GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Dechlorosoma suillum PS

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate Dsui_3339 Dsui_3339 branched-chain amino acid aminotransferase, group I

Query= reanno::BFirm:BPHYT_RS16285
         (307 letters)



>FitnessBrowser__PS:Dsui_3339
          Length = 306

 Score =  446 bits (1147), Expect = e-130
 Identities = 215/304 (70%), Positives = 254/304 (83%), Gaps = 1/304 (0%)

Query: 1   MSMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHT 60
           MSM+DRDG IW DGKL+ WR+A  H LTH+LHYGM VFEGVRAY+T D GTAIFRLQ+HT
Sbjct: 1   MSMSDRDGFIWQDGKLVPWREATTHALTHSLHYGMAVFEGVRAYQT-DKGTAIFRLQDHT 59

Query: 61  KRLLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIH 120
           +RL  SA IFQM +P+  E L  AQ EV+R N LES Y+RP+ + GSEK+GVS KG  +H
Sbjct: 60  QRLARSAHIFQMALPYSQEELNEAQKEVIRANNLESGYIRPLAFYGSEKMGVSPKGAKVH 119

Query: 121 VAIAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADG 180
           V IAAWPWGAYLGE+G+ +GIR+KTSSFTRHHVN++MVRAKASG Y+NSILAN EA+ DG
Sbjct: 120 VIIAAWPWGAYLGEEGMQRGIRIKTSSFTRHHVNITMVRAKASGNYMNSILANNEALTDG 179

Query: 181 YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEK 240
           YDEA+LLD +GYV EG+GEN F+V NGKLYTPDL+SCL+GITR TVI LA + GI+V+EK
Sbjct: 180 YDEAMLLDPEGYVCEGAGENIFIVKNGKLYTPDLTSCLEGITRATVIQLAGEMGIEVVEK 239

Query: 241 RITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKY 300
           RITRDEVY  DEAFFTGTAAEVTPIRELDNR IG G RGP+T+ LQ  +FD+VNG+S  +
Sbjct: 240 RITRDEVYCADEAFFTGTAAEVTPIRELDNRQIGVGHRGPVTKALQEKYFDVVNGRSAAH 299

Query: 301 ANWL 304
           A+WL
Sbjct: 300 ADWL 303


Lambda     K      H
   0.319    0.136    0.411 

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: 364
Number of extensions: 6
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: 307
Length of database: 306
Length adjustment: 27
Effective length of query: 280
Effective length of database: 279
Effective search space:    78120
Effective search space used:    78120
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 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate Dsui_3339 Dsui_3339 (branched-chain amino acid aminotransferase, group I)
to HMM TIGR01122 (ilvE: branched-chain amino acid aminotransferase (EC 2.6.1.42))

# 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/TIGR01122.hmm
# target sequence database:        /tmp/gapView.16884.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01122  [M=298]
Accession:   TIGR01122
Description: ilvE_I: branched-chain amino acid aminotransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.7e-143  463.2   0.1   1.9e-143  463.0   0.1    1.0  1  lcl|FitnessBrowser__PS:Dsui_3339  Dsui_3339 branched-chain amino a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_3339  Dsui_3339 branched-chain amino acid aminotransferase, group I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  463.0   0.1  1.9e-143  1.9e-143       1     298 []      11     306 .]      11     306 .] 0.99

  Alignments for each domain:
  == domain 1  score: 463.0 bits;  conditional E-value: 1.9e-143
                         TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvevtkev 77 
                                       w dG+lv++++a++h lth+lhYG++vfeG+RaY+tdkg+aifrl++h++Rl  sa+i+++ +pys+eel+e++kev
  lcl|FitnessBrowser__PS:Dsui_3339  11 WQDGKLVPWREATTHALTHSLHYGMAVFEGVRAYQTDKGTAIFRLQDHTQRLARSAHIFQMALPYSQEELNEAQKEV 87 
                                       99*************************************************************************** PP

                         TIGR01122  78 lrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsiptkakaag 154
                                       +r+nnl+s YiRpl+++G+e++g++p  ++kv+viiaaw+wgaylgee++++Gi++k+ssf+r++vn+ + +aka+g
  lcl|FitnessBrowser__PS:Dsui_3339  88 IRANNLESGYIRPLAFYGSEKMGVSP-KGAKVHVIIAAWPWGAYLGEEGMQRGIRIKTSSFTRHHVNITMVRAKASG 163
                                       **************************.6779********************************************** PP

                         TIGR01122 155 nYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdaviklakelgievkee 231
                                       nY+ns+la+ eal+ Gydea+lLd eGyv eG+Genifivk+g+l+tP++ +s+L+gitr +vi+la e+giev+e+
  lcl|FitnessBrowser__PS:Dsui_3339 164 NYMNSILANNEALTDGYDEAMLLDPEGYVCEGAGENIFIVKNGKLYTPDL-TSCLEGITRATVIQLAGEMGIEVVEK 239
                                       **************************************************.78************************ PP

                         TIGR01122 232 risreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekkeewltyv 298
                                       ri+r+e+y aDe+f+tGtaaevtPire+D+r+ig g+rGpvtk lqe++fd+v+g+  ++++wl  v
  lcl|FitnessBrowser__PS:Dsui_3339 240 RITRDEVYCADEAFFTGTAAEVTPIRELDNRQIGVGHRGPVTKALQEKYFDVVNGRSAAHADWLAFV 306
                                       ***************************************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (306 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: 00:00:00.01
# Mc/sec: 7.46
//
[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