GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Cupriavidus basilensis 4G11

Align 3-isopropylmalate dehydratase subunit LeuD (EC 4.2.1.33) (characterized)
to candidate RR42_RS01535 RR42_RS01535 3-isopropylmalate dehydratase

Query= ecocyc::LEUD-MONOMER
         (201 letters)



>FitnessBrowser__Cup4G11:RR42_RS01535
          Length = 215

 Score =  164 bits (414), Expect = 1e-45
 Identities = 89/182 (48%), Positives = 108/182 (59%), Gaps = 2/182 (1%)

Query: 11  LVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLDEKGQQPNPDFVLNFPQYQG 70
           L  PL   N+DTD I+PKQFL+ + + G    LF D RF D +G  P P F LN  +YQG
Sbjct: 12  LGAPLPIGNLDTDQIMPKQFLRIIDKAGLDRGLFYDMRF-DAQGV-PRPAFALNQARYQG 69

Query: 71  ASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNNQLLPVKLSDAEVD 130
           A +L+A  NFGCGSSREHA W L  YG + VIAPSF +IFY N+ NN+LL V L  AEVD
Sbjct: 70  AGVLVAGPNFGCGSSREHAVWGLQQYGIRAVIAPSFGEIFYSNAINNRLLLVMLPQAEVD 129

Query: 131 ELFALVKANPGIHFDVDLEAQEVKAGEKTYRFTIDAFRRHCMMNGLDSIGLTLQHDDAIA 190
            L A V  +     ++DL A  V AG   + FT+    R     GLD IG TL     IA
Sbjct: 130 ALMAAVSGSAPARIEIDLAAMSVSAGALRFAFTLAERHRTMFRQGLDMIGATLAQSSQIA 189

Query: 191 AY 192
           A+
Sbjct: 190 AF 191


Lambda     K      H
   0.322    0.138    0.421 

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: 128
Number of extensions: 4
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: 201
Length of database: 215
Length adjustment: 21
Effective length of query: 180
Effective length of database: 194
Effective search space:    34920
Effective search space used:    34920
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 RR42_RS01535 RR42_RS01535 (3-isopropylmalate dehydratase)
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.5772.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    3.8e-59  185.7   0.0    4.7e-59  185.5   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS01535  RR42_RS01535 3-isopropylmalate d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS01535  RR42_RS01535 3-isopropylmalate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.5   0.0   4.7e-59   4.7e-59      10     188 .]      12     188 ..       6     188 .. 0.96

  Alignments for each domain:
  == domain 1  score: 185.5 bits;  conditional E-value: 4.7e-59
                                 TIGR00171  10 lvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqgasillaren 78 
                                               l +pl   n+dtd+i+pkqfl+ i++ G+++ lfy+ r+ d++G  p p f ln+ +yqga +l+a+ n
  lcl|FitnessBrowser__Cup4G11:RR42_RS01535  12 LGAPLPIGNLDTDQIMPKQFLRIIDKAGLDRGLFYDMRF-DAQG-VPRPAFALNQARYQGAGVLVAGPN 78 
                                               67899999*******************************.****.9*********************** PP

                                 TIGR00171  79 fGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nkglkltvdl 146
                                               fGcGssreha w l++yG++ +iapsf++ify+n+++n+ll + l+++ev+ l+a v+     ++++dl
  lcl|FitnessBrowser__Cup4G11:RR42_RS01535  79 FGCGSSREHAVWGLQQYGIRAVIAPSFGEIFYSNAINNRLLLVMLPQAEVDALMAAVSgSAPARIEIDL 147
                                               **********************************************************88889****** PP

                                 TIGR00171 147 eaqkvkdsegkvysfeidefrkhcllnGldeigltlqkedei 188
                                                a+ v ++      f++ e ++ ++  Gld ig tl +  +i
  lcl|FitnessBrowser__Cup4G11:RR42_RS01535 148 AAMSVSAGA-LRFAFTLAERHRTMFRQGLDMIGATLAQSSQI 188
                                               *******99.99************************987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (188 nodes)
Target sequences:                          1  (215 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: 9.67
//
[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:

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