Alignments for a candidate for xylB in Desulfotomaculum hydrothermale Lam5

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylB in Desulfotomaculum hydrothermale Lam5

Align Xylulose kinase; Short=Xylulokinase; EC 2.7.1.17 (characterized, see rationale)
to candidate WP_008412468.1 DESHY_RS10055 xylulokinase

Query= uniprot:Q97FW4
         (500 letters)



>NCBI__GCF_000315365.1:WP_008412468.1
          Length = 510

 Score =  509 bits (1310), Expect = e-148
 Identities = 246/500 (49%), Positives = 342/500 (68%), Gaps = 7/500 (1%)

Query: 5   LGIDVGTSGTKTALFDECGNTIKTSTHEYELFQPQVGWAEQNPENWWTACVKGIREVIEK 64
           LGID+GT+G K  + DE G  +  +T EY L  P+ GWAEQNPE+W+ A    I  +I K
Sbjct: 6   LGIDIGTTGVKALVMDEQGRVVAQATREYPLHVPRPGWAEQNPEDWYKAACGAIATIISK 65

Query: 65  SKIDPLDIKGIGISGQMHGLVLIDKEYKVIRNSIIWCDQRTEKECTQITDTIGKEKLIRI 124
             I P  I+GIG++GQMHG V +D + KVIR +I+WCDQRT  EC QITD +G+ KLI +
Sbjct: 66  G-ISPGQIQGIGLTGQMHGSVFLDAQGKVIREAILWCDQRTADECRQITDLVGESKLIEL 124

Query: 125 TGNPALTGFTLSKLLWVRNNEPDNYKRIYKVLLPKDYIRFKLTGVFAAEVSDASGTQMLD 184
             NPAL GFT  K+LW+RN+EP+NYKR+ KVLLPKDYI +++TGVFA +VSDASG  +LD
Sbjct: 125 VSNPALAGFTAPKILWLRNHEPENYKRVAKVLLPKDYISWRMTGVFATDVSDASGMLLLD 184

Query: 185 INTRNWSEELLDDLRIDKNILPDVYESVVVSGCVIEKASKETKLAVNTPVVGGAGDQAAG 244
           +  R WS E+L  L I    L +V+ES  V G V  + + ET L    PVV GAGD AAG
Sbjct: 185 VVNRKWSSEMLAALEIPAAWLAEVFESPDVVGRVSARGAAETGLPEGIPVVAGAGDNAAG 244

Query: 245 AIGNGIVREGLISTVIGTSGVVFAATDTPRFDSKGRVHTLCHAVPNKWHIMGVTQGAGLS 304
           A+GNGI+  G+ +  +GTSGVVF  + TP  D  GR+HT CHAVP +WH+MGVT  AG S
Sbjct: 245 AVGNGIISPGMATASLGTSGVVFTPSQTPAVDRAGRLHTFCHAVPGQWHLMGVTMAAGGS 304

Query: 305 LNWFKRTFCAKEILESKEAGINIYDLLTEKASQSKPGSNGIIYLPYLMGERTPHIDPNVK 364
           L W++ TF  +E   ++  G + Y+L++++A+  +PG++G+I+LPYL GERTPH DP  +
Sbjct: 305 LRWYRDTFAGEERAVAQLTGRDPYELMSDEAALIEPGADGLIFLPYLSGERTPHADPLAR 364

Query: 365 GAFLGISLINNHNDFVRSILEGVGFSLKNCLDIIENMKVNIEEIRVSGGGAESSIWRQIL 424
           G F+G++L +    FVRSI+EGV FSLK+ L+I+  + + + ++R++GGG  S++WRQIL
Sbjct: 365 GVFVGMNLKHTKGHFVRSIMEGVAFSLKDTLEIMSGLGIALNDLRITGGGGRSAVWRQIL 424

Query: 425 SDIFNYELTTVKASEGPALGVAILAGVGAGIYNSVEEA----CDKIVKGNEKVMPNANLI 480
           +D+FN  L  ++ S+GPA G AIL  VGAG + SV EA    C +  +  ++V+P     
Sbjct: 425 ADVFNMPLQVMENSDGPAYGAAILGAVGAGCWQSVTEAVAATCSR--QQLQEVVPIPQNA 482

