Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate CCNA_02134 CCNA_02134 phosphogluconate dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__Caulo:CCNA_02134 Length = 602 Score = 733 bits (1892), Expect = 0.0 Identities = 365/600 (60%), Positives = 453/600 (75%), Gaps = 1/600 (0%) Query: 1 MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60 ++P + +VT R+VARS+ +R AYLA + A + P R KL CAN+AH A DK Sbjct: 3 LNPVIADVTARIVARSKDSRAAYLANMDRAIENQPGRAKLSCANWAHAFAASPGVDKLRA 62 Query: 61 RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120 NA N+ IVS+YNDMLSAHQP E +P IK A R++G+ QFAGG PAMCDGVTQG Sbjct: 63 LDPNAPNIGIVSAYNDMLSAHQPLEAYPALIKDAARDVGATAQFAGGVPAMCDGVTQGRP 122 Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180 GMELSL SR+VIA++TAVAL+H+ FD+AL LG+CDKIVPGL++GAL F HLP +FVP GP Sbjct: 123 GMELSLFSRDVIAMATAVALTHDAFDSALYLGVCDKIVPGLVIGALTFSHLPALFVPAGP 182 Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240 M SG+ N EKA +R YAEGK REELL +E SYH PGTCTFYGTANTNQ+LME+MG H Sbjct: 183 MTSGLPNSEKARIRALYAEGKVGREELLAAESASYHGPGTCTFYGTANTNQMLMELMGFH 242 Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300 LPG++FV+P TPLR+AL E+A++V +T + F P+G ++DE+S VN +V L ATGGS Sbjct: 243 LPGSAFVHPNTPLREALVKESARRVAAVTNKGNEFIPVGRMIDEKSFVNGVVGLMATGGS 302 Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360 TN LH+ A+A AAG+QLT +D+ D+S+ P L+ VYPNG AD+NHFQAAGGMAF+IREL Sbjct: 303 TNLALHIIAMAAAAGVQLTLEDLDDISKATPLLARVYPNGSADVNHFQAAGGMAFVIREL 362 Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420 L+AGL+HEDV T+AG GLS Y +EP L++G L WRDG ESLD I+RPV+ FS EGGL Sbjct: 363 LKAGLVHEDVQTIAGAGLSLYAKEPVLEDGMLTWRDGAHESLDPAIVRPVSDPFSKEGGL 422 Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480 R+M GNLGRGVMK+SAV +H ++EAP VFQ+Q+D AFK GEL++D V V+RFQGP Sbjct: 423 RLMAGNLGRGVMKISAVKPEHHVIEAPCAVFQEQEDFIAAFKRGELDRDVVVVVRFQGPS 482 Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540 +NGMPELH ++P + VL DRG KVALVTDGRMSGASGK PAAIHV+PEA GG LA V+D Sbjct: 483 ANGMPELHNLSPSISVLLDRGHKVALVTDGRMSGASGKTPAAIHVTPEAAKGGPLAYVQD 542 Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPAKGLLGNNVGSGRELFGFMRMAFSSAEQGASAF 600 GD+IRV+ G L++ VD AR PA + + G GRELFG+MR +A+ GAS F Sbjct: 543 GDVIRVNAETGELKIMVDEATLLARTPA-NVPASKPGFGRELFGWMRSGVGAADAGASVF 601 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: 1092 Number of extensions: 51 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: 602 Length adjustment: 37 Effective length of query: 571 Effective length of database: 565 Effective search space: 322615 Effective search space used: 322615 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 CCNA_02134 CCNA_02134 (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.5902.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.9e-297 971.3 0.5 8.8e-297 971.2 0.5 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_02134 CCNA_02134 phosphogluconate dehy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_02134 CCNA_02134 phosphogluconate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 971.2 0.5 8.8e-297 8.8e-297 2 600 .. 5 601 .. 4 602 .] 