Align xylulokinase; EC 2.7.1.17 (characterized)
to candidate WP_038015560.1 HA49_RS17420 xylulokinase
Query= CharProtDB::CH_003784 (484 letters) >NCBI__GCF_000757425.2:WP_038015560.1 Length = 489 Score = 504 bits (1299), Expect = e-147 Identities = 258/484 (53%), Positives = 326/484 (67%), Gaps = 6/484 (1%) Query: 1 MYIGIDLGTSGVKVILLNEQGEVVAAQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKALG 60 MY+GID+GTS +K ++++EQG++VA +LT+ RPHP WSEQDP+ WWQA RAM L Sbjct: 1 MYLGIDVGTSEIKTLVIDEQGKIVAFAGAELTIQRPHPHWSEQDPQSWWQALQRAMGQLR 60 Query: 61 DQHS--LQDVKALGIAGQMHGATLLDAQQRVLRPAILWNDGRCAQECTLLEARVPQSRVI 118 ++ + +KA+G++GQMHGA LLD Q VLRP ILWND R A++C L A+ P I Sbjct: 61 EKAAEHWSSIKAIGLSGQMHGAVLLDKQGEVLRPCILWNDTRSAEQCQQLTAKAPSLHRI 120 Query: 119 TGNLMMPGFTAPKLLWVQRHEPEIFRQIDKVLLPKDYLRLRMTGEFASDMSDAAGTMWLD 178 GNL MPGFTAPKLLWV RHEP+IF +I VLLPKDYLR RMTGEF SDMSD+AGT+WLD Sbjct: 121 AGNLAMPGFTAPKLLWVARHEPDIFARIAHVLLPKDYLRWRMTGEFISDMSDSAGTLWLD 180 Query: 179 VAKRDWSDVMLQACDLSRDQMPALYEGSEITGALLPEVAKAWGM-ATVPVVAGGGDNAAG 237 VAKRDWSD +LQACDL+R+ MPAL EGS G L PE+A W + A + V GGGDNAA Sbjct: 181 VAKRDWSDELLQACDLTREMMPALVEGSAAGGRLTPEIAAEWHLPAGLVVAGGGGDNAAS 240 Query: 238 AVGVGMVDANQAMLSLGTSGVYFAVSEGFLSKPESAVHSFCHALPQRWHLMSVMLSAASC 297 AVG+G V A +SLGTSGV F V+E + P+SAVH+FCHALPQRWH MSVMLSAAS Sbjct: 241 AVGIGAVRPGDAFISLGTSGVLFTVNECYRPNPQSAVHAFCHALPQRWHQMSVMLSAASA 300 Query: 298 LDWAAKLTGLSNVPALIAAAQ-QADESAEPVWFLPYLSGERTPHNNPQAKGVFFGLTHQH 356 L W ++ G + + D+ FLPYLSGERTPHN+PQA G F LTH Sbjct: 301 LRWVCQILGCDETTLMAEVGRLTLDQRRNAPIFLPYLSGERTPHNDPQASGSFHYLTHDV 360 Query: 357 GPNELARAVLEGVGYALADGMDVVHACGIKPQSVTLIGGGARSEYWRQMLADISGQQLDY 416 L AV+EG+ + LADG+ V++ G + +L+GGGARS W Q++AD+ + Sbjct: 361 TRAHLGYAVIEGITFGLADGLRVLNEAGTELSECSLVGGGARSAEWSQLIADVLNLPMIT 420 Query: 417 RTGGDVGPALGAARLAQIAANPEKSLIELLPQLPLEQSHLPDAQRYAAYQPRRETFRRLY 476 G + G ALGAARLA +A +++ + + P +Q P A + Q R + FR +Y Sbjct: 421 HEGSEAGGALGAARLAWLADGGDEAQVCVKP--AEKQRFQPQADHWEYLQKRLKAFRLMY 478 Query: 477 QQLL 480 QQ L Sbjct: 479 QQQL 482 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: 712 Number of extensions: 35 Number of successful extensions: 5 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: 489 Length adjustment: 34 Effective length of query: 450 Effective length of database: 455 Effective search space: 204750 Effective search space used: 204750 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 WP_038015560.1 HA49_RS17420 (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.2971122.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-187 609.6 0.0 2e-187 609.4 0.0 1.0 1 NCBI__GCF_000757425.2:WP_038015560.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000757425.2:WP_038015560.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 609.4 0.0 2e-187 2e-187 1 480 [. 