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.3987563.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 14.12
//
[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:

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:

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:

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:

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