Alignments for a candidate for nagA in Synechococcus elongatus PCC 7942

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Synechococcus elongatus PCC 7942

Align N-acetylglucosamine-6-phosphate deacetylase; GlcNAc 6-P deacetylase; Amidohydrolase domain-containing protein 2; EC 3.5.1.25 (characterized)
to candidate Synpcc7942_0440 Synpcc7942_0440 N-acetylglucosamine 6-phosphate deacetylase

Query= SwissProt::Q9Y303
         (409 letters)



>FitnessBrowser__SynE:Synpcc7942_0440
          Length = 375

 Score =  193 bits (491), Expect = 6e-54
 Identities = 129/353 (36%), Positives = 192/353 (54%), Gaps = 20/353 (5%)

Query: 57  DCGGRILAPGFIDVQINGGFGVDFSQATEDVGSGVALVARRILSHGVTSFCPTLVTSPPE 116
           D  G  L+ G ID+QING  G+ F +      + +  + RR+   GV +F PTLVTS   
Sbjct: 23  DLQGDWLSLGGIDLQINGALGLAFPEVQASDRNRLLAICRRLWEQGVDAFTPTLVTSSIA 82

Query: 117 VYHKVVPQIP---VKSGGPHGAGVLGLHLEGPFISREKRGAHPEAHLRSFEADAFQDLLA 173
            + + +  I     +   P  A +LGLHLEGP ++  KRGAHP+ HL+    +   ++  
Sbjct: 83  QFRQAIEAIADFVAQPLPPRHAKILGLHLEGPCLAESKRGAHPQEHLQPLTVEVLSEICG 142

Query: 174 TYGPLDNVRIVTLAPELGRSHEVIRALTARGICVSLGHSVADLRAAEDAVWSGATFITHL 233
            +  L  +RIVTLAPEL  + E I  L  +G+ VSLGHS A    A+ A   GAT +TH 
Sbjct: 143 DH--LAQIRIVTLAPELDPTGEAIAWLRQQGVIVSLGHSQATAEQAQVAFQQGATMVTHA 200

Query: 234 FNAMLPFHHRDPGIVG-LLTSDRLPAGRCIFYGMIADGTHTNPAALRIAHRA--HPQGLV 290
           FNAM P HHR PG++G  LT+D       +F G+IADG H +P  L++  RA    + L 
Sbjct: 201 FNAMPPLHHRQPGLLGAALTTD------TVFAGLIADGQHIDPIMLKLLLRAGEGDRRLF 254

Query: 291 LVTDAIPALGLGNGRHTLGQQEVEVDGLTAYVAGTKTLSGSIAPMDVCVRHFLQATGCSM 350
           LV+DA+  LGL +G++   ++++ V   T  +    TL+G+  P+   V++ ++   C  
Sbjct: 255 LVSDALAPLGLPDGQYPWDERQITVTAGTCRLE-DGTLAGTTLPLLAGVQNLVRWQVCEP 313

Query: 351 ESALEAASLHPAQLLGLEKSKGTLDFGADADFVVLDDSLHVQATYISGELVWQ 403
           E+A+  A+L P + LG++ S   L + +     +L    H   T   GEL WQ
Sbjct: 314 ETAIMLATLAPLRALGVDWSDPRLLYLSRPVCQLL--RWHQSDT---GELTWQ 361


Lambda     K      H
   0.322    0.139    0.422 

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: 452
Number of extensions: 27
Number of successful extensions: 6
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: 409
Length of database: 375
Length adjustment: 31
Effective length of query: 378
Effective length of database: 344
Effective search space:   130032
Effective search space used:   130032
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate Synpcc7942_0440 Synpcc7942_0440 (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.32423.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.3e-82  263.7   0.0    1.7e-82  263.3   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_0440  Synpcc7942_0440 N-acetylglucosam


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_0440  Synpcc7942_0440 N-acetylglucosamine 6-phosphate deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.3   0.0   1.7e-82   1.7e-82      38     349 ..      12     331 ..       3     335 .. 0.95

  Alignments for each domain:
  == domain 1  score: 263.3 bits;  conditional E-value: 1.7e-82
                                 TIGR00221  38 aele.eeikeidlkgnvltpGliDvqlnGcgGvdtnd.asv..etleimsealaksGvtsfLptlitre 102
                                               ++l+ ++ ++idl+g  l+ G iD+q+nG+ G  + + +++  + l  + ++l ++Gv +f ptl+t +
  lcl|FitnessBrowser__SynE:Synpcc7942_0440  12 DRLPpPQLRMIDLQGDWLSLGGIDLQINGALGLAFPEvQASdrNRLLAICRRLWEQGVDAFTPTLVTSS 80 
                                               55554899***************************9864545889************************ PP

                                 TIGR00221 103 deeikkavkvareylakekn...akiLGlhleGPflslekkGahpkeyirepdvellkkfldeagdvit 168
                                               + + ++a++++ +++a+      akiLGlhleGP l+  k+Gahp+e++++ +ve+l ++  +    i+
  lcl|FitnessBrowser__SynE:Synpcc7942_0440  81 IAQFRQAIEAIADFVAQPLPprhAKILGLHLEGPCLAESKRGAHPQEHLQPLTVEVLSEICGDHLAQIR 149
                                               ****************9754456*********************************9999999999*** PP

                                 TIGR00221 169 kvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynamskldhRepgviGav 237
                                               +vtlape+++t e i  l ++g+ivs+Gh++at e+++ af++G+t +th +nam++l+hR+pg++Ga+
  lcl|FitnessBrowser__SynE:Synpcc7942_0440 150 IVTLAPELDPTGEAIAWLRQQGVIVSLGHSQATAEQAQVAFQQGATMVTHAFNAMPPLHHRQPGLLGAA 218
                                               ********************************************************************* PP

                                 TIGR00221 238 LdeddvvteiiaDGlhihpknirlakkl.kgdsklvlvtDslaaagaklekfifaGkevyiredtlldk 305
                                               L  d v +++iaDG hi+p  ++l+ ++  gd +l lv D+la+ g++++++    +++++  +t+  +
  lcl|FitnessBrowser__SynE:Synpcc7942_0440 219 LTTDTVFAGLIADGQHIDPIMLKLLLRAgEGDRRLFLVSDALAPLGLPDGQYPWDERQITVTAGTCRLE 287
                                               **********************99877647999************************************ PP

                                 TIGR00221 306 ngtlaGssltmiegvknlvefveislsdvvrisslnparalgid 349
                                               +gtlaG++l ++ gv+nlv +  +  + ++ +++l p ralg+d
  lcl|FitnessBrowser__SynE:Synpcc7942_0440 288 DGTLAGTTLPLLAGVQNLVRWQVCEPETAIMLATLAPLRALGVD 331
                                               ******************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (375 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: 10.93
//
[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