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 L-asparaginase (EC 3.5.1.1) (characterized)
to candidate BPHYT_RS08815 BPHYT_RS08815 L-asparaginase

Query= reanno::BFirm:BPHYT_RS08815
         (347 letters)



>FitnessBrowser__BFirm:BPHYT_RS08815
          Length = 347

 Score =  662 bits (1707), Expect = 0.0
 Identities = 347/347 (100%), Positives = 347/347 (100%)

Query: 1   MNTSTSSSAMPSDEGAMPLLPRIVVLATGGTIAGAAASATNTSGYQAGVIGVEQLLAVVP 60
           MNTSTSSSAMPSDEGAMPLLPRIVVLATGGTIAGAAASATNTSGYQAGVIGVEQLLAVVP
Sbjct: 1   MNTSTSSSAMPSDEGAMPLLPRIVVLATGGTIAGAAASATNTSGYQAGVIGVEQLLAVVP 60

Query: 61  ALSTVARMEREQIASVDSKDMAMPLWTTLAQRINTLLADDEIDGVVVTHGTDTLEETAYL 120
           ALSTVARMEREQIASVDSKDMAMPLWTTLAQRINTLLADDEIDGVVVTHGTDTLEETAYL
Sbjct: 61  ALSTVARMEREQIASVDSKDMAMPLWTTLAQRINTLLADDEIDGVVVTHGTDTLEETAYL 120

Query: 121 LHLTIKSDKPVVLTAAMRPASALSADGPLNLLNAVTVAAQASARGQGVLVAFNNRIHSAR 180
           LHLTIKSDKPVVLTAAMRPASALSADGPLNLLNAVTVAAQASARGQGVLVAFNNRIHSAR
Sbjct: 121 LHLTIKSDKPVVLTAAMRPASALSADGPLNLLNAVTVAAQASARGQGVLVAFNNRIHSAR 180

Query: 181 DVVKTSTYAVDAFHSPEIGALGWVQDGRVEFQRGVVRPHTLATEFVIGAQWPHVEIVLSY 240
           DVVKTSTYAVDAFHSPEIGALGWVQDGRVEFQRGVVRPHTLATEFVIGAQWPHVEIVLSY
Sbjct: 181 DVVKTSTYAVDAFHSPEIGALGWVQDGRVEFQRGVVRPHTLATEFVIGAQWPHVEIVLSY 240

Query: 241 AGVSRIAVDALVAAGVRGIVVAGTGNGSIHASVQQALADAASQGVAVVRASRVGSGHVMR 300
           AGVSRIAVDALVAAGVRGIVVAGTGNGSIHASVQQALADAASQGVAVVRASRVGSGHVMR
Sbjct: 241 AGVSRIAVDALVAAGVRGIVVAGTGNGSIHASVQQALADAASQGVAVVRASRVGSGHVMR 300

Query: 301 NGAAADDALGFVSAGSLNPYKARVLLMLALAAGATGPMALQKIFDTY 347
           NGAAADDALGFVSAGSLNPYKARVLLMLALAAGATGPMALQKIFDTY
Sbjct: 301 NGAAADDALGFVSAGSLNPYKARVLLMLALAAGATGPMALQKIFDTY 347


Lambda     K      H
   0.317    0.129    0.360 

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: 478
Number of extensions: 6
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: 347
Length of database: 347
Length adjustment: 29
Effective length of query: 318
Effective length of database: 318
Effective search space:   101124
Effective search space used:   101124
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: 49 (23.5 bits)

Align candidate BPHYT_RS08815 BPHYT_RS08815 (L-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.18443.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.1e-120  388.7   2.0   1.3e-120  388.5   2.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS08815  BPHYT_RS08815 L-asparaginase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS08815  BPHYT_RS08815 L-asparaginase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  388.5   2.0  1.3e-120  1.3e-120      23     352 .]      19     347 .]       3     347 .] 0.96

  Alignments for each domain:
  == domain 1  score: 388.5 bits;  conditional E-value: 1.3e-120
                                TIGR00520  23 sLPnikilatGGtiagkgqssastaeYkvgklgvedLieavPelkeianiegeqivnvgsqdlneevllk 92 
                                               LP+i +latGGtiag+++s ++t++Y++g++gve+L+  vP l+ +a++e eqi+ v+s+d+   ++ +
  lcl|FitnessBrowser__BFirm:BPHYT_RS08815  19 LLPRIVVLATGGTIAGAAASATNTSGYQAGVIGVEQLLAVVPALSTVARMEREQIASVDSKDMAMPLWTT 88 
                                              59******************************************************************** PP

                                TIGR00520  93 lakrisealasddvdGivithGtDtleetayfldltvksdkPvvlvGamRpatsvsaDGplnLYnavsva 162
                                              la+ri++ la+d++dG+v+thGtDtleetay l lt+ksdkPvvl  amRpa+++saDGplnL nav+va
  lcl|FitnessBrowser__BFirm:BPHYT_RS08815  89 LAQRINTLLADDEIDGVVVTHGTDTLEETAYLLHLTIKSDKPVVLTAAMRPASALSADGPLNLLNAVTVA 158
                                              ********************************************************************** PP

                                TIGR00520 163 adeksagrGvlvvlndrilsarevtktnttsldtfkseeqGalGyiandkieyerepvkkhtletefdvs 232
                                              a+  ++g+Gvlv++n+ri sar+v+kt+t ++d+f+s e GalG ++++ +e++r +v++htl tef + 
  lcl|FitnessBrowser__BFirm:BPHYT_RS08815 159 AQASARGQGVLVAFNNRIHSARDVVKTSTYAVDAFHSPEIGALGWVQDGRVEFQRGVVRPHTLATEFVIG 228
                                              *******************************************************************886 PP

                                TIGR00520 233 kldeplPkvdiiYayqnlpeelvkavvdagakGivlagvGnGslsaaalkvleeaakesvvivrssRvad 302
                                                  + P+v+i+ +y++++   v+a+v ag +Giv+ag+GnGs++a+++++l++aa ++v++vr+sRv +
  lcl|FitnessBrowser__BFirm:BPHYT_RS08815 229 A---QWPHVEIVLSYAGVSRIAVDALVAAGVRGIVVAGTGNGSIHASVQQALADAASQGVAVVRASRVGS 295
                                              4...479*************************************************************** PP

                                TIGR00520 303 Gvvtkdaevddk.ealiasgtLnPqkaRvLLqLaLtkt.kdlekiqevfeey 352
                                              G v ++ + +d   +++++g+LnP kaRvLL+LaL+ +  ++  +q++f+ y
  lcl|FitnessBrowser__BFirm:BPHYT_RS08815 296 GHVMRNGAAADDaLGFVSAGSLNPYKARVLLMLALAAGaTGPMALQKIFDTY 347
                                              ****9988766659*********************97615688999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (352 nodes)
Target sequences:                          1  (347 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: 8.66
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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