Align phosphogluconate dehydratase (characterized)
to candidate WP_007677916.1 BN137_RS04825 phosphogluconate dehydratase
Query= CharProtDB::CH_024239 (603 letters) >NCBI__GCF_000319285.1:WP_007677916.1 Length = 603 Score = 1077 bits (2784), Expect = 0.0 Identities = 532/603 (88%), Positives = 566/603 (93%) Query: 1 MNPQLLRVTNRIIERSRETRSAYLARIEQAKTSTVHRSQLACGNLAHGFAACQPEDKASL 60 M+P+LLRVT RI ERSR TR AYLARIE+AK+ TVHR+ LACGNLAHGFAACQP+DKA+L Sbjct: 1 MHPKLLRVTKRITERSRATREAYLARIEEAKSQTVHRASLACGNLAHGFAACQPDDKAAL 60 Query: 61 KSMLRNNIAIITSYNDMLSAHQPYEHYPEIIRKALHEANAVGQVAGGVPAMCDGVTQGQD 120 KSMLRNNI IITSYNDMLSAHQPYE+YP+ IR ALH AV QVAGGVPAMCDGVTQGQD Sbjct: 61 KSMLRNNIGIITSYNDMLSAHQPYENYPQQIRDALHSVGAVAQVAGGVPAMCDGVTQGQD 120 Query: 121 GMELSLLSREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGP 180 GMELSLLSREVIAMSAAVGLSHNMFDGAL+LGVCDKIVPGL MAALSFGHLP VF+PSGP Sbjct: 121 GMELSLLSREVIAMSAAVGLSHNMFDGALYLGVCDKIVPGLVMAALSFGHLPGVFIPSGP 180 Query: 181 MASGLPNKEKVRIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQ 240 M+SGLPNKEKVRIRQLYAEGKVDR ALLESEAASYH PGTCTFYGTANTNQMV+EFMGMQ Sbjct: 181 MSSGLPNKEKVRIRQLYAEGKVDRAALLESEAASYHEPGTCTFYGTANTNQMVIEFMGMQ 240 Query: 241 LPGSSFVHPDSPLRDALTAAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGS 300 LPGSSFVHPD+PLR ALTAAAARQVTR+TGNGN+WMP+G+++DEKVVVNGIVALLATGGS Sbjct: 241 LPGSSFVHPDAPLRHALTAAAARQVTRLTGNGNDWMPLGRLVDEKVVVNGIVALLATGGS 300 Query: 301 TNHTMHLVAMARAAGIQINWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVREL 360 TNHTMHLVAMARAAGI INWDDFS+LS+ VPL+ARLYPNGPADINHFQAAGGVPVL+REL Sbjct: 301 TNHTMHLVAMARAAGIIINWDDFSELSEAVPLLARLYPNGPADINHFQAAGGVPVLMREL 360 Query: 361 LKAGLLHEDVNTVAGFGLSRYTLEPWLNNGELDWREGAEKSLDSNVIASFEQPFSHHGGT 420 LK GLLHEDVNTVAGFGL+RYT EPWLNNGEL WR+GA SLD +IA+ ++PFS HGGT Sbjct: 361 LKGGLLHEDVNTVAGFGLTRYTQEPWLNNGELAWRDGAAASLDDAIIATVDKPFSQHGGT 420 Query: 421 KVLSGNLGRAVMKTSAVPVENQVIEAPAVVFESQHDVMPAFEAGLLDRDCVVVVRHQGPK 480 KVLSGNLGRAVMKTSAVPVENQV+EAPAVVFESQHDV+PAFEAGLLDRDCVVVVRHQGPK Sbjct: 421 KVLSGNLGRAVMKTSAVPVENQVVEAPAVVFESQHDVLPAFEAGLLDRDCVVVVRHQGPK 480 Query: 481 ANGMPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRD 540 ANGMPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRD Sbjct: 481 ANGMPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRD 540 Query: 541 GDIIRVNGQTGELTLLVDEAELAAREPHIPDLSASRVGTGRELFSALREKLSGAEQGATC 600 GDIIRVNGQTGELTLLVD+A L+ RE PDLSA RVGTGRELF ALREKLSGAEQGATC Sbjct: 541 GDIIRVNGQTGELTLLVDDATLSQREAFHPDLSAQRVGTGRELFGALREKLSGAEQGATC 600 Query: 601 ITF 603 I F Sbjct: 601 IDF 603 Lambda K H 0.318 0.134 0.392 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: 1284 Number of extensions: 46 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: 603 Length of database: 603 Length adjustment: 37 Effective length of query: 566 Effective length of database: 566 Effective search space: 320356 Effective search space used: 320356 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_007677916.1 BN137_RS04825 (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.2344624.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 1095.3 0.1 0 1095.1 0.1 1.0 1 NCBI__GCF_000319285.1:WP_007677916.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000319285.1:WP_007677916.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1095.1 0.1 0 0 1 600 [. 