GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Magnetospirillum magneticum AMB-1

Align 3-isopropylmalate dehydratase small subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 (characterized)
to candidate WP_011386419.1 AMB_RS20565 3-isopropylmalate dehydratase small subunit

Query= SwissProt::Q1MA52
         (202 letters)



>NCBI__GCF_000009985.1:WP_011386419.1
          Length = 201

 Score =  310 bits (793), Expect = 1e-89
 Identities = 147/200 (73%), Positives = 168/200 (84%)

Query: 1   MDKFVKLTGVAAPLPVVNVDTDMIIPKDYLKTIKRTGLGTGLFAEARYNEDGSENPDFVL 60
           M+KF  LTGVAAPLP++NVDTDMIIPK +LKTIKRTGLG  LF E RY +DG E PDFVL
Sbjct: 1   MEKFTTLTGVAAPLPMINVDTDMIIPKQFLKTIKRTGLGKNLFDEMRYTQDGKEVPDFVL 60

Query: 61  NKPAYRDAKILVAGDNFGCGSSREHAPWALLDFGIRCVISTSFADIFYNNCFKNGILPIK 120
           NKPAYR AKILVAG NFGCGSSREHAPWA+ DFGIRCVI+ SFADIF+NNCFKNGILPIK
Sbjct: 61  NKPAYRSAKILVAGANFGCGSSREHAPWAIGDFGIRCVIAPSFADIFFNNCFKNGILPIK 120

Query: 121 VSQEDLDKLMDDASRGSNAILTVDLENLEITGPDGGLIKFDLDEFKRHCLLNGLDDIGLT 180
           + QE +DKL+DDA+RGSNAI+TVDL    ITGPDGG I F++D F++HCLLNGLDDIGLT
Sbjct: 121 LPQEQVDKLLDDANRGSNAIVTVDLARQVITGPDGGSISFEVDPFRKHCLLNGLDDIGLT 180

Query: 181 LEKGKAIDSFEKKNAASHPW 200
           L++   I +FE+    S PW
Sbjct: 181 LQREDKIAAFEESRKTSSPW 200


Lambda     K      H
   0.319    0.140    0.419 

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: 206
Number of extensions: 5
Number of successful extensions: 1
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: 202
Length of database: 201
Length adjustment: 21
Effective length of query: 181
Effective length of database: 180
Effective search space:    32580
Effective search space used:    32580
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_011386419.1 AMB_RS20565 (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.392479.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.8e-85  271.0   0.0    3.2e-85  270.8   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011386419.1  AMB_RS20565 3-isopropylmalate de


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011386419.1  AMB_RS20565 3-isopropylmalate dehydratase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  270.8   0.0   3.2e-85   3.2e-85       1     188 []       1     187 [.       1     187 [. 0.96

  Alignments for each domain:
  == domain 1  score: 270.8 bits;  conditional E-value: 3.2e-85
                                 TIGR00171   1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqg 69 
                                               m++f +ltG+++pl  +nvdtd iipkqflk+ikrtG+gk+lf e ry  ++G ++ p+fvln p y+ 
  lcl|NCBI__GCF_000009985.1:WP_011386419.1   1 MEKFTTLTGVAAPLPMINVDTDMIIPKQFLKTIKRTGLGKNLFDEMRY-TQDG-KEVPDFVLNKPAYRS 67 
                                               899*********************************************.6778.778************ PP

                                 TIGR00171  70 asillarenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.n 137
                                               a+il+a+ nfGcGssrehapwa+ d+G++ +iapsfadif+nn+fkng+lpi+l++e+v++ll   +  
  lcl|NCBI__GCF_000009985.1:WP_011386419.1  68 AKILVAGANFGCGSSREHAPWAIGDFGIRCVIAPSFADIFFNNCFKNGILPIKLPQEQVDKLLDDANrG 136
                                               **************************************************************9998745 PP

                                 TIGR00171 138 kglkltvdleaqkvkdsegkvysfeidefrkhcllnGldeigltlqkedei 188
                                               +   +tvdl  q ++  +g  +sfe+d+frkhcllnGld+igltlq+ed+i
  lcl|NCBI__GCF_000009985.1:WP_011386419.1 137 SNAIVTVDLARQVITGPDGGSISFEVDPFRKHCLLNGLDDIGLTLQREDKI 187
                                               556689*******************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (188 nodes)
Target sequences:                          1  (201 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: 14.04
//
[ok]

This GapMind analysis is from Apr 09 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:

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