Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate GFF2757 PGA1_c28000 phosphogluconate dehydratase Edd
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__Phaeo:GFF2757 Length = 607 Score = 699 bits (1805), Expect = 0.0 Identities = 349/606 (57%), Positives = 453/606 (74%), Gaps = 5/606 (0%) Query: 1 MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60 ++ V +VT+R++ARS R AYL +R A GP R L C+ AH A G ED+ L Sbjct: 3 LNQTVRDVTDRIIARSAKPRAAYLDRMRAAKGKGPARAHLSCSGQAHAYAATG-EDQMPL 61 Query: 61 RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120 A ++ IV++YNDMLSAHQP+E +P++I+ A+R +G Q AGG PAMCDGVTQGEA Sbjct: 62 AEGTAGHLGIVTAYNDMLSAHQPFETYPQRIRDAVRRVGGTAQVAGGVPAMCDGVTQGEA 121 Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180 GMELSL SR+ IA++T +ALSHN+FDA + LG+CDKIVPGL++GA FGHLP +F+P GP Sbjct: 122 GMELSLFSRDTIAMATGIALSHNVFDATVYLGVCDKIVPGLVIGAQVFGHLPAVFLPAGP 181 Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240 M SGISN +KA VRQ++A G+ R+ELL+SEM +YH PGTCTFYGTANTNQ+LME MGLH Sbjct: 182 MTSGISNDDKAKVRQKFAAGEIGRDELLKSEMAAYHGPGTCTFYGTANTNQMLMEFMGLH 241 Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300 LPG+SFVNP T +R ALT E A++ L+ ++TP+ +I+DER+ VN IV L TGGS Sbjct: 242 LPGSSFVNPGTDMRAALTEEGARRALALSALGNDYTPVCDILDERAYVNGIVGLMTTGGS 301 Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360 TN +H+ A+A+A GI L WQD ++LS+VVP L+ VYPNG AD+NHF AAGG+ ++I +L Sbjct: 302 TNLLIHLIAMARAGGIILDWQDFSELSDVVPLLARVYPNGLADVNHFHAAGGLGYVIGQL 361 Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420 L +G LH D TVAG GL YT EPFL + LVW+ G ESL++ I+RP + F P GGL Sbjct: 362 LNSGHLHSDTRTVAGSGLESYTAEPFLSDDGLVWKPGAAESLNDKIIRPASAPFQPTGGL 421 Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEK-DFVAVMRFQGP 479 + GNLG GVMK+SAVA +H++VEAPA VF DQ+++ AFKAGEL+K D + V+RFQGP Sbjct: 422 ARLSGNLGTGVMKISAVAPEHRMVEAPARVFHDQEEVKAAFKAGELDKGDMIIVVRFQGP 481 Query: 480 RSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVR 539 ++NGMPELH MTPFLG++Q RG KVALVTDGRMSGASGKIP+AIHV PEA GG ++++R Sbjct: 482 KANGMPELHSMTPFLGIMQGRGQKVALVTDGRMSGASGKIPSAIHVVPEALDGGPISKLR 541 Query: 540 DGDIIRVDGVKGTLELKVDADEFAAREP-AKGLLGNNVGSGRELFGFMRMAFSSAEQGAS 598 DGD++RVD + GTLE+K A+ F R+P L G+GRE+F R A +SA+ GA+ Sbjct: 542 DGDMVRVDALTGTLEVK--AEGFDDRDPVVADLSAYQHGTGREMFALFRNAVTSADTGAT 599 Query: 599 AFTSAL 604 F++ + Sbjct: 600 VFSTLI 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: 1079 Number of extensions: 43 Number of successful extensions: 5 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: 607 Length adjustment: 37 Effective length of query: 571 Effective length of database: 570 Effective search space: 325470 Effective search space used: 325470 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 GFF2757 PGA1_c28000 (phosphogluconate dehydratase Edd)
