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_013403936.1 CALHY_RS10535 xylulokinase

Query= uniprot:Q97FW4
         (500 letters)



>NCBI__GCF_000166355.1:WP_013403936.1
          Length = 502

 Score =  638 bits (1645), Expect = 0.0
 Identities = 300/498 (60%), Positives = 384/498 (77%)

Query: 3   YLLGIDVGTSGTKTALFDECGNTIKTSTHEYELFQPQVGWAEQNPENWWTACVKGIREVI 62
           Y +GIDVGTSGTKT L D  GN + T+T EY L+QPQ+GWAEQNPE+WW A VKGI+ V+
Sbjct: 2   YFIGIDVGTSGTKTILTDSKGNILATATFEYPLYQPQIGWAEQNPEDWWDASVKGIKAVL 61

Query: 63  EKSKIDPLDIKGIGISGQMHGLVLIDKEYKVIRNSIIWCDQRTEKECTQITDTIGKEKLI 122
           EKSK+DP ++K +G++GQMHGLV++DK Y VIR SIIWCDQRT KEC +IT+ IGKE+LI
Sbjct: 62  EKSKVDPKEVKAVGLTGQMHGLVMLDKNYNVIRPSIIWCDQRTAKECDEITEKIGKERLI 121

Query: 123 RITGNPALTGFTLSKLLWVRNNEPDNYKRIYKVLLPKDYIRFKLTGVFAAEVSDASGTQM 182
            IT NPALTGFT SK+LWVRNNEP NY+++YK+LLPKDYIRFKLTG FA +VSDASG Q+
Sbjct: 122 EITANPALTGFTASKILWVRNNEPQNYEKVYKILLPKDYIRFKLTGEFATDVSDASGMQL 181

Query: 183 LDINTRNWSEELLDDLRIDKNILPDVYESVVVSGCVIEKASKETKLAVNTPVVGGAGDQA 242
           LDI  R WS+E+L+ L IDK++L  VYES  V+G V  +AS+ T L   T VV G GDQA
Sbjct: 182 LDIKNRCWSDEVLEKLEIDKDLLGKVYESPEVTGKVSRQASEITGLWEGTLVVAGGGDQA 241

Query: 243 AGAIGNGIVREGLISTVIGTSGVVFAATDTPRFDSKGRVHTLCHAVPNKWHIMGVTQGAG 302
           AGA+GNGIV+ G+IS+ IG+SGVVFA  D  + D +GRVHT CHAVP KWH+MGVTQGAG
Sbjct: 242 AGAVGNGIVKTGVISSTIGSSGVVFAHLDEFKIDPQGRVHTFCHAVPGKWHVMGVTQGAG 301

Query: 303 LSLNWFKRTFCAKEILESKEAGINIYDLLTEKASQSKPGSNGIIYLPYLMGERTPHIDPN 362
           LSL WF+  F   E    +    + Y L+ ++A  + PGS+G+++LPYLMGERTP +DP 
Sbjct: 302 LSLKWFRDNFAHIEKAAFEFIDKDPYILMDQEAELANPGSDGLVFLPYLMGERTPILDPY 361

Query: 363 VKGAFLGISLINNHNDFVRSILEGVGFSLKNCLDIIENMKVNIEEIRVSGGGAESSIWRQ 422
            KG F GI+  +   +F+R+++EGV FSLKNCLDI+  M + ++E+RVSGGGA+S +WRQ
Sbjct: 362 AKGIFFGITAKHTRREFIRAVMEGVVFSLKNCLDILHEMGIEVKEVRVSGGGAKSKLWRQ 421

Query: 423 ILSDIFNYELTTVKASEGPALGVAILAGVGAGIYNSVEEACDKIVKGNEKVMPNANLIEV 482
           + +DIF  ++ T+ + EGPA G AILA VGAG+YN VEEACD +++  E   PN +L EV
Sbjct: 422 MQADIFEMDVWTLNSKEGPAFGAAILATVGAGVYNKVEEACDTMIQKVESCSPNKDLFEV 481

