Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate AO356_05220 AO356_05220 phosphogluconate dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_05220 Length = 608 Score = 1132 bits (2928), Expect = 0.0 Identities = 571/607 (94%), Positives = 590/607 (97%) Query: 1 MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60 MHPRVLEVTERL+ARSRATR+AYLALIR AASDGP RGKLQCANFAHGVAGCG+EDKH L Sbjct: 1 MHPRVLEVTERLIARSRATRQAYLALIRDAASDGPMRGKLQCANFAHGVAGCGTEDKHHL 60 Query: 61 RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120 RMMNAAN+AIVSSYNDMLSAHQPYE FPEQIKKALRE+GSVGQFAGGTPAMCDGVTQGEA Sbjct: 61 RMMNAANIAIVSSYNDMLSAHQPYETFPEQIKKALREIGSVGQFAGGTPAMCDGVTQGEA 120 Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180 GMELSLPSREVIALSTAVALSHNMFD ALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP Sbjct: 121 GMELSLPSREVIALSTAVALSHNMFDGALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180 Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240 M SGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH Sbjct: 181 MVSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240 Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300 LPGASFVNP TPLRDALT EAA QVTR+TKQSGNF PIGEIVDERSLVNSIVALHATGGS Sbjct: 241 LPGASFVNPNTPLRDALTREAAFQVTRMTKQSGNFMPIGEIVDERSLVNSIVALHATGGS 300 Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360 TNHTLHMPAIA AAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGM+FLIREL Sbjct: 301 TNHTLHMPAIAMAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMSFLIREL 360 Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420 LEAGLLHE+VNTV G GLSRYTQEPFL++G+LVWRDGPIESLDENILRPVARAFSPEGGL Sbjct: 361 LEAGLLHENVNTVLGHGLSRYTQEPFLEDGELVWRDGPIESLDENILRPVARAFSPEGGL 420 Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480 RVMEGNLGRGVMKVSAVAL++QIVEAPA+VFQDQQDLADAFKAG LEKDFVAVMRFQGPR Sbjct: 421 RVMEGNLGRGVMKVSAVALENQIVEAPAMVFQDQQDLADAFKAGLLEKDFVAVMRFQGPR 480 Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEA VGGALARV++ Sbjct: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAYVGGALARVQE 540 Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPAKGLLGNNVGSGRELFGFMRMAFSSAEQGASAF 600 GDIIRVDGVKGTLELKVDA+EFAAR PAKGLLGNN+G+GRELFGFMRMAFSSAEQGASAF Sbjct: 541 GDIIRVDGVKGTLELKVDAEEFAARTPAKGLLGNNIGTGRELFGFMRMAFSSAEQGASAF 600 Query: 601 TSALENL 607 TSALE L Sbjct: 601 TSALETL 607 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: 1375 Number of extensions: 48 Number of successful extensions: 1 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: 608 Length adjustment: 37 Effective length of query: 571 Effective length of database: 571 Effective search space: 326041 Effective search space used: 326041 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 AO356_05220 AO356_05220 (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.7210.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 1029.9 0.6 0 1029.7 0.6 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220 AO356_05220 phosphogluconate deh Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220 AO356_05220 phosphogluconate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1029.7 0.6 0 0 1 601 [] 2 601 .. 2 601 .. 0.99 Alignments for each domain: == domain 1 score: 1029.7 bits; conditional E-value: 0 TIGR01196 1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksek 63 h+r++e+ter+i+rs++tr++yl+ ir+a++ g++r++l c+n+ahgva + ++k +l+ ++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220 2 HPRVLEVTERLIARSRATRQAYLALIRDAASDGPMRGKLQCANFAHGVAGCGTEDKHHLRMMN 64 79************************************************************* PP TIGR01196 64 rknlaiitayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsll 126 +n+ai+++yndmlsahqp++++p++ikkal+e ++v+q agG+pamcdGvtqGe+Gmelsl lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220 65 AANIAIVSSYNDMLSAHQPYETFPEQIKKALREIGSVGQFAGGTPAMCDGVTQGEAGMELSLP 127 *************************************************************** PP TIGR01196 127 srdvialstaiglshnmfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkek 189 sr+vialsta++lshnmfdgal+lG+cdkivpGl+++al fGhlp++fvp+Gpm+sG++nkek lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220 128 SREVIALSTAVALSHNMFDGALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMVSGISNKEK 190 *************************************************************** PP TIGR01196 190 akvrqlfaeGkvdreellksemasyhapGtctfyGtansnqmlvelmGlhlpgasfvnpntpl 252 a vrq +aeGk++reell+sem+syh+pGtctfyGtan+nq+l+e+mGlhlpgasfvnpntpl lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220 191 ADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHLPGASFVNPNTPL 253 *************************************************************** PP TIGR01196 253 rdaltreaakrlarltakngevlplaelideksivnalvgllatGGstnhtlhlvaiaraaGi 315 rdaltreaa +++r+t ++g+++p++e++de+s+vn++v+l+atGGstnhtlh+ aia aaGi lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220 254 RDALTREAAFQVTRMTKQSGNFMPIGEIVDERSLVNSIVALHATGGSTNHTLHMPAIAMAAGI 316 *************************************************************** PP TIGR01196 316 ilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagkGlr 378 +l+w+d+ +ls++vp+l +vypnGkad+nhf+aaGG+sflirell++Gllhe+v+tv+g+Gl+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220 317 QLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMSFLIRELLEAGLLHENVNTVLGHGLS 379 *************************************************************** PP TIGR01196 379 rytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesr 441 ryt+epfledg+l++r+++ +slde+ilr+v + fs+eGGl++++GnlGr+v+kvsav+ e++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220 380 RYTQEPFLEDGELVWRDGPIESLDENILRPVARAFSPEGGLRVMEGNLGRGVMKVSAVALENQ 442 *************************************************************** PP TIGR01196 442 vieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkva 504 ++eapa+vf+dq++l++afkag le+d+vav+rfqGp++nGmpelhk+t++lGvlqdrgfkva lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220 443 IVEAPAMVFQDQQDLADAFKAGLLEKDFVAVMRFQGPRSNGMPELHKMTPFLGVLQDRGFKVA 505 *************************************************************** PP TIGR01196 505 lvtdGrlsGasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkarele 567 lvtdGr+sGasGk+paaihv+pea+ gGala++++Gd+ir+d+v+g le+ vd e++ar+++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220 506 LVTDGRMSGASGKIPAAIHVSPEAYVGGALARVQEGDIIRVDGVKGTLELKVDAEEFAARTPA 568 *************************************************************77 PP TIGR01196 568 eldlednelGlGrelfaalrekvssaeeGasslt 601 + l n++G+Grelf ++r + ssae+Gas++t lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220 569 K-GLLGNNIGTGRELFGFMRMAFSSAEQGASAFT 601 6.566789**********************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (601 nodes) Target sequences: 1 (608 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 7.53 // [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