Alignments for a candidate for leuC in Desulfotomaculum ruminis DSM 2154

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Desulfotomaculum ruminis DSM 2154

Align isopropylmalate/citramalate isomerase large subunit LeuC (EC 4.2.1.33; EC 4.2.1.35) (characterized)
to candidate WP_013840434.1 DESRU_RS01885 3-isopropylmalate dehydratase large subunit

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



>NCBI__GCF_000215085.1:WP_013840434.1
          Length = 420

 Score =  483 bits (1244), Expect = e-141
 Identities = 244/416 (58%), Positives = 299/416 (71%)

Query: 1   MAHTLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSFRAMGAKRVFDKDRV 60
           M  T+ +KIL     +     G+++  +V +VLANDITAP+AIK F  +G   V+DK+RV
Sbjct: 1   MPMTITEKILAAAAGKDYVKPGELINAKVDLVLANDITAPVAIKEFEKIGLPGVWDKERV 60

Query: 61  ALVMDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVV 120
           ALV DHF P KDI++A+Q K+ R+FA +  +THY+E G  G+EH LLPE GLVGPGDV++
Sbjct: 61  ALVPDHFVPNKDIKSAEQAKMVRDFAHKQELTHYFEVGRMGIEHCLLPEQGLVGPGDVII 120

Query: 121 GADSHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLIL 180
           GADSHTCTYG LGAFATG+GSTD+A AMALGETWFKVP +I+  F G L  +VG KDLIL
Sbjct: 121 GADSHTCTYGALGAFATGVGSTDLAAAMALGETWFKVPESIKFVFNGKLNPWVGGKDLIL 180

Query: 181 TLIGAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYCTT 240
             IG IGVDGALYRA+EF G AIE L ++GR TM NMAIEAGGK G+   D  T  Y   
Sbjct: 181 YTIGKIGVDGALYRAMEFCGEAIEQLSMDGRFTMCNMAIEAGGKNGIIQPDEITRQYVEG 240

Query: 241 AGRTGDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKDVTVQQVVIGSC 300
             +   T +++D  A Y     FDV+ + P VA PHLP+N + + E  +V + Q VIGSC
Sbjct: 241 RTKRPYTFYTSDPDAQYAEVHEFDVSKIEPQVAFPHLPENARSIREAGNVEIDQAVIGSC 300

Query: 301 TNGRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIVGPATC 360
           TNGR+ DLR AA VL+G+KV+R VR IV+P T  I+RQA+ EGL + F+EAG  V   TC
Sbjct: 301 TNGRMEDLRIAAQVLKGQKVNRRVRLIVIPGTQEIYRQAMHEGLFDIFLEAGAAVSTPTC 360

Query: 361 GPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVTGVITDP 416
           GPCLGG+MGILA GER IATTNRNF GRMG   SEVYLS PA AAASA+TG I+ P
Sbjct: 361 GPCLGGYMGILAQGERCIATTNRNFVGRMGHAGSEVYLSNPAVAAASAITGRISHP 416


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: 569
Number of extensions: 26
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: 420
Length adjustment: 32
Effective length of query: 387
Effective length of database: 388
Effective search space:   150156
Effective search space used:   150156
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_013840434.1 DESRU_RS01885 (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.7313.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-223  727.7   0.1   2.3e-223  727.5   0.1    1.0  1  lcl|NCBI__GCF_000215085.1:WP_013840434.1  DESRU_RS01885 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000215085.1:WP_013840434.1  DESRU_RS01885 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  727.5   0.1  2.3e-223  2.3e-223       1     419 []       3     419 ..       3     419 .. 1.00

  Alignments for each domain:
  == domain 1  score: 727.5 bits;  conditional E-value: 2.3e-223
                                 TIGR02083   1 mtlaekiladkagkeevkpgelilakldlvlgndvttplaikafkelgvkkvfdkdkvalvldhftpnk 69 
                                               mt++ekila  agk++vkpgeli ak+dlvl+nd+t+p+aik+f ++g   v dk++valv+dhf pnk
  lcl|NCBI__GCF_000215085.1:WP_013840434.1   3 MTITEKILAAAAGKDYVKPGELINAKVDLVLANDITAPVAIKEFEKIGLPGVWDKERVALVPDHFVPNK 71 
                                               9******************************************************************** PP

                                 TIGR02083  70 dikaaeqvklirefakekeiekyfeigelgvehallpekglvvsgdliigadshtctygalgafatgvg 138
                                               dik+aeq+k++r+fa+++e+ +yfe+g++g+eh+llpe+glv +gd+iigadshtctygalgafatgvg
  lcl|NCBI__GCF_000215085.1:WP_013840434.1  72 DIKSAEQAKMVRDFAHKQELTHYFEVGRMGIEHCLLPEQGLVGPGDVIIGADSHTCTYGALGAFATGVG 140
                                               ********************************************************************* PP

                                 TIGR02083 139 stdlavamatgkawfkvpeaikfvlkgklkdyvsakdlilkiigkigvdgalykslefsgeglkelsvd 207
                                               stdla+ama g++wfkvpe+ikfv++gkl+++v +kdlil++igkigvdgaly+++ef+ge++++ls+d
  lcl|NCBI__GCF_000215085.1:WP_013840434.1 141 STDLAAAMALGETWFKVPESIKFVFNGKLNPWVGGKDLILYTIGKIGVDGALYRAMEFCGEAIEQLSMD 209
                                               ********************************************************************* PP

                                 TIGR02083 208 drltianmaieagaktgifevdektieyvkgrakrelkiykadedakyervieidlselepqvafphlp 276
                                               +r+t++nmaieag+k+gi+++de+t +yv gr+kr +  y +d da+y +v e+d+s++epqvafphlp
  lcl|NCBI__GCF_000215085.1:WP_013840434.1 210 GRFTMCNMAIEAGGKNGIIQPDEITRQYVEGRTKRPYTFYTSDPDAQYAEVHEFDVSKIEPQVAFPHLP 278
                                               ********************************************************************* PP

                                 TIGR02083 277 entkeideaekeeikidqvvigsctngrledlrlaaeilkgkkvakevrliilpasqkvylealkegll 345
                                               en+++i ea+  +++idq+vigsctngr+edlr+aa++lkg+kv++ vrli++p++q++y +a++egl 
  lcl|NCBI__GCF_000215085.1:WP_013840434.1 279 ENARSIREAG--NVEIDQAVIGSCTNGRMEDLRIAAQVLKGQKVNRRVRLIVIPGTQEIYRQAMHEGLF 345
                                               **********..********************************************************* PP

                                 TIGR02083 346 eifieagavvstptcgpclgghmgilaegeravsttnrnfvgrmghpksevylaspavaaasaikgkia 414
                                               +if+eaga+vstptcgpclgg+mgila+ger+++ttnrnfvgrmgh  sevyl+ pavaaasai+g+i+
  lcl|NCBI__GCF_000215085.1:WP_013840434.1 346 DIFLEAGAAVSTPTCGPCLGGYMGILAQGERCIATTNRNFVGRMGHAGSEVYLSNPAVAAASAITGRIS 414
                                               ********************************************************************* PP

                                 TIGR02083 415 speev 419
                                               +peev
  lcl|NCBI__GCF_000215085.1:WP_013840434.1 415 HPEEV 419
                                               ***97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (419 nodes)
Target sequences:                          1  (420 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: 11.04
//
[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