0.99 Alignments for each domain: == domain 1 score: 971.2 bits; conditional E-value: 8.8e-297 TIGR01196 2 srlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitayn 74 + +a++t+ri++rsk+ r +yl+++ a ++ + r++l+c+n ah++aa + +k+ + +n++i++ayn lcl|FitnessBrowser__Caulo:CCNA_02134 5 PVIADVTARIVARSKDSRAAYLANMDRAIENQPGRAKLSCANWAHAFAASPGVDKLRALDPNAPNIGIVSAYN 77 56899******************************************************************** PP TIGR01196 75 dmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdga 147 dmlsahqp++ yp+lik+a+++ +a+aq agGvpamcdGvtqG++Gmelsl+srdvia++ta++l+h+ fd+a lcl|FitnessBrowser__Caulo:CCNA_02134 78 DMLSAHQPLEAYPALIKDAARDVGATAQFAGGVPAMCDGVTQGRPGMELSLFSRDVIAMATAVALTHDAFDSA 150 ************************************************************************* PP TIGR01196 148 lflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtc 220 l+lGvcdkivpGl+i+al+f hlpa+fvpaGpm+sGl+n+eka++r l+aeGkv+reell++e+asyh+pGtc lcl|FitnessBrowser__Caulo:CCNA_02134 151 LYLGVCDKIVPGLVIGALTFSHLPALFVPAGPMTSGLPNSEKARIRALYAEGKVGREELLAAESASYHGPGTC 223 ************************************************************************* PP TIGR01196 221 tfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgl 293 tfyGtan+nqml+elmG+hlpg++fv+pntplr+al++e+a+r+a++t+k++e++p++++ideks+vn++vgl lcl|FitnessBrowser__Caulo:CCNA_02134 224 TFYGTANTNQMLMELMGFHLPGSAFVHPNTPLREALVKESARRVAAVTNKGNEFIPVGRMIDEKSFVNGVVGL 296 ************************************************************************* PP TIGR01196 294 latGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllh 366 +atGGstn +lh++a+a aaG++l+ +dl+++s+ pllarvypnG+advnhf+aaGG++f+irellk+Gl+h lcl|FitnessBrowser__Caulo:CCNA_02134 297 MATGGSTNLALHIIAMAAAAGVQLTLEDLDDISKATPLLARVYPNGSADVNHFQAAGGMAFVIRELLKAGLVH 369 ************************************************************************* PP TIGR01196 367 edvetvagkGlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkee 439 edv+t+ag Gl+ y+kep+ledg l++r++a++sld +i+r+v++pfs+eGGl+l+ GnlGr+v+k+savk+e lcl|FitnessBrowser__Caulo:CCNA_02134 370 EDVQTIAGAGLSLYAKEPVLEDGMLTWRDGAHESLDPAIVRPVSDPFSKEGGLRLMAGNLGRGVMKISAVKPE 442 ************************************************************************* PP TIGR01196 440 srvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrls 512 ++vieap+ vf++q++++aafk+gel+rd+v+vvrfqGp anGmpelh l + + vl+drg+kvalvtdGr+s lcl|FitnessBrowser__Caulo:CCNA_02134 443 HHVIEAPCAVFQEQEDFIAAFKRGELDRDVVVVVRFQGPSANGMPELHNLSPSISVLLDRGHKVALVTDGRMS 515 ************************************************************************* PP TIGR01196 513 GasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaa 585 GasGk paaihvtpea++gG+la ++dGd+ir++a +gel+++vd+a l ar+++++ +++ G Grelf lcl|FitnessBrowser__Caulo:CCNA_02134 516 GASGKTPAAIHVTPEAAKGGPLAYVQDGDVIRVNAETGELKIMVDEATLLARTPANV--PASKPGFGRELFGW 586 *****************************************************8766..5667799******* PP TIGR01196 586 lrekvssaeeGassl 600 +r+ v++a+ Gas++ lcl|FitnessBrowser__Caulo:CCNA_02134 587 MRSGVGAADAGASVF 601 ************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (601 nodes) Target sequences: 1 (602 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: 11.39 // [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