GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Pseudomonas stutzeri RCH2

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate GFF2539 Psest_2589 3-isopropylmalate dehydrogenase

Query= BRENDA::P96197
         (360 letters)



>FitnessBrowser__psRCH2:GFF2539
          Length = 360

 Score =  538 bits (1387), Expect = e-158
 Identities = 294/365 (80%), Positives = 307/365 (84%), Gaps = 10/365 (2%)

Query: 1   MSKQILVLPGDGIGPEIMAEAVKVLQLANEKYQLGFVLGYDELGGAAVDKYGVPLADETL 60
           MSKQILVLPGDGIGPEIMAEAVKVLQLAN+K+QL F L YDELGGAAVDKYGVPLADETL
Sbjct: 1   MSKQILVLPGDGIGPEIMAEAVKVLQLANDKFQLDFELSYDELGGAAVDKYGVPLADETL 60

Query: 61  ERARRRCHPARRRRRSEMGRHR-PGHPPGARPAENPFAT----GPVRQPAPGVLYPQLAE 115
           ERAR     A       +G  +     P  RP           G      P +LYPQLAE
Sbjct: 61  ERARA----ADAILLGAVGGPKWDTIDPAIRPERGLLKIRSQLGLFGNLRPALLYPQLAE 116

Query: 116 ASTLRPEVVAGLDILIVRELTGGIYFGAPRESRLLANGERMAYDTLPYSESEIRRIAKVG 175
           AS+L+PE+VAGLDILIVRELTGGIYFG PRES++L +GERMAYDTLPYSESEIRRIAKVG
Sbjct: 117 ASSLKPEIVAGLDILIVRELTGGIYFGQPRESKVLESGERMAYDTLPYSESEIRRIAKVG 176

Query: 176 FDMARVRGKKLCSVDKANVLASSQLWRAVVEEVAKDYPDVVLSHMYVDNAAMQLVRAPKQ 235
           FDMA VR KKLCSVDKANVLASSQLWRAVVEEVAK YPDV LSHMYVDNAAMQLVRAPKQ
Sbjct: 177 FDMAMVRNKKLCSVDKANVLASSQLWRAVVEEVAKYYPDVELSHMYVDNAAMQLVRAPKQ 236

Query: 236 FDVIVTDNMFGDILSDEASMLTGSIGMLPSASLDADNKGMYEPCHGSRRPDIAGKGIANP 295
           FDVIVTDNMFGDILSDEASMLTGSIGMLPSASLDA NKGMYEPCHGS  PDIAG+GIANP
Sbjct: 237 FDVIVTDNMFGDILSDEASMLTGSIGMLPSASLDAGNKGMYEPCHGS-APDIAGQGIANP 295

Query: 296 LATILSVSMMLRYSFGQVEAANAIEQAVSKVLDQGLRTGDIWSEGCRKVGTAEMGDAVVA 355
           LATILSVSMMLRYSF QV AA+AIEQAVS VLDQGLRTGDIWSEGC KVGT  MGDAVVA
Sbjct: 296 LATILSVSMMLRYSFNQVAAADAIEQAVSDVLDQGLRTGDIWSEGCTKVGTQAMGDAVVA 355

Query: 356 ALATL 360
           ALA L
Sbjct: 356 ALAKL 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: 499
Number of extensions: 12
Number of successful extensions: 3
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: 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 GFF2539 Psest_2589 (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.19034.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.1e-163  529.3   0.0   2.4e-163  529.1   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF2539  Psest_2589 3-isopropylmalate deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF2539  Psest_2589 3-isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  529.1   0.0  2.4e-163  2.4e-163       1     348 [.       4     352 ..       4     353 .. 0.99

  Alignments for each domain:
  == domain 1  score: 529.1 bits;  conditional E-value: 2.4e-163
                           TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGpk 75 
                                         +i vLpGDgiGpe++aea+kvL+  +++f+l++e ++ ++GGaa+d++g Pl++etl+ +++ada+LlgavGGpk
  lcl|FitnessBrowser__psRCH2:GFF2539   4 QILVLPGDGIGPEIMAEAVKVLQLANDKFQLDFELSYDELGGAAVDKYGVPLADETLERARAADAILLGAVGGPK 78 
                                         589************************************************************************ PP

                           TIGR00169  76 WdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkereeaee 150
                                         Wd+  + +rPe+gLLk+r +l+lf nLrPa l+++L ++s+lk+eiv g+D+++vreLtgGiYfG+p+e++  e+
  lcl|FitnessBrowser__psRCH2:GFF2539  79 WDTIDPAIRPERGLLKIRSQLGLFGNLRPALLYPQLAEASSLKPEIVAGLDILIVRELTGGIYFGQPRESKVLES 153
                                         ***********************************************************************9998 PP

                           TIGR00169 151 .ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyiDnaam 224
                                          e+ a+dt  Y+++ei+ria+v+f +a+ r+kk++svDkanvL+ss+lWr +vee+ak yPdvel+h+y+Dnaam
  lcl|FitnessBrowser__psRCH2:GFF2539 154 gERMAYDTLPYSESEIRRIAKVGFDMAMVRNKKLCSVDKANVLASSQLWRAVVEEVAKYYPDVELSHMYVDNAAM 228
                                         8************************************************************************** PP

                           TIGR00169 225 qLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpiaailsaa 299
                                         qLv++P+q+dv+vt+n+fGDilsDeas++tGs+G+LPsasl    ++++ep hgsapdiag+gianp+a+ils++
  lcl|FitnessBrowser__psRCH2:GFF2539 229 QLVRAPKQFDVIVTDNMFGDILSDEASMLTGSIGMLPSASLDAGNKGMYEPCHGSAPDIAGQGIANPLATILSVS 303
                                         *************************************************************************** PP

                           TIGR00169 300 lllryslnleeaaeaieaavkkvleegkrtedlaseattavstkeveee 348
                                         ++lrys+n+  aa+aie+av+ vl++g rt d+ se++t+v+t+++++ 
  lcl|FitnessBrowser__psRCH2:GFF2539 304 MMLRYSFNQVAAADAIEQAVSDVLDQGLRTGDIWSEGCTKVGTQAMGDA 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.81
//
[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