Align xylulokinase; EC 2.7.1.17 (characterized)
to candidate 17625 b3564 xylulokinase (NCBI)
Query= CharProtDB::CH_003784 (484 letters) >FitnessBrowser__Keio:17625 Length = 484 Score = 977 bits (2525), Expect = 0.0 Identities = 484/484 (100%), Positives = 484/484 (100%) Query: 1 MYIGIDLGTSGVKVILLNEQGEVVAAQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKALG 60 MYIGIDLGTSGVKVILLNEQGEVVAAQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKALG Sbjct: 1 MYIGIDLGTSGVKVILLNEQGEVVAAQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKALG 60 Query: 61 DQHSLQDVKALGIAGQMHGATLLDAQQRVLRPAILWNDGRCAQECTLLEARVPQSRVITG 120 DQHSLQDVKALGIAGQMHGATLLDAQQRVLRPAILWNDGRCAQECTLLEARVPQSRVITG Sbjct: 61 DQHSLQDVKALGIAGQMHGATLLDAQQRVLRPAILWNDGRCAQECTLLEARVPQSRVITG 120 Query: 121 NLMMPGFTAPKLLWVQRHEPEIFRQIDKVLLPKDYLRLRMTGEFASDMSDAAGTMWLDVA 180 NLMMPGFTAPKLLWVQRHEPEIFRQIDKVLLPKDYLRLRMTGEFASDMSDAAGTMWLDVA Sbjct: 121 NLMMPGFTAPKLLWVQRHEPEIFRQIDKVLLPKDYLRLRMTGEFASDMSDAAGTMWLDVA 180 Query: 181 KRDWSDVMLQACDLSRDQMPALYEGSEITGALLPEVAKAWGMATVPVVAGGGDNAAGAVG 240 KRDWSDVMLQACDLSRDQMPALYEGSEITGALLPEVAKAWGMATVPVVAGGGDNAAGAVG Sbjct: 181 KRDWSDVMLQACDLSRDQMPALYEGSEITGALLPEVAKAWGMATVPVVAGGGDNAAGAVG 240 Query: 241 VGMVDANQAMLSLGTSGVYFAVSEGFLSKPESAVHSFCHALPQRWHLMSVMLSAASCLDW 300 VGMVDANQAMLSLGTSGVYFAVSEGFLSKPESAVHSFCHALPQRWHLMSVMLSAASCLDW Sbjct: 241 VGMVDANQAMLSLGTSGVYFAVSEGFLSKPESAVHSFCHALPQRWHLMSVMLSAASCLDW 300 Query: 301 AAKLTGLSNVPALIAAAQQADESAEPVWFLPYLSGERTPHNNPQAKGVFFGLTHQHGPNE 360 AAKLTGLSNVPALIAAAQQADESAEPVWFLPYLSGERTPHNNPQAKGVFFGLTHQHGPNE Sbjct: 301 AAKLTGLSNVPALIAAAQQADESAEPVWFLPYLSGERTPHNNPQAKGVFFGLTHQHGPNE 360 Query: 361 LARAVLEGVGYALADGMDVVHACGIKPQSVTLIGGGARSEYWRQMLADISGQQLDYRTGG 420 LARAVLEGVGYALADGMDVVHACGIKPQSVTLIGGGARSEYWRQMLADISGQQLDYRTGG Sbjct: 361 LARAVLEGVGYALADGMDVVHACGIKPQSVTLIGGGARSEYWRQMLADISGQQLDYRTGG 420 Query: 421 DVGPALGAARLAQIAANPEKSLIELLPQLPLEQSHLPDAQRYAAYQPRRETFRRLYQQLL 480 DVGPALGAARLAQIAANPEKSLIELLPQLPLEQSHLPDAQRYAAYQPRRETFRRLYQQLL Sbjct: 421 DVGPALGAARLAQIAANPEKSLIELLPQLPLEQSHLPDAQRYAAYQPRRETFRRLYQQLL 480 Query: 481 PLMA 484 PLMA Sbjct: 481 PLMA 484 Lambda K H 0.319 0.134 0.409 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: 904 Number of extensions: 21 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: 484 Length of database: 484 Length adjustment: 34 Effective length of query: 450 Effective length of database: 450 Effective search space: 202500 Effective search space used: 202500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
Align candidate 17625 b3564 (xylulokinase (NCBI))
