Alignments for a candidate for nagA in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Dyella japonica UNC79MFTsu3.2

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate N515DRAFT_0589 N515DRAFT_0589 N-acetylglucosamine-6-phosphate deacetylase

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



>FitnessBrowser__Dyella79:N515DRAFT_0589
          Length = 386

 Score =  378 bits (971), Expect = e-109
 Identities = 202/373 (54%), Positives = 253/373 (67%), Gaps = 1/373 (0%)

Query: 4   ALINGRVLTESGVVEGKAVLVKDGLILDVIEAAQTPSDAKPR-DLKGGLLVPGFIDTQVN 62
           AL+NGRVL + G     AVLV+ G I  ++ A     D   R DL+G LL+PGFID QVN
Sbjct: 9   ALVNGRVLADHGPRNDLAVLVRGGRIEALVPAGDPSLDKATRHDLQGRLLLPGFIDVQVN 68

Query: 63  GGGGVLFNDAPTVETIATIGAAHRRFGTTGFLPTLISDDLRVVDQAMRATEEAIARGVPG 122
           GGGG+LFN APTV+T+  I AAHRRFGTTG LPTLI+D   V+  A+ A + AIA GVPG
Sbjct: 69  GGGGLLFNAAPTVDTLRGIAAAHRRFGTTGMLPTLITDTADVMHAALEAVDAAIAEGVPG 128

Query: 123 VLGLHIEGPFLNPKRKGIHDAGKFRVIDDEALALLTSLKRGKTLVTLAPERTTPQIIRRL 182
           +LG+H+EGPFL P RKGIHDA  FR+ D   +A +    RG  ++TLAPER   + IR+L
Sbjct: 129 ILGIHLEGPFLAPARKGIHDANLFRLPDAADIADIARKHRGVVMMTLAPERVPLETIRQL 188

Query: 183 ADAGVIVAAGHTNALYATMRQALEHGLTGFTHLFNAMSPLTSREPGAVGAALESPDAWCG 242
           + AGVIV AGHT A YATMR AL+ G++GFTHL+NAM+PL SR+PG VGAAL+ P +WCG
Sbjct: 189 SAAGVIVVAGHTAADYATMRAALDAGVSGFTHLYNAMTPLGSRDPGVVGAALDDPHSWCG 248

Query: 243 IIVDGRHVDPVVLKIALRTRALDRFMLVTDAMPTVGLPDKRFNLQGRDIRVVDGVCVDDH 302
           +IVD  HV P  L++A+  +A  + +LVTDAMP VG  D  + L G+ I   DGVC  D 
Sbjct: 249 LIVDLHHVHPASLRVAIAAKARGKSVLVTDAMPPVGADDPTYVLNGQTIVARDGVCQSDD 308

Query: 303 GTLAGSDLDMIGAVRNAIDLLDLSLDDAVMMASHAPASFLGLGHGRGLIAPGYAADLCLL 362
           G LAGS LDM   VR+ ++ + L L +A  MAS  PA++LGL    G I  G  AD  +L
Sbjct: 309 GVLAGSALDMATGVRHLVNAVGLPLAEASRMASAYPAAWLGLERELGRIVAGQRADFAVL 368

Query: 363 NDRLEVAATWIDG 375
           +D L V  TWI G
Sbjct: 369 DDALVVQETWIGG 381


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: 525
Number of extensions: 25
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: 386
Length adjustment: 30
Effective length of query: 348
Effective length of database: 356
Effective search space:   123888
Effective search space used:   123888
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 N515DRAFT_0589 N515DRAFT_0589 (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.32130.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
    4.6e-99  317.8   0.0    5.7e-99  317.5   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0589  N515DRAFT_0589 N-acetylglucosami


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0589  N515DRAFT_0589 N-acetylglucosamine-6-phosphate deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  317.5   0.0   5.7e-99   5.7e-99       5     378 ..       8     380 ..       5     382 .. 0.97

  Alignments for each domain:
  == domain 1  score: 317.5 bits;  conditional E-value: 5.7e-99
                                    TIGR00221   5 lllkdkailtendvlddsavvindekikavvteaele.eeikeidlkgnvltpGliDvqlnGcgGv 69 
                                                  l+l + ++l ++   +d av+++++ i+a+v+  +   ++  + dl+g  l+pG+iDvq+nG+gG 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0589   8 LALVNGRVLADHGPRNDLAVLVRGGRIEALVPAGDPSlDKATRHDLQGRLLLPGFIDVQVNGGGGL 73 
                                                  689999*************************9866554889999********************** PP

                                    TIGR00221  70 dtndasv.etleimsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPf 134
                                                   +n a + +tl  +  a  + G+t+ Lptlit   + ++ a++++ +++a+     iLG+hleGPf
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0589  74 LFNAAPTvDTLRGIAAAHRRFGTTGMLPTLITDTADVMHAALEAVDAAIAEGVP-GILGIHLEGPF 138
                                                  ***97655*****************************************99877.8********** PP

                                    TIGR00221 135 lslekkGahpkeyirepdvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtna 200
                                                  l++ +kG+h  +  r pd++ + ++  +  +v+ ++tlap e+++ e i++l  ag+iv aGht a
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0589 139 LAPARKGIHDANLFRLPDAADIADIARKHRGVV-MMTLAP-ERVPLETIRQLSAAGVIVVAGHTAA 202
                                                  ********************99***99999987.7*****.99*********************** PP

                                    TIGR00221 201 tyeelkeafkaGitfathlynamskldhRepgviGavLdeddvvteiiaDGlhihpknirlakklk 266
                                                  +y+++++a  aG++  thlynam++l  R+pgv+Ga+Ld+    +++i+D +h+hp+ +r+a  +k
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0589 203 DYATMRAALDAGVSGFTHLYNAMTPLGSRDPGVVGAALDDPHSWCGLIVDLHHVHPASLRVAIAAK 268
                                                  ****************************************************************** PP

                                    TIGR00221 267 gdsklvlvtDslaaagaklekfifaGkevyiredtlldkngtlaGssltmiegvknlvefveisls 332
                                                     k vlvtD++ + ga++ +++ +G+++  r++ +  ++g laGs+l m  gv++lv+ v+++l+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0589 269 ARGKSVLVTDAMPPVGADDPTYVLNGQTIVARDGVCQSDDGVLAGSALDMATGVRHLVNAVGLPLA 334
                                                  ****************************************************************** PP

                                    TIGR00221 333 dvvrisslnparalgiddrlGsvakGkdanLavltkdfeviltive 378
                                                  ++ r++s +pa  lg++  lG + +G+ a+ avl+    v+ t + 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0589 335 EASRMASAYPAAWLGLERELGRIVAGQRADFAVLDDALVVQETWIG 380
                                                  ************************************9999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (386 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: 10.87
//
[ok]

This GapMind analysis is from Sep 17 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