNF+GRMGSL+SEV+LS PA AAASAV G I DP+ L
Sbjct: 361 GPCLGGHMGILAGGERSIATTNRNFRGRMGSLQSEVFLSNPAVAAASAVAGEIIDPAAL 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: 619
Number of extensions: 14
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 WP_027722228.1 H589_RS0111935 (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.2841674.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-194  632.5   3.0   1.9e-194  632.3   3.0    1.0  1  NCBI__GCF_000425265.1:WP_027722228.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000425265.1:WP_027722228.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  632.3   3.0  1.9e-194  1.9e-194       2     417 ..       4     417 ..       3     419 .] 0.99

  Alignments for each domain:
  == domain 1  score: 632.3 bits;  conditional E-value: 1.9e-194
                             TIGR02083   2 tlaekiladkagkeevkpgelilakldlvlgndvttplaikafkelgvkkvfdkdkvalvldhftpnkdikaa 74 
                                           tla+kil  ++     ++g+++  ++ +vl+nd+t+plaik+fk +g+++vfdkdkvalv dhftpnkdi +a
  NCBI__GCF_000425265.1:WP_027722228.1   4 TLAQKILQAHTDETVKEAGQIVRCNVSMVLANDITAPLAIKSFKAMGADQVFDKDKVALVCDHFTPNKDIDSA 76 
                                           89**********99999******************************************************** PP

                             TIGR02083  75 eqvklirefakekeiekyfeigelgvehallpekglvvsgdliigadshtctygalgafatgvgstdlavama 147
                                           eqvk++refa+ek+i +y+e ge+gvehallpe glv + d++igadshtctyg lgafatg+gstd+a+ama
  NCBI__GCF_000425265.1:WP_027722228.1  77 EQVKVVREFAHEKNITHYYEGGEVGVEHALLPELGLVGPSDIVIGADSHTCTYGGLGAFATGMGSTDIAGAMA 149
                                           ************************************************************************* PP

                             TIGR02083 148 tgkawfkvpeaikfvlkgklkdyvsakdlilkiigkigvdgalykslefsgeglkelsvddrltianmaieag 220
                                            g++wfkvp +ik+ ++g   +yvsakd il++ig+igv galyk+lefsg +++++s+++r+tianmaieag
  NCBI__GCF_000425265.1:WP_027722228.1 150 LGETWFKVPPSIKVEIEGTPGKYVSAKDYILNLIGTIGVSGALYKALEFSGSVVDDMSIEGRMTIANMAIEAG 222
                                           ************************************************************************* PP

                             TIGR02083 221 aktgifevdektieyvkgrakrelkiykadedakyervieidlselepqvafphlpentkeideaekeeikid 293
                                           +k g+f+vd kt+ey +  ++      +ade a yerv++id+  ++pq+a phlp+n k+ide++  ++ki 
  NCBI__GCF_000425265.1:WP_027722228.1 223 GKVGLFPVDSKTLEYCQAAGRTGDVELRADEGAVYERVVKIDVTGMKPQIACPHLPDNVKPIDEVK--NMKIH 293
                                           *****************9999999999**************************************9..99*** PP

                             TIGR02083 294 qvvigsctngrledlrlaaeilkgkkvakevrliilpasqkvylealkeglleifieagavvstptcgpclgg 366
                                           q+vigsctngr++dlr+aae+lkg+k  k+vrli+lpa+++++++alkegl+eif+++ga+v++ tcgpclgg
  NCBI__GCF_000425265.1:WP_027722228.1 294 QAVIGSCTNGRISDLRIAAEVLKGRKADKNVRLIVLPATPSIWKQALKEGLIEIFMDSGAIVGPATCGPCLGG 366
                                           ************************************************************************* PP

                             TIGR02083 367 hmgilaegeravsttnrnfvgrmghpksevylaspavaaasaikgkiaspe 417
                                           hmgila ger+++ttnrnf grmg  +sev+l+ pavaaasa++g+i +p 
  NCBI__GCF_000425265.1:WP_027722228.1 367 HMGILAGGERSIATTNRNFRGRMGSLQSEVFLSNPAVAAASAVAGEIIDPA 417
                                           *************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (419 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 17.38
//
[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