Alignments for a candidate for nagA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Burkholderia phytofirmans PsJN

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate BPHYT_RS02730 BPHYT_RS02730 N-acetylglucosamine-6-phosphate deacetylase

Query= reanno::BFirm:BPHYT_RS02730
         (367 letters)



>FitnessBrowser__BFirm:BPHYT_RS02730
          Length = 367

 Score =  728 bits (1880), Expect = 0.0
 Identities = 367/367 (100%), Positives = 367/367 (100%)

Query: 1   MLTGNILTTDGWIHGTLEYENGRITALTGERADPSTNDAPYILPGFIDLHVHGGGGSDVM 60
           MLTGNILTTDGWIHGTLEYENGRITALTGERADPSTNDAPYILPGFIDLHVHGGGGSDVM
Sbjct: 1   MLTGNILTTDGWIHGTLEYENGRITALTGERADPSTNDAPYILPGFIDLHVHGGGGSDVM 60

Query: 61  EGGSAIETITRTHARYGTTSLLATTMTAPRDELMAVVAELGNNARIRTPGGARVLGVHLE 120
           EGGSAIETITRTHARYGTTSLLATTMTAPRDELMAVVAELGNNARIRTPGGARVLGVHLE
Sbjct: 61  EGGSAIETITRTHARYGTTSLLATTMTAPRDELMAVVAELGNNARIRTPGGARVLGVHLE 120

Query: 121 GPYINPGKLGAQPDAAVSAVMDEVLKYLSIAPIRVVTLAPEIAGHMEIISEMAARGVRVQ 180
           GPYINPGKLGAQPDAAVSAVMDEVLKYLSIAPIRVVTLAPEIAGHMEIISEMAARGVRVQ
Sbjct: 121 GPYINPGKLGAQPDAAVSAVMDEVLKYLSIAPIRVVTLAPEIAGHMEIISEMAARGVRVQ 180

Query: 181 LGHSLGTYDDAVAALKHGACGFTHLFNAMSPLHHRNPGLVGAALAHAEFAEIIPDLLHVH 240
           LGHSLGTYDDAVAALKHGACGFTHLFNAMSPLHHRNPGLVGAALAHAEFAEIIPDLLHVH
Sbjct: 181 LGHSLGTYDDAVAALKHGACGFTHLFNAMSPLHHRNPGLVGAALAHAEFAEIIPDLLHVH 240

Query: 241 PGAIRAALRAIPRLYVVTDSTSATGMPDGEYRLGSQHVTKCLGGVRLADGTLAGSTLTMD 300
           PGAIRAALRAIPRLYVVTDSTSATGMPDGEYRLGSQHVTKCLGGVRLADGTLAGSTLTMD
Sbjct: 241 PGAIRAALRAIPRLYVVTDSTSATGMPDGEYRLGSQHVTKCLGGVRLADGTLAGSTLTMD 300

Query: 301 QALRNLVSIGLPIADVSNRLSRYAADYLGIEDRGRIARGAWADVVVFDRELALSATYVEG 360
           QALRNLVSIGLPIADVSNRLSRYAADYLGIEDRGRIARGAWADVVVFDRELALSATYVEG
Sbjct: 301 QALRNLVSIGLPIADVSNRLSRYAADYLGIEDRGRIARGAWADVVVFDRELALSATYVEG 360

Query: 361 EAIVEYA 367
           EAIVEYA
Sbjct: 361 EAIVEYA 367


Lambda     K      H
   0.319    0.136    0.399 

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: 615
Number of extensions: 23
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: 367
Length of database: 367
Length adjustment: 30
Effective length of query: 337
Effective length of database: 337
Effective search space:   113569
Effective search space used:   113569
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate BPHYT_RS02730 BPHYT_RS02730 (N-acetylglucosamine-6-phosphate deacetylase)
to HMM TIGR00221 (nagA: N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25))

# 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/TIGR00221.hmm
# target sequence database:        /tmp/gapView.31231.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00221  [M=380]
Accession:   TIGR00221
Description: nagA: N-acetylglucosamine-6-phosphate deacetylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
      5e-84  268.4   0.0    6.1e-84  268.1   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS02730  BPHYT_RS02730 N-acetylglucosamin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS02730  BPHYT_RS02730 N-acetylglucosamine-6-phosphate deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.1   0.0   6.1e-84   6.1e-84      50     379 ..      38     360 ..      22     361 .. 0.92

  Alignments for each domain:
  == domain 1  score: 268.1 bits;  conditional E-value: 6.1e-84
                                TIGR00221  50 kgnvltpGliDvqlnGcgGvdtndasvetleimsealaksGvtsfLptlitredeeikkavkvare..yl 117
                                              ++ +++pG+iD++++G+gG d+++   +++e + ++ a++G+ts L+t++t++ +e+   v    +   +
  lcl|FitnessBrowser__BFirm:BPHYT_RS02730  38 DAPYILPGFIDLHVHGGGGSDVMEGG-SAIETITRTHARYGTTSLLATTMTAPRDELMAVVAELGNnaRI 106
                                              5689******************9854.678888999********************99888766431034 PP

                                TIGR00221 118 akeknakiLGlhleGPflslekkGahpkeyirepdvellkkfldeagdvitkvtlapeekqtaeliskll 187
                                                  +a++LG+hleGP++++ k Ga+p   +     e+  k+l  a   i+ vtlape  +++e+is+++
  lcl|FitnessBrowser__BFirm:BPHYT_RS02730 107 RTPGGARVLGVHLEGPYINPGKLGAQPDAAVSAVMDEV-LKYLSIA--PIRVVTLAPEIAGHMEIISEMA 173
                                              44445********************************9.5666665..69******************** PP

                                TIGR00221 188 eagiivsaGhtnatyeelkeafkaGitfathlynamskldhRepgviGavLdeddvvteiiaDGlhihpk 257
                                                g+ v++Gh+  ty+ + +a k G+   thl+nams+l+hR+pg++Ga+L+++++ +eii D lh+hp 
  lcl|FitnessBrowser__BFirm:BPHYT_RS02730 174 ARGVRVQLGHSLGTYDDAVAALKHGACGFTHLFNAMSPLHHRNPGLVGAALAHAEF-AEIIPDLLHVHPG 242
                                              *****************************************************887.7************ PP

                                TIGR00221 258 nirlakklkgdsklvlvtDslaaagaklekfifaGkevyiredtlldkngtlaGssltmiegvknlvefv 327
                                              +ir a ++  + +l +vtDs++a g++++++  + ++v+   +++  ++gtlaGs+ltm ++++nlv  +
  lcl|FitnessBrowser__BFirm:BPHYT_RS02730 243 AIRAALRA--IPRLYVVTDSTSATGMPDGEYRLGSQHVTKCLGGVRLADGTLAGSTLTMDQALRNLVSIG 310
                                              ***98766..566*******************************************************99 PP

                                TIGR00221 328 eislsdvvrisslnparalgiddrlGsvakGkdanLavltkdfeviltiveg 379
                                               ++++dv +  s ++a  lgi+dr G +a+G  a+++v++++  +  t veg
  lcl|FitnessBrowser__BFirm:BPHYT_RS02730 311 -LPIADVSNRLSRYAADYLGIEDR-GRIARGAWADVVVFDRELALSATYVEG 360
                                              .***********************.************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (367 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: 8.07
//
[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