Alignments for a candidate for xylB in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylB in Cereibacter sphaeroides ATCC 17029

Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate WP_011841914.1 RSPH17029_RS14315 xylulokinase

Query= reanno::Dino:3608604
         (480 letters)



>NCBI__GCF_000015985.1:WP_011841914.1
          Length = 478

 Score =  687 bits (1772), Expect = 0.0
 Identities = 346/478 (72%), Positives = 386/478 (80%), Gaps = 1/478 (0%)

Query: 1   MYLGLDLGTSGLKAVLIDENQALVAEATAPLEVARPHPGWSEQMPCDWLAATEAAMAALG 60
           MY+GLDLGTSGLK +LID  Q ++AEA APL V+RPH GWSEQ P DW+AA EA M  L 
Sbjct: 1   MYIGLDLGTSGLKGILIDAEQRVLAEAVAPLAVSRPHEGWSEQSPADWIAAAEAVMDQLA 60

Query: 61  ARADLSGVRAIGLSGQMHGATLLDASHEVLRPCILWNDTRAAAEAAALDADPAFRSVTGN 120
           A+  LS V+ IGLSGQMHGATLLDAS EVLRPCILWNDTR+ AEA ALDADP FR+VTGN
Sbjct: 61  AQG-LSEVKGIGLSGQMHGATLLDASDEVLRPCILWNDTRSHAEAMALDADPRFRAVTGN 119

Query: 121 IVFPGFTAPKLAWVRAHEPDVFDRTALVLLPKDYLRLWLTGEAVAEMSDAAGTSWLDTGA 180
           IVFPGFTAPKL WV  HEP + +R A VLLPKDYLRLWLTGE VAEMSDAAGTSWLD GA
Sbjct: 120 IVFPGFTAPKLVWVERHEPAIRERVAKVLLPKDYLRLWLTGEHVAEMSDAAGTSWLDVGA 179

Query: 181 RDWSAPLLAATGLSRDHMPRLVEGSEVSGTLRDSLADAWGLPRGVPVAGGGGDNAASGIG 240
           RDWS  LLA TGL+R+ MPRLVEGS VSG LR +LA  WGLP+GV VAGGGGDNAAS +G
Sbjct: 180 RDWSDALLAVTGLTREAMPRLVEGSAVSGALRPALAARWGLPQGVAVAGGGGDNAASAVG 239

Query: 241 MGVVRAGDGFVSLGTSGVLFAACDAYAPDPATAVHTFCHALPETWHQMGVILAATDALNW 300
           +GVVRAG+ FVSLGTSGVLFAA D Y P P TAVHTFCHALP  WHQMGVILAATDALNW
Sbjct: 240 VGVVRAGEAFVSLGTSGVLFAANDGYQPAPETAVHTFCHALPGAWHQMGVILAATDALNW 299

Query: 301 FARTCGTDAATLTGGLGPLQAPGRPVFLPYLGGERTPHNDAAIRGAFARIDHAADRDALA 360
           +AR  G +A+ LT  LG LQAPGR +FLPYLGGERTP NDAAIRGAF  ++HA DR A  
Sbjct: 300 YARLVGQEASALTKELGGLQAPGRTLFLPYLGGERTPLNDAAIRGAFTGLEHATDRAAGT 359

Query: 361 RAVLEGVAFAFRDSFDALAATGTRLERLVAVGGGAKSDTWVRMIATLIGLPIDLPQAGDY 420
           RAVLEGV FA RD  DALAATGTRLE L+AVGGG++SD W+  IAT + +P+ LP AGD+
Sbjct: 360 RAVLEGVTFAIRDCRDALAATGTRLESLIAVGGGSRSDYWLSAIATALDVPVLLPAAGDF 419

Query: 421 GGAFGAARLGMMAATGQGAALATRPPIARSLDPVPALADAFGEAHATYRATYTALKGL 478
           GGAFGAARL +MAATG GA +AT PPIAR+L P   L  AF +AHA +RA  TA++ L
Sbjct: 420 GGAFGAARLALMAATGAGAEVATLPPIARTLSPDRGLTAAFDDAHARHRAAQTAIRSL 477


