Alignments for a candidate for leuC in Arcobacter nitrofigilis DSM 7299

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Arcobacter nitrofigilis DSM 7299

Align isopropylmalate/citramalate isomerase large subunit LeuC (EC 4.2.1.33; EC 4.2.1.35) (characterized)
to candidate WP_013134112.1 ARNIT_RS01500 3-isopropylmalate dehydratase large subunit

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



>NCBI__GCF_000092245.1:WP_013134112.1
          Length = 422

 Score =  393 bits (1009), Expect = e-114
 Identities = 202/423 (47%), Positives = 278/423 (65%), Gaps = 5/423 (1%)

Query: 1   MAHTLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSFRAMGAKRVFDKDRV 60
           M  T+ +KI   H    +  AG+IVR  + MV+ NDIT P++I++F   G +++ + D  
Sbjct: 1   MGQTITEKIFSEHVGHEVY-AGEIVRSPIDMVIGNDITTPISIRAFEEGGFEKLANPDGF 59

Query: 61  ALVMDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVV 120
           A+V+DHF P KDI +A Q +++R+FA +  +  +++  D G+EHALLPE GLV PGDV++
Sbjct: 60  AIVLDHFIPAKDIASANQARISRDFAEKHNLKLFFDEKDMGIEHALLPEKGLVLPGDVII 119

Query: 121 GADSHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLIL 180
           GADSHTCT+G LGAF+TG+GSTD++  M  G  WFKVP +I+  F G    Y+  KDLIL
Sbjct: 120 GADSHTCTHGALGAFSTGMGSTDISFGMITGGNWFKVPESIKVVFKGKPGPYITGKDLIL 179

Query: 181 TLIGAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYCTT 240
            +I  +GVDGALY+ALEF G +I  L ++ R ++ NMAIEAG K G+ A D  T  +  +
Sbjct: 180 EIIRILGVDGALYKALEFTGDSIPYLSMDDRFSLCNMAIEAGAKNGIVAYDEVTKEFLDS 239

Query: 241 AG--RTGDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEV--KDVTVQQVV 296
               R       +D  A Y + +  DV  + PV+A P LP N   V++    ++ V QV 
Sbjct: 240 RDSLRAQPKIHYSDDDATYCQVIEIDVEALNPVIAYPFLPSNGHSVNQAVEDNIRVDQVF 299

Query: 297 IGSCTNGRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIVG 356
           IGSCTNGR+ D + AA +L G+KV+R VR I+ P T  I R+A + G I+T ++AG +V 
Sbjct: 300 IGSCTNGRLSDFKVAAQLLEGKKVARHVRLILTPGTQKILREATKLGYIDTLVDAGGVVS 359

Query: 357 PATCGPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVTGVITDP 416
             TCG CLGG+MGIL D E  I+TTNRNF GRMGS  S++YLS  A AAASA++G ITDP
Sbjct: 360 NPTCGACLGGYMGILGDDEVCISTTNRNFVGRMGSRSSKIYLSNTAVAAASAISGYITDP 419

Query: 417 STL 419
            +L
Sbjct: 420 RSL 422


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: 494
Number of extensions: 16
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: 422
Length adjustment: 32
Effective length of query: 387
Effective length of database: 390
Effective search space:   150930
Effective search space used:   150930
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_013134112.1 ARNIT_RS01500 (3-isopropylmalate dehydratase large subunit)
to HMM TIGR02086 (3-isopropylmalate dehydratase, large subunit)

# 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/TIGR02086.hmm
# target sequence database:        /tmp/gapView.10662.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02086  [M=411]
Accession:   TIGR02086
Description: IPMI_arch: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.7e-157  507.8   0.0   1.1e-156  507.6   0.0    1.0  1  lcl|NCBI__GCF_000092245.1:WP_013134112.1  ARNIT_RS01500 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092245.1:WP_013134112.1  ARNIT_RS01500 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  507.6   0.0  1.1e-156  1.1e-156       1     410 [.       3     420 ..       3     421 .. 0.97

