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.6310.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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 6.10
//
[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