Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_019865040.1 METMI_RS0104465 phosphogluconate dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >NCBI__GCF_000384075.1:WP_019865040.1 Length = 606 Score = 741 bits (1913), Expect = 0.0 Identities = 360/600 (60%), Positives = 455/600 (75%), Gaps = 2/600 (0%) Query: 1 MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60 MHP + +VT+ ++ RS TREAYL I GA GP R L C N AHG A CG+ +K L Sbjct: 1 MHPLLEKVTKEVIDRSHRTREAYLVCIDGAIGKGPHRSVLGCGNLAHGFAACGAGEKLDL 60 Query: 61 RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120 AN+ I+SSYNDMLSAH+PY+ P IK+A+ G V QFAGG PAMCDG+TQG+A Sbjct: 61 AGDKKANIGIISSYNDMLSAHEPYKDAPALIKEAISAAGGVAQFAGGVPAMCDGITQGQA 120 Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180 GMELSL SR+VIA+STA+ LSHNMFD AL LG+CDKIVPGL+MGAL FGHLP +FVP GP Sbjct: 121 GMELSLFSRDVIAMSTAIGLSHNMFDGALYLGVCDKIVPGLLMGALSFGHLPAVFVPAGP 180 Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240 MPSGI+NKEK+ RQ+YAEGK R ELLESE KSYHSPGTCTFYGTAN+NQ+++E+MGLH Sbjct: 181 MPSGITNKEKSRARQQYAEGKIGRAELLESESKSYHSPGTCTFYGTANSNQMMVEMMGLH 240 Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300 LPG+SFVNPYTPLRD LT AA+QV + T +F PIG +++E++++N+++ L ATGGS Sbjct: 241 LPGSSFVNPYTPLRDELTKAAARQVLKFTALGNDFRPIGHVINEKAILNALIGLLATGGS 300 Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360 TNHT+H+ AIA+ AGI + W D +LS+ +P ++ +YPNG AD+NHFQAAGGM LI EL Sbjct: 301 TNHTMHLVAIARMAGIIINWNDFDNLSKAIPLITKIYPNGPADVNHFQAAGGMGVLIAEL 360 Query: 361 LEAGLLHEDVNTVAGR-GLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGG 419 L+ G++HED+ T+ R G+ +YTQEP + G LVW P SLD ++ V + F+P GG Sbjct: 361 LKHGMMHEDILTIGDRHGMGQYTQEPKIIGGNLVWEASPAASLDTEVIATVEKPFAPGGG 420 Query: 420 LRVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGP 479 + ++ GNLGRG+ KVSAV+ HQ+VEAPAVVF DQ ++ AFK GEL DFVAV+RFQGP Sbjct: 421 IHLIRGNLGRGISKVSAVSEDHQVVEAPAVVFDDQDEMMAAFKRGELNHDFVAVLRFQGP 480 Query: 480 RSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVR 539 R+NGMPELHK+TP LG+LQD+G+KVAL+TDGRMSGASGK+P+AIH+ PE GG LA+VR Sbjct: 481 RANGMPELHKLTPALGLLQDKGYKVALLTDGRMSGASGKVPSAIHMYPECINGGPLAKVR 540 Query: 540 DGDIIRVDGVKGTLELKVDADEFAAREPAKGLLGN-NVGSGRELFGFMRMAFSSAEQGAS 598 +GDII ++ G + + VD EF R P + N + G GRE+FG R ++AE GAS Sbjct: 541 NGDIISLNIKTGDVNVLVDETEFNGRLPEENSAKNHHFGMGREMFGGFRQGATTAETGAS 600 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: 1157 Number of extensions: 49 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: 606 Length adjustment: 37 Effective length of query: 571 Effective length of database: 569 Effective search space: 324899 Effective search space used: 324899 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_019865040.1 METMI_RS0104465 (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.2067481.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-305 998.2 0.6 6.6e-305 998.0 0.6 1.0 1 NCBI__GCF_000384075.1:WP_019865040.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000384075.1:WP_019865040.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 998.0 0.6 6.6e-305 6.6e-305 1 600 [. 2 602 .. 2 603 .. 