Lambda     K      H
   0.320    0.135    0.418 

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: 783
Number of extensions: 34
Number of successful extensions: 2
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: 480
Length of database: 478
Length adjustment: 34
Effective length of query: 446
Effective length of database: 444
Effective search space:   198024
Effective search space used:   198024
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 WP_011841914.1 RSPH17029_RS14315 (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.234057.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.5e-167  541.6   0.1   8.8e-167  541.3   0.1    1.0  1  NCBI__GCF_000015985.1:WP_011841914.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015985.1:WP_011841914.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  541.3   0.1  8.8e-167  8.8e-167       1     447 [.       3     440 ..       3     471 .. 0.95

  Alignments for each domain:
  == domain 1  score: 541.3 bits;  conditional E-value: 8.8e-167
                             TIGR01312   1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeikaisi 73 
                                           +G+DlgTs++K +l+d++++v+a++ a+l+v++p++gwsEq p +w++a e ++++l ++     +e+k+i++
  NCBI__GCF_000015985.1:WP_011841914.1   3 IGLDLGTSGLKGILIDAEQRVLAEAVAPLAVSRPHEGWSEQSPADWIAAAEAVMDQLAAQGL---SEVKGIGL 72 
                                           7********************************************************99955...8******* PP

                             TIGR01312  74 sGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllWvrkhepevfa 146
                                           sGQmHg++lLD++++vlrp+iLWnDtr+++e+  l+++    +++++tgn++++gfTapKl+Wv +hep + +
  NCBI__GCF_000015985.1:WP_011841914.1  73 SGQMHGATLLDASDEVLRPCILWNDTRSHAEAMALDADP---RFRAVTGNIVFPGFTAPKLVWVERHEPAIRE 142
                                           ***********************************9988...7****************************** PP

                             TIGR01312 147 riakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPklvessekaGkvreeva 219
                                           r+akvlLPkDylr++Ltge+v+e+sDA+GT ++dv  r+ws++ll+ + l ++++P+lve+s+++G++r+++a
  NCBI__GCF_000015985.1:WP_011841914.1 143 RVAKVLLPKDYLRLWLTGEHVAEMSDAAGTSWLDVGARDWSDALLAVTGLTREAMPRLVEGSAVSGALRPALA 215
                                           ************************************************************************* PP

                             TIGR01312 220 kklGleegvkvaaGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesdpegavhsFchalpgkwyplg 292
                                           +++Gl +gv va+Gggdnaa+A+G+g+v++g+++vslGtSGv++a++d +++ pe+avh+Fchalpg+w+++g
  NCBI__GCF_000015985.1:WP_011841914.1 216 ARWGLPQGVAVAGGGGDNAASAVGVGVVRAGEAFVSLGTSGVLFAANDGYQPAPETAVHTFCHALPGAWHQMG 288
                                           ************************************************************************* PP

                             TIGR01312 293 vtlsatsalewlkellgeldveelneeaekvevgaegvlllPylsGERtPhldpqargsliGltanttradla 365
                                           v+l+at+al+w ++l+g  + ++l++e    ++     l+lPyl GERtP +d+++rg ++Gl+++t ra  +
  NCBI__GCF_000015985.1:WP_011841914.1 289 VILAATDALNWYARLVG-QEASALTKELGGLQAP-GRTLFLPYLGGERTPLNDAAIRGAFTGLEHATDRAAGT 359
                                           *****************.8888999999988888.67889********************************* PP

                             TIGR01312 366 rAvlegvafalrdsldilkelkglkikeirliGGGaksevwrqiladilglevvvpe.eeegaalGaAilAai 437
                                           rAvlegv+fa+rd  d+l + +g++++++ ++GGG++s++w+  +a+ l+++v  p+  + g a+GaA+lA++
  NCBI__GCF_000015985.1:WP_011841914.1 360 RAVLEGVTFAIRDCRDALAA-TGTRLESLIAVGGGSRSDYWLSAIATALDVPVLLPAaGDFGGAFGAARLALM 431
                                           *******************9.77*********************************989************** PP

                             TIGR01312 438 algekdlvee 447
                                           a++ +  +e+
  NCBI__GCF_000015985.1:WP_011841914.1 432 AATGA-GAEV 440
                                           *9842.3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (478 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 29.39
//
[ok]

This GapMind analysis is from Apr 10 2024. 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