Alignments for a candidate for nagA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Pseudomonas simiae WCS417

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate GFF4491 PS417_22985 N-acetylglucosamine-6-phosphate deacetylase

Query= reanno::WCS417:GFF4491
         (368 letters)



>FitnessBrowser__WCS417:GFF4491
          Length = 368

 Score =  739 bits (1907), Expect = 0.0
 Identities = 368/368 (100%), Positives = 368/368 (100%)

Query: 1   MSEDNILTPDGWIRGRLVHEHGKVIAIEGTPCDPAENDLPYLLPGFIDLHVHGGGGADIM 60
           MSEDNILTPDGWIRGRLVHEHGKVIAIEGTPCDPAENDLPYLLPGFIDLHVHGGGGADIM
Sbjct: 1   MSEDNILTPDGWIRGRLVHEHGKVIAIEGTPCDPAENDLPYLLPGFIDLHVHGGGGADIM 60

Query: 61  EGGAAFETITRTHVRFGTTSLLATTMTAPVEEISRVLGQLGTFCERRPAGSARVLGVHLE 120
           EGGAAFETITRTHVRFGTTSLLATTMTAPVEEISRVLGQLGTFCERRPAGSARVLGVHLE
Sbjct: 61  EGGAAFETITRTHVRFGTTSLLATTMTAPVEEISRVLGQLGTFCERRPAGSARVLGVHLE 120

Query: 121 GPYINPGKLGAQPNFAHTALMAEVEAYLRLAPIRVITIAPEIAGHDGLIRALSERGVRMQ 180
           GPYINPGKLGAQPNFAHTALMAEVEAYLRLAPIRVITIAPEIAGHDGLIRALSERGVRMQ
Sbjct: 121 GPYINPGKLGAQPNFAHTALMAEVEAYLRLAPIRVITIAPEIAGHDGLIRALSERGVRMQ 180

Query: 181 IGHTLGSYEEGVAALAAGATSFTHLYNAMSPLHHREPGIVGAALAHAKFAELIPDLLHVH 240
           IGHTLGSYEEGVAALAAGATSFTHLYNAMSPLHHREPGIVGAALAHAKFAELIPDLLHVH
Sbjct: 181 IGHTLGSYEEGVAALAAGATSFTHLYNAMSPLHHREPGIVGAALAHAKFAELIPDLLHVH 240

Query: 241 PGAMRVALRSIPCLYCVTDSTAAAGMPDGEYKLGSHTVTKCLGGVRLADGTLAGSTLTMD 300
           PGAMRVALRSIPCLYCVTDSTAAAGMPDGEYKLGSHTVTKCLGGVRLADGTLAGSTLTMD
Sbjct: 241 PGAMRVALRSIPCLYCVTDSTAAAGMPDGEYKLGSHTVTKCLGGVRLADGTLAGSTLTMD 300

Query: 301 QALRNLVKIGLPISEASQRLSQFPADYLGLEERGRLQPGSFADCVRLDRSLTLTDVMVEG 360
           QALRNLVKIGLPISEASQRLSQFPADYLGLEERGRLQPGSFADCVRLDRSLTLTDVMVEG
Sbjct: 301 QALRNLVKIGLPISEASQRLSQFPADYLGLEERGRLQPGSFADCVRLDRSLTLTDVMVEG 360

Query: 361 ETIDFKNA 368
           ETIDFKNA
Sbjct: 361 ETIDFKNA 368


Lambda     K      H
   0.320    0.138    0.411 

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: 721
Number of extensions: 16
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: 368
Length of database: 368
Length adjustment: 30
Effective length of query: 338
Effective length of database: 338
Effective search space:   114244
Effective search space used:   114244
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 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate GFF4491 PS417_22985 (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.18590.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    9.6e-77  244.4   0.0    1.2e-76  244.1   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF4491  PS417_22985 N-acetylglucosamine-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4491  PS417_22985 N-acetylglucosamine-6-phosphate deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.1   0.0   1.2e-76   1.2e-76      53     379 ..      41     360 ..      29     361 .. 0.94

  Alignments for each domain:
  == domain 1  score: 244.1 bits;  conditional E-value: 1.2e-76
                           TIGR00221  53 vltpGliDvqlnGcgGvdtnd..asvetleimsealaksGvtsfLptlitredeeikkavkvareylakekn..a 123
                                         +l+pG+iD++++G+gG+d+++  a++et+    ++  + G+ts L+t++t++ eei++ +     +  + ++  a
  lcl|FitnessBrowser__WCS417:GFF4491  41 YLLPGFIDLHVHGGGGADIMEggAAFETI---TRTHVRFGTTSLLATTMTAPVEEISRVLGQLGTFCERRPAgsA 112
                                         89******************965666776...5678899****************************9998777* PP

                           TIGR00221 124 kiLGlhleGPflslekkGahpkeyirepdvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGht 198
                                         ++LG+hleGP++++ k Ga+p ++ + + ++ ++ +l  a   i+ +t+ape  ++  li+ l e g+ +++Ght
  lcl|FitnessBrowser__WCS417:GFF4491 113 RVLGVHLEGPYINPGKLGAQP-NFAHTALMAEVEAYLRLA--PIRVITIAPEIAGHDGLIRALSERGVRMQIGHT 184
                                         *******************86.788888766669999987..59******************************* PP

                           TIGR00221 199 natyeelkeafkaGitfathlynamskldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvl 273
                                            yee  +a  aG+t  thlynams+l+hRepg++Ga+L+++ + +e+i D lh+hp ++r+a +   +  l  
  lcl|FitnessBrowser__WCS417:GFF4491 185 LGSYEEGVAALAAGATSFTHLYNAMSPLHHREPGIVGAALAHAKF-AELIPDLLHVHPGAMRVALR--SIPCLYC 256
                                         ******************************************775.8***************9865..5666*** PP

                           TIGR00221 274 vtDslaaagaklekfifaGkevyiredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgi 348
                                         vtDs+aaag++++++  + ++v+   +++  ++gtlaGs+ltm ++++nlv  + +++s++ +  s++pa  lg+
  lcl|FitnessBrowser__WCS417:GFF4491 257 VTDSTAAAGMPDGEYKLGSHTVTKCLGGVRLADGTLAGSTLTMDQALRNLVKIG-LPISEASQRLSQFPADYLGL 330
                                         ****************************************************99.******************** PP

                           TIGR00221 349 ddrlGsvakGkdanLavltkdfeviltiveg 379
                                         ++r G ++ G  a+ + l++   ++  +veg
  lcl|FitnessBrowser__WCS417:GFF4491 331 EER-GRLQPGSFADCVRLDRSLTLTDVMVEG 360
                                         ***.*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (368 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: 11.72
//
[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