GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Enterococcus termitis LMG 8895

Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate WP_069663815.1 BCR25_RS11865 3-isopropylmalate dehydrogenase

Query= SwissProt::P12010
         (366 letters)



>NCBI__GCF_001730305.1:WP_069663815.1
          Length = 346

 Score =  378 bits (970), Expect = e-109
 Identities = 194/356 (54%), Positives = 250/356 (70%), Gaps = 10/356 (2%)

Query: 1   MKMKLAVLPGDGIGPEVMDAAIRVLKTVLDNDGHEAVFENALIGGAAIDEAGTPLPEETL 60
           M  ++  LPGDGIG E+MD+A+ +L  ++  D  +   E    GGA IDE G PLP+ETL
Sbjct: 1   MSRRIVALPGDGIGTEIMDSALNILAEIMVQDNLDFDIERFAFGGAGIDEKGDPLPQETL 60

Query: 61  DICRRSDAILLGAVGGPKWDHNPASLRPEKGLLGLRKEMGLFANLRPVKAYATLLNASPL 120
           + C ++DAILLGA+GGPKWD+ P   RPE+GLLGLRK +GLFAN+RP+     +++ SPL
Sbjct: 61  EACEQADAILLGAIGGPKWDNAPK--RPEQGLLGLRKALGLFANIRPISVPDAVVHLSPL 118

Query: 121 KRERVENVDLVIVRELTGGLYFGRPSERRGPGENEVVDTLAYTREEIERIIEKAFQLAQI 180
           K E V  VD V+VRELTGG+YFG     +  GE +  D   Y++ EI+RII KAF++AQ 
Sbjct: 119 KEENVRGVDFVVVRELTGGIYFGE----KQLGETQASDLCTYSKAEIQRIIRKAFEIAQT 174

Query: 181 RRKKLASVDKANVLESSRMWREIAEETAKKYPDVELSHMLVDSTSMQLIANPGQFDVIVT 240
           R KK+ SVDKANVL +S++WR+ AEE AK++PD  L + LVDS +M +I  P QFDVIVT
Sbjct: 175 RNKKVTSVDKANVLATSKLWRQTAEEVAKEFPDCTLENQLVDSAAMVMIQKPKQFDVIVT 234

Query: 241 ENMFGDILSDEASVITGSLGMLPSASLRSDRFGMYEPVHGSAPDIAGQGKANPLGTVLSA 300
           EN+FGDILSDEASVI GSLGM+PSAS       +YEP+HGSAPDIA Q  ANP+  +LS 
Sbjct: 235 ENLFGDILSDEASVIPGSLGMMPSASHSETGPSLYEPIHGSAPDIANQNIANPMSMILSV 294

Query: 301 ALMLRYSFGLEKEAAAIEKAVDDVLQDGYCTGDLQVANGKVVSTIELTDRLIEKLN 356
           A+MLR SFGLE+ A  IE A D V+  G  T DL    G   +T E T+ +I++L+
Sbjct: 295 AMMLRQSFGLEESAKKIEAACDCVMNQGILTTDL----GGKATTTEFTEAVIKELH 346


Lambda     K      H
   0.316    0.135    0.379 

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: 368
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: 366
Length of database: 346
Length adjustment: 29
Effective length of query: 337
Effective length of database: 317
Effective search space:   106829
Effective search space used:   106829
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_069663815.1 BCR25_RS11865 (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.3447451.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.9e-151  488.9   0.1   4.4e-151  488.8   0.1    1.0  1  NCBI__GCF_001730305.1:WP_069663815.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001730305.1:WP_069663815.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  488.8   0.1  4.4e-151  4.4e-151       1     348 [.       4     344 ..       4     345 .. 0.98

  Alignments for each domain:
  == domain 1  score: 488.8 bits;  conditional E-value: 4.4e-151
                             TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGG 73 
                                           +i+ LpGDgiG e++++al++L ++  + +l+++ e++ +GGa id++g+Plp+etl+ac++ada+Llga+GG
  NCBI__GCF_001730305.1:WP_069663815.1   4 RIVALPGDGIGTEIMDSALNILAEIMVQDNLDFDIERFAFGGAGIDEKGDPLPQETLEACEQADAILLGAIGG 76 
                                           699********************************************************************** PP

                             TIGR00169  74 pkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkere 146
                                           pkWdn    +rPe+gLL lrk l+lfan+rP+ + +++++lsplkee v+gvD+vvvreLtgGiYfGe++  e
  NCBI__GCF_001730305.1:WP_069663815.1  77 PKWDNA--PKRPEQGLLGLRKALGLFANIRPISVPDAVVHLSPLKEENVRGVDFVVVRELTGGIYFGEKQLGE 147
                                           ******..67*********************************************************987655 PP

                             TIGR00169 147 eaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyi 219
                                                ++a d  +Y+k ei+ri+r+afe+a++r+kkvtsvDkanvL++s+lWr+t+ee+ake+Pd +le++++
  NCBI__GCF_001730305.1:WP_069663815.1 148 -----TQASDLCTYSKAEIQRIIRKAFEIAQTRNKKVTSVDKANVLATSKLWRQTAEEVAKEFPDCTLENQLV 215
                                           .....48****************************************************************** PP

                             TIGR00169 220 DnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpi 292
                                           D+aam ++++P+q+dv+vt+nlfGDilsDeasvi+GslG++Psas s++g  l+ep+hgsapdia+++ianp+
  NCBI__GCF_001730305.1:WP_069663815.1 216 DSAAMVMIQKPKQFDVIVTENLFGDILSDEASVIPGSLGMMPSASHSETGPSLYEPIHGSAPDIANQNIANPM 288
                                           ************************************************************************* PP

                             TIGR00169 293 aailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkeveee 348
                                           ++ils+a++lr+s++lee+a++ieaa + v+++g+ t+dl+++att+ +t++v +e
  NCBI__GCF_001730305.1:WP_069663815.1 289 SMILSVAMMLRQSFGLEESAKKIEAACDCVMNQGILTTDLGGKATTTEFTEAVIKE 344
                                           **************************************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (346 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: 25.65
//
[ok]

This GapMind analysis is from Jul 26 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