GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Pseudomonas stutzeri RCH2

Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate GFF2540 Psest_2590 3-isopropylmalate dehydratase, small subunit

Query= uniprot:Q845W4
         (216 letters)



>FitnessBrowser__psRCH2:GFF2540
          Length = 215

 Score =  321 bits (823), Expect = 6e-93
 Identities = 151/210 (71%), Positives = 173/210 (82%)

Query: 1   MEKFTVHTGVVAPLDRENVDTDAIIPKQFLKSIKRTGFGPNAFDEWRYLDHGEPGQDNSK 60
           M+ FT HTG+V PLDR NVDTD IIPKQFLKSIKRTGFGPN FDEWRYLD G+P QD S+
Sbjct: 1   MKAFTQHTGLVCPLDRANVDTDQIIPKQFLKSIKRTGFGPNLFDEWRYLDVGQPNQDCSQ 60

Query: 61  RPLNPDFVLNQPRYQGASILVTRKNFGCGSSREHAPWALQQYGFRAIIAPSFADIFFNNC 120
           RP+N DFVLN PRY+GAS+L+ R+NFGCGSSREHAPWAL++YGFR IIAPSFADIF+NN 
Sbjct: 61  RPVNKDFVLNFPRYRGASVLLARENFGCGSSREHAPWALEEYGFRTIIAPSFADIFYNNS 120

Query: 121 FKNGLLPIVLTEQQVDHLINETVAFNGYQLTIDLEAQVVRTPDGRDYPFEITAFRKYCLL 180
           FKNGLLPIVL E++VD L  +  A  GYQLT+DL AQVV  PDG+ Y FE+ AFRK+CLL
Sbjct: 121 FKNGLLPIVLKEEEVDELFAQAEASEGYQLTVDLAAQVVTRPDGKQYSFEVDAFRKHCLL 180

Query: 181 NGFDDIGLTLRHADKIRQFEAERLAKQPWL 210
           NG DDIGLTL+ A+ I+ FEA     QPWL
Sbjct: 181 NGLDDIGLTLQDAEAIKTFEARHQQNQPWL 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: 220
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: 216
Length of database: 215
Length adjustment: 22
Effective length of query: 194
Effective length of database: 193
Effective search space:    37442
Effective search space used:    37442
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 GFF2540 Psest_2590 (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.28992.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    4.3e-93  296.4   0.0    5.1e-93  296.2   0.0    1.1  1  lcl|FitnessBrowser__psRCH2:GFF2540  Psest_2590 3-isopropylmalate deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF2540  Psest_2590 3-isopropylmalate dehydratase, small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.2   0.0   5.1e-93   5.1e-93       1     188 []       1     196 [.       1     196 [. 0.94

  Alignments for each domain:
  == domain 1  score: 296.2 bits;  conditional E-value: 5.1e-93
                           TIGR00171   1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkep.......npefvlnvpqyq 68 
                                         mk f ++tGlv pld+anvdtd+iipkqflk ikrtGfg +lf ewryld+   ++       n +fvln+p+y+
  lcl|FitnessBrowser__psRCH2:GFF2540   1 MKAFTQHTGLVCPLDRANVDTDQIIPKQFLKSIKRTGFGPNLFDEWRYLDVGQPNQdcsqrpvNKDFVLNFPRYR 75 
                                         899**********************************************9643222122223488********** PP

                           TIGR00171  69 gasillarenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nkglkl 142
                                         gas+llarenfGcGssrehapwal++yGf++iiapsfadifynnsfkngllpi l+eeev+el+a+ +  +g +l
  lcl|FitnessBrowser__psRCH2:GFF2540  76 GASVLLARENFGCGSSREHAPWALEEYGFRTIIAPSFADIFYNNSFKNGLLPIVLKEEEVDELFAQAEaSEGYQL 150
                                         ******************************************************************9989***** PP

                           TIGR00171 143 tvdleaqkvkdsegkvysfeidefrkhcllnGldeigltlqkedei 188
                                         tvdl aq v+  +gk+ysfe+d+frkhcllnGld+igltlq  ++i
  lcl|FitnessBrowser__psRCH2:GFF2540 151 TVDLAAQVVTRPDGKQYSFEVDAFRKHCLLNGLDDIGLTLQDAEAI 196
                                         *****************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (188 nodes)
Target sequences:                          1  (215 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 6.25
//
[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