GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Caldicellulosiruptor kronotskyensis 2002

Align isopropylmalate/citramalate isomerase large subunit LeuC (EC 4.2.1.33; EC 4.2.1.35) (characterized)
to candidate WP_013429581.1 CALKRO_RS02690 3-isopropylmalate dehydratase large subunit

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



>NCBI__GCF_000166775.1:WP_013429581.1
          Length = 429

 Score =  480 bits (1236), Expect = e-140
 Identities = 232/417 (55%), Positives = 300/417 (71%), Gaps = 1/417 (0%)

Query: 4   TLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSFRAMGAKRVFDKDRVALV 63
           T++QKIL  H  +   + G ++   V +VL ND+T P+AIK F  +G  RVFDKD++A+V
Sbjct: 6   TMSQKILAYHAGKEYVEPGDLIFANVDLVLGNDVTTPVAIKEFEKIGIDRVFDKDKIAIV 65

Query: 64  MDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVVGAD 123
            DHFTP KDI++AQQ K+ REFA++  +T+Y+E G+ G+EHALLPE GLV PGD+V+GAD
Sbjct: 66  PDHFTPNKDIKSAQQCKMVREFAKKYEITNYFEVGEMGIEHALLPEKGLVVPGDLVIGAD 125

Query: 124 SHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLILTLI 183
           SHTCTYG LGAF+TG+GSTD+A AMA G+ WFKVP  I+    G    +   KD+IL +I
Sbjct: 126 SHTCTYGALGAFSTGIGSTDMACAMATGKCWFKVPEAIKFILYGKKTGWTSGKDIILHII 185

Query: 184 GAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYCTTAGR 243
           G IGVDGALY+++E+ G  +++L ++ R T+ANMAIEAG K G+F  D KT+ Y      
Sbjct: 186 GMIGVDGALYKSMEYTGEGLKSLSMDDRFTIANMAIEAGAKNGIFEVDEKTIEYVKQHST 245

Query: 244 TGDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKD-VTVQQVVIGSCTN 302
                F AD  A Y +    D++ + P VA PHLP+N K + E+ + + + QVVIGSCTN
Sbjct: 246 KPYKIFKADEDAEYSQVFEIDISKIRPTVAFPHLPENTKTIDEITEKIYIDQVVIGSCTN 305

Query: 303 GRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIVGPATCGP 362
           GRI DLR AA +L+GRKV + +RCI+ P T  I++QAL+EGLIE F++AGC+V   TCGP
Sbjct: 306 GRIEDLRIAAKILKGRKVKKGLRCIIFPTTQNIYKQALKEGLIEIFIDAGCVVSTPTCGP 365

Query: 363 CLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVTGVITDPSTL 419
           CLGGHMGILADGE+A+ATTNRNF GRMG   SEVYLS PA AAASAV G I  P  L
Sbjct: 366 CLGGHMGILADGEKALATTNRNFVGRMGHPNSEVYLSSPAIAAASAVLGYIGSPEEL 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: 519
Number of extensions: 20
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: 429
Length adjustment: 32
Effective length of query: 387
Effective length of database: 397
Effective search space:   153639
Effective search space used:   153639
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: 51 (24.3 bits)

Align candidate WP_013429581.1 CALKRO_RS02690 (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.2414192.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.4e-240  782.3   3.4   6.1e-240  782.2   3.4    1.0  1  NCBI__GCF_000166775.1:WP_013429581.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166775.1:WP_013429581.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  782.2   3.4  6.1e-240  6.1e-240       1     419 []       5     422 ..       5     422 .. 1.00

  Alignments for each domain:
  == domain 1  score: 782.2 bits;  conditional E-value: 6.1e-240
                             TIGR02083   1 mtlaekiladkagkeevkpgelilakldlvlgndvttplaikafkelgvkkvfdkdkvalvldhftpnkdika 73 
                                           mt+++kila +agke+v+pg+li a++dlvlgndvttp+aik+f ++g+++vfdkdk+a+v+dhftpnkdik+
  NCBI__GCF_000166775.1:WP_013429581.1   5 MTMSQKILAYHAGKEYVEPGDLIFANVDLVLGNDVTTPVAIKEFEKIGIDRVFDKDKIAIVPDHFTPNKDIKS 77 
                                           9************************************************************************ PP

                             TIGR02083  74 aeqvklirefakekeiekyfeigelgvehallpekglvvsgdliigadshtctygalgafatgvgstdlavam 146
                                           a+q+k++refak+ ei +yfe+ge+g+ehallpekglvv+gdl+igadshtctygalgaf+tg+gstd+a am
  NCBI__GCF_000166775.1:WP_013429581.1  78 AQQCKMVREFAKKYEITNYFEVGEMGIEHALLPEKGLVVPGDLVIGADSHTCTYGALGAFSTGIGSTDMACAM 150
                                           ************************************************************************* PP

                             TIGR02083 147 atgkawfkvpeaikfvlkgklkdyvsakdlilkiigkigvdgalykslefsgeglkelsvddrltianmaiea 219
                                           atgk+wfkvpeaikf l gk   + s+kd+il+iig+igvdgalyks+e++geglk+ls+ddr+tianmaiea
  NCBI__GCF_000166775.1:WP_013429581.1 151 ATGKCWFKVPEAIKFILYGKKTGWTSGKDIILHIIGMIGVDGALYKSMEYTGEGLKSLSMDDRFTIANMAIEA 223
                                           ************************************************************************* PP

                             TIGR02083 220 gaktgifevdektieyvkgrakrelkiykadedakyervieidlselepqvafphlpentkeideaekeeiki 292
                                           gak+gifevdektieyvk+ +++ +ki+kadeda+y++v+eid+s+++p+vafphlpentk+ide++ e+i i
  NCBI__GCF_000166775.1:WP_013429581.1 224 GAKNGIFEVDEKTIEYVKQHSTKPYKIFKADEDAEYSQVFEIDISKIRPTVAFPHLPENTKTIDEIT-EKIYI 295
                                           ******************************************************************9.9**** PP

                             TIGR02083 293 dqvvigsctngrledlrlaaeilkgkkvakevrliilpasqkvylealkeglleifieagavvstptcgpclg 365
                                           dqvvigsctngr+edlr+aa+ilkg+kv+k +r+ii+p++q++y++alkegl+eifi+ag+vvstptcgpclg
  NCBI__GCF_000166775.1:WP_013429581.1 296 DQVVIGSCTNGRIEDLRIAAKILKGRKVKKGLRCIIFPTTQNIYKQALKEGLIEIFIDAGCVVSTPTCGPCLG 368
                                           ************************************************************************* PP

                             TIGR02083 366 ghmgilaegeravsttnrnfvgrmghpksevylaspavaaasaikgkiaspeev 419
                                           ghmgila+ge+a++ttnrnfvgrmghp+sevyl+spa+aaasa+ g+i spee+
  NCBI__GCF_000166775.1:WP_013429581.1 369 GHMGILADGEKALATTNRNFVGRMGHPNSEVYLSSPAIAAASAVLGYIGSPEEL 422
                                           ***************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (419 nodes)
Target sequences:                          1  (429 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: 26.30
//
[ok]

This GapMind analysis is from Jul 26 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:

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:

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:

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:

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