Alignments for a candidate for astB in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for astB in Burkholderia phytofirmans PsJN

Align Succinylarginine dihydrolase (EC 3.5.3.23) (characterized)
to candidate BPHYT_RS07715 BPHYT_RS07715 N-succinylarginine dihydrolase

Query= reanno::MR1:201844
         (444 letters)



>FitnessBrowser__BFirm:BPHYT_RS07715
          Length = 446

 Score =  530 bits (1365), Expect = e-155
 Identities = 272/447 (60%), Positives = 325/447 (72%), Gaps = 4/447 (0%)

Query: 1   MKHFEANFDGLVGPTHNYAGLSFGNVASLNNAALVSNPKAAAKQGLQKAKALADLGMIQG 60
           M+  EANFDGLVGPTHNYAGLSFGNVAS NN   ++NPKAAA+QGL+K K LADLG  QG
Sbjct: 1   MQATEANFDGLVGPTHNYAGLSFGNVASQNNEKSIANPKAAARQGLRKMKQLADLGFHQG 60

Query: 61  MLAPQERPDLNTLRRIGFSGSDAQVLQQAAKTAPALLNACCSASSMWTANAATVSPSADT 120
           +L PQERP +  LR +GFSG DA V+ + AK AP LL A  SAS+MWTANAATVSPSADT
Sbjct: 61  VLPPQERPSMRLLRELGFSGDDATVIARVAKDAPELLAAASSASAMWTANAATVSPSADT 120

Query: 121 RDGKLHFTPANLVDKLHRSIEPITTGRILTATFNDPHYFYHHNHLPEHNSFGDEGAANHT 180
            DG++HFTPANL  KLHR+IE  +T R L A FND   F  H  LP   + GDEGAANHT
Sbjct: 121 HDGRVHFTPANLCSKLHRAIEHESTRRTLRAIFNDADRFVVHEALPGTPALGDEGAANHT 180

Query: 181 RLCQEYGHAGVELFVYGQEATNPHAPKPLKFPARQTLEASMAIARLHQLEEDNCVFIQQN 240
           R C +Y   GVE FVYG+       P+P +FPARQT EAS A+A  H L E   V+ QQN
Sbjct: 181 RFCADYAARGVEFFVYGRSEYR-RGPEPKRFPARQTFEASRAVAHRHGLAEAATVYAQQN 239

Query: 241 PAVIDQGVFHNDVIAVGNQNVLFYHEQAFLNTQAKLDEIKRK---LDTELYFIEVPTAKV 297
           P VID GVFHNDVIAVGN+N LF H+ AF+   A  DE++ K   L  +   IEVP A+V
Sbjct: 240 PDVIDAGVFHNDVIAVGNRNTLFCHQLAFVEQNAVYDELRSKLTELKADFNVIEVPDAQV 299

Query: 298 SINDAVKSYLFNTQIITLPSGEMAIIAPTDCQENPAVYAYLNELLSLNTPIKQVLYFDVK 357
           S+ DAV SYLFN+Q++T P G+  ++ P +C+ENP V AYL+ L S   PI  VL FD++
Sbjct: 300 SVADAVTSYLFNSQLLTRPDGKQVLVVPQECRENPRVAAYLDGLTSHAGPIDDVLVFDLR 359

Query: 358 QSMQNGGGPACLRLRVAMNEREVAAVNQHTLLTDALFTRLNTWVEKHYRDRLSTEDLADP 417
           +SM+NGGGPACLRLRV +++ E AAV Q   + D LF RL+TW+EKHYRDRL+  DL DP
Sbjct: 360 ESMKNGGGPACLRLRVVLDDAERAAVTQGVWINDTLFGRLDTWIEKHYRDRLAPADLTDP 419

Query: 418 QLVIESRTALDELTQIMKLGSVYPFQR 444
           QL+ ESRTALDELTQI+ LGS+Y FQR
Sbjct: 420 QLLAESRTALDELTQILGLGSLYDFQR 446


Lambda     K      H
   0.318    0.132    0.387 

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: 542
Number of extensions: 19
Number of successful extensions: 3
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: 444
Length of database: 446
Length adjustment: 32
Effective length of query: 412
Effective length of database: 414
Effective search space:   170568
Effective search space used:   170568
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate BPHYT_RS07715 BPHYT_RS07715 (N-succinylarginine dihydrolase)
to HMM TIGR03241 (astB: succinylarginine dihydrolase (EC 3.5.3.23))

