Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate BPHYT_RS16735 BPHYT_RS16735 phosphogluconate dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__BFirm:BPHYT_RS16735 Length = 634 Score = 764 bits (1973), Expect = 0.0 Identities = 379/601 (63%), 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 HSQLLKVTQRVVERSKPTREAYLARIHQAQGKFPARGALSCANLAHGFAGLEGNDKLVIK 64 Query: 62 MMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAG 121 + N+ IVSSYN+MLSAH PY+++P+ IK+A RE G V QFAGG PAMCDGVTQG AG Sbjct: 65 QIREPNIGIVSSYNEMLSAHAPYKNYPDIIKQAARENGGVAQFAGGVPAMCDGVTQGNAG 124 Query: 122 MELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPM 181 MELSL SREVIA+STAVAL+HNMFDAAL LGICDKIVPGL++GAL+FGH+PTIFVP GPM Sbjct: 125 MELSLFSREVIAMSTAVALTHNMFDAALCLGICDKIVPGLLIGALQFGHIPTIFVPAGPM 184 Query: 182 PSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHL 241 SG+SN +KA RQ +A G+ R LLE+E +YHS GTCTFYGTAN+NQ+LMEVMGLHL Sbjct: 185 GSGLSNDDKAKTRQLFATGQCDRGALLEAEAAAYHSHGTCTFYGTANSNQMLMEVMGLHL 244 Query: 242 PGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGST 301 P ++FV+P+TPLRDALT +AA++V LT + GN+TPIG +VDE+++VN IVAL ATGGST Sbjct: 245 PSSAFVHPHTPLRDALTAQAARRVLELTVERGNYTPIGHVVDEKAIVNGIVALLATGGST 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 P+GGLR Sbjct: 365 EGGLLHEDVNTVAGKGLKHYTEEPKLIDGKLQWVPGAQASEDTAVLRGIKEPFQPDGGLR 424 Query: 422 VMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRS 481 +M+G LGRGV+K+SAVA QH+ V+APA+VF Q+ + +AF GEL++DF+AV+RFQG R+ Sbjct: 425 LMQGKLGRGVIKISAVAAQHRKVKAPAIVFDSQEAVQEAFDKGELKRDFIAVVRFQGARA 484 Query: 482 NGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDG 541 NGMPELH++TP LGVLQD+GF VALVTDGRMSGASGK+PA IH+SPEA + G + +VR G Sbjct: 485 NGMPELHRLTPLLGVLQDQGFHVALVTDGRMSGASGKVPAVIHLSPEALLQGPIGKVRTG 544 Query: 542 DIIRVDGVKGTLELKVDADEFAAREPA--KGLLGNNVGSGRELFGFMRMAFSSAEQGASA 599 D++ +D G L++++DA E+AAR A + N VG GRELF R A + AEQGAS Sbjct: 545 DMLVIDAEAGVLDIEIDAAEWAARPNAVPQHQAENEVGFGRELFSVFRAAAAPAEQGASV 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: 1168 Number of extensions: 43 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: 634 Length adjustment: 37 Effective length of query: 571 Effective length of database: 597 Effective search space: 340887 Effective search space used: 340887 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 BPHYT_RS16735 BPHYT_RS16735 (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.27502.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-300 982.6 1.1 3.4e-300 982.5 1.1 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS16735 BPHYT_RS16735 phosphogluconate d Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS16735 BPHYT_RS16735 phosphogluconate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 982.5 1.1 3.4e-300 3.4e-300 1 600 [. 5 605 .. 5 606 .. 