Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate RR42_RS06125 RR42_RS06125 phosphogluconate dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__Cup4G11:RR42_RS06125 Length = 628 Score = 724 bits (1868), Expect = 0.0 Identities = 371/607 (61%), Positives = 458/607 (75%), Gaps = 11/607 (1%) Query: 1 MHPRVLEVTERLVARSRATREAYLALIRGAASD-GPQRGKLQCANFAHGVAGCGSEDKHS 59 +H V VTER++ARS+ +R AYLA A + GP RG L CAN AHG+A + DK Sbjct: 5 LHAEVHAVTERVIARSQRSRAAYLARCERAQQEMGPLRG-LSCANLAHGLAALPAHDKLK 63 Query: 60 LRMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGE 119 LR+ +AAN+ IV++YNDMLSAHQPYE +P I++A R +G+V Q AGG PAMCDG+TQG Sbjct: 64 LRVEHAANLGIVTAYNDMLSAHQPYERYPGVIREAARAVGAVAQVAGGVPAMCDGITQGN 123 Query: 120 AGMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGG 179 AGMELSL SR+ IA++TAV+LSHN FDAA+MLG+CDKIVPGL+MGAL+FGHLP +FVP G Sbjct: 124 AGMELSLFSRDAIAMATAVSLSHNTFDAAVMLGVCDKIVPGLLMGALQFGHLPVVFVPAG 183 Query: 180 PMPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGL 239 PM +G+SNKEKA VRQ YA G+ RE LLE+E ++YH GTCTFYGTAN+NQ LME+MGL Sbjct: 184 PMSTGLSNKEKARVRQLYATGQVGREALLEAECEAYHGAGTCTFYGTANSNQFLMEIMGL 243 Query: 240 HLPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGG 299 H+PGA+FV+P + LRDALT AAQ+ LT + G++ P+ IVDER+++N++V L ATGG Sbjct: 244 HMPGAAFVHPDSGLRDALTAAAAQRALALTARGGDYLPLARIVDERAVINAVVGLLATGG 303 Query: 300 STNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRE 359 STNHT+H+ A+A+AAGI + W D LS + P L+ VYPNG AD+NHF AAGG+A++IR+ Sbjct: 304 STNHTIHLVAMARAAGILIDWDDFDRLSRITPLLARVYPNGSADVNHFHAAGGVAYVIRQ 363 Query: 360 LLEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGG 419 LL AGLLHEDV TVAGRGL+RYTQEP + +G L WRDG S D +L A FS EGG Sbjct: 364 LLSAGLLHEDVETVAGRGLARYTQEPVMIDGVLQWRDGAAVSGDATVLATAAEPFSAEGG 423 Query: 420 LRVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGP 479 LR+++GNLGRG++KVSAVA +H++VEAPA VF Q+ L AF+AGE D +AV+RFQGP Sbjct: 424 LRLLQGNLGRGMIKVSAVADEHRVVEAPARVFDSQEQLQAAFEAGEFTGDMIAVVRFQGP 483 Query: 480 RSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVR 539 +NGMPELH++TP LG LQD G KVALVTDGRMSGASGK+PA IHV PEA GG LARVR Sbjct: 484 NANGMPELHRLTPVLGSLQDAGHKVALVTDGRMSGASGKVPAVIHVGPEALAGGPLARVR 543 Query: 540 DGDIIRVDGVKGTLELKVDAD---EFAAREPAKGLLGN----NVGSGRELFGFMRMAFSS 592 DGD IRVD V GTLE A+ + A R A +L + N GR LFG R Sbjct: 544 DGDRIRVDAVAGTLEWLGAANGDGDLATR--ASAVLPDDAFANFSVGRGLFGLFRRNARI 601 Query: 593 AEQGASA 599 AE+G SA Sbjct: 602 AEEGGSA 608 Lambda K H 0.318 0.134 0.386 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: 1155 Number of extensions: 47 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: 608 Length of database: 628 Length adjustment: 37 Effective length of query: 571 Effective length of database: 591 Effective search space: 337461 Effective search space used: 337461 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: 53 (25.0 bits)
Align candidate RR42_RS06125 RR42_RS06125 (phosphogluconate dehydratase)
to HMM TIGR01196 (edd: phosphogluconate dehydratase (EC 4.2.1.12))
