Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate H281DRAFT_04278 H281DRAFT_04278 6-phosphogluconate dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__Burk376:H281DRAFT_04278 Length = 641 Score = 759 bits (1960), Expect = 0.0 Identities = 376/601 (62%), Positives = 470/601 (78%), Gaps = 2/601 (0%) Query: 2 HPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSLR 61 H ++L+VT+R+V RS+ TREAYLA I A P RG L CAN AHG AG DK ++ Sbjct: 5 HSQLLKVTQRVVERSKPTREAYLARIHEAQGRFPARGALSCANLAHGFAGLEGNDKLVIK 64 Query: 62 MMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAG 121 + NV IVSSYN+MLSAH PY+++P+ IK+A RE G V QFAGG PAMCDG+TQG AG Sbjct: 65 QIREPNVGIVSSYNEMLSAHAPYKNYPDIIKQAARENGGVAQFAGGVPAMCDGITQGNAG 124 Query: 122 MELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPM 181 MELSL SREVIA+STAVAL+HNMFDAAL LGICDKIVPGL++GAL+FGHLPTIFVP GPM Sbjct: 125 MELSLFSREVIAMSTAVALTHNMFDAALCLGICDKIVPGLLIGALQFGHLPTIFVPAGPM 184 Query: 182 PSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHL 241 SG+SN +KA RQ++A G+ R+ LLE+E +YH GTCTFYGTAN+NQ+LME+MGLHL Sbjct: 185 TSGLSNDDKAKTRQQFATGQCGRDALLEAEAAAYHGHGTCTFYGTANSNQMLMEIMGLHL 244 Query: 242 PGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGST 301 PG++FV+P+TPLRDALT +AA++V LT + G++ PIG ++DE+++VN IVAL ATGGST Sbjct: 245 PGSAFVHPHTPLRDALTAQAARRVLDLTVERGHYMPIGHVIDEKAIVNGIVALLATGGST 304 Query: 302 NHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRELL 361 NHTLH+ AIA+AAGI + W D LS+ VP L+ +YPNGKAD+NHF AAGG+AFL+R LL Sbjct: 305 NHTLHLVAIARAAGIVIDWDDFDTLSQAVPLLAKIYPNGKADVNHFHAAGGVAFLVRNLL 364 Query: 362 EAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGLR 421 E GLLHEDVNTVAG+GL YT+EP L +GKL W G S D +LR + F +GGLR Sbjct: 365 EGGLLHEDVNTVAGKGLHHYTEEPKLLDGKLQWVPGVQASEDTAVLRGIKEPFQADGGLR 424 Query: 422 VMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRS 481 +M+G LGRGV+K+SAVA QH+ V+APA+VF Q+ + +AF GEL++DF+AV+RFQG R+ Sbjct: 425 LMQGKLGRGVIKISAVAQQHRKVKAPAIVFDSQEAVQEAFDNGELKRDFIAVVRFQGARA 484 Query: 482 NGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDG 541 NGMPELH++TP LGVLQD+GF VALVTDGRMSGASGK+PA IH+SPEA + G + +VR G Sbjct: 485 NGMPELHRLTPLLGVLQDQGFHVALVTDGRMSGASGKVPAVIHLSPEALLQGPIGKVRSG 544 Query: 542 DIIRVDGVKGTLELKVDADEFAAREPAKGL--LGNNVGSGRELFGFMRMAFSSAEQGASA 599 D++ +D G L++++D E+AAR A L N VG GRELFG R A + AEQGAS Sbjct: 545 DMLVIDAEAGVLDIEIDPAEWAARPNAVPLHQAENEVGFGRELFGVFRAAAAPAEQGASV 604 Query: 600 F 600 F Sbjct: 605 F 605 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: 1192 Number of extensions: 49 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: 641 Length adjustment: 37 Effective length of query: 571 Effective length of database: 604 Effective search space: 344884 Effective search space used: 344884 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: 54 (25.4 bits)
Align candidate H281DRAFT_04278 H281DRAFT_04278 (6-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.25666.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-299 980.2 0.8 1.9e-299 980.0 0.8 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_04278 H281DRAFT_04278 6-phosphoglucona Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_04278 H281DRAFT_04278 6-phosphogluconate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 980.0 0.8 1.9e-299 1.9e-299 1 600 [. 5 605 .. 5 606 .. 