GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Pseudomonas fluorescens GW456-L13

Align 3-isopropylmalate dehydratase small subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 (characterized)
to candidate PfGW456L13_3593 3-isopropylmalate dehydratase small subunit (EC 4.2.1.33)

Query= SwissProt::Q1MA52
         (202 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3593
          Length = 202

 Score =  192 bits (487), Expect = 5e-54
 Identities = 95/200 (47%), Positives = 132/200 (66%)

Query: 1   MDKFVKLTGVAAPLPVVNVDTDMIIPKDYLKTIKRTGLGTGLFAEARYNEDGSENPDFVL 60
           M  F  ++G AAPL   N+DTD+I+PK +LK I R GL  GLF + R+ E G  NP F+L
Sbjct: 1   MQPFDFVSGSAAPLLASNIDTDVIMPKQFLKGIDRKGLDKGLFFDLRFLESGEPNPGFIL 60

Query: 61  NKPAYRDAKILVAGDNFGCGSSREHAPWALLDFGIRCVISTSFADIFYNNCFKNGILPIK 120
           N+PA+ DA  LV G NFGCGSSREHA W L   GIR +I TSFA IFY+NC +NG+L I+
Sbjct: 61  NQPAWNDAAFLVVGPNFGCGSSREHAVWGLKQVGIRALIGTSFAGIFYDNCQRNGVLAIQ 120

Query: 121 VSQEDLDKLMDDASRGSNAILTVDLENLEITGPDGGLIKFDLDEFKRHCLLNGLDDIGLT 180
           +++  L+++    S  + A ++V+L    I   DG +I F +DE ++  LL GLD +G T
Sbjct: 121 LTEVQLNQIAALTSNPATARISVNLPEQTIELADGNVIPFGIDELRKQSLLLGLDAVGTT 180

Query: 181 LEKGKAIDSFEKKNAASHPW 200
           L++ + I SFE ++ A +PW
Sbjct: 181 LQRAEQIRSFEARHLAENPW 200


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: 126
Number of extensions: 4
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: 202
Length of database: 202
Length adjustment: 21
Effective length of query: 181
Effective length of database: 181
Effective search space:    32761
Effective search space used:    32761
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 PfGW456L13_3593 (3-isopropylmalate dehydratase small subunit (EC 4.2.1.33))
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.8768.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
    5.4e-63  198.3   0.0    6.1e-63  198.1   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3593  3-isopropylmalate dehydratase sm


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3593  3-isopropylmalate dehydratase small subunit (EC 4.2.1.33)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.1   0.0   6.1e-63   6.1e-63       1     188 []       1     187 [.       1     187 [. 0.97

  Alignments for each domain:
  == domain 1  score: 198.1 bits;  conditional E-value: 6.1e-63
                                               TIGR00171   1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGke 55 
                                                             m++f   +G ++pl + n+dtd i+pkqflk i+r G++k lf++ r+l e G e
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3593   1 MQPFDFVSGSAAPLLASNIDTDVIMPKQFLKGIDRKGLDKGLFFDLRFL-ESG-E 53 
                                                             899999******************************************6.567.9 PP

                                               TIGR00171  56 pnpefvlnvpqyqgasillarenfGcGssrehapwalkdyGfkviiapsfadify 110
                                                             pnp f+ln+p +++a  l+++ nfGcGssreha w lk+ G++ +i  sfa ify
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3593  54 PNPGFILNQPAWNDAAFLVVGPNFGCGSSREHAVWGLKQVGIRALIGTSFAGIFY 108
                                                             ******************************************************* PP

                                               TIGR00171 111 nnsfkngllpirlseeeveellalvknkg.lkltvdleaqkvkdsegkvysfeid 164
                                                             +n+ +ng+l i+l+e +++++ al +n++  +++v+l++q+++ ++g+v+ f id
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3593 109 DNCQRNGVLAIQLTEVQLNQIAALTSNPAtARISVNLPEQTIELADGNVIPFGID 163
                                                             **************************875279*********************** PP

                                               TIGR00171 165 efrkhcllnGldeigltlqkedei 188
                                                             e rk+ ll Gld +g tlq+ ++i
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3593 164 ELRKQSLLLGLDAVGTTLQRAEQI 187
                                                             ********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (188 nodes)
Target sequences:                          1  (202 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: 6.94
//
[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