Alignments for a candidate for xylB in Phyllobacterium brassicacearum STM 196

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylB in Phyllobacterium brassicacearum STM 196

Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate WP_106712328.1 CU102_RS17150 xylulokinase

Query= reanno::Smeli:SMc03164
         (484 letters)



>NCBI__GCF_003010955.1:WP_106712328.1
          Length = 484

 Score =  730 bits (1885), Expect = 0.0
 Identities = 353/480 (73%), Positives = 401/480 (83%)

Query: 1   MYLGLDLGTSGVKAMLMDGEQRIIGSASGALDVDRPHPGWSEQDPADWIRAAEEAIARLR 60
           MYLGLDLGTSGVKA+L+D +Q +I S +G LD+ RP  GWSEQDP+ WI+A E A+A +R
Sbjct: 1   MYLGLDLGTSGVKALLIDEKQSVIASGTGILDISRPQSGWSEQDPSHWIKATEGAVAAVR 60

Query: 61  ETHAQALAAVRGIGLSGQMHGATLLDEGDAVLRPCILWNDTRSFREAAALDGDPQFRALT 120
            TH + LAAV+GIGLSGQMHGATLLD GD VLRPCILWNDTRS +EAA  D +P FRAL+
Sbjct: 61  ATHGKELAAVKGIGLSGQMHGATLLDAGDQVLRPCILWNDTRSHKEAAEFDSNPIFRALS 120

Query: 121 GNIVFPGFTAPKLAWVRENEPEIFARVRWVLLPKDYLRLWLTGEHMSEMSDSAGTSWLDT 180
           GNIVFPGFTAPK+AWV+ NEP++FA++  VLLPKDYLRLWLTGEH+SEMSD+AGTSWLD 
Sbjct: 121 GNIVFPGFTAPKIAWVKNNEPDVFAKLSRVLLPKDYLRLWLTGEHVSEMSDAAGTSWLDV 180

Query: 181 GKRKWSASLLAATHLEERQMPDLVEGTDAAGTLRPELAARWGMGPGVVVAGGAGDNAASA 240
           GKR WS  LLAAT L+   MP LVEGT+ +G L+ +LAARWGMG  VVVAGGAGDNAASA
Sbjct: 181 GKRAWSPELLAATGLDASFMPSLVEGTEVSGKLKADLAARWGMGTSVVVAGGAGDNAASA 240

Query: 241 CGMGTVGEGQAFVSLGTSGVLFAANASYLPNPESAVHAFCHALPNTWHQMGVILSATDAL 300
           CGMGTV EG AFVSLGTSGVLFAAN++YLPNP+SAVH FCHALPNTWHQMGVILSATDAL
Sbjct: 241 CGMGTVAEGHAFVSLGTSGVLFAANSAYLPNPQSAVHTFCHALPNTWHQMGVILSATDAL 300

Query: 301 NWHSGVTGRSAAELTSELGESLKAPGSVTFLPYLSGERTPHNDATIRGVFAGLGHESSRA 360
           NW++G+  R  AELT ELG+ L+AP  VTFLPYLSGERTP ND+ IRG F GL H S RA
Sbjct: 301 NWYAGIASRQPAELTGELGDQLRAPSGVTFLPYLSGERTPLNDSAIRGSFHGLEHASDRA 360

Query: 361 VLTQAVLEGVSFAIRDSLEALRAAGTKLKRVTAIGGGSRSRYWLSSIATALNLPVDLPAD 420
           VLTQAVLEGV+FA RD L AL AAGTKL+RVTA+GGGSRS YWL +IATALN+PVD+PAD
Sbjct: 361 VLTQAVLEGVAFAFRDCLHALAAAGTKLERVTAVGGGSRSTYWLKAIATALNIPVDVPAD 420

Query: 421 GDFGAAFGAARLGLIAATGADPAAVCTAPETAETIAPEASLVPAYEDAYQRYRRLYPAIK 480
           GDFGAAFGAARLGLIAA   DP A+C AP T  TI PE +L  A++ AY RY  LYPA+K
Sbjct: 421 GDFGAAFGAARLGLIAAENGDPRAICAAPSTDYTIEPETALTDAFDAAYNRYHNLYPALK 480


Lambda     K      H
   0.317    0.132    0.401 

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: 778
Number of extensions: 28
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: 484
Length of database: 484
Length adjustment: 34
Effective length of query: 450
Effective length of database: 450
Effective search space:   202500
Effective search space used:   202500
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_106712328.1 CU102_RS17150 (xylulokinase)
to HMM TIGR01312 (xylB: xylulokinase (EC 2.7.1.17))

