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

GapMind for catabolism of small carbon sources

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

Align Xylose isomerase (EC 5.3.1.5) (characterized)
to candidate Pf6N2E2_1454 Xylose isomerase (EC 5.3.1.5)

Query= reanno::pseudo5_N2C3_1:AO356_28500
         (438 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1454
          Length = 438

 Score =  879 bits (2270), Expect = 0.0
 Identities = 422/438 (96%), Positives = 430/438 (98%)

Query: 1   MPYFPGVDKIRYEGPASDSPLAFRHYDANRLVLGKPMREHLRMAVCYWHTFVWPGSDVFG 60
           M YFP VDKIRYEG ASDSPLAFRHYDAN+LVLGKPMREHLRMAVCYWHTFVWPGSDVFG
Sbjct: 1   MSYFPAVDKIRYEGAASDSPLAFRHYDANKLVLGKPMREHLRMAVCYWHTFVWPGSDVFG 60

Query: 61  AGTFKRPWQHAGDPMEVAIGKAEAAFEFFSKLGIDYYCFHDTDVAPEGGSLKEYRNHFAQ 120
           AGTFKRPWQHAGDPME+AIGKAEAAFEFFSKLGIDYYCFHDTDVAPEG SLKEYR HFAQ
Sbjct: 61  AGTFKRPWQHAGDPMEMAIGKAEAAFEFFSKLGIDYYCFHDTDVAPEGTSLKEYREHFAQ 120

Query: 121 MIDHLERHQEQTGIKLLWGTANCFSNPRFAAGAASNPDPEVFACAAAQVFSAMNATQRLK 180
           M+DHLERHQEQTGIKLLWGTANCFSNPRFAAGAASNPDPEVFACAAAQVFSAMNATQRLK
Sbjct: 121 MVDHLERHQEQTGIKLLWGTANCFSNPRFAAGAASNPDPEVFACAAAQVFSAMNATQRLK 180

Query: 181 GANYVLWGGREGYETLLNTDLKHEREQLGRFMRMVVEHKHKIGFKGDLLIEPKPQEPTKH 240
           G+NYVLWGGREGYETLLNTDLK EREQLGRFMRMVVEHKHKIGFKGDLLIEPKPQEPTKH
Sbjct: 181 GSNYVLWGGREGYETLLNTDLKREREQLGRFMRMVVEHKHKIGFKGDLLIEPKPQEPTKH 240

Query: 241 QYDYDSATVFGFLQQFGLENEIKVNIEANHATLAGHSFHHEIATAVSLGIFGSIDANRGD 300
           QYDYDSATVFGFLQQFGLENEIKVNIEANHATLAGHSFHHEIATAVSLGIFGSIDANRGD
Sbjct: 241 QYDYDSATVFGFLQQFGLENEIKVNIEANHATLAGHSFHHEIATAVSLGIFGSIDANRGD 300

Query: 301 PQNGWDTDQFPNSVEEMTLATYEILKAGGFGNGGFNFDSKVRRQSVDDIDLFHGHVAAMD 360
           PQNGWDTDQFPNSVEEMTLATYEILKAGGF NGGFNFDSKVRRQSVD++DLFHGHVAAMD
Sbjct: 301 PQNGWDTDQFPNSVEEMTLATYEILKAGGFTNGGFNFDSKVRRQSVDELDLFHGHVAAMD 360

Query: 361 VLALALERAAAMVQNDQLQQFKDQRYAGWQQPFGKAVLAGDFSLESLAEHAFTNELNPQA 420
           VLALALERAAAMVQNDQLQQFKDQRYAGWQQPFG+AVLAG+FSL SLAEHAFTNELNPQA
Sbjct: 361 VLALALERAAAMVQNDQLQQFKDQRYAGWQQPFGQAVLAGEFSLASLAEHAFTNELNPQA 420

Query: 421 VSGRQEMLENVVNRFIYP 438
           VSGRQEMLENVVNRFIYP
Sbjct: 421 VSGRQEMLENVVNRFIYP 438


Lambda     K      H
   0.321    0.136    0.424 

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: 839
Number of extensions: 23
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: 438
Length of database: 438
Length adjustment: 32
Effective length of query: 406
Effective length of database: 406
Effective search space:   164836
Effective search space used:   164836
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: 51 (24.3 bits)