2 601 .. 2 602 .. 1.00 Alignments for each domain: == domain 1 score: 1095.1 bits; conditional E-value: 0 TIGR01196 1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitay 73 h++l+++t+ri+ers++tre+yl++i++ak+++++r++l+cgnlahg+aa+++++k++lks+ r+n++iit+y NCBI__GCF_000319285.1:WP_007677916.1 2 HPKLLRVTKRITERSRATREAYLARIEEAKSQTVHRASLACGNLAHGFAACQPDDKAALKSMLRNNIGIITSY 74 79*********************************************************************** PP TIGR01196 74 ndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdg 146 ndmlsahqp+++yp++i++al+ +avaqvagGvpamcdGvtqG+dGmelsllsr+via+s+a+glshnmfdg NCBI__GCF_000319285.1:WP_007677916.1 75 NDMLSAHQPYENYPQQIRDALHSVGAVAQVAGGVPAMCDGVTQGQDGMELSLLSREVIAMSAAVGLSHNMFDG 147 ************************************************************************* PP TIGR01196 147 alflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGt 219 al+lGvcdkivpGl++aalsfGhlp+vf+p+Gpm+sGl+nkek+++rql+aeGkvdr +ll+se+asyh+pGt NCBI__GCF_000319285.1:WP_007677916.1 148 ALYLGVCDKIVPGLVMAALSFGHLPGVFIPSGPMSSGLPNKEKVRIRQLYAEGKVDRAALLESEAASYHEPGT 220 ************************************************************************* PP TIGR01196 220 ctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvg 292 ctfyGtan+nqm++e+mG++lpg+sfv+p++plr+alt++aa++++rlt+++++++pl++l+dek++vn++v+ NCBI__GCF_000319285.1:WP_007677916.1 221 CTFYGTANTNQMVIEFMGMQLPGSSFVHPDAPLRHALTAAAARQVTRLTGNGNDWMPLGRLVDEKVVVNGIVA 293 ************************************************************************* PP TIGR01196 293 llatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGll 365 llatGGstnht+hlva+araaGii+nwdd+sels+ vpllar+ypnG ad+nhf+aaGG+++l+rellk Gll NCBI__GCF_000319285.1:WP_007677916.1 294 LLATGGSTNHTMHLVAMARAAGIIINWDDFSELSEAVPLLARLYPNGPADINHFQAAGGVPVLMRELLKGGLL 366 ************************************************************************* PP TIGR01196 366 hedvetvagkGlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavke 438 hedv+tvag Gl ryt+ep+l++g+l +r++a +sld++i+++vdkpfs++GG+k+l+GnlGrav+k+sav NCBI__GCF_000319285.1:WP_007677916.1 367 HEDVNTVAGFGLTRYTQEPWLNNGELAWRDGAAASLDDAIIATVDKPFSQHGGTKVLSGNLGRAVMKTSAVPV 439 ************************************************************************* PP TIGR01196 439 esrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrl 511 e++v+eapa+vf++q+++l+af+ag l+rd+v+vvr+qGpkanGmpelhkl+++lGvl+dr+fk+alvtdGrl NCBI__GCF_000319285.1:WP_007677916.1 440 ENQVVEAPAVVFESQHDVLPAFEAGLLDRDCVVVVRHQGPKANGMPELHKLMPPLGVLLDRCFKIALVTDGRL 512 ************************************************************************* PP TIGR01196 512 sGasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfa 584 sGasGkvp+aihvtpea++gG lak+rdGd+ir+++++gel++lvdda l re ++dl+++++G+Grelf NCBI__GCF_000319285.1:WP_007677916.1 513 SGASGKVPSAIHVTPEAYDGGLLAKVRDGDIIRVNGQTGELTLLVDDATLSQREAFHPDLSAQRVGTGRELFG 585 ************************************************************************* PP TIGR01196 585 alrekvssaeeGassl 600 alrek+s+ae+Ga+++ NCBI__GCF_000319285.1:WP_007677916.1 586 ALREKLSGAEQGATCI 601 *************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (601 nodes) Target sequences: 1 (603 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: 22.32 // [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