Alignments for a candidate for iolG in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolG in Pseudomonas fluorescens FW300-N2E2

Align inositol 2-dehydrogenase (EC 1.1.1.18) (characterized)
to candidate Pf6N2E2_1002 Myo-inositol 2-dehydrogenase (EC 1.1.1.18)

Query= BRENDA::O68965
         (330 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1002
          Length = 333

 Score =  279 bits (713), Expect = 8e-80
 Identities = 150/330 (45%), Positives = 206/330 (62%), Gaps = 4/330 (1%)

Query: 3   VRFGLLGAGRIGKVHAKAVSGNADARLVAVADAFPAAAEAIAGAYGCEVRT--IDAIEAA 60
           +R  +LGAGRIGK+HA  V+ N   +LV +AD +     A+A   GCE       AIE  
Sbjct: 2   LRIAVLGAGRIGKIHAANVATNPRTKLVVIADPWKEGVNALAMQLGCEAAYDYASAIERT 61

Query: 61  ADIDAVVICTPTDTHADLIERFARAGKAIFCEKPIDLDAERVRACLKVVSDTKAKLMVGF 120
            D+DAV I TPT+ H +L+ +  R GK + CEKPID+D ER +A +  +     ++M+ F
Sbjct: 62  -DVDAVFIGTPTEFHIELMLQAVRLGKPVICEKPIDMDYERAKAAVDELERLNGRVMLAF 120

Query: 121 NRRFDPHFMAVRKAIDDGRIGEVEMVTITSRDPSAPPVDYIKRSGGIFRDMTIHDFDMAR 180
           NRRFDP ++ +R+AIDDG IG V  V ITSRDP+     Y++ SGGIFRDMTIHDFDMAR
Sbjct: 121 NRRFDPDYLRLRRAIDDGEIGVVRQVIITSRDPALAARAYLETSGGIFRDMTIHDFDMAR 180

Query: 181 FLLGEEPVSVTATAAVLIDKAIGDAGDYDSVSVILQTASGKQAIISNSRRATYGYDQRIE 240
            LLGEEPV V A  + L+D  +    DYDSV V+++TASG+Q  I+  R A YG+DQR+E
Sbjct: 181 SLLGEEPVEVFAVGSRLVDPTLESIPDYDSVMVLMRTASGRQCHINCCREAVYGFDQRLE 240

Query: 241 VHGSKGAVAAENQRPVSIEIATGDGY-TRPPLHDFFMTRYTEAYANEIESFIAAIEKGAE 299
           V GSKG +  EN R  S+     +      PL +FF+ R+ ++Y  E+ SF+ A+E  + 
Sbjct: 241 VSGSKGMLLNENHRTNSVRRYGAEATDVADPLLNFFLERHADSYKIELNSFLDAVENNSP 300

Query: 300 IAPSGNDGLAALALADAAVRSVAEKRQISI 329
           +  +  DGL AL LA+ A  S    + + +
Sbjct: 301 MPATPRDGLRALRLANCASESAETGKVVRV 330


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: 301
Number of extensions: 9
Number of successful extensions: 3
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: 333
Length adjustment: 28
Effective length of query: 302
Effective length of database: 305
Effective search space:    92110
Effective search space used:    92110
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 Pf6N2E2_1002 (Myo-inositol 2-dehydrogenase (EC 1.1.1.18))
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.7970.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   9.9e-119  382.0   0.0   1.1e-118  381.8   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1002  Myo-inositol 2-dehydrogenase (EC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1002  Myo-inositol 2-dehydrogenase (EC 1.1.1.18)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  381.8   0.0  1.1e-118  1.1e-118       1     330 []       1     329 [.       1     329 [. 0.98

  Alignments for each domain:
  == domain 1  score: 381.8 bits;  conditional E-value: 1.1e-118
                                      TIGR04380   1 klkigiiGaGRigkvHaenlakkvpeaelaavvdvaeeaakelaeklgieevvedveailedpe 64 
                                                    +l+i+++GaGRigk+Ha n+a++ p+++l+ ++d+ +e +++la +lg  e++ d+++++e+++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1002   1 MLRIAVLGAGRIGKIHAANVATN-PRTKLVVIADPWKEGVNALAMQLGC-EAAYDYASAIERTD 62 
                                                    689********************.*************************.77788********* PP

                                      TIGR04380  65 vdAvliasptdtHaeliveaakagkhifcEKPidldleeikealkavekagvklqiGfnRRFDa 128
                                                    vdAv+i +pt++H+el+ +a++ gk ++cEKPid+d e++k+a++++e+ + ++++ fnRRFD+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1002  63 VDAVFIGTPTEFHIELMLQAVRLGKPVICEKPIDMDYERAKAAVDELERLNGRVMLAFNRRFDP 126
                                                    **************************************************************** PP

                                      TIGR04380 129 nfaevkklveagkiGklellritsrDPapppveyvkvsGglflDmtiHDfDmarfllgseveev 192
                                                     + ++++++++g+iG ++++ itsrDPa+++++y+++sGg+f+DmtiHDfDmar llg+e++ev
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1002 127 DYLRLRRAIDDGEIGVVRQVIITSRDPALAARAYLETSGGIFRDMTIHDFDMARSLLGEEPVEV 190
                                                    **************************************************************** PP

                                      TIGR04380 193 yaagsvlvdpeleeagdvdtavvvlkfengalaviensrraayGYdqrvEvfGskGslraendt 256
                                                    +a+gs+lvdp+le + d+d+++v++++++g+ ++i+ +r+a+yG+dqr+Ev GskG+l  en++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1002 191 FAVGSRLVDPTLESIPDYDSVMVLMRTASGRQCHINCCREAVYGFDQRLEVSGSKGMLLNENHR 254
                                                    **************************************************************** PP

                                      TIGR04380 257 estvvlsdeegv.raekpenfFleRyaeayraeikafvdailedkevsvtaeDglkalklalaa 319
                                                    +++v+++++e + +a+   nfFleR+a++y+ e+++f+da++++++++ t +Dgl+al+la+ a
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1002 255 TNSVRRYGAEATdVADPLLNFFLERHADSYKIELNSFLDAVENNSPMPATPRDGLRALRLANCA 318
                                                    *********9995677889********************************************* PP

                                      TIGR04380 320 krsleegravk 330
                                                    ++s+e+g++v+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1002 319 SESAETGKVVR 329
                                                    *******9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (333 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: 11.38
//
[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