Align Xylulose kinase; Short=Xylulokinase; EC 2.7.1.17 (characterized, see rationale)
to candidate 353949 BT4423 xylulose kinase (NCBI ptt file)
Query= uniprot:Q97FW4 (500 letters) >FitnessBrowser__Btheta:353949 Length = 505 Score = 331 bits (848), Expect = 4e-95 Identities = 173/493 (35%), Positives = 279/493 (56%), Gaps = 5/493 (1%) Query: 3 YLLGIDVGTSGTKTALFDECGNTIKTSTHEYELFQPQVGWAEQNPENWWTACVKGIREVI 62 Y+L D+GTSG K LFDE G I + T Y AEQNP +WW A V + ++ Sbjct: 2 YILAHDLGTSGNKATLFDESGLLIASRTAAYPTDYASGNRAEQNPHHWWKAIVDTTQALL 61 Query: 63 EKSKIDPLDIKGIGISGQMHGLVLIDKEYKVIRNSIIWCDQRTEKECTQITDTIGKEKLI 122 E + P DI G+ +SGQM G + IDK+ +R +++CDQR+++E ++T+ I Sbjct: 62 EL--VSPNDIAGVALSGQMMGCLCIDKDGNPLRPHMLYCDQRSQEEEAKLTEKIDPLHFY 119 Query: 123 RITGNPALTGFTLSKLLWVRNNEPDNYKRIYKVLLPKDYIRFKLTGVFAAEVSDASGTQM 182 ITG+ +++ KL+WV+ +EP+ + + K+L KDYI ++L G A + SDASGT Sbjct: 120 EITGHRISASYSVEKLMWVKKHEPEIFAQTAKMLNAKDYINYRLCGTIATDPSDASGTNA 179 Query: 183 LDINTRNWSEELLDDLRIDKNILPDVYESVVVSGCVIEKASKETKLAVNTPVVGGAGDQA 242 D+N WSEE+++ +D ++ P+V S+ V G + +A++ET L TPV+ G GD + Sbjct: 180 YDLNRWQWSEEIIEAAELDLSLFPEVRSSIDVIGEITNEAARETGLLAGTPVICGGGDGS 239 Query: 243 AGAIGNGIVREGLISTVIGTSGVVFAATDTPRFDSKGRVHTLCHAVPNKWHIMGVTQGAG 302 +G G V G +G+S V + P D + R H VP H G Q AG Sbjct: 240 CAGVGVGCVAPGTAYNYLGSSSWVALTVEKPIVDEQRRTMNWAHVVPGMLHPSGTMQAAG 299 Query: 303 LSLNWFKRTFCAKEILESKEAGINIYDLLTEKASQSKPGSNGIIYLPYLMGERTPHIDPN 362 S NW C E + ++G ++++L+ E+ S G+N +++LPY++GERTP + + Sbjct: 300 SSYNWMINQLCQNEQALAAQSGRSVFELIDEQIIASPIGANKLLFLPYMLGERTPRWNVD 359 Query: 363 VKGAFLGISLINNHNDFVRSILEGVGFSLKNCLDIIENMKVNIEEIRVSGGGAESSIWRQ 422 KGAF+G++L + H D +R+++EGV +L ++I V I+ + V GG A++ +WRQ Sbjct: 360 AKGAFIGLTLGHKHGDMLRAVMEGVTLNLGFIINIFRK-HVPIDRMTVIGGCAQNPVWRQ 418 Query: 423 ILSDIFNYELTTVK-ASEGPALGVAILAGVGAGIYNSVEEACDKIVKGNEKVMPNANLIE 481 +++DI+ E+ E ++G AILAG+GAG++ D+ V+ + V P ++ Sbjct: 419 MMADIYQAEIRVPNYLEEATSMGAAILAGIGAGVFPDF-SVIDRFVRIEQTVQPIPENVK 477 Query: 482 VYSKVYEVYNSAY 494 Y V++ AY Sbjct: 478 KYEAWMPVFDQAY 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: 612 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: 505 Length adjustment: 34 Effective length of query: 466 Effective length of database: 471 Effective search space: 219486 Effective search space used: 219486 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 353949 BT4423 (xylulose kinase (NCBI ptt file))
