Alignments for a candidate for leuB in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Pseudomonas putida KT2440

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate PP_1988 PP_1988 3-isopropylmalate dehydrogenase

Query= BRENDA::P96197
         (360 letters)



>FitnessBrowser__Putida:PP_1988
          Length = 360

 Score =  524 bits (1350), Expect = e-153
 Identities = 284/376 (75%), Positives = 307/376 (81%), Gaps = 32/376 (8%)

Query: 1   MSKQILVLPGDGIGPEIMAEAVKVLQLANEKYQLGFVLGYDELGGAAVDKYGVPLADETL 60
           MSKQIL+LPGDGIGPEIMAEAVKVL+LAN+K+QLGF L +D +GGAA+DK+GVPLADETL
Sbjct: 1   MSKQILILPGDGIGPEIMAEAVKVLELANDKFQLGFSLAHDVIGGAAIDKHGVPLADETL 60

Query: 61  ERARR------------RCHPARRRRRSEMG----RHRPGHPPGARPAENPFATGPVRQP 104
           ERAR+            +     R  R E G    R + G     RPA            
Sbjct: 61  ERARKADAVLLGAVGGPKWDKIERDIRPERGLLKIRSQLGLFANLRPA------------ 108

Query: 105 APGVLYPQLAEASTLRPEVVAGLDILIVRELTGGIYFGAPRESRLLANGERMAYDTLPYS 164
              +LYPQLA+AS+L+PE+V+GLDILIVRELTGGIYFGAPR  R L  GER AYDTLPYS
Sbjct: 109 ---ILYPQLADASSLKPEIVSGLDILIVRELTGGIYFGAPRGQRELEGGERQAYDTLPYS 165

Query: 165 ESEIRRIAKVGFDMARVRGKKLCSVDKANVLASSQLWRAVVEEVAKDYPDVVLSHMYVDN 224
           ESE+RRIA+VGFDMARVRGKKLCSVDKANVLASSQLWR VVE+VAKDYPDV LSHMYVDN
Sbjct: 166 ESEVRRIARVGFDMARVRGKKLCSVDKANVLASSQLWREVVEDVAKDYPDVELSHMYVDN 225

Query: 225 AAMQLVRAPKQFDVIVTDNMFGDILSDEASMLTGSIGMLPSASLDADNKGMYEPCHGSRR 284
           AAMQLVRAPKQFDV+VTDNMFGDILSDEASMLTGSIGMLPSASLDADNKGMYEPCHGS  
Sbjct: 226 AAMQLVRAPKQFDVMVTDNMFGDILSDEASMLTGSIGMLPSASLDADNKGMYEPCHGS-A 284

Query: 285 PDIAGKGIANPLATILSVSMMLRYSFGQVEAANAIEQAVSKVLDQGLRTGDIWSEGCRKV 344
           PDIAG GIANPLATILSVSMMLRYSF Q  AA AIE+AVS VLDQGLRTGDI+SEGCRKV
Sbjct: 285 PDIAGLGIANPLATILSVSMMLRYSFNQSAAAEAIEKAVSLVLDQGLRTGDIFSEGCRKV 344

Query: 345 GTAEMGDAVVAALATL 360
           GT EMGDAVVAAL  L
Sbjct: 345 GTQEMGDAVVAALRNL 360


Lambda     K      H
   0.318    0.135    0.393 

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: 473
Number of extensions: 11
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 360
Length of database: 360
Length adjustment: 29
Effective length of query: 331
Effective length of database: 331
Effective search space:   109561
Effective search space used:   109561
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: 49 (23.5 bits)

Align candidate PP_1988 PP_1988 (3-isopropylmalate dehydrogenase)
to HMM TIGR00169 (leuB: 3-isopropylmalate dehydrogenase (EC 1.1.1.85))

# 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/TIGR00169.hmm
# target sequence database:        /tmp/gapView.8370.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00169  [M=349]
Accession:   TIGR00169
Description: leuB: 3-isopropylmalate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.4e-165  535.2   0.0   3.9e-165  535.0   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_1988  PP_1988 3-isopropylmalate dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_1988  PP_1988 3-isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  535.0   0.0  3.9e-165  3.9e-165       1     348 [.       4     352 ..       4     353 .. 0.99

  Alignments for each domain:
  == domain 1  score: 535.0 bits;  conditional E-value: 3.9e-165
                           TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGpk 75 
                                         +i +LpGDgiGpe++aea+kvL+  +++f+l +   +  iGGaaid++g Pl++etl+ +++adavLlgavGGpk
  lcl|FitnessBrowser__Putida:PP_1988   4 QILILPGDGIGPEIMAEAVKVLELANDKFQLGFSLAHDVIGGAAIDKHGVPLADETLERARKADAVLLGAVGGPK 78 
                                         589************************************************************************ PP

                           TIGR00169  76 WdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkereeaee 150
                                         Wd+  rd+rPe+gLLk+r +l+lfanLrPa l+++L ++s+lk+eiv+g+D+++vreLtgGiYfG p++++e e 
  lcl|FitnessBrowser__Putida:PP_1988  79 WDKIERDIRPERGLLKIRSQLGLFANLRPAILYPQLADASSLKPEIVSGLDILIVRELTGGIYFGAPRGQRELEG 153
                                         *********************************************************************999887 PP

                           TIGR00169 151 .ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyiDnaam 224
                                          e++a+dt  Y+++e++riarv+f +ar r kk++svDkanvL+ss+lWr++ve++ak+yPdvel+h+y+Dnaam
  lcl|FitnessBrowser__Putida:PP_1988 154 gERQAYDTLPYSESEVRRIARVGFDMARVRGKKLCSVDKANVLASSQLWREVVEDVAKDYPDVELSHMYVDNAAM 228
                                         8************************************************************************** PP

                           TIGR00169 225 qLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpiaailsaa 299
                                         qLv++P+q+dv+vt+n+fGDilsDeas++tGs+G+LPsasl  + ++++ep hgsapdiag gianp+a+ils++
  lcl|FitnessBrowser__Putida:PP_1988 229 QLVRAPKQFDVMVTDNMFGDILSDEASMLTGSIGMLPSASLDADNKGMYEPCHGSAPDIAGLGIANPLATILSVS 303
                                         *************************************************************************** PP

                           TIGR00169 300 lllryslnleeaaeaieaavkkvleegkrtedlaseattavstkeveee 348
                                         ++lrys+n++ aaeaie+av+ vl++g rt d+ se++ +v+t+e+++ 
  lcl|FitnessBrowser__Putida:PP_1988 304 MMLRYSFNQSAAAEAIEKAVSLVLDQGLRTGDIFSEGCRKVGTQEMGDA 352
                                         **********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (360 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: 00:00:00.01
# Mc/sec: 7.57
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis