Alignments for a candidate for leuC in Desulfobacca acetoxidans DSM 11109

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Desulfobacca acetoxidans DSM 11109

Align isopropylmalate/citramalate isomerase large subunit LeuC (EC 4.2.1.33; EC 4.2.1.35) (characterized)
to candidate WP_013707452.1 DESAC_RS12565 3-isopropylmalate dehydratase large subunit

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



>NCBI__GCF_000195295.1:WP_013707452.1
          Length = 421

 Score =  493 bits (1269), Expect = e-144
 Identities = 242/416 (58%), Positives = 296/416 (71%)

Query: 4   TLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSFRAMGAKRVFDKDRVALV 63
           T+ +KIL  H      + GQ++  RV + L NDITAP+AIK FR  GA +V+D +RV LV
Sbjct: 6   TITEKILAAHAGLDYVEPGQLINARVDIALGNDITAPIAIKEFRQAGALKVYDPERVVLV 65

Query: 64  MDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVVGAD 123
            DHF P KDI +A Q +  R FA+E  + HYY+GG+ GVEHALLPE G+VGPGD+V+GAD
Sbjct: 66  ADHFAPNKDIPSAIQCQTLRRFAQEQKLRHYYDGGEMGVEHALLPEKGIVGPGDLVIGAD 125

Query: 124 SHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLILTLI 183
           SHTCTYGGLGAFATG+GSTD+A  M  GE+WFKVP T+   FTG LP +VG KDLIL LI
Sbjct: 126 SHTCTYGGLGAFATGVGSTDLAATMITGESWFKVPETMLFIFTGQLPQWVGGKDLILFLI 185

Query: 184 GAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYCTTAGR 243
           G IGVDGALY A+EF G  +  L +  R+TM NMAIEAG K G+ A D  T  Y      
Sbjct: 186 GQIGVDGALYNAMEFTGEVVARLPMSDRLTMCNMAIEAGAKNGIIAPDDITREYVANRAL 245

Query: 244 TGDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKDVTVQQVVIGSCTNG 303
              T F++D GA Y     +DV+GM P +A PHLP+N  P+S+V  V + Q VIGSCTNG
Sbjct: 246 RAVTFFASDPGANYHSVREYDVSGMEPQIAFPHLPENTHPLSQVGAVPIDQAVIGSCTNG 305

Query: 304 RIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIVGPATCGPC 363
           R+ D+R AA VL+GRKV+R VR I++PATP I+RQ L+EGL E F++AG ++ P TCGPC
Sbjct: 306 RLEDMRLAAQVLKGRKVARGVRLIIIPATPWIYRQCLKEGLFEIFLDAGAVISPPTCGPC 365

Query: 364 LGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVTGVITDPSTL 419
           LGGHMG+L  GE AIATTNRNF GRMG  ES++YL+ PA  AASAV G I  P  L
Sbjct: 366 LGGHMGVLGPGETAIATTNRNFVGRMGHPESKLYLANPAVTAASAVAGRIVGPQAL 421


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: 573
Number of extensions: 29
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: 421
Length adjustment: 32
Effective length of query: 387
Effective length of database: 389
Effective search space:   150543
Effective search space used:   150543
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_013707452.1 DESAC_RS12565 (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.20471.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.3e-208  677.6   0.0   3.7e-208  677.5   0.0    1.0  1  lcl|NCBI__GCF_000195295.1:WP_013707452.1  DESAC_RS12565 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000195295.1:WP_013707452.1  DESAC_RS12565 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  677.5   0.0  3.7e-208  3.7e-208       1     418 [.       5     420 ..       5     421 .] 1.00

  Alignments for each domain:
  == domain 1  score: 677.5 bits;  conditional E-value: 3.7e-208
                                 TIGR02083   1 mtlaekiladkagkeevkpgelilakldlvlgndvttplaikafkelgvkkvfdkdkvalvldhftpnk 69 
                                               mt++ekila +ag+++v+pg+li a++d++lgnd+t+p+aik+f+++g+ kv+d+++v+lv dhf+pnk
  lcl|NCBI__GCF_000195295.1:WP_013707452.1   5 MTITEKILAAHAGLDYVEPGQLINARVDIALGNDITAPIAIKEFRQAGALKVYDPERVVLVADHFAPNK 73 
                                               9******************************************************************** PP

                                 TIGR02083  70 dikaaeqvklirefakekeiekyfeigelgvehallpekglvvsgdliigadshtctygalgafatgvg 138
                                               di +a q++ +r+fa+e+++++y++ ge+gvehallpekg+v +gdl+igadshtctyg lgafatgvg
  lcl|NCBI__GCF_000195295.1:WP_013707452.1  74 DIPSAIQCQTLRRFAQEQKLRHYYDGGEMGVEHALLPEKGIVGPGDLVIGADSHTCTYGGLGAFATGVG 142
                                               ********************************************************************* PP

                                 TIGR02083 139 stdlavamatgkawfkvpeaikfvlkgklkdyvsakdlilkiigkigvdgalykslefsgeglkelsvd 207
                                               stdla++m+tg++wfkvpe++ f + g+l ++v +kdlil +ig+igvdgaly ++ef+ge++ +l + 
  lcl|NCBI__GCF_000195295.1:WP_013707452.1 143 STDLAATMITGESWFKVPETMLFIFTGQLPQWVGGKDLILFLIGQIGVDGALYNAMEFTGEVVARLPMS 211
                                               ********************************************************************* PP

                                 TIGR02083 208 drltianmaieagaktgifevdektieyvkgrakrelkiykadedakyervieidlselepqvafphlp 276
                                               drlt++nmaieagak+gi+ +d++t eyv +ra r +  + +d  a+y+ v e+d+s +epq+afphlp
  lcl|NCBI__GCF_000195295.1:WP_013707452.1 212 DRLTMCNMAIEAGAKNGIIAPDDITREYVANRALRAVTFFASDPGANYHSVREYDVSGMEPQIAFPHLP 280
                                               ********************************************************************* PP

                                 TIGR02083 277 entkeideaekeeikidqvvigsctngrledlrlaaeilkgkkvakevrliilpasqkvylealkegll 345
                                               ent+++++++   + idq+vigsctngrled+rlaa++lkg+kva+ vrlii+pa++ +y ++lkegl 
  lcl|NCBI__GCF_000195295.1:WP_013707452.1 281 ENTHPLSQVG--AVPIDQAVIGSCTNGRLEDMRLAAQVLKGRKVARGVRLIIIPATPWIYRQCLKEGLF 347
                                               **********..9******************************************************** PP

                                 TIGR02083 346 eifieagavvstptcgpclgghmgilaegeravsttnrnfvgrmghpksevylaspavaaasaikgkia 414
                                               eif++agav+s+ptcgpclgghmg+l  ge a++ttnrnfvgrmghp+s++yla pav+aasa++g+i+
  lcl|NCBI__GCF_000195295.1:WP_013707452.1 348 EIFLDAGAVISPPTCGPCLGGHMGVLGPGETAIATTNRNFVGRMGHPESKLYLANPAVTAASAVAGRIV 416
                                               ********************************************************************* PP

                                 TIGR02083 415 spee 418
                                                p+ 
  lcl|NCBI__GCF_000195295.1:WP_013707452.1 417 GPQA 420
                                               **86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (419 nodes)
Target sequences:                          1  (421 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 0.01s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 6.37
//
[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