Alignments for a candidate for iolE in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolE in Pseudomonas simiae WCS417

Align Myo-inosose-2 dehydratase (EC 4.2.1.44) (characterized)
to candidate GFF2325 PS417_11855 xylose isomerase

Query= reanno::WCS417:GFF2325
         (295 letters)



>FitnessBrowser__WCS417:GFF2325
          Length = 295

 Score =  602 bits (1552), Expect = e-177
 Identities = 295/295 (100%), Positives = 295/295 (100%)

Query: 1   MPAIRIGINPISWSNDDLPALGGETPLSTALSEGKDIGYEGFELNGKFPKDAKGVGDVLR 60
           MPAIRIGINPISWSNDDLPALGGETPLSTALSEGKDIGYEGFELNGKFPKDAKGVGDVLR
Sbjct: 1   MPAIRIGINPISWSNDDLPALGGETPLSTALSEGKDIGYEGFELNGKFPKDAKGVGDVLR 60

Query: 61  PYDLALVSGWYSSRLARRSVAEEIEAIAGHVELLKHNGATVLVYGEVADSIQGSRIRLIE 120
           PYDLALVSGWYSSRLARRSVAEEIEAIAGHVELLKHNGATVLVYGEVADSIQGSRIRLIE
Sbjct: 61  PYDLALVSGWYSSRLARRSVAEEIEAIAGHVELLKHNGATVLVYGEVADSIQGSRIRLIE 120

Query: 121 RPRFHSEQAWQDYADKLTELARFTLSQGVRLAYHHHMGAYVESPEDIDQLMRRTGPEVGL 180
           RPRFHSEQAWQDYADKLTELARFTLSQGVRLAYHHHMGAYVESPEDIDQLMRRTGPEVGL
Sbjct: 121 RPRFHSEQAWQDYADKLTELARFTLSQGVRLAYHHHMGAYVESPEDIDQLMRRTGPEVGL 180

Query: 181 LFDSGHCYMGGGEPIEVLRKHIDRVCHVHFKDVRKAVVQLARNQMWSFPDCIVNGTFTVP 240
           LFDSGHCYMGGGEPIEVLRKHIDRVCHVHFKDVRKAVVQLARNQMWSFPDCIVNGTFTVP
Sbjct: 181 LFDSGHCYMGGGEPIEVLRKHIDRVCHVHFKDVRKAVVQLARNQMWSFPDCIVNGTFTVP 240

Query: 241 GDGDIDFAELLDVLLAAQYEGWLVVEAEQDPAVAPSYIYAKKGYDTLRALLNERT 295
           GDGDIDFAELLDVLLAAQYEGWLVVEAEQDPAVAPSYIYAKKGYDTLRALLNERT
Sbjct: 241 GDGDIDFAELLDVLLAAQYEGWLVVEAEQDPAVAPSYIYAKKGYDTLRALLNERT 295


Lambda     K      H
   0.319    0.138    0.421 

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: 489
Number of extensions: 11
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: 295
Length of database: 295
Length adjustment: 26
Effective length of query: 269
Effective length of database: 269
Effective search space:    72361
Effective search space used:    72361
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 GFF2325 PS417_11855 (xylose isomerase)
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.29786.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     8e-118  379.2   0.0   9.1e-118  379.0   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF2325  PS417_11855 xylose isomerase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF2325  PS417_11855 xylose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.0   0.0  9.1e-118  9.1e-118       2     289 ..       4     290 ..       3     291 .. 0.98

  Alignments for each domain:
  == domain 1  score: 379.0 bits;  conditional E-value: 9.1e-118
                           TIGR04379   2 vklgiaPiaWvndDlpelggdttleqvlseaaeagfsgtElgnkfpkdpavLkaaleerglelvsgwfsalllek 76 
                                         +++gi+Pi+W+ndDlp lgg+t+l+++lse + +g++g+El  kfpkd++ + ++l+ ++l+lvsgw+s++l+++
  lcl|FitnessBrowser__WCS417:GFF2325   4 IRIGINPISWSNDDLPALGGETPLSTALSEGKDIGYEGFELNGKFPKDAKGVGDVLRPYDLALVSGWYSSRLARR 78 
                                         89************************************************************************* PP

                           TIGR04379  77 sveeeieavrehlellkalgakvivvaEvgksiqgdkdtplaerpkl.teeeweelaeklnklgeilkekglkla 150
                                         sv+eeiea++ h+ellk+ ga+v+v++Ev++siqg+ ++ l erp++ +e+ w+++a+kl++l+++  ++g++la
  lcl|FitnessBrowser__WCS417:GFF2325  79 SVAEEIEAIAGHVELLKHNGATVLVYGEVADSIQGS-RIRLIERPRFhSEQAWQDYADKLTELARFTLSQGVRLA 152
                                         ***********************************9.899999999956778*********************** PP

                           TIGR04379 151 yHhHlgtvveteeeidrlmeltdpelvgllyDtGHlvfagedplavlekyadRiahvHlKDvRkevleevrkekk 225
                                         yHhH+g++ve+ e+id+lm  t+pe vgll+D+GH +++g++p++vl+k++dR++hvH+KDvRk+v++ +r++ +
  lcl|FitnessBrowser__WCS417:GFF2325 153 YHHHMGAYVESPEDIDQLMRRTGPE-VGLLFDSGHCYMGGGEPIEVLRKHIDRVCHVHFKDVRKAVVQLARNQMW 226
                                         *************************.************************************************* PP

                           TIGR04379 226 sFldavlkGvftvPGdGcidfeeilealkakdYeGWlvvEaEqDPakaepleyakkakkyleel 289
                                         sF d++++G ftvPGdG+idf+e+l+ l a++YeGWlvvEaEqDPa+a+++ yakk++++l++l
  lcl|FitnessBrowser__WCS417:GFF2325 227 SFPDCIVNGTFTVPGDGDIDFAELLDVLLAAQYEGWLVVEAEQDPAVAPSYIYAKKGYDTLRAL 290
                                         ************************************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (290 nodes)
Target sequences:                          1  (295 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: 11.12
//
[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