GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Burkholderia phytofirmans PsJN

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate BPHYT_RS16285 BPHYT_RS16285 branched-chain amino acid aminotransferase

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



>FitnessBrowser__BFirm:BPHYT_RS16285
          Length = 307

 Score =  624 bits (1609), Expect = 0.0
 Identities = 307/307 (100%), Positives = 307/307 (100%)

Query: 1   MSMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHT 60
           MSMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHT
Sbjct: 1   MSMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHT 60

Query: 61  KRLLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIH 120
           KRLLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIH
Sbjct: 61  KRLLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIH 120

Query: 121 VAIAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADG 180
           VAIAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADG
Sbjct: 121 VAIAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADG 180

Query: 181 YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEK 240
           YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEK
Sbjct: 181 YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEK 240

Query: 241 RITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKY 300
           RITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKY
Sbjct: 241 RITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKY 300

Query: 301 ANWLTKI 307
           ANWLTKI
Sbjct: 301 ANWLTKI 307


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: 553
Number of extensions: 5
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: 307
Length of database: 307
Length adjustment: 27
Effective length of query: 280
Effective length of database: 280
Effective search space:    78400
Effective search space used:    78400
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 BPHYT_RS16285 BPHYT_RS16285 (branched-chain amino acid aminotransferase)
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.20155.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   3.9e-140  452.2   0.0   4.4e-140  452.0   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS16285  BPHYT_RS16285 branched-chain ami


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS16285  BPHYT_RS16285 branched-chain amino acid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  452.0   0.0  4.4e-140  4.4e-140       1     298 []      11     307 .]      11     307 .] 0.99

  Alignments for each domain:
  == domain 1  score: 452.0 bits;  conditional E-value: 4.4e-140
                                TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdk.glaifrlkehveRlydsakilrleipyskee 69 
                                              w+dG+l+d++dak+hvlth+lhYG+gvfeG+RaY+t + g+aifrl+eh++Rl++saki+++++p+ +e+
  lcl|FitnessBrowser__BFirm:BPHYT_RS16285  11 WMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADgGTAIFRLQEHTKRLLNSAKIFQMDVPFDHET 80 
                                              9**********************************987689***************************** PP

                                TIGR01122  70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfr 139
                                              l  ++ ev+r+n+l+s+Y+Rp+++vG+e+lg+++k + +++v+iaaw+wgaylge+++ kGi+vk+ssf+
  lcl|FitnessBrowser__BFirm:BPHYT_RS16285  81 LAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGN-TIHVAIAAWPWGAYLGEDGIAKGIRVKTSSFT 149
                                              **********************************655.9******************************* PP

                                TIGR01122 140 raavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiL 209
                                              r++vn+ + +aka+g Y+ns+la++ea++ Gydea+lLd +Gyv+eGsGen+f+v++g+l+tP++ +s+L
  lcl|FitnessBrowser__BFirm:BPHYT_RS16285 150 RHHVNVSMVRAKASGWYVNSILANQEAIADGYDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDL-SSCL 218
                                              *****************************************************************.88** PP

                                TIGR01122 210 kgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqea 279
                                              +gitrd+vi+la++ gi+v e+ri+r+e+yt De+f+tGtaaevtPire+D+r+ig+g rGp+t+klq+ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS16285 219 DGITRDTVITLARDAGIQVIEKRITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSG 288
                                              ********************************************************************** PP

                                TIGR01122 280 ffdlvegktekkeewltyv 298
                                              ffd+v+gk +k+++wlt++
  lcl|FitnessBrowser__BFirm:BPHYT_RS16285 289 FFDIVNGKSDKYANWLTKI 307
                                              ****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (307 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: 00:00:00.01
# Mc/sec: 7.91
//
[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