Alignments for a candidate for nagA in Marinomonas arctica 328

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Marinomonas arctica 328

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate WP_111609148.1 DK187_RS20445 N-acetylglucosamine-6-phosphate deacetylase

Query= reanno::ANA3:7025964
         (378 letters)



>NCBI__GCF_003259225.1:WP_111609148.1
          Length = 387

 Score =  324 bits (831), Expect = 2e-93
 Identities = 180/375 (48%), Positives = 238/375 (63%), Gaps = 5/375 (1%)

Query: 5   LIAEQLFDGEAFHRDVPVTIEDGLIASLDTASGAK--EIRYPGTLVPGFIDVQVNGGGGA 62
           + AE+LFDGE +  +  VT +  +I S+++A+     EI     L PGFIDV VNGGGGA
Sbjct: 9   VFAERLFDGEHWLTNQLVTFKGQMIESVESATMPTNGEIERLDVLAPGFIDVHVNGGGGA 68

Query: 63  LFNSSPTVACIETIGKAHARFGTTGFLPTLITDDVQVMAKAADAVASAVAQKSAGVLGVH 122
           LFN +PT+  +  +   HA+FGT   +PTLI+DD  VM++A  AV  A+ Q  AG+LG+H
Sbjct: 69  LFNHTPTIEALARMVAVHAQFGTVAMMPTLISDDYDVMSQAHHAVCQALEQNMAGILGMH 128

Query: 123 FEGPHLSVPKKGVHPQGFIREITEAELAIFCR-QDLGIRVVTLAPENVSPEVIRLLVESG 181
           +EGP+L+  +KGVH +  +R+ TE  L+        G  +VTLAPE V    I  LV  G
Sbjct: 129 YEGPYLNPIRKGVHNESKLRKPTEGTLSTLLNVSRSGKLMVTLAPEQVPEGFIEWLVSEG 188

Query: 182 VKVCLGHSNADYDTVVAALAAGATGFTHLYNAMSPLGSREPGVVGAAIESE-TAWCGLIV 240
             VC+GHS A YD    A+ +G  GFTHL+NAM+PL SREPGVVGAA++++   WCGLI 
Sbjct: 189 AIVCIGHSAASYDQARQAVMSGVRGFTHLFNAMTPLVSREPGVVGAALQTDLPTWCGLIA 248

Query: 241 DGHHVHPAAARVALRAKPRGKVMLVTDAMPPVGMDDETSFELFGTQVLRVGDRLNAVTGE 300
           DGHHVHPAA RVA+ AK    ++LVTDA+  VG  DE      G +V R   ++    G 
Sbjct: 249 DGHHVHPAAMRVAIAAKGSEHMLLVTDAIQSVG-SDEKEMPFLGKKVRRSEGKVTTEDGT 307

Query: 301 LAGCVLDMATAVENSVKMLGLPLGEALRMASLYPAEFLGIAESVGRLAVGQRADLVLLDN 360
           LAG  LDMATAV N++ ++G    EAL+MASL PAEFLG+    GR+  G RA LV L+ 
Sbjct: 308 LAGSDLDMATAVRNAISLIGRTPAEALQMASLRPAEFLGLEHQFGRIKPGYRASLVALNE 367

Query: 361 QYKVLANYIAGNAVY 375
            + V A +I G  V+
Sbjct: 368 DFVVKATWIDGQKVW 382


Lambda     K      H
   0.320    0.137    0.396 

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: 374
Number of extensions: 15
Number of successful extensions: 5
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: 387
Length adjustment: 30
Effective length of query: 348
Effective length of database: 357
Effective search space:   124236
Effective search space used:   124236
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_111609148.1 DK187_RS20445 (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.1648738.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    8.8e-90  287.3   0.0    1.1e-89  287.0   0.0    1.0  1  NCBI__GCF_003259225.1:WP_111609148.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003259225.1:WP_111609148.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.0   0.0   1.1e-89   1.1e-89      11     379 ..      13     378 ..       3     379 .. 0.94

  Alignments for each domain:
  == domain 1  score: 287.0 bits;  conditional E-value: 1.1e-89
                             TIGR00221  11 ailtendvlddsavvindekikavvtea.eleeeikeidlkgnvltpGliDvqlnGcgGvdtndasv.etlei 81 
                                           +++ ++  l ++ v  ++++i++v +   + + ei++ d    vl+pG+iDv++nG+gG+ +n + + e+l  
  NCBI__GCF_003259225.1:WP_111609148.1  13 RLFDGEHWLTNQLVTFKGQMIESVESATmPTNGEIERLD----VLAPGFIDVHVNGGGGALFNHTPTiEALAR 81 
                                           67788899***************9654314445666555....89*******************7666***** PP

                             TIGR00221  82 msealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyirepdve 154
                                           m    a+ G+++ +ptli+ + + +++a +++ ++l ++ +  iLG+h eGP+l++ +kG+h+++ +r+p+  
  NCBI__GCF_003259225.1:WP_111609148.1  82 MVAVHAQFGTVAMMPTLISDDYDVMSQAHHAVCQALEQNMA-GILGMHYEGPYLNPIRKGVHNESKLRKPTEG 153
                                           ********************************999988776.9****************************** PP

                             TIGR00221 155 llkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynamskld 227
                                            l  +l+ +     +vtlap e+++  +i+ l+ +g iv +Gh+ a y+++++a+  G+   thl+nam++l 
  NCBI__GCF_003259225.1:WP_111609148.1 154 TLSTLLNVSRSGKLMVTLAP-EQVPEGFIEWLVSEGAIVCIGHSAASYDQARQAVMSGVRGFTHLFNAMTPLV 225
                                           ******999888889*****.9999************************************************ PP

                             TIGR00221 228 hRepgviGavLded.dvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGkevyire 299
                                            Repgv+Ga+L+ d    +++iaDG+h+hp+++r+a  +kg+  ++lvtD++++ g + +++ f Gk+v   e
  NCBI__GCF_003259225.1:WP_111609148.1 226 SREPGVVGAALQTDlPTWCGLIADGHHVHPAAMRVAIAAKGSEHMLLVTDAIQSVGSDEKEMPFLGKKVRRSE 298
                                           ***********9953468******************************************************* PP

                             TIGR00221 300 dtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkdfev 372
                                           +++  ++gtlaGs l m  +v+n++   + + +++++++sl pa  lg++++ G ++ G+ a L++l++df v
  NCBI__GCF_003259225.1:WP_111609148.1 299 GKVTTEDGTLAGSDLDMATAVRNAISLIGRTPAEALQMASLRPAEFLGLEHQFGRIKPGYRASLVALNEDFVV 371
                                           ************************************************************************* PP

                             TIGR00221 373 iltiveg 379
                                           + t ++g
  NCBI__GCF_003259225.1:WP_111609148.1 372 KATWIDG 378
                                           ***9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (387 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: 17.05
//
[ok]

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

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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