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.28899.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-126 408.7 0.0 1.8e-126 408.4 0.0 1.0 1 lcl|FitnessBrowser__Btheta:353949 BT4423 xylulose kinase (NCBI ptt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:353949 BT4423 xylulose kinase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 408.4 0.0 1.8e-126 1.8e-126 4 480 .. 7 490 .. 4 491 .. 0.96 Alignments for each domain: == domain 1 score: 408.4 bits; conditional E-value: 1.8e-126 TIGR01312 4 DlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeikaisisGQmHg 79 DlgTs+ Ka l de+g +ias +a++++ + +++Eq+p++w++a+ +++++lle + +++i+++++sGQm g lcl|FitnessBrowser__Btheta:353949 7 DLGTSGNKATLFDESGLLIASRTAAYPTDYASGNRAEQNPHHWWKAIVDTTQALLELVS--PNDIAGVALSGQMMG 80 9********************************************************77..8************** PP TIGR01312 80 lvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllWvrkhepevfariakvlLPk 155 +D++g++lrp +L++D+r++ee ++l+e++ ++ e+tg + +++ + Kl+Wv+khepe+fa++ak+l k lcl|FitnessBrowser__Btheta:353949 81 CLCIDKDGNPLRPHMLYCDQRSQEEEAKLTEKIDPLHFYEITGHRISASYSVEKLMWVKKHEPEIFAQTAKMLNAK 156 **********************************99**************************************** PP TIGR01312 156 DylrykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPklvessekaGkvreevakklGleegvkva 231 Dy++y+L g+++t+ sDAsGT +d ++ +ws+e+++a++l+ sl+P++ +s +++G++++e+a+++Gl +g++v+ lcl|FitnessBrowser__Btheta:353949 157 DYINYRLCGTIATDPSDASGTNAYDLNRWQWSEEIIEAAELDLSLFPEVRSSIDVIGEITNEAARETGLLAGTPVI 232 **************************************************************************** PP TIGR01312 232 aGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesdpegavhsFchalpgkwyplgvtlsatsalewlkel 307 +Gggd ++ +G+g v++g++ lG+S v + +k+ +d++ + +++h++pg +p g + +a+s+ +w+ + lcl|FitnessBrowser__Btheta:353949 233 CGGGDGSCAGVGVGCVAPGTAYNYLGSSSWVALTVEKPIVDEQRRTMNWAHVVPGMLHPSGTMQAAGSSYNWMINQ 308 ************************************************************************9987 PP TIGR01312 308 lg...........eldveelneeaekvevgaegvlllPylsGERtPhldpqargsliGltanttradlarAvlegv 372 l ++ +e ++e++ ++++ga+ +l+lPy+ GERtP + +a+g +iGlt +++ d+ rAv+egv lcl|FitnessBrowser__Btheta:353949 309 LCqneqalaaqsgRSVFELIDEQIIASPIGANKLLFLPYMLGERTPRWNVDAKGAFIGLTLGHKHGDMLRAVMEGV 384 76455555555444567889999***************************************************** PP TIGR01312 373 afalrdsldilkelkglkikeirliGGGaksevwrqiladilglevvvpe.eeegaalGaAilAaialgekdlvee 447 ++ l ++i+++ + ++i+++++iGG a+++vwrq++adi ++e++vp+ ee++++GaAilA i++g + ++++ lcl|FitnessBrowser__Btheta:353949 385 TLNLGFIINIFRK-H-VPIDRMTVIGGCAQNPVWRQMMADIYQAEIRVPNyLEEATSMGAAILAGIGAGVFPDFSV 458 *************.4.9*********************************99*******************99999 PP TIGR01312 448 cseavvkqkesvepiaenveayeelyerykkly 480 ++++v +++v+pi env++ye + ++ + y lcl|FitnessBrowser__Btheta:353949 459 IDRFVRI-EQTVQPIPENVKKYEAWMPVFDQAY 490 9887655.5566***********9999998876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (505 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 9.31 // [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