GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylA in Pseudomonas fluorescens FW300-N2C3

Align Xylose isomerase (EC 5.3.1.5) (characterized)
to candidate AO356_28500 AO356_28500 xylose isomerase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_28500
          Length = 438

 Score =  910 bits (2352), Expect = 0.0
 Identities = 438/438 (100%), Positives = 438/438 (100%)

Query: 1   MPYFPGVDKIRYEGPASDSPLAFRHYDANRLVLGKPMREHLRMAVCYWHTFVWPGSDVFG 60
           MPYFPGVDKIRYEGPASDSPLAFRHYDANRLVLGKPMREHLRMAVCYWHTFVWPGSDVFG
Sbjct: 1   MPYFPGVDKIRYEGPASDSPLAFRHYDANRLVLGKPMREHLRMAVCYWHTFVWPGSDVFG 60

Query: 61  AGTFKRPWQHAGDPMEVAIGKAEAAFEFFSKLGIDYYCFHDTDVAPEGGSLKEYRNHFAQ 120
           AGTFKRPWQHAGDPMEVAIGKAEAAFEFFSKLGIDYYCFHDTDVAPEGGSLKEYRNHFAQ
Sbjct: 61  AGTFKRPWQHAGDPMEVAIGKAEAAFEFFSKLGIDYYCFHDTDVAPEGGSLKEYRNHFAQ 120

Query: 121 MIDHLERHQEQTGIKLLWGTANCFSNPRFAAGAASNPDPEVFACAAAQVFSAMNATQRLK 180
           MIDHLERHQEQTGIKLLWGTANCFSNPRFAAGAASNPDPEVFACAAAQVFSAMNATQRLK
Sbjct: 121 MIDHLERHQEQTGIKLLWGTANCFSNPRFAAGAASNPDPEVFACAAAQVFSAMNATQRLK 180

Query: 181 GANYVLWGGREGYETLLNTDLKHEREQLGRFMRMVVEHKHKIGFKGDLLIEPKPQEPTKH 240
           GANYVLWGGREGYETLLNTDLKHEREQLGRFMRMVVEHKHKIGFKGDLLIEPKPQEPTKH
Sbjct: 181 GANYVLWGGREGYETLLNTDLKHEREQLGRFMRMVVEHKHKIGFKGDLLIEPKPQEPTKH 240

Query: 241 QYDYDSATVFGFLQQFGLENEIKVNIEANHATLAGHSFHHEIATAVSLGIFGSIDANRGD 300
           QYDYDSATVFGFLQQFGLENEIKVNIEANHATLAGHSFHHEIATAVSLGIFGSIDANRGD
Sbjct: 241 QYDYDSATVFGFLQQFGLENEIKVNIEANHATLAGHSFHHEIATAVSLGIFGSIDANRGD 300

Query: 301 PQNGWDTDQFPNSVEEMTLATYEILKAGGFGNGGFNFDSKVRRQSVDDIDLFHGHVAAMD 360
           PQNGWDTDQFPNSVEEMTLATYEILKAGGFGNGGFNFDSKVRRQSVDDIDLFHGHVAAMD
Sbjct: 301 PQNGWDTDQFPNSVEEMTLATYEILKAGGFGNGGFNFDSKVRRQSVDDIDLFHGHVAAMD 360

Query: 361 VLALALERAAAMVQNDQLQQFKDQRYAGWQQPFGKAVLAGDFSLESLAEHAFTNELNPQA 420
           VLALALERAAAMVQNDQLQQFKDQRYAGWQQPFGKAVLAGDFSLESLAEHAFTNELNPQA
Sbjct: 361 VLALALERAAAMVQNDQLQQFKDQRYAGWQQPFGKAVLAGDFSLESLAEHAFTNELNPQA 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: 863
Number of extensions: 25
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 AO356_28500 AO356_28500 (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.1650.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   1.6e-206  672.2   0.2   1.8e-206  672.1   0.2    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28500  AO356_28500 xylose isomerase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28500  AO356_28500 xylose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  672.1   0.2  1.8e-206  1.8e-206       1     435 []       3     436 ..       3     436 .. 0.99

  Alignments for each domain:
  == domain 1  score: 672.1 bits;  conditional E-value: 1.8e-206
                                       TIGR02630   1 ffeeiekvkyeGkdsknplafkyynpeeviegkkmkdhlrfavayWhtlaaegaDpfGagtae 63 
                                                     +f++++k++yeG+ s++plaf++y++++++ gk m++hlr+av+yWht+ + g+D fGagt++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28500   3 YFPGVDKIRYEGPASDSPLAFRHYDANRLVLGKPMREHLRMAVCYWHTFVWPGSDVFGAGTFK 65 
                                                     8************************************************************** PP

                                       TIGR02630  64 rpwdkeltdaldkakakvdaafelleklgveyycfhDvDiapegaslketnanldeivdllke 126
                                                     rpw++   d+++ a  k++aafe+++klg++yycfhD+D+apeg slke+ +++ +++d+l+ 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28500  66 RPWQH-AGDPMEVAIGKAEAAFEFFSKLGIDYYCFHDTDVAPEGGSLKEYRNHFAQMIDHLER 127
                                                     ***95.6******************************************************** PP

                                       TIGR02630 127 kqketgvklLWgtanlfshpryvaGaatspdadvfayaaaqvkkalevtkklggenyvfWGGr 189
                                                     +q++tg+klLWgtan+fs+pr++aGaa +pd++vfa aaaqv  a+++t++l g nyv+WGGr
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28500 128 HQEQTGIKLLWGTANCFSNPRFAAGAASNPDPEVFACAAAQVFSAMNATQRLKGANYVLWGGR 190
                                                     *************************************************************** PP

                                       TIGR02630 190 eGyetLlntdlkleldnlarflklavdyakkigfkgqlliePkPkePtkhqyDfDaatvlafl 252
                                                     eGyetLlntdlk e+++l+rf++++v++++kigfkg+lliePkP+ePtkhqyD+D+atv++fl
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28500 191 EGYETLLNTDLKHEREQLGRFMRMVVEHKHKIGFKGDLLIEPKPQEPTKHQYDYDSATVFGFL 253
                                                     *************************************************************** PP

                                       TIGR02630 253 kkydLdkdfklnieanhatLaghtfehelrvarelgllGsiDanrgdlllGWDtDefptdvye 315
                                                     ++++L++++k+nieanhatLagh+f+he+++a +lg++GsiDanrgd ++GWDtD+fp++v+e
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28500 254 QQFGLENEIKVNIEANHATLAGHSFHHEIATAVSLGIFGSIDANRGDPQNGWDTDQFPNSVEE 316
                                                     *************************************************************** PP

                                       TIGR02630 316 atlamyevlkagglakGGlnfdakvrresldaeDlllahiagmDafarglkvaaklledgale 378
                                                     +tla ye+lkagg+++GG+nfd+kvrr+s+d  Dl+++h+a+mD +a++l+ aa+++++++l+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28500 317 MTLATYEILKAGGFGNGGFNFDSKVRRQSVDDIDLFHGHVAAMDVLALALERAAAMVQNDQLQ 379
                                                     *************************************************************** PP

                                       TIGR02630 379 klveeryesfdseiGkeieegkadleelekyalekeeeaekksgrqelleslinkyl 435
                                                     ++ ++ry+++++ +Gk++++g  +le+l+++a ++e +++  sgrqe+le+++n+++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28500 380 QFKDQRYAGWQQPFGKAVLAGDFSLESLAEHAFTNELNPQAVSGRQEMLENVVNRFI 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: 00:00:00.02
# Mc/sec: 8.27
//
[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