GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Cupriavidus basilensis 4G11

Align 3-isopropylmalate dehydratase (EC 4.2.1.33) (characterized)
to candidate RR42_RS21080 RR42_RS21080 3-isopropylmalate dehydratase

Query= BRENDA::Q58673
         (168 letters)



>FitnessBrowser__Cup4G11:RR42_RS21080
          Length = 170

 Score =  140 bits (352), Expect = 1e-38
 Identities = 72/160 (45%), Positives = 105/160 (65%), Gaps = 5/160 (3%)

Query: 7   GRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGGKNFGCG 66
           GR+W+FG+NVDTD + P  ++     EE+A+  + G  P+FP  V+PGD++V G+NFG G
Sbjct: 12  GRIWRFGDNVDTDQMAPGTHMK-GGVEEIARHCLAGLRPEFPAAVRPGDLLVAGRNFGVG 70

Query: 67  SSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDELEVNLET 126
           SSRE AP  L+  G++ VIA SFA +FYRNAIN+GLP++ C   +  V   D     LE 
Sbjct: 71  SSREQAPQALRHLGLAAVIAPSFAGLFYRNAINLGLPVLVCHDATRLV---DGAAARLEL 127

Query: 127 GE-IKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKKKMA 165
           G+    L  G  +  + +PEF+  +L+AGGL+P+LK ++A
Sbjct: 128 GQACLVLPDGSRVACEPIPEFLHALLQAGGLVPHLKARLA 167


Lambda     K      H
   0.317    0.139    0.405 

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: 101
Number of extensions: 3
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: 168
Length of database: 170
Length adjustment: 18
Effective length of query: 150
Effective length of database: 152
Effective search space:    22800
Effective search space used:    22800
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: 43 (21.2 bits)

Align candidate RR42_RS21080 RR42_RS21080 (3-isopropylmalate dehydratase)
to HMM TIGR02087 (3-isopropylmalate dehydratase, small subunit)

# 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/TIGR02087.hmm
# target sequence database:        /tmp/gapView.3792.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02087  [M=157]
Accession:   TIGR02087
Description: LEUD_arch: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.7e-54  169.9   0.0    1.9e-54  169.8   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS21080  RR42_RS21080 3-isopropylmalate d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS21080  RR42_RS21080 3-isopropylmalate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.8   0.0   1.9e-54   1.9e-54       1     156 [.      12     164 ..      12     165 .. 0.97

  Alignments for each domain:
  == domain 1  score: 169.8 bits;  conditional E-value: 1.9e-54
                                 TIGR02087   1 GrvwkfGddvdtdaiiPgrylrttdlkelakhamegidpefakkvreGdvivaGknfGiGssreqaala 69 
                                               Gr+w+fGd+vdtd++ Pg  + +  ++e+a+h+++g++pef+  vr+Gd++vaG+nfG+Gssreqa+ a
  lcl|FitnessBrowser__Cup4G11:RR42_RS21080  12 GRIWRFGDNVDTDQMAPGTHM-KGGVEEIARHCLAGLRPEFPAAVRPGDLLVAGRNFGVGSSREQAPQA 79 
                                               9******************99.5789******************************************* PP

                                 TIGR02087  70 lkaaGvaaviaesfarifyrnainvGlplivaedvtelikdGdevevdlekgeirkvakkevlkleele 138
                                               l+++G+aavia sfa +fyrnain Glp++v +d+t l+ dG   +++l +  ++ +++ + + +e+++
  lcl|FitnessBrowser__Cup4G11:RR42_RS21080  80 LRHLGLAAVIAPSFAGLFYRNAINLGLPVLVCHDATRLV-DGAAARLELGQACLV-LPDGSRVACEPIP 146
                                               ***********************************9999.7************99.8************ PP

                                 TIGR02087 139 dllleileeGGlleylkk 156
                                               ++l  +l++GGl+ +lk 
  lcl|FitnessBrowser__Cup4G11:RR42_RS21080 147 EFLHALLQAGGLVPHLKA 164
                                               **************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (157 nodes)
Target sequences:                          1  (170 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: 7.45
//
[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