Alignments for a candidate for nagA in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Shewanella amazonensis SB2B

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate 6936759 Sama_0946 N-acetylglucosamine-6-phosphate deacetylase (RefSeq)

Query= reanno::SB2B:6936759
         (377 letters)



>FitnessBrowser__SB2B:6936759
          Length = 377

 Score =  748 bits (1930), Expect = 0.0
 Identities = 377/377 (100%), Positives = 377/377 (100%)

Query: 1   MKTTLIAERLFDGEQFHHNVPLTVEDGQVLALDTVAGCAEVRLQGTLVPGFIDVQVNGGG 60
           MKTTLIAERLFDGEQFHHNVPLTVEDGQVLALDTVAGCAEVRLQGTLVPGFIDVQVNGGG
Sbjct: 1   MKTTLIAERLFDGEQFHHNVPLTVEDGQVLALDTVAGCAEVRLQGTLVPGFIDVQVNGGG 60

Query: 61  GVLFNDTPTVAAIEAIGAAHARFGTTGYLPTLITDKVETMARAADAAAEAIAKGSTGVLG 120
           GVLFNDTPTVAAIEAIGAAHARFGTTGYLPTLITDKVETMARAADAAAEAIAKGSTGVLG
Sbjct: 61  GVLFNDTPTVAAIEAIGAAHARFGTTGYLPTLITDKVETMARAADAAAEAIAKGSTGVLG 120

Query: 121 VHFEGPHLSVPKKGVHPESHIRRIGDRELEIFARQDLGLKVVTLAPENVSPEVICALVDV 180
           VHFEGPHLSVPKKGVHPESHIRRIGDRELEIFARQDLGLKVVTLAPENVSPEVICALVDV
Sbjct: 121 VHFEGPHLSVPKKGVHPESHIRRIGDRELEIFARQDLGLKVVTLAPENVSPEVICALVDV 180

Query: 181 GVKVCLGHSNADYATTVAALEAGATGFTHLYNAMSALTSREPGVVGAAIDSDEAWCGLIV 240
           GVKVCLGHSNADYATTVAALEAGATGFTHLYNAMSALTSREPGVVGAAIDSDEAWCGLIV
Sbjct: 181 GVKVCLGHSNADYATTVAALEAGATGFTHLYNAMSALTSREPGVVGAAIDSDEAWCGLIV 240

Query: 241 DGHHVHSAAARIAIKAKPRGKVMLVTDAMPPVGMDDNASFELFGIQVVRQGDKLNALTGE 300
           DGHHVHSAAARIAIKAKPRGKVMLVTDAMPPVGMDDNASFELFGIQVVRQGDKLNALTGE
Sbjct: 241 DGHHVHSAAARIAIKAKPRGKVMLVTDAMPPVGMDDNASFELFGIQVVRQGDKLNALTGE 300

Query: 301 LAGCVLDMAGAVQNTVDMLGLPQAEAIRMASLYPAAFLGIDNRVGTLSVGKQADMVLLDD 360
           LAGCVLDMAGAVQNTVDMLGLPQAEAIRMASLYPAAFLGIDNRVGTLSVGKQADMVLLDD
Sbjct: 301 LAGCVLDMAGAVQNTVDMLGLPQAEAIRMASLYPAAFLGIDNRVGTLSVGKQADMVLLDD 360

Query: 361 NGRCRGTWIGGRQVFGL 377
           NGRCRGTWIGGRQVFGL
Sbjct: 361 NGRCRGTWIGGRQVFGL 377


Lambda     K      H
   0.320    0.137    0.402 

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: 593
Number of extensions: 13
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: 377
Length of database: 377
Length adjustment: 30
Effective length of query: 347
Effective length of database: 347
Effective search space:   120409
Effective search space used:   120409
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 6936759 Sama_0946 (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.1825.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    3.6e-94  301.7   0.1    3.9e-94  301.6   0.1    1.0  1  lcl|FitnessBrowser__SB2B:6936759  Sama_0946 N-acetylglucosamine-6-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6936759  Sama_0946 N-acetylglucosamine-6-phosphate deacetylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  301.6   0.1   3.9e-94   3.9e-94      20     379 ..      18     371 ..       1     372 [. 0.90

  Alignments for each domain:
  == domain 1  score: 301.6 bits;  conditional E-value: 3.9e-94
                         TIGR00221  20 ddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtndasv.etleimsealaksGvtsfL 95 
                                       ++    ++d+++ a+ t+a    +  e+ l+g +l pG+iDvq+nG+gGv +nd+ +  ++e +  a a+ G+t++L
  lcl|FitnessBrowser__SB2B:6936759  18 HNVPLTVEDGQVLALDTVA----GCAEVRLQG-TLVPGFIDVQVNGGGGVLFNDTPTvAAIEAIGAAHARFGTTGYL 89 
                                       5555555555555555544....345566776.589******************6555******************* PP

                         TIGR00221  96 ptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyirep.dvellkkfldeagdvitkvt 171
                                       ptlit + e + +a  +a e++ak     +LG+h+eGP+ls+ kkG+hp+++ir++ d el + f  +  + ++ vt
  lcl|FitnessBrowser__SB2B:6936759  90 PTLITDKVETMARAADAAAEAIAKGST-GVLGVHFEGPHLSVPKKGVHPESHIRRIgDREL-EIFARQDLG-LKVVT 163
                                       ************************998.9*************************9845666.666666555.79*** PP

                         TIGR00221 172 lapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynamskldhRepgviGavLdeddvvteii 248
                                       lap e++  e+i  l++ g+ v +Gh+na+y++  +a +aG+t  thlynams l+ Repgv+Ga++d+d+  +++i
  lcl|FitnessBrowser__SB2B:6936759 164 LAP-ENVSPEVICALVDVGVKVCLGHSNADYATTVAALEAGATGFTHLYNAMSALTSREPGVVGAAIDSDEAWCGLI 239
                                       ***.99*********************************************************************** PP

                         TIGR00221 249 aDGlhihpknirlakklkgdsklvlvtDslaaagak.lekfifaGkevyiredtlldkngtlaGssltmiegvknlv 324
                                       +DG+h+h +++r+a k+k   k++lvtD++ + g++   +f+  G +v  ++d+l    g laG +l m  +v+n v
  lcl|FitnessBrowser__SB2B:6936759 240 VDGHHVHSAAARIAIKAKPRGKVMLVTDAMPPVGMDdNASFELFGIQVVRQGDKLNALTGELAGCVLDMAGAVQNTV 316
                                       **********************************995679************************************* PP

                         TIGR00221 325 efveislsdvvrisslnparalgiddrlGsvakGkdanLavltkdfeviltiveg 379
                                       +  +++ ++++r++sl+pa  lgid+r G++++Gk+a++++l+ + +  +t + g
  lcl|FitnessBrowser__SB2B:6936759 317 DMLGLPQAEAIRMASLYPAAFLGIDNRVGTLSVGKQADMVLLDDNGRCRGTWIGG 371
                                       ********************************************99998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (377 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 0.01s 00:00:00.01 Elapsed: 00:00:00.03
# Mc/sec: 3.98
//
[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:

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