Alignments for a candidate for nagA in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Halomonas desiderata SP1

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate WP_086511253.1 BZY95_RS17925 N-acetylglucosamine-6-phosphate deacetylase

Query= reanno::Caulo:CCNA_00452
         (378 letters)



>NCBI__GCF_002151265.1:WP_086511253.1
          Length = 377

 Score =  347 bits (890), Expect = e-100
 Identities = 194/372 (52%), Positives = 241/372 (64%), Gaps = 2/372 (0%)

Query: 6   INGRVLTESGVVEGKAVLVKDGLILDVIEAAQTPSDAKPR-DLKGGLLVPGFIDTQVNGG 64
           +NGRV     + +   V ++   I  ++ A +TP     R +L+G LL PGFID QVNGG
Sbjct: 1   MNGRVFDGERLRDDVHVAIEGETIQALLPADETPPAGAERCNLEGRLLAPGFIDLQVNGG 60

Query: 65  GGVLFNDAPTVETIATIGAAHRRFGTTGFLPTLISDDLRVVDQAMRATEEAIARGVPGVL 124
           GG LFN+AP+VETI  I  +HRR GTTG L TLISD   V+  A+ A  +A+ + +PG+L
Sbjct: 61  GGHLFNEAPSVETIQAIMTSHRRHGTTGLLVTLISDRREVMQAALNAARQALEQRLPGLL 120

Query: 125 GLHIEGPFLNPKRKGIHDAGKFRVIDDEALALLTSLKR-GKTLVTLAPERTTPQIIRRLA 183
           GLH+EGP+LNP RKGIH A   R  + +ALALLT L   G TLVTLAPE      IR L 
Sbjct: 121 GLHLEGPYLNPARKGIHPAAAIRPPEPDALALLTGLGDVGVTLVTLAPECVPEGFIRSLV 180

Query: 184 DAGVIVAAGHTNALYATMRQALEHGLTGFTHLFNAMSPLTSREPGAVGAALESPDAWCGI 243
           + GV VAAGHT+A  AT+++AL+ GL GFTHLFNAMSPL SREPG VG AL    +WC +
Sbjct: 181 ERGVQVAAGHTDADLATLQRALDEGLHGFTHLFNAMSPLGSREPGTVGTALADTASWCSV 240

Query: 244 IVDGRHVDPVVLKIALRTRALDRFMLVTDAMPTVGLPDKRFNLQGRDIRVVDGVCVDDHG 303
           IVDG HV P  L+IAL  +   R +LVTDAMP+ G    RF L G  I   +G  V+  G
Sbjct: 241 IVDGHHVHPASLRIALAAKPRGRLLLVTDAMPSAGSDQDRFTLFGEMIERRNGRLVNSAG 300

Query: 304 TLAGSDLDMIGAVRNAIDLLDLSLDDAVMMASHAPASFLGLGHGRGLIAPGYAADLCLLN 363
           TLAG+DL M  AV N   +L + L++A+ MAS  PA  LGLG   G I PGY ADL LL+
Sbjct: 301 TLAGADLTMERAVANTHQMLGVPLEEALRMASRYPAECLGLGWQLGWIRPGYRADLVLLD 360

Query: 364 DRLEVAATWIDG 375
           + L V  TW+ G
Sbjct: 361 EALRVCMTWVGG 372


Lambda     K      H
   0.321    0.140    0.410 

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: 475
Number of extensions: 14
Number of successful extensions: 2
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: 377
Length adjustment: 30
Effective length of query: 348
Effective length of database: 347
Effective search space:   120756
Effective search space used:   120756
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 WP_086511253.1 BZY95_RS17925 (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.6337.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    5.4e-96  307.7   0.0    5.9e-96  307.6   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086511253.1  BZY95_RS17925 N-acetylglucosamin


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086511253.1  BZY95_RS17925 N-acetylglucosamine-6-phosphate deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.6   0.0   5.9e-96   5.9e-96      10     379 ..       3     372 ..       1     373 [. 0.96

  Alignments for each domain:
  == domain 1  score: 307.6 bits;  conditional E-value: 5.9e-96
                                 TIGR00221  10 kailtendvlddsavvindekikavvteaele.eeikeidlkgnvltpGliDvqlnGcgGvdtnd.asv 76 
                                                +++ ++   dd  v i++e i+a+ + +e +  + ++ +l+g  l+pG+iD+q+nG+gG+ +n+  sv
  lcl|NCBI__GCF_002151265.1:WP_086511253.1   3 GRVFDGERLRDDVHVAIEGETIQALLPADETPpAGAERCNLEGRLLAPGFIDLQVNGGGGHLFNEaPSV 71 
                                               678888888899******************994578899**************************4566 PP

                                 TIGR00221  77 etleimsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpk 145
                                               et++ +     ++G+t+ L tli+   e ++ a+++ar++l +     +LGlhleGP+l++ +kG+hp 
  lcl|NCBI__GCF_002151265.1:WP_086511253.1  72 ETIQAIMTSHRRHGTTGLLVTLISDRREVMQAALNAARQALEQRLP-GLLGLHLEGPYLNPARKGIHPA 139
                                               ***988888999*****************************99988.8********************* PP

                                 TIGR00221 146 eyirepdvellkkfldeagdv.itkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGi 213
                                                 ir+p+++    +l+  gdv +t vtlap e ++  +i++l+e g+ v aGht+a++++l+ a   G 
  lcl|NCBI__GCF_002151265.1:WP_086511253.1 140 AAIRPPEPDA-LALLTGLGDVgVTLVTLAP-ECVPEGFIRSLVERGVQVAAGHTDADLATLQRALDEGL 206
                                               ********99.68999999976999*****.89999********************************* PP

                                 TIGR00221 214 tfathlynamskldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaag 282
                                                  thl+nams+l  Repg +G++L++    + +i+DG+h+hp+ +r+a  +k   +l+lvtD++ +ag
  lcl|NCBI__GCF_002151265.1:WP_086511253.1 207 HGFTHLFNAMSPLGSREPGTVGTALADTASWCSVIVDGHHVHPASLRIALAAKPRGRLLLVTDAMPSAG 275
                                               ********************************************************************* PP

                                 TIGR00221 283 aklekfifaGkevyiredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddr 351
                                                + ++f+  G+ +  r+++l+++ gtlaG+ ltm  +v n     +++l++++r++s +pa  lg+  +
  lcl|NCBI__GCF_002151265.1:WP_086511253.1 276 SDQDRFTLFGEMIERRNGRLVNSAGTLAGADLTMERAVANTHQMLGVPLEEALRMASRYPAECLGLGWQ 344
                                               ********************************************************************* PP

                                 TIGR00221 352 lGsvakGkdanLavltkdfeviltiveg 379
                                               lG +  G+ a+L++l++  +v +t v g
  lcl|NCBI__GCF_002151265.1:WP_086511253.1 345 LGWIRPGYRADLVLLDEALRVCMTWVGG 372
                                               **********************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (377 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: 00:00:00.01
# Mc/sec: 12.25
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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