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.4096.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.15
//
[ok]

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

Links

Downloads

Related tools

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