Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_004689073.1 BIBO1_RS18110 phosphogluconate dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >NCBI__GCF_000182725.1:WP_004689073.1 Length = 607 Score = 738 bits (1906), Expect = 0.0 Identities = 365/601 (60%), Positives = 455/601 (75%), Gaps = 2/601 (0%) Query: 2 HPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSLR 61 H R+ E+TER+ RS+ TREAYL +R AAS+ P+R L CAN AHG A CG DK +L Sbjct: 7 HKRIQEITERIRERSKPTREAYLDRVREAASNKPKRSFLGCANLAHGFAACGPHDKAALT 66 Query: 62 MMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAG 121 N+ I+++YNDMLSAHQP+E FP+ IK+A RE G V Q AGG PAMCDGVTQG AG Sbjct: 67 ADVVPNLGIITAYNDMLSAHQPFETFPQLIKQAAREAGGVAQVAGGVPAMCDGVTQGFAG 126 Query: 122 MELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPM 181 MELSL SREVIA++TAV LSH+MFDAA+ LG+CDKIVPGL++GAL FGHLP +F+P GPM Sbjct: 127 MELSLFSREVIAMATAVGLSHDMFDAAVYLGVCDKIVPGLIVGALTFGHLPAVFIPAGPM 186 Query: 182 PSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHL 241 SG+ N EKA RQ YAEGK R ELLESE KSYH PGTCTFYGTAN+NQ+LME+MGLHL Sbjct: 187 TSGLPNDEKAKTRQLYAEGKVGRAELLESESKSYHGPGTCTFYGTANSNQMLMEIMGLHL 246 Query: 242 PGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGST 301 PGASF+NP TPLRDALT EAA++ +T +TP+GE++DERS+VN +V L+ATGGST Sbjct: 247 PGASFINPGTPLRDALTREAAKRALAITALGNEYTPVGEMIDERSIVNGVVGLNATGGST 306 Query: 302 NHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRELL 361 NHT+H+ A+A AAGI+LTW D++ +S+VVP L+ VYPNG AD+NHF AAGGM FLIRELL Sbjct: 307 NHTIHLIAMAAAAGIKLTWHDISQISDVVPLLARVYPNGLADVNHFHAAGGMGFLIRELL 366 Query: 362 EAGLLHEDVNTVAGRGLSRYTQEPFL-DNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420 + GLLHEDV TV G GL Y EP L +G +V P +S D+ +L +A F P GG+ Sbjct: 367 DGGLLHEDVRTVWGEGLRPYAIEPKLGPDGNVVREAAPEKSGDDKVLAKIAAPFQPTGGI 426 Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480 +V+ GN+G ++KVSAV + ++EAPA VF DQ +L AFKAG+L DF+AV+R+QGP+ Sbjct: 427 KVLSGNIGNAIIKVSAVKPERHVIEAPAKVFNDQAELQAAFKAGDLTGDFIAVVRYQGPK 486 Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540 +NGMPELHK+ LG+LQDRG +VALVTDGR+SGASGK+P+AIHV+PEA GG + ++R Sbjct: 487 ANGMPELHKLMTVLGILQDRGQRVALVTDGRLSGASGKVPSAIHVTPEALDGGMIGKIRT 546 Query: 541 GDIIRVDGVKGTLELKVDADEFAAR-EPAKGLLGNNVGSGRELFGFMRMAFSSAEQGASA 599 GDIIR+D + GTLE+ ++ +R E L GN G GRELF R A++GAS Sbjct: 547 GDIIRLDAINGTLEVLLNQAVLDSRIEERPDLSGNEYGMGRELFRAFRQIAGRADEGASV 606 Query: 600 F 600 F Sbjct: 607 F 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: 1099 Number of extensions: 46 Number of successful extensions: 3 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 WP_004689073.1 BIBO1_RS18110 (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.678590.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 1054.2 0.2 0 1054.1 0.2 1.0 1 NCBI__GCF_000182725.1:WP_004689073.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000182725.1:WP_004689073.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1054.1 0.2 0 0 1 600 [. 7 607 .] 7 607 .] 