Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate HSERO_RS05520 HSERO_RS05520 phosphogluconate dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__HerbieS:HSERO_RS05520 Length = 623 Score = 746 bits (1925), Expect = 0.0 Identities = 367/608 (60%), Positives = 462/608 (75%), Gaps = 8/608 (1%) Query: 1 MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60 ++ + VT+R+ RSR R AYL + A G QRG L C N AHG A + DK L Sbjct: 3 LNATLASVTQRIAERSRPYRTAYLERLEAARRKGAQRGALACTNLAHGFAAFPANDKLKL 62 Query: 61 RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120 + A ++AIVS+YNDMLSAHQP+E FP+ IK A RE G+V QFAGG+PAMCDGVTQG+A Sbjct: 63 KEDKAPSLAIVSAYNDMLSAHQPFERFPQIIKDAAREAGAVAQFAGGSPAMCDGVTQGQA 122 Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180 GMELSL SR+ IA++TA+ALSHNMFDAAL LG+CDKIVPGL++GAL FGHLP +FVP GP Sbjct: 123 GMELSLFSRDAIAMATAIALSHNMFDAALYLGVCDKIVPGLLIGALHFGHLPAVFVPAGP 182 Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240 M SG+SN +K +RQ Y GK R ELLE+E KSYH GTCTFYGTAN+NQ+LME MGLH Sbjct: 183 MTSGMSNSDKVKIRQLYTAGKIGRAELLEAESKSYHGAGTCTFYGTANSNQMLMEAMGLH 242 Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300 LPGA+F+ P TPLRDALT AA+Q ++T +TP+G ++DE+S+VN+IVALHATGGS Sbjct: 243 LPGAAFITPNTPLRDALTAAAAKQAAKITDLGTQYTPVGRMIDEKSIVNAIVALHATGGS 302 Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360 TNHTLH+ AIA+AAGI + W D LS VVP ++ +YPNG AD+NHF AAGG F++REL Sbjct: 303 TNHTLHLVAIAKAAGIVIDWDDFDKLSAVVPLITKIYPNGTADVNHFHAAGGTGFVLREL 362 Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFL----DNGK---LVWRDGPIESLDENILRPVARA 413 ++AGL+H+DV T+ G+GL ++ +EP L +NG+ + W D P +S DE +L VA+ Sbjct: 363 IDAGLMHDDVTTILGQGLRQHCKEPMLAAEGENGRPGIVTWHDAPAQSGDEGVLGTVAKP 422 Query: 414 FSPEGGLRVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAV 473 F+ +GGL++++GNLGR V+K+SAV +H++VEAPAVVF Q+ AFKAG+L++DFVAV Sbjct: 423 FAADGGLKLLQGNLGRAVIKISAVKPEHRVVEAPAVVFHSQEAFMAAFKAGQLDRDFVAV 482 Query: 474 MRFQGPRSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGG 533 + FQGPR+NGMPELH +TP LG+LQD+G VALVTDGRMSGASGK+PAAIHV+PE GG Sbjct: 483 ITFQGPRANGMPELHALTPALGILQDKGRHVALVTDGRMSGASGKVPAAIHVTPEVLGGG 542 Query: 534 ALARVRDGDIIRVDGVKGTLELKVDADEFAAR-EPAKGLLGNNVGSGRELFGFMRMAFSS 592 L RVRDGDIIR+D GTLE KVDA E+AAR + + L GN G GRELF R A + Sbjct: 543 PLGRVRDGDIIRLDAEAGTLEAKVDATEWAARSQDSSDLSGNQHGMGRELFSLFRNAVGT 602 Query: 593 AEQGASAF 600 AE+G + F Sbjct: 603 AEEGGATF 610 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: 1134 Number of extensions: 52 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: 608 Length of database: 623 Length adjustment: 37 Effective length of query: 571 Effective length of database: 586 Effective search space: 334606 Effective search space used: 334606 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 HSERO_RS05520 HSERO_RS05520 (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.1039.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-305 999.3 2.1 3.1e-305 999.1 2.1 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS05520 HSERO_RS05520 phosphogluconate d Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS05520 HSERO_RS05520 phosphogluconate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 999.1 2.1 3.1e-305 3.1e-305 2 600 .. 5 610 .. 4 611 .. 