Align Aconitate hydratase B; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_057687520.1 ABB28_RS16835 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= SwissProt::Q8ZRS8 (865 letters) >NCBI__GCF_001431535.1:WP_057687520.1 Length = 863 Score = 1261 bits (3264), Expect = 0.0 Identities = 625/859 (72%), Positives = 728/859 (84%), Gaps = 8/859 (0%) Query: 1 MLEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEA 60 MLE YR HVAERAA GI P PL A Q A ++ELLK PP GE EFLLDLL +RVP GVD+A Sbjct: 1 MLEAYRHHVAERAALGIPPLPLTAQQTADVIELLKNPPAGEAEFLLDLLTHRVPAGVDDA 60 Query: 61 AYVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120 A VKA +LAA+A G +PL+S E+A ELLGTM GGYN+ PL+ LDDA + IAA AL Sbjct: 61 AKVKASYLAAIAFGSEQNPLISRERATELLGTMLGGYNVAPLVQLLDDATVGSIAAAALK 120 Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFKVTGETNTD 180 +TLL+FD F+DV+EKAKAGN A+ V+QSWADAEWF SRP +A+ +T+TVFKV GETNTD Sbjct: 121 NTLLVFDAFHDVQEKAKAGNANAQSVLQSWADAEWFTSRPEVAQSMTLTVFKVPGETNTD 180 Query: 181 DLSPAPDAWSRPDIPLHAQAMLKNARE--GIEPDQPGVVGPIKQIEALQKKGYPLAYVGD 238 DLSPAPDA +RPDIPLHA AMLKN R P++ G GPI++I +L+ KG+ +AYVGD Sbjct: 181 DLSPAPDATTRPDIPLHALAMLKNKRPDAAFVPEEDGKRGPIQEILSLKDKGHLVAYVGD 240 Query: 239 VVGTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDV 298 VVGTGSSRKSATNSVLWF G+DIP +PNKR GG+CLG KIAPIF+NTMEDAGALPIE+DV Sbjct: 241 VVGTGSSRKSATNSVLWFTGEDIPFIPNKRFGGVCLGSKIAPIFYNTMEDAGALPIELDV 300 Query: 299 SNLNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAR 358 + + GDVI++ PY G+ + GE++A F++K+DVL DEVRAGGRIPLI+GRGLT KAR Sbjct: 301 TQMEHGDVIELRPYDGKALKN--GEVIAEFQVKSDVLFDEVRAGGRIPLIVGRGLTAKAR 358 Query: 359 EALGLPHSDVFRQAKDVAESSRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQD 415 EALG+P +D+FR A++ +GFSLAQKMVGRACG+ +G+RPG YCEPKMTSVGSQD Sbjct: 359 EALGMPVTDLFRLPVQPADTGKGFSLAQKMVGRACGLPEGQGMRPGTYCEPKMTSVGSQD 418 Query: 416 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPG 475 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDV THHTLP+FI RGG+SLRPG Sbjct: 419 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVKTHHTLPEFISTRGGISLRPG 478 Query: 476 DGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR 535 DGVIHSWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPESVLVR Sbjct: 479 DGVIHSWLNRMLLPDTVGTGGDSHTRFPVGISFPAGSGLVAFAAATGVMPLDMPESVLVR 538 Query: 536 FKGKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFEL 595 FKGKMQPG+TLRDLV+AIPLYAIK GLLTV K GKKNIFSGRILEIEGLPDLKVEQAFEL Sbjct: 539 FKGKMQPGVTLRDLVNAIPLYAIKAGLLTVAKAGKKNIFSGRILEIEGLPDLKVEQAFEL 598 Query: 596 TDASAERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADP 655 +DASAERSAAGC++ L+K PI+EYLTSNI LL+WMIAEGY D R+L+RRI M++WLADP Sbjct: 599 SDASAERSAAGCSVHLDKAPIIEYLTSNITLLQWMIAEGYQDPRSLQRRIDKMKEWLADP 658 Query: 656 QLLEADADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIG 715 QLL DADAEYAAVI+IDLADI EPI+ PNDPDD ++LS+V G KIDEVFIGSCMTNIG Sbjct: 659 QLLAPDADAEYAAVIEIDLADIHEPIVACPNDPDDVKMLSEVAGAKIDEVFIGSCMTNIG 718 Query: 716 HFRAAGKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGN 775 HFRAA KLL+ K +PT+LWVAPPT+MDA++LT EG+Y FG +GAR+E+PGCSLCMGN Sbjct: 719 HFRAAAKLLEG-KRDIPTKLWVAPPTKMDASELTREGHYGTFGSAGARMEMPGCSLCMGN 777 Query: 776 QARVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDK 835 QA+V +GATV STSTRNFPNRLG +NV+L SAELAA+ + +G++PT EEY V ++ Sbjct: 778 QAQVREGATVFSTSTRNFPNRLGRNSNVYLGSAELAAICSRLGRIPTKEEYMADVGVLEA 837 Query: 836 TAVDTYRYLNFDQLSQYTE 854 + + YRY+NFDQ+ +Y E Sbjct: 838 SGAEIYRYMNFDQIEEYQE 856 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: 2096 Number of extensions: 78 Number of successful extensions: 5 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: 863 Length adjustment: 42 Effective length of query: 823 Effective length of database: 821 Effective search space: 675683 Effective search space used: 675683 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 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