0.99 Alignments for each domain: == domain 1 score: 1054.1 bits; conditional E-value: 0 TIGR01196 1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitay 73 h r++eiteri ersk+tre+yl+++r+a+++ ++rs lgc+nlahg+aa+ +++k++l+ + ++nl+iitay NCBI__GCF_000182725.1:WP_004689073.1 7 HKRIQEITERIRERSKPTREAYLDRVREAASNKPKRSFLGCANLAHGFAACGPHDKAALTADVVPNLGIITAY 79 689********************************************************************** PP TIGR01196 74 ndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdg 146 ndmlsahqpf+++p+lik+a++ea++vaqvagGvpamcdGvtqG +Gmelsl+sr+via++ta+glsh+mfd+ NCBI__GCF_000182725.1:WP_004689073.1 80 NDMLSAHQPFETFPQLIKQAAREAGGVAQVAGGVPAMCDGVTQGFAGMELSLFSREVIAMATAVGLSHDMFDA 152 ************************************************************************* PP TIGR01196 147 alflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGt 219 a++lGvcdkivpGl+++al+fGhlpavf+paGpm+sGl+n+ekak+rql+aeGkv+r ell+se++syh+pGt NCBI__GCF_000182725.1:WP_004689073.1 153 AVYLGVCDKIVPGLIVGALTFGHLPAVFIPAGPMTSGLPNDEKAKTRQLYAEGKVGRAELLESESKSYHGPGT 225 ************************************************************************* PP TIGR01196 220 ctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvg 292 ctfyGtansnqml+e+mGlhlpgasf+np tplrdaltreaakr+ ++ta ++e++p++e+ide+sivn++vg NCBI__GCF_000182725.1:WP_004689073.1 226 CTFYGTANSNQMLMEIMGLHLPGASFINPGTPLRDALTREAAKRALAITALGNEYTPVGEMIDERSIVNGVVG 298 ************************************************************************* PP TIGR01196 293 llatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGll 365 l atGGstnht+hl+a+a aaGi l+w+d+s++sd+vpllarvypnG advnhf+aaGG++flirell+ Gll NCBI__GCF_000182725.1:WP_004689073.1 299 LNATGGSTNHTIHLIAMAAAAGIKLTWHDISQISDVVPLLARVYPNGLADVNHFHAAGGMGFLIRELLDGGLL 371 ************************************************************************* PP TIGR01196 366 hedvetvagkGlrrytkepfle.dgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavk 437 hedv+tv g+Glr y++ep+l dg+++++ a+eks d+++l+k+ pf+++GG+k+l+Gn+G a+ikvsavk NCBI__GCF_000182725.1:WP_004689073.1 372 HEDVRTVWGEGLRPYAIEPKLGpDGNVVREAAPEKSGDDKVLAKIAAPFQPTGGIKVLSGNIGNAIIKVSAVK 444 *********************846************************************************* PP TIGR01196 438 eesrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGr 510 +e +vieapa+vf+dqael+aafkag+l +d++avvr+qGpkanGmpelhkl+tvlG+lqdrg++valvtdGr NCBI__GCF_000182725.1:WP_004689073.1 445 PERHVIEAPAKVFNDQAELQAAFKAGDLTGDFIAVVRYQGPKANGMPELHKLMTVLGILQDRGQRVALVTDGR 517 ************************************************************************* PP TIGR01196 511 lsGasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelf 583 lsGasGkvp+aihvtpeal+gG + kir+Gd+irlda+ng levl ++a l++r e++dl+ ne+G+Grelf NCBI__GCF_000182725.1:WP_004689073.1 518 LSGASGKVPSAIHVTPEALDGGMIGKIRTGDIIRLDAINGTLEVLLNQAVLDSRIEERPDLSGNEYGMGRELF 590 ************************************************************************* PP TIGR01196 584 aalrekvssaeeGassl 600 a+r++++ a+eGas++ NCBI__GCF_000182725.1:WP_004689073.1 591 RAFRQIAGRADEGASVF 607 **************986 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 33.88 // [ok]
This GapMind analysis is from Sep 24 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