Alignments for a candidate for xylA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylA in Pseudomonas simiae WCS417

Align Xylose isomerase (EC 5.3.1.5) (characterized)
to candidate GFF2146 PS417_10945 xylose isomerase

Query= reanno::WCS417:GFF2146
         (438 letters)



>FitnessBrowser__WCS417:GFF2146
          Length = 438

 Score =  907 bits (2343), Expect = 0.0
 Identities = 438/438 (100%), Positives = 438/438 (100%)

Query: 1   MPYFPGVEKVRFEGPSSDAPLAFRHYDANKLILGKPMREHLRMAACYWHTFVWPGADMFG 60
           MPYFPGVEKVRFEGPSSDAPLAFRHYDANKLILGKPMREHLRMAACYWHTFVWPGADMFG
Sbjct: 1   MPYFPGVEKVRFEGPSSDAPLAFRHYDANKLILGKPMREHLRMAACYWHTFVWPGADMFG 60

Query: 61  VGTFKRPWQRSGDPMELAIGKADAAFEFFSKLGIDYYSFHDTDVAPEGSSLKEYRHHFAQ 120
           VGTFKRPWQRSGDPMELAIGKADAAFEFFSKLGIDYYSFHDTDVAPEGSSLKEYRHHFAQ
Sbjct: 61  VGTFKRPWQRSGDPMELAIGKADAAFEFFSKLGIDYYSFHDTDVAPEGSSLKEYRHHFAQ 120

Query: 121 MVDHLERHQEHTGIKLLWGTANCFSNPRFAAGAASNPDPEVFAYAAAQVFSAMNATLRLK 180
           MVDHLERHQEHTGIKLLWGTANCFSNPRFAAGAASNPDPEVFAYAAAQVFSAMNATLRLK
Sbjct: 121 MVDHLERHQEHTGIKLLWGTANCFSNPRFAAGAASNPDPEVFAYAAAQVFSAMNATLRLK 180

Query: 181 GSNYVLWGGREGYETLLNTDLKREREQLGRFMRMVVEHKHKIGFKGDLLIEPKPQEPTKH 240
           GSNYVLWGGREGYETLLNTDLKREREQLGRFMRMVVEHKHKIGFKGDLLIEPKPQEPTKH
Sbjct: 181 GSNYVLWGGREGYETLLNTDLKREREQLGRFMRMVVEHKHKIGFKGDLLIEPKPQEPTKH 240

Query: 241 QYDYDSATVFGFLHEYGLEHEIKVNIEANHATLAGHSFHHEIATAVSLGIFGSIDANRGD 300
           QYDYDSATVFGFLHEYGLEHEIKVNIEANHATLAGHSFHHEIATAVSLGIFGSIDANRGD
Sbjct: 241 QYDYDSATVFGFLHEYGLEHEIKVNIEANHATLAGHSFHHEIATAVSLGIFGSIDANRGD 300

Query: 301 PQNGWDTDQFPNSVEEMTLATYEILKAGGFKNGGYNFDSKVRRQSLDDVDLFHGHVAAMD 360
           PQNGWDTDQFPNSVEEMTLATYEILKAGGFKNGGYNFDSKVRRQSLDDVDLFHGHVAAMD
Sbjct: 301 PQNGWDTDQFPNSVEEMTLATYEILKAGGFKNGGYNFDSKVRRQSLDDVDLFHGHVAAMD 360

Query: 361 VLALALERAAAMVENDRLQQFKDQRYAGWQQPLGQAVLAGEFSLESLAEHAFAHELDPQA 420
           VLALALERAAAMVENDRLQQFKDQRYAGWQQPLGQAVLAGEFSLESLAEHAFAHELDPQA
Sbjct: 361 VLALALERAAAMVENDRLQQFKDQRYAGWQQPLGQAVLAGEFSLESLAEHAFAHELDPQA 420

