GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagA in Lactobacillus silagei IWT126

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate WP_054654192.1 CES79_RS04380 N-acetylglucosamine-6-phosphate deacetylase

Query= BRENDA::Q8Y8E8
         (377 letters)



>NCBI__GCF_002217945.1:WP_054654192.1
          Length = 381

 Score =  456 bits (1173), Expect = e-133
 Identities = 217/371 (58%), Positives = 273/371 (73%)

Query: 5   VITNATIYTGKGVLENAFVRFDKQILEVGSMADFQADKAEEVIDAKGQKLVPGFIDVHSH 64
           V+ +ATIYTG+ V+ + ++RFDK I  VG M+D+QA   ++V    G+ +VPGFIDVH+H
Sbjct: 4   VLKHATIYTGEEVISDGYIRFDKTIEAVGQMSDYQAQPNDDVKFVNGKVIVPGFIDVHTH 63

Query: 65  GGYSFDAMDADPEALRKQVNGMLNEGITTYFPTTMTQSHENIEKALKVINEVAQTEPVIG 124
           GGY FD+MD D + + K VN M+ EGITT FPTTMTQS++NI  A+  I E A+  PVI 
Sbjct: 64  GGYGFDSMDGDADQINKMVNHMVKEGITTVFPTTMTQSNDNIAHAMTGIKEAAKVNPVIK 123

Query: 125 GIHLEGPFVSKVFKGAQPEEYIQAPDLELFKKWFDISGGLIKLVTYAPEHDTSADFENLC 184
           G+HLEGPF++ ++KGAQPE+YI+ PD+ L   W  +SGGL+KL+TYAPE   S  FE+ C
Sbjct: 124 GVHLEGPFIAAIYKGAQPEKYIKDPDVSLLDHWNKLSGGLVKLITYAPEDKGSRVFEDYC 183

Query: 185 FELGVVPSIGHSNDVREHLKTSKATHATHLYNACHRMTHREPGVPGHVLLERGINAELIV 244
               +VPS+GHSN  R  +  S+ATH THLYNA     HREPGV GH +LE  + AELI 
Sbjct: 184 LSHNIVPSVGHSNATRAQMLASRATHVTHLYNAQREFKHREPGVTGHAMLEENMYAELIC 243

Query: 245 DGIHVHPDMVKLAYQMKGPEHLCIITDSMRAKGMPEGKSELGGQTVIVKDKQARLEDGTL 304
           DG H+ PDM+KLAY  KGP  + ++TDSMRAKGMPEG SELGGQ VIVKDKQARLE G L
Sbjct: 244 DGFHIVPDMIKLAYDQKGPHRIELVTDSMRAKGMPEGISELGGQKVIVKDKQARLETGNL 303

Query: 305 AGSVLTYDDGFRNMIKFTGCSVEEAVLMSSGNQAREFNLTQKGAIEAGKDADFNLLDEDL 364
           AGSVL YDD FRN++ FTGC +EEAVLM+S NQA EF LTQKG +  G DAD N+ D  L
Sbjct: 304 AGSVLRYDDAFRNVMAFTGCGIEEAVLMTSVNQAEEFGLTQKGKLLPGLDADLNVFDRTL 363

Query: 365 HITATYSFGKK 375
           ++  TYS+G++
Sbjct: 364 NLQTTYSYGRE 374


Lambda     K      H
   0.317    0.135    0.391 

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: 521
Number of extensions: 22
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: 381
Length adjustment: 30
Effective length of query: 347
Effective length of database: 351
Effective search space:   121797
Effective search space used:   121797
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_054654192.1 CES79_RS04380 (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.2017385.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    4.5e-93  298.1   0.8      5e-93  298.0   0.8    1.0  1  NCBI__GCF_002217945.1:WP_054654192.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002217945.1:WP_054654192.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.0   0.8     5e-93     5e-93       4     376 ..       2     369 ..       1     373 [. 0.96

  Alignments for each domain:
  == domain 1  score: 298.0 bits;  conditional E-value: 5e-93
                             TIGR00221   4 slllkdkailtendvlddsavvindekikavvteaele..eeikeidlkgnvltpGliDvqlnGcgGvdtnda 74 
                                           s +lk+ +i+t+++v+ d+++   d+ i+av   ++ +  ++ +   ++g v+ pG+iDv+ +G++G d +d 
  NCBI__GCF_002217945.1:WP_054654192.1   2 STVLKHATIYTGEEVISDGYIRF-DKTIEAVGQMSDYQaqPNDDVKFVNGKVIVPGFIDVHTHGGYGFDSMDG 73 
                                           57899***************876.899****77665554488888899************************* PP

                             TIGR00221  75 svetleimsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkey 147
                                             + +++m ++  k+G+t+  pt++t+++++i +a+  ++e+   ++   i G+hleGPf++   kGa+p++y
  NCBI__GCF_002217945.1:WP_054654192.1  74 DADQINKMVNHMVKEGITTVFPTTMTQSNDNIAHAMTGIKEAAKVNPV--IKGVHLEGPFIAAIYKGAQPEKY 144
                                           ****************************************98777776..99********************* PP

                             TIGR00221 148 irepdvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathly 220
                                           i++pdv ll ++ + +g++++ +t ape+k+ + +   +l ++i+ s+Gh+nat +++ ++    +t++thly
  NCBI__GCF_002217945.1:WP_054654192.1 145 IKDPDVSLLDHWNKLSGGLVKLITYAPEDKGSRVFEDYCLSHNIVPSVGHSNATRAQMLAS---RATHVTHLY 214
                                           *********************************************************9876...58******* PP

                             TIGR00221 221 namskldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGk 293
                                           na  +++hRepgv G ++ e+++++e+i DG hi p  i+la   kg  ++ lvtDs++a+g++ +  + +G+
  NCBI__GCF_002217945.1:WP_054654192.1 215 NAQREFKHREPGVTGHAMLEENMYAELICDGFHIVPDMIKLAYDQKGPHRIELVTDSMRAKGMPEGISELGGQ 287
                                           ************************************************************************* PP

                             TIGR00221 294 evyiredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavl 366
                                           +v ++++++  + g laGs+l+  ++ +n++ f+++ ++++v ++s n a   g+ ++ G +  G da+L+v+
  NCBI__GCF_002217945.1:WP_054654192.1 288 KVIVKDKQARLETGNLAGSVLRYDDAFRNVMAFTGCGIEEAVLMTSVNQAEEFGLTQK-GKLLPGLDADLNVF 359
                                           ********************************************************99.************** PP

                             TIGR00221 367 tkdfevilti 376
                                           ++  +++ t 
  NCBI__GCF_002217945.1:WP_054654192.1 360 DRTLNLQTTY 369
                                           *****99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (381 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: 00:00:00.00
# Mc/sec: 18.49
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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