GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Pseudomonas putida KT2440

Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate PP_1986 PP_1986 3-isopropylmalate dehydratase small subunit

Query= uniprot:Q845W4
         (216 letters)



>FitnessBrowser__Putida:PP_1986
          Length = 214

 Score =  325 bits (832), Expect = 5e-94
 Identities = 154/210 (73%), Positives = 176/210 (83%)

Query: 1   MEKFTVHTGVVAPLDRENVDTDAIIPKQFLKSIKRTGFGPNAFDEWRYLDHGEPGQDNSK 60
           M+ FT HTG+VAPLDR NVDTD IIPKQFLKSIKRTGFGPN FDEWRYLD G+P QDNSK
Sbjct: 1   MKAFTQHTGIVAPLDRANVDTDQIIPKQFLKSIKRTGFGPNLFDEWRYLDVGQPYQDNSK 60

Query: 61  RPLNPDFVLNQPRYQGASILVTRKNFGCGSSREHAPWALQQYGFRAIIAPSFADIFFNNC 120
           RPLN +FVLN  RYQGAS+L+ R+NFGCGSSREHAPWAL +YGFR+IIAPSFADIFFNN 
Sbjct: 61  RPLNEEFVLNHARYQGASVLLARENFGCGSSREHAPWALDEYGFRSIIAPSFADIFFNNS 120

Query: 121 FKNGLLPIVLTEQQVDHLINETVAFNGYQLTIDLEAQVVRTPDGRDYPFEITAFRKYCLL 180
           FKNGLLPI+L++++VD L  +  A  GYQLTIDL+AQ V  PDG+   FEI AFRK+CLL
Sbjct: 121 FKNGLLPIILSDEEVDELFKQVEANPGYQLTIDLQAQAVTRPDGKVLHFEIDAFRKHCLL 180

Query: 181 NGFDDIGLTLRHADKIRQFEAERLAKQPWL 210
           NG DDIGLTL+ +D I+ FEA+  A QPWL
Sbjct: 181 NGLDDIGLTLQDSDAIKAFEAKHRASQPWL 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: 233
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: 216
Length of database: 214
Length adjustment: 22
Effective length of query: 194
Effective length of database: 192
Effective search space:    37248
Effective search space used:    37248
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 PP_1986 PP_1986 (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.2319.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    7.2e-94  299.0   0.0    8.8e-94  298.7   0.0    1.1  1  lcl|FitnessBrowser__Putida:PP_1986  PP_1986 3-isopropylmalate dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_1986  PP_1986 3-isopropylmalate dehydratase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.7   0.0   8.8e-94   8.8e-94       1     188 []       1     196 [.       1     196 [. 0.94

  Alignments for each domain:
  == domain 1  score: 298.7 bits;  conditional E-value: 8.8e-94
                           TIGR00171   1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryld......ekGkep.npefvlnvpqyq 68 
                                         mk f ++tG+v+pld+anvdtd+iipkqflk ikrtGfg +lf ewryld      ++ k p n efvln+ +yq
  lcl|FitnessBrowser__Putida:PP_1986   1 MKAFTQHTGIVAPLDRANVDTDQIIPKQFLKSIKRTGFGPNLFDEWRYLDvgqpyqDNSKRPlNEEFVLNHARYQ 75 
                                         899*********************************************98333322233333488********** PP

                           TIGR00171  69 gasillarenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nkglkl 142
                                         gas+llarenfGcGssrehapwal++yGf++iiapsfadif+nnsfkngllpi ls+eev+el+++v+ n+g +l
  lcl|FitnessBrowser__Putida:PP_1986  76 GASVLLARENFGCGSSREHAPWALDEYGFRSIIAPSFADIFFNNSFKNGLLPIILSDEEVDELFKQVEaNPGYQL 150
                                         *******************************************************************99****** PP

                           TIGR00171 143 tvdleaqkvkdsegkvysfeidefrkhcllnGldeigltlqkedei 188
                                         t+dl+aq v+  +gkv +feid+frkhcllnGld+igltlq  d+i
  lcl|FitnessBrowser__Putida:PP_1986 151 TIDLQAQAVTRPDGKVLHFEIDAFRKHCLLNGLDDIGLTLQDSDAI 196
                                         ******************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (188 nodes)
Target sequences:                          1  (214 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 7.30
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Links

Downloads

Related tools

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