GapMind for Amino acid biosynthesis

 

Aligments for a candidate for leuD in Pedobacter sp. GW460-11-11-14-LB5

Align 3-isopropylmalate dehydratase small subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate CA265_RS15840 CA265_RS15840 3-isopropylmalate dehydratase small subunit

Query= SwissProt::P04787
         (201 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS15840 CA265_RS15840
           3-isopropylmalate dehydratase small subunit
          Length = 195

 Score =  178 bits (452), Expect = 5e-50
 Identities = 93/194 (47%), Positives = 126/194 (64%), Gaps = 7/194 (3%)

Query: 3   EKFTQHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLDEKGQQPNPEFV 62
           +KFT+ T  VVPL+  N+DTD IIP +FL+  TR GFG +LF DWR+  E   QP  +FV
Sbjct: 2   KKFTKLTSAVVPLNIENIDTDQIIPARFLKATTREGFGENLFRDWRY--ENDNQPKADFV 59

Query: 63  LNFPEYQGASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNNQLLPV 122
           +N P Y G  +L+A +NFGCGSSREHA WA+ D GF  VI+  FADIF GN+ NN LLP+
Sbjct: 60  MNNPTYSG-QVLVAGKNFGCGSSREHAAWAIQDAGFDAVISSFFADIFKGNALNNGLLPI 118

Query: 123 TLSDAQVDELFALVKANPGIKFEVDLEAQ---VVKAGDKTYSFKIDDFRRHCMLNGLDSI 179
            +SD  + ++F  V  NP    EVDLE Q   +V+ G +  SF+I+ +++ C++NG D I
Sbjct: 119 QVSDEFLAQIFKAVDNNPKSALEVDLENQTVTIVETGAQE-SFEINPYKKSCLINGYDDI 177

Query: 180 GLTLQHEDAIAAYE 193
              L  +  I  +E
Sbjct: 178 DFILNQKQLIEEFE 191


Lambda     K      H
   0.321    0.138    0.416 

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: 152
Number of extensions: 7
Number of successful extensions: 4
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: 195
Length adjustment: 20
Effective length of query: 181
Effective length of database: 175
Effective search space:    31675
Effective search space used:    31675
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 CA265_RS15840 CA265_RS15840 (3-isopropylmalate dehydratase small subunit)
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.7794.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
      4e-69  218.3   0.4    4.5e-69  218.1   0.4    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS15840  CA265_RS15840 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS15840  CA265_RS15840 3-isopropylmalate dehydratase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.1   0.4   4.5e-69   4.5e-69       1     186 [.       1     185 [.       1     187 [. 0.95

  Alignments for each domain:
  == domain 1  score: 218.1 bits;  conditional E-value: 4.5e-69
                                  TIGR00171   1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyq 68 
                                                mk+f klt  vvpl+  n+dtd+iip +flk+ +r Gfg++lf +wry  e+ ++p+++fv+n p+y 
  lcl|FitnessBrowser__Pedo557:CA265_RS15840   1 MKKFTKLTSAVVPLNIENIDTDQIIPARFLKATTREGFGENLFRDWRY--ENDNQPKADFVMNNPTYS 66 
                                                899*********************************************..66668************9 PP

                                  TIGR00171  69 gasillarenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk 136
                                                g ++l+a++nfGcGssreha wa++d Gf  +i+  fadif +n+++ngllpi++s+e + ++++ v 
  lcl|FitnessBrowser__Pedo557:CA265_RS15840  67 G-QVLVAGKNFGCGSSREHAAWAIQDAGFDAVISSFFADIFKGNALNNGLLPIQVSDEFLAQIFKAVD 133
                                                8.79***************************************************************9 PP

                                  TIGR00171 137 .nkglkltvdleaqkvkdse.gkvysfeidefrkhcllnGldeigltlqked 186
                                                 n+   l+vdle+q+v+  e g + sfei++++k cl+nG+d+i + l++++
  lcl|FitnessBrowser__Pedo557:CA265_RS15840 134 nNPKSALEVDLENQTVTIVEtGAQESFEINPYKKSCLINGYDDIDFILNQKQ 185
                                                778889**********9877369**********************9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (188 nodes)
Target sequences:                          1  (195 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: 4.97
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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