GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Cupriavidus basilensis 4G11

Align 3-isopropylmalate dehydratase small subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 (characterized)
to candidate RR42_RS22775 RR42_RS22775 3-isopropylmalate dehydratase

Query= SwissProt::Q1MA52
         (202 letters)



>FitnessBrowser__Cup4G11:RR42_RS22775
          Length = 208

 Score =  187 bits (475), Expect = 1e-52
 Identities = 95/201 (47%), Positives = 127/201 (63%), Gaps = 2/201 (0%)

Query: 1   MDKFVKLTGVAAPLPVVNVDTDMIIPKDYLKTIKRTGLGTGLFAEARYNEDGSENPDFVL 60
           M  F  +TG A PL   NVDTD+II  + L  + R  LG       RY  DGSE+P  V 
Sbjct: 1   MQPFTVVTGAAVPLLRANVDTDVIIRIERLTALPREQLGPYALEALRYRADGSEDPGCVF 60

Query: 61  NKPAYRDAKILVAGDNFGCGSSREHAPWALLDFGIRCVISTSFADIFYNNCFKNGILPIK 120
           N+PA+R A +L+AG NFGCGSSRE A WAL+  G+RCVI+ S+ DIFYNNCF+NG+LPI+
Sbjct: 61  NQPAFRGAPVLLAGANFGCGSSREGAVWALMGLGVRCVIAPSYGDIFYNNCFQNGVLPIR 120

Query: 121 VSQEDLDKLMDDASRGSNAILTVDLENLEITGPDGGLIKFDLDEFKRHCLLNGLDDIGLT 180
           +  E +  L   A   S A + VDL +  ++ PDG  + F +D  +R  LL+GLDDIGLT
Sbjct: 121 LPAEAVQALA--AQCASGAPVRVDLASATLSAPDGATVAFPVDRLRREALLHGLDDIGLT 178

Query: 181 LEKGKAIDSFEKKNAASHPWA 201
           L+    I ++++ +    PWA
Sbjct: 179 LKDDALIRAWQQADRTRRPWA 199


Lambda     K      H
   0.319    0.140    0.419 

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: 138
Number of extensions: 2
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: 202
Length of database: 208
Length adjustment: 21
Effective length of query: 181
Effective length of database: 187
Effective search space:    33847
Effective search space used:    33847
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: 45 (21.9 bits)

Align candidate RR42_RS22775 RR42_RS22775 (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.27420.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    6.1e-57  178.5   0.0    7.1e-57  178.3   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS22775  RR42_RS22775 3-isopropylmalate d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS22775  RR42_RS22775 3-isopropylmalate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.3   0.0   7.1e-57   7.1e-57       1     186 [.       1     183 [.       1     185 [. 0.95

  Alignments for each domain:
  == domain 1  score: 178.3 bits;  conditional E-value: 7.1e-57
                                 TIGR00171   1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqg 69 
                                               m++f   tG +vpl +anvdtd ii  + l ++ r  +g +++   ry+ ++G +++p  v+n+p ++g
  lcl|FitnessBrowser__Cup4G11:RR42_RS22775   1 MQPFTVVTGAAVPLLRANVDTDVIIRIERLTALPREQLGPYALEALRYR-ADG-SEDPGCVFNQPAFRG 67 
                                               899*********************************************6.556.678999********* PP

                                 TIGR00171  70 asillarenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvknk 138
                                               a +lla+ nfGcGssre a wal   G++ +iaps++difynn+f+ng+lpirl+ e v+ l a+   +
  lcl|FitnessBrowser__Cup4G11:RR42_RS22775  68 APVLLAGANFGCGSSREGAVWALMGLGVRCVIAPSYGDIFYNNCFQNGVLPIRLPAEAVQALAAQC-AS 135
                                               *********************************************************998877766.57 PP

                                 TIGR00171 139 glkltvdleaqkvkdsegkvysfeidefrkhcllnGldeigltlqked 186
                                               g  + vdl + ++ + +g ++ f +d  r++ ll Gld+igltl+ + 
  lcl|FitnessBrowser__Cup4G11:RR42_RS22775 136 GAPVRVDLASATLSAPDGATVAFPVDRLRREALLHGLDDIGLTLKDDA 183
                                               999*****************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (188 nodes)
Target sequences:                          1  (208 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: 8.37
//
[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