# 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/TIGR01196.hmm # target sequence database: /tmp/gapView.22110.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01196 [M=601] Accession: TIGR01196 Description: edd: phosphogluconate dehydratase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-291 953.7 3.5 2e-291 953.5 3.5 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS06125 RR42_RS06125 phosphogluconate de Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS06125 RR42_RS06125 phosphogluconate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 953.5 3.5 2e-291 2e-291 1 600 [. 6 609 .. 6 610 .. 0.97 Alignments for each domain: == domain 1 score: 953.5 bits; conditional E-value: 2e-291 TIGR01196 1 hsrlaeiteriierskktrekylekirsakt.kgklrstlgcgnlahgvaalsesekvelksekrknla 68 h+++ ++ter+i+rs++ r +yl++ + a++ +g+lr+ l+c+nlahg+aal+ ++k++l+ e+ +nl+ lcl|FitnessBrowser__Cup4G11:RR42_RS06125 6 HAEVHAVTERVIARSQRSRAAYLARCERAQQeMGPLRG-LSCANLAHGLAALPAHDKLKLRVEHAANLG 73 678999********************999872567776.****************************** PP TIGR01196 69 iitayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstai 137 i+tayndmlsahqp+++yp++i++a++ +avaqvagGvpamcdG+tqG++Gmelsl+srd ia++ta+ lcl|FitnessBrowser__Cup4G11:RR42_RS06125 74 IVTAYNDMLSAHQPYERYPGVIREAARAVGAVAQVAGGVPAMCDGITQGNAGMELSLFSRDAIAMATAV 142 ********************************************************************* PP TIGR01196 138 glshnmfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreel 206 +lshn fd+a++lGvcdkivpGll++al fGhlp vfvpaGpm++Gl+nkeka+vrql+a G+v+re+l lcl|FitnessBrowser__Cup4G11:RR42_RS06125 143 SLSHNTFDAAVMLGVCDKIVPGLLMGALQFGHLPVVFVPAGPMSTGLSNKEKARVRQLYATGQVGREAL 211 ********************************************************************* PP TIGR01196 207 lksemasyhapGtctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevl 275 l++e ++yh++GtctfyGtansnq+l+e+mGlh+pga+fv+p++ lrdalt++aa+r+ +lta++g++l lcl|FitnessBrowser__Cup4G11:RR42_RS06125 212 LEAECEAYHGAGTCTFYGTANSNQFLMEIMGLHMPGAAFVHPDSGLRDALTAAAAQRALALTARGGDYL 280 ********************************************************************* PP TIGR01196 276 plaelideksivnalvgllatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvn 344 pla+++de++++na+vgllatGGstnht+hlva+araaGi+++wdd++ ls + pllarvypnG+advn lcl|FitnessBrowser__Cup4G11:RR42_RS06125 281 PLARIVDERAVINAVVGLLATGGSTNHTIHLVAMARAAGILIDWDDFDRLSRITPLLARVYPNGSADVN 349 ********************************************************************* PP TIGR01196 345 hfeaaGGlsflirellkeGllhedvetvagkGlrrytkepfledgkleyreaaeksldedilrkvdkpf 413 hf+aaGG++++ir+ll++Gllhedvetvag+Gl ryt+ep++ dg l++r++a s d +l+++ +pf lcl|FitnessBrowser__Cup4G11:RR42_RS06125 350 HFHAAGGVAYVIRQLLSAGLLHEDVETVAGRGLARYTQEPVMIDGVLQWRDGAAVSGDATVLATAAEPF 418 ********************************************************************* PP TIGR01196 414 saeGGlkllkGnlGravikvsavkeesrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanG 482 saeGGl+ll+GnlGr++ikvsav++e+rv+eapa+vf++q++l+aaf+age+ +d++avvrfqGp+anG lcl|FitnessBrowser__Cup4G11:RR42_RS06125 419 SAEGGLRLLQGNLGRGMIKVSAVADEHRVVEAPARVFDSQEQLQAAFEAGEFTGDMIAVVRFQGPNANG 487 ********************************************************************* PP TIGR01196 483 mpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakirdGdlirldavnge 551 mpelh+lt+vlG lqd g+kvalvtdGr+sGasGkvpa ihv peal+gG+la++rdGd+ir+dav+g lcl|FitnessBrowser__Cup4G11:RR42_RS06125 488 MPELHRLTPVLGSLQDAGHKVALVTDGRMSGASGKVPAVIHVGPEALAGGPLARVRDGDRIRVDAVAGT 556 ********************************************************************* PP TIGR01196 552 levl...vddaelkareleel.dlednelGlGrelfaalrekvssaeeGassl 600 le l d +l++r + l d +++ +Gr lf +r+++ aeeG+s+l lcl|FitnessBrowser__Cup4G11:RR42_RS06125 557 LEWLgaaNGDGDLATRASAVLpDDAFANFSVGRGLFGLFRRNARIAEEGGSAL 609 **99332346779999877651677799*********************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (601 nodes) Target sequences: 1 (628 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 9.69 // [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