Alignments for a candidate for nagA in Moritella dasanensis ArB 0140

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Moritella dasanensis ArB 0140

Align N-acetylglucosamine 6-phosphate deacetylase (NagA) (EC 3.5.1.25) (characterized)
to candidate WP_017220790.1 A923_RS0106160 N-acetylglucosamine-6-phosphate deacetylase

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



>NCBI__GCF_000276805.1:WP_017220790.1
          Length = 378

 Score =  491 bits (1264), Expect = e-143
 Identities = 238/374 (63%), Positives = 296/374 (79%)

Query: 1   MYALTNCKIYTGNDVLVKHAVIINGDKIEAVCPIESLPSEMNVVDLNGANLSPGFIDLQL 60
           MYALTNC IYT + VL +H VI++G+ I  +  +   P+++  +DL GA+L+ GFIDLQL
Sbjct: 1   MYALTNCTIYTNDSVLTEHCVIVDGEYIHDLVSVADCPADIEKIDLAGASLTAGFIDLQL 60

Query: 61  NGCGGVMFNDEITAETIDIMHKANLKSGCTSFLPTLITSSDENMRQAIAAAREYQAKYPN 120
           NGCGGV+FN +I+ +T++IM + N + GCTS+LPT IT++D  M+ AI     Y AK+ N
Sbjct: 61  NGCGGVLFNTDISVKTLEIMQETNERFGCTSYLPTFITATDGAMKSAIETMAAYLAKHSN 120

Query: 121 QSLGLHLEGPYLNVMKKGIHSVDFIRPSDDTMIDTICANSDVIAKVTLAPENNKPEHIEK 180
           Q+LGLHLEGPYL+V KKGIHS D IR S+  MID I  NS VI+KVTLAPEN  P HI++
Sbjct: 121 QALGLHLEGPYLSVAKKGIHSSDLIRRSEQAMIDHISNNSAVISKVTLAPENTDPAHIKQ 180

Query: 181 LVKAGIVVSIGHTNATYSEARKSFESGITFATHLFNAMTPMVGREPGVVGAIYDTPEVYA 240
           LV A ++VS+GHTNATY+E  + F++G  FATHLFNAMT + GR+PGVVGAIYD  +VYA
Sbjct: 181 LVAADVLVSVGHTNATYTECMQGFDAGARFATHLFNAMTSITGRDPGVVGAIYDHQDVYA 240

Query: 241 GIIADGFHVDYANIRIAHKIKGEKLVLVTDATAPAGAEMDYFIFVGKKVYYRDGKCVDEN 300
           GII DG HVDYAN+R++HK+ GEKLVLVTDA APAGA+++ F FVG +V+YRDGKCV  +
Sbjct: 241 GIIVDGHHVDYANVRMSHKLMGEKLVLVTDAVAPAGADIESFDFVGTEVFYRDGKCVGAD 300

Query: 301 GTLGGSALTMIEAVQNTVEHVGIALDEALRMATLYPAKAIGVDEKLGRIKKGMIANLTVF 360
           GTLGGSALTMIEAV+NTV+HVG+ LDE LRMA LYPAKAIGVD+KLG I KG +ANLT F
Sbjct: 301 GTLGGSALTMIEAVENTVKHVGLPLDETLRMANLYPAKAIGVDDKLGSIAKGKVANLTAF 360

Query: 361 DRDFNVKATVVNGQ 374
           D DF V  T+VNGQ
Sbjct: 361 DADFTVIKTIVNGQ 374


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: 485
Number of extensions: 12
Number of successful extensions: 1
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: 378
Length adjustment: 30
Effective length of query: 348
Effective length of database: 348
Effective search space:   121104
Effective search space used:   121104
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_017220790.1 A923_RS0106160 (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.1371608.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-147  477.9   6.3   1.2e-147  477.7   6.3    1.0  1  NCBI__GCF_000276805.1:WP_017220790.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000276805.1:WP_017220790.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  477.7   6.3  1.2e-147  1.2e-147       4     380 .]       1     374 [.       1     374 [. 0.98

  Alignments for each domain:
  == domain 1  score: 477.7 bits;  conditional E-value: 1.2e-147
                             TIGR00221   4 slllkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtnd.as 75 
                                           +++l++++i+t+  vl ++ v++++e i+++v++a+ + +i++idl g+ lt+G+iD+qlnGcgGv +n   s
  NCBI__GCF_000276805.1:WP_017220790.1   1 MYALTNCTIYTNDSVLTEHCVIVDGEYIHDLVSVADCPADIEKIDLAGASLTAGFIDLQLNGCGGVLFNTdIS 73 
                                           69******************************************************************96489 PP

                             TIGR00221  76 vetleimsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyi 148
                                           v+tleim+e++++ G+ts+Lpt+it+ d+ +k+a++++ +ylak+ n ++LGlhleGP+ls+ kkG+h  + i
  NCBI__GCF_000276805.1:WP_017220790.1  74 VKTLEIMQETNERFGCTSYLPTFITATDGAMKSAIETMAAYLAKHSN-QALGLHLEGPYLSVAKKGIHSSDLI 145
                                           9**********************************************.************************* PP

                             TIGR00221 149 repdvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlyn 221
                                           r+++ ++  + + +++ vi+kvtlap e++    i++l+ a++ vs+Ghtnaty e  ++f aG+ fathl+n
  NCBI__GCF_000276805.1:WP_017220790.1 146 RRSEQAM-IDHISNNSAVISKVTLAP-ENTDPAHIKQLVAADVLVSVGHTNATYTECMQGFDAGARFATHLFN 216
                                           ******9.99****************.666677899************************************* PP

                             TIGR00221 222 amskldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGke 294
                                           am+ +++R+pgv+Ga+ d++dv+++ii+DG+h++++n+r+ +kl g+ klvlvtD++a+aga++e+f f+G e
  NCBI__GCF_000276805.1:WP_017220790.1 217 AMTSITGRDPGVVGAIYDHQDVYAGIIVDGHHVDYANVRMSHKLMGE-KLVLVTDAVAPAGADIESFDFVGTE 288
                                           ***********************************************.************************* PP

                             TIGR00221 295 vyiredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavlt 367
                                           v++r+++++ ++gtl Gs+ltmie+v n v +v+++l++ +r+++l+pa+a+g+dd+lGs+akGk+anL++++
  NCBI__GCF_000276805.1:WP_017220790.1 289 VFYRDGKCVGADGTLGGSALTMIEAVENTVKHVGLPLDETLRMANLYPAKAIGVDDKLGSIAKGKVANLTAFD 361
                                           ************************************************************************* PP

                             TIGR00221 368 kdfeviltivegk 380
                                            df vi+tiv+g+
  NCBI__GCF_000276805.1:WP_017220790.1 362 ADFTVIKTIVNGQ 374
                                           ***********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (378 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 19.27
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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