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.1132.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.32
//
[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:

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:

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:

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:

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