Alignments for a candidate for nagA in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Bacteroides thetaiotaomicron VPI-5482

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate 350204 BT0676 N-acetylglucosamine-6-phosphate deacetylase (NCBI ptt file)

Query= BRENDA::Q8Y8E8
         (377 letters)



>FitnessBrowser__Btheta:350204
          Length = 390

 Score =  183 bits (464), Expect = 8e-51
 Identities = 124/379 (32%), Positives = 199/379 (52%), Gaps = 14/379 (3%)

Query: 6   ITNATIYTGKGVLENAFVRF-DKQILEVGSMADFQADKAEEVIDAKGQKLVPGFIDVHSH 64
           I N  I T +G L++  V   D +ILEV + +D     A  VIDA+G  +VPGF+ +H+H
Sbjct: 5   IINGRILTPQGWLKDGSVLICDGKILEVTN-SDLAVIGAT-VIDARGMTIVPGFVSMHAH 62

Query: 65  GGYSFDAMDADPEALRKQVNGMLNEGITTYFPTTMTQSHENIEKALKVINE-VAQTEPVI 123
           GG   D  +A  EA R      L  G T  FPT  + S E I +A+ V  + + + E  I
Sbjct: 63  GGGGHDFTEATEEAFRIAATAHLKHGATGIFPTLSSTSFERIYQAVDVCEKLMKEPESPI 122

Query: 124 GGIHLEGPFVSKVFKGAQPEEYIQAPDLELFKKWFDISGGLIKLVTYAPEHDTSADFENL 183
            G+H+EGP+++    G+Q + +++ PD   +    + +   IK    +PE   + DF   
Sbjct: 123 LGLHIEGPYLNPKMAGSQYDGFLKTPDENEYVPLLEHT-SCIKRWDISPELHGAHDFAKY 181

Query: 184 CFELGVVPSIGHSNDVREHLKTSKA---THATHLYNAC----HRMTHREPGVPGHVLLER 236
               G++ ++ H+    + +K + A   +HA H YNA      R  ++  G    V L  
Sbjct: 182 TRSKGIMTAVTHTEAEYDEIKAAYAVGFSHAAHFYNAMPGFHKRREYKYEGTVESVYLTD 241

Query: 237 GINAELIVDGIHVHPDMVKLAYQMKGPEHLCIITDSMRAKGMPEGKSELGGQTVIVKDKQ 296
           G+  E+I DGIH+   ++KL Y++KG E+ C++TD++ A    EG   +  + +I     
Sbjct: 242 GMTVEVIADGIHLPATILKLVYKLKGVENTCLVTDAL-AYAANEGNEPIDPRYIIEDGVC 300

Query: 297 ARLEDGTLAGSVLTYDDGFRNMIKFTGCSVEEAVLMSSGNQAREFNLT-QKGAIEAGKDA 355
              +   LAGS+ T D   R M+K     +E+AV M+S   AR   ++ +KGA+  GKDA
Sbjct: 301 KMADHSALAGSLATMDVLVRTMVKKASIPLEDAVRMASETPARLIGVSDRKGALSKGKDA 360

Query: 356 DFNLLDEDLHITATYSFGK 374
           D  +LD++L++   +S GK
Sbjct: 361 DIVILDKELNVRCVWSMGK 379


Lambda     K      H
   0.317    0.135    0.391 

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: 396
Number of extensions: 19
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: 377
Length of database: 390
Length adjustment: 30
Effective length of query: 347
Effective length of database: 360
Effective search space:   124920
Effective search space used:   124920
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 350204 BT0676 (N-acetylglucosamine-6-phosphate deacetylase (NCBI ptt file))
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.12726.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    2.5e-84  269.4   0.1    2.8e-84  269.2   0.1    1.0  1  lcl|FitnessBrowser__Btheta:350204  BT0676 N-acetylglucosamine-6-pho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:350204  BT0676 N-acetylglucosamine-6-phosphate deacetylase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.2   0.1   2.8e-84   2.8e-84       6     373 ..       4     372 ..       1     379 [. 0.91

  Alignments for each domain:
  == domain 1  score: 269.2 bits;  conditional E-value: 2.8e-84
                          TIGR00221   6 llkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtndasvetlei 81 
                                         +++ +ilt +  l+d+ v+i d+ki +v+ ++    +   id++g ++ pG++ ++ +G+gG+d+ +a+ e++ i
  lcl|FitnessBrowser__Btheta:350204   4 QIINGRILTPQGWLKDGSVLICDGKILEVTNSDLAVIGATVIDARGMTIVPGFVSMHAHGGGGHDFTEATEEAFRI 79 
                                        58899****************************999**************************************** PP

                          TIGR00221  82 msealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyirepdvellk 157
                                           a  k+G+t+  ptl +++ e i +av v+ +   ke+++ iLGlh+eGP+l+++ +G +   +++ pd + ++
  lcl|FitnessBrowser__Btheta:350204  80 AATAHLKHGATGIFPTLSSTSFERIYQAVDVCEKL-MKEPESPILGLHIEGPYLNPKMAGSQYDGFLKTPDENEYV 154
                                        ******************************99665.566666*****************************99978 PP

                          TIGR00221 158 kfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynamskld.hRep. 231
                                         +l e +  i++  + pe+++  ++++    +gi+  + ht+a+y+e+k+a+ +G ++a h+ynam+ ++  Re  
  lcl|FitnessBrowser__Btheta:350204 155 PLL-EHTSCIKRWDISPELHGAHDFAKYTRSKGIMTAVTHTEAEYDEIKAAYAVGFSHAAHFYNAMPGFHkRREYk 229
                                        776.66789*************************************************************666752 PP

                          TIGR00221 232 ..gviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGkevyiredtlld. 304
                                          g + +v   d++++e+iaDG+h   + ++l  klkg    +lvtD+la a+ + ++ i   +  yi ed++ + 
  lcl|FitnessBrowser__Btheta:350204 230 yeGTVESVYLTDGMTVEVIADGIHLPATILKLVYKLKGVENTCLVTDALAYAANEGNEPI---DPRYIIEDGVCKm 302
                                        225666678899*************************************98877655544...3334444444443 PP

                          TIGR00221 305 .kngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkdfevi 373
                                         ++  laGs  tm   v+ +v  + i+l+d+vr++s+ par +g+ dr+G+++kGkda++++l+k+ +v 
  lcl|FitnessBrowser__Btheta:350204 303 aDHSALAGSLATMDVLVRTMVKKASIPLEDAVRMASETPARLIGVSDRKGALSKGKDADIVILDKELNVR 372
                                        47789**************************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (390 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: 00:00:00.01
# Mc/sec: 11.32
//
[ok]

This GapMind analysis is from Sep 17 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 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