Alignments for a candidate for xylB in Clostridium tyrobutyricum FAM22553

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylB in Clostridium tyrobutyricum FAM22553

Align Xylulose kinase; Short=Xylulokinase; EC 2.7.1.17 (characterized, see rationale)
to candidate WP_039653479.1 PN53_RS12045 xylulokinase

Query= uniprot:Q97FW4
         (500 letters)



>NCBI__GCF_000816635.1:WP_039653479.1
          Length = 512

 Score =  601 bits (1550), Expect = e-176
 Identities = 284/498 (57%), Positives = 375/498 (75%)

Query: 1   MRYLLGIDVGTSGTKTALFDECGNTIKTSTHEYELFQPQVGWAEQNPENWWTACVKGIRE 60
           M Y+LGID+GTSGTKTALFDE G TI +S +EY+L+QP++GWAEQ+P++WW A + GIR 
Sbjct: 1   MPYVLGIDIGTSGTKTALFDENGKTISSSLNEYKLYQPRIGWAEQDPQDWWKAVILGIRT 60

Query: 61  VIEKSKIDPLDIKGIGISGQMHGLVLIDKEYKVIRNSIIWCDQRTEKECTQITDTIGKEK 120
           V+ +S I P  IK IG+SGQMHGLV++DK+ +++R SIIWCDQRT +EC  IT+ +GK++
Sbjct: 61  VLSESGIIPEKIKAIGLSGQMHGLVMLDKQLRILRPSIIWCDQRTNEECIDITEIVGKQR 120

Query: 121 LIRITGNPALTGFTLSKLLWVRNNEPDNYKRIYKVLLPKDYIRFKLTGVFAAEVSDASGT 180
           LI IT NPALTGFT SK++WV+ +EP+ Y++ YK+LLPKDYIRF LTG FA EVSDASG 
Sbjct: 121 LIEITANPALTGFTASKIIWVKKHEPEIYEKAYKILLPKDYIRFMLTGEFATEVSDASGM 180

Query: 181 QMLDINTRNWSEELLDDLRIDKNILPDVYESVVVSGCVIEKASKETKLAVNTPVVGGAGD 240
           Q+LDI  RNWS E+L  L+ID N+L  VYES  ++G + + A++ T L  +T VVGGAGD
Sbjct: 181 QLLDIAKRNWSSEMLSKLQIDVNLLGKVYESQEITGKINKYAAELTGLKEDTLVVGGAGD 240

Query: 241 QAAGAIGNGIVREGLISTVIGTSGVVFAATDTPRFDSKGRVHTLCHAVPNKWHIMGVTQG 300
           QAAGAIGNGIV+ G++S+ IGTS VVFA TD    D KGRVHT C+A+PN WH+MGVTQ 
Sbjct: 241 QAAGAIGNGIVKSGMVSSTIGTSRVVFAYTDKAVIDRKGRVHTFCYAIPNTWHVMGVTQS 300

Query: 301 AGLSLNWFKRTFCAKEILESKEAGINIYDLLTEKASQSKPGSNGIIYLPYLMGERTPHID 360
           AGLSL WF+  FC  E   +   G +IY+ L ++AS SKPG  G+IYLPYLMGERTPH+D
Sbjct: 301 AGLSLKWFRDNFCNYEKESANLIGTDIYEFLNKEASMSKPGCEGLIYLPYLMGERTPHLD 360

Query: 361 PNVKGAFLGISLINNHNDFVRSILEGVGFSLKNCLDIIENMKVNIEEIRVSGGGAESSIW 420
           P  +G F G++  +  ND +R+I+EGVG+SLK+C+D+I  M +N  ++R SGGG +S +W
Sbjct: 361 PLARGVFFGLTSRHKKNDMLRAIMEGVGYSLKDCMDVINEMGINSNQVRASGGGGKSHLW 420

Query: 421 RQILSDIFNYELTTVKASEGPALGVAILAGVGAGIYNSVEEACDKIVKGNEKVMPNANLI 480
           RQI +D+FN E+TTV ++EGP+LG AILA VG G Y+SV EACD I+       P  +  
Sbjct: 421 RQIQADMFNTEVTTVNSNEGPSLGAAILALVGIGQYSSVREACDNIIYNISSQKPIYDNS 480

Query: 481 EVYSKVYEVYNSAYPKIK 498
            +Y++ + +Y   Y  +K
Sbjct: 481 ILYNRYHSIYKGIYKCLK 498


Lambda     K      H
   0.317    0.136    0.404 

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: 724
Number of extensions: 19
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: 500
Length of database: 512
Length adjustment: 34
Effective length of query: 466
Effective length of database: 478
Effective search space:   222748
Effective search space used:   222748
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 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate WP_039653479.1 PN53_RS12045 (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.1161001.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.2e-176  571.3   0.0   8.6e-176  571.1   0.0    1.1  1  NCBI__GCF_000816635.1:WP_039653479.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000816635.1:WP_039653479.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  571.1   0.0  8.6e-176  8.6e-176       1     480 [.       5     494 ..       5     495 .. 0.96

  Alignments for each domain:
  == domain 1  score: 571.1 bits;  conditional E-value: 8.6e-176
                             TIGR01312   1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeikaisi 73 
                                           lGiD+gTs++K+ l de+g+ i s+ +++++++p+ gw+Eqdp++w++a+   ++++l+++   +++ikai++
  NCBI__GCF_000816635.1:WP_039653479.1   5 LGIDIGTSGTKTALFDENGKTISSSLNEYKLYQPRIGWAEQDPQDWWKAVILGIRTVLSESGIIPEKIKAIGL 77 
                                           7************************************************************************ PP

                             TIGR01312  74 sGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllWvrkhepevfa 146
                                           sGQmHglv+LD++ ++lrp i+W+D+rt+eec +++e +g+++l+e+t n al+gfTa+K++Wv+khepe+++
  NCBI__GCF_000816635.1:WP_039653479.1  78 SGQMHGLVMLDKQLRILRPSIIWCDQRTNEECIDITEIVGKQRLIEITANPALTGFTASKIIWVKKHEPEIYE 150
                                           ************************************************************************* PP

                             TIGR01312 147 riakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPklvessekaGkvreeva 219
                                           +  k+lLPkDy+r++Ltge++te+sDAsG  l+d++kr+ws+e+l++l+++ +ll k++es+e++Gk+++ +a
  NCBI__GCF_000816635.1:WP_039653479.1 151 KAYKILLPKDYIRFMLTGEFATEVSDASGMQLLDIAKRNWSSEMLSKLQIDVNLLGKVYESQEITGKINKYAA 223
                                           ************************************************************************* PP

                             TIGR01312 220 kklGleegvkvaaGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesdpegavhsFchalpgkwyplg 292
                                           + +Gl+e++ v++G+gd+aagAiG givk+g v+  +GtS vv+a++dka+ d +g+vh+Fc a p++w+ +g
  NCBI__GCF_000816635.1:WP_039653479.1 224 ELTGLKEDTLVVGGAGDQAAGAIGNGIVKSGMVSSTIGTSRVVFAYTDKAVIDRKGRVHTFCYAIPNTWHVMG 296
                                           ************************************************************************* PP

                             TIGR01312 293 vtlsatsalewlkellg...........eldveelneeaekvevgaegvlllPylsGERtPhldpqargsliG 354
                                           vt sa+ +l+w+++++            +  +e ln+ea+ +++g eg+++lPyl+GERtPhldp arg+++G
  NCBI__GCF_000816635.1:WP_039653479.1 297 VTQSAGLSLKWFRDNFCnyekesanligTDIYEFLNKEASMSKPGCEGLIYLPYLMGERTPHLDPLARGVFFG 369
                                           **************99866554443332223566899************************************ PP

                             TIGR01312 355 ltanttradlarAvlegvafalrdsldilkelkglkikeirliGGGaksevwrqiladilglevvvpeeeega 427
                                           lt++++++d+ rA++egv ++l+d +d+++e  g++++++r+ GGG ks++wrqi+ad++++ev++ +++eg+
  NCBI__GCF_000816635.1:WP_039653479.1 370 LTSRHKKNDMLRAIMEGVGYSLKDCMDVINE-MGINSNQVRASGGGGKSHLWRQIQADMFNTEVTTVNSNEGP 441
                                           *******************************.66*************************************** PP

                             TIGR01312 428 alGaAilAaialgekdlveecseavvkqkesvepiaenveayeelyerykkly 480
                                           +lGaAilA+++ g++++v e+ + ++ + +s +pi  n   y++ ++ yk +y
  NCBI__GCF_000816635.1:WP_039653479.1 442 SLGAAILALVGIGQYSSVREACDNIIYNISSQKPIYDNSILYNRYHSIYKGIY 494
                                           *************8888877777777777777******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (512 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 30.27
//
[ok]

This GapMind analysis is from Apr 09 2024. 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