Align phosphogluconate dehydratase (characterized)
to candidate 7024978 Shewana3_2149 phosphogluconate dehydratase (RefSeq)
Query= CharProtDB::CH_024239 (603 letters) >FitnessBrowser__ANA3:7024978 Length = 608 Score = 814 bits (2103), Expect = 0.0 Identities = 406/598 (67%), Positives = 487/598 (81%) Query: 1 MNPQLLRVTNRIIERSRETRSAYLARIEQAKTSTVHRSQLACGNLAHGFAACQPEDKASL 60 M+ + VT+RII RS+ +R AYLA + A+ VHRS L+CGNLAHGFAAC P+DK SL Sbjct: 1 MHSVVQSVTDRIIARSKASREAYLAALNDARNHGVHRSSLSCGNLAHGFAACSPDDKNSL 60 Query: 61 KSMLRNNIAIITSYNDMLSAHQPYEHYPEIIRKALHEANAVGQVAGGVPAMCDGVTQGQD 120 + + + NI IIT++NDMLSAHQPYE YPE+++KA E +V QVAGGVPAMCDGVTQGQ Sbjct: 61 RQLTKANIGIITAFNDMLSAHQPYETYPELLKKACQEVGSVAQVAGGVPAMCDGVTQGQP 120 Query: 121 GMELSLLSREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGP 180 GMELSLLSREVIAM+ AVGLSHNMFDGAL LG+CDKIVPGL + ALSFGHLP +FVP+GP Sbjct: 121 GMELSLLSREVIAMATAVGLSHNMFDGALLLGICDKIVPGLLIGALSFGHLPMLFVPAGP 180 Query: 181 MASGLPNKEKVRIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQ 240 M SG+PNKEK RIRQ +A+GKVDR LLE+EA SYH+ GTCTFYGTAN+NQ+++E MG+Q Sbjct: 181 MKSGIPNKEKARIRQQFAQGKVDRAQLLEAEAQSYHSAGTCTFYGTANSNQLMLEVMGLQ 240 Query: 241 LPGSSFVHPDSPLRDALTAAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGS 300 LPGSSFV+PD PLR+AL AA+QV R+T G ++ PIG++++EK VVNGIVALLATGGS Sbjct: 241 LPGSSFVNPDDPLREALNKMAAKQVCRLTELGTQYSPIGEVVNEKSVVNGIVALLATGGS 300 Query: 301 TNHTMHLVAMARAAGIQINWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVREL 360 TN TMH+VA ARAAGI +NWDDFS+LSD VPL+AR+YPNG ADINHF AAGG+ L++EL Sbjct: 301 TNLTMHIVAAARAAGIIVNWDDFSELSDAVPLLARVYPNGHADINHFHAAGGMAFLIKEL 360 Query: 361 LKAGLLHEDVNTVAGFGLSRYTLEPWLNNGELDWREGAEKSLDSNVIASFEQPFSHHGGT 420 L AGLLHEDVNTVAGFGL RYT EP L +GEL W +G SLD+ V+ S PF ++GG Sbjct: 361 LDAGLLHEDVNTVAGFGLRRYTQEPKLLDGELRWVDGPTVSLDTEVLTSVATPFQNNGGL 420 Query: 421 KVLSGNLGRAVMKTSAVPVENQVIEAPAVVFESQHDVMPAFEAGLLDRDCVVVVRHQGPK 480 K+L GNLGRAV+K SAV +++V+EAPAVV + Q+ + F++G LDRDCVVVV+ QGPK Sbjct: 421 KLLKGNLGRAVIKVSAVQEKHRVVEAPAVVIDDQNKLDALFKSGALDRDCVVVVKGQGPK 480 Query: 481 ANGMPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRD 540 ANGMPELHKL P LG L D+ FK+AL+TDGR+SGASGKVP+AIH+TPEA DGGL+AKV+D Sbjct: 481 ANGMPELHKLTPLLGSLQDKGFKVALMTDGRMSGASGKVPAAIHLTPEAIDGGLIAKVQD 540 Query: 541 GDIIRVNGQTGELTLLVDEAELAAREPHIPDLSASRVGTGRELFSALREKLSGAEQGA 598 GD+IRV+ TGEL+LLV +AELAAR DL SR G GRELF ALR LS E GA Sbjct: 541 GDLIRVDALTGELSLLVSDAELAARTAAEIDLRHSRYGMGRELFGALRSNLSSPETGA 598 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: 1058 Number of extensions: 30 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: 608 Length adjustment: 37 Effective length of query: 566 Effective length of database: 571 Effective search space: 323186 Effective search space used: 323186 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 7024978 Shewana3_2149 (phosphogluconate dehydratase (RefSeq))
