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

GapMind for catabolism of small carbon sources

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

Align glucosamine-6-phosphate deaminase (EC 3.5.99.6) (characterized)
to candidate 353653 BT4127 glucosamine-6-phosphate isomerase (NCBI ptt file)

Query= BRENDA::P0A759
         (266 letters)



>FitnessBrowser__Btheta:353653
          Length = 270

 Score =  356 bits (914), Expect = e-103
 Identities = 172/263 (65%), Positives = 208/263 (79%)

Query: 1   MRLIPLTTAEQVGKWAARHIVNRINAFKPTADRPFVLGLPTGGTPMTTYKALVEMHKAGQ 60
           MRLI     + V +WAA ++  +I A  PT ++PFVLG PTG +P+  YKAL++++K G 
Sbjct: 1   MRLIIQPDYQSVSQWAAHYVAAKIKAANPTPEKPFVLGCPTGSSPLGMYKALIDLNKKGI 60

Query: 61  VSFKHVVTFNMDEYVGLPKEHPESYYSFMHRNFFDHVDIPAENINLLNGNAPDIDAECRQ 120
           VSF++VVTFNMDEYVGLPKEHPESYYSFM  NFF H+DI  EN N+LNGNAPD+DAEC +
Sbjct: 61  VSFQNVVTFNMDEYVGLPKEHPESYYSFMWNNFFSHIDIKKENTNILNGNAPDLDAECAR 120

Query: 121 YEEKIRSYGKIHLFMGGVGNDGHIAFNEPASSLASRTRIKTLTHDTRVANSRFFDNDVNQ 180
           YEEKI+SYG I LFMGG+G DGHIAFNEP SSL SRTR KTLT DT +ANSRFFDND+N+
Sbjct: 121 YEEKIKSYGGIDLFMGGIGPDGHIAFNEPGSSLTSRTRQKTLTTDTIIANSRFFDNDINK 180

Query: 181 VPKYALTVGVGTLLDAEEVMILVLGSQKALALQAAVEGCVNHMWTISCLQLHPKAIMVCD 240
           VPK ALTVGVGT+L A+EVMI+V G  KA AL  AVEG +  MWTIS LQ+H K I+VCD
Sbjct: 181 VPKTALTVGVGTVLSAKEVMIIVNGHNKARALYHAVEGSITQMWTISALQMHEKGIIVCD 240

Query: 241 EPSTMELKVKTLRYFNELEAENI 263
           + +T ELKV T RYF ++EA ++
Sbjct: 241 DAATEELKVGTYRYFKDIEAGHL 263


Lambda     K      H
   0.320    0.135    0.405 

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: 245
Number of extensions: 4
Number of successful extensions: 1
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: 266
Length of database: 270
Length adjustment: 25
Effective length of query: 241
Effective length of database: 245
Effective search space:    59045
Effective search space used:    59045
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: 47 (22.7 bits)

Align candidate 353653 BT4127 (glucosamine-6-phosphate isomerase (NCBI ptt file))
to HMM TIGR00502 (nagB: glucosamine-6-phosphate deaminase (EC 3.5.99.6))

# 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/TIGR00502.hmm
# target sequence database:        /tmp/gapView.31870.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00502  [M=259]
Accession:   TIGR00502
Description: nagB: glucosamine-6-phosphate deaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   5.1e-134  431.5   0.0   5.8e-134  431.3   0.0    1.0  1  lcl|FitnessBrowser__Btheta:353653  BT4127 glucosamine-6-phosphate i


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:353653  BT4127 glucosamine-6-phosphate isomerase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  431.3   0.0  5.8e-134  5.8e-134       1     259 []       1     259 [.       1     259 [. 1.00

  Alignments for each domain:
  == domain 1  score: 431.3 bits;  conditional E-value: 5.8e-134
                          TIGR00502   1 mklliletyeelsklaariiaekinefkpdaerpfvlGlatGgtPvglykqlielykagkvsfkkvvtfnldeyvg 76 
                                        m+l+i + y+ +s++aa+++a ki++ +p+ e+pfvlG +tG++P+g+yk+li+l+k g vsf++vvtfn+deyvg
  lcl|FitnessBrowser__Btheta:353653   1 MRLIIQPDYQSVSQWAAHYVAAKIKAANPTPEKPFVLGCPTGSSPLGMYKALIDLNKKGIVSFQNVVTFNMDEYVG 76 
                                        9*************************************************************************** PP

                          TIGR00502  77 lseehPesyhsfmyenffqhidikpeninilnGnaddleaecrryeekikslGkidlfllGiGadGhiafnePgss 152
                                        l++ehPesy+sfm++nff+hidik+en nilnGna+dl+aec ryeekiks+G+idlf++GiG dGhiafnePgss
  lcl|FitnessBrowser__Btheta:353653  77 LPKEHPESYYSFMWNNFFSHIDIKKENTNILNGNAPDLDAECARYEEKIKSYGGIDLFMGGIGPDGHIAFNEPGSS 152
                                        **************************************************************************** PP

                          TIGR00502 153 lesrtrvktltedtiiansrffegdvnkvPkkaltvGiktildskevlllvsGkekaeavkklvegsvnedvtisa 228
                                        l+srtr ktlt dtiiansrff++d+nkvPk+altvG++t+l++kev+++v+G++ka+a+ ++vegs+++++tisa
  lcl|FitnessBrowser__Btheta:353653 153 LTSRTRQKTLTTDTIIANSRFFDNDINKVPKTALTVGVGTVLSAKEVMIIVNGHNKARALYHAVEGSITQMWTISA 228
                                        **************************************************************************** PP

                          TIGR00502 229 lqlhkkvivvadeeaaqelkvktlkyfnele 259
                                        lq+h+k i+v+d +a++elkv+t +yf+++e
  lcl|FitnessBrowser__Btheta:353653 229 LQMHEKGIIVCDDAATEELKVGTYRYFKDIE 259
                                        *****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (259 nodes)
Target sequences:                          1  (270 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 6.53
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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