Query: 421 VSGRQEMLEGVVNRFIYR 438
           VSGRQEMLEGVVNRFIYR
Sbjct: 421 VSGRQEMLEGVVNRFIYR 438


Lambda     K      H
   0.320    0.136    0.420 

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: 952
Number of extensions: 35
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 GFF2146 PS417_10945 (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.11330.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.1e-204  666.3   0.2   1.2e-204  666.1   0.2    1.0  1  lcl|FitnessBrowser__WCS417:GFF2146  PS417_10945 xylose isomerase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF2146  PS417_10945 xylose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  666.1   0.2  1.2e-204  1.2e-204       1     435 []       3     436 ..       3     436 .. 0.99

  Alignments for each domain:
  == domain 1  score: 666.1 bits;  conditional E-value: 1.2e-204
                           TIGR02630   1 ffeeiekvkyeGkdsknplafkyynpeeviegkkmkdhlrfavayWhtlaaegaDpfGagtaerpwdkeltdald 75 
                                         +f+++ekv++eG++s+ plaf++y+++++i gk m++hlr+a +yWht+ + gaD+fG gt++rpw++   d+++
  lcl|FitnessBrowser__WCS417:GFF2146   3 YFPGVEKVRFEGPSSDAPLAFRHYDANKLILGKPMREHLRMAACYWHTFVWPGADMFGVGTFKRPWQR-SGDPME 76 
                                         8*****************************************************************95.6***** PP

                           TIGR02630  76 kakakvdaafelleklgveyycfhDvDiapegaslketnanldeivdllkekqketgvklLWgtanlfshpryva 150
                                          a  k+daafe+++klg++yy+fhD+D+apeg+slke+ +++ ++vd+l+ +q++tg+klLWgtan+fs+pr++a
  lcl|FitnessBrowser__WCS417:GFF2146  77 LAIGKADAAFEFFSKLGIDYYSFHDTDVAPEGSSLKEYRHHFAQMVDHLERHQEHTGIKLLWGTANCFSNPRFAA 151
                                         *************************************************************************** PP

                           TIGR02630 151 GaatspdadvfayaaaqvkkalevtkklggenyvfWGGreGyetLlntdlkleldnlarflklavdyakkigfkg 225
                                         Gaa +pd++vfayaaaqv  a+++t +l g nyv+WGGreGyetLlntdlk+e+++l+rf++++v++++kigfkg
  lcl|FitnessBrowser__WCS417:GFF2146 152 GAASNPDPEVFAYAAAQVFSAMNATLRLKGSNYVLWGGREGYETLLNTDLKREREQLGRFMRMVVEHKHKIGFKG 226
                                         *************************************************************************** PP

                           TIGR02630 226 qlliePkPkePtkhqyDfDaatvlaflkkydLdkdfklnieanhatLaghtfehelrvarelgllGsiDanrgdl 300
                                         +lliePkP+ePtkhqyD+D+atv++fl++y+L++++k+nieanhatLagh+f+he+++a +lg++GsiDanrgd 
  lcl|FitnessBrowser__WCS417:GFF2146 227 DLLIEPKPQEPTKHQYDYDSATVFGFLHEYGLEHEIKVNIEANHATLAGHSFHHEIATAVSLGIFGSIDANRGDP 301
                                         *************************************************************************** PP

                           TIGR02630 301 llGWDtDefptdvyeatlamyevlkagglakGGlnfdakvrresldaeDlllahiagmDafarglkvaaklledg 375
                                         ++GWDtD+fp++v+e+tla ye+lkagg+++GG nfd+kvrr+sld  Dl+++h+a+mD +a++l+ aa+++e++
  lcl|FitnessBrowser__WCS417:GFF2146 302 QNGWDTDQFPNSVEEMTLATYEILKAGGFKNGGYNFDSKVRRQSLDDVDLFHGHVAAMDVLALALERAAAMVEND 376
                                         *************************************************************************** PP

                           TIGR02630 376 aleklveeryesfdseiGkeieegkadleelekyalekeeeaekksgrqelleslinkyl 435
                                         +l+++ ++ry+++++ +G+++++g+ +le+l+++a  +e +++  sgrqe+le ++n+++
  lcl|FitnessBrowser__WCS417:GFF2146 377 RLQQFKDQRYAGWQQPLGQAVLAGEFSLESLAEHAFAHELDPQAVSGRQEMLEGVVNRFI 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 9.28
//
[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