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.12694.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7e-201 653.8 0.0 8e-201 653.6 0.0 1.0 1 lcl|FitnessBrowser__Keio:17625 b3564 xylulokinase (NCBI) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:17625 b3564 xylulokinase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 653.6 0.0 8e-201 8e-201 1 481 [] 3 477 .. 3 477 .. 0.99 Alignments for each domain: == domain 1 score: 653.6 bits; conditional E-value: 8e-201 TIGR01312 1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeikaisisGQmHg 79 +GiDlgTs+vK++l++e+gev+a ++++ltv++p+p wsEqdpe+w++a+++a+k+l ++++ +++ka++i+GQmHg lcl|FitnessBrowser__Keio:17625 3 IGIDLGTSGVKVILLNEQGEVVAAQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKALGDQHS--LQDVKALGIAGQMHG 79 8***********************************************************88..5************** PP TIGR01312 80 lvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllWvrkhepevfariakvlLPkDyl 158 ++lLD++++vlrpaiLWnD r+a+ec+ le++++ +++ +tgnl+++gfTapKllWv++hepe+f++i+kvlLPkDyl lcl|FitnessBrowser__Keio:17625 80 ATLLDAQQRVLRPAILWNDGRCAQECTLLEARVP--QSRVITGNLMMPGFTAPKLLWVQRHEPEIFRQIDKVLLPKDYL 156 *********************************9..88899************************************** PP TIGR01312 159 rykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPklvessekaGkvreevakklGleegvkvaaGggdn 237 r+++tge+++++sDA+GT+++dv+kr+ws+ +l+a+dl+++++P+l+e+se++G++ +evak++G+ ++v+v+aGggdn lcl|FitnessBrowser__Keio:17625 157 RLRMTGEFASDMSDAAGTMWLDVAKRDWSDVMLQACDLSRDQMPALYEGSEITGALLPEVAKAWGM-ATVPVVAGGGDN 234 ******************************************************************.99********** PP TIGR01312 238 aagAiGlgivkegkvlvslGtSGvvlavedkaesdpegavhsFchalpgkwyplgvtlsatsalewlkellgeldveel 316 aagA+G+g+v+++++++slGtSGv++av++ s+pe+avhsFchalp++w+ ++v+lsa+s+l+w+++l+g ++v +l lcl|FitnessBrowser__Keio:17625 235 AAGAVGVGMVDANQAMLSLGTSGVYFAVSEGFLSKPESAVHSFCHALPQRWHLMSVMLSAASCLDWAAKLTGLSNVPAL 313 ******************************************************************************* PP TIGR01312 317 neeaekvevgaegvlllPylsGERtPhldpqargsliGltanttradlarAvlegvafalrdsldilkelkglkikeir 395 ++a++++++ae+v++lPylsGERtPh++pqa+g+++Glt+++ ++larAvlegv +al+d++d++++ +g+k+++++ lcl|FitnessBrowser__Keio:17625 314 IAAAQQADESAEPVWFLPYLSGERTPHNNPQAKGVFFGLTHQHGPNELARAVLEGVGYALADGMDVVHA-CGIKPQSVT 391 ********************************************************************9.88******* PP TIGR01312 396 liGGGaksevwrqiladilglevvvpe.eeegaalGaAilAaialg.ekdlveecseavvkqkesvepiaenveayeel 472 liGGGa+se+wrq+ladi+g+++++++ + g+alGaA+lA+ia++ ek+l+e++++ +q++ p+a++++ay+ + lcl|FitnessBrowser__Keio:17625 392 LIGGGARSEYWRQMLADISGQQLDYRTgGDVGPALGAARLAQIAANpEKSLIELLPQLPLEQSHL--PDAQRYAAYQPR 468 ***************************99*****************9999**********99999..************ PP TIGR01312 473 yerykklye 481 e++++ly+ lcl|FitnessBrowser__Keio:17625 469 RETFRRLYQ 477 ******996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (484 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 8.31 // [ok]
This GapMind analysis is from Sep 17 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