GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Dechlorosoma suillum PS

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

Query= BRENDA::O86428
         (307 letters)



>FitnessBrowser__PS:Dsui_2030
          Length = 308

 Score =  372 bits (956), Expect = e-108
 Identities = 180/304 (59%), Positives = 225/304 (74%)

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

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

Query: 121 IIAAWSWGAYMGEEALQQGIKVRTSSFTRHHVNISMTRAKSNGAYINSMLALQEAISGGA 180
           ++AAW WGAY+G +AL+QGI+VR SS+ RHH N+ M RAK+   Y NS+LA++EA   G 
Sbjct: 121 MVAAWPWGAYLGGDALEQGIRVRISSYARHHPNVQMCRAKAISTYSNSILAVREARRDGY 180

Query: 181 DEAMMLDPEGYVAEGSGENIFIIKDGVIYTPEVTACLNGITRNTILTLAAEHGFKLVEKR 240
           DEA++LD EGYVAEGSGEN+F+++DG +  PE T+ L+GITR +I  LA E G  L  KR
Sbjct: 181 DEALLLDTEGYVAEGSGENLFLVRDGELLEPETTSALDGITRRSIHVLAREAGLTLRAKR 240

Query: 241 ITRDEVYIADEAFFTGTAAEVTPIREVDGRKIGAGRRGPVTEKLQKAYFDLVSGKTEAHA 300
           ITRDEVY ADE F TGTAAEVTP+ EVD R IG G+ GPVT  LQ+ YF  V G+ EAHA
Sbjct: 241 ITRDEVYCADEVFLTGTAAEVTPVVEVDRRSIGTGQPGPVTRLLQQRYFACVRGEDEAHA 300

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


Lambda     K      H
   0.319    0.134    0.394 

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: 383
Number of extensions: 9
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.25153.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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 10.69
//
[ok]

This GapMind analysis is from Apr 09 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:

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:

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:

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:

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