GapMind for Amino acid biosynthesis

 

Aligments for a candidate for leuD in Bacteroides thetaiotaomicron VPI-5482

Align 3-isopropylmalate dehydratase small subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate 351387 BT1859 3-isopropylmalate dehydratase small subunit (NCBI ptt file)

Query= SwissProt::P04787
         (201 letters)



>FitnessBrowser__Btheta:351387
          Length = 200

 Score =  157 bits (397), Expect = 1e-43
 Identities = 88/196 (44%), Positives = 123/196 (62%), Gaps = 7/196 (3%)

Query: 4   KFTQHTGLVVPLDAANVDTDAIIPKQFLQKVTRTG--FGAHLFNDWRFLDEKGQQPNPEF 61
           KF   T   VPL   NVDTD IIP +FL+  TR    FG +LF DWR+  +     N +F
Sbjct: 5   KFNIITSTCVPLPLENVDTDQIIPARFLKATTREEKFFGDNLFRDWRYNADGSL--NKDF 62

Query: 62  VLNFPEYQGASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNNQLLP 121
           VLN P Y G  IL+A +NFG GSSREHA WA+  YGF+VV++  FADI   N  NN +LP
Sbjct: 63  VLNDPTYSG-QILVAGKNFGSGSSREHAAWAIAGYGFRVVVSSFFADIHKNNELNNFVLP 121

Query: 122 VTLSDAQVDELFALVKANPGIKFEVDLEAQVV--KAGDKTYSFKIDDFRRHCMLNGLDSI 179
           V +++  + ELF  + A+P ++ EV+L  Q +  KA  K+  F+I+ +++ C++NGLD I
Sbjct: 122 VVVTEGFLQELFDSIFADPKMEVEVNLPEQTITNKATGKSEHFEINAYKKLCLMNGLDDI 181

Query: 180 GLTLQHEDAIAAYENK 195
              L +++ I  +ENK
Sbjct: 182 DFLLSNKNKIEEWENK 197


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: 140
Number of extensions: 9
Number of successful extensions: 5
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: 200
Length adjustment: 21
Effective length of query: 180
Effective length of database: 179
Effective search space:    32220
Effective search space used:    32220
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 351387 BT1859 (3-isopropylmalate dehydratase small subunit (NCBI ptt file))
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.26914.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    4.2e-56  175.8   0.2    4.7e-56  175.7   0.2    1.0  1  lcl|FitnessBrowser__Btheta:351387  BT1859 3-isopropylmalate dehydra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:351387  BT1859 3-isopropylmalate dehydratase small subunit (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.7   0.2   4.7e-56   4.7e-56       4     188 .]       6     191 ..       1     191 [. 0.93

  Alignments for each domain:
  == domain 1  score: 175.7 bits;  conditional E-value: 4.7e-56
                          TIGR00171   4 fkkltGlvvpldkanvdtdaiipkqflkkikrtG..fgkhlfyewryldekGkepnpefvlnvpqyqgasillare 77 
                                        f   t  +vpl   nvdtd+iip +flk+ +r    fg +lf +wry +++G + n +fvln p+y g +il+a++
  lcl|FitnessBrowser__Btheta:351387   6 FNIITSTCVPLPLENVDTDQIIPARFLKATTREEkfFGDNLFRDWRY-NADG-SLNKDFVLNDPTYSG-QILVAGK 78 
                                        667788999*********************9964449**********.8888.89***********97.7****** PP

                          TIGR00171  78 nfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nkglkltvdleaqkvk 152
                                        nfG Gssreha wa++ yGf+v+++  fadi  nn ++n +lp+ ++e  ++el+  +  ++ ++++v+l++q+++
  lcl|FitnessBrowser__Btheta:351387  79 NFGSGSSREHAAWAIAGYGFRVVVSSFFADIHKNNELNNFVLPVVVTEGFLQELFDSIFaDPKMEVEVNLPEQTIT 154
                                        *******************************************************999879999***********8 PP

                          TIGR00171 153 d.segkvysfeidefrkhcllnGldeigltlqkedei 188
                                        + + gk  +fei++++k cl+nGld+i + l ++++i
  lcl|FitnessBrowser__Btheta:351387 155 NkATGKSEHFEINAYKKLCLMNGLDDIDFLLSNKNKI 191
                                        62678************************99988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (188 nodes)
Target sequences:                          1  (200 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: 6.47
//
[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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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