GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagA in Bacteroides clarus YIT 12056

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate WP_009120426.1 BUB52_RS15205 N-acetylglucosamine-6-phosphate deacetylase

Query= BRENDA::Q8Y5F6
         (377 letters)



>NCBI__GCF_900129655.1:WP_009120426.1
          Length = 388

 Score =  185 bits (470), Expect = 2e-51
 Identities = 105/342 (30%), Positives = 187/342 (54%), Gaps = 20/342 (5%)

Query: 45  DGNGRLLIPGMIDVHIHGAKNYDMMDGSTESIQAVSMACAETGCTSFLVTSVSSSLEDLI 104
           D  G  ++PG + +H HG   +D  + + E+ +++  A    G TSF  T  SS  + L 
Sbjct: 46  DAKGMYIVPGFVCMHAHGGGGHDFNECTEEAFRSIIDAHLAHGATSFYPTISSSPFDKLH 105

Query: 105 QMIRQTKKVIGKEKGAKIAGIHLEGPYLNIEKKGMQNPAHLRHPDLKEMKKIFDEADGLI 164
           Q  +  ++++  E  + + G+H+EGPYLN +  G Q    ++  D +E +++ +    + 
Sbjct: 106 QAAKVCERLMA-EPDSPVLGLHIEGPYLNRKMAGEQFADQVKEIDEQEYRELVESTRCIC 164

Query: 165 KMVTIAPELPGGIELIDFLKKRGVVVAIAHSNATYEEAQDAFEKGASHITHCFNAMPAIH 224
           +    +PELPG +E   +L+++G++ A++H+ A Y+  + A+E G +H  H +NAMP  H
Sbjct: 165 RW-DASPELPGALEFASYLREKGILAAVSHTEAEYDGIRAAYEAGFTHAAHFYNAMPGFH 223

Query: 225 HRA----PGLVAAALENDSISVQAIVDGVHLHPGIVRLIHKIKGPDKMVLTTDAL----- 275
            R      G V +    D ++++ I DG+HL   I++L +K+KG +   L TDAL     
Sbjct: 224 KRREYKYEGTVESVYLTDGMTIELIADGIHLPSTILKLAYKLKGVEHTCLVTDALSCAAT 283

Query: 276 QAMGVGDGEYIFGGHQVTVTEGVARLQD-GTLASSTVTMNKSLRLSNEFGINLQDTIQMA 334
           +   + D  YI       + +GV +L D  +LA S  TM+  +R   + GI L D ++MA
Sbjct: 284 EGKEINDPRYI-------IEDGVCKLADRSSLAGSIATMDVLVRTMAKAGIPLGDALRMA 336

Query: 335 TSTPADILGM-KNLGRIEKGYSADLVLLDKKFEVLSTWINGE 375
           + TPA I+G+    G ++K   AD++++DK+  + + W  G+
Sbjct: 337 SETPARIMGVYDRKGSLQKDKDADILIMDKELNIRAVWQAGK 378


Lambda     K      H
   0.317    0.134    0.380 

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: 388
Number of extensions: 22
Number of successful extensions: 6
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: 388
Length adjustment: 30
Effective length of query: 347
Effective length of database: 358
Effective search space:   124226
Effective search space used:   124226
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_009120426.1 BUB52_RS15205 (N-acetylglucosamine-6-phosphate deacetylase)
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.3137108.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    8.2e-80  254.5   0.0    9.1e-80  254.3   0.0    1.0  1  NCBI__GCF_900129655.1:WP_009120426.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900129655.1:WP_009120426.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.3   0.0   9.1e-80   9.1e-80       6     374 ..       4     372 ..       1     378 [. 0.92

  Alignments for each domain:
  == domain 1  score: 254.3 bits;  conditional E-value: 9.1e-80
                             TIGR00221   6 llkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtndasvet 78 
                                            +++ +i+t +  l+++ v+++d+ki +v+  +    + + id+kg ++ pG++ ++ +G+gG+d+n+++ e+
  NCBI__GCF_900129655.1:WP_009120426.1   4 QIINGRIFTPQGWLNEGSVLMRDGKILEVTNCDLALIGARLIDAKGMYIVPGFVCMHAHGGGGHDFNECTEEA 76 
                                           58899************************9999999************************************* PP

                             TIGR00221  79 leimsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyirep 151
                                           +  + +a   +G+tsf pt+ + + +++++a kv+   +a+ ++  +LGlh+eGP+l+ + +G +  + ++e+
  NCBI__GCF_900129655.1:WP_009120426.1  77 FRSIIDAHLAHGATSFYPTISSSPFDKLHQAAKVCERLMAEPDS-PVLGLHIEGPYLNRKMAGEQFADQVKEI 148
                                           ***99999***************************888877666.**************************** PP

                             TIGR00221 152 dvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynams 224
                                           d + ++++  e++  i +    pe+ +  e++s l e+gi + + ht+a+y+ +++a++aG t+a h+ynam+
  NCBI__GCF_900129655.1:WP_009120426.1 149 DEQEYREL-VESTRCICRWDASPELPGALEFASYLREKGILAAVSHTEAEYDGIRAAYEAGFTHAAHFYNAMP 220
                                           *9997776.57889*********************************************************** PP

                             TIGR00221 225 kld.hRep...gviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGk 293
                                            ++  Re    g + +v   d+++ e+iaDG+h   + ++la klkg    +lvtD+l+ a   +e  +++  
  NCBI__GCF_900129655.1:WP_009120426.1 221 GFHkRREYkyeGTVESVYLTDGMTIELIADGIHLPSTILKLAYKLKGVEHTCLVTDALSCA--ATEGKEINDP 291
                                           ***666752225666678899************************************9755..5555566766 PP

                             TIGR00221 294 evyiredtlld.kngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLav 365
                                              i+++ +   +   laGs+ tm   v+ +   + i+l d++r++s+ par++g+ dr+Gs++k kda++ +
  NCBI__GCF_900129655.1:WP_009120426.1 292 RYIIEDGVCKLaDRSSLAGSIATMDVLVRTMAKAG-IPLGDALRMASETPARIMGVYDRKGSLQKDKDADILI 363
                                           6667777776646789***************9988.************************************* PP

                             TIGR00221 366 ltkdfevil 374
                                           ++k+ ++  
  NCBI__GCF_900129655.1:WP_009120426.1 364 MDKELNIRA 372
                                           *****9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (388 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 27.02
//
[ok]

This GapMind analysis is from Sep 24 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