Alignments for a candidate for nagB in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagB in Shewanella loihica PV-4

Align Glucosamine-6-phosphate deaminase (EC 3.5.99.6) (characterized)
to candidate 5208303 Shew_0815 glucosamine-6-phosphate isomerase (RefSeq)

Query= reanno::PV4:5208303
         (268 letters)



>FitnessBrowser__PV4:5208303
          Length = 268

 Score =  518 bits (1335), Expect = e-152
 Identities = 268/268 (100%), Positives = 268/268 (100%)

Query: 1   MQIVILKDSAEVAEYGANLIINQLKRKPDSVLGLATGSTPVSLYQRLVAANQAGAVSFEG 60
           MQIVILKDSAEVAEYGANLIINQLKRKPDSVLGLATGSTPVSLYQRLVAANQAGAVSFEG
Sbjct: 1   MQIVILKDSAEVAEYGANLIINQLKRKPDSVLGLATGSTPVSLYQRLVAANQAGAVSFEG 60

Query: 61  VTSFNLDEYLGLEGSHPQSYRYFMDSQLFDAIDINKANTHVPPGDAEDPIAACEAYEAQI 120
           VTSFNLDEYLGLEGSHPQSYRYFMDSQLFDAIDINKANTHVPPGDAEDPIAACEAYEAQI
Sbjct: 61  VTSFNLDEYLGLEGSHPQSYRYFMDSQLFDAIDINKANTHVPPGDAEDPIAACEAYEAQI 120

Query: 121 QAAGGIDIQLLGIGRNGHIGFNEPSSGLMSRTRVKTLTQATIEDNARFFAEGEYQPHLSI 180
           QAAGGIDIQLLGIGRNGHIGFNEPSSGLMSRTRVKTLTQATIEDNARFFAEGEYQPHLSI
Sbjct: 121 QAAGGIDIQLLGIGRNGHIGFNEPSSGLMSRTRVKTLTQATIEDNARFFAEGEYQPHLSI 180

Query: 181 TMGIGTILDAKKVLLLATGESKADAIRAAVEGALSAACPASALQLHRDAVLVIDEAAASK 240
           TMGIGTILDAKKVLLLATGESKADAIRAAVEGALSAACPASALQLHRDAVLVIDEAAASK
Sbjct: 181 TMGIGTILDAKKVLLLATGESKADAIRAAVEGALSAACPASALQLHRDAVLVIDEAAASK 240

Query: 241 LADKEFYRHIEAENQLLQARLAALKAGE 268
           LADKEFYRHIEAENQLLQARLAALKAGE
Sbjct: 241 LADKEFYRHIEAENQLLQARLAALKAGE 268


Lambda     K      H
   0.316    0.132    0.363 

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: 353
Number of extensions: 5
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: 268
Length of database: 268
Length adjustment: 25
Effective length of query: 243
Effective length of database: 243
Effective search space:    59049
Effective search space used:    59049
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: 47 (22.7 bits)

Align candidate 5208303 Shew_0815 (glucosamine-6-phosphate isomerase (RefSeq))
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.5794.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
    4.5e-96  307.1   0.0    5.1e-96  307.0   0.0    1.0  1  lcl|FitnessBrowser__PV4:5208303  Shew_0815 glucosamine-6-phosphat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208303  Shew_0815 glucosamine-6-phosphate isomerase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.0   0.0   5.1e-96   5.1e-96       1     252 [.       1     246 [.       1     253 [. 0.97

  Alignments for each domain:
  == domain 1  score: 307.0 bits;  conditional E-value: 5.1e-96
                        TIGR00502   1 mklliletyeelsklaariiaekinefkpdaerpfvlGlatGgtPvglykqlielykagkvsfkkvvtfnldeyvgls 78 
                                      m+++il+   e++++ a+ i+++++  kpd     vlGlatG+tPv+ly++l+  ++ag vsf+ v+ fnldey+gl+
  lcl|FitnessBrowser__PV4:5208303   1 MQIVILKDSAEVAEYGANLIINQLKR-KPD-S---VLGLATGSTPVSLYQRLVAANQAGAVSFEGVTSFNLDEYLGLE 73 
                                      89************************.999.5...9****************************************** PP

                        TIGR00502  79 eehPesyhsfmyenffqhidikpeninilnGnaddleaecrryeekikslGkidlfllGiGadGhiafnePgsslesr 156
                                       +hP+sy +fm +++f+ idi++ n +++ G+a+d  a+c+ ye +i+ +G+id++llGiG++Ghi+fneP+s l sr
  lcl|FitnessBrowser__PV4:5208303  74 GSHPQSYRYFMDSQLFDAIDINKANTHVPPGDAEDPIAACEAYEAQIQAAGGIDIQLLGIGRNGHIGFNEPSSGLMSR 151
                                      ****************************************************************************** PP

                        TIGR00502 157 trvktltedtiiansrffegdvnkvPkkaltvGiktildskevlllvsGkekaeavkklvegsvnedvtisalqlhkk 234
                                      trvktlt+ ti  n+rff  + +  P+ ++t+Gi+tild+k+vlll++G++ka+a++++veg+++   ++salqlh++
  lcl|FitnessBrowser__PV4:5208303 152 TRVKTLTQATIEDNARFFA-EGEYQPHLSITMGIGTILDAKKVLLLATGESKADAIRAAVEGALSAACPASALQLHRD 228
                                      ******************9.77888***************************************************** PP

                        TIGR00502 235 vivvadeeaaqelkvktl 252
                                      +++v+de+aa++l  k +
  lcl|FitnessBrowser__PV4:5208303 229 AVLVIDEAAASKLADKEF 246
                                      ************987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (259 nodes)
Target sequences:                          1  (268 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# 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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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