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 350204 BT0676 N-acetylglucosamine-6-phosphate deacetylase (NCBI ptt file)

Query= BRENDA::Q8Y8E8
         (377 letters)



>FitnessBrowser__Btheta:350204
          Length = 390

 Score =  183 bits (464), Expect = 8e-51
 Identities = 124/379 (32%), Positives = 199/379 (52%), Gaps = 14/379 (3%)

Query: 6   ITNATIYTGKGVLENAFVRF-DKQILEVGSMADFQADKAEEVIDAKGQKLVPGFIDVHSH 64
           I N  I T +G L++  V   D +ILEV + +D     A  VIDA+G  +VPGF+ +H+H
Sbjct: 5   IINGRILTPQGWLKDGSVLICDGKILEVTN-SDLAVIGAT-VIDARGMTIVPGFVSMHAH 62

Query: 65  GGYSFDAMDADPEALRKQVNGMLNEGITTYFPTTMTQSHENIEKALKVINE-VAQTEPVI 123
           GG   D  +A  EA R      L  G T  FPT  + S E I +A+ V  + + + E  I
Sbjct: 63  GGGGHDFTEATEEAFRIAATAHLKHGATGIFPTLSSTSFERIYQAVDVCEKLMKEPESPI 122

Query: 124 GGIHLEGPFVSKVFKGAQPEEYIQAPDLELFKKWFDISGGLIKLVTYAPEHDTSADFENL 183
            G+H+EGP+++    G+Q + +++ PD   +    + +   IK    +PE   + DF   
Sbjct: 123 LGLHIEGPYLNPKMAGSQYDGFLKTPDENEYVPLLEHT-SCIKRWDISPELHGAHDFAKY 181

Query: 184 CFELGVVPSIGHSNDVREHLKTSKA---THATHLYNAC----HRMTHREPGVPGHVLLER 236
               G++ ++ H+    + +K + A   +HA H YNA      R  ++  G    V L  
Sbjct: 182 TRSKGIMTAVTHTEAEYDEIKAAYAVGFSHAAHFYNAMPGFHKRREYKYEGTVESVYLTD 241

Query: 237 GINAELIVDGIHVHPDMVKLAYQMKGPEHLCIITDSMRAKGMPEGKSELGGQTVIVKDKQ 296
           G+  E+I DGIH+   ++KL Y++KG E+ C++TD++ A    EG   +  + +I     
Sbjct: 242 GMTVEVIADGIHLPATILKLVYKLKGVENTCLVTDAL-AYAANEGNEPIDPRYIIEDGVC 300

Query: 297 ARLEDGTLAGSVLTYDDGFRNMIKFTGCSVEEAVLMSSGNQAREFNLT-QKGAIEAGKDA 355
              +   LAGS+ T D   R M+K     +E+AV M+S   AR   ++ +KGA+  GKDA
Sbjct: 301 KMADHSALAGSLATMDVLVRTMVKKASIPLEDAVRMASETPARLIGVSDRKGALSKGKDA 360

Query: 356 DFNLLDEDLHITATYSFGK 374
           D  +LD++L++   +S GK
Sbjct: 361 DIVILDKELNVRCVWSMGK 379


Lambda     K      H
   0.317    0.135    0.391 

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: 396
Number of extensions: 19
Number of successful extensions: 6
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: 390
Length adjustment: 30
Effective length of query: 347
Effective length of database: 360
Effective search space:   124920
Effective search space used:   124920
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 350204 BT0676 (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.4651.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    2.5e-84  269.4   0.1    2.8e-84  269.2   0.1    1.0  1  lcl|FitnessBrowser__Btheta:350204  BT0676 N-acetylglucosamine-6-pho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:350204  BT0676 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 !  269.2   0.1   2.8e-84   2.8e-84       6     373 ..       4     372 ..       1     379 [. 0.91

  Alignments for each domain:
  == domain 1  score: 269.2 bits;  conditional E-value: 2.8e-84
                          TIGR00221   6 llkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtndasvetlei 81 
                                         +++ +ilt +  l+d+ v+i d+ki +v+ ++    +   id++g ++ pG++ ++ +G+gG+d+ +a+ e++ i
  lcl|FitnessBrowser__Btheta:350204   4 QIINGRILTPQGWLKDGSVLICDGKILEVTNSDLAVIGATVIDARGMTIVPGFVSMHAHGGGGHDFTEATEEAFRI 79 
                                        58899****************************999**************************************** PP

                          TIGR00221  82 msealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyirepdvellk 157
                                           a  k+G+t+  ptl +++ e i +av v+ +   ke+++ iLGlh+eGP+l+++ +G +   +++ pd + ++
  lcl|FitnessBrowser__Btheta:350204  80 AATAHLKHGATGIFPTLSSTSFERIYQAVDVCEKL-MKEPESPILGLHIEGPYLNPKMAGSQYDGFLKTPDENEYV 154
                                        ******************************99665.566666*****************************99978 PP

                          TIGR00221 158 kfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynamskld.hRep. 231
                                         +l e +  i++  + pe+++  ++++    +gi+  + ht+a+y+e+k+a+ +G ++a h+ynam+ ++  Re  
  lcl|FitnessBrowser__Btheta:350204 155 PLL-EHTSCIKRWDISPELHGAHDFAKYTRSKGIMTAVTHTEAEYDEIKAAYAVGFSHAAHFYNAMPGFHkRREYk 229
                                        776.66789*************************************************************666752 PP

                          TIGR00221 232 ..gviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGkevyiredtlld. 304
                                          g + +v   d++++e+iaDG+h   + ++l  klkg    +lvtD+la a+ + ++ i   +  yi ed++ + 
  lcl|FitnessBrowser__Btheta:350204 230 yeGTVESVYLTDGMTVEVIADGIHLPATILKLVYKLKGVENTCLVTDALAYAANEGNEPI---DPRYIIEDGVCKm 302
                                        225666678899*************************************98877655544...3334444444443 PP

                          TIGR00221 305 .kngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkdfevi 373
                                         ++  laGs  tm   v+ +v  + i+l+d+vr++s+ par +g+ dr+G+++kGkda++++l+k+ +v 
  lcl|FitnessBrowser__Btheta:350204 303 aDHSALAGSLATMDVLVRTMVKKASIPLEDAVRMASETPARLIGVSDRKGALSKGKDADIVILDKELNVR 372
                                        47789**************************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (390 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: 8.27
//
[ok]

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

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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