GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvE in Desulfovibrio vulgaris Miyazaki F

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate 8501549 DvMF_2268 branched-chain amino acid aminotransferase (RefSeq)

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



>lcl|FitnessBrowser__Miya:8501549 DvMF_2268 branched-chain amino
           acid aminotransferase (RefSeq)
          Length = 307

 Score =  357 bits (915), Expect = e-103
 Identities = 170/302 (56%), Positives = 219/302 (72%)

Query: 3   MADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTKR 62
           M  +   IW DGK + W +A +HVLTHTLHYG+GVFEG+RAYK ADGG+A+FRL+EH +R
Sbjct: 1   MVQKAETIWFDGKQVPWDEANVHVLTHTLHYGVGVFEGIRAYKCADGGSAVFRLREHMQR 60

Query: 63  LLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIHVA 122
           LLNSAKI +M +P+  + L  A  E ++ NKL   Y+RP+ +VG+  +GV    N +   
Sbjct: 61  LLNSAKILRMVIPYTVDQLVDAVEETLKRNKLAEGYIRPLSFVGAGAMGVYPGDNPVQTI 120

Query: 123 IAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYD 182
           IA WPWGAYLG + +  GIRVKTSSF RHHVN  M +AKA G YVNS+LA  EA ADGYD
Sbjct: 121 IATWPWGAYLGAEALEHGIRVKTSSFCRHHVNAMMTKAKACGNYVNSVLAKMEAKADGYD 180

Query: 183 EALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEKRI 242
           E L+LD  G+VSE +GEN F+V    + T  L+S LDGITR+++ITLAR+ G +V+E++ 
Sbjct: 181 EGLMLDTQGFVSEATGENIFIVRGKLIKTTPLTSVLDGITRNSLITLARELGYEVVEQQF 240

Query: 243 TRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKYAN 302
           TRDE+Y  DEAFF GTAAE+TPIRE+D R IG G  GP+T+ LQ  +F  V G++  YA+
Sbjct: 241 TRDELYIADEAFFCGTAAELTPIREVDLRVIGQGTAGPVTKHLQGEYFKAVKGENPAYAH 300

Query: 303 WL 304
           WL
Sbjct: 301 WL 302


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: 334
Number of extensions: 6
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 8501549 DvMF_2268 (branched-chain amino acid aminotransferase (RefSeq))
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.20715.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.6e-133  430.4   0.0   1.8e-133  430.2   0.0    1.0  1  lcl|FitnessBrowser__Miya:8501549  DvMF_2268 branched-chain amino a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501549  DvMF_2268 branched-chain amino acid aminotransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  430.2   0.0  1.8e-133  1.8e-133       1     296 [.       9     303 ..       9     305 .. 0.99

  Alignments for each domain:
  == domain 1  score: 430.2 bits;  conditional E-value: 1.8e-133
                         TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdk.glaifrlkehveRlydsakilrleipyskeelvevtke 76 
                                       w+dG+ v++++a+vhvlth+lhYG gvfeGiRaY+  + g+a+frl+eh++Rl++sakilr+ ipy+ ++lv+++ e
  lcl|FitnessBrowser__Miya:8501549   9 WFDGKQVPWDEANVHVLTHTLHYGVGVFEGIRAYKCADgGSAVFRLREHMQRLLNSAKILRMVIPYTVDQLVDAVEE 85 
                                       9**********************************866599************************************ PP

                         TIGR01122  77 vlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsiptkakaa 153
                                       +l++n+l + YiRpl +vGa+ +g++p  d +v+ iia+w+wgaylg+eale+Gi+vk+ssf r++vn+++tkaka 
  lcl|FitnessBrowser__Miya:8501549  86 TLKRNKLAEGYIRPLSFVGAGAMGVYP-GDNPVQTIIATWPWGAYLGAEALEHGIRVKTSSFCRHHVNAMMTKAKAC 161
                                       ***************************.999********************************************** PP

                         TIGR01122 154 gnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdaviklakelgievke 230
                                       gnY+ns+lak+ea++ Gyde+++Ld++G+v+e +Genifiv+   ++t p+ +s+L+gitr+++i+la+elg+ev+e
  lcl|FitnessBrowser__Miya:8501549 162 GNYVNSVLAKMEAKADGYDEGLMLDTQGFVSEATGENIFIVRGKLIKTTPL-TSVLDGITRNSLITLARELGYEVVE 237
                                       **************************************************9.78*********************** PP

                         TIGR01122 231 erisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekkeewlt 296
                                       ++++r+ely+aDe+f+ Gtaae+tPirevD r ig+g++Gpvtk+lq ++f+ v+g+++++++wl+
  lcl|FitnessBrowser__Miya:8501549 238 QQFTRDELYIADEAFFCGTAAELTPIREVDLRVIGQGTAGPVTKHLQGEYFKAVKGENPAYAHWLH 303
                                       ****************************************************************97 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.92
//
[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, 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