Alignments for a candidate for nagA in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Bacteroides thetaiotaomicron VPI-5482

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate 353114 BT3588 N-acetylglucosamine-6-phosphate deacetylase (NCBI ptt file)

Query= BRENDA::Q8Y5F6
         (377 letters)



>FitnessBrowser__Btheta:353114
          Length = 395

 Score =  221 bits (563), Expect = 3e-62
 Identities = 136/369 (36%), Positives = 211/369 (57%), Gaps = 15/369 (4%)

Query: 19  VVITEGNLIKEVCSTTPEKYSDEPTFDGNGRLLIPGMIDVHIHGAKNYDMMDGSTESIQA 78
           +V   G + + V S      +D+   D N + + PG ID+H+HG   +D MDG+ E+   
Sbjct: 23  MVCRNGKIEQIVSSEAYIPQADDRIIDANQQYVSPGFIDIHVHGGGGHDFMDGTVEAFLG 82

Query: 79  VSMACAETGCTSFLVTSVSSSLEDLIQM--IRQTKKVIGKEKGAKIAGIHLEGPYLNIEK 136
           V+   A  G T+ + T+++S+ E+L+    + Q  K + K KGA+  G+HLEGPY + ++
Sbjct: 83  VAETHARYGTTAMVPTTLTSTNEELMTTFAVYQKAKSLNK-KGAQFIGLHLEGPYFSPKQ 141

Query: 137 KGMQNPAHLRHPDLKEMKKIFDEADGLIKMVTIAPELPGGIELIDFLKKRGVVVAIAHSN 196
            G Q+P HL+ P   E   I + +  +++  +IAPEL G IEL + L    ++ +IAH++
Sbjct: 142 CGAQDPNHLKTPHPDEYNTILEASQDIVRW-SIAPELAGAIELGEKLNSCHILPSIAHTD 200

Query: 197 ATYEEAQDAFEKGASHITHCFNAMPAIH----HRAPGLVAAALENDSISVQAIVDGVHLH 252
           A YEE   A+E G +HITH ++AM  I     +R  G+V AA   D ++V+ I DG+HL 
Sbjct: 201 AIYEEVVKAYEAGYTHITHLYSAMSTITRRNAYRYAGVVEAAYLIDGMTVEIIADGIHLP 260

Query: 253 PGIVRLIHKIKGPDKMVLTTDALQAMGVGDGEYIFG----GHQVTVTEGVARLQD-GTLA 307
             +++ ++K KG DK  L TDA++  G+ DGE I G    G +V + +GVA+L D    A
Sbjct: 261 KPLLQFVYKFKGADKTALCTDAMRGAGMPDGESILGSLTNGQKVIIEDGVAKLPDRSAFA 320

Query: 308 SSTVTMNKSLR-LSNEFGINLQDTIQMATSTPADILGM-KNLGRIEKGYSADLVLLDKKF 365
            S  T ++ +R + N  GI L D I+M T TPA IL +    G +E+G  AD+V  D + 
Sbjct: 321 GSVATADRLVRTMINIAGIPLIDAIRMITLTPARILHVDSQKGSLEEGKDADIVTFDNQI 380

Query: 366 EVLSTWING 374
            V +T   G
Sbjct: 381 NVTTTISKG 389


Lambda     K      H
   0.317    0.134    0.380 

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: 384
Number of extensions: 21
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: 377
Length of database: 395
Length adjustment: 30
Effective length of query: 347
Effective length of database: 365
Effective search space:   126655
Effective search space used:   126655
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate 353114 BT3588 (N-acetylglucosamine-6-phosphate deacetylase (NCBI ptt file))
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.32410.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    1.5e-86  276.6   1.6    1.7e-86  276.5   1.6    1.0  1  lcl|FitnessBrowser__Btheta:353114  BT3588 N-acetylglucosamine-6-pho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:353114  BT3588 N-acetylglucosamine-6-phosphate deacetylase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.5   1.6   1.7e-86   1.7e-86      20     379 ..      19     389 ..       1     390 [. 0.91

  Alignments for each domain:
  == domain 1  score: 276.5 bits;  conditional E-value: 1.7e-86
                          TIGR00221  20 ddsavvindekikavvteaele..eeikeidlkgnvltpGliDvqlnGcgGvdtndasvetleimsealaksGvts 93 
                                         ++ +v +++ki+++v+++      + + id++ ++++pG+iD++++G+gG+d++d +ve++  + e+ a++G+t+
  lcl|FitnessBrowser__Btheta:353114  19 TNKIMVCRNGKIEQIVSSEAYIpqADDRIIDANQQYVSPGFIDIHVHGGGGHDFMDGTVEAFLGVAETHARYGTTA 94 
                                        68888999*******9998877224456789999****************************************** PP

                          TIGR00221  94 fLptlitredeeikkavkvareylake.knakiLGlhleGPflslekkGahpkeyirepdvellkkfldeagdvit 168
                                         +pt++t  +ee+  +  v +++++ + k+a+ +GlhleGP++s+++ Ga+ +++++ p ++   + + ea++ i 
  lcl|FitnessBrowser__Btheta:353114  95 MVPTTLTSTNEELMTTFAVYQKAKSLNkKGAQFIGLHLEGPYFSPKQCGAQDPNHLKTPHPDE-YNTILEASQDIV 169
                                        ****************99999988765156********************************9.566777888899 PP

                          TIGR00221 169 kvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynamskldhRe....pgviGavLde 240
                                        +  +ape+ + +el +kl    i  s+ ht+a yee+ +a++aG t++thly ams ++ R+     gv+ a+   
  lcl|FitnessBrowser__Btheta:353114 170 RWSIAPELAGAIELGEKLNSCHILPSIAHTDAIYEEVVKAYEAGYTHITHLYSAMSTITRRNayryAGVVEAAYLI 245
                                        99*********************************************************98844336999999999 PP

                          TIGR00221 241 ddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfi....faGkevyiredtlld.kngtlaG 311
                                        d++++eiiaDG+h    +++   k kg  k  l tD+++ ag+++++ i     +G++v i+++ +   +    aG
  lcl|FitnessBrowser__Btheta:353114 246 DGMTVEIIADGIHLPKPLLQFVYKFKGADKTALCTDAMRGAGMPDGESIlgslTNGQKVIIEDGVAKLpDRSAFAG 321
                                        9*******************************************88876222258*******99997768899*** PP

                          TIGR00221 312 ssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkdfeviltiveg 379
                                        s+ t    v+ +++ ++i+l d++r+ +l par+l +d ++Gs+++Gkda+++ ++++++v+ ti +g
  lcl|FitnessBrowser__Btheta:353114 322 SVATADRLVRTMINIAGIPLIDAIRMITLTPARILHVDSQKGSLEEGKDADIVTFDNQINVTTTISKG 389
                                        *****************************************************************887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (395 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.34
//
[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