GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Streptacidiphilus oryzae TH49

Align 3-isopropylmalate dehydratase small subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 (characterized)
to candidate WP_037572524.1 BS73_RS14590 3-isopropylmalate dehydratase small subunit

Query= SwissProt::Q8NQV7
         (197 letters)



>NCBI__GCF_000744815.1:WP_037572524.1
          Length = 198

 Score =  242 bits (618), Expect = 3e-69
 Identities = 126/195 (64%), Positives = 146/195 (74%), Gaps = 1/195 (0%)

Query: 1   MEKFTTYTGVGVPLQRSNVDTDQIIPAVYLKRVTRTGFEDGLFSNWRQNDPNFVLNTDTY 60
           MEKFT +TG  VPL+RSNVDTDQIIPA +LK+VTRTGFEDGLF  WR+ D +FVLN    
Sbjct: 1   MEKFTVHTGRAVPLRRSNVDTDQIIPAHWLKKVTRTGFEDGLFEAWRK-DESFVLNDPVR 59

Query: 61  KNGSVLVAGPDFGTGSSREHAVWALMDYGFRAVFSSRFADIFRGNSGKAGMLTGIMEQSD 120
           K  +VLVAGPDFGTGSSREHAVWAL +YGF+AV S RFADIFRGNS K G+LT I+    
Sbjct: 60  KGATVLVAGPDFGTGSSREHAVWALQNYGFKAVISPRFADIFRGNSLKNGLLTVILPAET 119

Query: 121 IELLWKLMEQTPGLELTVNLEKQIVTAGDVVISFEVDPYIRWRLMEGLDDAGLTLRKLDE 180
           +E L  L+E  P  E+TV+LE + V A  V  SFE+D   RWRL+ GLDD  +TL + D 
Sbjct: 120 VEALQALVEADPQAEITVDLENREVRAQGVTASFELDENARWRLLNGLDDISITLDQEDA 179

Query: 181 IEDYEAKRPAFKPRT 195
           I  YEAKRPAFKPRT
Sbjct: 180 IAAYEAKRPAFKPRT 194


Lambda     K      H
   0.319    0.137    0.409 

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: 192
Number of extensions: 4
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: 197
Length of database: 198
Length adjustment: 20
Effective length of query: 177
Effective length of database: 178
Effective search space:    31506
Effective search space used:    31506
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 (21.7 bits)
S2: 45 (21.9 bits)

Align candidate WP_037572524.1 BS73_RS14590 (3-isopropylmalate dehydratase small subunit)
to HMM TIGR00171 (leuD: 3-isopropylmalate dehydratase, small 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/TIGR00171.hmm
# target sequence database:        /tmp/gapView.3985134.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00171  [M=188]
Accession:   TIGR00171
Description: leuD: 3-isopropylmalate dehydratase, small 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    4.4e-63  198.6   0.0    5.2e-63  198.4   0.0    1.1  1  NCBI__GCF_000744815.1:WP_037572524.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_037572524.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.4   0.0   5.2e-63   5.2e-63       1     188 []       1     180 [.       1     180 [. 0.97

  Alignments for each domain:
  == domain 1  score: 198.4 bits;  conditional E-value: 5.2e-63
                             TIGR00171   1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqgasil 73 
                                           m++f  +tG +vpl + nvdtd+iip  +lkk++rtGf+  lf  wr         +  fvln p+ +ga++l
  NCBI__GCF_000744815.1:WP_037572524.1   1 MEKFTVHTGRAVPLRRSNVDTDQIIPAHWLKKVTRTGFEDGLFEAWRK--------DESFVLNDPVRKGATVL 65 
                                           899********************************************7........456************** PP

                             TIGR00171  74 larenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nkglkltvd 145
                                           +a+ +fG Gssreha wal++yGfk +i+p fadif +ns+kngll + l+ e+ve l alv+ ++  ++tvd
  NCBI__GCF_000744815.1:WP_037572524.1  66 VAGPDFGTGSSREHAVWALQNYGFKAVISPRFADIFRGNSLKNGLLTVILPAETVEALQALVEaDPQAEITVD 138
                                           **************************************************************989999***** PP

                             TIGR00171 146 leaqkvkdsegkvysfeidefrkhcllnGldeigltlqkedei 188
                                           le+++v++  g + sfe+de  +  llnGld+i++tl +ed+i
  NCBI__GCF_000744815.1:WP_037572524.1 139 LENREVRAQ-GVTASFELDENARWRLLNGLDDISITLDQEDAI 180
                                           ******975.69*****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (188 nodes)
Target sequences:                          1  (198 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 13.95
//
[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