0.99 Alignments for each domain: == domain 1 score: 998.0 bits; conditional E-value: 6.6e-305 TIGR01196 1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitay 73 h+ l+++t+ +i+rs++tre+yl i a kg++rs+lgcgnlahg+aa+ ek++l+ +k++n++ii++y NCBI__GCF_000384075.1:WP_019865040.1 2 HPLLEKVTKEVIDRSHRTREAYLVCIDGAIGKGPHRSVLGCGNLAHGFAACGAGEKLDLAGDKKANIGIISSY 74 67799******************************************************************** PP TIGR01196 74 ndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdg 146 ndmlsah+p+k+ p+lik+a+ a++vaq agGvpamcdG+tqG++Gmelsl+srdvia+staiglshnmfdg NCBI__GCF_000384075.1:WP_019865040.1 75 NDMLSAHEPYKDAPALIKEAISAAGGVAQFAGGVPAMCDGITQGQAGMELSLFSRDVIAMSTAIGLSHNMFDG 147 ************************************************************************* PP TIGR01196 147 alflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGt 219 al+lGvcdkivpGll++alsfGhlpavfvpaGpm+sG++nkek+++rq++aeGk++r ell+se++syh+pGt NCBI__GCF_000384075.1:WP_019865040.1 148 ALYLGVCDKIVPGLLMGALSFGHLPAVFVPAGPMPSGITNKEKSRARQQYAEGKIGRAELLESESKSYHSPGT 220 ************************************************************************* PP TIGR01196 220 ctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvg 292 ctfyGtansnqm+ve+mGlhlpg+sfvnp+tplrd+lt++aa+++ + ta ++++ p++++i+ek+i+nal+g NCBI__GCF_000384075.1:WP_019865040.1 221 CTFYGTANSNQMMVEMMGLHLPGSSFVNPYTPLRDELTKAAARQVLKFTALGNDFRPIGHVINEKAILNALIG 293 ************************************************************************* PP TIGR01196 293 llatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGll 365 llatGGstnht+hlvaiar aGii+nw+d+++ls+ +pl++++ypnG advnhf+aaGG+++li+ellk+G++ NCBI__GCF_000384075.1:WP_019865040.1 294 LLATGGSTNHTMHLVAIARMAGIIINWNDFDNLSKAIPLITKIYPNGPADVNHFQAAGGMGVLIAELLKHGMM 366 ************************************************************************* PP TIGR01196 366 hedvetvag.kGlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavk 437 hed+ t+ + +G+ +yt+ep++ g+l+++ ++ +sld++++++v+kpf++ GG++l++GnlGr++ kvsav NCBI__GCF_000384075.1:WP_019865040.1 367 HEDILTIGDrHGMGQYTQEPKIIGGNLVWEASPAASLDTEVIATVEKPFAPGGGIHLIRGNLGRGISKVSAVS 439 *******9989************************************************************** PP TIGR01196 438 eesrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGr 510 e+++v+eapa+vf+dq e++aafk+gel++d+vav+rfqGp+anGmpelhklt++lG+lqd+g+kval+tdGr NCBI__GCF_000384075.1:WP_019865040.1 440 EDHQVVEAPAVVFDDQDEMMAAFKRGELNHDFVAVLRFQGPRANGMPELHKLTPALGLLQDKGYKVALLTDGR 512 ************************************************************************* PP TIGR01196 511 lsGasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelf 583 +sGasGkvp+aih+ pe+++gG+lak+r+Gd+i l+ ++g+++vlvd++e++ r +ee ++ ++G+Gre+f NCBI__GCF_000384075.1:WP_019865040.1 513 MSGASGKVPSAIHMYPECINGGPLAKVRNGDIISLNIKTGDVNVLVDETEFNGRLPEENSAKNHHFGMGREMF 585 ************************************************************************* PP TIGR01196 584 aalrekvssaeeGassl 600 +r+ +++ae+Gas l NCBI__GCF_000384075.1:WP_019865040.1 586 GGFRQGATTAETGASNL 602 **************876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (601 nodes) Target sequences: 1 (606 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 18.42 // [ok]
This GapMind analysis is from Apr 09 2024. 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