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.14565.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 6.43
//
[ok]

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

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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