Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate AO353_25905 AO353_25905 xylulose kinase
Query= reanno::pseudo6_N2E2:Pf6N2E2_805 (495 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25905 Length = 497 Score = 805 bits (2080), Expect = 0.0 Identities = 400/497 (80%), Positives = 437/497 (87%), Gaps = 2/497 (0%) Query: 1 MANQQLFLGIDCGTQGTKALILDATSGQVLGLGAAAHSMISGANGRREQDTQQWLDAFTQ 60 M+ + LFLGIDCGTQGTKALILD+ SG+VLG GAAAHS+IS ANGRREQD QWL+A T Sbjct: 1 MSIRNLFLGIDCGTQGTKALILDSRSGKVLGQGAAAHSLISSANGRREQDPAQWLEALTL 60 Query: 61 ATHQALAAAGVDGQAILGIGVSGQQHGLVLLDDQGQVLRPAKLWCDTETTPENDRLLAHL 120 AT QAL AA + G+ ILGIGVSGQQHGLVLLD+QGQVLRPAKLWCDTETT EN RLLAHL Sbjct: 61 ATRQALLAANISGREILGIGVSGQQHGLVLLDEQGQVLRPAKLWCDTETTAENQRLLAHL 120 Query: 121 GGEDGSLERLGVVIAPGYTVSKLLWTREQHPQVFERIASVLLPHDFLNYWLTGRHCSEYG 180 GGE GSLERLGV IAPGYTVSKLLWT EQHPQ+F RIA +LLPHD+LNYWLTGR CSE+G Sbjct: 121 GGESGSLERLGVAIAPGYTVSKLLWTEEQHPQIFARIAHILLPHDYLNYWLTGRCCSEFG 180 Query: 181 DASGTGYFNVRTRQWDVQLLQHIDPSARLQAALPELIEAHQPVGRILPAIAAHLGINPEA 240 DASGTGYFNVR+RQWD+QLL+ IDPS RLQAALPEL+EAHQ VG ILP IA LGINP+A Sbjct: 181 DASGTGYFNVRSRQWDLQLLRDIDPSGRLQAALPELLEAHQAVGTILPDIAERLGINPKA 240 Query: 241 VVASGGGDNMMGAIGTGNIQPGVITMSLGSSGTVYAYAAEPAVSPQPSVATFCSSSGGWL 300 +VASGGGDNMMGA+GTGNIQPG ITMSLGSSGTVYAYA +P VSP +VATFCSSSGGWL Sbjct: 241 LVASGGGDNMMGALGTGNIQPGAITMSLGSSGTVYAYAEQPNVSPDAAVATFCSSSGGWL 300 Query: 301 PLICTMNLTNATGAIRELLDLDIDAFNALVAKAPIGAEGVCMLPFLNGERVPALPHATGS 360 PLICTMNLTNAT A+REL DLD+ FNA V ++PIGAEGV MLPFLNGERVPALPHATGS Sbjct: 301 PLICTMNLTNATSAVRELFDLDLSQFNARVEQSPIGAEGVSMLPFLNGERVPALPHATGS 360 Query: 361 LLGLTTTNLTRANLCRAVVEGTTFGLRYGLDLLRANGLQAQSIRLIGGGSKSAQWRQIVA 420 LLGL +NLT+ANLCRAVVEGTTFGLRYGLDLLR NGLQ++SIRL GGGSKS WRQ+VA Sbjct: 361 LLGLNMSNLTQANLCRAVVEGTTFGLRYGLDLLRHNGLQSRSIRLTGGGSKSPAWRQMVA 420 Query: 421 DTMDTTVICTEQSEAAALGAAIQAAWCHS--GSQTGLAELCERCVKLDPSSETRPIAAHV 478 D M+T V+CTE SEAAALGAAIQAAWC S G+Q L LCERCV LDPSSET+P+AA+V Sbjct: 421 DIMNTPVVCTEHSEAAALGAAIQAAWCESAAGTQQSLLALCERCVSLDPSSETQPVAANV 480 Query: 479 AASQQAYERYRQHVATL 495 AA QQAYERYRQ VATL Sbjct: 481 AAYQQAYERYRQQVATL 497 Lambda K H 0.318 0.133 0.402 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: 891 Number of extensions: 31 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: 495 Length of database: 497 Length adjustment: 34 Effective length of query: 461 Effective length of database: 463 Effective search space: 213443 Effective search space used: 213443 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 (21.7 bits) S2: 52 (24.6 bits)
Align candidate AO353_25905 AO353_25905 (xylulose kinase)
