Alignments for a candidate for leuC in Desulfitobacterium hafniense DCB-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Desulfitobacterium hafniense DCB-2

Align isopropylmalate/citramalate isomerase large subunit LeuC (EC 4.2.1.33; EC 4.2.1.35) (characterized)
to candidate WP_026198993.1 DHAF_RS12325 3-isopropylmalate dehydratase large subunit

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



>NCBI__GCF_000021925.1:WP_026198993.1
          Length = 421

 Score =  464 bits (1194), Expect = e-135
 Identities = 231/417 (55%), Positives = 294/417 (70%), Gaps = 1/417 (0%)

Query: 1   MAHTLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSFRAMGAKRVFDKDRV 60
           MA T+ +KIL  H        GQ++  ++ + LANDIT P++I+ F   G + V+DK +V
Sbjct: 1   MAMTITEKILAEHAGLDKVVPGQLITAQLDLALANDITGPVSIREFEKFGVETVWDKTKV 60

Query: 61  ALVMDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVV 120
           ALV DHFTP KDI +A+  K  REFA++ G+ HY+E G  GVEH LLPE G+  PGDV++
Sbjct: 61  ALVPDHFTPNKDIASAELSKALREFAKKQGIVHYWEQGRVGVEHCLLPEQGVTLPGDVII 120

Query: 121 GADSHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGT-LPAYVGAKDLI 179
           GADSHTCTYG LGAFATG+GSTD+A  MA GE WF++P +I+  F GT    +V  KDLI
Sbjct: 121 GADSHTCTYGALGAFATGVGSTDLAAGMATGEAWFRIPESIKFIFKGTNFQPWVSGKDLI 180

Query: 180 LTLIGAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYCT 239
           L  IG IGVDGA YR++EF G  I AL ++GR+TM NMA+EAG K G+   D KTL Y  
Sbjct: 181 LYTIGKIGVDGARYRSMEFTGEGIAALSMDGRLTMCNMAVEAGAKNGIIPPDEKTLAYVN 240

Query: 240 TAGRTGDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKDVTVQQVVIGS 299
              +     + +D  A Y     +DV  +   VA PHLP+N KPVSE K + + QVVIGS
Sbjct: 241 ERAKRPYKVYHSDPDAQYVEVYEWDVADIPLQVAFPHLPENAKPVSEGKGIKIDQVVIGS 300

Query: 300 CTNGRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIVGPAT 359
           CTNGR+ D++ AA +L+G+KV  DVR IV+P T  I++QA++EGLI+ F++AG +V   T
Sbjct: 301 CTNGRLEDMQVAAQILKGQKVHGDVRLIVIPGTQDIYKQAMQEGLIDIFIDAGAVVSTPT 360

Query: 360 CGPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVTGVITDP 416
           CGPCLGG+MGILA GERA++TTNRNF GRMG  ESEVYLSGPA AAASAVTG I+ P
Sbjct: 361 CGPCLGGYMGILAKGERALSTTNRNFVGRMGHPESEVYLSGPAVAAASAVTGEISHP 417


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: 508
Number of extensions: 16
Number of successful extensions: 2
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_026198993.1 DHAF_RS12325 (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.25480.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-219  714.3   0.1   2.9e-219  714.1   0.1    1.0  1  lcl|NCBI__GCF_000021925.1:WP_026198993.1  DHAF_RS12325 3-isopropylmalate d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021925.1:WP_026198993.1  DHAF_RS12325 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  714.1   0.1  2.9e-219  2.9e-219       1     419 []       3     420 ..       3     420 .. 0.99

  Alignments for each domain:
  == domain 1  score: 714.1 bits;  conditional E-value: 2.9e-219
                                 TIGR02083   1 mtlaekiladkagkeevkpgelilakldlvlgndvttplaikafkelgvkkvfdkdkvalvldhftpnk 69 
                                               mt++ekila++ag+++v pg+li+a+ldl+l+nd+t p++i++f ++gv+ v dk kvalv+dhftpnk
  lcl|NCBI__GCF_000021925.1:WP_026198993.1   3 MTITEKILAEHAGLDKVVPGQLITAQLDLALANDITGPVSIREFEKFGVETVWDKTKVALVPDHFTPNK 71 
                                               9******************************************************************** PP

                                 TIGR02083  70 dikaaeqvklirefakekeiekyfeigelgvehallpekglvvsgdliigadshtctygalgafatgvg 138
                                               di +ae +k +refak+++i +y+e g++gveh+llpe+g+ ++gd+iigadshtctygalgafatgvg
  lcl|NCBI__GCF_000021925.1:WP_026198993.1  72 DIASAELSKALREFAKKQGIVHYWEQGRVGVEHCLLPEQGVTLPGDVIIGADSHTCTYGALGAFATGVG 140
                                               ********************************************************************* PP

                                 TIGR02083 139 stdlavamatgkawfkvpeaikfvlkg.klkdyvsakdlilkiigkigvdgalykslefsgeglkelsv 206
                                               stdla++matg+awf++pe+ikf +kg +++++vs+kdlil++igkigvdga y+s+ef+geg+  ls+
  lcl|NCBI__GCF_000021925.1:WP_026198993.1 141 STDLAAGMATGEAWFRIPESIKFIFKGtNFQPWVSGKDLILYTIGKIGVDGARYRSMEFTGEGIAALSM 209
                                               **************************9569*************************************** PP

                                 TIGR02083 207 ddrltianmaieagaktgifevdektieyvkgrakrelkiykadedakyervieidlselepqvafphl 275
                                               d+rlt++nma+eagak+gi+++dekt++yv++rakr +k+y++d da+y++v e d+ ++  qvafphl
  lcl|NCBI__GCF_000021925.1:WP_026198993.1 210 DGRLTMCNMAVEAGAKNGIIPPDEKTLAYVNERAKRPYKVYHSDPDAQYVEVYEWDVADIPLQVAFPHL 278
                                               ********************************************************************* PP

                                 TIGR02083 276 pentkeideaekeeikidqvvigsctngrledlrlaaeilkgkkvakevrliilpasqkvylealkegl 344
                                               pen+k+++e +   ikidqvvigsctngrled+++aa+ilkg+kv  +vrli++p++q++y++a++egl
  lcl|NCBI__GCF_000021925.1:WP_026198993.1 279 PENAKPVSEGK--GIKIDQVVIGSCTNGRLEDMQVAAQILKGQKVHGDVRLIVIPGTQDIYKQAMQEGL 345
                                               ********988..9******************************************************* PP

                                 TIGR02083 345 leifieagavvstptcgpclgghmgilaegeravsttnrnfvgrmghpksevylaspavaaasaikgki 413
                                               ++ifi+agavvstptcgpclgg+mgila+gera+sttnrnfvgrmghp+sevyl+ pavaaasa++g+i
  lcl|NCBI__GCF_000021925.1:WP_026198993.1 346 IDIFIDAGAVVSTPTCGPCLGGYMGILAKGERALSTTNRNFVGRMGHPESEVYLSGPAVAAASAVTGEI 414
                                               ********************************************************************* PP

                                 TIGR02083 414 aspeev 419
                                               ++peev
  lcl|NCBI__GCF_000021925.1:WP_026198993.1 415 SHPEEV 420
                                               ****97 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.42
//
[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