3 478 .. 3 479 .. 0.97 Alignments for each domain: == domain 1 score: 609.4 bits; conditional E-value: 2e-187 TIGR01312 1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeikaisi 73 lGiD+gTs++K+l++de+g+++a + a+lt+++p+p+wsEqdp++w++al++a+ +l+eka+e++++ikai++ NCBI__GCF_000757425.2:WP_038015560.1 3 LGIDVGTSEIKTLVIDEQGKIVAFAGAELTIQRPHPHWSEQDPQSWWQALQRAMGQLREKAAEHWSSIKAIGL 75 7************************************************************************ PP TIGR01312 74 sGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllWvrkhepevfa 146 sGQmHg+vlLD++g+vlrp+iLWnDtr+ae+c++l+++++ +l++++gnla++gfTapKllWv +hep++fa NCBI__GCF_000757425.2:WP_038015560.1 76 SGQMHGAVLLDKQGEVLRPCILWNDTRSAEQCQQLTAKAP--SLHRIAGNLAMPGFTAPKLLWVARHEPDIFA 146 ***************************************9..******************************* PP TIGR01312 147 riakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPklvessekaGkvreeva 219 ria+vlLPkDylr+++tge+++++sD++GTl++dv+kr+ws+ell+a+dl ++++P+lve+s+ G++++e+a NCBI__GCF_000757425.2:WP_038015560.1 147 RIAHVLLPKDYLRWRMTGEFISDMSDSAGTLWLDVAKRDWSDELLQACDLTREMMPALVEGSAAGGRLTPEIA 219 ************************************************************************* PP TIGR01312 220 kklGleegvkvaaGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesdpegavhsFchalpgkwyplg 292 +++ l +g va+Gggdnaa+A+G+g+v++g++++slGtSGv+++v++ ++++p++avh+Fchalp++w++++ NCBI__GCF_000757425.2:WP_038015560.1 220 AEWHLPAGLVVAGGGGDNAASAVGIGAVRPGDAFISLGTSGVLFTVNECYRPNPQSAVHAFCHALPQRWHQMS 292 ************************************************************************* PP TIGR01312 293 vtlsatsalewlkellgeldveelneeaekvevg..aegvlllPylsGERtPhldpqargsliGltanttrad 363 v+lsa+sal w++++lg d ++l++e+ + + + ++ ++lPylsGERtPh+dpqa+gs++ lt++ tra+ NCBI__GCF_000757425.2:WP_038015560.1 293 VMLSAASALRWVCQILG-CDETTLMAEVGRLTLDqrRNAPIFLPYLSGERTPHNDPQASGSFHYLTHDVTRAH 364 *****************.89999999999887664489*********************************** PP TIGR01312 364 larAvlegvafalrdsldilkelkglkikeirliGGGaksevwrqiladilglevvvpe.eeegaalGaAilA 435 l +Av+eg++f+l+d+l +l+e +g++++e++l+GGGa+s+ w q++ad+l+l++ ++e +e g alGaA+lA NCBI__GCF_000757425.2:WP_038015560.1 365 LGYAVIEGITFGLADGLRVLNE-AGTELSECSLVGGGARSAEWSQLIADVLNLPMITHEgSEAGGALGAARLA 436 **********************.67*********************************988999********* PP TIGR01312 436 aialgekdlveecseavvkqkesvepiaenveayeelyerykkly 480 +a g d++++c + kq+ +p+a + e +++++ ++ +y NCBI__GCF_000757425.2:WP_038015560.1 437 WLADGG-DEAQVCVKPAEKQR--FQPQADHWEYLQKRLKAFRLMY 478 999986.78999988876665..5599999999999999998877 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (489 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 0.02s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 13.12 // [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