0.99 Alignments for each domain: == domain 1 score: 982.5 bits; conditional E-value: 3.4e-300 TIGR01196 1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaii 70 hs+l+++t+r++ersk+tre+yl++i++a+ k + r++l+c+nlahg+a l+ ++k+ +k+ +++n++i+ lcl|FitnessBrowser__BFirm:BPHYT_RS16735 5 HSQLLKVTQRVVERSKPTREAYLARIHQAQGKFPARGALSCANLAHGFAGLEGNDKLVIKQIREPNIGIV 74 89******************************************************************** PP TIGR01196 71 tayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaigls 140 ++yn+mlsah p+k+ypd+ik+a++e+++vaq agGvpamcdGvtqG++Gmelsl+sr+via+sta++l+ lcl|FitnessBrowser__BFirm:BPHYT_RS16735 75 SSYNEMLSAHAPYKNYPDIIKQAARENGGVAQFAGGVPAMCDGVTQGNAGMELSLFSREVIAMSTAVALT 144 ********************************************************************** PP TIGR01196 141 hnmfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellkse 210 hnmfd+al+lG+cdkivpGlli+al fGh+p++fvpaGpm sGl+n++kak+rqlfa G+ dr +ll++e lcl|FitnessBrowser__BFirm:BPHYT_RS16735 145 HNMFDAALCLGICDKIVPGLLIGALQFGHIPTIFVPAGPMGSGLSNDDKAKTRQLFATGQCDRGALLEAE 214 ********************************************************************** PP TIGR01196 211 masyhapGtctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplael 280 +a+yh+ GtctfyGtansnqml+e+mGlhlp+++fv+p+tplrdalt++aa+r+ +lt + g+++p++++ lcl|FitnessBrowser__BFirm:BPHYT_RS16735 215 AAAYHSHGTCTFYGTANSNQMLMEVMGLHLPSSAFVHPHTPLRDALTAQAARRVLELTVERGNYTPIGHV 284 ********************************************************************** PP TIGR01196 281 ideksivnalvgllatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaG 350 +dek+ivn++v+llatGGstnhtlhlvaiaraaGi+++wdd++ ls+ vplla++ypnGkadvnhf+aaG lcl|FitnessBrowser__BFirm:BPHYT_RS16735 285 VDEKAIVNGIVALLATGGSTNHTLHLVAIARAAGIVIDWDDFDTLSQAVPLLAKIYPNGKADVNHFHAAG 354 ********************************************************************** PP TIGR01196 351 GlsflirellkeGllhedvetvagkGlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlk 420 G++fl+r+ll+ Gllhedv+tvagkGl++yt+ep+l dgkl++ ++a++s d+++lr +++pf+++GGl+ lcl|FitnessBrowser__BFirm:BPHYT_RS16735 355 GVAFLVRNLLEGGLLHEDVNTVAGKGLKHYTEEPKLIDGKLQWVPGAQASEDTAVLRGIKEPFQPDGGLR 424 ********************************************************************** PP TIGR01196 421 llkGnlGravikvsavkeesrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklt 490 l++G lGr+vik+sav+ ++r+++apaivf++q+ +++af++gel+rd++avvrfqG +anGmpelh+lt lcl|FitnessBrowser__BFirm:BPHYT_RS16735 425 LMQGKLGRGVIKISAVAAQHRKVKAPAIVFDSQEAVQEAFDKGELKRDFIAVVRFQGARANGMPELHRLT 494 ********************************************************************** PP TIGR01196 491 tvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddae 560 + lGvlqd+gf valvtdGr+sGasGkvpa ih++peal +G++ k+r+Gd++ +da +g l++ +d ae lcl|FitnessBrowser__BFirm:BPHYT_RS16735 495 PLLGVLQDQGFHVALVTDGRMSGASGKVPAVIHLSPEALLQGPIGKVRTGDMLVIDAEAGVLDIEIDAAE 564 ********************************************************************** PP TIGR01196 561 lkareleeld.lednelGlGrelfaalrekvssaeeGassl 600 ++ar + ++ +ne+G Grelf+ +r +++ ae+Gas++ lcl|FitnessBrowser__BFirm:BPHYT_RS16735 565 WAARPNAVPQhQAENEVGFGRELFSVFRAAAAPAEQGASVF 605 *****99998466799**********************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (601 nodes) Target sequences: 1 (634 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: 11.61 // [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