Align Aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_046009357.1 OLEAN_RS11565 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= reanno::Dino:3608667 (930 letters) >NCBI__GCF_000967895.1:WP_046009357.1 Length = 928 Score = 1356 bits (3509), Expect = 0.0 Identities = 698/933 (74%), Positives = 785/933 (84%), Gaps = 10/933 (1%) Query: 1 MSLYTAYLEEIAARKEQ-GLQPKPIDDAALTSEIIAQIKDPAHEHRADSLQFFIYNTLPG 59 MSLYT YLEEI RK GL PKPID A L SEIIAQIKD + R SL FFIYNT+PG Sbjct: 1 MSLYTEYLEEIEVRKNDLGLNPKPIDTADLLSEIIAQIKDTGNAAREASLDFFIYNTIPG 60 Query: 60 TTSAAGAKAQFLKEIILGESVVAEITPDFAFELLSHMRGGPSVEVLLDIALGDDASLAAQ 119 TTSAA KA FLK+I LG VAEITP+FA E LSHM+GGPSVE LLDIAL DDA A Sbjct: 61 TTSAAVVKAAFLKDIALGTETVAEITPEFALEQLSHMKGGPSVEALLDIALSDDAQAKA- 119 Query: 120 AAEVLKTQVFLYEADTDRLKAAHEAGNAVATGILQSYARAEFFTTLPEIEDEIEVVTYIA 179 A EVLK+QVFLYEADT R+ A +AGNA+A +L+SYA AEFFT LPEI +I+VVTYIA Sbjct: 120 AGEVLKSQVFLYEADTSRIADAFKAGNAIAKDLLESYAAAEFFTKLPEIPAKIDVVTYIA 179 Query: 180 AEGDISTDLLSPGNQAHSRSDRELHGKCMISEAAQKEIEALKLQHPGKRVMLIAEKGTMG 239 AEGDISTDLLSPGNQ+HSR+DRELHG+CMI+ AQ+EI AL +HP +VMLIAEKGTMG Sbjct: 180 AEGDISTDLLSPGNQSHSRADRELHGQCMITPEAQQEIVALGKKHPNAKVMLIAEKGTMG 239 Query: 240 VGSSRMSGVNNVALWTGKQASPYVPFVNIAPVVAGTNGISPIFMTTVGVTGGIGIDLKNW 299 VGSSRMSGVNNVALW G++ SPY+PF+N APVVAGTNGI+PIF+TTVGVTGGIG+DLKNW Sbjct: 240 VGSSRMSGVNNVALWAGEKTSPYIPFINNAPVVAGTNGIAPIFLTTVGVTGGIGLDLKNW 299 Query: 300 VKKVDGDGNPILNNDGNPILEQKYSVDTGTVLKIDTKARKLMSADGGEELADVSSAFSPQ 359 VKKVD +GN + + +G+ +LE+ YSV TGTVL IDT A+KL + D +EL DVS AFSPQ Sbjct: 300 VKKVDAEGNTVKDANGDNVLEEAYSVATGTVLTIDTAAKKLYNGD--KELVDVSDAFSPQ 357 Query: 360 AVEFMKAGGSYAVVFGKKLQTLAAETLGVEPTPVFAPAKEISHEGQGLTAVEKIFNANAR 419 VEFMKAGGSYA+ FGKKLQT AAETLG++ VFAP+KEIS EGQGLTAVEKIFN NA Sbjct: 358 KVEFMKAGGSYALTFGKKLQTFAAETLGIQAPTVFAPSKEISVEGQGLTAVEKIFNRNAV 417 Query: 420 GVTPGKVLHAGSDVRVQVNIVGSQDTTGLMTSQELEAMAATVLSPTVDGAYQSGCHTASV 479 GV LH GSDVRV+VNIVGSQDTTG MT QELE+MAA+ +SP+VDGA+QSGCHTASV Sbjct: 418 GVASSTPLHTGSDVRVKVNIVGSQDTTGPMTCQELESMAASTISPSVDGAFQSGCHTASV 477 Query: 480 WDLKAQANTPRLMAFMHKFGLITARDPKGVYHSMTDVIHKVLNDITVSDWDIIIGGDSHT 