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.25366.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 8.30
//
[ok]

This GapMind analysis is from Sep 17 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