Alignments for a candidate for nagA in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Shewanella sp. ANA-3

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate 7025964 Shewana3_3112 N-acetylglucosamine 6-phosphate deacetylase (RefSeq)

Query= reanno::ANA3:7025964
         (378 letters)



>FitnessBrowser__ANA3:7025964
          Length = 378

 Score =  742 bits (1916), Expect = 0.0
 Identities = 378/378 (100%), Positives = 378/378 (100%)

Query: 1   MKFTLIAEQLFDGEAFHRDVPVTIEDGLIASLDTASGAKEIRYPGTLVPGFIDVQVNGGG 60
           MKFTLIAEQLFDGEAFHRDVPVTIEDGLIASLDTASGAKEIRYPGTLVPGFIDVQVNGGG
Sbjct: 1   MKFTLIAEQLFDGEAFHRDVPVTIEDGLIASLDTASGAKEIRYPGTLVPGFIDVQVNGGG 60

Query: 61  GALFNSSPTVACIETIGKAHARFGTTGFLPTLITDDVQVMAKAADAVASAVAQKSAGVLG 120
           GALFNSSPTVACIETIGKAHARFGTTGFLPTLITDDVQVMAKAADAVASAVAQKSAGVLG
Sbjct: 61  GALFNSSPTVACIETIGKAHARFGTTGFLPTLITDDVQVMAKAADAVASAVAQKSAGVLG 120

Query: 121 VHFEGPHLSVPKKGVHPQGFIREITEAELAIFCRQDLGIRVVTLAPENVSPEVIRLLVES 180
           VHFEGPHLSVPKKGVHPQGFIREITEAELAIFCRQDLGIRVVTLAPENVSPEVIRLLVES
Sbjct: 121 VHFEGPHLSVPKKGVHPQGFIREITEAELAIFCRQDLGIRVVTLAPENVSPEVIRLLVES 180

Query: 181 GVKVCLGHSNADYDTVVAALAAGATGFTHLYNAMSPLGSREPGVVGAAIESETAWCGLIV 240
           GVKVCLGHSNADYDTVVAALAAGATGFTHLYNAMSPLGSREPGVVGAAIESETAWCGLIV
Sbjct: 181 GVKVCLGHSNADYDTVVAALAAGATGFTHLYNAMSPLGSREPGVVGAAIESETAWCGLIV 240

Query: 241 DGHHVHPAAARVALRAKPRGKVMLVTDAMPPVGMDDETSFELFGTQVLRVGDRLNAVTGE 300
           DGHHVHPAAARVALRAKPRGKVMLVTDAMPPVGMDDETSFELFGTQVLRVGDRLNAVTGE
Sbjct: 241 DGHHVHPAAARVALRAKPRGKVMLVTDAMPPVGMDDETSFELFGTQVLRVGDRLNAVTGE 300

Query: 301 LAGCVLDMATAVENSVKMLGLPLGEALRMASLYPAEFLGIAESVGRLAVGQRADLVLLDN 360
           LAGCVLDMATAVENSVKMLGLPLGEALRMASLYPAEFLGIAESVGRLAVGQRADLVLLDN
Sbjct: 301 LAGCVLDMATAVENSVKMLGLPLGEALRMASLYPAEFLGIAESVGRLAVGQRADLVLLDN 360

Query: 361 QYKVLANYIAGNAVYVRP 378
           QYKVLANYIAGNAVYVRP
Sbjct: 361 QYKVLANYIAGNAVYVRP 378


Lambda     K      H
   0.320    0.137    0.396 

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: 596
Number of extensions: 15
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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate 7025964 Shewana3_3112 (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.7684.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    1.3e-95  306.5   0.0    1.4e-95  306.4   0.0    1.0  1  lcl|FitnessBrowser__ANA3:7025964  Shewana3_3112 N-acetylglucosamin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7025964  Shewana3_3112 N-acetylglucosamine 6-phosphate deacetylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.4   0.0   1.4e-95   1.4e-95       5     380 .]       3     372 ..       1     372 [. 0.94

  Alignments for each domain:
  == domain 1  score: 306.4 bits;  conditional E-value: 1.4e-95
                         TIGR00221   5 lllkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtndasv.etle 80 
                                       + l+  +++ ++ + +d  v i+d++i ++ t      + kei  +g+ l pG+iDvq+nG+gG+ +n   +   +e
  lcl|FitnessBrowser__ANA3:7025964   3 FTLIAEQLFDGEAFHRDVPVTIEDGLIASLDTA----SGAKEIRYPGT-LVPGFIDVQVNGGGGALFNSSPTvACIE 74 
                                       5667778889999999***********998776....57789999985.89*****************96555**** PP

                         TIGR00221  81 imsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyirepdvellk 157
                                        + +a a+ G+t+fLptlit + + + ka  ++  ++a+ k+a +LG+h+eGP+ls+ kkG+hp+ +ire++ + l 
  lcl|FitnessBrowser__ANA3:7025964  75 TIGKAHARFGTTGFLPTLITDDVQVMAKAADAVASAVAQ-KSAGVLGVHFEGPHLSVPKKGVHPQGFIREITEAEL- 149
                                       ******************************999998876.566***************************986553. PP

                         TIGR00221 158 kfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynamskldhRepgvi 234
                                        + +     i+ vtlap e++  e+i+ l+e g+ v +Gh+na+y+++ +a  aG+t  thlynams+l  Repgv+
  lcl|FitnessBrowser__ANA3:7025964 150 AIFCRQDLGIRVVTLAP-ENVSPEVIRLLVESGVKVCLGHSNADYDTVVAALAAGATGFTHLYNAMSPLGSREPGVV 225
                                       566667777********.99********************************************************* PP

                         TIGR00221 235 GavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagakle.kfifaGkevyiredtlldkngtla 310
                                       Ga+++++   +++i+DG+h+hp+++r+a ++k   k++lvtD++ + g+++e +f+  G +v   +d+l    g la
  lcl|FitnessBrowser__ANA3:7025964 226 GAAIESETAWCGLIVDGHHVHPAAARVALRAKPRGKVMLVTDAMPPVGMDDEtSFELFGTQVLRVGDRLNAVTGELA 302
                                       *************************************************96538*********************** PP

                         TIGR00221 311 GssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkdfeviltivegk 380
                                       G +l m  +v n v   +++l +++r++sl+pa  lgi +  G +a+G+ a+L++l+++++v    + g+
  lcl|FitnessBrowser__ANA3:7025964 303 GCVLDMATAVENSVKMLGLPLGEALRMASLYPAEFLGIAESVGRLAVGQRADLVLLDNQYKVLANYIAGN 372
                                       **************************************************************98888775 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: 00:00:00.02
# Mc/sec: 6.35
//
[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