GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Leptospirillum ferrooxidans C2-3

Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate WP_014449006.1 LFE_RS04105 3-isopropylmalate dehydratase small subunit

Query= curated2:A1K4A2
         (212 letters)



>NCBI__GCF_000284315.1:WP_014449006.1
          Length = 208

 Score =  239 bits (611), Expect = 2e-68
 Identities = 116/211 (54%), Positives = 151/211 (71%), Gaps = 8/211 (3%)

Query: 1   MKPFTVLDAIVAPLDRANVDTDAIIPKQFLKSIKRSGFGPNLFDEWRYLDVGQPGQDCSN 60
           M+ F  L +IV P+DRANVDTDAIIPKQFLK+I R+G G +LF +WRYL  G        
Sbjct: 1   MEAFKTLKSIVIPIDRANVDTDAIIPKQFLKTIHRTGLGKSLFYDWRYLSDGVT------ 54

Query: 61  RPKNPDFVLNQARYQGAQVLLARDNFGCGSSREHAPWALEDYGFRVIIAPSFADIFFNNS 120
              NPDFV+NQ RY+G ++LL+R+NFG GSSREHAPWAL D+G + IIAPSFADIF+NN 
Sbjct: 55  --PNPDFVINQTRYKGGRILLSRENFGSGSSREHAPWALLDFGIKAIIAPSFADIFYNNC 112

Query: 121 FKNGLLPIKLDAAELDVLFQQCEATEGYRLKVDLAAQTITRPDGKAIAFDVDPFRKECLL 180
           FKNG+LPI++D   +D LF++ + T GY+ +++L +Q I  PDG+ I F++D F K+CLL
Sbjct: 113 FKNGILPIRIDRMIVDGLFKEIDRTPGYQAEINLESQLILLPDGRTIPFEIDAFLKKCLL 172

Query: 181 NGWDDIGLTLRHADKIRDFEAKRRAEHPYYF 211
            G DDI LT      I  +E +RR E P+ F
Sbjct: 173 EGLDDISLTFEKKALITSYEDRRRKEAPWLF 203


Lambda     K      H
   0.323    0.141    0.441 

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: 168
Number of extensions: 3
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: 212
Length of database: 208
Length adjustment: 21
Effective length of query: 191
Effective length of database: 187
Effective search space:    35717
Effective search space used:    35717
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)

Align candidate WP_014449006.1 LFE_RS04105 (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.3313996.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.5e-83  264.6   0.0    3.1e-83  264.3   0.0    1.1  1  NCBI__GCF_000284315.1:WP_014449006.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000284315.1:WP_014449006.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  264.3   0.0   3.1e-83   3.1e-83       1     185 [.       1     185 [.       1     188 [. 0.98

  Alignments for each domain:
  == domain 1  score: 264.3 bits;  conditional E-value: 3.1e-83
                             TIGR00171   1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqgasil 73 
                                           m+ fk+l+ +v+p+d+anvdtdaiipkqflk+i+rtG+gk lfy+wryl ++G  pnp+fv+n+ +y+g  il
  NCBI__GCF_000284315.1:WP_014449006.1   1 MEAFKTLKSIVIPIDRANVDTDAIIPKQFLKTIHRTGLGKSLFYDWRYL-SDGVTPNPDFVINQTRYKGGRIL 72 
                                           899*********************************************6.5689******************* PP

                             TIGR00171  74 larenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nkglkltvd 145
                                           l+renfG Gssrehapwal d+G+k iiapsfadifynn+fkng+lpir+++ +v+ l++ +   +g + +++
  NCBI__GCF_000284315.1:WP_014449006.1  73 LSRENFGSGSSREHAPWALLDFGIKAIIAPSFADIFYNNCFKNGILPIRIDRMIVDGLFKEIDrTPGYQAEIN 145
                                           **************************************************************9899******* PP

                             TIGR00171 146 leaqkvkdsegkvysfeidefrkhcllnGldeigltlqke 185
                                           le+q +   +g+++ feid+f k+cll+Gld+i+lt+ k+
  NCBI__GCF_000284315.1:WP_014449006.1 146 LESQLILLPDGRTIPFEIDAFLKKCLLEGLDDISLTFEKK 185
                                           ************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (188 nodes)
Target sequences:                          1  (208 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: 10.48
//
[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:

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