0.99 Alignments for each domain: == domain 1 score: 980.0 bits; conditional E-value: 1.9e-299 TIGR01196 1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrkn 66 hs+l+++t+r++ersk+tre+yl++i++a+ + + r++l+c+nlahg+a l+ ++k+ +k+ +++n lcl|FitnessBrowser__Burk376:H281DRAFT_04278 5 HSQLLKVTQRVVERSKPTREAYLARIHEAQGRFPARGALSCANLAHGFAGLEGNDKLVIKQIREPN 70 89**************************************************************** PP TIGR01196 67 laiitayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvia 132 ++i+++yn+mlsah p+k+ypd+ik+a++e+++vaq agGvpamcdG+tqG++Gmelsl+sr+via lcl|FitnessBrowser__Burk376:H281DRAFT_04278 71 VGIVSSYNEMLSAHAPYKNYPDIIKQAARENGGVAQFAGGVPAMCDGITQGNAGMELSLFSREVIA 136 ****************************************************************** PP TIGR01196 133 lstaiglshnmfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfae 198 +sta++l+hnmfd+al+lG+cdkivpGlli+al fGhlp++fvpaGpm+sGl+n++kak+rq+fa lcl|FitnessBrowser__Burk376:H281DRAFT_04278 137 MSTAVALTHNMFDAALCLGICDKIVPGLLIGALQFGHLPTIFVPAGPMTSGLSNDDKAKTRQQFAT 202 ****************************************************************** PP TIGR01196 199 GkvdreellksemasyhapGtctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrl 264 G+ +r++ll++e+a+yh+ GtctfyGtansnqml+e+mGlhlpg++fv+p+tplrdalt++aa+r+ lcl|FitnessBrowser__Burk376:H281DRAFT_04278 203 GQCGRDALLEAEAAAYHGHGTCTFYGTANSNQMLMEIMGLHLPGSAFVHPHTPLRDALTAQAARRV 268 ****************************************************************** PP TIGR01196 265 arltakngevlplaelideksivnalvgllatGGstnhtlhlvaiaraaGiilnwddlselsdlvp 330 lt + g+++p++++idek+ivn++v+llatGGstnhtlhlvaiaraaGi+++wdd++ ls+ vp lcl|FitnessBrowser__Burk376:H281DRAFT_04278 269 LDLTVERGHYMPIGHVIDEKAIVNGIVALLATGGSTNHTLHLVAIARAAGIVIDWDDFDTLSQAVP 334 ****************************************************************** PP TIGR01196 331 llarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagkGlrrytkepfledgkleyrea 396 lla++ypnGkadvnhf+aaGG++fl+r+ll+ Gllhedv+tvagkGl++yt+ep+l dgkl++ ++ lcl|FitnessBrowser__Burk376:H281DRAFT_04278 335 LLAKIYPNGKADVNHFHAAGGVAFLVRNLLEGGLLHEDVNTVAGKGLHHYTEEPKLLDGKLQWVPG 400 ****************************************************************** PP TIGR01196 397 aeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivfkdqaellaafka 462 +++s d+++lr +++pf+a+GGl+l++G lGr+vik+sav++++r+++apaivf++q+ +++af++ lcl|FitnessBrowser__Burk376:H281DRAFT_04278 401 VQASEDTAVLRGIKEPFQADGGLRLMQGKLGRGVIKISAVAQQHRKVKAPAIVFDSQEAVQEAFDN 466 ****************************************************************** PP TIGR01196 463 gelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpea 528 gel+rd++avvrfqG +anGmpelh+lt+ lGvlqd+gf valvtdGr+sGasGkvpa ih++pea lcl|FitnessBrowser__Burk376:H281DRAFT_04278 467 GELKRDFIAVVRFQGARANGMPELHRLTPLLGVLQDQGFHVALVTDGRMSGASGKVPAVIHLSPEA 532 ****************************************************************** PP TIGR01196 529 legGalakirdGdlirldavngelevlvddaelkareleeld.lednelGlGrelfaalrekvssa 593 l +G++ k+r Gd++ +da +g l++ +d ae++ar + + +ne+G Grelf +r +++ a lcl|FitnessBrowser__Burk376:H281DRAFT_04278 533 LLQGPIGKVRSGDMLVIDAEAGVLDIEIDPAEWAARPNAVPLhQAENEVGFGRELFGVFRAAAAPA 598 ************************************877654277899****************** PP TIGR01196 594 eeGassl 600 e+Gas++ lcl|FitnessBrowser__Burk376:H281DRAFT_04278 599 EQGASVF 605 ****998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (601 nodes) Target sequences: 1 (641 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: 00:00:00.03 # Mc/sec: 10.69 // [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