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.9616.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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 11.88
//
[ok]

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

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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