GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Cupriavidus basilensis 4G11

Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate RR42_RS24180 RR42_RS24180 3-isopropylmalate dehydratase

Query= uniprot:Q845W4
         (216 letters)



>FitnessBrowser__Cup4G11:RR42_RS24180
          Length = 216

 Score =  372 bits (954), Expect = e-108
 Identities = 175/216 (81%), Positives = 189/216 (87%)

Query: 1   MEKFTVHTGVVAPLDRENVDTDAIIPKQFLKSIKRTGFGPNAFDEWRYLDHGEPGQDNSK 60
           MEKFT+H G+VAPLDR NVDTDAIIPKQFLKSIKRTGFGPN FDEWRY D GEPG DNSK
Sbjct: 1   MEKFTIHRGLVAPLDRGNVDTDAIIPKQFLKSIKRTGFGPNLFDEWRYKDVGEPGMDNSK 60

Query: 61  RPLNPDFVLNQPRYQGASILVTRKNFGCGSSREHAPWALQQYGFRAIIAPSFADIFFNNC 120
           RPLNPDFVLNQPRYQGASIL+ R+NFGCGSSREHAPWAL QYGF A+IAPSFADIFFNNC
Sbjct: 61  RPLNPDFVLNQPRYQGASILLARRNFGCGSSREHAPWALTQYGFHAVIAPSFADIFFNNC 120

Query: 121 FKNGLLPIVLTEQQVDHLINETVAFNGYQLTIDLEAQVVRTPDGRDYPFEITAFRKYCLL 180
           +KNGLLP+VLTEQQVDHL NET AF GYQLTIDL+ Q V T  G+ Y F+I  FRKYC+L
Sbjct: 121 YKNGLLPVVLTEQQVDHLFNETNAFKGYQLTIDLDKQAVITASGQGYEFDIAPFRKYCML 180

Query: 181 NGFDDIGLTLRHADKIRQFEAERLAKQPWLNNKLVG 216
           NGFDDI LTLRHADKI+ FEAER+AK PWL  +L G
Sbjct: 181 NGFDDIRLTLRHADKIKVFEAERVAKMPWLKPRLAG 216


Lambda     K      H
   0.322    0.141    0.437 

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: 258
Number of extensions: 6
Number of successful extensions: 1
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: 216
Length of database: 216
Length adjustment: 22
Effective length of query: 194
Effective length of database: 194
Effective search space:    37636
Effective search space used:    37636
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_RS24180 RR42_RS24180 (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.13661.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    3.1e-85  270.8   0.0    3.6e-85  270.6   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS24180  RR42_RS24180 3-isopropylmalate d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS24180  RR42_RS24180 3-isopropylmalate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  270.6   0.0   3.6e-85   3.6e-85       1     188 []       1     196 [.       1     196 [. 0.94

  Alignments for each domain:
  == domain 1  score: 270.6 bits;  conditional E-value: 3.6e-85
                                 TIGR00171   1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryld..ekGkep.....npefvl 62 
                                               m++f  + Glv+pld+ nvdtdaiipkqflk ikrtGfg +lf ewry+d  e G ++     np+fvl
  lcl|FitnessBrowser__Cup4G11:RR42_RS24180   1 MEKFTIHRGLVAPLDRGNVDTDAIIPKQFLKSIKRTGFGPNLFDEWRYKDvgEPGMDNskrplNPDFVL 69 
                                               899*********************************************9843234332222359***** PP

                                 TIGR00171  63 nvpqyqgasillarenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveel 131
                                               n+p+yqgasillar nfGcGssrehapwal++yGf  +iapsfadif+nn++kngllp+ l+e++v++l
  lcl|FitnessBrowser__Cup4G11:RR42_RS24180  70 NQPRYQGASILLARRNFGCGSSREHAPWALTQYGFHAVIAPSFADIFFNNCYKNGLLPVVLTEQQVDHL 138
                                               ********************************************************************* PP

                                 TIGR00171 132 lalvk.nkglkltvdleaqkvkdsegkvysfeidefrkhcllnGldeigltlqkedei 188
                                               ++  +  kg +lt+dl++q v ++ g+ y+f+i +frk c+lnG+d+i ltl++ d+i
  lcl|FitnessBrowser__Cup4G11:RR42_RS24180 139 FNETNaFKGYQLTIDLDKQAVITASGQGYEFDIAPFRKYCMLNGFDDIRLTLRHADKI 196
                                               **99889*************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (188 nodes)
Target sequences:                          1  (216 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 6.28
//
[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