Alignments for a candidate for ilvE in Paraburkholderia phymatum STM815

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Paraburkholderia phymatum STM815

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_012399873.1 BPHY_RS02290 branched-chain amino acid transaminase

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



>NCBI__GCF_000020045.1:WP_012399873.1
          Length = 307

 Score =  599 bits (1545), Expect = e-176
 Identities = 295/307 (96%), Positives = 301/307 (98%)

Query: 1   MSMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHT 60
           MSMADRDGKIWMDGKLIDWRDA+IHVLTHTLHYGMGVFEGVRAYKTADGGT+IFRL+EHT
Sbjct: 1   MSMADRDGKIWMDGKLIDWRDARIHVLTHTLHYGMGVFEGVRAYKTADGGTSIFRLKEHT 60

Query: 61  KRLLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIH 120
           KRLLNSAKIFQMDVPFDHETLAAAQ EVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIH
Sbjct: 61  KRLLNSAKIFQMDVPFDHETLAAAQREVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIH 120

Query: 121 VAIAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADG 180
           VAIAAWPWGAYLGEDGI KGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEA ADG
Sbjct: 121 VAIAAWPWGAYLGEDGIKKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEATADG 180

Query: 181 YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEK 240
           YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLA+DAGI+VIEK
Sbjct: 181 YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLAKDAGIEVIEK 240

Query: 241 RITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKY 300
           RITRDEVYT DEAFFTGTAAEVTPIRELDNRTIGSG RGPITEKLQSGFFDIVNGKS KY
Sbjct: 241 RITRDEVYTADEAFFTGTAAEVTPIRELDNRTIGSGTRGPITEKLQSGFFDIVNGKSAKY 300

Query: 301 ANWLTKI 307
           A+WLTKI
Sbjct: 301 AHWLTKI 307


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: 525
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 WP_012399873.1 BPHY_RS02290 (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.881371.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.9e-141  454.8   0.1   6.6e-141  454.7   0.1    1.0  1  NCBI__GCF_000020045.1:WP_012399873.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000020045.1:WP_012399873.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  454.7   0.1  6.6e-141  6.6e-141       1     298 []      11     307 .]      11     307 .] 0.99

  Alignments for each domain:
  == domain 1  score: 454.7 bits;  conditional E-value: 6.6e-141
                             TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdk.glaifrlkehveRlydsakilrleipyskeelve 72 
                                           w+dG+l+d++da++hvlth+lhYG+gvfeG+RaY+t + g+ ifrlkeh++Rl++saki+++++p+ +e+l  
  NCBI__GCF_000020045.1:WP_012399873.1  11 WMDGKLIDWRDARIHVLTHTLHYGMGVFEGVRAYKTADgGTSIFRLKEHTKRLLNSAKIFQMDVPFDHETLAA 83 
                                           9**********************************987689******************************** PP

                             TIGR01122  73 vtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavns 145
                                           +++ev+r+n+l+s+Y+Rp+++vG+e+lg+++k + +++v+iaaw+wgaylge++++kGi+vk+ssf+r++vn+
  NCBI__GCF_000020045.1:WP_012399873.1  84 AQREVVRENKLESCYLRPIIWVGSEKLGVSAKGN-TIHVAIAAWPWGAYLGEDGIKKGIRVKTSSFTRHHVNV 155
                                           *******************************655.9************************************* PP

                             TIGR01122 146 iptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdavi 218
                                            + +aka+g Y+ns+la++ea++ Gydea+lLd +Gyv+eGsGen+f+v++g+l+tP++ +s+L+gitrd+vi
  NCBI__GCF_000020045.1:WP_012399873.1 156 SMVRAKASGWYVNSILANQEATADGYDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDL-SSCLDGITRDTVI 227
                                           ***********************************************************.88*********** PP

                             TIGR01122 219 klakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekk 291
                                           +lak+ giev e+ri+r+e+ytaDe+f+tGtaaevtPire+D+r+ig+g+rGp+t+klq+ ffd+v+gk  k+
  NCBI__GCF_000020045.1:WP_012399873.1 228 TLAKDAGIEVIEKRITRDEVYTADEAFFTGTAAEVTPIRELDNRTIGSGTRGPITEKLQSGFFDIVNGKSAKY 300
                                           ************************************************************************* PP

                             TIGR01122 292 eewltyv 298
                                           ++wlt++
  NCBI__GCF_000020045.1:WP_012399873.1 301 AHWLTKI 307
                                           ****986 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 12.23
//
[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