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.
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:
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