539 WD KA+ANTP+LMAFM+ FG+ITARDPKGVYHSMTDVIHKVLNDIT+ D IIIGGDSHT Sbjct: 478 WDNKAKANTPKLMAFMNDFGVITARDPKGVYHSMTDVIHKVLNDITIDDRAIIIGGDSHT 537 Query: 540 RMSKGVAFGADSGTVALALATGEATMPIPESVKVTFKGKMADHMDFRDVVHATQAQMLAQ 599 RMSKGVAFGADSGTVA+ALATGE MPIPESVKVTFKG+M DH+DFRDVVH+TQAQML + Sbjct: 538 RMSKGVAFGADSGTVAIALATGECAMPIPESVKVTFKGQMKDHIDFRDVVHSTQAQMLNK 597 Query: 600 HGDNVFQGRVIEVHIGTLLADQAFTFTDWTAEMKAKASICISNDDTLIESLEIAKQRIQV 659 G+NVFQGRVIEV IGTLLADQAFTFTDWTAEMKAKASICIS DDTL++SLE++K RIQ+ Sbjct: 598 FGENVFQGRVIEVQIGTLLADQAFTFTDWTAEMKAKASICISTDDTLVQSLELSKARIQI 657 Query: 660 MIDKGMDNDVQMLAGLIAKANARIAEIRSGEKPALKPDDTARYFAEVVVDLDQIVEPMIA 719 MI+KGMDN ML GLI A+ RIA I+SGE+PAL PDDTA YFAE+VVDLD I EPMIA Sbjct: 658 MINKGMDNATNMLQGLIDLADKRIAGIQSGEEPALAPDDTATYFAEMVVDLDLIDEPMIA 717 Query: 720 DPDVHNADVSKRYTHDTIRPISYYGAEKKIDLGFVGSCMVHKGDVKIVAQMLRNLEKANG 779 DPDV+N D SKRYTHD IR S+Y +K+DLGFVGSCMVHKGD++I+A MLRNLEK NG Sbjct: 718 DPDVNNEDASKRYTHDVIRQASFYDG-RKVDLGFVGSCMVHKGDMQIIAAMLRNLEK-NG 775 Query: 780 EVKFKAPLVLAAPTYNIIDELKEEGDWDVLQKYAGFEFDDSAPKEKARTEYENILYLERP 839 + F +PLV+A PTYNI+DELK EGDW+VL KYAGF FDDS PKE ART+YENI+YLERP Sbjct: 776 PITFNSPLVVAPPTYNIVDELKAEGDWEVLAKYAGFTFDDSHPKEAARTKYENIMYLERP 835 Query: 840 GCNLCMGNQEKAAKGDTVLATSTRLFQGRVVADSETKKGESLLGSTPVVVLSAILGRTPT 899 GCNLCMGNQEKA GDTVLATSTRLFQGRVV DS KKGESLLGSTP+VVL++ILGR PT Sbjct: 836 GCNLCMGNQEKAEAGDTVLATSTRLFQGRVVEDSTEKKGESLLGSTPMVVLASILGRFPT 895 Query: 900 VEEYKTAVEGINLTKFAPP----LTPPIDAKSV 928 + EYK AVEGINLT FAPP P I K+V Sbjct: 896 IAEYKAAVEGINLTSFAPPSEDLARPAIPLKAV 928 Lambda K H 0.316 0.132 0.374 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: 2249 Number of extensions: 74 Number of successful extensions: 6 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: 930 Length of database: 928 Length adjustment: 43 Effective length of query: 887 Effective length of database: 885 Effective search space: 784995 Effective search space used: 784995 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 (21.6 bits) S2: 57 (26.6 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