Alignments for a candidate for nagA in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Sinorhizobium meliloti 1021

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate SMc02878 SMc02878 N-acetylglucosamine-6-phosphate deacetylase

Query= reanno::MR1:202606
         (378 letters)



>FitnessBrowser__Smeli:SMc02878
          Length = 386

 Score =  314 bits (804), Expect = 3e-90
 Identities = 182/382 (47%), Positives = 234/382 (61%), Gaps = 9/382 (2%)

Query: 2   KFTLIAEQLFDGESFHQDVPVTIEDGLIASFDTA----LGAKEVRYTGTL-VPGFIDVQV 56
           K T+   ++FDG  +H    + IE G + +   A     G + +   G L VPGFID+QV
Sbjct: 4   KKTISGARIFDGIDWHDGAALVIEAGHVKAIAPAGSVPAGGETIDARGLLLVPGFIDLQV 63

Query: 57  NGGGGALFNTSPTVACIETIGKAHARFGTTGFLPTLITDNVQVMAKAADAVALAVAQKSA 116
           NGGGGAL N  P++  I  I  AHA+FGTT  LPTLITD   V   A  A   A A    
Sbjct: 64  NGGGGALLNEKPSLESIRQICAAHAQFGTTALLPTLITDTRAVRTAAIAAGIEAKAAAVP 123

Query: 117 GVLGVHFEGPHLSVPKKGVHPQGFIREITEAELA--IFCRQDLGIRVVTLAPENVSPEVI 174
           G LG+H EGPHLSV +KG H    IR + + +LA  + C + L   ++T+APEN + E +
Sbjct: 124 GFLGLHLEGPHLSVARKGAHDPALIRPMGDDDLAEILACAKALSRLMLTVAPENATKEQV 183

Query: 175 RLLVESGVKVCLGHSNADYDTVVAALKAGATGFTHLYNAMSPLGSREPGVVGAAIESETA 234
           R L ++GV V LGH++ DYDT  A  KAGA   THL+NAMS LG REPGVVGAA+ + T 
Sbjct: 184 RALADAGVVVSLGHTDVDYDTACAYAKAGARTVTHLFNAMSGLGHREPGVVGAALSTGTL 243

Query: 235 WCGLIVDGHHVHPAAARIALRAKP-RGKMMLVTDAMPPVGMDDETSFELFGTQVLRVGDR 293
             G+I DG HVHPA+  IALR K   G++ LVTDAM P+G  D+TSF L G ++LR G R
Sbjct: 244 HAGMIADGFHVHPASMGIALRGKKGPGQIFLVTDAMSPIG-TDQTSFFLNGREILRQGGR 302

Query: 294 LNAVTGELAGCVLDMASAVHNTVNMLGLPLGEALRMAALYPAEFLGIADSVGRLAVGQRA 353
           L    G LAG  +DM S+V      LGLP+ EA+RMA+ YPA+ +GIA   GRL  G  A
Sbjct: 303 LTLADGTLAGADVDMLSSVRFVHQKLGLPIEEAVRMASAYPADAMGIASHKGRLLPGTDA 362

Query: 354 DLVLLDNQYQVLANYIAGNAVY 375
           D VLL  +  + + +I G  V+
Sbjct: 363 DFVLLTPELAMKSTWIGGETVF 384


Lambda     K      H
   0.321    0.137    0.400 

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: 423
Number of extensions: 15
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: 378
Length of database: 386
Length adjustment: 30
Effective length of query: 348
Effective length of database: 356
Effective search space:   123888
Effective search space used:   123888
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 SMc02878 SMc02878 (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.20153.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    2.1e-93  299.2   0.0    2.3e-93  299.1   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc02878  SMc02878 N-acetylglucosamine-6-p


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc02878  SMc02878 N-acetylglucosamine-6-phosphate deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.1   0.0   2.3e-93   2.3e-93       3     379 ..       3     380 ..       1     381 [. 0.95

  Alignments for each domain:
  == domain 1  score: 299.1 bits;  conditional E-value: 2.3e-93
                           TIGR00221   3 eslllkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtndasv. 76 
                                          +  +   +i+ + d  d  a vi+ + +ka+ +    + + ++id++g  l pG+iD+q+nG+gG+  n++ + 
  lcl|FitnessBrowser__Smeli:SMc02878   3 AKKTISGARIFDGIDWHDGAALVIEAGHVKAIAPAGSVPAGGETIDARGLLLVPGFIDLQVNGGGGALLNEKPSl 77 
                                         5566788899************************************************************96555 PP

                           TIGR00221  77 etleimsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyirep 151
                                         e++  +  a a+ G+t+ Lptlit      + a+ + +e++a+      LGlhleGP+ls+ +kGah +  ir+ 
  lcl|FitnessBrowser__Smeli:SMc02878  78 ESIRQICAAHAQFGTTALLPTLITDTRAVRTAAIAAGIEAKAAAVP-GFLGLHLEGPHLSVARKGAHDPALIRPM 151
                                         *****************************************99988.8*************************98 PP

                           TIGR00221 152 .dvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynamsk 225
                                          d +l + + ++ +    ++t+ap e+ t e ++ l++ag++vs+Ght+ +y+++ + +kaG+  +thl+nams 
  lcl|FitnessBrowser__Smeli:SMc02878 152 gDDDLAEILACAKALSRLMLTVAP-ENATKEQVRALADAGVVVSLGHTDVDYDTACAYAKAGARTVTHLFNAMSG 225
                                         35667666777777777889****.999*********************************************** PP

                           TIGR00221 226 ldhRepgviGavLdeddvvteiiaDGlhihpknirlakk.lkgdsklvlvtDslaaagaklekfifaGkevyire 299
                                         l hRepgv+Ga+L  + + +++iaDG h+hp+ + +a +  kg  ++ lvtD++++ g++  +f  +G+e+  ++
  lcl|FitnessBrowser__Smeli:SMc02878 226 LGHREPGVVGAALSTGTLHAGMIADGFHVHPASMGIALRgKKGPGQIFLVTDAMSPIGTDQTSFFLNGREILRQG 300
                                         **********************************99866267999****************************** PP

                           TIGR00221 300 dtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkdfevil 374
                                         ++l  ++gtlaG+ + m+ +v+ +    +++++++vr++s +pa a+gi  ++G +  G da+ ++lt++  ++ 
  lcl|FitnessBrowser__Smeli:SMc02878 301 GRLTLADGTLAGADVDMLSSVRFVHQKLGLPIEEAVRMASAYPADAMGIASHKGRLLPGTDADFVLLTPELAMKS 375
                                         *************************************************************************** PP

                           TIGR00221 375 tiveg 379
                                         t + g
  lcl|FitnessBrowser__Smeli:SMc02878 376 TWIGG 380
                                         98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (386 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: 11.77
//
[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