Alignments for a candidate for nagA in Caldicellulosiruptor kronotskyensis 2002

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Caldicellulosiruptor kronotskyensis 2002

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate WP_013429178.1 CALKRO_RS00520 N-acetylglucosamine-6-phosphate deacetylase

Query= BRENDA::Q8DN83
         (383 letters)



>NCBI__GCF_000166775.1:WP_013429178.1
          Length = 380

 Score =  199 bits (506), Expect = 1e-55
 Identities = 121/345 (35%), Positives = 184/345 (53%), Gaps = 8/345 (2%)

Query: 41  EVIDYTGYSIAPGLVDTHIHGYAGVDVMDNNIEGTLHTMSEGLLSTGVTSFLPTTLTATY 100
           E+ID   + ++PG VD H HG  GVD  D   E  L T+       GVT+ LPT ++A +
Sbjct: 42  EIIDRRDFILSPGFVDKHTHGIGGVDFFDTT-ENDLKTIQNYYFKHGVTTILPTIVSAPF 100

Query: 101 EQLLAVTENLGNHYKEAT-GAKIRGIYYEGPYFTETFKGAQNPTYMRDPGVEEFHSWQKA 159
           E +  +   +    K+      I GI+ EGP+     KGA +  +++ P VE+       
Sbjct: 101 ENIYKLARAIKEAKKDPNFKLNIPGIFLEGPFINPAKKGAHDERFLQMPTVEKLEELISN 160

Query: 160 ANGLLNKIALAPER-DGVEDFVRTVTGEGVTVALGHSNATFDEAKKAVDAGASVWVHAYN 218
               +  IALAPE  D    F+       + ++LGH+ ++F++A KA   GA   VH +N
Sbjct: 161 CEEKIIDIALAPELLDNPNKFISKAIEHKINISLGHTESSFEQAAKAHTLGAKNIVHLFN 220

Query: 219 GMRGLTHRELGMVGAMYQLPHTYAELICDGHHVDPKACEILIKQKGTENIALITDCMTAG 278
            M  L HR+   +     L     ELICD  H+ P+  ++  K KG ENI LI+D + A 
Sbjct: 221 AMPQLHHRQ-NSITTYALLNDIKVELICDLIHLSPEIIKLTYKLKGAENIILISDSIAAT 279

Query: 279 GLEDGDYMLGEFPVVVANGTARLKSTGNLAGSILKLKDGLKNVVEWGIANPHEAVMMASF 338
            L DG+Y LG   V V NG  +L + G +AGS L +   +KN+V+ GI    +A+M A++
Sbjct: 280 DLSDGEYSLGSLRVKVENGICKL-ADGTIAGSTLTIDKAVKNLVKIGI-RLEDALMAATY 337

Query: 339 NPAKSVHIDDVCGQIREGYDADFIVLDKDLELVATYLDGVKRYQA 383
           NP+K   ++  C  I+EG+ ADF+++D+DL +   Y+ G   Y+A
Sbjct: 338 NPSKLFSLE--CATIKEGFRADFVLMDEDLNVKEVYVGGELVYKA 380


Lambda     K      H
   0.317    0.137    0.410 

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: 449
Number of extensions: 27
Number of successful extensions: 7
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: 383
Length of database: 380
Length adjustment: 30
Effective length of query: 353
Effective length of database: 350
Effective search space:   123550
Effective search space used:   123550
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_013429178.1 CALKRO_RS00520 (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.2183621.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.6e-81  259.4   2.1    2.8e-81  259.3   2.1    1.0  1  NCBI__GCF_000166775.1:WP_013429178.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166775.1:WP_013429178.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  259.3   2.1   2.8e-81   2.8e-81      10     378 ..       8     373 ..       1     375 [. 0.94

  Alignments for each domain:
  == domain 1  score: 259.3 bits;  conditional E-value: 2.8e-81
                             TIGR00221  10 kailtendvlddsavvindekikavvteaele.eeikeidlkgnvltpGliDvqlnGcgGvdtndasvetlei 81 
                                           k+i+ ++ +++d+  v++d++i    t++  +  + + id +  +l+pG++D + +G+gGvd+ d++ + l+ 
  NCBI__GCF_000166775.1:WP_013429178.1   8 KKIFNGYSFIRDNVLVVEDGIILG--TQNGIDiGKDEIIDRRDFILSPGFVDKHTHGIGGVDFFDTTENDLKT 78 
                                           689*******************75..66666634456789999****************************** PP

                             TIGR00221  82 msealaksGvtsfLptlitredeeikkavkvareylakekn..akiLGlhleGPflslekkGahpkeyirepd 152
                                           +++   k+Gvt+ Lpt+++++ e+i k  ++++e++ k++n   +i G+ leGPf+++ kkGah + +++ p+
  NCBI__GCF_000166775.1:WP_013429178.1  79 IQNYYFKHGVTTILPTIVSAPFENIYKLARAIKEAK-KDPNfkLNIPGIFLEGPFINPAKKGAHDERFLQMPT 150
                                           ***************************999999987.4555457899************************** PP

                             TIGR00221 153 vellkkfldeagdvitkvtlapee.kqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynams 224
                                           ve l++++ +  + i  + lape+ +++ ++isk +e+ i++s+Ght+  +e++ +a   G+  + hl+nam+
  NCBI__GCF_000166775.1:WP_013429178.1 151 VEKLEELISNCEEKIIDIALAPELlDNPNKFISKAIEHKINISLGHTESSFEQAAKAHTLGAKNIVHLFNAMP 223
                                           **********************96378899******************************************* PP

                             TIGR00221 225 kldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGkevyi 297
                                           +l+hR+  +   +L + d+ +e+i D +h  p+ i+l+ klkg   ++l+ Ds+aa  ++++++  +   v +
  NCBI__GCF_000166775.1:WP_013429178.1 224 QLHHRQNSITTYALLN-DIKVELICDLIHLSPEIIKLTYKLKGAENIILISDSIAATDLSDGEYSLGSLRVKV 295
                                           *******999999998.******************************************************** PP

                             TIGR00221 298 redtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkdf 370
                                           +++ +  ++gt+aGs+lt+ ++vknlv  + i l+d++ ++++np++   ++    ++++G  a+ +++++d 
  NCBI__GCF_000166775.1:WP_013429178.1 296 ENGICKLADGTIAGSTLTIDKAVKNLVKIG-IRLEDALMAATYNPSKLFSLECA--TIKEGFRADFVLMDEDL 365
                                           ****************************99.********************987..***************** PP

                             TIGR00221 371 eviltive 378
                                           +v+   v 
  NCBI__GCF_000166775.1:WP_013429178.1 366 NVKEVYVG 373
                                           **987775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (380 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: 00:00:00.00
# Mc/sec: 14.78
//
[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