Alignments for a candidate for leuC in Hippea alviniae EP5-r

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Hippea alviniae EP5-r

Align isopropylmalate/citramalate isomerase large subunit LeuC (EC 4.2.1.33; EC 4.2.1.35) (characterized)
to candidate WP_022670322.1 G415_RS0104090 3-isopropylmalate dehydratase large subunit

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



>NCBI__GCF_000420385.1:WP_022670322.1
          Length = 424

 Score =  431 bits (1107), Expect = e-125
 Identities = 222/416 (53%), Positives = 289/416 (69%), Gaps = 4/416 (0%)

Query: 4   TLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSFRAMGAKRVFDKDRVALV 63
           T++QKIL + ++     AG+IV   V +  ANDITAP+AI   + +G   VFDK++VAL+
Sbjct: 5   TISQKILAKKSNRDFLKAGEIVLADVDLAFANDITAPIAIDFVKRLGVD-VFDKNKVALI 63

Query: 64  MDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVVGAD 123
            DHFTP KDI +A Q K+ R+F RE  +  Y+E G+ G+EHALLPE G + PG +VVGAD
Sbjct: 64  PDHFTPNKDINSANQCKIMRDFVREKDLPLYWETGEVGIEHALLPEQGYIKPGMLVVGAD 123

Query: 124 SHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLILTLI 183
           SHTCT+G LGAFATG+GSTDV  A A G++WF+VP +I+  + G    +V  KDLIL  I
Sbjct: 124 SHTCTHGALGAFATGMGSTDVGFAFATGKSWFRVPESIKFIYKGKRNKWVYGKDLILYTI 183

Query: 184 GAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYC--TTA 241
           G IGV GALY+++EF G AI+ L +E R+TM NMA+EAG K G+   D  T+ Y      
Sbjct: 184 GKIGVAGALYKSMEFTGDAIKELSMEDRLTMCNMAVEAGAKNGIIEPDDITIEYLKERDI 243

Query: 242 GRTGDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVK-DVTVQQVVIGSC 300
            R+      +D  A Y   +  DV+ + P VA PHLP N K +SE+K D+ + Q  IGSC
Sbjct: 244 DRSEYEILKSDDDAEYSDIIEIDVSNIEPQVAFPHLPSNTKGISEIKEDIKIDQAFIGSC 303

Query: 301 TNGRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIVGPATC 360
           TNGRI DLREAA VL+G KV++ VR I++PAT  +++QAL+EGL + F+EAG ++   TC
Sbjct: 304 TNGRISDLREAAKVLKGNKVAKYVRLIIIPATVEVYKQALKEGLFDIFLEAGAVISTPTC 363

Query: 361 GPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVTGVITDP 416
           GPCLGG+MGILADGE  I+T+NRNF GRMGS ++ VYLS PA AAASAV G I  P
Sbjct: 364 GPCLGGYMGILADGEVCISTSNRNFVGRMGSKKAYVYLSSPAVAAASAVAGKIIHP 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: 505
Number of extensions: 23
Number of successful extensions: 4
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: 424
Length adjustment: 32
Effective length of query: 387
Effective length of database: 392
Effective search space:   151704
Effective search space used:   151704
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_022670322.1 G415_RS0104090 (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.3184393.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.6e-208  676.3   1.8   9.7e-208  676.1   1.8    1.0  1  NCBI__GCF_000420385.1:WP_022670322.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000420385.1:WP_022670322.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  676.1   1.8  9.7e-208  9.7e-208       1     419 []       4     422 ..       4     422 .. 0.99

  Alignments for each domain:
  == domain 1  score: 676.1 bits;  conditional E-value: 9.7e-208
                             TIGR02083   1 mtlaekiladkagkeevkpgelilakldlvlgndvttplaikafkelgvkkvfdkdkvalvldhftpnkdika 73 
                                           mt+++kila+k+ ++ +k+ge++la++dl+++nd+t+p+ai+  k+lgv+ vfdk+kval++dhftpnkdi +
  NCBI__GCF_000420385.1:WP_022670322.1   4 MTISQKILAKKSNRDFLKAGEIVLADVDLAFANDITAPIAIDFVKRLGVD-VFDKNKVALIPDHFTPNKDINS 75 
                                           9*********************************************9996.9********************* PP

                             TIGR02083  74 aeqvklirefakekeiekyfeigelgvehallpekglvvsgdliigadshtctygalgafatgvgstdlavam 146
                                           a+q+k++r+f +ek++  y+e+ge+g+ehallpe+g +++g l++gadshtct+galgafatg+gstd+  a+
  NCBI__GCF_000420385.1:WP_022670322.1  76 ANQCKIMRDFVREKDLPLYWETGEVGIEHALLPEQGYIKPGMLVVGADSHTCTHGALGAFATGMGSTDVGFAF 148
                                           ************************************************************************* PP

                             TIGR02083 147 atgkawfkvpeaikfvlkgklkdyvsakdlilkiigkigvdgalykslefsgeglkelsvddrltianmaiea 219
                                           atgk+wf+vpe+ikf +kgk +++v +kdlil++igkigv galyks+ef+g+++kels++drlt++nma+ea
  NCBI__GCF_000420385.1:WP_022670322.1 149 ATGKSWFRVPESIKFIYKGKRNKWVYGKDLILYTIGKIGVAGALYKSMEFTGDAIKELSMEDRLTMCNMAVEA 221
                                           ************************************************************************* PP

                             TIGR02083 220 gaktgifevdektieyvkgrak..relkiykadedakyervieidlselepqvafphlpentkeideaekeei 290
                                           gak+gi+e+d++tiey k+r +   e++i k+d+da+y+ +ieid+s++epqvafphlp+ntk i+e++ e+i
  NCBI__GCF_000420385.1:WP_022670322.1 222 GAKNGIIEPDDITIEYLKERDIdrSEYEILKSDDDAEYSDIIEIDVSNIEPQVAFPHLPSNTKGISEIK-EDI 293
                                           ********************7522689****************************************98.9** PP

                             TIGR02083 291 kidqvvigsctngrledlrlaaeilkgkkvakevrliilpasqkvylealkeglleifieagavvstptcgpc 363
                                           kidq+ igsctngr++dlr aa++lkg+kvak vrlii+pa+ +vy++alkegl +if+eagav+stptcgpc
  NCBI__GCF_000420385.1:WP_022670322.1 294 KIDQAFIGSCTNGRISDLREAAKVLKGNKVAKYVRLIIIPATVEVYKQALKEGLFDIFLEAGAVISTPTCGPC 366
                                           ************************************************************************* PP

                             TIGR02083 364 lgghmgilaegeravsttnrnfvgrmghpksevylaspavaaasaikgkiaspeev 419
                                           lgg+mgila+ge+++st+nrnfvgrmg  k+ vyl+spavaaasa++gki +p+ev
  NCBI__GCF_000420385.1:WP_022670322.1 367 LGGYMGILADGEVCISTSNRNFVGRMGSKKAYVYLSSPAVAAASAVAGKIIHPDEV 422
                                           *****************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (419 nodes)
Target sequences:                          1  (424 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 18.31
//
[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