Alignments for a candidate for leuC in Nitratiruptor tergarcus DSM 16512

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Nitratiruptor tergarcus DSM 16512

Align isopropylmalate/citramalate isomerase large subunit LeuC (EC 4.2.1.33; EC 4.2.1.35) (characterized)
to candidate WP_084274801.1 B8779_RS01390 3-isopropylmalate dehydratase large subunit

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



>NCBI__GCF_900176045.1:WP_084274801.1
          Length = 421

 Score =  445 bits (1144), Expect = e-129
 Identities = 223/422 (52%), Positives = 289/422 (68%), Gaps = 4/422 (0%)

Query: 1   MAHTLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSFRAMGAKRVFDKDRV 60
           M  T+ +KI   H    +  AG+IV C + M++ NDIT P++IK+FR  GAK++   D  
Sbjct: 1   MGQTITEKIFSEHVGREVK-AGEIVECELDMIIGNDITTPISIKAFRESGAKKLAKPDNF 59

Query: 61  ALVMDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVV 120
           A+V+DHF P KDI +A Q K++REFA E  + H+++  D G+EHALLPE GLV PGDV++
Sbjct: 60  AIVLDHFIPAKDIASANQAKISREFAYEHNLKHFFDEKDMGIEHALLPEKGLVVPGDVII 119

Query: 121 GADSHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLIL 180
           GADSHTCT+G LGAFATG+GSTD+A  M  G+ WFKVPP+I+  +TG L  YV  KDLIL
Sbjct: 120 GADSHTCTHGALGAFATGMGSTDLAYGMITGKNWFKVPPSIKVVYTGKLDEYVYGKDLIL 179

Query: 181 TLIGAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYCTT 240
            LI  IGVDGALY+ALEF G  IE LD++GR ++ NMAIEAG K G+ A D  T  +   
Sbjct: 180 ELIRRIGVDGALYKALEFTGDTIENLDMDGRFSLCNMAIEAGAKNGIIAVDEITKAFLAD 239

Query: 241 AGRTGDTAFS-ADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEV--KDVTVQQVVI 297
                +     +D  A YE+ +  DV  + PV+A PHLP N +P+SE    D+ V QV I
Sbjct: 240 KDLAREPKIHYSDEDAEYEQVIEIDVNSLEPVIAFPHLPSNGRPISEAAKMDLKVDQVFI 299

Query: 298 GSCTNGRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIVGP 357
           GSCTNGR+ D+  AA +L+GRKV+R  R IV PAT  I ++A ++G I+  ++AG +V  
Sbjct: 300 GSCTNGRLSDIAIAAEILKGRKVARHTRMIVTPATQKILKEAEKQGYIDILIDAGAVVSN 359

Query: 358 ATCGPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVTGVITDPS 417
            TCG CLGG+MGILAD ER ++TTNRNF GRMG+  SE+YL+  A AAASAV G I DP 
Sbjct: 360 PTCGACLGGYMGILADNERCVSTTNRNFIGRMGARTSEIYLANSAVAAASAVAGKIADPR 419

Query: 418 TL 419
            L
Sbjct: 420 EL 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: 520
Number of extensions: 21
Number of successful extensions: 3
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_084274801.1 B8779_RS01390 (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.1572581.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-198  646.0   3.0   1.6e-198  645.8   3.0    1.0  1  NCBI__GCF_900176045.1:WP_084274801.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900176045.1:WP_084274801.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  645.8   3.0  1.6e-198  1.6e-198       2     419 .]       4     421 .]       3     421 .] 0.99

  Alignments for each domain:
  == domain 1  score: 645.8 bits;  conditional E-value: 1.6e-198
                             TIGR02083   2 tlaekiladkagkeevkpgelilakldlvlgndvttplaikafkelgvkkvfdkdkvalvldhftpnkdikaa 74 
                                           t++eki++++ g+e vk+ge++  +ld+++gnd+ttp++ikaf+e g+kk+ ++d+ a+vldhf p kdi +a
  NCBI__GCF_900176045.1:WP_084274801.1   4 TITEKIFSEHVGRE-VKAGEIVECELDMIIGNDITTPISIKAFRESGAKKLAKPDNFAIVLDHFIPAKDIASA 75 
                                           89***********9.********************************************************** PP

                             TIGR02083  75 eqvklirefakekeiekyfeigelgvehallpekglvvsgdliigadshtctygalgafatgvgstdlavama 147
                                           +q+k++refa e++++++f+  ++g+ehallpekglvv+gd+iigadshtct+galgafatg+gstdla +m+
  NCBI__GCF_900176045.1:WP_084274801.1  76 NQAKISREFAYEHNLKHFFDEKDMGIEHALLPEKGLVVPGDVIIGADSHTCTHGALGAFATGMGSTDLAYGMI 148
                                           ************************************************************************* PP

                             TIGR02083 148 tgkawfkvpeaikfvlkgklkdyvsakdlilkiigkigvdgalykslefsgeglkelsvddrltianmaieag 220
                                           tgk wfkvp +ik+v+ gkl +yv +kdlil++i  igvdgalyk+lef+g+++++l +d+r++++nmaieag
  NCBI__GCF_900176045.1:WP_084274801.1 149 TGKNWFKVPPSIKVVYTGKLDEYVYGKDLILELIRRIGVDGALYKALEFTGDTIENLDMDGRFSLCNMAIEAG 221
                                           ************************************************************************* PP

                             TIGR02083 221 aktgifevdektieyvkgra.krelkiykadedakyervieidlselepqvafphlpentkeideaekeeiki 292
                                           ak+gi+ vde+t ++  ++   re ki+ +deda+ye+vieid+++lep +afphlp+n ++i+ea+k+++k+
  NCBI__GCF_900176045.1:WP_084274801.1 222 AKNGIIAVDEITKAFLADKDlAREPKIHYSDEDAEYEQVIEIDVNSLEPVIAFPHLPSNGRPISEAAKMDLKV 294
                                           ***************9887537999************************************************ PP

                             TIGR02083 293 dqvvigsctngrledlrlaaeilkgkkvakevrliilpasqkvylealkeglleifieagavvstptcgpclg 365
                                           dqv igsctngrl+d+++aaeilkg+kva+++r+i+ pa+qk+ +ea k+g+++i+i+agavvs ptcg clg
  NCBI__GCF_900176045.1:WP_084274801.1 295 DQVFIGSCTNGRLSDIAIAAEILKGRKVARHTRMIVTPATQKILKEAEKQGYIDILIDAGAVVSNPTCGACLG 367
                                           ************************************************************************* PP

                             TIGR02083 366 ghmgilaegeravsttnrnfvgrmghpksevylaspavaaasaikgkiaspeev 419
                                           g+mgila++er+vsttnrnf+grmg  +se+yla  avaaasa++gkia+p+e+
  NCBI__GCF_900176045.1:WP_084274801.1 368 GYMGILADNERCVSTTNRNFIGRMGARTSEIYLANSAVAAASAVAGKIADPREL 421
                                           ***************************************************986 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 26.31
//
[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 2024 update 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 original 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