Alignments for a candidate for nagA in Rhodobacter johrii JA192

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Rhodobacter johrii JA192

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate WP_069332780.1 C8J29_RS16310 N-acetylglucosamine-6-phosphate deacetylase

Query= reanno::MR1:202606
         (378 letters)



>NCBI__GCF_003046325.1:WP_069332780.1
          Length = 377

 Score =  226 bits (577), Expect = 6e-64
 Identities = 155/379 (40%), Positives = 204/379 (53%), Gaps = 19/379 (5%)

Query: 1   MKFTLIAEQLFDGESFHQDVPVTIEDGLIASF---DTALGAKEVRYTGTLVPGFIDVQVN 57
           M   L    LFDG  F +D  + + DG +A+      A G +  +  G L PG ID+QVN
Sbjct: 1   MSIVLRGATLFDGTGF-RDGDLLLGDGRVAAILPPGEAPGQRVEQVEGILAPGLIDLQVN 59

Query: 58  GGGGALFNTSPTVACIETIGKAHARFGTTGFLPTLITDNVQVMAKAADAVALAVAQKSAG 117
           G GG + + + T A    I  +    G    LPTL+TD       AA A  +A AQ++AG
Sbjct: 60  GSGGVMLDGTATAATFAHICASQEGLGVLHVLPTLVTDR-----PAAVARVIAAAQEAAG 114

Query: 118 ---VLGVHFEGPHLSVPKKGVHPQGFIREITEAELAIFCR--QDLGIRVVTLAPENVSPE 172
              +LG+H EGPH+   KKG H    +R + EA+LA++    + L   ++TL+P    PE
Sbjct: 115 TPGLLGLHLEGPHIDPAKKGAHDGDLVRPLEEADLALYLEAARSLPRLMLTLSPSAARPE 174

Query: 173 VIRLLVESGVKVCLGHSNADYDTVVAALKAGATGFTHLYNAMSPLGSREPGVVGAAIESE 232
            I  L  +G+ V LGH++   D    A  AGA   THL+NAMSPLG REPG+ GAA+ S 
Sbjct: 175 EIAALAAAGIVVSLGHTDCTMDEARRAFAAGAACVTHLFNAMSPLGHREPGLPGAALTSP 234

Query: 233 TAWCGLIVDGHHVHPAAARIALRAKPRGKMMLVTDAMPPVGMDDETSFELFGTQVLRVGD 292
               GLI DGHHV P   RIAL AKP G + LV+D M   G D +  FEL G ++LR   
Sbjct: 235 VP-TGLIADGHHVAPELIRIALAAKPEG-LFLVSDCMAVAGTDLD-GFELNGRRILRREG 291

Query: 293 RLNAVTGELAGCVLDMASAVHNTVNMLGLPLGEALRMAALYPAEFLGIADSVGRLAVGQR 352
           RL   +G LAG  L +  A+ N ++  G+    AL MA   PA  +G  D +G LA G  
Sbjct: 292 RLTLASGTLAGADLTLPQAIRNLLH-FGVSPERALAMATSTPARAIGRPD-LGCLAPGAP 349

Query: 353 ADLVLLDNQYQVLANYIAG 371
           ADLVLL       A + AG
Sbjct: 350 ADLVLLTPDLYPTALWRAG 368


Lambda     K      H
   0.321    0.137    0.400 

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: 408
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: 378
Length of database: 377
Length adjustment: 30
Effective length of query: 348
Effective length of database: 347
Effective search space:   120756
Effective search space used:   120756
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: 50 (23.9 bits)

Align candidate WP_069332780.1 C8J29_RS16310 (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.256310.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    4.9e-78  248.6   0.0    6.2e-78  248.3   0.0    1.0  1  NCBI__GCF_003046325.1:WP_069332780.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003046325.1:WP_069332780.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.3   0.0   6.2e-78   6.2e-78      20     370 ..      17     359 ..       3     363 .. 0.92

  Alignments for each domain:
  == domain 1  score: 248.3 bits;  conditional E-value: 6.2e-78
                             TIGR00221  20 ddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtndasv.etleimsealaksGv 91 
                                           +d+  ++ d+ + a+ +  e + + ++++    +l+pGliD+q+nG gGv+ + +++  t+  +    +  Gv
  NCBI__GCF_003046325.1:WP_069332780.1  17 RDGDLLLGDGRVAAILPPGEAP-G-QRVEQVEGILAPGLIDLQVNGSGGVMLDGTATaATFAHICASQEGLGV 87 
                                           5677778888888888877665.3.334444469*******************987779************** PP

                             TIGR00221  92 tsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyirepdvellkkfldeag 164
                                              Lptl+t     + + + +a+e+ +  ++  +LGlhleGP++ + kkGah  + +r+ + + l  +l++a 
  NCBI__GCF_003046325.1:WP_069332780.1  88 LHVLPTLVTDRPAAVARVIAAAQEAAGT-PG--LLGLHLEGPHIDPAKKGAHDGDLVRPLEEADLALYLEAAR 157
                                           *******************999998765.55..8************************998777788998888 PP

                             TIGR00221 165 dvitkv.tlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynamskldhRepgviGa 236
                                            + + + tl p      e i  l+ agi+vs+Ght+ t++e++ af aG++ +thl+nams+l hRepg+ Ga
  NCBI__GCF_003046325.1:WP_069332780.1 158 SLPRLMlTLSP-SAARPEEIAALAAAGIVVSLGHTDCTMDEARRAFAAGAACVTHLFNAMSPLGHREPGLPGA 229
                                           876654499**.7777788899*************************************************** PP

                             TIGR00221 237 vLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGkevyiredtlldkngtl 309
                                           +L +  v t++iaDG+h+ p++ir+a  +k +  l lv D +a ag++l+ f+ +G+ +  re++l  ++gtl
  NCBI__GCF_003046325.1:WP_069332780.1 230 ALTS-PVPTGLIADGHHVAPELIRIALAAKPE-GLFLVSDCMAVAGTDLDGFELNGRRILRREGRLTLASGTL 300
                                           ***9.9**************************.9*************************************** PP

                             TIGR00221 310 aGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkdf 370
                                           aG+ lt+ ++++nl+ f+ +s + ++ +++  para+g  d  G +a G  a+L++lt+d 
  NCBI__GCF_003046325.1:WP_069332780.1 301 AGADLTLPQAIRNLLHFG-VSPERALAMATSTPARAIGRPDL-GCLAPGAPADLVLLTPDL 359
                                           *****************9.*******************9997.****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (377 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: 16.25
//
[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