Alignments for a candidate for nagA in Gracilibacillus halophilus YIM-C55.5

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Gracilibacillus halophilus YIM-C55.5

Align N-acetylglucosamine 6-phosphate deacetylase (NagA;BSU35010) (EC 3.5.1.25) (characterized)
to candidate WP_003465246.1 J416_RS03840 N-acetylglucosamine-6-phosphate deacetylase

Query= CAZy::CAB15506.1
         (396 letters)



>NCBI__GCF_000359605.1:WP_003465246.1
          Length = 395

 Score =  386 bits (991), Expect = e-112
 Identities = 198/387 (51%), Positives = 264/387 (68%), Gaps = 5/387 (1%)

Query: 6   LIKDIAIVTENEVIKNGYVGINDGKISTVST----ERPKEPYSKEIQAPADSVLLPGMID 61
           +IKD+ I +E  + ++GY+ + DG I+ +      ++ K    + IQ    SVL+PGMID
Sbjct: 5   IIKDVTIYSETGIYQHGYIQVEDGIITAIGDVNQLDQEKSRTLQVIQPSYKSVLIPGMID 64

Query: 62  IHIHGGYGADTMDASFSTLDIMSSRLPEEGTTSFLATTITQEHGNISQALVNAREWKAAE 121
           +HIHG  GADTMDA+   +  M++ LP+EGTTSFLATT+TQE   I +ALVN   +   +
Sbjct: 65  VHIHGVAGADTMDATQEAIQTMATHLPKEGTTSFLATTMTQEEAAIEEALVNVSTYMR-D 123

Query: 122 ESSLLGAELLGIHLEGPFVSPKRAGAQPKEWIRPSDVELFKKWQQEAGGLIKIVTLAPEE 181
            SS   AE+LGIHLEGPF+S KRAGAQP E ++  D+E+F++WQQ A   I++VTLAPEE
Sbjct: 124 ASSNGTAEVLGIHLEGPFLSKKRAGAQPVEHMKQPDIEMFQRWQQLANYNIRLVTLAPEE 183

Query: 182 DQHFELIRHLKDESIIASMGHTDADSALLSDAAKAGASHMTHLYNAMSPFHHREPGVIGT 241
                LI+HL D  ++AS+GH+DA    +  A KAGA+H+THL+N M   HHREPGV G 
Sbjct: 184 QNGMHLIQHLNDSGVVASVGHSDATYEEVEQAVKAGATHVTHLFNGMRGLHHREPGVAGA 243

Query: 242 ALAHDGFVTELIADGIHSHPLAAKLAFLAKGSSKLILITDSMRAKGLKDGVYEFGGQSVT 301
           AL HD    E+IADGIH  P   K+A+  K S +++LI+D++RAK LK G Y+ GGQ V 
Sbjct: 244 ALLHDELFVEMIADGIHIRPEIVKIAYRQKTSDRVLLISDAIRAKCLKQGSYDLGGQDVQ 303

Query: 302 VRGRTALLSDGTLAGSILKMNEGARHMREFTNCSWTDIANITSENAAKQLGIFDRKGSVT 361
           V    A LSDGTLAGSILKM +   +M  FT+CS  D+  +T+ N AKQLG+ DRKGS+ 
Sbjct: 304 VGETRATLSDGTLAGSILKMKDAMHNMFTFTDCSMEDMIQMTASNPAKQLGVDDRKGSIA 363

Query: 362 VGKDADLVIVSSDCEVILTICRGNIAF 388
           VGKDADLV++    EV +T CRG +A+
Sbjct: 364 VGKDADLVLLDDTLEVEMTFCRGKLAY 390


Lambda     K      H
   0.316    0.132    0.377 

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: 443
Number of extensions: 17
Number of successful extensions: 3
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: 396
Length of database: 395
Length adjustment: 31
Effective length of query: 365
Effective length of database: 364
Effective search space:   132860
Effective search space used:   132860
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_003465246.1 J416_RS03840 (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.2275307.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.8e-129  415.8   5.4   9.5e-129  415.5   5.4    1.0  1  NCBI__GCF_000359605.1:WP_003465246.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000359605.1:WP_003465246.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.5   5.4  9.5e-129  9.5e-129       6     380 .]       5     387 ..       2     387 .. 0.96

  Alignments for each domain:
  == domain 1  score: 415.5 bits;  conditional E-value: 9.5e-129
                             TIGR00221   6 llkdkailtendvlddsavvindekikavvteaele....eeikeidlkg.nvltpGliDvqlnGcgGvdtnd 73 
                                           ++kd++i+ e  + + +++ ++d++i+a+  +++l+       + i+    +vl pG+iDv+++G+ G+dt+d
  NCBI__GCF_000359605.1:WP_003465246.1   5 IIKDVTIYSETGIYQHGYIQVEDGIITAIGDVNQLDqeksRTLQVIQPSYkSVLIPGMIDVHIHGVAGADTMD 77 
                                           799**************************99998885333445666655579********************* PP

                             TIGR00221  74 asvetleimsealaksGvtsfLptlitredeeikkavkvareylakekn...akiLGlhleGPflslekkGah 143
                                           a+ e+++ m  +l+k+G+tsfL+t++t+e+  i++a++++  y+    +   a++LG+hleGPfls +++Ga+
  NCBI__GCF_000359605.1:WP_003465246.1  78 ATQEAIQTMATHLPKEGTTSFLATTMTQEEAAIEEALVNVSTYMRDASSngtAEVLGIHLEGPFLSKKRAGAQ 150
                                           *******************************************987766689********************* PP

                             TIGR00221 144 pkeyirepdvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfa 216
                                           p+e++++pd+e+++ +++ a   i+ vtlapee++ + li++l + g+++s+Gh++atyee+++a+kaG+t++
  NCBI__GCF_000359605.1:WP_003465246.1 151 PVEHMKQPDIEMFQRWQQLANYNIRLVTLAPEEQNGMHLIQHLNDSGVVASVGHSDATYEEVEQAVKAGATHV 223
                                           ************************************************************************* PP

                             TIGR00221 217 thlynamskldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfi 289
                                           thl+n m  l+hRepgv+Ga+L +d++ +e+iaDG+hi p+ +++a + k + +++l+ D+++a+++k +++ 
  NCBI__GCF_000359605.1:WP_003465246.1 224 THLFNGMRGLHHREPGVAGAALLHDELFVEMIADGIHIRPEIVKIAYRQKTSDRVLLISDAIRAKCLKQGSYD 296
                                           ************************************************************************* PP

                             TIGR00221 290 faGkevyiredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdan 362
                                            +G++v + e ++  ++gtlaGs+l+m ++++n+  f+++s++d++++++ npa++lg+ddr+Gs+a+Gkda+
  NCBI__GCF_000359605.1:WP_003465246.1 297 LGGQDVQVGETRATLSDGTLAGSILKMKDAMHNMFTFTDCSMEDMIQMTASNPAKQLGVDDRKGSIAVGKDAD 369
                                           ************************************************************************* PP

                             TIGR00221 363 Lavltkdfeviltivegk 380
                                           L++l+   ev +t ++gk
  NCBI__GCF_000359605.1:WP_003465246.1 370 LVLLDDTLEVEMTFCRGK 387
                                           ****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (395 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 21.23
//
[ok]

This GapMind analysis is from Sep 24 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 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