Alignments for a candidate for iolG in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolG in Dinoroseobacter shibae DFL-12

Align inositol 2-dehydrogenase (EC 1.1.1.18) (characterized)
to candidate 3607857 Dshi_1265 Inositol 2-dehydrogenase (RefSeq)

Query= BRENDA::O68965
         (330 letters)



>FitnessBrowser__Dino:3607857
          Length = 327

 Score =  336 bits (861), Expect = 5e-97
 Identities = 173/315 (54%), Positives = 215/315 (68%)

Query: 3   VRFGLLGAGRIGKVHAKAVSGNADARLVAVADAFPAAAEAIAGAYGCEVRTIDAIEAAAD 62
           ++ GLLG GRIG+VHA+++S  A+ARLVAVADA P AA+A+A   G EVR  + I  A D
Sbjct: 1   MKLGLLGCGRIGQVHARSLSRIAEARLVAVADAVPEAAQALAARAGAEVRGSEEIITAPD 60

Query: 63  IDAVVICTPTDTHADLIERFARAGKAIFCEKPIDLDAERVRACLKVVSDTKAKLMVGFNR 122
           IDAV++ TPT  H + I   A AGKAIFCEKPIDL AER   C + V       +  FNR
Sbjct: 61  IDAVIVATPTTLHFEQIHAIAAAGKAIFCEKPIDLSAERAAQCQQAVEAAGVPFLTAFNR 120

Query: 123 RFDPHFMAVRKAIDDGRIGEVEMVTITSRDPSAPPVDYIKRSGGIFRDMTIHDFDMARFL 182
           RFDP F  +   + DG IGE+EMV ITSRDP+ PP+ YI+ SGG+FRDM IHDFDMARFL
Sbjct: 121 RFDPSFAHLHDQVRDGAIGEIEMVVITSRDPAPPPISYIESSGGLFRDMMIHDFDMARFL 180

Query: 183 LGEEPVSVTATAAVLIDKAIGDAGDYDSVSVILQTASGKQAIISNSRRATYGYDQRIEVH 242
           LGEEP  + A  + L+D AIG AGD D+  V L+TASG+   I+NSRRATYGYDQRIEVH
Sbjct: 181 LGEEPAEIHAFGSCLVDPAIGAAGDIDTAMVTLRTASGRLCQINNSRRATYGYDQRIEVH 240

Query: 243 GSKGAVAAENQRPVSIEIATGDGYTRPPLHDFFMTRYTEAYANEIESFIAAIEKGAEIAP 302
           GSKG + A NQ    +  A+G G+T     DFF+ RY  AY  E+  F+ A+ +G+ +  
Sbjct: 241 GSKGMLQAANQPAHLVTQASGGGFTAARSMDFFLERYEAAYLAEMTHFVDAVTRGSPLKA 300

Query: 303 SGNDGLAALALADAA 317
           +  DG+AA  LAD A
Sbjct: 301 TIADGVAAQRLADTA 315


Lambda     K      H
   0.320    0.134    0.379 

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: 313
Number of extensions: 10
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: 327
Length adjustment: 28
Effective length of query: 302
Effective length of database: 299
Effective search space:    90298
Effective search space used:    90298
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: 49 (23.5 bits)

Align candidate 3607857 Dshi_1265 (Inositol 2-dehydrogenase (RefSeq))
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.724.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   7.2e-130  418.6   0.5     8e-130  418.5   0.5    1.0  1  lcl|FitnessBrowser__Dino:3607857  Dshi_1265 Inositol 2-dehydrogena


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3607857  Dshi_1265 Inositol 2-dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.5   0.5    8e-130    8e-130       2     328 ..       1     324 [.       1     326 [. 0.99

  Alignments for each domain:
  == domain 1  score: 418.5 bits;  conditional E-value: 8e-130
                         TIGR04380   2 lkigiiGaGRigkvHaenlakkvpeaelaavvdvaeeaakelaeklgieevvedveailedpevdAvliasptdtHa 78 
                                       +k+g++G GRig+vHa++l++   ea+l+av+d++ eaa++la++ g+   v+  e+i++ p++dAv++a+pt++H 
  lcl|FitnessBrowser__Dino:3607857   1 MKLGLLGCGRIGQVHARSLSRI-AEARLVAVADAVPEAAQALAARAGA--EVRGSEEIITAPDIDAVIVATPTTLHF 74 
                                       589****************986.*************************..88899********************** PP

                         TIGR04380  79 eliveaakagkhifcEKPidldleeikealkavekagvklqiGfnRRFDanfaevkklveagkiGklellritsrDP 155
                                       e+i + a+agk+ifcEKPidl+ e++ ++++ave+agv+++  fnRRFD++fa+++++v++g iG++e++ itsrDP
  lcl|FitnessBrowser__Dino:3607857  75 EQIHAIAAAGKAIFCEKPIDLSAERAAQCQQAVEAAGVPFLTAFNRRFDPSFAHLHDQVRDGAIGEIEMVVITSRDP 151
                                       ***************************************************************************** PP

                         TIGR04380 156 apppveyvkvsGglflDmtiHDfDmarfllgseveevyaagsvlvdpeleeagdvdtavvvlkfengalaviensrr 232
                                       appp++y+++sGglf+Dm+iHDfDmarfllg+e+ e++a gs+lvdp+++ agd+dta+v+l++++g+l+ i+nsrr
  lcl|FitnessBrowser__Dino:3607857 152 APPPISYIESSGGLFRDMMIHDFDMARFLLGEEPAEIHAFGSCLVDPAIGAAGDIDTAMVTLRTASGRLCQINNSRR 228
                                       ***************************************************************************** PP

                         TIGR04380 233 aayGYdqrvEvfGskGslraendtestvvlsdeegvraekpenfFleRyaeayraeikafvdailedkevsvtaeDg 309
                                       a+yGYdqr+Ev+GskG+l+a+n+ ++ v+ ++  g++a+++  fFleRy++ay ae+++fvda++++++ + t+ Dg
  lcl|FitnessBrowser__Dino:3607857 229 ATYGYDQRIEVHGSKGMLQAANQPAHLVTQASGGGFTAARSMDFFLERYEAAYLAEMTHFVDAVTRGSPLKATIADG 305
                                       ***************************************************************************** PP

                         TIGR04380 310 lkalklalaakrsleegra 328
                                       ++a++la+ a+ + ++g++
  lcl|FitnessBrowser__Dino:3607857 306 VAAQRLADTADTARKTGKV 324
                                       *************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (327 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: 10.68
//
[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