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.16949.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.6e-190 617.2 0.0 9.8e-190 617.0 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905 AO353_25905 xylulose kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905 AO353_25905 xylulose kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 617.0 0.0 9.8e-190 9.8e-190 1 479 [. 8 493 .. 8 495 .. 0.99 Alignments for each domain: == domain 1 score: 617.0 bits; conditional E-value: 9.8e-190 TIGR01312 1 lGiDlgTssvKallvd.ekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakee 64 lGiD+gT+++Kal++d +g+v+++g+a++++is+++g++Eqdp +wleal+ a++++l +a+ + lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905 8 LGIDCGTQGTKALILDsRSGKVLGQGAAAHSLISSANGRREQDPAQWLEALTLATRQALLAANIS 72 7***************99*********************************************** PP TIGR01312 65 kkeikaisisGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelg.eeelleltgnlaleg 128 +ei +i++sGQ+HglvlLDe+g+vlrpa+LW+Dt+t++e+++l ++lg e+ +le++g ++++g lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905 73 GREILGIGVSGQQHGLVLLDEQGQVLRPAKLWCDTETTAENQRLLAHLGgESGSLERLGVAIAPG 137 *************************************************9*************** PP TIGR01312 129 fTapKllWvrkhepevfariakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellka 193 +T++KllW+ +++p++faria++lLP+Dyl+y+Ltg+ ++e +DAsGT++f+v+ r+w+ +ll+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905 138 YTVSKLLWTEEQHPQIFARIAHILLPHDYLNYWLTGRCCSEFGDASGTGYFNVRSRQWDLQLLRD 202 ***************************************************************** PP TIGR01312 194 ldle...esllPklvessekaGkvreevakklGleegvkvaaGggdnaagAiGlgivkegkvlvs 255 +d++ +++lP+l+e+++ +G++ +++a++lG++ + va+Gggdn++gA+G+g++++g++++s lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905 203 IDPSgrlQAALPELLEAHQAVGTILPDIAERLGINPKALVASGGGDNMMGALGTGNIQPGAITMS 267 ****99999******************************************************** PP TIGR01312 256 lGtSGvvlavedkaesdpegavhsFchalpgkwyplgvtlsatsalewlkellgeldveelneea 320 lG+SG+v+a++++++++p++av++Fc+++ g+w+pl++t+++t+a++ ++el+ ld++++n+ + lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905 268 LGSSGTVYAYAEQPNVSPDAAVATFCSSS-GGWLPLICTMNLTNATSAVRELFD-LDLSQFNARV 330 *****************************.************************.********** PP TIGR01312 321 ekvevgaegvlllPylsGERtPhldpqargsliGlt.anttradlarAvlegvafalrdsldilk 384 e++++gaegv++lP+l+GER+P+l p+a+gsl+Gl+ +n t+a+l+rAv+eg++f+lr++ld+l+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905 331 EQSPIGAEGVSMLPFLNGERVPAL-PHATGSLLGLNmSNLTQANLCRAVVEGTTFGLRYGLDLLR 394 ************************.***********8999************************* PP TIGR01312 385 elkglkikeirliGGGaksevwrqiladilglevvvpeeeegaalGaAilAaialg....ekdlv 445 + +gl++++irl+GGG+ks++wrq++adi++++vv++e++e+aalGaAi+Aa++++ +++l+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905 395 H-NGLQSRSIRLTGGGSKSPAWRQMVADIMNTPVVCTEHSEAAALGAAIQAAWCESaagtQQSLL 458 *.88**************************************************99888778899 PP TIGR01312 446 eecseavvkqkes.vepiaenveayeelyerykkl 479 ++c+++v+ + +s ++p+a+nv+ay+++yery++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905 459 ALCERCVSLDPSSeTQPVAANVAAYQQAYERYRQQ 493 **********9999******************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (497 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: 00:00:00.02 # Mc/sec: 9.22 // [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