Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate GFF2930 PS417_14990 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= BRENDA::P36683 (865 letters) >FitnessBrowser__WCS417:GFF2930 Length = 869 Score = 1375 bits (3560), Expect = 0.0 Identities = 668/859 (77%), Positives = 759/859 (88%), Gaps = 3/859 (0%) Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60 MLE YRKH+ ERAA GI P+PL+A Q A LVELLKNPPAGEEEFL+DL+TNR+PPGVDEA Sbjct: 1 MLEAYRKHIEERAALGIVPQPLNAEQTAGLVELLKNPPAGEEEFLVDLITNRIPPGVDEA 60 Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120 AYVKAGFL+A+AKGEA SPL+ ++A+ELLGTMQGGYNI L++ LDDA LAP+AA L Sbjct: 61 AYVKAGFLSALAKGEATSPLIDKKRAVELLGTMQGGYNIVTLVELLDDAALAPVAAAQLK 120 Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180 HTLLMFD F+DV EKA+ GNE+AK V+QSWAD EWF NRP LA+K+++ VFKVTGETNTD Sbjct: 121 HTLLMFDAFHDVAEKARNGNEHAKAVIQSWADGEWFRNRPTLADKISLRVFKVTGETNTD 180 Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240 DLSPAPDAWSRPDIPLHALAMLK AREGI PD+ G GP+KQIE ++ +GFP+AYVGDVV Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKMAREGIVPDEQGKTGPMKQIEEMRGQGFPIAYVGDVV 240 Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300 GTGSSRKSATNSVLWF GDD+P+VPNKR GG C G KIAPIF+NTMEDAGALPIE DV+N Sbjct: 241 GTGSSRKSATNSVLWFFGDDVPYVPNKRAGGFCFGSKIAPIFYNTMEDAGALPIEFDVTN 300 Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360 +NMGDVID+YP+ G+V H T E++ TFE+KT VL+DEVRAGGRIPLIIGRGLT KAR Sbjct: 301 MNMGDVIDLYPHAGKVCKHGTDEVITTFEMKTPVLLDEVRAGGRIPLIIGRGLTDKARAE 360 Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417 LGL +D+F+ + ++ +GF+LAQKMVG+ACG+ KG+RPG YCEPKMT+VGSQDTT Sbjct: 361 LGLGPTDLFKLPEAPVDTGKGFTLAQKMVGKACGLPEGKGVRPGTYCEPKMTTVGSQDTT 420 Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDG 477 GPMTRDELKDLACLGFS DLVMQSFCHTAAYPKP+DV THHTLPDFIM RGGVSLRPGDG Sbjct: 421 GPMTRDELKDLACLGFSTDLVMQSFCHTAAYPKPIDVTTHHTLPDFIMTRGGVSLRPGDG 480 Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537 +IHSWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPES+LVRFK Sbjct: 481 IIHSWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAATGVMPLDMPESILVRFK 540 Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597 GKM+PGITLRDLVHAIP YAI+ GLLTVEKKGKKN FSGRILEIEGL DL +EQAFEL+D Sbjct: 541 GKMKPGITLRDLVHAIPYYAIQSGLLTVEKKGKKNAFSGRILEIEGLNDLTLEQAFELSD 600 Query: 598 ASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPEL 657 ASAERSAAGCTIKL+KE I EYLNSNI LL+WMI EGYGD RTLERR Q ME W+ NPEL Sbjct: 601 ASAERSAAGCTIKLSKESITEYLNSNITLLRWMIGEGYGDPRTLERRAQAMEAWVKNPEL 660 Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHF 717 +EADADAEYA +I+IDLA+I EPILCAPNDPDDAR LS+V GEKIDEVFIGSCMTNIGHF Sbjct: 661 MEADADAEYAEIIEIDLAEINEPILCAPNDPDDARLLSSVAGEKIDEVFIGSCMTNIGHF 720 Query: 718 RAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777 RAAGKLL+ KGQLPTRLW++PPT+MDA QLTEEGYY ++GK+GAR+E+PGCSLCMGNQA Sbjct: 721 RAAGKLLEQVKGQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQA 780 Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837 RV +TVVSTSTRNFPNRLG GANV+LASAELAAVA+ +G+LPT EEY Y A++D A Sbjct: 781 RVEPNSTVVSTSTRNFPNRLGDGANVYLASAELAAVASTLGRLPTVEEYMGYAAKLDTMA 840 Query: 838 VDTYRYLNFNQLSQYTEKA 856 D YRYLNF+Q++++ + A Sbjct: 841 SDVYRYLNFDQIAEFRKIA 859 Lambda K H 0.317 0.136 0.400 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: 2185 Number of extensions: 74 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: 865 Length of database: 869 Length adjustment: 42 Effective length of query: 823 Effective length of database: 827 Effective search space: 680621 Effective search space used: 680621 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: 56 (26.2 bits)
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