Alignments for a candidate for ilvE in Paraburkholderia sp. CCGE1002

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Paraburkholderia sp. CCGE1002

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_013090429.1 BC1002_RS12695 branched-chain amino acid transaminase

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



>NCBI__GCF_000092885.1:WP_013090429.1
          Length = 307

 Score =  598 bits (1542), Expect = e-176
 Identities = 293/307 (95%), Positives = 299/307 (97%)

Query: 1   MSMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHT 60
           MSMADRDGKIWMDGKLI+WRDAKIHVLTHTLHYGMGVFEGVRAYKTADG TAIFRLQEHT
Sbjct: 1   MSMADRDGKIWMDGKLIEWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGATAIFRLQEHT 60

Query: 61  KRLLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIH 120
           KRLLNSAKIFQMDVPFDHETLAAAQ EVVRENKL+SCYLRPIIWVGSEKLGVSAKGNTIH
Sbjct: 61  KRLLNSAKIFQMDVPFDHETLAAAQREVVRENKLDSCYLRPIIWVGSEKLGVSAKGNTIH 120

Query: 121 VAIAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADG 180
           VAIAAWPWGAYLGEDGI KGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADG
Sbjct: 121 VAIAAWPWGAYLGEDGITKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADG 180

Query: 181 YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEK 240
           YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARD GIQVIEK
Sbjct: 181 YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDMGIQVIEK 240

Query: 241 RITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKY 300
           RITRDEVYTCDEAFFTGTAAEVTPIRELDNR IG+G RGPITEKLQS FFD+VNGK +KY
Sbjct: 241 RITRDEVYTCDEAFFTGTAAEVTPIRELDNRKIGAGVRGPITEKLQSAFFDVVNGKGEKY 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: 537
Number of extensions: 4
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_013090429.1 BC1002_RS12695 (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.29053.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-140  453.9   0.1   1.3e-140  453.7   0.1    1.0  1  lcl|NCBI__GCF_000092885.1:WP_013090429.1  BC1002_RS12695 branched-chain am


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092885.1:WP_013090429.1  BC1002_RS12695 branched-chain amino acid transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  453.7   0.1  1.3e-140  1.3e-140       1     298 []      11     307 .]      11     307 .] 0.98

  Alignments for each domain:
  == domain 1  score: 453.7 bits;  conditional E-value: 1.3e-140
                                 TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdk.glaifrlkehveRlydsakilrleipyske 68 
                                               w+dG+l++++dak+hvlth+lhYG+gvfeG+RaY+t +  +aifrl+eh++Rl++saki+++++p+ +e
  lcl|NCBI__GCF_000092885.1:WP_013090429.1  11 WMDGKLIEWRDAKIHVLTHTLHYGMGVFEGVRAYKTADgATAIFRLQEHTKRLLNSAKIFQMDVPFDHE 79 
                                               9**********************************9983579*************************** PP

                                 TIGR01122  69 elvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvss 137
                                               +l  +++ev+r+n+l+s+Y+Rp+++vG+e+lg+++k + +++v+iaaw+wgaylge+++ kGi+vk+ss
  lcl|NCBI__GCF_000092885.1:WP_013090429.1  80 TLAAAQREVVRENKLDSCYLRPIIWVGSEKLGVSAKGN-TIHVAIAAWPWGAYLGEDGITKGIRVKTSS 147
                                               ***********************************655.9***************************** PP

                                 TIGR01122 138 frraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvse 206
                                               f+r++vn+ + +aka+g Y+ns+la++ea++ Gydea+lLd +Gyv+eGsGen+f+v++g+l+tP++ +
  lcl|NCBI__GCF_000092885.1:WP_013090429.1 148 FTRHHVNVSMVRAKASGWYVNSILANQEAIADGYDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDL-S 215
                                               *******************************************************************.8 PP

                                 TIGR01122 207 siLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkk 275
                                               s+L+gitrd+vi+la+++gi+v e+ri+r+e+yt De+f+tGtaaevtPire+D+rkig+g rGp+t+k
  lcl|NCBI__GCF_000092885.1:WP_013090429.1 216 SCLDGITRDTVITLARDMGIQVIEKRITRDEVYTCDEAFFTGTAAEVTPIRELDNRKIGAGVRGPITEK 284
                                               8******************************************************************** PP

                                 TIGR01122 276 lqeaffdlvegktekkeewltyv 298
                                               lq+affd+v+gk ek+++wlt++
  lcl|NCBI__GCF_000092885.1:WP_013090429.1 285 LQSAFFDVVNGKGEKYAHWLTKI 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 10.48
//
[ok]

This GapMind analysis is from Apr 10 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:

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