GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Miya:8501549
          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.23901.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: 6.87
//
[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