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.1164870.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 17.33
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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