Query: 481 EVYSKVYEVYNSAYPKIKDI 500
             Y K+Y++Y   YP ++ +
Sbjct: 483 ARYQKIYQIYIDTYPPLQPL 502


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: 644
Number of extensions: 27
Number of successful extensions: 3
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: 510
Length adjustment: 34
Effective length of query: 466
Effective length of database: 476
Effective search space:   221816
Effective search space used:   221816
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_008412468.1 DESHY_RS10055 (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.1108508.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.6e-180  585.5   0.0   4.4e-180  585.2   0.0    1.1  1  NCBI__GCF_000315365.1:WP_008412468.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000315365.1:WP_008412468.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  585.2   0.0  4.4e-180  4.4e-180       1     480 [.       6     496 ..       6     497 .. 0.97

  Alignments for each domain:
  == domain 1  score: 585.2 bits;  conditional E-value: 4.4e-180
                             TIGR01312   1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeikaisi 73 
                                           lGiD+gT++vKal++de+g+v+a+++ ++++  p+pgw+Eq+pe+w++a + a++++++k   ++ +i++i++
  NCBI__GCF_000315365.1:WP_008412468.1   6 LGIDIGTTGVKALVMDEQGRVVAQATREYPLHVPRPGWAEQNPEDWYKAACGAIATIISK-GISPGQIQGIGL 77 
                                           7*********************************************************99.558********* PP

                             TIGR01312  74 sGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllWvrkhepevfa 146
                                           +GQmHg v LD++gkv+r aiLW+D+rta ec+++++ +ge++l+el+ n al+gfTapK+lW+r+hepe+++
  NCBI__GCF_000315365.1:WP_008412468.1  78 TGQMHGSVFLDAQGKVIREAILWCDQRTADECRQITDLVGESKLIELVSNPALAGFTAPKILWLRNHEPENYK 150
                                           ************************************************************************* PP

                             TIGR01312 147 riakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPklvessekaGkvreeva 219
                                           r+akvlLPkDy+ +++tg ++t++sDAsG ll+dv +r+ws+e+l+al+++ ++l +++es +++G+v++  a
  NCBI__GCF_000315365.1:WP_008412468.1 151 RVAKVLLPKDYISWRMTGVFATDVSDASGMLLLDVVNRKWSSEMLAALEIPAAWLAEVFESPDVVGRVSARGA 223
                                           ************************************************************************* PP

                             TIGR01312 220 kklGleegvkvaaGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesdpegavhsFchalpgkwyplg 292
                                           +++Gl eg++v+aG+gdnaagA+G gi+++g ++ slGtSGvv++ ++++ +d +g++h+Fcha+pg+w+ +g
  NCBI__GCF_000315365.1:WP_008412468.1 224 AETGLPEGIPVVAGAGDNAAGAVGNGIISPGMATASLGTSGVVFTPSQTPAVDRAGRLHTFCHAVPGQWHLMG 296
                                           ************************************************************************* PP

                             TIGR01312 293 vtlsatsalewlkellg...........eldveelneeaekvevgaegvlllPylsGERtPhldpqargsliG 354
                                           vt++a+ +l w +++++           +  +e +  ea+ +e+ga+g+++lPylsGERtPh+dp arg+++G
  NCBI__GCF_000315365.1:WP_008412468.1 297 VTMAAGGSLRWYRDTFAgeeravaqltgRDPYELMSDEAALIEPGADGLIFLPYLSGERTPHADPLARGVFVG 369
                                           ***************99776655544444567888999*********************************** PP

                             TIGR01312 355 ltanttradlarAvlegvafalrdsldilkelkglkikeirliGGGaksevwrqiladilglevvvpeeeega 427
                                           ++ ++t+ +++r+++egvaf+l+d+l+i+  l+ + ++++r++GGG +s+vwrqilad+++++++v e++ g+
  NCBI__GCF_000315365.1:WP_008412468.1 370 MNLKHTKGHFVRSIMEGVAFSLKDTLEIMSGLG-IALNDLRITGGGGRSAVWRQILADVFNMPLQVMENSDGP 441
                                           *******************************55.*************************************** PP

                             TIGR01312 428 alGaAilAaialg.ekdlveecseavvkqkes.vepiaenveayeelyerykkly 480
                                           a+GaAil+a+++g +++ +e +++++++q+ + v pi +n+++y+++y+ y + y
  NCBI__GCF_000315365.1:WP_008412468.1 442 AYGAAILGAVGAGcWQSVTEAVAATCSRQQLQeVVPIPQNAARYQKIYQIYIDTY 496
                                           *************88888888888888888777******************8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (510 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: 24.00
//
[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