Alignments for a candidate for ilvE in Rhodanobacter denitrificans FW104-10B01

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Rhodanobacter denitrificans FW104-10B01

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_027490420.1 LRK54_RS10340 branched-chain amino acid transaminase

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



>NCBI__GCF_021560695.1:WP_027490420.1
          Length = 333

 Score =  355 bits (911), Expect = e-103
 Identities = 177/300 (59%), Positives = 226/300 (75%), Gaps = 3/300 (1%)

Query: 8   WIWQNGQIKPWREATTHVMSHALHYGSSVFEGIRSYATPDGAAIFRLTDHLKRLYQSAKI 67
           ++W NG+IKPW EA+ HV +HALHYGSSVFEG R YATP G A FRL DH +RL++SA++
Sbjct: 5   FLWHNGRIKPWAEASVHVSTHALHYGSSVFEGERVYATPRGPAYFRLADHTRRLFESARV 64

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

Query: 126 GPYLGPEALESGIDACVSSWQRFAPNTIPAGAKAGGNYLSGQLIAREARRLGFGEGIALA 185
           G YLG EA E G D CVSSW R APNTIP+ AKAGGNYLS QLI  EARR G+ EGIAL 
Sbjct: 125 GAYLG-EAAERGADICVSSWHRPAPNTIPSWAKAGGNYLSSQLIGLEARRNGYDEGIALG 183

Query: 186 NTGLLSEGAGENLFLVFDGVLHTTPASASILTGITRHTLITLAREDGIEVIERDIPREYL 245
           + GLLSEGAGENLFLV +G L T P+SA IL GITR +++ LA   GI V ER++PRE L
Sbjct: 184 HGGLLSEGAGENLFLVKNGRLLTPPSSAGILAGITRDSVLALAAGLGIAVEERELPREAL 243

Query: 246 YLCDELLMCGTAAEITPIRSVDGKKIGSGKAGRVTRRMQELFFGLFNGKTNDQWGWLEPV 305
           Y  DE+ M GTAAEITP+RSVD K +G G  G VT+++++ FFGLF+G+T D+ GWL  V
Sbjct: 244 YSADEVFMTGTAAEITPVRSVDRKAVGKGAPGPVTQQLRQAFFGLFDGRTEDRHGWLSVV 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: 350
Number of extensions: 18
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: 333
Length adjustment: 27
Effective length of query: 278
Effective length of database: 306
Effective search space:    85068
Effective search space used:    85068
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 WP_027490420.1 LRK54_RS10340 (branched-chain amino acid transaminase)
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.1801252.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.6e-120  387.1   0.0     3e-120  386.9   0.0    1.0  1  NCBI__GCF_021560695.1:WP_027490420.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_021560695.1:WP_027490420.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  386.9   0.0    3e-120    3e-120       1     298 []       7     303 ..       7     303 .. 0.99

  Alignments for each domain:
  == domain 1  score: 386.9 bits;  conditional E-value: 3e-120
                             TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvev 73 
                                           w +G++ ++++a vhv thalhYG++vfeG R+Y t++g+a frl +h+ Rl++sa+++++e+ ys++e++ +
  NCBI__GCF_021560695.1:WP_027490420.1   7 WHNGRIKPWAEASVHVSTHALHYGSSVFEGERVYATPRGPAYFRLADHTRRLFESARVYEIEVGYSEDEINAA 79 
                                           99*********************************************************************** PP

                             TIGR01122  74 tkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsi 146
                                           + e++r+n + saY+Rp+v++Ga++lg+ +k +++vev+i+a++wgaylge a e+G ++ vss++r a+n+i
  NCBI__GCF_021560695.1:WP_027490420.1  80 CLELIRANAMPSAYVRPIVFRGAGGLGVLAKDGAPVEVAIMAMAWGAYLGE-AAERGADICVSSWHRPAPNTI 151
                                           **************************************************6.89******************* PP

                             TIGR01122 147 ptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdavik 219
                                           p+ aka+gnYl+s+l++ ea+r+Gyde+i+L + G ++eG+Gen+f+vk+g lltPp s  iL gitrd+v+ 
  NCBI__GCF_021560695.1:WP_027490420.1 152 PSWAKAGGNYLSSQLIGLEARRNGYDEGIALGHGGLLSEGAGENLFLVKNGRLLTPPSSAGILAGITRDSVLA 224
                                           ************************************************************************* PP

                             TIGR01122 220 lakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekke 292
                                           la+ lgi v+e+++ re+ly aDevf+tGtaae+tP+r+vD + +g+g  Gpvt++l++aff l+ g+te+++
  NCBI__GCF_021560695.1:WP_027490420.1 225 LAAGLGIAVEERELPREALYSADEVFMTGTAAEITPVRSVDRKAVGKGAPGPVTQQLRQAFFGLFDGRTEDRH 297
                                           ************************************************************************* PP

                             TIGR01122 293 ewltyv 298
                                           +wl+ v
  NCBI__GCF_021560695.1:WP_027490420.1 298 GWLSVV 303
                                           **9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (333 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 16.67
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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:

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