GapMind for Amino acid biosynthesis

 

Aligments for a candidate for leuD in Marinobacter adhaerens HP15

Align 3-isopropylmalate dehydratase small subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate GFF1876 HP15_1833 isopropylmalate isomerase small subunit

Query= SwissProt::P04787
         (201 letters)



>lcl|FitnessBrowser__Marino:GFF1876 HP15_1833 isopropylmalate
           isomerase small subunit
          Length = 215

 Score =  228 bits (581), Expect = 6e-65
 Identities = 112/198 (56%), Positives = 145/198 (73%), Gaps = 8/198 (4%)

Query: 7   QHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLDE-KGQQP------NP 59
           QH G+V P+D +NVDTD IIPKQFL+ + RTGFG +LF++ R++DE K  Q       NP
Sbjct: 6   QHQGVVAPMDRSNVDTDMIIPKQFLKSIKRTGFGPNLFDELRYMDEGKPDQDCSTRPINP 65

Query: 60  EFVLNFPEYQGASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNNQL 119
           +FVLN   Y+ AS+LLAR NFGCGSSREHAPWAL D+GF+V+IAPSFADIFY N F N L
Sbjct: 66  DFVLNQDRYKNASVLLARRNFGCGSSREHAPWALEDFGFRVIIAPSFADIFYNNCFKNGL 125

Query: 120 LPVTLSDAQVDELFALVKANPGIKFEVDLEAQVVKA-GDKTYSFKIDDFRRHCMLNGLDS 178
           LP+ L +  VD LF  V+ + G +  VDLEA+ V     +T++F++DDFRRHC+LNGLD 
Sbjct: 126 LPIVLPEEIVDRLFREVEQSEGYQLAVDLEARTVTTPSGETFTFEVDDFRRHCLLNGLDD 185

Query: 179 IGLTLQHEDAIAAYENKQ 196
           IG+TL+  + I +YE  +
Sbjct: 186 IGVTLEDAELIRSYEESR 203


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: 169
Number of extensions: 7
Number of successful extensions: 3
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: 215
Length adjustment: 21
Effective length of query: 180
Effective length of database: 194
Effective search space:    34920
Effective search space used:    34920
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 GFF1876 HP15_1833 (isopropylmalate isomerase 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.18763.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    9.7e-87  275.7   0.0    1.2e-86  275.4   0.0    1.1  1  lcl|FitnessBrowser__Marino:GFF1876  HP15_1833 isopropylmalate isomer


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF1876  HP15_1833 isopropylmalate isomerase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.4   0.0   1.2e-86   1.2e-86       1     186 [.       1     194 [.       1     196 [. 0.94

  Alignments for each domain:
  == domain 1  score: 275.4 bits;  conditional E-value: 1.2e-86
                           TIGR00171   1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkep.......npefvlnvpqyq 68 
                                         m+ +k+++G+v+p+d+ nvdtd iipkqflk ikrtGfg +lf e ry+de   ++       np+fvln+++y+
  lcl|FitnessBrowser__Marino:GFF1876   1 MRALKQHQGVVAPMDRSNVDTDMIIPKQFLKSIKRTGFGPNLFDELRYMDEGKPDQdcstrpiNPDFVLNQDRYK 75 
                                         7899********************************************9875433323333458*********** PP

                           TIGR00171  69 gasillarenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nkglkl 142
                                         +as+llar nfGcGssrehapwal+d+Gf+viiapsfadifynn+fkngllpi l+ee+v+ l+  v+  +g +l
  lcl|FitnessBrowser__Marino:GFF1876  76 NASVLLARRNFGCGSSREHAPWALEDFGFRVIIAPSFADIFYNNCFKNGLLPIVLPEEIVDRLFREVEqSEGYQL 150
                                         *******************************************************************989***** PP

                           TIGR00171 143 tvdleaqkvkdsegkvysfeidefrkhcllnGldeigltlqked 186
                                         +vdlea++v++  g++ +fe+d+fr+hcllnGld+ig+tl   +
  lcl|FitnessBrowser__Marino:GFF1876 151 AVDLEARTVTTPSGETFTFEVDDFRRHCLLNGLDDIGVTLEDAE 194
                                         ****************************************8776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (188 nodes)
Target sequences:                          1  (215 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: 4.87
//
[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 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