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.16844.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: 10.02
//
[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:

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:

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:

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:

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