Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate GFF1853 Psest_1892 6-phosphogluconate dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__psRCH2:GFF1853 Length = 609 Score = 977 bits (2526), Expect = 0.0 Identities = 482/609 (79%), Positives = 545/609 (89%), Gaps = 1/609 (0%) Query: 1 MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGS-EDKHS 59 MHPRVLEVTERLV RSR TRE YLA++ AAS+GPQRG LQCANFAHGVAGC S +DK S Sbjct: 1 MHPRVLEVTERLVERSRKTRERYLAMMAAAASEGPQRGGLQCANFAHGVAGCNSPQDKQS 60 Query: 60 LRMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGE 119 LR+MNA NVAIVS+YNDMLSAHQPYEHFPE I++ALRE+GSVGQFAGG PAMCDGVTQGE Sbjct: 61 LRLMNAVNVAIVSAYNDMLSAHQPYEHFPEMIRQALREIGSVGQFAGGVPAMCDGVTQGE 120 Query: 120 AGMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGG 179 AGME+SL SREVIA+STAVALSHNMFDAALMLGICDKIVPGLM+GALRFGHLPTIFVPGG Sbjct: 121 AGMEMSLASREVIAMSTAVALSHNMFDAALMLGICDKIVPGLMIGALRFGHLPTIFVPGG 180 Query: 180 PMPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGL 239 PMPSGI NK KA+VRQRYAEGKA+REELLESEMKSYHSPGTCTFYGTANTNQ++ME+MGL Sbjct: 181 PMPSGIPNKAKAEVRQRYAEGKASREELLESEMKSYHSPGTCTFYGTANTNQVVMEIMGL 240 Query: 240 HLPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGG 299 HLPG+SFVNPYTPLRDALT EAAQQVTRLT Q+GN+TP+ ++VDE+S+VNS+VAL+ATGG Sbjct: 241 HLPGSSFVNPYTPLRDALTREAAQQVTRLTHQAGNYTPLCQVVDEKSIVNSVVALNATGG 300 Query: 300 STNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRE 359 STNHTLH+PA A+AAGIQLTW+DMADLSEVVPTL+ VYPNG+AD+NHF A GG+ F++R Sbjct: 301 STNHTLHIPAFARAAGIQLTWKDMADLSEVVPTLAKVYPNGQADVNHFHACGGVPFMVRT 360 Query: 360 LLEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGG 419 LL+AGLLHEDV+TV G+GL RY QEPFLD +LVWRDGP +SLDE+ILRP R FSPEGG Sbjct: 361 LLDAGLLHEDVHTVVGKGLRRYIQEPFLDGDRLVWRDGPTQSLDESILRPAERPFSPEGG 420 Query: 420 LRVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGP 479 LRV+EGNLGRGV K+SAVA +H++VEAPA VF DQ +LA AFKAGELE+DF+AV+RFQGP Sbjct: 421 LRVLEGNLGRGVTKISAVAPEHRVVEAPARVFIDQSELAAAFKAGELERDFIAVVRFQGP 480 Query: 480 RSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVR 539 ++NGMPELHK+TPFLGVLQDRG+KVALVTDGRMSGASGK+PAAIHV PEA GG LARVR Sbjct: 481 KANGMPELHKLTPFLGVLQDRGYKVALVTDGRMSGASGKVPAAIHVCPEALDGGPLARVR 540 Query: 540 DGDIIRVDGVKGTLELKVDADEFAAREPAKGLLGNNVGSGRELFGFMRMAFSSAEQGASA 599 DGDI+RVDG G L VD E+ AREPA +G GRELF FMR +FS+AEQGASA Sbjct: 541 DGDILRVDGESGELLALVDPVEWGAREPAIRPEDVGIGCGRELFAFMRASFSTAEQGASA 600 Query: 600 FTSALENLK 608 FT +LE L+ Sbjct: 601 FTESLEALR 609 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: 1230 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: 609 Length adjustment: 37 Effective length of query: 571 Effective length of database: 572 Effective search space: 326612 Effective search space used: 326612 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 GFF1853 Psest_1892 (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.28674.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1036.7 0.0 0 1036.6 0.0 1.0 1 lcl|FitnessBrowser__psRCH2:GFF1853 Psest_1892 6-phosphogluconate de Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF1853 Psest_1892 6-phosphogluconate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1036.6 0.0 0 0 1 601 [] 2 602 .. 2 602 .. 