  Alignments for each domain:
  == domain 1  score: 507.6 bits;  conditional E-value: 1.1e-156
                                 TIGR02086   1 ktlaekilsekvGkevkaGeivevkvDlvmvhDgtgplvikalrelg.akvekkekivlvfDhvvPapt 68 
                                               +t++eki+se+vG+ev aGeiv   +D+v+ +D t+p  i+a++e g +k  +++   +v+Dh +Pa++
  lcl|NCBI__GCF_000092245.1:WP_013134112.1   3 QTITEKIFSEHVGHEVYAGEIVRSPIDMVIGNDITTPISIRAFEEGGfEKLANPDGFAIVLDHFIPAKD 71 
                                               699******************************************8899999***************** PP

                                 TIGR02086  69 veaaelqkeirefakelgikv.f.dvgeGichqvlvekgyakpgkvvvgaDshtttsGalgafatGlGa 135
                                               + +a+  +  r+fa ++++k  f + + Gi h +l ekg++ pg+v++gaDsht+t+Galgaf+tG+G+
  lcl|NCBI__GCF_000092245.1:WP_013134112.1  72 IASANQARISRDFAEKHNLKLfFdEKDMGIEHALLPEKGLVLPGDVIIGADSHTCTHGALGAFSTGMGS 140
                                               ********************97525688***************************************** PP

                                 TIGR02086 136 tDvalalatGktWlkvPesikveleGkleekvtakDvileivkelgadgatykaieftgeeiealslde 204
                                               tD+++ ++tG +W+kvPesikv+++Gk+  ++t+kD+ilei++ lg dga yka+eftg++i  ls+d+
  lcl|NCBI__GCF_000092245.1:WP_013134112.1 141 TDISFGMITGGNWFKVPESIKVVFKGKPGPYITGKDLILEIIRILGVDGALYKALEFTGDSIPYLSMDD 209
                                               ********************************************************************* PP

                                 TIGR02086 205 Rltlsnlaveagakaglvepdeetleylkkrrge...frilkadedakyeeeieidlseleplvavPhs 270
                                               R++l+n+a+eagak+g+v  de t+e+l +r +     +i ++d+da+y + ieid+++l+p++a P+ 
  lcl|NCBI__GCF_000092245.1:WP_013134112.1 210 RFSLCNMAIEAGAKNGIVAYDEVTKEFLDSRDSLraqPKIHYSDDDATYCQVIEIDVEALNPVIAYPFL 278
                                               ****************************99877666799****************************** PP

                                 TIGR02086 271 vdnvkevee.veg.teidqvfiGsCtnGRledlkiaaeilegrevhkdvrlivvPasrkvyekaleeGl 337
                                               + n+++v++ ve  +++dqvfiGsCtnGRl+d+k+aa++leg++v+++vrli +P  +k++++a++ G+
  lcl|NCBI__GCF_000092245.1:WP_013134112.1 279 PSNGHSVNQaVEDnIRVDQVFIGSCTNGRLSDFKVAAQLLEGKKVARHVRLILTPGTQKILREATKLGY 347
                                               *******97466569****************************************************** PP

                                 TIGR02086 338 ietlveaGaiiltpgCGPClGahlGvladgevivsttnRnfkGRmGspkaeiYLasPavaavsaveGei 406
                                               i+tlv+aG ++ +p+CG ClG ++G+l+d+ev++sttnRnf GRmGs++++iYL++ avaa+sa++G+i
  lcl|NCBI__GCF_000092245.1:WP_013134112.1 348 IDTLVDAGGVVSNPTCGACLGGYMGILGDDEVCISTTNRNFVGRMGSRSSKIYLSNTAVAAASAISGYI 416
                                               ********************************************************************* PP

                                 TIGR02086 407 tdpe 410
                                               tdp+
  lcl|NCBI__GCF_000092245.1:WP_013134112.1 417 TDPR 420
                                               ***8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (411 nodes)
Target sequences:                          1  (422 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: 10.31
//
[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