Alignments for a candidate for iolG in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolG in Burkholderia phytofirmans PsJN

Align Myo-inositol 2-dehydrogenase (EC 1.1.1.18) (characterized)
to candidate BPHYT_RS13885 BPHYT_RS13885 myo-inositol 2-dehydrogenase

Query= reanno::HerbieS:HSERO_RS12095
         (330 letters)



>FitnessBrowser__BFirm:BPHYT_RS13885
          Length = 338

 Score =  480 bits (1236), Expect = e-140
 Identities = 237/327 (72%), Positives = 274/327 (83%)

Query: 2   IDVAIFGAGRIGKIHAANIAAQAGVRLKYVCDVHAESAAELAQRHGAQVGRVEQVLDDSS 61
           IDVA+FGAGRIGKIHAAN+A Q GVRLKYV DV+ E+AA LA  HGAQV  ++  + D+S
Sbjct: 8   IDVAVFGAGRIGKIHAANLARQPGVRLKYVVDVNREAAAALAAEHGAQVADIDGAMGDAS 67

Query: 62  VAAVVIASSTDTHADLILRAAAAGKAIFCEKPVDLDLQRAQACAEAVRAAGVTCMIGFQR 121
           + A VI SSTDTHADLIL++AA  K +FCEKPVDL L+RA+ACA+AV  AGV CMIGFQR
Sbjct: 68  IGATVICSSTDTHADLILQSAAQKKHVFCEKPVDLTLERARACADAVERAGVVCMIGFQR 127

Query: 122 RFDPTFESLSRRLEAGEIGDPEMLLVTSRDPGAPPLSYIASSGGIFKDMLIHDFDIFRWI 181
           RFDPTF +L  RL+AGEIG PEML+VTSRDPGAPP+ YI  SGGIFKDMLIHDFDIFRWI
Sbjct: 128 RFDPTFSALKARLDAGEIGTPEMLVVTSRDPGAPPVEYIKHSGGIFKDMLIHDFDIFRWI 187

Query: 182 LADEAVSVFATGSCLTDPAIATAGDVDSTAVTLTTRSGRLCQINTSRRAAYGYDQRFEVL 241
           L DEA ++ ATGSCL+DPAIA AGD+DSTAVT+ T+ GRLCQINT+RRAAYGYDQRFEVL
Sbjct: 188 LDDEAETLHATGSCLSDPAIAEAGDIDSTAVTIRTKRGRLCQINTARRAAYGYDQRFEVL 247

Query: 242 GSKGMLQAGNHRPTEVVAATASQVGSDLPEHFFLERYRAAYAREMAHFFQAMQSGAPVRT 301
           GS GMLQAGN RPTEV A + ++V SD+PE FFLERYRAAYA E+AHFF A+  G PVRT
Sbjct: 248 GSHGMLQAGNVRPTEVTAYSKTEVSSDVPEAFFLERYRAAYAHEIAHFFDAVTHGKPVRT 307

Query: 302 SIEDGVKALQLAEAAATSWRERRIVSL 328
           ++ DG+KAL+LAEAA  SWRE R + L
Sbjct: 308 TVADGLKALELAEAATRSWREGRAIKL 334


Lambda     K      H
   0.321    0.132    0.380 

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: 374
Number of extensions: 7
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: 330
Length of database: 338
Length adjustment: 28
Effective length of query: 302
Effective length of database: 310
Effective search space:    93620
Effective search space used:    93620
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 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate BPHYT_RS13885 BPHYT_RS13885 (myo-inositol 2-dehydrogenase)
to HMM TIGR04380 (iolG: inositol 2-dehydrogenase (EC 1.1.1.18))

# 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/TIGR04380.hmm
# target sequence database:        /tmp/gapView.24743.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR04380  [M=330]
Accession:   TIGR04380
Description: myo_inos_iolG: inositol 2-dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   6.1e-130  418.8   0.8   6.9e-130  418.7   0.8    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS13885  BPHYT_RS13885 myo-inositol 2-deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS13885  BPHYT_RS13885 myo-inositol 2-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.7   0.8  6.9e-130  6.9e-130       2     330 .]       8     333 ..       7     333 .. 0.99

  Alignments for each domain:
  == domain 1  score: 418.7 bits;  conditional E-value: 6.9e-130
                                TIGR04380   2 lkigiiGaGRigkvHaenlakkvpeaelaavvdvaeeaakelaeklgieevvedveailedpevdAvlia 71 
                                              ++++++GaGRigk+Ha nla++ p+++l++vvdv++eaa++la++ g+  +v+d++ ++ d+ + A +i+
  lcl|FitnessBrowser__BFirm:BPHYT_RS13885   8 IDVAVFGAGRIGKIHAANLARQ-PGVRLKYVVDVNREAAAALAAEHGA--QVADIDGAMGDASIGATVIC 74 
                                              689*******************.*************************..999***************** PP

                                TIGR04380  72 sptdtHaeliveaakagkhifcEKPidldleeikealkavekagvklqiGfnRRFDanfaevkklveagk 141
                                              s+tdtHa+li ++a+++kh+fcEKP+dl+le+++++++ave+agv ++iGf+RRFD++f+++k++++ag+
  lcl|FitnessBrowser__BFirm:BPHYT_RS13885  75 SSTDTHADLILQSAAQKKHVFCEKPVDLTLERARACADAVERAGVVCMIGFQRRFDPTFSALKARLDAGE 144
                                              ********************************************************************** PP

                                TIGR04380 142 iGklellritsrDPapppveyvkvsGglflDmtiHDfDmarfllgseveevyaagsvlvdpeleeagdvd 211
                                              iG++e+l +tsrDP +ppvey+k+sGg+f Dm iHDfD+ r++l++e e  +a+gs+l dp+++eagd+d
  lcl|FitnessBrowser__BFirm:BPHYT_RS13885 145 IGTPEMLVVTSRDPGAPPVEYIKHSGGIFKDMLIHDFDIFRWILDDEAETLHATGSCLSDPAIAEAGDID 214
                                              ********************************************************************** PP

                                TIGR04380 212 tavvvlkfengalaviensrraayGYdqrvEvfGskGslraendtestvvlsdeegvraekpenfFleRy 281
                                              +++v+++++ g+l+ i+ +rraayGYdqr Ev+Gs+G+l+a n+++++v+ +++++v+++ pe fFleRy
  lcl|FitnessBrowser__BFirm:BPHYT_RS13885 215 STAVTIRTKRGRLCQINTARRAAYGYDQRFEVLGSHGMLQAGNVRPTEVTAYSKTEVSSDVPEAFFLERY 284
                                              ********************************************************************** PP

                                TIGR04380 282 aeayraeikafvdailedkevsvtaeDglkalklalaakrsleegravk 330
                                              ++ay++ei++f+da++++k+v  t+ Dglkal+la+aa+rs +egra+k
  lcl|FitnessBrowser__BFirm:BPHYT_RS13885 285 RAAYAHEIAHFFDAVTHGKPVRTTVADGLKALELAEAATRSWREGRAIK 333
                                              *********************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (338 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 11.78
//
[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