Alignments for a candidate for ilvE in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ilvE in Paraburkholderia bryophila 376MFSha3.1

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate H281DRAFT_04193 H281DRAFT_04193 branched chain amino acid aminotransferase apoenzyme

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



>FitnessBrowser__Burk376:H281DRAFT_04193
          Length = 307

 Score =  610 bits (1574), Expect = e-179
 Identities = 301/307 (98%), Positives = 304/307 (99%)

Query: 1   MSMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHT 60
           MSMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHT
Sbjct: 1   MSMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHT 60

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

Query: 121 VAIAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADG 180
           VAIAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADG
Sbjct: 121 VAIAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADG 180

Query: 181 YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEK 240
           YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARD GI VIEK
Sbjct: 181 YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDMGIPVIEK 240

Query: 241 RITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKY 300
           RITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIG+GARGPITEKLQSGFFDIVNGKS+KY
Sbjct: 241 RITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGAGARGPITEKLQSGFFDIVNGKSEKY 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: 539
Number of extensions: 5
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 H281DRAFT_04193 H281DRAFT_04193 (branched chain amino acid aminotransferase apoenzyme)
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.carbon/TIGR01122.hmm
# target sequence database:        /tmp/gapView.25890.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   7.5e-141  454.5   0.0   8.3e-141  454.4   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_04193  H281DRAFT_04193 branched chain a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_04193  H281DRAFT_04193 branched chain amino acid aminotransferase apoenzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  454.4   0.0  8.3e-141  8.3e-141       1     298 []      11     307 .]      11     307 .] 0.99

  Alignments for each domain:
  == domain 1  score: 454.4 bits;  conditional E-value: 8.3e-141
                                    TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdk.glaifrlkehveRlydsakilrleipy 65 
                                                  w+dG+l+d++dak+hvlth+lhYG+gvfeG+RaY+t + g+aifrl+eh++Rl++saki+++++p+
  lcl|FitnessBrowser__Burk376:H281DRAFT_04193  11 WMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADgGTAIFRLQEHTKRLLNSAKIFQMDVPF 76 
                                                  9**********************************987689************************* PP

                                    TIGR01122  66 skeelvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGi 131
                                                   +e+l  +++ev+r+n+l+s+Y+Rp+++vG+e+lg+++k + +++v+iaaw+wgaylge+++ kGi
  lcl|FitnessBrowser__Burk376:H281DRAFT_04193  77 DHETLAAAQREVVRENKLESCYLRPIIWVGSEKLGVSAKGN-TIHVAIAAWPWGAYLGEDGIAKGI 141
                                                  **************************************655.9*********************** PP

                                    TIGR01122 132 kvkvssfrraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdg 197
                                                  +vk+ssf+r++vn+ + +aka+g Y+ns+la++ea++ Gydea+lLd +Gyv+eGsGen+f+v++g
  lcl|FitnessBrowser__Burk376:H281DRAFT_04193 142 RVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYDEALLLDVDGYVSEGSGENFFLVNNG 207
                                                  ****************************************************************** PP

                                    TIGR01122 198 vlltPpvsesiLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrk 263
                                                  +l+tP++ +s+L+gitrd+vi+la+++gi v e+ri+r+e+yt De+f+tGtaaevtPire+D+r+
  lcl|FitnessBrowser__Burk376:H281DRAFT_04193 208 KLYTPDL-SSCLDGITRDTVITLARDMGIPVIEKRITRDEVYTCDEAFFTGTAAEVTPIRELDNRT 272
                                                  *******.88******************************************************** PP

                                    TIGR01122 264 igegkrGpvtkklqeaffdlvegktekkeewltyv 298
                                                  ig+g rGp+t+klq+ ffd+v+gk ek+++wlt++
  lcl|FitnessBrowser__Burk376:H281DRAFT_04193 273 IGAGARGPITEKLQSGFFDIVNGKSEKYAHWLTKI 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.03
# Mc/sec: 2.69
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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

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 catabolism of small carbon sources