Alignments for a candidate for xylA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylA in Burkholderia phytofirmans PsJN

Align Xylose isomerase (EC 5.3.1.5) (characterized)
to candidate BPHYT_RS32825 BPHYT_RS32825 xylose isomerase

Query= reanno::BFirm:BPHYT_RS32825
         (440 letters)



>FitnessBrowser__BFirm:BPHYT_RS32825
          Length = 440

 Score =  909 bits (2348), Expect = 0.0
 Identities = 440/440 (100%), Positives = 440/440 (100%)

Query: 1   MSYFEHIPEIRYEGPQSDNPLAYRHYDKSKKVLGKTLEEHLRIAVCYWHTFVWPGVDIFG 60
           MSYFEHIPEIRYEGPQSDNPLAYRHYDKSKKVLGKTLEEHLRIAVCYWHTFVWPGVDIFG
Sbjct: 1   MSYFEHIPEIRYEGPQSDNPLAYRHYDKSKKVLGKTLEEHLRIAVCYWHTFVWPGVDIFG 60

Query: 61  QGTFRRPWQQAGDAMERAQQKADSAFEFFSKLGTPYYTFHDTDVSPEGSNLKEYSENFLR 120
           QGTFRRPWQQAGDAMERAQQKADSAFEFFSKLGTPYYTFHDTDVSPEGSNLKEYSENFLR
Sbjct: 61  QGTFRRPWQQAGDAMERAQQKADSAFEFFSKLGTPYYTFHDTDVSPEGSNLKEYSENFLR 120

Query: 121 ITDYLARKQESTGIKLLWGTANLFSHPRYAAGAATSPDPEVFAFAATQVRHALDATQRLG 180
           ITDYLARKQESTGIKLLWGTANLFSHPRYAAGAATSPDPEVFAFAATQVRHALDATQRLG
Sbjct: 121 ITDYLARKQESTGIKLLWGTANLFSHPRYAAGAATSPDPEVFAFAATQVRHALDATQRLG 180

Query: 181 GDNYVLWGGREGYDTLLNTDLVRERDQLARFLHMVVDHAHKIGFKGSLLIEPKPQEPTKH 240
           GDNYVLWGGREGYDTLLNTDLVRERDQLARFLHMVVDHAHKIGFKGSLLIEPKPQEPTKH
Sbjct: 181 GDNYVLWGGREGYDTLLNTDLVRERDQLARFLHMVVDHAHKIGFKGSLLIEPKPQEPTKH 240

Query: 241 QYDYDVATVHGFLLQHGLDKEIRVNIEANHATLAGHSFHHEIATAYALGIFGSVDANRGD 300
           QYDYDVATVHGFLLQHGLDKEIRVNIEANHATLAGHSFHHEIATAYALGIFGSVDANRGD
Sbjct: 241 QYDYDVATVHGFLLQHGLDKEIRVNIEANHATLAGHSFHHEIATAYALGIFGSVDANRGD 300

Query: 301 PQNGWDTDQFPNSVEELTLAFYEILKHGGFTTGGMNFDSKVRRQSVDPEDLFYGHIGAID 360
           PQNGWDTDQFPNSVEELTLAFYEILKHGGFTTGGMNFDSKVRRQSVDPEDLFYGHIGAID
Sbjct: 301 PQNGWDTDQFPNSVEELTLAFYEILKHGGFTTGGMNFDSKVRRQSVDPEDLFYGHIGAID 360

Query: 361 NLALAVERAAVLIENDRLDQFKRQRYSGWDAEFGRKISSGDYSLSALAEEAMARGLNPQH 420
           NLALAVERAAVLIENDRLDQFKRQRYSGWDAEFGRKISSGDYSLSALAEEAMARGLNPQH
Sbjct: 361 NLALAVERAAVLIENDRLDQFKRQRYSGWDAEFGRKISSGDYSLSALAEEAMARGLNPQH 420

Query: 421 ASGHQELMENIVNQAIYSGR 440
           ASGHQELMENIVNQAIYSGR
Sbjct: 421 ASGHQELMENIVNQAIYSGR 440


Lambda     K      H
   0.319    0.136    0.414 

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: 892
Number of extensions: 19
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: 440
Length of database: 440
Length adjustment: 32
Effective length of query: 408
Effective length of database: 408
Effective search space:   166464
Effective search space used:   166464
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: 51 (24.3 bits)

Align candidate BPHYT_RS32825 BPHYT_RS32825 (xylose isomerase)
to HMM TIGR02630 (xylA: xylose isomerase (EC 5.3.1.5))

