GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagA in Psychromonas ossibalaenae JAMM 0738

Align N-acetylglucosamine 6-phosphate deacetylase (NagA) (EC 3.5.1.25) (characterized)
to candidate WP_033298634.1 G327_RS0118820 N-acetylglucosamine-6-phosphate deacetylase

Query= CAZy::BAA22834.1
         (378 letters)



>NCBI__GCF_000381745.1:WP_033298634.1
          Length = 379

 Score =  308 bits (789), Expect = 2e-88
 Identities = 158/374 (42%), Positives = 232/374 (62%), Gaps = 4/374 (1%)

Query: 2   YALTNCKIYTGNDVLVKHAVIINGDKIEAVCPIESLPSEMNV-VDLNGANLSPGFIDLQL 60
           +ALTN  ++ G+ VL    ++I G  I++V P+ES+ S   + +   G   + GFIDLQL
Sbjct: 5   FALTNVDVFDGDKVLNNQVIVIEGQTIKSVAPMESVTSLPEIQIASPGLLATAGFIDLQL 64

Query: 61  NGCGGVMFNDEITAETIDIMHKANLKSGCTSFLPTLITSSDENMRQAIAAAREYQAKYPN 120
           NGCGGV+ N  I  +T+ +M+  NL SG T +LPTL+TSS  ++ +A+      +     
Sbjct: 65  NGCGGVLLNSAIEEKTLTVMNHTNLISGTTQYLPTLVTSSQADLCKAVELVEGLKNPEEQ 124

Query: 121 QSLGLHLEGPYLNVMKKGIHSVDFIRPSDDTMIDTICANSDVIAKVTLAPENNKPEHIEK 180
             LGLHLEGP++N  KKG H+  +IR  D    D +  +   +  +T+APE    E I K
Sbjct: 125 GILGLHLEGPFINKKKKGAHAQQYIRELDTAAADYLTEHKSAVKVLTVAPECVSQEVINK 184

Query: 181 LVKAGIVVSIGHTNATYSEARKSFESGITFATHLFNAMTPMVGREPGVVGAIYDTPEVYA 240
           L  AGI+VS+GHTNATY +     + GI  ATHL+NAMTP+  REPG VG + +    Y+
Sbjct: 185 LTSAGIIVSMGHTNATYEQLEN--KQGIVMATHLYNAMTPLTSREPGAVGYVLN-HRPYS 241

Query: 241 GIIADGFHVDYANIRIAHKIKGEKLVLVTDATAPAGAEMDYFIFVGKKVYYRDGKCVDEN 300
           GII DG H D+A +R+AH+  GE+L +VTDA  PAG ++  F   G   +   GKC   +
Sbjct: 242 GIIVDGIHSDFAAVRLAHEHLGERLFMVTDAVTPAGTDLTEFDMAGTAAFVSQGKCHFAD 301

Query: 301 GTLGGSALTMIEAVQNTVEHVGIALDEALRMATLYPAKAIGVDEKLGRIKKGMIANLTVF 360
           GT+ G+++TMI+ + N ++ VG++ +EALRMA+LYPA+A+ +  + GRIK G  AN+T+ 
Sbjct: 302 GTIAGASITMIKGIHNLIDKVGLSREEALRMASLYPAQAVNMAHQYGRIKAGYKANITLL 361

Query: 361 DRDFNVKATVVNGQ 374
           + D  V +    G+
Sbjct: 362 NADNEVNSVYQMGR 375


Lambda     K      H
   0.318    0.135    0.388 

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: 362
Number of extensions: 11
Number of successful extensions: 4
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: 379
Length adjustment: 30
Effective length of query: 348
Effective length of database: 349
Effective search space:   121452
Effective search space used:   121452
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_033298634.1 G327_RS0118820 (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.3446755.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-108  348.8   4.1   2.1e-108  348.6   4.1    1.0  1  NCBI__GCF_000381745.1:WP_033298634.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000381745.1:WP_033298634.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  348.6   4.1  2.1e-108  2.1e-108       4     373 ..       4     368 ..       1     374 [. 0.97

  Alignments for each domain:
  == domain 1  score: 348.6 bits;  conditional E-value: 2.1e-108
                             TIGR00221   4 slllkdkailtendvlddsavvindekikavvteaele..eeikeidlkgnvltpGliDvqlnGcgGvdtnda 74 
                                            ++l+++ ++ +  vl+++ +vi+++ ik+v + +     +ei +i  +g   t+G+iD+qlnGcgGv  n a
  NCBI__GCF_000381745.1:WP_033298634.1   4 AFALTNVDVFDGDKVLNNQVIVIEGQTIKSVAPMESVTslPEI-QIASPGLLATAGFIDLQLNGCGGVLLNSA 75 
                                           5799*****************************9999855565.578899999******************98 PP

                             TIGR00221  75 sv.etleimsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpke 146
                                              +tl +m++++  sG+t++Lptl+t ++ ++ kav+ +   ++ e++  iLGlhleGPf++ +kkGah ++
  NCBI__GCF_000381745.1:WP_033298634.1  76 IEeKTLTVMNHTNLISGTTQYLPTLVTSSQADLCKAVELVEGLKNPEEQ-GILGLHLEGPFINKKKKGAHAQQ 147
                                           7769*****************************************9999.9********************** PP

                             TIGR00221 147 yirepdvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathl 219
                                           yire d +   ++l+e    ++ +t+ap e +  e+i+kl+ agiivs+Ghtnatye+l++  k+Gi  athl
  NCBI__GCF_000381745.1:WP_033298634.1 148 YIRELDTAA-ADYLTEHKSAVKVLTVAP-ECVSQEVINKLTSAGIIVSMGHTNATYEQLEN--KQGIVMATHL 216
                                           ********9.******************.999***************************86..89******** PP

                             TIGR00221 220 ynamskldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaG 292
                                           ynam++l+ Repg++G vL++   +++ii+DG+h++++++rla+   g+ +l +vtD++++ag++l +f +aG
  NCBI__GCF_000381745.1:WP_033298634.1 217 YNAMTPLTSREPGAVGYVLNH-RPYSGIIVDGIHSDFAAVRLAHEHLGE-RLFMVTDAVTPAGTDLTEFDMAG 287
                                           *********************.889************************.*********************** PP

                             TIGR00221 293 kevyiredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLav 365
                                              ++ ++++  ++gt+aG+s+tmi+g++nl++ v++s ++++r++sl+pa+a+++ ++ G +++G+ an+++
  NCBI__GCF_000381745.1:WP_033298634.1 288 TAAFVSQGKCHFADGTIAGASITMIKGIHNLIDKVGLSREEALRMASLYPAQAVNMAHQYGRIKAGYKANITL 360
                                           ************************************************************************* PP

                             TIGR00221 366 ltkdfevi 373
                                           l+ d ev 
  NCBI__GCF_000381745.1:WP_033298634.1 361 LNADNEVN 368
                                           ****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (379 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: 16.04
//
[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:

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:

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:

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:

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