Query: 483 YSKVYEVYNSAYPKIKDI 500
           Y K Y++YNS YP++KD+
Sbjct: 482 YRKTYKLYNSIYPRVKDL 499


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: 787
Number of extensions: 36
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: 500
Length of database: 502
Length adjustment: 34
Effective length of query: 466
Effective length of database: 468
Effective search space:   218088
Effective search space used:   218088
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_013403936.1 CALHY_RS10535 (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.2988505.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     8e-183  594.2   0.0   9.5e-183  594.0   0.0    1.0  1  NCBI__GCF_000166355.1:WP_013403936.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166355.1:WP_013403936.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  594.0   0.0  9.5e-183  9.5e-183       1     480 [.       4     493 ..       4     494 .. 0.97

  Alignments for each domain:
  == domain 1  score: 594.0 bits;  conditional E-value: 9.5e-183
                             TIGR01312   1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeikaisi 73 
                                           +GiD+gTs++K++l d+kg+++a+++ ++++++p+ gw+Eq+pe+w++a  + +k++lek+k+++ke+ka+++
  NCBI__GCF_000166355.1:WP_013403936.1   4 IGIDVGTSGTKTILTDSKGNILATATFEYPLYQPQIGWAEQNPEDWWDASVKGIKAVLEKSKVDPKEVKAVGL 76 
                                           7************************************************************************ PP

                             TIGR01312  74 sGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllWvrkhepevfa 146
                                           +GQmHglv+LD++ +v+rp i+W+D+rta+ec+e++e++g+e+l+e+t n al+gfTa+K+lWvr++ep++++
  NCBI__GCF_000166355.1:WP_013403936.1  77 TGQMHGLVMLDKNYNVIRPSIIWCDQRTAKECDEITEKIGKERLIEITANPALTGFTASKILWVRNNEPQNYE 149
                                           ************************************************************************* PP

                             TIGR01312 147 riakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPklvessekaGkvreeva 219
                                           ++ k+lLPkDy+r+kLtge++t++sDAsG  l+d+k+r+ws+e+l++l+++++ll k++es e++Gkv+ ++ 
  NCBI__GCF_000166355.1:WP_013403936.1 150 KVYKILLPKDYIRFKLTGEFATDVSDASGMQLLDIKNRCWSDEVLEKLEIDKDLLGKVYESPEVTGKVSRQAS 222
                                           ************************************************************************* PP

                             TIGR01312 220 kklGleegvkvaaGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesdpegavhsFchalpgkwyplg 292
                                           + +Gl eg+ v+aGggd+aagA+G givk g+++  +G+SGvv+a  d+ + dp+g+vh+Fcha+pgkw+ +g
  NCBI__GCF_000166355.1:WP_013403936.1 223 EITGLWEGTLVVAGGGDQAAGAVGNGIVKTGVISSTIGSSGVVFAHLDEFKIDPQGRVHTFCHAVPGKWHVMG 295
                                           ************************************************************************* PP

                             TIGR01312 293 vtlsatsalewlkellg...........eldveelneeaekvevgaegvlllPylsGERtPhldpqargsliG 354
                                           vt  a+ +l+w++++++           +  +  +++eae +++g++g+++lPyl+GERtP ldp a+g+++G
  NCBI__GCF_000166355.1:WP_013403936.1 296 VTQGAGLSLKWFRDNFAhiekaafefidKDPYILMDQEAELANPGSDGLVFLPYLMGERTPILDPYAKGIFFG 368
                                           ****************95553333332222233467899********************************** PP

                             TIGR01312 355 ltanttradlarAvlegvafalrdsldilkelkglkikeirliGGGaksevwrqiladilglevvvpeeeega 427
                                           +ta++tr ++ rAv+egv+f+l++ ldil+e  g+++ke+r+ GGGaks++wrq++adi+++ v + +++eg+
  NCBI__GCF_000166355.1:WP_013403936.1 369 ITAKHTRREFIRAVMEGVVFSLKNCLDILHE-MGIEVKEVRVSGGGAKSKLWRQMQADIFEMDVWTLNSKEGP 440
                                           *******************************.66*************************************** PP

                             TIGR01312 428 alGaAilAaialgekdlveecseavvkqkesvepiaenveayeelyerykkly 480
                                           a+GaAilA++++g +++vee+ ++++++ es +p++   e y+++y+ y+++y
  NCBI__GCF_000166355.1:WP_013403936.1 441 AFGAAILATVGAGVYNKVEEACDTMIQKVESCSPNKDLFEVYRKTYKLYNSIY 493
                                           *************999**99999999999999*****************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (502 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: 00:00:00.00
# Mc/sec: 26.53
//
[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:

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:

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:

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:

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