Alignments for a candidate for iolE in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolE in Burkholderia phytofirmans PsJN

Align Myo-inosose-2 dehydratase (EC 4.2.1.44) (characterized)
to candidate BPHYT_RS13920 BPHYT_RS13920 xylose isomerase

Query= reanno::BFirm:BPHYT_RS13920
         (305 letters)



>FitnessBrowser__BFirm:BPHYT_RS13920
          Length = 305

 Score =  620 bits (1599), Expect = 0.0
 Identities = 305/305 (100%), Positives = 305/305 (100%)

Query: 1   MTAFDVRIGINPLSWMNDDLPSLGGETPLEVALTEGREIGYQGFELGNKFPREPQALKSL 60
           MTAFDVRIGINPLSWMNDDLPSLGGETPLEVALTEGREIGYQGFELGNKFPREPQALKSL
Sbjct: 1   MTAFDVRIGINPLSWMNDDLPSLGGETPLEVALTEGREIGYQGFELGNKFPREPQALKSL 60

Query: 61  LAQYDLALVSGWYSGRLARRSVEEEIAEVGPHLELLAQNGATAMVYGEVADSIQGAAQPL 120
           LAQYDLALVSGWYSGRLARRSVEEEIAEVGPHLELLAQNGATAMVYGEVADSIQGAAQPL
Sbjct: 61  LAQYDLALVSGWYSGRLARRSVEEEIAEVGPHLELLAQNGATAMVYGEVADSIQGAAQPL 120

Query: 121 YQRPRFFSEKQWADYAARVDEFARYTLSRGVRLAYHHHMGAYVETPADVDQLMARTSDAV 180
           YQRPRFFSEKQWADYAARVDEFARYTLSRGVRLAYHHHMGAYVETPADVDQLMARTSDAV
Sbjct: 121 YQRPRFFSEKQWADYAARVDEFARYTLSRGVRLAYHHHMGAYVETPADVDQLMARTSDAV 180

Query: 181 GLLFDAGHITFAGGDPLAVLDKHIGRVCHVHCKDVRPAVMKLARNRNWSFLDAVIAGAFT 240
           GLLFDAGHITFAGGDPLAVLDKHIGRVCHVHCKDVRPAVMKLARNRNWSFLDAVIAGAFT
Sbjct: 181 GLLFDAGHITFAGGDPLAVLDKHIGRVCHVHCKDVRPAVMKLARNRNWSFLDAVIAGAFT 240

Query: 241 VPGDGAVNFPAIIERLKRHGYCGWLVVEAEQDPVVAPSFEYAQKGYKTLRALVDAPLDGT 300
           VPGDGAVNFPAIIERLKRHGYCGWLVVEAEQDPVVAPSFEYAQKGYKTLRALVDAPLDGT
Sbjct: 241 VPGDGAVNFPAIIERLKRHGYCGWLVVEAEQDPVVAPSFEYAQKGYKTLRALVDAPLDGT 300

Query: 301 EQEAA 305
           EQEAA
Sbjct: 301 EQEAA 305


Lambda     K      H
   0.320    0.137    0.417 

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: 469
Number of extensions: 5
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: 305
Length of database: 305
Length adjustment: 27
Effective length of query: 278
Effective length of database: 278
Effective search space:    77284
Effective search space used:    77284
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: 48 (23.1 bits)

Align candidate BPHYT_RS13920 BPHYT_RS13920 (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.24475.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
     6e-125  402.5   0.0   6.8e-125  402.4   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS13920  BPHYT_RS13920 xylose isomerase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS13920  BPHYT_RS13920 xylose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  402.4   0.0  6.8e-125  6.8e-125       2     289 ..       6     292 ..       5     293 .. 0.98

  Alignments for each domain:
  == domain 1  score: 402.4 bits;  conditional E-value: 6.8e-125
                                TIGR04379   2 vklgiaPiaWvndDlpelggdttleqvlseaaeagfsgtElgnkfpkdpavLkaaleerglelvsgwfsa 71 
                                              v++gi+P++W+ndDlp+lgg+t+le +l+e +e+g++g+Elgnkfp++p++Lk++l +++l+lvsgw+s+
  lcl|FitnessBrowser__BFirm:BPHYT_RS13920   6 VRIGINPLSWMNDDLPSLGGETPLEVALTEGREIGYQGFELGNKFPREPQALKSLLAQYDLALVSGWYSG 75 
                                              89******************************************************************** PP

                                TIGR04379  72 llleksveeeieavrehlellkalgakvivvaEvgksiqgdkdtplaerpkl.teeeweelaeklnklge 140
                                              +l+++sveeei++v  hlell++ ga+++v++Ev++siqg   +pl +rp++ +e++w+++a++++++++
  lcl|FitnessBrowser__BFirm:BPHYT_RS13920  76 RLARRSVEEEIAEVGPHLELLAQNGATAMVYGEVADSIQGA-AQPLYQRPRFfSEKQWADYAARVDEFAR 144
                                              ****************************************9.899****66549**************** PP

                                TIGR04379 141 ilkekglklayHhHlgtvveteeeidrlmeltdpelvgllyDtGHlvfagedplavlekyadRiahvHlK 210
                                              +  ++g++layHhH+g++vet +++d+lm+ t+++ vgll+D+GH++fag+dplavl+k++ R++hvH+K
  lcl|FitnessBrowser__BFirm:BPHYT_RS13920 145 YTLSRGVRLAYHHHMGAYVETPADVDQLMARTSDA-VGLLFDAGHITFAGGDPLAVLDKHIGRVCHVHCK 213
                                              *********************************99.********************************** PP

                                TIGR04379 211 DvRkevleevrkekksFldavlkGvftvPGdGcidfeeilealkakdYeGWlvvEaEqDPakaepleyak 280
                                              DvR++v++ +r++++sFldav++G+ftvPGdG+++f +i+e lk+++Y GWlvvEaEqDP +a+++eya+
  lcl|FitnessBrowser__BFirm:BPHYT_RS13920 214 DVRPAVMKLARNRNWSFLDAVIAGAFTVPGDGAVNFPAIIERLKRHGYCGWLVVEAEQDPVVAPSFEYAQ 283
                                              ********************************************************************** PP

                                TIGR04379 281 kakkyleel 289
                                              k++k+l++l
  lcl|FitnessBrowser__BFirm:BPHYT_RS13920 284 KGYKTLRAL 292
                                              *****9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (290 nodes)
Target sequences:                          1  (305 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: 8.69
//
[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