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.11340.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 1028.8 1.3 0 1028.6 1.3 1.0 1 lcl|FitnessBrowser__ANA3:7024978 Shewana3_2149 phosphogluconate d Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7024978 Shewana3_2149 phosphogluconate dehydratase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1028.6 1.3 0 0 1 599 [. 2 600 .. 2 602 .. 1.00 Alignments for each domain: == domain 1 score: 1028.6 bits; conditional E-value: 0 TIGR01196 1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitayndml 77 hs ++++t+rii+rsk+ re+yl+ +++a+++g++rs+l+cgnlahg+aa+s+++k +l++ +++n++iita+ndml lcl|FitnessBrowser__ANA3:7024978 2 HSVVQSVTDRIIARSKASREAYLAALNDARNHGVHRSSLSCGNLAHGFAACSPDDKNSLRQLTKANIGIITAFNDML 78 678999*********************************************************************** PP TIGR01196 78 sahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdgalflGvcd 154 sahqp+++yp+l+kka+qe ++vaqvagGvpamcdGvtqG++Gmelsllsr+via++ta+glshnmfdgal+lG+cd lcl|FitnessBrowser__ANA3:7024978 79 SAHQPYETYPELLKKACQEVGSVAQVAGGVPAMCDGVTQGQPGMELSLLSREVIAMATAVGLSHNMFDGALLLGICD 155 ***************************************************************************** PP TIGR01196 155 kivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtctfyGtansnqm 231 kivpGlli+alsfGhlp +fvpaGpm sG++nkeka++rq+fa+Gkvdr +ll++e++syh++GtctfyGtansnq+ lcl|FitnessBrowser__ANA3:7024978 156 KIVPGLLIGALSFGHLPMLFVPAGPMKSGIPNKEKARIRQQFAQGKVDRAQLLEAEAQSYHSAGTCTFYGTANSNQL 232 ***************************************************************************** PP TIGR01196 232 lvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgllatGGstnhtlhlva 308 ++e+mGl+lpg+sfvnp+ plr+al + aak++ rlt + ++ p++e+++eks+vn++v+llatGGstn t+h+va lcl|FitnessBrowser__ANA3:7024978 233 MLEVMGLQLPGSSFVNPDDPLREALNKMAAKQVCRLTELGTQYSPIGEVVNEKSVVNGIVALLATGGSTNLTMHIVA 309 ***************************************************************************** PP TIGR01196 309 iaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagkGlrrytkepf 385 araaGii+nwdd+selsd vpllarvypnG+ad+nhf+aaGG++fli+ell++Gllhedv+tvag Glrryt+ep+ lcl|FitnessBrowser__ANA3:7024978 310 AARAAGIIVNWDDFSELSDAVPLLARVYPNGHADINHFHAAGGMAFLIKELLDAGLLHEDVNTVAGFGLRRYTQEPK 386 ***************************************************************************** PP TIGR01196 386 ledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivfkdqaellaafka 462 l dg+l++ +++ sld+++l +v +pf+++GGlkllkGnlGravikvsav+e++rv+eapa+v +dq++l a fk+ lcl|FitnessBrowser__ANA3:7024978 387 LLDGELRWVDGPTVSLDTEVLTSVATPFQNNGGLKLLKGNLGRAVIKVSAVQEKHRVVEAPAVVIDDQNKLDALFKS 463 ***************************************************************************** PP TIGR01196 463 gelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakird 539 g l+rd+v+vv+ qGpkanGmpelhklt+ lG lqd+gfkval+tdGr+sGasGkvpaaih+tpea++gG +ak++d lcl|FitnessBrowser__ANA3:7024978 464 GALDRDCVVVVKGQGPKANGMPELHKLTPLLGSLQDKGFKVALMTDGRMSGASGKVPAAIHLTPEAIDGGLIAKVQD 540 ***************************************************************************** PP TIGR01196 540 GdlirldavngelevlvddaelkareleeldlednelGlGrelfaalrekvssaeeGass 599 Gdlir+da +gel++lv dael+ar+ +e+dl ++++G+Grelf alr+++ss e+Ga s lcl|FitnessBrowser__ANA3:7024978 541 GDLIRVDALTGELSLLVSDAELAARTAAEIDLRHSRYGMGRELFGALRSNLSSPETGARS 600 *********************************************************986 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 9.66 // [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