Alignments for a candidate for nagA in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Shewanella loihica PV-4

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate 5208606 Shew_1117 N-acetylglucosamine-6-phosphate deacetylase (RefSeq)

Query= reanno::PV4:5208606
         (376 letters)



>FitnessBrowser__PV4:5208606
          Length = 376

 Score =  746 bits (1927), Expect = 0.0
 Identities = 376/376 (100%), Positives = 376/376 (100%)

Query: 1   MKQTLIAERVFDGEHFHHNQAITIEDGRIVSFDRASDVEPILLAGTLVPGFIDVQVNGGG 60
           MKQTLIAERVFDGEHFHHNQAITIEDGRIVSFDRASDVEPILLAGTLVPGFIDVQVNGGG
Sbjct: 1   MKQTLIAERVFDGEHFHHNQAITIEDGRIVSFDRASDVEPILLAGTLVPGFIDVQVNGGG 60

Query: 61  GALFNDAPSVEKIKTIGQAHARFGTTGFLPTLITDEIEVMRAAADAVAEALALNTPGVLG 120
           GALFNDAPSVEKIKTIGQAHARFGTTGFLPTLITDEIEVMRAAADAVAEALALNTPGVLG
Sbjct: 61  GALFNDAPSVEKIKTIGQAHARFGTTGFLPTLITDEIEVMRAAADAVAEALALNTPGVLG 120

Query: 121 IHFEGPHLSVPKKGVHPANYIRRISDEELAVFARNDLGTKVVTLAPENVAPEVIHALVEC 180
           IHFEGPHLSVPKKGVHPANYIRRISDEELAVFARNDLGTKVVTLAPENVAPEVIHALVEC
Sbjct: 121 IHFEGPHLSVPKKGVHPANYIRRISDEELAVFARNDLGTKVVTLAPENVAPEVIHALVEC 180

Query: 181 GVRVCLGHSNADYDTVIKALEAGATGFTHLFNAMSPMDSRAPGMVGAALESQDAWCGLIV 240
           GVRVCLGHSNADYDTVIKALEAGATGFTHLFNAMSPMDSRAPGMVGAALESQDAWCGLIV
Sbjct: 181 GVRVCLGHSNADYDTVIKALEAGATGFTHLFNAMSPMDSRAPGMVGAALESQDAWCGLIV 240

Query: 241 DGHHVHPASAKVAIAAKPRGKVMLVTDAMPPVGMDDNASFELFGTQVVRRGDRLNAVTGE 300
           DGHHVHPASAKVAIAAKPRGKVMLVTDAMPPVGMDDNASFELFGTQVVRRGDRLNAVTGE
Sbjct: 241 DGHHVHPASAKVAIAAKPRGKVMLVTDAMPPVGMDDNASFELFGTQVVRRGDRLNAVTGE 300

Query: 301 LAGCVLDMIGAVNNSVSMLGVAHEEALRMAARYPAEFIGHRQRGVFTIGARADMVLLGSD 360
           LAGCVLDMIGAVNNSVSMLGVAHEEALRMAARYPAEFIGHRQRGVFTIGARADMVLLGSD
Sbjct: 301 LAGCVLDMIGAVNNSVSMLGVAHEEALRMAARYPAEFIGHRQRGVFTIGARADMVLLGSD 360

Query: 361 NQVARTYIDGQLVYQA 376
           NQVARTYIDGQLVYQA
Sbjct: 361 NQVARTYIDGQLVYQA 376


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: 649
Number of extensions: 14
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: 376
Length of database: 376
Length adjustment: 30
Effective length of query: 346
Effective length of database: 346
Effective search space:   119716
Effective search space used:   119716
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 5208606 Shew_1117 (N-acetylglucosamine-6-phosphate deacetylase (RefSeq))
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.19732.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
    1.9e-94  302.6   0.0    2.2e-94  302.5   0.0    1.0  1  lcl|FitnessBrowser__PV4:5208606  Shew_1117 N-acetylglucosamine-6-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208606  Shew_1117 N-acetylglucosamine-6-phosphate deacetylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.5   0.0   2.2e-94   2.2e-94       6     379 ..       4     370 ..       1     371 [. 0.94

  Alignments for each domain:
  == domain 1  score: 302.5 bits;  conditional E-value: 2.2e-94
                        TIGR00221   6 llkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtnd.asvetleim 82 
                                       l+  +++ ++ + +++a+ i+d+ i +    +    +++ i l   +l pG+iDvq+nG+gG+ +nd  sve ++ +
  lcl|FitnessBrowser__PV4:5208606   4 TLIAERVFDGEHFHHNQAITIEDGRIVSFDRAS----DVEPILLA-GTLVPGFIDVQVNGGGGALFNDaPSVEKIKTI 76 
                                      57788999*****************98765554....45556555.5799******************4466****** PP

                        TIGR00221  83 sealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyirepdvellkkfl 160
                                       +a a+ G+t+fLptlit e+e ++ a  ++ e+la +    +LG+h+eGP+ls+ kkG+hp +yir+++ e l  f 
  lcl|FitnessBrowser__PV4:5208606  77 GQAHARFGTTGFLPTLITDEIEVMRAAADAVAEALALNTP-GVLGIHFEGPHLSVPKKGVHPANYIRRISDEELAVFA 153
                                      ************************************9988.9**************************9888767776 PP

                        TIGR00221 161 deagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynamskldhRepgviGavL 238
                                       +  +  + vtlap e++  e+i+ l+e g+ v +Gh+na+y+++++a +aG+t  thl+nams++d R pg++Ga+L
  lcl|FitnessBrowser__PV4:5208606 154 RNDLG-TKVVTLAP-ENVAPEVIHALVECGVRVCLGHSNADYDTVIKALEAGATGFTHLFNAMSPMDSRAPGMVGAAL 229
                                      66555.5899****.99************************************************************* PP

                        TIGR00221 239 deddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagak.lekfifaGkevyiredtlldkngtlaGsslt 315
                                      +++d  +++i+DG+h+hp+ +++a  +k   k++lvtD++ + g++   +f+  G +v  r+d+l    g laG +l 
  lcl|FitnessBrowser__PV4:5208606 230 ESQDAWCGLIVDGHHVHPASAKVAIAAKPRGKVMLVTDAMPPVGMDdNASFELFGTQVVRRGDRLNAVTGELAGCVLD 307
                                      ********************************************995679**************************** PP

                        TIGR00221 316 miegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkdfeviltiveg 379
                                      mi +v n v   +++ ++++r+++ +pa  +g  +r G  + G  a++++l +d +v +t ++g
  lcl|FitnessBrowser__PV4:5208606 308 MIGAVNNSVSMLGVAHEEALRMAARYPAEFIGHRQR-GVFTIGARADMVLLGSDNQVARTYIDG 370
                                      *********************************999.***********************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (376 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: 00:00:00.01
# Mc/sec: 9.78
//
[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