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_046009357.1 OLEAN_RS11565 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= SwissProt::Q8ZRS8 (865 letters) >NCBI__GCF_000967895.1:WP_046009357.1 Length = 928 Score = 328 bits (842), Expect = 7e-94 Identities = 283/926 (30%), Positives = 431/926 (46%), Gaps = 113/926 (12%) Query: 4 EYRKHVAERAAQ-GIVPKPLD-ATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEAA 61 EY + + R G+ PKP+D A ++ ++ +K E LD I PG AA Sbjct: 6 EYLEEIEVRKNDLGLNPKPIDTADLLSEIIAQIKDTGNAAREASLDFFIYNTIPGTTSAA 65 Query: 62 YVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLID-ALDDAKLAPIAAKALS 120 VKA FL +A G T ++PE A+E L M+GG ++ L+D AL D A A + L Sbjct: 66 VVKAAFLKDIALGTETVAEITPEFALEQLSHMKGGPSVEALLDIALSDDAQAKAAGEVLK 125 Query: 121 HTLLMFD-NFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKI-TVTVFKVTGETN 178 + +++ + + + KAGN AK +++S+A AE+F P + KI VT G+ + Sbjct: 126 SQVFLYEADTSRIADAFKAGNAIAKDLLESYAAAEFFTKLPEIPAKIDVVTYIAAEGDIS 185 Query: 179 TDDLSPAPDAWSRPDIPLHAQAMLKNAREGIEPDQPGVVGPIKQIEALQKKGYPLAYVGD 238 TD LSP + SR D LH Q M+ + E G P ++ + +KG Sbjct: 186 TDLLSPGNQSHSRADRELHGQCMITPEAQQ-EIVALGKKHPNAKVMLIAEKG-------- 236 Query: 239 VVGTGSSRKSATNSV-LWFMGDDIPNVPNKRGGGLCLGGK-IAPIFF------------- 283 +G GSSR S N+V LW P +P + G IAPIF Sbjct: 237 TMGVGSSRMSGVNNVALWAGEKTSPYIPFINNAPVVAGTNGIAPIFLTTVGVTGGIGLDL 296 Query: 284 -----------NTMEDAGALPIEVDVSNLNMGDVIDVYPYKGEVRNHETGELLATFELKT 332 NT++DA + + ++ G V+ + ++ N + EL+ + + Sbjct: 297 KNWVKKVDAEGNTVKDANGDNVLEEAYSVATGTVLTIDTAAKKLYNGDK-ELVDVSDAFS 355 Query: 333 DVLIDEVRAGGRIPLIIGRGLTTKAREALGLPHSDVFRQAKDVAESSRGFSLAQKMVGR- 391 ++ ++AGG L G+ L T A E LG+ VF +K+++ +G + +K+ R Sbjct: 356 PQKVEFMKAGGSYALTFGKKLQTFAAETLGIQAPTVFAPSKEISVEGQGLTAVEKIFNRN 415 Query: 392 ACGVKGIRP---GAYCEPKMTSVGSQDTTGPMTRDELKDLAC--LGFSADLVMQSFCHTA 446 A GV P G+ K+ VGSQDTTGPMT EL+ +A + S D QS CHTA Sbjct: 416 AVGVASSTPLHTGSDVRVKVNIVGSQDTTGPMTCQELESMAASTISPSVDGAFQSGCHTA 475 Query: 447 AYPKPVDVTTHHTLPDFIMNRGGVSLRPGDGVIHSW-------LNRMLLPD-TVGTGGDS 498 + L F+ + G ++ R GV HS LN + + D + GGDS Sbjct: 476 SVWDNKAKANTPKLMAFMNDFGVITARDPKGVYHSMTDVIHKVLNDITIDDRAIIIGGDS 535 Query: 499 HTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKMQPGITLRDLVHAIPLYAI 558 HTR G++F A SG VA A ATG + +PESV V FKG+M+ I RD+VH+ + Sbjct: 536 HTRMSKGVAFGADSGTVAIALATGECAMPIPESVKVTFKGQMKDHIDFRDVVHSTQAQML 595 Query: 559 KQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASAERSAAGCTIKLNKEPIVE 618 K +N+F GR++E++ + L +QAF TD +AE A + +V+ Sbjct: 596 --------NKFGENVFQGRVIEVQ-IGTLLADQAFTFTDWTAEMKAKASICISTDDTLVQ 646 Query: 619 YLTSNIVLLKWMIAEGYGDRRTL--------ERRIQGMEKWLADPQLLEADADAEYAAVI 670 L + ++ MI +G + + ++RI G++ + L D A Y A + Sbjct: 647 SLELSKARIQIMINKGMDNATNMLQGLIDLADKRIAGIQS--GEEPALAPDDTATYFAEM 704 Query: 671 DIDLADIKEPILCAP---NDPDDARLLSDV-------QGEKIDEVFIGSCMTNIGHFRAA 720 +DL I EP++ P N+ R DV G K+D F+GSCM + G + Sbjct: 705 VVDLDLIDEPMIADPDVNNEDASKRYTHDVIRQASFYDGRKVDLGFVGSCMVHKGDMQII 764 Query: 721 GKLLDNHKGQLP----TRLWVAPPTRMDAAQLTEEGYYSVFG------------KSGAR- 763 +L N + P + L VAPPT +L EG + V K AR Sbjct: 765 AAMLRNLEKNGPITFNSPLVVAPPTYNIVDELKAEGDWEVLAKYAGFTFDDSHPKEAART 824 Query: 764 -------IEIPGCSLCMGNQARVADGATVVSTSTRNFPNRLGTGA-----NVFLASAELA 811 +E PGC+LCMGNQ + G TV++TSTR F R+ + L S + Sbjct: 825 KYENIMYLERPGCNLCMGNQEKAEAGDTVLATSTRLFQGRVVEDSTEKKGESLLGSTPMV 884 Query: 812 AVAALIGKLPTPEEYQTYVAQVDKTA 837 +A+++G+ PT EY+ V ++ T+ Sbjct: 885 VLASILGRFPTIAEYKAAVEGINLTS 910 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: 1710 Number of extensions: 84 Number of successful extensions: 11 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: 928 Length adjustment: 43 Effective length of query: 822 Effective length of database: 885 Effective search space: 727470 Effective search space used: 727470 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 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