0.98 Alignments for each domain: == domain 1 score: 999.1 bits; conditional E-value: 3.1e-305 TIGR01196 2 srlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlai 69 + la++t+ri ers+++r +yle++++a++kg +r++l+c+nlahg+aa + ++k++lk++k + lai lcl|FitnessBrowser__HerbieS:HSERO_RS05520 5 ATLASVTQRIAERSRPYRTAYLERLEAARRKGAQRGALACTNLAHGFAAFPANDKLKLKEDKAPSLAI 72 56899*************************************************************** PP TIGR01196 70 itayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstai 137 ++ayndmlsahqpf+++p++ik+a++ea+avaq agG pamcdGvtqG++Gmelsl+srd ia++tai lcl|FitnessBrowser__HerbieS:HSERO_RS05520 73 VSAYNDMLSAHQPFERFPQIIKDAAREAGAVAQFAGGSPAMCDGVTQGQAGMELSLFSRDAIAMATAI 140 ******************************************************************** PP TIGR01196 138 glshnmfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdree 205 +lshnmfd+al+lGvcdkivpGlli+al fGhlpavfvpaGpm+sG++n++k+k+rql++ Gk++r e lcl|FitnessBrowser__HerbieS:HSERO_RS05520 141 ALSHNMFDAALYLGVCDKIVPGLLIGALHFGHLPAVFVPAGPMTSGMSNSDKVKIRQLYTAGKIGRAE 208 ******************************************************************** PP TIGR01196 206 llksemasyhapGtctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltaknge 273 ll++e++syh++GtctfyGtansnqml+e mGlhlpga+f+ pntplrdalt++aak++a++t + + lcl|FitnessBrowser__HerbieS:HSERO_RS05520 209 LLEAESKSYHGAGTCTFYGTANSNQMLMEAMGLHLPGAAFITPNTPLRDALTAAAAKQAAKITDLGTQ 276 ******************************************************************** PP TIGR01196 274 vlplaelideksivnalvgllatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGka 341 ++p++++ideksivna+v+l+atGGstnhtlhlvaia+aaGi+++wdd+++ls +vpl++++ypnG+a lcl|FitnessBrowser__HerbieS:HSERO_RS05520 277 YTPVGRMIDEKSIVNAIVALHATGGSTNHTLHLVAIAKAAGIVIDWDDFDKLSAVVPLITKIYPNGTA 344 ******************************************************************** PP TIGR01196 342 dvnhfeaaGGlsflirellkeGllhedvetvagkGlrrytkepfl....edgk...leyreaaeksld 402 dvnhf+aaGG +f++rel+++Gl+h+dv+t++g+Glr+++kep+l e+g+ +++++a+ +s d lcl|FitnessBrowser__HerbieS:HSERO_RS05520 345 DVNHFHAAGGTGFVLRELIDAGLMHDDVTTILGQGLRQHCKEPMLaaegENGRpgiVTWHDAPAQSGD 412 ********************************************94433233244499********** PP TIGR01196 403 edilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivfkdqaellaafkagelerdlv 470 e +l +v kpf+a+GGlkll+GnlGravik+savk+e+rv+eapa+vf++q+ ++aafkag+l+rd+v lcl|FitnessBrowser__HerbieS:HSERO_RS05520 413 EGVLGTVAKPFAADGGLKLLQGNLGRAVIKISAVKPEHRVVEAPAVVFHSQEAFMAAFKAGQLDRDFV 480 ******************************************************************** PP TIGR01196 471 avvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakir 538 av+ fqGp+anGmpelh lt++lG+lqd+g valvtdGr+sGasGkvpaaihvtpe l gG+l ++r lcl|FitnessBrowser__HerbieS:HSERO_RS05520 481 AVITFQGPRANGMPELHALTPALGILQDKGRHVALVTDGRMSGASGKVPAAIHVTPEVLGGGPLGRVR 548 ******************************************************************** PP TIGR01196 539 dGdlirldavngelevlvddaelkareleeldlednelGlGrelfaalrekvssaeeGassl 600 dGd+irlda +g le vd +e++ar+ ++ dl+ n+ G+Grelf+ +r++v++aeeG++++ lcl|FitnessBrowser__HerbieS:HSERO_RS05520 549 DGDIIRLDAEAGTLEAKVDATEWAARSQDSSDLSGNQHGMGRELFSLFRNAVGTAEEGGATF 610 ***********************************************************988 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (601 nodes) Target sequences: 1 (623 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: 12.50 // [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