GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Pseudomonas stutzeri RCH2

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate GFF445 Psest_0450 branched-chain amino acid aminotransferase, group I

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



>FitnessBrowser__psRCH2:GFF445
          Length = 307

 Score =  619 bits (1596), Expect = 0.0
 Identities = 307/307 (100%), Positives = 307/307 (100%)

Query: 1   MSMADRDGVIWYDGELVQWRDATTHVLTHTLHYGMGVFEGVRAYNTPDGTAIFRLQAHTD 60
           MSMADRDGVIWYDGELVQWRDATTHVLTHTLHYGMGVFEGVRAYNTPDGTAIFRLQAHTD
Sbjct: 1   MSMADRDGVIWYDGELVQWRDATTHVLTHTLHYGMGVFEGVRAYNTPDGTAIFRLQAHTD 60

Query: 61  RLFDSAHIMNMPMPYSKEEINEATRAAVRENNLESAYIRPMVFYGSEGMGLRASGLKVHV 120
           RLFDSAHIMNMPMPYSKEEINEATRAAVRENNLESAYIRPMVFYGSEGMGLRASGLKVHV
Sbjct: 61  RLFDSAHIMNMPMPYSKEEINEATRAAVRENNLESAYIRPMVFYGSEGMGLRASGLKVHV 120

Query: 121 IVAAWHWGAYMGDEALELGIKVRTSSFTRHHVNITMTRAKSNGAYINSMLALQEAISGGA 180
           IVAAWHWGAYMGDEALELGIKVRTSSFTRHHVNITMTRAKSNGAYINSMLALQEAISGGA
Sbjct: 121 IVAAWHWGAYMGDEALELGIKVRTSSFTRHHVNITMTRAKSNGAYINSMLALQEAISGGA 180

Query: 181 DEALMLDPEGYVAEGSGENIFIIKDGVIYTPEVTACLNGITRGTVLTLAAEHGLKIVEKR 240
           DEALMLDPEGYVAEGSGENIFIIKDGVIYTPEVTACLNGITRGTVLTLAAEHGLKIVEKR
Sbjct: 181 DEALMLDPEGYVAEGSGENIFIIKDGVIYTPEVTACLNGITRGTVLTLAAEHGLKIVEKR 240

Query: 241 ITRDEVYIADEAFFTGTAAEVTPIREVDGRAIGIGRRGPITEKLQKAYFDLVTGKTDAHA 300
           ITRDEVYIADEAFFTGTAAEVTPIREVDGRAIGIGRRGPITEKLQKAYFDLVTGKTDAHA
Sbjct: 241 ITRDEVYIADEAFFTGTAAEVTPIREVDGRAIGIGRRGPITEKLQKAYFDLVTGKTDAHA 300

Query: 301 EWRTLVK 307
           EWRTLVK
Sbjct: 301 EWRTLVK 307


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: 533
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: 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 GFF445 Psest_0450 (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.24391.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   5.2e-147  474.7   0.4   5.8e-147  474.6   0.4    1.0  1  lcl|FitnessBrowser__psRCH2:GFF445  Psest_0450 branched-chain amino 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF445  Psest_0450 branched-chain amino acid aminotransferase, group I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  474.6   0.4  5.8e-147  5.8e-147       1     298 []      11     306 ..      11     306 .. 0.99

  Alignments for each domain:
  == domain 1  score: 474.6 bits;  conditional E-value: 5.8e-147
                          TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvevtke 76 
                                        w+dGelv+++da++hvlth+lhYG+gvfeG+RaY+t++g+aifrl+ h++Rl+dsa+i+++++pyskee++e+t+ 
  lcl|FitnessBrowser__psRCH2:GFF445  11 WYDGELVQWRDATTHVLTHTLHYGMGVFEGVRAYNTPDGTAIFRLQAHTDRLFDSAHIMNMPMPYSKEEINEATRA 86 
                                        9*************************************************************************** PP

                          TIGR01122  77 vlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsiptkaka 152
                                        ++r+nnl+saYiRp+v++G+e++gl++ ++lkv+vi+aaw+wgay+g+eale Gikv++ssf+r++vn+ +t+ak+
  lcl|FitnessBrowser__psRCH2:GFF445  87 AVRENNLESAYIRPMVFYGSEGMGLRA-SGLKVHVIVAAWHWGAYMGDEALELGIKVRTSSFTRHHVNITMTRAKS 161
                                        ***************************.9*********************************************** PP

                          TIGR01122 153 agnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdaviklakelgiev 228
                                        +g+Y+ns+la +ea++ G+dea++Ld eGyvaeGsGenifi+kdgv++tP+v +++L+gitr +v++la+e+g+++
  lcl|FitnessBrowser__psRCH2:GFF445 162 NGAYINSMLALQEAISGGADEALMLDPEGYVAEGSGENIFIIKDGVIYTPEV-TACLNGITRGTVLTLAAEHGLKI 236
                                        ****************************************************.78********************* PP

                          TIGR01122 229 keerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekkeewltyv 298
                                        +e+ri+r+e+y+aDe+f+tGtaaevtPirevDgr ig g+rGp+t+klq+a+fdlv+gkt++++ew t v
  lcl|FitnessBrowser__psRCH2:GFF445 237 VEKRITRDEVYIADEAFFTGTAAEVTPIREVDGRAIGIGRRGPITEKLQKAYFDLVTGKTDAHAEWRTLV 306
                                        ******************************************************************9976 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.55
//
[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