GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Dyella japonica UNC79MFTsu3.2

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate N515DRAFT_0573 N515DRAFT_0573 branched-chain amino acid aminotransferase

Query= reanno::Dyella79:N515DRAFT_2015
         (305 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0573
          Length = 313

 Score =  383 bits (984), Expect = e-111
 Identities = 185/300 (61%), Positives = 234/300 (78%), Gaps = 3/300 (1%)

Query: 8   WIWQNGQIKPWREATTHVMSHALHYGSSVFEGIRSYATPDGAAIFRLTDHLKRLYQSAKI 67
           ++W NGQIKPW EAT HV +HALHYGSSVFEG R YATP G A FRL DH +RL++SA++
Sbjct: 5   FLWHNGQIKPWTEATVHVSTHALHYGSSVFEGERVYATPQGPAYFRLADHTRRLFESARV 64

Query: 68  YDMVLPYSQDQIAAACRDVIKQNGLGAAYLRPVAYRGLGGFGLSAE--TPIDVAVAAWPM 125
           Y++ + YS+D+I AAC +VI+ N +G+AY+RP+ +RG GG G+ A+   P+DVA+ A   
Sbjct: 65  YEIEVGYSEDEINAACMEVIRANRMGSAYVRPIVFRGAGGLGVLAKPGAPVDVAIMAMEW 124

Query: 126 GPYLGPEALESGIDACVSSWQRFAPNTIPAGAKAGGNYLSGQLIAREARRLGFGEGIALA 185
           G YLG +A E G D CVSSWQR APNT+P+ AKAGGNYLS QLI  EARR G+ EGIAL 
Sbjct: 125 GAYLG-DAREQGADVCVSSWQRPAPNTVPSWAKAGGNYLSSQLIGLEARRGGYAEGIALG 183

Query: 186 NTGLLSEGAGENLFLVFDGVLHTTPASASILTGITRHTLITLAREDGIEVIERDIPREYL 245
           + GLLSEGAGEN+F+V +G L T P SA IL GITR T++TLA + GI+V ERD+PRE L
Sbjct: 184 HNGLLSEGAGENVFVVKNGKLLTPPTSAGILAGITRDTVMTLAEDLGIKVEERDLPREAL 243

Query: 246 YLCDELLMCGTAAEITPIRSVDGKKIGSGKAGRVTRRMQELFFGLFNGKTNDQWGWLEPV 305
           Y  DE+ M GTAAEITP+RSVD K +G+G+ G +TR +Q+ FFGLF+G+T+D+WGWL PV
Sbjct: 244 YTADEVFMTGTAAEITPVRSVDRKPVGTGRPGPITRALQDAFFGLFDGRTDDRWGWLAPV 303


Lambda     K      H
   0.320    0.138    0.425 

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: 353
Number of extensions: 13
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: 305
Length of database: 313
Length adjustment: 27
Effective length of query: 278
Effective length of database: 286
Effective search space:    79508
Effective search space used:    79508
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 N515DRAFT_0573 N515DRAFT_0573 (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.29132.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   3.7e-125  403.0   0.0   4.2e-125  402.8   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0573  N515DRAFT_0573 branched-chain am


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0573  N515DRAFT_0573 branched-chain amino acid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  402.8   0.0  4.2e-125  4.2e-125       1     298 []       7     303 ..       7     303 .. 0.99

  Alignments for each domain:
  == domain 1  score: 402.8 bits;  conditional E-value: 4.2e-125
                                    TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipys 66 
                                                  w +G++ ++ +a+vhv thalhYG++vfeG R+Y t++g+a frl +h+ Rl++sa+++++e+ ys
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0573   7 WHNGQIKPWTEATVHVSTHALHYGSSVFEGERVYATPQGPAYFRLADHTRRLFESARVYEIEVGYS 72 
                                                  99**************************************************************** PP

                                    TIGR01122  67 keelvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGik 132
                                                  ++e++ +++ev+r+n + saY+Rp+v++Ga++lg+ +k +++v+v+i+a+ewgaylg+ a e+G +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0573  73 EDEINAACMEVIRANRMGSAYVRPIVFRGAGGLGVLAKPGAPVDVAIMAMEWGAYLGD-AREQGAD 137
                                                  *********************************************************6.9****** PP

                                    TIGR01122 133 vkvssfrraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgv 198
                                                  v vss++r a+n++p+ aka+gnYl+s+l++ ea+r Gy e+i+L ++G ++eG+Gen+f+vk+g+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0573 138 VCVSSWQRPAPNTVPSWAKAGGNYLSSQLIGLEARRGGYAEGIALGHNGLLSEGAGENVFVVKNGK 203
                                                  ****************************************************************** PP

                                    TIGR01122 199 lltPpvsesiLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrki 264
                                                  lltPp+s  iL gitrd+v++la++lgi+v+e+ + re+lytaDevf+tGtaae+tP+r+vD + +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0573 204 LLTPPTSAGILAGITRDTVMTLAEDLGIKVEERDLPREALYTADEVFMTGTAAEITPVRSVDRKPV 269
                                                  ****************************************************************** PP

                                    TIGR01122 265 gegkrGpvtkklqeaffdlvegktekkeewltyv 298
                                                  g g+ Gp+t+ lq+aff l+ g+t+++++wl +v
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0573 270 GTGRPGPITRALQDAFFGLFDGRTDDRWGWLAPV 303
                                                  ******************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (313 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: 00:00:00.00
# Mc/sec: 10.57
//
[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