Alignments for a candidate for iolE in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolE in Pseudomonas fluorescens FW300-N1B4

Align Myo-inosose-2 dehydratase (EC 4.2.1.44) (characterized)
to candidate Pf1N1B4_4275 Inosose dehydratase (EC 4.2.1.44)

Query= reanno::pseudo3_N2E3:AO353_21340
         (297 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4275
          Length = 297

 Score =  579 bits (1492), Expect = e-170
 Identities = 281/294 (95%), Positives = 289/294 (98%)

Query: 1   MPAIRIGINPISWSNDDLPALGGETPLSTALSEGKEIGYEGFELNGKFPKDAKGVGDVLR 60
           MPAIRIGINPISWSNDDLP+LGGETPLSTALSEGK+IGYEGFELNGKFPKDAKGVGDVLR
Sbjct: 1   MPAIRIGINPISWSNDDLPSLGGETPLSTALSEGKDIGYEGFELNGKFPKDAKGVGDVLR 60

Query: 61  PYDLALVSGWYSSRLARRSVAEEIEAIGSHVELLAKNGAKVLVYGEVADSIQGQRIPLVE 120
           PYDLALVSGWYSSRLARRSVAEEI+AI SHVELLAKNGAKVLVYGEVADSIQGQRIPLVE
Sbjct: 61  PYDLALVSGWYSSRLARRSVAEEIDAIASHVELLAKNGAKVLVYGEVADSIQGQRIPLVE 120

Query: 121 RPRFHTEQAWQEYADKLNELARFTLSQGVRLAYHHHMGAYVESPADIDKLMSLTGSEVGL 180
           RPRFHTEQAWQEYADKL ELARFTLSQGVRLAYHHHMGAYVESPADIDKLM+LTGSEVGL
Sbjct: 121 RPRFHTEQAWQEYADKLTELARFTLSQGVRLAYHHHMGAYVESPADIDKLMALTGSEVGL 180

Query: 181 LFDSGHCYMGGGEPLEVLRKHIGRICHVHFKDVRKPVVQLARNNLWSFPDCIINGTFTVP 240
           LFDSGHCYMGGGEPL+VLRKHI RICHVHFKDVRKPVVQLARNNLWSFPDCIINGTFTVP
Sbjct: 181 LFDSGHCYMGGGEPLQVLRKHIERICHVHFKDVRKPVVQLARNNLWSFPDCIINGTFTVP 240

Query: 241 GDGDIDFAALLDVLLAADYHGWLVVEAEQDPAVAPSYVYAKKGYETLRALLDQR 294
           GDGDIDF ALLDVLL ADYHGWLVVEAEQDPAVAPSYVYAKKGY+TLRALL++R
Sbjct: 241 GDGDIDFGALLDVLLGADYHGWLVVEAEQDPAVAPSYVYAKKGYDTLRALLEER 294


Lambda     K      H
   0.319    0.138    0.420 

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: 438
Number of extensions: 8
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: 297
Length of database: 297
Length adjustment: 26
Effective length of query: 271
Effective length of database: 271
Effective search space:    73441
Effective search space used:    73441
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate Pf1N1B4_4275 (Inosose dehydratase (EC 4.2.1.44))
to HMM TIGR04379 (iolE: myo-inosose-2 dehydratase (EC 4.2.1.44))

# 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/TIGR04379.hmm
# target sequence database:        /tmp/gapView.28830.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR04379  [M=290]
Accession:   TIGR04379
Description: myo_inos_iolE: myo-inosose-2 dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   6.4e-118  379.5   0.0   7.2e-118  379.3   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4275  Inosose dehydratase (EC 4.2.1.44


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4275  Inosose dehydratase (EC 4.2.1.44)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.3   0.0  7.2e-118  7.2e-118       2     289 ..       4     290 ..       3     291 .. 0.99

  Alignments for each domain:
  == domain 1  score: 379.3 bits;  conditional E-value: 7.2e-118
                                      TIGR04379   2 vklgiaPiaWvndDlpelggdttleqvlseaaeagfsgtElgnkfpkdpavLkaaleerglelv 65 
                                                    +++gi+Pi+W+ndDlp+lgg+t+l+++lse + +g++g+El  kfpkd++ + ++l+ ++l+lv
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4275   4 IRIGINPISWSNDDLPSLGGETPLSTALSEGKDIGYEGFELNGKFPKDAKGVGDVLRPYDLALV 67 
                                                    89************************************************************** PP

                                      TIGR04379  66 sgwfsallleksveeeieavrehlellkalgakvivvaEvgksiqgdkdtplaerpkl.teeew 128
                                                    sgw+s++l+++sv+eei+a+++h+ell++ gakv+v++Ev++siqg+ ++pl erp++ te+ w
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4275  68 SGWYSSRLARRSVAEEIDAIASHVELLAKNGAKVLVYGEVADSIQGQ-RIPLVERPRFhTEQAW 130
                                                    **********************************************9.9******99977889* PP

                                      TIGR04379 129 eelaeklnklgeilkekglklayHhHlgtvveteeeidrlmeltdpelvgllyDtGHlvfaged 192
                                                    +e+a+kl++l+++  ++g++layHhH+g++ve+ ++id+lm+lt+ e vgll+D+GH +++g++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4275 131 QEYADKLTELARFTLSQGVRLAYHHHMGAYVESPADIDKLMALTGSE-VGLLFDSGHCYMGGGE 193
                                                    *********************************************99.**************** PP

                                      TIGR04379 193 plavlekyadRiahvHlKDvRkevleevrkekksFldavlkGvftvPGdGcidfeeilealkak 256
                                                    pl+vl+k+++Ri+hvH+KDvRk v++ +r++ +sF d++++G ftvPGdG+idf ++l+ l  +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4275 194 PLQVLRKHIERICHVHFKDVRKPVVQLARNNLWSFPDCIINGTFTVPGDGDIDFGALLDVLLGA 257
                                                    **************************************************************** PP

                                      TIGR04379 257 dYeGWlvvEaEqDPakaepleyakkakkyleel 289
                                                    dY+GWlvvEaEqDPa+a+++ yakk++++l++l
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4275 258 DYHGWLVVEAEQDPAVAPSYVYAKKGYDTLRAL 290
                                                    *****************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (290 nodes)
Target sequences:                          1  (297 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.50
//
[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