# 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/TIGR03241.hmm
# target sequence database:        /tmp/gapView.7411.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03241  [M=443]
Accession:   TIGR03241
Description: arg_catab_astB: succinylarginine dihydrolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.6e-242  791.1   0.1   1.8e-242  791.0   0.1    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS07715  BPHYT_RS07715 N-succinylarginine


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS07715  BPHYT_RS07715 N-succinylarginine dihydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  791.0   0.1  1.8e-242  1.8e-242       1     443 []       3     445 ..       3     445 .. 1.00

  Alignments for each domain:
  == domain 1  score: 791.0 bits;  conditional E-value: 1.8e-242
                                TIGR03241   1 ayevnfdGlvGlthnyaGlsfGnkastsnkksvsnpklaakqGllkmkaladlGfkqgvlapqerpdiaa 70 
                                              a e+nfdGlvG+thnyaGlsfGn+as++n+ks++npk+aa+qGl+kmk+ladlGf+qgvl+pqerp+++ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS07715   3 ATEANFDGLVGPTHNYAGLSFGNVASQNNEKSIANPKAAARQGLRKMKQLADLGFHQGVLPPQERPSMRL 72 
                                              579******************************************************************* PP

                                TIGR03241  71 lrklGfsGsdeevlekaareapellsavssassmwtanaatvspsadtadgrvhftaanlnnkfhrsiea 140
                                              lr+lGfsG+d+ v++++a++apell+a+ssas+mwtanaatvspsadt dgrvhft+anl++k+hr+ie+
  lcl|FitnessBrowser__BFirm:BPHYT_RS07715  73 LRELGFSGDDATVIARVAKDAPELLAAASSASAMWTANAATVSPSADTHDGRVHFTPANLCSKLHRAIEH 142
                                              ********************************************************************** PP

                                TIGR03241 141 ettervlkaifadekkfavhealpavallGdeGaanhtrlgaeydepgvelfvyGraalerepkpkrypa 210
                                              e+t+r+l+aif+d ++f+vhealp + +lGdeGaanhtr++a+y + gve+fvyGr++++r+p+pkr+pa
  lcl|FitnessBrowser__BFirm:BPHYT_RS07715 143 ESTRRTLRAIFNDADRFVVHEALPGTPALGDEGAANHTRFCADYAARGVEFFVYGRSEYRRGPEPKRFPA 212
                                              ********************************************************************** PP

                                TIGR03241 211 rqtleasqavarlhqleeekvvyaqqnpdvidqGvfhndviavsnrevlfhhekaflnqsqvldelrakl 280
                                              rqt+eas+ava++h+l+e+++vyaqqnpdvid+Gvfhndviav+nr++lf+h+ af++q++v+delr+kl
  lcl|FitnessBrowser__BFirm:BPHYT_RS07715 213 RQTFEASRAVAHRHGLAEAATVYAQQNPDVIDAGVFHNDVIAVGNRNTLFCHQLAFVEQNAVYDELRSKL 282
                                              ********************************************************************** PP

                                TIGR03241 281 aalgqelvaievpdaevsvedavssylfnsqllskedgkmllvvpeecreneavwayldelvaadgpike 350
                                              + l++++++ievpda+vsv+dav+sylfnsqll++ dgk++lvvp+ecren++v+ayld l+++ gpi++
  lcl|FitnessBrowser__BFirm:BPHYT_RS07715 283 TELKADFNVIEVPDAQVSVADAVTSYLFNSQLLTRPDGKQVLVVPQECRENPRVAAYLDGLTSHAGPIDD 352
                                              ********************************************************************** PP

                                TIGR03241 351 vkvfdlresmknGGGpaclrlrvvlndaelaavnpkvllsdalfatlnkwvdrhyrdrlsakdladpqll 420
                                              v vfdlresmknGGGpaclrlrvvl+dae+aav + v+++d+lf +l++w+++hyrdrl+ +dl+dpqll
  lcl|FitnessBrowser__BFirm:BPHYT_RS07715 353 VLVFDLRESMKNGGGPACLRLRVVLDDAERAAVTQGVWINDTLFGRLDTWIEKHYRDRLAPADLTDPQLL 422
                                              ********************************************************************** PP

                                TIGR03241 421 vesrtaldeltqilnlGsvyefq 443
                                               esrtaldeltqil+lGs+y+fq
  lcl|FitnessBrowser__BFirm:BPHYT_RS07715 423 AESRTALDELTQILGLGSLYDFQ 445
                                              **********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (446 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: 12.14
//
[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