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-acetylgalactosamine-6-phosphate deacetylase; GalNAc-6-P deacetylase; N-acetylglucosamine-6-phosphate deacetylase; GlcNAc-6-P deacetylase; EC 3.5.1.-; EC 3.5.1.25 (characterized)
to candidate 7025546 Shewana3_2697 N-acetylglucosamine 6-phosphate deacetylase (RefSeq)

Query= SwissProt::A0KYQ5
         (394 letters)



>FitnessBrowser__ANA3:7025546
          Length = 394

 Score =  788 bits (2034), Expect = 0.0
 Identities = 394/394 (100%), Positives = 394/394 (100%)

Query: 1   MKPNTDFMLIADGAKVLTQGNLTEHCAIEVSDGIICGLKSTISAEWTADKPHYRLTSGTL 60
           MKPNTDFMLIADGAKVLTQGNLTEHCAIEVSDGIICGLKSTISAEWTADKPHYRLTSGTL
Sbjct: 1   MKPNTDFMLIADGAKVLTQGNLTEHCAIEVSDGIICGLKSTISAEWTADKPHYRLTSGTL 60

Query: 61  VAGFIDTQVNGGGGLMFNHVPTLETLRLMMQAHRQFGTTAMLPTVITDDIEVMQAAADAV 120
           VAGFIDTQVNGGGGLMFNHVPTLETLRLMMQAHRQFGTTAMLPTVITDDIEVMQAAADAV
Sbjct: 61  VAGFIDTQVNGGGGLMFNHVPTLETLRLMMQAHRQFGTTAMLPTVITDDIEVMQAAADAV 120

Query: 121 AEAIDCQVPGIIGIHFEGPHLSVAKRGCHPPAHLRGITEREWLLYLRQDLGVRLITLAPE 180
           AEAIDCQVPGIIGIHFEGPHLSVAKRGCHPPAHLRGITEREWLLYLRQDLGVRLITLAPE
Sbjct: 121 AEAIDCQVPGIIGIHFEGPHLSVAKRGCHPPAHLRGITEREWLLYLRQDLGVRLITLAPE 180

Query: 181 SVTPEQIKRLVASGAIISLGHSNADGETVLKAIEAGASGFTHLYNGMSALTSREPGMVGA 240
           SVTPEQIKRLVASGAIISLGHSNADGETVLKAIEAGASGFTHLYNGMSALTSREPGMVGA
Sbjct: 181 SVTPEQIKRLVASGAIISLGHSNADGETVLKAIEAGASGFTHLYNGMSALTSREPGMVGA 240

Query: 241 AFASENTYCGIILDGQHVHPISALAAWRAKGTEHLMLVTDAMSPLGSDQTEFQFFDGKVV 300
           AFASENTYCGIILDGQHVHPISALAAWRAKGTEHLMLVTDAMSPLGSDQTEFQFFDGKVV
Sbjct: 241 AFASENTYCGIILDGQHVHPISALAAWRAKGTEHLMLVTDAMSPLGSDQTEFQFFDGKVV 300

Query: 301 REGMTLRDQHGSLAGSVLDMASAVRYAATELNLGLSNAVQMATRTPAEFIQRPQLGDIAE 360
           REGMTLRDQHGSLAGSVLDMASAVRYAATELNLGLSNAVQMATRTPAEFIQRPQLGDIAE
Sbjct: 301 REGMTLRDQHGSLAGSVLDMASAVRYAATELNLGLSNAVQMATRTPAEFIQRPQLGDIAE 360

Query: 361 GKQADWVWLDDDQRVLAVWIAGELLYQAEQARFA 394
           GKQADWVWLDDDQRVLAVWIAGELLYQAEQARFA
Sbjct: 361 GKQADWVWLDDDQRVLAVWIAGELLYQAEQARFA 394


Lambda     K      H
   0.320    0.134    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: 712
Number of extensions: 9
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: 394
Length of database: 394
Length adjustment: 31
Effective length of query: 363
Effective length of database: 363
Effective search space:   131769
Effective search space used:   131769
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 7025546 Shewana3_2697 (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.13726.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    5.2e-83  265.0   0.0    6.3e-83  264.7   0.0    1.0  1  lcl|FitnessBrowser__ANA3:7025546  Shewana3_2697 N-acetylglucosamin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7025546  Shewana3_2697 N-acetylglucosamine 6-phosphate deacetylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  264.7   0.0   6.3e-83   6.3e-83       6     378 ..       9     381 ..       5     383 .. 0.91

  Alignments for each domain:
  == domain 1  score: 264.7 bits;  conditional E-value: 6.3e-83
                         TIGR00221   6 llkd.kailtendvlddsavvindekikavvteaele..eeikeidlkgnvltpGliDvqlnGcgGvdtndasv.et 78 
                                       l+ d  ++lt+ +  +  a+ + d++i  + ++   e   +  +  l + +l +G+iD q+nG+gG ++n   + et
  lcl|FitnessBrowser__ANA3:7025546   9 LIADgAKVLTQGNLTEHCAIEVSDGIICGLKSTISAEwtADKPHYRLTSGTLVAGFIDTQVNGGGGLMFNHVPTlET 85 
                                       444415799******************98876544443277777889999*********************7666** PP

                         TIGR00221  79 leimsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyirepdvel 155
                                       l  m +a  + G+t+ Lpt+it ++e ++ a  ++ e++  +    i+G+h+eGP+ls+ k+G hp+ ++r ++   
  lcl|FitnessBrowser__ANA3:7025546  86 LRLMMQAHRQFGTTAMLPTVITDDIEVMQAAADAVAEAIDCQVP-GIIGIHFEGPHLSVAKRGCHPPAHLRGITERE 161
                                       ***************************************99988.8**************************98766 PP

                         TIGR00221 156 lkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynamskldhRepg 232
                                          +l +  + ++ +tlap e++t e i++l+  g i+s+Gh+na+ e++ +a++aG++  thlyn ms l+ Repg
  lcl|FitnessBrowser__ANA3:7025546 162 WLLYLRQDLG-VRLITLAP-ESVTPEQIKRLVASGAIISLGHSNADGETVLKAIEAGASGFTHLYNGMSALTSREPG 236
                                       5556655555.689*****.999****************************************************** PP

                         TIGR00221 233 viGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGkevyiredtlldkngtl 309
                                       ++Ga+ ++++ +++ii DG h+hp  ++ a ++kg   l+lvtD++++ g +  +f+f   +v  ++ tl d++g l
  lcl|FitnessBrowser__ANA3:7025546 237 MVGAAFASENTYCGIILDGQHVHPISALAAWRAKGTEHLMLVTDAMSPLGSDQTEFQFFDGKVVREGMTLRDQHGSL 313
                                       *****************************************************9999988888777888888***** PP

                         TIGR00221 310 aGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkdfeviltive 378
                                       aGs+l m  +v+ +    ++ ls++v++++  pa  +    +lG +a+Gk+a+ + l+ d +v    + 
  lcl|FitnessBrowser__ANA3:7025546 314 AGSVLDMASAVRYAATELNLGLSNAVQMATRTPAEFIQR-PQLGDIAEGKQADWVWLDDDQRVLAVWIA 381
                                       **************99999*****************985.567*****************999876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (394 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: 9.39
//
[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