Aligments for a candidate for ilvE in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Aligments for a candidate for ilvE in Pseudomonas fluorescens GW456-L13

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate PfGW456L13_4923 Branched-chain amino acid aminotransferase (EC 2.6.1.42)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4923
          Length = 293

 Score =  219 bits (557), Expect = 8e-62
 Identities = 114/266 (42%), Positives = 162/266 (60%), Gaps = 5/266 (1%)

Query: 6   RDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTKRLLN 65
           R+G IW+DG+ ++W  A++HVLTH LHY   V+EG R Y        IF+L+EH++RL  
Sbjct: 11  REGVIWLDGEFVEWSRAQLHVLTHGLHYASTVYEGERVYNGR-----IFKLREHSERLYR 65

Query: 66  SAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIHVAIAA 125
           SA+     +P++   L AA  E+++ NK+   YLRP+ W GSE +  SA+ N +HVAIA 
Sbjct: 66  SAQWMDFAIPYEMAELEAASHELLQRNKVADGYLRPVAWRGSEMISTSARFNRVHVAIAC 125

Query: 126 WPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYDEAL 185
           W W +Y        GIR+KT+S+ R   + S   AKASG Y  + L+  +A   GY +AL
Sbjct: 126 WQWPSYFDPAARMAGIRLKTASWRRPPPSSSPFEAKASGHYQIATLSKHDAENTGYHDAL 185

Query: 186 LLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEKRITRD 245
           +LD  G+V+E +  N F V    L+TP     L+GITR TVI LA+    QV+E+ I   
Sbjct: 186 MLDWRGHVAEATSANVFFVKGRTLHTPLPDCFLNGITRQTVIELAKALDYQVVERTILPT 245

Query: 246 EVYTCDEAFFTGTAAEVTPIRELDNR 271
           E+   DE F TGTAAE+TP++ +D +
Sbjct: 246 ELGDFDECFLTGTAAEITPVQSIDEQ 271


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: 258
Number of extensions: 6
Number of successful extensions: 2
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: 293
Length adjustment: 27
Effective length of query: 280
Effective length of database: 266
Effective search space:    74480
Effective search space used:    74480
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 PfGW456L13_4923 (Branched-chain amino acid aminotransferase (EC 2.6.1.42))
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.13310.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
    3.1e-83  265.3   0.0    3.6e-83  265.1   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4923  Branched-chain amino acid aminot


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4923  Branched-chain amino acid aminotransferase (EC 2.6.1.42)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.1   0.0   3.6e-83   3.6e-83       1     265 [.      16     274 ..      16     292 .. 0.97

  Alignments for each domain:
  == domain 1  score: 265.1 bits;  conditional E-value: 3.6e-83
                                               TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlyds 55 
                                                             wldGe+v++  a++hvlth+lhY ++v+eG R+Y++    +if+l+eh eRly s
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4923  16 WLDGEFVEWSRAQLHVLTHGLHYASTVYEGERVYNG----RIFKLREHSERLYRS 66 
                                                             9***********************************....9************** PP

                                               TIGR01122  56 akilrleipyskeelvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkve 110
                                                             a+ +++ ipy   el  + +e+l++n++ + Y+Rp++++G+e +  +++ + +v+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4923  67 AQWMDFAIPYEMAELEAASHELLQRNKVADGYLRPVAWRGSEMISTSARFN-RVH 120
                                                             ************************************************998.9** PP

                                               TIGR01122 111 viiaawewgaylgeealekGikvkvssfrraavnsiptkakaagnYlnsllakse 165
                                                             v+ia w+w+ y++  a   Gi+ k++s+rr  ++s p +aka+g Y  ++l k++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4923 121 VAIACWQWPSYFDPAARMAGIRLKTASWRRPPPSSSPFEAKASGHYQIATLSKHD 175
                                                             ******************************************************* PP

                                               TIGR01122 166 alraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdavikl 220
                                                             a ++Gy++a++Ld  G+vae +  n+f vk  +l tP   +  L+gitr++vi+l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4923 176 AENTGYHDALMLDWRGHVAEATSANVFFVKGRTLHTPLP-DCFLNGITRQTVIEL 229
                                                             *************************************99.99************* PP

                                               TIGR01122 221 akelgievkeerisreelytaDevfltGtaaevtPirevDgrkig 265
                                                             ak l ++v+e++i  +el   De fltGtaae+tP++++D+++  
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4923 230 AKALDYQVVERTILPTELGDFDECFLTGTAAEITPVQSIDEQHYR 274
                                                             ****************************************98754 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (293 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: 6.35
//
[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