Alignments for a candidate for ans in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for ans in Burkholderia phytofirmans PsJN

Align Glutaminase-asparaginase; L-ASNase/L-GLNase; L-asparagine/L-glutamine amidohydrolase; EC 3.5.1.38 (characterized)
to candidate BPHYT_RS21005 BPHYT_RS21005 asparaginase

Query= SwissProt::O68897
         (362 letters)



>FitnessBrowser__BFirm:BPHYT_RS21005
          Length = 330

 Score =  329 bits (844), Expect = 6e-95
 Identities = 160/331 (48%), Positives = 233/331 (70%), Gaps = 2/331 (0%)

Query: 32  TKLANVVILATGGTIAGAGASAANSATYQAAKVGIEQLIAGVPELSQIANVRGEQVMQIA 91
           T  AN+V++ TGGTIAG G ++ N++TY  + +GI++++  +P   ++AN+R EQ++Q  
Sbjct: 2   TAKANIVVIGTGGTIAGQGKASVNTSTYMCSVLGIDEILGSIPHAGELANLRAEQLLQTG 61

Query: 92  SESINNENLLQLGRRVAELADSKDVDGIVITHGTDTLEETAYFLNLVEKTDKPIIVVGSM 151
           SE+ NN +LL +G RVAEL    DVDG+VITHGTDT+EETAYFL+L  K+ KP++VVGSM
Sbjct: 62  SENFNNTHLLAIGNRVAELLARNDVDGVVITHGTDTIEETAYFLHLTLKSAKPVVVVGSM 121

Query: 152 RPGTAMSADGMLNLYNAVAVAGSKDARGKGVLVTMNDEIQSGRDVSKMINIKTEAFKSPW 211
           RP +AMS+D  LNLY+A+AVA    +RG G LV  N+EI + RDV K  + K +AF+SP+
Sbjct: 122 RPPSAMSSDAALNLYDALAVATHPSSRGLGTLVVANNEIHTARDVVKSNSFKLDAFRSPY 181

Query: 212 GPLGMVVEGKSYWFRLPAKRHTMDSEFDIKTIKSLPDVEIAYGYGNVSDTAVKALAQAGA 271
           G LG V+EG   ++R PA+ HT+D+ + I T++SLP V+I Y YG +   A+ A+  A A
Sbjct: 182 GALGYVIEGAPRYYRRPARAHTLDTPWSITTLRSLPKVDIVYAYGALEPGAISAIT-ANA 240

Query: 272 KAIIHAGTGNGSVSSKVVPALQELRKQGVQIIRSSHVNAGGFVLRNAEQPDDKYDWVVAH 331
           + +I+ GTGNG+V+S ++  L++  ++GV ++R+S   + G VL N  QPD +Y W+   
Sbjct: 241 RGLIYVGTGNGNVASHLIDPLRDAARRGVHVVRASRTGS-GIVLHNGAQPDHEYGWLTVD 299

Query: 332 DLNPQKARILAMVALTKTQDSKELQRMFWEY 362
           D  PQKARIL  +ALT+T D+  LQ +F  Y
Sbjct: 300 DQIPQKARILLTLALTQTDDTAALQAVFERY 330


Lambda     K      H
   0.315    0.130    0.361 

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: 251
Number of extensions: 9
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: 362
Length of database: 330
Length adjustment: 29
Effective length of query: 333
Effective length of database: 301
Effective search space:   100233
Effective search space used:   100233
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 (21.5 bits)
S2: 49 (23.5 bits)

Align candidate BPHYT_RS21005 BPHYT_RS21005 (asparaginase)
to HMM TIGR00520 (L-asparaginase, type II (EC 3.5.1.1))

# 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/TIGR00520.hmm
# target sequence database:        /tmp/gapView.25704.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00520  [M=352]
Accession:   TIGR00520
Description: asnASE_II: L-asparaginase, type II
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   3.6e-108  347.5   0.1   4.3e-108  347.3   0.1    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS21005  BPHYT_RS21005 asparaginase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS21005  BPHYT_RS21005 asparaginase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  347.3   0.1  4.3e-108  4.3e-108      26     352 .]       6     330 .]       2     330 .] 0.97

  Alignments for each domain:
  == domain 1  score: 347.3 bits;  conditional E-value: 4.3e-108
                                TIGR00520  26 nikilatGGtiagkgqssastaeYkvgklgvedLieavPelkeianiegeqivnvgsqdlneevllklak 95 
                                              ni +++tGGtiag+g+ s +t+ Y   +lg+++++ ++P+  e+an++ eq+ + gs+++n+++ll + +
  lcl|FitnessBrowser__BFirm:BPHYT_RS21005   6 NIVVIGTGGTIAGQGKASVNTSTYMCSVLGIDEILGSIPHAGELANLRAEQLLQTGSENFNNTHLLAIGN 75 
                                              899******************************************************************* PP

                                TIGR00520  96 risealasddvdGivithGtDtleetayfldltvksdkPvvlvGamRpatsvsaDGplnLYnavsvaade 165
                                              r+ e la +dvdG+vithGtDt+eetayfl lt+ks kPvv+vG+mRp +++s+D +lnLY+a++va+++
  lcl|FitnessBrowser__BFirm:BPHYT_RS21005  76 RVAELLARNDVDGVVITHGTDTIEETAYFLHLTLKSAKPVVVVGSMRPPSAMSSDAALNLYDALAVATHP 145
                                              ********************************************************************** PP

                                TIGR00520 166 ksagrGvlvvlndrilsarevtktnttsldtfkseeqGalGyiandkieyerepvkkhtletefdvskld 235
                                               s+g G+lvv n++i  ar+v+k n+ +ld+f+s  +GalGy+ ++  +y+r+p++ htl+t++++  l 
  lcl|FitnessBrowser__BFirm:BPHYT_RS21005 146 SSRGLGTLVVANNEIHTARDVVKSNSFKLDAFRSP-YGALGYVIEGAPRYYRRPARAHTLDTPWSITTLR 214
                                              **********************************9.********************************** PP

                                TIGR00520 236 eplPkvdiiYayqnlpeelvkavvdagakGivlagvGnGslsaaalkvleeaakesvvivrssRvadGvv 305
                                              + lPkvdi+Yay +l +  + a++ + a+G++  g+GnG++  +  + l +aa+++v +vr+sR+ +G+v
  lcl|FitnessBrowser__BFirm:BPHYT_RS21005 215 S-LPKVDIVYAYGALEPGAISAITAN-ARGLIYVGTGNGNVASHLIDPLRDAARRGVHVVRASRTGSGIV 282
                                              *.*************99999988766.9****************************************** PP

                                TIGR00520 306 tkdaevddk.ealiasgtLnPqkaRvLLqLaLtktkdlekiqevfeey 352
                                               ++ +  d+ ++ ++ +   PqkaR+LL LaLt+t d+  +q+vfe y
  lcl|FitnessBrowser__BFirm:BPHYT_RS21005 283 LHNGAQPDHeYGWLTVDDQIPQKARILLTLALTQTDDTAALQAVFERY 330
                                              99876655559**********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (352 nodes)
Target sequences:                          1  (330 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.31
//
[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