Alignments for a candidate for nagA in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Pedobacter sp. GW460-11-11-14-LB5

Align N-acetylglucosamine 6-phosphate deacetylase (NagA) (EC 3.5.1.25) (characterized)
to candidate CA265_RS18930 CA265_RS18930 N-acetylglucosamine-6-phosphate deacetylase

Query= CAZy::BAA22834.1
         (378 letters)



>FitnessBrowser__Pedo557:CA265_RS18930
          Length = 363

 Score =  239 bits (609), Expect = 1e-67
 Identities = 136/372 (36%), Positives = 209/372 (56%), Gaps = 16/372 (4%)

Query: 4   LTNCKIYTGNDVLVKHAVIINGDKIEAVCPIESLPSEMNVVDLNGANLSPGFIDLQLNGC 63
           +TN   +  N++     ++I G  I  +   E+  +  ++         PGFIDLQ+ G 
Sbjct: 5   ITNTSYFQDNEIKSNQDILIEGSTISIINSSENKETSQSLT-------IPGFIDLQIYGA 57

Query: 64  GGVMFNDEITAETIDIMHKANLKSGCTSFLPTLITSSDENMRQAIAAAREYQAKYPNQSL 123
            G +F+ + T E++ IM    LK G T FL  + T+S E     I AA+E+++   N  L
Sbjct: 58  AGRLFSADPTVESLTIMEDDLLKKGTTGFLACMATNSSEVFNACIKAAKEHRSAAKN-CL 116

Query: 124 GLHLEGPYLNVMKKGIHSVDFIRPSD-DTMIDTICANSDVIAKVTLAPENNKPEHIEKLV 182
           GLHLEGP+LN  + G H   F+R +  D + + I     VI  +T+APE    E I+ L+
Sbjct: 117 GLHLEGPFLNPKRLGAHVPAFVRKASLDEIKELIDFGDGVIKMMTIAPEIQDDEVIQYLL 176

Query: 183 KAGIVVSIGHTNATYSEARKSFESGITFATHLFNAMTPMVGREPGVVGAIYDTPEVYAGI 242
             G+VVS+GH+NAT+ EA  ++  GI   THLFNAM+P+  REPG+  A+++  +  A I
Sbjct: 177 DHGVVVSLGHSNATFDEATAAYNKGIQTTTHLFNAMSPIHHREPGIPTAVFNHNKAMASI 236

Query: 243 IADGFHVDYANIRIAHKIKGEKLVLVTDATAPAGAEMDYFIFVGKKVYYRDGKCVDENGT 302
           IADG HVD+  ++ A K+  E+L L+TDA           +        ++ K V  +GT
Sbjct: 237 IADGQHVDFEVLKFAQKLLKERLFLITDAVTACSTGPYQHV-------EKENKYVMPDGT 289

Query: 303 LGGSALTMIEAVQNTVEHVGIALDEALRMATLYPAKAIGVDEKLGRIKKGMIANLTVFDR 362
           L GS++TM++AV+N V H  I+L + ++M TLYPA+ IG++     I  G  ANL V D 
Sbjct: 290 LSGSSITMLQAVKNCVTHCAISLSDGVKMGTLYPAQLIGIENLTATIATGHQANLLVLDD 349

Query: 363 DFNVKATVVNGQ 374
           + ++K  +  G+
Sbjct: 350 ELSLKEVIFRGE 361


Lambda     K      H
   0.318    0.135    0.388 

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: 326
Number of extensions: 11
Number of successful extensions: 4
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: 363
Length adjustment: 30
Effective length of query: 348
Effective length of database: 333
Effective search space:   115884
Effective search space used:   115884
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate CA265_RS18930 CA265_RS18930 (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.10663.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-97  313.0   2.5    1.6e-97  312.8   2.5    1.1  1  lcl|FitnessBrowser__Pedo557:CA265_RS18930  CA265_RS18930 N-acetylglucosamin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS18930  CA265_RS18930 N-acetylglucosamine-6-phosphate deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  312.8   2.5   1.6e-97   1.6e-97       6     379 ..       4     360 ..       1     361 [. 0.93

  Alignments for each domain:
  == domain 1  score: 312.8 bits;  conditional E-value: 1.6e-97
                                  TIGR00221   6 llkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtnd 73 
                                                ++++++ + +n++  ++ ++i++  i+ + +++++e+         +   pG+iD+q+ G+ G  +  
  lcl|FitnessBrowser__Pedo557:CA265_RS18930   4 VITNTSYFQDNEIKSNQDILIEGSTISIINSSENKET-------SQSLTIPGFIDLQIYGAAGRLFSA 64 
                                                578889999999999999***9999987766555543.......346678**************9975 PP

                                  TIGR00221  74 .asvetleimsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekk 140
                                                  +ve+l im++ l k+G+t+fL+ + t++ e  +  +k+a+e+ ++ kn   LGlhleGPfl++++ 
  lcl|FitnessBrowser__Pedo557:CA265_RS18930  65 dPTVESLTIMEDDLLKKGTTGFLACMATNSSEVFNACIKAAKEHRSAAKN--CLGLHLEGPFLNPKRL 130
                                                2778**********************************************..9*************** PP

                                  TIGR00221 141 GahpkeyirepdvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkea 208
                                                Gah + ++r+++ + +k+++d   +vi+++t+ap e q  e+i+ ll++g++vs+Gh+nat++e+++a
  lcl|FitnessBrowser__Pedo557:CA265_RS18930 131 GAHVPAFVRKASLDEIKELIDFGDGVIKMMTIAP-EIQDDEVIQYLLDHGVVVSLGHSNATFDEATAA 197
                                                *************999******************.88999**************************** PP

                                  TIGR00221 209 fkaGitfathlynamskldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtD 276
                                                +++Gi  +thl+nams+++hRepg+  av +++  ++ iiaDG h++++ ++ a+kl  + +l l+tD
  lcl|FitnessBrowser__Pedo557:CA265_RS18930 198 YNKGIQTTTHLFNAMSPIHHREPGIPTAVFNHNKAMASIIADGQHVDFEVLKFAQKLLKE-RLFLITD 264
                                                ******************************************************999888.8****** PP

                                  TIGR00221 277 slaaagaklekfifaGkevyiredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnpar 344
                                                +++a +  ++ ++ +      +e++ +  +gtl+Gss+tm+++vkn v ++ islsd v++ +l+pa+
  lcl|FitnessBrowser__Pedo557:CA265_RS18930 265 AVTACS--TGPYQHV-----EKENKYVMPDGTLSGSSITMLQAVKNCVTHCAISLSDGVKMGTLYPAQ 325
                                                **9854..4666554.....367888999*************************************** PP

                                  TIGR00221 345 algiddrlGsvakGkdanLavltkdfeviltiveg 379
                                                 +gi++   ++a+G++anL vl+ +  ++  i +g
  lcl|FitnessBrowser__Pedo557:CA265_RS18930 326 LIGIENLTATIATGHQANLLVLDDELSLKEVIFRG 360
                                                *****************************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (363 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.07
//
[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