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.21832.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-288 943.1 0.5 3.1e-288 942.9 0.5 1.0 1 lcl|FitnessBrowser__Phaeo:GFF2757 PGA1_c28000 phosphogluconate deh Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF2757 PGA1_c28000 phosphogluconate dehydratase Edd # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 942.9 0.5 3.1e-288 3.1e-288 3 600 .. 6 601 .. 4 602 .. 0.99 Alignments for each domain: == domain 1 score: 942.9 bits; conditional E-value: 3.1e-288 TIGR01196 3 rlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitayndmls 78 + ++t+rii+rs+k r +yl+++r+ak kg+ r++l+c+ ah++aa e ++++l++ + +l+i+tayndmls lcl|FitnessBrowser__Phaeo:GFF2757 6 TVRDVTDRIIARSAKPRAAYLDRMRAAKGKGPARAHLSCSGQAHAYAATGE-DQMPLAEGTAGHLGIVTAYNDMLS 80 5789*******************************************9886.689********************* PP TIGR01196 79 ahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdgalflGvcd 154 ahqpf++yp+ i++a+++ +++aqvagGvpamcdGvtqGe+Gmelsl+srd ia++t+i+lshn+fd++++lGvcd lcl|FitnessBrowser__Phaeo:GFF2757 81 AHQPFETYPQRIRDAVRRVGGTAQVAGGVPAMCDGVTQGEAGMELSLFSRDTIAMATGIALSHNVFDATVYLGVCD 156 **************************************************************************** PP TIGR01196 155 kivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtctfyGtansnq 230 kivpGl+i+a fGhlpavf+paGpm+sG++n++kakvrq fa G ++r+ellksema+yh+pGtctfyGtan+nq lcl|FitnessBrowser__Phaeo:GFF2757 157 KIVPGLVIGAQVFGHLPAVFLPAGPMTSGISNDDKAKVRQKFAAGEIGRDELLKSEMAAYHGPGTCTFYGTANTNQ 232 **************************************************************************** PP TIGR01196 231 mlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgllatGGstnhtlhl 306 ml+e+mGlhlpg+sfvnp t++r alt+e a+r+ +l a +++++p+++++de++ vn++vgl++tGGstn +hl lcl|FitnessBrowser__Phaeo:GFF2757 233 MLMEFMGLHLPGSSFVNPGTDMRAALTEEGARRALALSALGNDYTPVCDILDERAYVNGIVGLMTTGGSTNLLIHL 308 **************************************************************************** PP TIGR01196 307 vaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagkGlrrytk 382 +a+ara Giil+w+d+selsd+vpllarvypnG advnhf+aaGGl+++i +ll++G lh d++tvag+Gl+ yt lcl|FitnessBrowser__Phaeo:GFF2757 309 IAMARAGGIILDWQDFSELSDVVPLLARVYPNGLADVNHFHAAGGLGYVIGQLLNSGHLHSDTRTVAGSGLESYTA 384 **************************************************************************** PP TIGR01196 383 epfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivfkdqaella 458 epfl+d+ l+++++a +sl+++i+r+++ pf+++GGl l+GnlG +v+k+sav++e+r++eapa+vf+dq+e++a lcl|FitnessBrowser__Phaeo:GFF2757 385 EPFLSDDGLVWKPGAAESLNDKIIRPASAPFQPTGGLARLSGNLGTGVMKISAVAPEHRMVEAPARVFHDQEEVKA 460 **************************************************************************** PP TIGR01196 459 afkageler.dlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGa 533 afkagel++ d+++vvrfqGpkanGmpelh +t++lG++q rg+kvalvtdGr+sGasGk+p+aihv peal+gG+ lcl|FitnessBrowser__Phaeo:GFF2757 461 AFKAGELDKgDMIIVVRFQGPKANGMPELHSMTPFLGIMQGRGQKVALVTDGRMSGASGKIPSAIHVVPEALDGGP 536 *******955****************************************************************** PP TIGR01196 534 lakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaalrekvssaeeGassl 600 + k+rdGd++r+da +g lev + + + r + dl++ + G+Gre+fa +r++v+sa++Ga+++ lcl|FitnessBrowser__Phaeo:GFF2757 537 ISKLRDGDMVRVDALTGTLEVKAEGF--DDRDPVVADLSAYQHGTGREMFALFRNAVTSADTGATVF 601 ********************987765..6888999*****************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (601 nodes) Target sequences: 1 (607 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 7.33 // [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