Alignments for a candidate for iolG in Sinorhizobium fredii NGR234

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolG in Sinorhizobium fredii NGR234

Align Myo-inositol 2-dehydrogenase (EC 1.1.1.18) (characterized)
to candidate WP_012706497.1 NGR_RS02130 inositol 2-dehydrogenase

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



>NCBI__GCF_000018545.1:WP_012706497.1
          Length = 335

 Score =  289 bits (740), Expect = 6e-83
 Identities = 154/325 (47%), Positives = 199/325 (61%)

Query: 4   VAIFGAGRIGKIHAANIAAQAGVRLKYVCDVHAESAAELAQRHGAQVGRVEQVLDDSSVA 63
           VA+FGAGR+G IHAA +  ++   L  + D H  SA  LA  HG +V   + V DD  V 
Sbjct: 10  VAVFGAGRMGAIHAATLVRRSDACLAGIVDAHLPSAERLAAEHGVRVLEEDAVFDDEDVD 69

Query: 64  AVVIASSTDTHADLILRAAAAGKAIFCEKPVDLDLQRAQACAEAVRAAGVTCMIGFQRRF 123
           AVVIAS+ D+H  LILR+ AA KAIFCEKP+  DL+  Q+ A+ V A  +  ++ F RRF
Sbjct: 70  AVVIASAADSHPHLILRSVAARKAIFCEKPLARDLEAVQSVAKVVEATKLPFLLAFNRRF 129

Query: 124 DPTFESLSRRLEAGEIGDPEMLLVTSRDPGAPPLSYIASSGGIFKDMLIHDFDIFRWILA 183
           DP F +L+ RL  GEIG  E+ ++TSRDP  PP+ Y+  SGG+F++  IHD D+ RW+  
Sbjct: 130 DPDFVALASRLRGGEIGAVELAILTSRDPSPPPIDYVVKSGGVFRETTIHDIDVARWLTG 189

Query: 184 DEAVSVFATGSCLTDPAIATAGDVDSTAVTLTTRSGRLCQINTSRRAAYGYDQRFEVLGS 243
           +E +SV AT S LT  A+  A   D+  VT+T  SG +  IN S RAAYGYDQR EVLG 
Sbjct: 190 EEPISVHATASALTTVAMKEAKLPDTVVVTMTMPSGAIVSINNSWRAAYGYDQRVEVLGE 249

Query: 244 KGMLQAGNHRPTEVVAATASQVGSDLPEHFFLERYRAAYAREMAHFFQAMQSGAPVRTSI 303
            GML+  N     V    AS      PE FFLERY  AY  E+ +F  A+  G  +   +
Sbjct: 250 LGMLKLANRLQNGVTQMGASGTWKSNPEPFFLERYANAYNAELDYFISALWEGRTISPGV 309

Query: 304 EDGVKALQLAEAAATSWRERRIVSL 328
            DGVKALQ+A AA  S R  + V+L
Sbjct: 310 ADGVKALQIAYAAEQSARTGQTVTL 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: 227
Number of extensions: 2
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: 335
Length adjustment: 28
Effective length of query: 302
Effective length of database: 307
Effective search space:    92714
Effective search space used:    92714
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 WP_012706497.1 NGR_RS02130 (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.1929734.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.3e-113  362.9   0.0   7.1e-113  362.8   0.0    1.0  1  NCBI__GCF_000018545.1:WP_012706497.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000018545.1:WP_012706497.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  362.8   0.0  7.1e-113  7.1e-113       2     329 ..       8     332 ..       7     333 .. 0.99

  Alignments for each domain:
  == domain 1  score: 362.8 bits;  conditional E-value: 7.1e-113
                             TIGR04380   2 lkigiiGaGRigkvHaenlakkvpeaelaavvdvaeeaakelaeklgieevvedveailedpevdAvliaspt 74 
                                           l+++++GaGR+g++Ha +l+++  +a+la +vd++ ++a++la++ g+  +v + +a+++d++vdAv+ias++
  NCBI__GCF_000018545.1:WP_012706497.1   8 LRVAVFGAGRMGAIHAATLVRR-SDACLAGIVDAHLPSAERLAAEHGV--RVLEEDAVFDDEDVDAVVIASAA 77 
                                           78********************.*************************..666689***************** PP

                             TIGR04380  75 dtHaeliveaakagkhifcEKPidldleeikealkavekagvklqiGfnRRFDanfaevkklveagkiGklel 147
                                           d H +li ++++a+k+ifcEKP++ dle++++++k+ve++++++++ fnRRFD+ f ++ ++++ g+iG++el
  NCBI__GCF_000018545.1:WP_012706497.1  78 DSHPHLILRSVAARKAIFCEKPLARDLEAVQSVAKVVEATKLPFLLAFNRRFDPDFVALASRLRGGEIGAVEL 150
                                           ************************************************************************* PP

                             TIGR04380 148 lritsrDPapppveyvkvsGglflDmtiHDfDmarfllgseveevyaagsvlvdpeleeagdvdtavvvlkfe 220
                                              tsrDP+ppp++yv +sGg+f+ +tiHD+D+ar+l+g+e+ +v+a++s+l   +++ea+  dt+vv++ + 
  NCBI__GCF_000018545.1:WP_012706497.1 151 AILTSRDPSPPPIDYVVKSGGVFRETTIHDIDVARWLTGEEPISVHATASALTTVAMKEAKLPDTVVVTMTMP 223
                                           ************************************************************************* PP

                             TIGR04380 221 ngalaviensrraayGYdqrvEvfGskGslraendtestvvlsdeegvraekpenfFleRyaeayraeikafv 293
                                           +ga+  i+ns+raayGYdqrvEv+G+ G+l+++n+ ++ v+ ++++g+ +++pe fFleRya+ay+ae++ f+
  NCBI__GCF_000018545.1:WP_012706497.1 224 SGAIVSINNSWRAAYGYDQRVEVLGELGMLKLANRLQNGVTQMGASGTWKSNPEPFFLERYANAYNAELDYFI 296
                                           ************************************************************************* PP

                             TIGR04380 294 dailedkevsvtaeDglkalklalaakrsleegrav 329
                                            a+ e+++ s+++ Dg+kal++a aa++s+++g++v
  NCBI__GCF_000018545.1:WP_012706497.1 297 SALWEGRTISPGVADGVKALQIAYAAEQSARTGQTV 332
                                           *********************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (335 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: 00:00:00.00
# Mc/sec: 23.71
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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