Alignments for a candidate for nagA in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Paraburkholderia bryophila 376MFSha3.1

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate H281DRAFT_05506 H281DRAFT_05506 N-acetylglucosamine 6-phosphate deacetylase (EC 3.5.1.25)

Query= reanno::WCS417:GFF4491
         (368 letters)



>FitnessBrowser__Burk376:H281DRAFT_05506
          Length = 376

 Score =  410 bits (1055), Expect = e-119
 Identities = 202/363 (55%), Positives = 268/363 (73%), Gaps = 4/363 (1%)

Query: 5   NILTPDGWIRGRLVHEHGKVIA-IEGTPCDPAENDLPYLLPGFIDLHVHGGGGADIMEGG 63
           NILTP GW+ GR+V +   +IA IEG+P         Y+LPGFIDLHVHGGGG D+M+G 
Sbjct: 3   NILTPKGWVLGRVVVDAAGLIARIEGSPVTSPLLAAGYVLPGFIDLHVHGGGGTDLMDGE 62

Query: 64  AAFETITRTHVRFGTTSLLATTMTAPVEEISRVLGQLGTFCER-RPAGSARVLGVHLEGP 122
            A   + +TH  +GTTS LATTMTAP +++    G LG    + R  G +R+LGVHLEGP
Sbjct: 63  TAACVVAKTHAEYGTTSFLATTMTAPEDDLRVATGHLGAAIRKPRGPGQSRILGVHLEGP 122

Query: 123 YINPGKLGAQPNFAHTALMAEVEAYLRLAPIRVITIAPEIAGHDGLIRALSERGVRMQIG 182
           ++N  K G+QP     A  AE++  L +A +R++T+APEI G   +IR L ERG+R+Q+G
Sbjct: 123 FLNANKRGSQPAHTRCAAPAELDELLNIAHVRLVTLAPEIEGQLAIIRKLVERGIRVQLG 182

Query: 183 HTLGSYEEGVAALAAGATSFTHLYNAMSPLHHREPGIVGAALAHAKFAELIPDLLHVHPG 242
           H+ G+YE+G+AAL  GAT F HL+NAMS +HHR+PGIVG A AHA++AE+IPDLLHVHPG
Sbjct: 183 HSTGTYEQGLAALQCGATGFAHLFNAMSGMHHRDPGIVGVAFAHAEYAEMIPDLLHVHPG 242

Query: 243 AMRVALRSIPCLYCVTDSTAAAGMPDGEYKLGSHTV--TKCLGGVRLADGTLAGSTLTMD 300
           A++ A R+IP LYC+TDS +A GM +GE+ LG+  V   +C  GVRLADGTLA STLTMD
Sbjct: 243 AVKAAFRAIPKLYCITDSCSAVGMGEGEFTLGAQKVFRRRCESGVRLADGTLAASTLTMD 302

Query: 301 QALRNLVKIGLPISEASQRLSQFPADYLGLEERGRLQPGSFADCVRLDRSLTLTDVMVEG 360
           +ALRNLV +G+ I++AS RLS+FPAD+LGL++RGRL PG++ D V L ++L L +V +EG
Sbjct: 303 EALRNLVSLGMTIADASDRLSRFPADFLGLQDRGRLVPGAWGDYVALSQNLALEEVCIEG 362

Query: 361 ETI 363
           E +
Sbjct: 363 EHV 365


Lambda     K      H
   0.320    0.138    0.411 

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: 510
Number of extensions: 24
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: 368
Length of database: 376
Length adjustment: 30
Effective length of query: 338
Effective length of database: 346
Effective search space:   116948
Effective search space used:   116948
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: 49 (23.5 bits)

Align candidate H281DRAFT_05506 H281DRAFT_05506 (N-acetylglucosamine 6-phosphate deacetylase (EC 3.5.1.25))
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.10751.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
    4.2e-74  235.7   0.0    5.1e-74  235.4   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_05506  H281DRAFT_05506 N-acetylglucosam


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_05506  H281DRAFT_05506 N-acetylglucosamine 6-phosphate deacetylase (EC 3.5.1.25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.4   0.0   5.1e-74   5.1e-74      50     379 ..      37     362 ..      25     363 .. 0.93

  Alignments for each domain:
  == domain 1  score: 235.4 bits;  conditional E-value: 5.1e-74
                                    TIGR00221  50 kgnvltpGliDvqlnGcgGvdtndasvetleimsealaksGvtsfLptlitredeeikkavkvare 115
                                                   + +++pG+iD++++G+gG+d +d  + +  ++ ++ a++G+tsfL+t++t+++++++ a     +
  lcl|FitnessBrowser__Burk376:H281DRAFT_05506  37 AAGYVLPGFIDLHVHGGGGTDLMDGETAAC-VVAKTHAEYGTTSFLATTMTAPEDDLRVATGHLGA 101
                                                  56799*******************776554.6789999**************************** PP

                                    TIGR00221 116 ylakekn...akiLGlhleGPflslekkGahpkeyirepdvellkkfldeagdvitkvtlapeekq 178
                                                  ++ k ++   ++iLG+hleGPfl+ +k+G +p +    + +el  ++l+    +++ vtlape ++
  lcl|FitnessBrowser__Burk376:H281DRAFT_05506 102 AIRKPRGpgqSRILGVHLEGPFLNANKRGSQPAHTRCAAPAEL-DELLNI--AHVRLVTLAPEIEG 164
                                                  ***99988889*******************9987766667777.888865..59************ PP

                                    TIGR00221 179 taelisklleagiivsaGhtnatyeelkeafkaGitfathlynamskldhRepgviGavLdeddvv 244
                                                  +  +i+kl+e gi v++Gh+  tye+  +a + G+t   hl+nams ++hR+pg++G + ++++ +
  lcl|FitnessBrowser__Burk376:H281DRAFT_05506 165 QLAIIRKLVERGIRVQLGHSTGTYEQGLAALQCGATGFAHLFNAMSGMHHRDPGIVGVAFAHAE-Y 229
                                                  **************************************************************65.9 PP

                                    TIGR00221 245 teiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGkevyir..edtlldkngt 308
                                                  +e+i D lh+hp +++ a+++  + kl  +tDs +a g+  ++f+ + ++v+ r  e ++  ++gt
  lcl|FitnessBrowser__Burk376:H281DRAFT_05506 230 AEMIPDLLHVHPGAVKAAFRA--IPKLYCITDSCSAVGMGEGEFTLGAQKVFRRrcESGVRLADGT 293
                                                  9*****************987..678*************************98844566777**** PP

                                    TIGR00221 309 laGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkdfevil 374
                                                  la s+ltm e+++nlv  + ++++d+    s +pa  lg++dr G +  G   + ++l+++  +  
  lcl|FitnessBrowser__Burk376:H281DRAFT_05506 294 LAASTLTMDEALRNLVSLG-MTIADASDRLSRFPADFLGLQDR-GRLVPGAWGDYVALSQNLALEE 357
                                                  *****************99.***********************.******************9999 PP

                                    TIGR00221 375 tiveg 379
                                                    +eg
  lcl|FitnessBrowser__Burk376:H281DRAFT_05506 358 VCIEG 362
                                                  98887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (376 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: 12.81
//
[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