# 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/TIGR02630.hmm
# target sequence database:        /tmp/gapView.28566.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02630  [M=435]
Accession:   TIGR02630
Description: xylose_isom_A: xylose isomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.5e-207  675.7   0.1   1.7e-207  675.5   0.1    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS32825  BPHYT_RS32825 xylose isomerase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS32825  BPHYT_RS32825 xylose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  675.5   0.1  1.7e-207  1.7e-207       1     435 []       3     436 ..       3     436 .. 0.99

  Alignments for each domain:
  == domain 1  score: 675.5 bits;  conditional E-value: 1.7e-207
                                TIGR02630   1 ffeeiekvkyeGkdsknplafkyynpeeviegkkmkdhlrfavayWhtlaaegaDpfGagtaerpwdkel 70 
                                              +fe+i +++yeG++s+npla+++y++ + + gk++++hlr av+yWht+ + g D fG+gt++rpw++  
  lcl|FitnessBrowser__BFirm:BPHYT_RS32825   3 YFEHIPEIRYEGPQSDNPLAYRHYDKSKKVLGKTLEEHLRIAVCYWHTFVWPGVDIFGQGTFRRPWQQ-A 71 
                                              8*****************************************************************96.6 PP

                                TIGR02630  71 tdaldkakakvdaafelleklgveyycfhDvDiapegaslketnanldeivdllkekqketgvklLWgta 140
                                               da+++a++k+d afe+++klg +yy+fhD+D++peg++lke+++n+ +i+d+l  kq++tg+klLWgta
  lcl|FitnessBrowser__BFirm:BPHYT_RS32825  72 GDAMERAQQKADSAFEFFSKLGTPYYTFHDTDVSPEGSNLKEYSENFLRITDYLARKQESTGIKLLWGTA 141
                                              ********************************************************************** PP

                                TIGR02630 141 nlfshpryvaGaatspdadvfayaaaqvkkalevtkklggenyvfWGGreGyetLlntdlkleldnlarf 210
                                              nlfshpry+aGaatspd++vfa+aa+qv++al++t++lgg+nyv+WGGreGy+tLlntdl +e+d+larf
  lcl|FitnessBrowser__BFirm:BPHYT_RS32825 142 NLFSHPRYAAGAATSPDPEVFAFAATQVRHALDATQRLGGDNYVLWGGREGYDTLLNTDLVRERDQLARF 211
                                              ********************************************************************** PP

                                TIGR02630 211 lklavdyakkigfkgqlliePkPkePtkhqyDfDaatvlaflkkydLdkdfklnieanhatLaghtfehe 280
                                              l+++vd+a+kigfkg+lliePkP+ePtkhqyD+D+atv++fl +++Ldk++++nieanhatLagh+f+he
  lcl|FitnessBrowser__BFirm:BPHYT_RS32825 212 LHMVVDHAHKIGFKGSLLIEPKPQEPTKHQYDYDVATVHGFLLQHGLDKEIRVNIEANHATLAGHSFHHE 281
                                              ********************************************************************** PP

                                TIGR02630 281 lrvarelgllGsiDanrgdlllGWDtDefptdvyeatlamyevlkagglakGGlnfdakvrresldaeDl 350
                                              +++a +lg++Gs+Danrgd ++GWDtD+fp++v+e+tla+ye+lk+gg+++GG+nfd+kvrr+s+d+eDl
  lcl|FitnessBrowser__BFirm:BPHYT_RS32825 282 IATAYALGIFGSVDANRGDPQNGWDTDQFPNSVEELTLAFYEILKHGGFTTGGMNFDSKVRRQSVDPEDL 351
                                              ********************************************************************** PP

                                TIGR02630 351 llahiagmDafarglkvaaklledgaleklveeryesfdseiGkeieegkadleelekyalekeeeaekk 420
                                              +++hi+++D +a++++ aa l+e+++l+++ ++ry+++d e+G++i +g  +l+ l+++a+ ++ ++++ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS32825 352 FYGHIGAIDNLALAVERAAVLIENDRLDQFKRQRYSGWDAEFGRKISSGDYSLSALAEEAMARGLNPQHA 421
                                              ********************************************************************** PP

                                TIGR02630 421 sgrqelleslinkyl 435
                                              sg+qel+e+++n+ +
  lcl|FitnessBrowser__BFirm:BPHYT_RS32825 422 SGHQELMENIVNQAI 436
                                              ************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (435 nodes)
Target sequences:                          1  (440 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: 00:00:00.03
# Mc/sec: 5.91
//
[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