# 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/TIGR01312.hmm
# target sequence database:        /tmp/gapView.2411753.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01312  [M=481]
Accession:   TIGR01312
Description: XylB: xylulokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.4e-180  584.7   0.0   7.3e-180  584.5   0.0    1.0  1  NCBI__GCF_003010955.1:WP_106712328.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010955.1:WP_106712328.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  584.5   0.0  7.3e-180  7.3e-180       1     480 [.       3     476 ..       3     477 .. 0.98

  Alignments for each domain:
  == domain 1  score: 584.5 bits;  conditional E-value: 7.3e-180
                             TIGR01312   1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeikaisi 73 
                                           lG+DlgTs+vKall+dek++viasg+  l++++p++gwsEqdp++w++a+e a++++++++ +e +++k+i++
  NCBI__GCF_003010955.1:WP_106712328.1   3 LGLDLGTSGVKALLIDEKQSVIASGTGILDISRPQSGWSEQDPSHWIKATEGAVAAVRATHGKELAAVKGIGL 75 
                                           7************************************************************************ PP

                             TIGR01312  74 sGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllWvrkhepevfa 146
                                           sGQmHg++lLD+ ++vlrp+iLWnDtr+++e++e++++     +++l gn++++gfTapK++Wv+++ep+vfa
  NCBI__GCF_003010955.1:WP_106712328.1  76 SGQMHGATLLDAGDQVLRPCILWNDTRSHKEAAEFDSNP---IFRALSGNIVFPGFTAPKIAWVKNNEPDVFA 145
                                           ************************************998...599**************************** PP

                             TIGR01312 147 riakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPklvessekaGkvreeva 219
                                           +++ vlLPkDylr++Ltge+v+e+sDA+GT ++dv kr+ws ell+a+ l+ s +P+lve++e++Gk+++++a
  NCBI__GCF_003010955.1:WP_106712328.1 146 KLSRVLLPKDYLRLWLTGEHVSEMSDAAGTSWLDVGKRAWSPELLAATGLDASFMPSLVEGTEVSGKLKADLA 218
                                           ************************************************************************* PP

                             TIGR01312 220 kklGleegvkvaaGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesdpegavhsFchalpgkwyplg 292
                                           +++G+ ++v va+G+gdnaa+A+G+g+v+eg+++vslGtSGv++a++ ++ ++p++avh+Fchalp++w+++g
  NCBI__GCF_003010955.1:WP_106712328.1 219 ARWGMGTSVVVAGGAGDNAASACGMGTVAEGHAFVSLGTSGVLFAANSAYLPNPQSAVHTFCHALPNTWHQMG 291
                                           ************************************************************************* PP

                             TIGR01312 293 vtlsatsalewlkellgeldveelneeaekvevgaegvlllPylsGERtPhldpqargsliGltanttradla 365
                                           v+lsat+al+w + + ++   e + e+ ++ ++   gv++lPylsGERtP +d+++rgs++Gl++++ ra l+
  NCBI__GCF_003010955.1:WP_106712328.1 292 VILSATDALNWYAGIASRQPAELTGELGDQLRAP-SGVTFLPYLSGERTPLNDSAIRGSFHGLEHASDRAVLT 363
                                           *****************99999999999999998.8************************************* PP

                             TIGR01312 366 rAvlegvafalrdsldilkelkglkikeirliGGGaksevwrqiladilglevvvpe.eeegaalGaAilAai 437
                                           +Avlegvafa+rd l++l + +g+k+++++++GGG++s++w++ +a+ l+ +v+vp+  + gaa+GaA+l++i
  NCBI__GCF_003010955.1:WP_106712328.1 364 QAVLEGVAFAFRDCLHALAA-AGTKLERVTAVGGGSRSTYWLKAIATALNIPVDVPAdGDFGAAFGAARLGLI 435
                                           *******************9.77*********************************999************** PP

                             TIGR01312 438 algekdlveecseavvkqkesvepiaenveayeelyerykkly 480
                                           a+++ d  + c++  ++++ +  p+++ + a + +y+ry++ly
  NCBI__GCF_003010955.1:WP_106712328.1 436 AAENGDPRAICAAPSTDYTIE--PETALTDAFDAAYNRYHNLY 476
                                           ***999******999999888..*****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (484 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: 15.83
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 2024 update 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