Alignments for a candidate for ilvE in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Synechococcus elongatus PCC 7942

Align branched-chain-amino-acid transaminase (EC 2.6.1.42); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate Synpcc7942_1029 Synpcc7942_1029 branched-chain amino acid aminotransferase

Query= BRENDA::P54691
         (305 letters)



>FitnessBrowser__SynE:Synpcc7942_1029
          Length = 304

 Score =  457 bits (1177), Expect = e-133
 Identities = 219/303 (72%), Positives = 260/303 (85%)

Query: 1   MHKFLPIAYFEDKFVPFEDAKISVATHALHYGTAAFGGLRGIPDPEDPGTILLFRLDRHG 60
           M+ FLP A+F  + VPF +A++S+ATHALHYGT AFGGLRGIPDPE+P  +LLFRLDRH 
Sbjct: 1   MNDFLPYAFFRGQLVPFPEAQLSIATHALHYGTGAFGGLRGIPDPENPDRVLLFRLDRHC 60

Query: 61  DRLSKSAKFLHYDISAEKIKEVIVDFVKKNQPDKSFYIRPLVYSSGLGIAPRLHNLEKDF 120
            RLS+SAKFLH+++SAE+I + I  FV+KNQP +SFYIRP VY+S LGIAPRLHN+EKDF
Sbjct: 61  QRLSQSAKFLHFELSAEEIFKAIEAFVQKNQPSQSFYIRPFVYTSDLGIAPRLHNIEKDF 120

Query: 121 LVYGLEMGDYLAADGVSCRISSWYRQEDRSFPLRGKISAAYITSALAKTEAVESGFDEAI 180
            +YGL++GDYL+ +GVSCRISSWYRQEDRS PLRGKIS AYI S+LAKTEAV SGFDEAI
Sbjct: 121 FIYGLQLGDYLSPEGVSCRISSWYRQEDRSLPLRGKISGAYIASSLAKTEAVASGFDEAI 180

Query: 181 LMNSQGKVCEATGMNVFMVRNGQIVTPGNEQDILEGITRDSILTIAADLGIPTCQRPIDK 240
           LMNSQGKVCEATGMN+FMVRNG+++TPG +QDILEGITRDS++ +A DLGIP  QRPIDK
Sbjct: 181 LMNSQGKVCEATGMNLFMVRNGRLITPGYDQDILEGITRDSVIRVAQDLGIPVDQRPIDK 240

Query: 241 SELMIADEVFLSGTAAKITPVKRIENFTLGGDRPITEKLRSVLTAVTENREPKYQDWVFK 300
           SEL IADEVFLSGTAAK+TPVK++EN+    DRPIT+++R  LT +TE R   YQDWVF 
Sbjct: 241 SELFIADEVFLSGTAAKVTPVKQVENYLTPCDRPITDQIRQQLTLITEGRLAAYQDWVFP 300

Query: 301 IPL 303
           I L
Sbjct: 301 IAL 303


Lambda     K      H
   0.320    0.138    0.406 

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: 10
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: 305
Length of database: 304
Length adjustment: 27
Effective length of query: 278
Effective length of database: 277
Effective search space:    77006
Effective search space used:    77006
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 Synpcc7942_1029 Synpcc7942_1029 (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.30232.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    5.4e-82  261.3   0.0    6.1e-82  261.1   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_1029  Synpcc7942_1029 branched-chain a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_1029  Synpcc7942_1029 branched-chain amino acid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.1   0.0   6.1e-82   6.1e-82       1     296 [.       9     299 ..       9     301 .. 0.94

  Alignments for each domain:
  == domain 1  score: 261.1 bits;  conditional E-value: 6.1e-82
                                 TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdk...glaifrlkehveRlydsakilrleipys 66 
                                               ++ G+lv++ +a++++ thalhYGtg f G+R    ++      +frl+ h++Rl +sak l++e  +s
  lcl|FitnessBrowser__SynE:Synpcc7942_1029   9 FFRGQLVPFPEAQLSIATHALHYGTGAFGGLRGIPDPEnpdRVLLFRLDRHCQRLSQSAKFLHFE--LS 75 
                                               789*****************************9865542327789***************98876..68 PP

                                 TIGR01122  67 keelvevtkevlrknnlks.aYiRplvyvGaedlglkpk.vdlkveviiaawewgaylgeealekGikv 133
                                               +ee+ +++   ++kn+ ++  YiRp vy  + dlg+ p+  +++ + +i+  ++g yl      +G++ 
  lcl|FitnessBrowser__SynE:Synpcc7942_1029  76 AEEIFKAIEAFVQKNQPSQsFYIRPFVY--TSDLGIAPRlHNIEKDFFIYGLQLGDYLSP----EGVSC 138
                                               9*************9976659*******..89*******999*****************7....6**** PP

                                 TIGR01122 134 kvssfrraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltP 202
                                               ++ss+ r+++ s+p + k +g+Y+ s lak+ea+++G+deail++++G v e +G n+f+v++g l+tP
  lcl|FitnessBrowser__SynE:Synpcc7942_1029 139 RISSWYRQEDRSLPLRGKISGAYIASSLAKTEAVASGFDEAILMNSQGKVCEATGMNLFMVRNGRLITP 207
                                               ********************************************************************* PP

                                 TIGR01122 203 pvsesiLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGp 271
                                                  + iL+gitrd+vi++a++lgi v +++i ++el++aDevfl+Gtaa vtP+++v++      +  p
  lcl|FitnessBrowser__SynE:Synpcc7942_1029 208 GYDQDILEGITRDSVIRVAQDLGIPVDQRPIDKSELFIADEVFLSGTAAKVTPVKQVENYLTPCDR--P 274
                                               **********************************************************98766554..9 PP

                                 TIGR01122 272 vtkklqeaffdlvegktekkeewlt 296
                                               +t +++++   ++eg+  ++++w+ 
  lcl|FitnessBrowser__SynE:Synpcc7942_1029 275 ITDQIRQQLTLITEGRLAAYQDWVF 299
                                               **********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (304 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: 6.54
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis