Alignments for a candidate for xylB in Caldicellulosiruptor hydrothermalis 108

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylB in Caldicellulosiruptor hydrothermalis 108

Align Xylulose kinase; Short=Xylulokinase; EC 2.7.1.17 (characterized, see rationale)
to candidate WP_013402101.1 CALHY_RS00630 xylulokinase

Query= uniprot:Q97FW4
         (500 letters)



>NCBI__GCF_000166355.1:WP_013402101.1
          Length = 497

 Score =  302 bits (773), Expect = 2e-86
 Identities = 164/500 (32%), Positives = 271/500 (54%), Gaps = 10/500 (2%)

Query: 1   MRYLLGIDVGTSGTKTALFDECGNTIKTSTHEYELFQPQVGWAEQNPENWWTACVKGIRE 60
           M  +L ID+GT+  K  +FD  GN +  +  EY  + PQ+ WAEQ+P +WW   V+GI+E
Sbjct: 1   MEKILTIDIGTTACKVIVFDLQGNILAKANREYPTYTPQIEWAEQDPLDWWNEVVEGIKE 60

Query: 61  VIEKSKIDPLDIKGIGISGQMHGLVLIDKEYKVIRNSIIWCDQRTEKECTQITDTIGKEK 120
           V + +  D   I  IG+S Q   +V IDKE  V+  +I W D+R+  E  +I+   GK+ 
Sbjct: 61  VAQAAGAD--GIVAIGLSSQRETVVPIDKEGNVLSRAISWMDRRSRLEAEEISHQFGKDT 118

Query: 121 LIRITGNPALTGFTLSKLLWVRNNEPDNYKRIYKVLLPKDYIRFKLTGVFAAEVSDASGT 180
           + +ITG    + FT +KLLW++ ++P+  ++ Y  L PK++I + LTG  A + S AS T
Sbjct: 119 IHKITGLIPDSTFTATKLLWLKKHQPEILQKAYIFLQPKEFIGYMLTGEAATDHSLASRT 178

Query: 181 QMLDINTRNWSEELLDDLRIDKNILPDVYESVVVSGCVIEKASKETKLAVNTPVVGGAGD 240
            M D+N R W E++ + + +  +  P +  +  V G + E  +K   L    PVV G GD
Sbjct: 179 MMFDVNKRQWWEDIFEFVGVKTSQFPRLCYADEVIGYLKEDVAKILGLKSGIPVVSGGGD 238

Query: 241 QAAGAIGNGIVREGLISTVIGTSGVVFAATDTPRFDSKGRVHTLCHAVPNKWHIMGVTQG 300
           +   A+G GIV   ++ +    + V  ++   P      RV   CH + + + I      
Sbjct: 239 RPLEALGAGIVGSRVMESTGTATNVSMSSNKVPE-SLDPRVVCSCHVIRDHYLIEQGINT 297

Query: 301 AGLSLNWFKRTFCAKEILESKEAGINIYDLLTEKASQSKPGSNGIIYLPYLMGERTPHID 360
           +G  L W +  F   E    KE G N+Y+L+  +A  S PG+NG++ LP+ MG R    +
Sbjct: 298 SGTILRWIRDNFYRGE----KEKGENVYELIDSEAESSSPGANGVVLLPFFMGSRATRWN 353

Query: 361 PNVKGAFLGISLINNHNDFVRSILEGVGFSLKNCLDIIENMKVNIEEIRVSGGGAESSIW 420
           P+ KG   G++L ++  D  R++LEG+ + ++ C++I+E+M +  E I   GGGA+S +W
Sbjct: 354 PDAKGVLFGLTLTHSRADIARAVLEGISYEIRACIEILESMGLKAESIVSMGGGAKSRVW 413

Query: 421 RQILSDIFNYELTTVKASEGPALGVAILAGVGAGIYNSVEEACDKIVKGNEKVMPNANLI 480
            +I +DI    +   K  E  + G  +LA    G   S+ E   +++    +  P++   
Sbjct: 414 SKIKADILGKNVVVEKVQEAASKGAMLLASYAIGARESLIEEKREVL---FEYQPDSKNH 470

Query: 481 EVYSKVYEVYNSAYPKIKDI 500
           E+Y++VYE+YN  Y  +  +
Sbjct: 471 EIYNRVYEIYNQLYNSVSPL 490


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: 639
Number of extensions: 26
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 500
Length of database: 497
Length adjustment: 34
Effective length of query: 466
Effective length of database: 463
Effective search space:   215758
Effective search space used:   215758
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_013402101.1 CALHY_RS00630 (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.4175829.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-124  402.2   0.0   1.6e-124  402.0   0.0    1.0  1  NCBI__GCF_000166355.1:WP_013402101.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166355.1:WP_013402101.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  402.0   0.0  1.6e-124  1.6e-124       2     481 .]       6     485 ..       5     485 .. 0.94

  Alignments for each domain:
  == domain 1  score: 402.0 bits;  conditional E-value: 1.6e-124
                             TIGR01312   2 GiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeikaisis 74 
                                            iD+gT+++K+++ d +g+++a+++ ++++++p+  w+Eqdp +w++ + e +ke+ ++a    + i ai++s
  NCBI__GCF_000166355.1:WP_013402101.1   6 TIDIGTTACKVIVFDLQGNILAKANREYPTYTPQIEWAEQDPLDWWNEVVEGIKEVAQAAG--ADGIVAIGLS 76 
                                           69*********************************************************99..599******* PP

                             TIGR01312  75 GQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllWvrkhepevfar 147
                                            Q   +v +D+eg+vl  ai W D r+  e+ee++++ g+++++++tg ++   fTa+KllW++kh+pe+ ++
  NCBI__GCF_000166355.1:WP_013402101.1  77 SQRETVVPIDKEGNVLSRAISWMDRRSRLEAEEISHQFGKDTIHKITGLIPDSTFTATKLLWLKKHQPEILQK 149
                                           ************************************************************************* PP

                             TIGR01312 148 iakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPklvessekaGkvreevak 220
                                              +l Pk ++ y+Ltge++t++s As T++fdv+kr+w +++++ + +++s++P+l+ ++e++G ++e+vak
  NCBI__GCF_000166355.1:WP_013402101.1 150 AYIFLQPKEFIGYMLTGEAATDHSLASRTMMFDVNKRQWWEDIFEFVGVKTSQFPRLCYADEVIGYLKEDVAK 222
                                           ************************************************************************* PP

                             TIGR01312 221 klGleegvkvaaGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesdpegavhsFchalpgkwyplgv 293
                                            lGl++g++v++Gggd    A+G+giv +  v+ s Gt   v + ++k  ++ + +v   ch+  ++++    
  NCBI__GCF_000166355.1:WP_013402101.1 223 ILGLKSGIPVVSGGGDRPLEALGAGIVGS-RVMESTGTATNVSMSSNKVPESLDPRVVCSCHVIRDHYLIEQG 294
                                           *************************8875.6899******************************777777777 PP

                             TIGR01312 294 tlsatsalewlkellg.......eldveelneeaekvevgaegvlllPylsGERtPhldpqargsliGltant 359
                                           +   ++ l w+++++        e  +e ++ eae +++ga+gv+llP+++G R    +p+a+g+l+Glt ++
  NCBI__GCF_000166355.1:WP_013402101.1 295 INTSGTILRWIRDNFYrgekekgENVYELIDSEAESSSPGANGVVLLPFFMGSRATRWNPDAKGVLFGLTLTH 367
                                           7778999********87775554445677889999************************************** PP

                             TIGR01312 360 tradlarAvlegvafalrdsldilkelkglkikeirliGGGaksevwrqiladilglevvvpeeeegaalGaA 432
                                           +rad+arAvleg+++ +r+ ++il++  glk ++i+++GGGaks+vw +i adilg++vvv++ +e+a+ Ga 
  NCBI__GCF_000166355.1:WP_013402101.1 368 SRADIARAVLEGISYEIRACIEILES-MGLKAESIVSMGGGAKSRVWSKIKADILGKNVVVEKVQEAASKGAM 439
                                           **************************.66******************************************** PP

                             TIGR01312 433 ilAaialgekdlveecseavvkqkesvepiaenveayeelyerykklye 481
                                            lA +a g     e++ e+  +   +++p+ +n+e y+++ye y++ly+
  NCBI__GCF_000166355.1:WP_013402101.1 440 LLASYAIGAR---ESLIEEKREVLFEYQPDSKNHEIYNRVYEIYNQLYN 485
                                           *******954...34444444444557899****************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (497 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 32.40
//
[ok]

This GapMind analysis is from Sep 24 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 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