Align candidate Pf6N2E2_1454 (Xylose isomerase (EC 5.3.1.5))
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.20172.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.8e-207  675.4   0.5     2e-207  675.2   0.5    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1454  Xylose isomerase (EC 5.3.1.5)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1454  Xylose isomerase (EC 5.3.1.5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  675.2   0.5    2e-207    2e-207       1     435 []       3     436 ..       3     436 .. 0.99

  Alignments for each domain:
  == domain 1  score: 675.2 bits;  conditional E-value: 2e-207
                                      TIGR02630   1 ffeeiekvkyeGkdsknplafkyynpeeviegkkmkdhlrfavayWhtlaaegaDpfGagtaer 64 
                                                    +f+ ++k++yeG  s++plaf++y++++++ gk m++hlr+av+yWht+ + g+D fGagt++r
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1454   3 YFPAVDKIRYEGAASDSPLAFRHYDANKLVLGKPMREHLRMAVCYWHTFVWPGSDVFGAGTFKR 66 
                                                    89************************************************************** PP

                                      TIGR02630  65 pwdkeltdaldkakakvdaafelleklgveyycfhDvDiapegaslketnanldeivdllkekq 128
                                                    pw++   d++++a  k++aafe+++klg++yycfhD+D+apeg+slke+ +++ ++vd+l+ +q
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1454  67 PWQH-AGDPMEMAIGKAEAAFEFFSKLGIDYYCFHDTDVAPEGTSLKEYREHFAQMVDHLERHQ 129
                                                    **95.6********************************************************** PP

                                      TIGR02630 129 ketgvklLWgtanlfshpryvaGaatspdadvfayaaaqvkkalevtkklggenyvfWGGreGy 192
                                                    ++tg+klLWgtan+fs+pr++aGaa +pd++vfa aaaqv  a+++t++l g nyv+WGGreGy
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1454 130 EQTGIKLLWGTANCFSNPRFAAGAASNPDPEVFACAAAQVFSAMNATQRLKGSNYVLWGGREGY 193
                                                    **************************************************************** PP

                                      TIGR02630 193 etLlntdlkleldnlarflklavdyakkigfkgqlliePkPkePtkhqyDfDaatvlaflkkyd 256
                                                    etLlntdlk+e+++l+rf++++v++++kigfkg+lliePkP+ePtkhqyD+D+atv++fl++++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1454 194 ETLLNTDLKREREQLGRFMRMVVEHKHKIGFKGDLLIEPKPQEPTKHQYDYDSATVFGFLQQFG 257
                                                    **************************************************************** PP

                                      TIGR02630 257 LdkdfklnieanhatLaghtfehelrvarelgllGsiDanrgdlllGWDtDefptdvyeatlam 320
                                                    L++++k+nieanhatLagh+f+he+++a +lg++GsiDanrgd ++GWDtD+fp++v+e+tla 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1454 258 LENEIKVNIEANHATLAGHSFHHEIATAVSLGIFGSIDANRGDPQNGWDTDQFPNSVEEMTLAT 321
                                                    **************************************************************** PP

                                      TIGR02630 321 yevlkagglakGGlnfdakvrresldaeDlllahiagmDafarglkvaaklledgaleklveer 384
                                                    ye+lkagg+++GG+nfd+kvrr+s+d+ Dl+++h+a+mD +a++l+ aa+++++++l+++ ++r
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1454 322 YEILKAGGFTNGGFNFDSKVRRQSVDELDLFHGHVAAMDVLALALERAAAMVQNDQLQQFKDQR 385
                                                    **************************************************************** PP

                                      TIGR02630 385 yesfdseiGkeieegkadleelekyalekeeeaekksgrqelleslinkyl 435
                                                    y+++++ +G+++++g+ +l++l+++a ++e +++  sgrqe+le+++n+++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1454 386 YAGWQQPFGQAVLAGEFSLASLAEHAFTNELNPQAVSGRQEMLENVVNRFI 436
                                                    ************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (435 nodes)
Target sequences:                          1  (438 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.49
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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