0.99 Alignments for each domain: == domain 1 score: 1036.6 bits; conditional E-value: 0 TIGR01196 1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaals.esekvelksekrknlaiitayn 74 h+r++e+ter++ers+ktre+yl+++ +a+++g++r+ l c+n+ahgva ++ +++k++l+ ++ n+ai++ayn lcl|FitnessBrowser__psRCH2:GFF1853 2 HPRVLEVTERLVERSRKTRERYLAMMAAAASEGPQRGGLQCANFAHGVAGCNsPQDKQSLRLMNAVNVAIVSAYN 76 79***********************************************9963799******************* PP TIGR01196 75 dmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdgalf 149 dmlsahqp++++p++i++al+e ++v+q agGvpamcdGvtqGe+Gme+sl+sr+via+sta++lshnmfd+al+ lcl|FitnessBrowser__psRCH2:GFF1853 77 DMLSAHQPYEHFPEMIRQALREIGSVGQFAGGVPAMCDGVTQGEAGMEMSLASREVIAMSTAVALSHNMFDAALM 151 *************************************************************************** PP TIGR01196 150 lGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtctfyG 224 lG+cdkivpGl+i+al fGhlp++fvp+Gpm+sG++nk ka+vrq +aeGk++reell+sem+syh+pGtctfyG lcl|FitnessBrowser__psRCH2:GFF1853 152 LGICDKIVPGLMIGALRFGHLPTIFVPGGPMPSGIPNKAKAEVRQRYAEGKASREELLESEMKSYHSPGTCTFYG 226 *************************************************************************** PP TIGR01196 225 tansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgllatGGs 299 tan+nq+++e+mGlhlpg+sfvnp+tplrdaltreaa++++rlt ++g+++pl++++deksivn++v+l atGGs lcl|FitnessBrowser__psRCH2:GFF1853 227 TANTNQVVMEIMGLHLPGSSFVNPYTPLRDALTREAAQQVTRLTHQAGNYTPLCQVVDEKSIVNSVVALNATGGS 301 *************************************************************************** PP TIGR01196 300 tnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvag 374 tnhtlh+ a+araaGi+l+w+d+ +ls++vp+la+vypnG+advnhf+a+GG++f++r ll++Gllhedv+tv+g lcl|FitnessBrowser__psRCH2:GFF1853 302 TNHTLHIPAFARAAGIQLTWKDMADLSEVVPTLAKVYPNGQADVNHFHACGGVPFMVRTLLDAGLLHEDVHTVVG 376 *************************************************************************** PP TIGR01196 375 kGlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaiv 449 kGlrry +epfl+ ++l++r+++ +slde+ilr++++pfs+eGGl++l+GnlGr+v k+sav++e+rv+eapa+v lcl|FitnessBrowser__psRCH2:GFF1853 377 KGLRRYIQEPFLDGDRLVWRDGPTQSLDESILRPAERPFSPEGGLRVLEGNLGRGVTKISAVAPEHRVVEAPARV 451 *************************************************************************** PP TIGR01196 450 fkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihv 524 f dq+el+aafkagelerd++avvrfqGpkanGmpelhklt++lGvlqdrg+kvalvtdGr+sGasGkvpaaihv lcl|FitnessBrowser__psRCH2:GFF1853 452 FIDQSELAAAFKAGELERDFIAVVRFQGPKANGMPELHKLTPFLGVLQDRGYKVALVTDGRMSGASGKVPAAIHV 526 *************************************************************************** PP TIGR01196 525 tpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaalrekvssaeeGass 599 +peal+gG+la++rdGd++r+d+ +gel lvd +e+ are+ + +ed +G+Grelfa++r s+ae+Gas+ lcl|FitnessBrowser__psRCH2:GFF1853 527 CPEALDGGPLARVRDGDILRVDGESGELLALVDPVEWGAREP-AIRPEDVGIGCGRELFAFMRASFSTAEQGASA 600 *****************************************5.6899**************************99 PP TIGR01196 600 lt 601 +t lcl|FitnessBrowser__psRCH2:GFF1853 601 FT 602 86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (601 nodes) Target sequences: 1 (609 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: 11.95 // [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