GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Thiohalospira halophila DSM 15071 HL 3

Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate WP_093427306.1 BM272_RS03350 3-isopropylmalate dehydratase small subunit

Query= uniprot:Q845W4
         (216 letters)



>NCBI__GCF_900112605.1:WP_093427306.1
          Length = 218

 Score =  318 bits (816), Expect = 4e-92
 Identities = 152/210 (72%), Positives = 168/210 (80%)

Query: 1   MEKFTVHTGVVAPLDRENVDTDAIIPKQFLKSIKRTGFGPNAFDEWRYLDHGEPGQDNSK 60
           ME  T H G+VAPLDR NVDTDAIIPKQFLKS+KRTGFGPN FDEWRYLDHGEPGQD+S+
Sbjct: 1   MEALTHHQGLVAPLDRANVDTDAIIPKQFLKSVKRTGFGPNLFDEWRYLDHGEPGQDHSQ 60

Query: 61  RPLNPDFVLNQPRYQGASILVTRKNFGCGSSREHAPWALQQYGFRAIIAPSFADIFFNNC 120
           R  NPDFVLNQPRY+GASIL+ R+NFGCGSSREHAPWAL  YGFR IIAPSFADIF+NNC
Sbjct: 61  RRENPDFVLNQPRYRGASILLARENFGCGSSREHAPWALADYGFRVIIAPSFADIFYNNC 120

Query: 121 FKNGLLPIVLTEQQVDHLINETVAFNGYQLTIDLEAQVVRTPDGRDYPFEITAFRKYCLL 180
           FKNGLLP+VL  + VD L  ET A  GY+LT+DL AQ V TP G   PFE+   RK  LL
Sbjct: 121 FKNGLLPVVLDAETVDRLFRETAATEGYELTVDLAAQTVTTPGGEAIPFEVDPARKRRLL 180

Query: 181 NGFDDIGLTLRHADKIRQFEAERLAKQPWL 210
            G DDIGLTL +AD IR +EA R  + PWL
Sbjct: 181 EGLDDIGLTLEYADAIRAYEARRREEAPWL 210


Lambda     K      H
   0.322    0.141    0.437 

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: 215
Number of extensions: 3
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: 216
Length of database: 218
Length adjustment: 22
Effective length of query: 194
Effective length of database: 196
Effective search space:    38024
Effective search space used:    38024
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 (21.9 bits)
S2: 45 (21.9 bits)

Align candidate WP_093427306.1 BM272_RS03350 (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.2900691.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    4.9e-87  276.7   0.0    7.3e-87  276.1   0.0    1.2  1  NCBI__GCF_900112605.1:WP_093427306.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900112605.1:WP_093427306.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.1   0.0   7.3e-87   7.3e-87       1     188 []       1     196 [.       1     196 [. 0.94

  Alignments for each domain:
  == domain 1  score: 276.1 bits;  conditional E-value: 7.3e-87
                             TIGR00171   1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewrylde..kGke.....pnpefvlnvpq 66 
                                           m+ + +++Glv+pld+anvdtdaiipkqflk +krtGfg +lf ewryld+   G++     +np+fvln+p+
  NCBI__GCF_900112605.1:WP_093427306.1   1 MEALTHHQGLVAPLDRANVDTDAIIPKQFLKSVKRTGFGPNLFDEWRYLDHgePGQDhsqrrENPDFVLNQPR 73 
                                           88999*******************************************9852245432222279********* PP

                             TIGR00171  67 yqgasillarenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nk 138
                                           y+gasillarenfGcGssrehapwal+dyGf+viiapsfadifynn+fkngllp+ l+ e+v+ l+   +  +
  NCBI__GCF_900112605.1:WP_093427306.1  74 YRGASILLARENFGCGSSREHAPWALADYGFRVIIAPSFADIFYNNCFKNGLLPVVLDAETVDRLFRETAaTE 146
                                           ******************************************************************999879* PP

                             TIGR00171 139 glkltvdleaqkvkdsegkvysfeidefrkhcllnGldeigltlqkedei 188
                                           g +ltvdl aq+v++  g+ + fe+d+ rk+ ll+Gld+igltl   d+i
  NCBI__GCF_900112605.1:WP_093427306.1 147 GYELTVDLAAQTVTTPGGEAIPFEVDPARKRRLLEGLDDIGLTLEYADAI 196
                                           ********************************************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (188 nodes)
Target sequences:                          1  (218 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: 13.29
//
[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