Alignments for a candidate for nagA in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate WP_052304712.1 NPUN_RS26665 N-acetylglucosamine-6-phosphate deacetylase

Query= BRENDA::Q8Y5F6
         (377 letters)



>NCBI__GCF_000020025.1:WP_052304712.1
          Length = 406

 Score =  194 bits (493), Expect = 4e-54
 Identities = 116/357 (32%), Positives = 208/357 (58%), Gaps = 13/357 (3%)

Query: 10  YKENELIDAVVITEGNLIKEVCST-TPEKYSDEPTFDGNGRLLIPGMIDVHIHGAKNYDM 68
           YK+ +++   ++ E ++I+++    T E  S     +  G  +  G +D+ I+GA     
Sbjct: 19  YKDLQML---LVDEEDIIEQILPMGTVEARSRASLINVAGDWISLGGVDLQINGALGLAF 75

Query: 69  MDGSTES---IQAVSMACAETGCTSFLVTSVSSSLEDLIQMIRQTKKVIGKEK-GAKIAG 124
            D + E+   +Q +S      G   FL T V++S+E++ + +    +V+  +  GAKI G
Sbjct: 76  PDLTAENAHKLQEISQFLWNVGVDGFLPTLVTTSVENIQRSLAIIAEVLPNQPAGAKILG 135

Query: 125 IHLEGPYLNIEKKGMQNPAHLRHPDLKEMKKIFDEADGLIKMVTIAPELPGGIELIDFLK 184
           +HLEGP+LN++K+G     +L    +  +K++  +   ++K++T+APEL    E+I +L+
Sbjct: 136 VHLEGPFLNLQKRGAHPAEYLLPLTMDRVKRVLGDYAYIVKVITLAPELDFTGEVIPYLR 195

Query: 185 KRGVVVAIAHSNATYEEAQDAFEKGASHITHCFNAMPAIHHRAPGLVAAALENDSISVQA 244
             G+ V++ HS AT  +AQ AFE+GA+ +TH FNAMPA+HHR PGL+ AA+ +  +    
Sbjct: 196 SLGITVSLGHSQATSAQAQCAFEQGATMVTHAFNAMPALHHREPGLLGAAITHPDVMCGF 255

Query: 245 IVDGVHLHPGIVRLIHKIKGPDK-MVLTTDALQAMGVGDGEYIFGGHQVTVTEGVARLQD 303
           I DG H+ P +++++ +    +K + L +DAL  +G+ DG Y +   Q+ V  G ARL D
Sbjct: 256 IADGEHVSPMMLQILLRASYQEKGLFLVSDALSPLGLSDGVYPWDSRQIEVKNGTARLAD 315

Query: 304 GTLASSTVTMNKSLRLSNEFGI-NLQDTIQMATSTPADILGMKNLGRIEKGYSADLV 359
           GTL+ +T+ +   ++   ++GI +++  I +AT+ P   +G+     I K  SA+L+
Sbjct: 316 GTLSGTTLPLLVGVQNLVKWGICDVESAIALATNAPRKAIGLPG---IVKSQSANLL 369


Lambda     K      H
   0.317    0.134    0.380 

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: 361
Number of extensions: 13
Number of successful extensions: 2
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: 377
Length of database: 406
Length adjustment: 31
Effective length of query: 346
Effective length of database: 375
Effective search space:   129750
Effective search space used:   129750
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_052304712.1 NPUN_RS26665 (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.2351127.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    8.8e-83  264.3   0.0    1.2e-82  263.8   0.0    1.0  1  NCBI__GCF_000020025.1:WP_052304712.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000020025.1:WP_052304712.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.8   0.0   1.2e-82   1.2e-82      27     348 ..      29     357 ..      18     371 .. 0.93

  Alignments for each domain:
  == domain 1  score: 263.8 bits;  conditional E-value: 1.2e-82
                             TIGR00221  27 ndekikavvteaele..eeikeidlkgnvltpGliDvqlnGcgGvdtndasv...etleimsealaksGvtsf 94 
                                           ++++i+++ +    e       i++ g  ++ G +D+q+nG+ G  + d +      l+ +s+ l + Gv +f
  NCBI__GCF_000020025.1:WP_052304712.1  29 EEDIIEQILPMGTVEarSRASLINVAGDWISLGGVDLQINGALGLAFPDLTAenaHKLQEISQFLWNVGVDGF 101
                                           567999**999988844566789**************************77723355667777889******* PP

                             TIGR00221  95 Lptlitredeeikkavkvareylakekn.akiLGlhleGPflslekkGahpkeyirepdvellkkfldeagdv 166
                                           Lptl+t++ e+i++++ ++ e l ++++ akiLG+hleGPfl+l+k+Gahp ey+ + +++ +k  l + + +
  NCBI__GCF_000020025.1:WP_052304712.1 102 LPTLVTTSVENIQRSLAIIAEVLPNQPAgAKILGVHLEGPFLNLQKRGAHPAEYLLPLTMDRVKRVLGDYAYI 174
                                           **********************9888766******************************************** PP

                             TIGR00221 167 itkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynamskldhRepgviGavLd 239
                                           ++ +tlape++ t e+i+ l   gi vs+Gh++at+++++ af++G+t +th +nam+ l+hRepg++Ga++ 
  NCBI__GCF_000020025.1:WP_052304712.1 175 VKVITLAPELDFTGEVIPYLRSLGITVSLGHSQATSAQAQCAFEQGATMVTHAFNAMPALHHREPGLLGAAIT 247
                                           ************************************************************************* PP

                             TIGR00221 240 eddvvteiiaDGlhihpknirlakklkgdsk.lvlvtDslaaagaklekfifaGkevyiredtlldkngtlaG 311
                                           + dv+++ iaDG h+ p  ++++ ++  + k l lv D+l++ g++++++    +++ ++++t+  ++gtl+G
  NCBI__GCF_000020025.1:WP_052304712.1 248 HPDVMCGFIADGEHVSPMMLQILLRASYQEKgLFLVSDALSPLGLSDGVYPWDSRQIEVKNGTARLADGTLSG 320
                                           *******************99999987766659**************************************** PP

                             TIGR00221 312 ssltmiegvknlvefveislsdvvrisslnparalgi 348
                                           ++l ++ gv+nlv ++ + ++ ++ +++  p +a+g+
  NCBI__GCF_000020025.1:WP_052304712.1 321 TTLPLLVGVQNLVKWGICDVESAIALATNAPRKAIGL 357
                                           ***********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (406 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: 00:00:00.00
# Mc/sec: 25.00
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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