Aligments for a candidate for ilvE in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Aligments for a candidate for ilvE in Dechlorosoma suillum PS

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate Dsui_2030 Dsui_2030 branched-chain amino acid aminotransferase, group I

Query= reanno::psRCH2:GFF445
         (307 letters)



>lcl|FitnessBrowser__PS:Dsui_2030 Dsui_2030 branched-chain amino
           acid aminotransferase, group I
          Length = 308

 Score =  367 bits (943), Expect = e-106
 Identities = 178/304 (58%), Positives = 225/304 (74%)

Query: 1   MSMADRDGVIWYDGELVQWRDATTHVLTHTLHYGMGVFEGVRAYNTPDGTAIFRLQAHTD 60
           MSM +RDG IW DG  + WRDA  HVL+HTLHYG G FEG+RAY TP G AIFRL+ H  
Sbjct: 1   MSMENRDGFIWLDGHWLPWRDAKVHVLSHTLHYGYGCFEGIRAYATPRGPAIFRLEEHLR 60

Query: 61  RLFDSAHIMNMPMPYSKEEINEATRAAVRENNLESAYIRPMVFYGSEGMGLRASGLKVHV 120
           RL DSAHI+ + +P+S+ E+ +  R AV  N L+SAYIRP+VF G E +G+  +G + HV
Sbjct: 61  RLADSAHILAIDLPWSRAELAQVCREAVSRNGLDSAYIRPLVFLGPEKVGVDPAGAQTHV 120

Query: 121 IVAAWHWGAYMGDEALELGIKVRTSSFTRHHVNITMTRAKSNGAYINSMLALQEAISGGA 180
           +VAAW WGAY+G +ALE GI+VR SS+ RHH N+ M RAK+   Y NS+LA++EA   G 
Sbjct: 121 MVAAWPWGAYLGGDALEQGIRVRISSYARHHPNVQMCRAKAISTYSNSILAVREARRDGY 180

Query: 181 DEALMLDPEGYVAEGSGENIFIIKDGVIYTPEVTACLNGITRGTVLTLAAEHGLKIVEKR 240
           DEAL+LD EGYVAEGSGEN+F+++DG +  PE T+ L+GITR ++  LA E GL +  KR
Sbjct: 181 DEALLLDTEGYVAEGSGENLFLVRDGELLEPETTSALDGITRRSIHVLAREAGLTLRAKR 240

Query: 241 ITRDEVYIADEAFFTGTAAEVTPIREVDGRAIGIGRRGPITEKLQKAYFDLVTGKTDAHA 300
           ITRDEVY ADE F TGTAAEVTP+ EVD R+IG G+ GP+T  LQ+ YF  V G+ +AHA
Sbjct: 241 ITRDEVYCADEVFLTGTAAEVTPVVEVDRRSIGTGQPGPVTRLLQQRYFACVRGEDEAHA 300

Query: 301 EWRT 304
           +W T
Sbjct: 301 DWLT 304


Lambda     K      H
   0.319    0.135    0.400 

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: 354
Number of extensions: 7
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: 308
Length adjustment: 27
Effective length of query: 280
Effective length of database: 281
Effective search space:    78680
Effective search space used:    78680
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 Dsui_2030 Dsui_2030 (branched-chain amino acid aminotransferase, group I)
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.31581.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   7.4e-130  418.4   0.0   8.3e-130  418.2   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_2030  Dsui_2030 branched-chain amino a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_2030  Dsui_2030 branched-chain amino acid aminotransferase, group I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.2   0.0  8.3e-130  8.3e-130       1     297 [.      11     305 ..      11     306 .. 0.99

  Alignments for each domain:
  == domain 1  score: 418.2 bits;  conditional E-value: 8.3e-130
                         TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvevtkev 77 
                                       wldG+ ++++dakvhvl+h+lhYG g feGiRaY t++g+aifrl+eh+ Rl dsa+il +++p+s+ el +v++e+
  lcl|FitnessBrowser__PS:Dsui_2030  11 WLDGHWLPWRDAKVHVLSHTLHYGYGCFEGIRAYATPRGPAIFRLEEHLRRLADSAHILAIDLPWSRAELAQVCREA 87 
                                       9**************************************************************************** PP

                         TIGR01122  78 lrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsiptkakaag 154
                                       + +n+l+saYiRplv++G e++g++p ++++++v++aaw+wgaylg +ale+Gi+v++ss++r+++n+ + +aka +
  lcl|FitnessBrowser__PS:Dsui_2030  88 VSRNGLDSAYIRPLVFLGPEKVGVDP-AGAQTHVMVAAWPWGAYLGGDALEQGIRVRISSYARHHPNVQMCRAKAIS 163
                                       **************************.999*********************************************** PP

                         TIGR01122 155 nYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdaviklakelgievkee 231
                                       +Y ns+la  ea+r Gydea+lLd+eGyvaeGsGen+f+v+dg+ll P++ +s+L+gitr ++  la+e g++++ +
  lcl|FitnessBrowser__PS:Dsui_2030 164 TYSNSILAVREARRDGYDEALLLDTEGYVAEGSGENLFLVRDGELLEPET-TSALDGITRRSIHVLAREAGLTLRAK 239
                                       *************************************************9.78************************ PP

                         TIGR01122 232 risreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekkeewlty 297
                                       ri+r+e+y aDevfltGtaaevtP++evD r+ig g+ Gpvt+ lq+++f  v+g++e++++wlt+
  lcl|FitnessBrowser__PS:Dsui_2030 240 RITRDEVYCADEVFLTGTAAEVTPVVEVDRRSIGTGQPGPVTRLLQQRYFACVRGEDEAHADWLTP 305
                                       ****************************************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (308 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: 9.06
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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, or view the source code, or see 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