Align 2-methylisocitrate dehydratase (EC 4.2.1.99) (characterized)
to candidate BPHYT_RS33980 BPHYT_RS33980 aconitate hydratase
Query= reanno::acidovorax_3H11:Ac3H11_1140 (980 letters) >FitnessBrowser__BFirm:BPHYT_RS33980 Length = 905 Score = 1313 bits (3399), Expect = 0.0 Identities = 682/970 (70%), Positives = 768/970 (79%), Gaps = 74/970 (7%) Query: 14 HAFANTLKSFRTASGKDGQFYSLPALAKQFP-EIKRLPVSIRIVLESVLRNCDGRKVTPE 72 H TLK F + SGK G+FYSLP L K +I RLPVSIRIVLESVLRN DG+K+ E Sbjct: 3 HNLHKTLKEFDSGSGK-GKFYSLPQLGKALNIKIDRLPVSIRIVLESVLRNYDGKKIAEE 61 Query: 73 HVEQLARWAPNAERKDEIPFVVSRVVLQDFTGVPLLADLAAMRSVAAKLGKNPKKIEPLV 132 H+EQLA W P A R DEIPFVVSRVVLQDFTGVPLLAD+AAMR VA +GK+PK IEPLV Sbjct: 62 HIEQLANWKPTAARVDEIPFVVSRVVLQDFTGVPLLADIAAMRGVAKHMGKDPKSIEPLV 121 Query: 133 PVDLVVDHSIMIDHYGKKNSLDLNMKLEFQRNRERYEFMKWGMQAFDTFGVVPPGFGIVH 192 PVDLVVDHS+ IDH+ +KN+LDLNMKLEFQRN ERY+FMKWGMQAFDTF VVPPG GIVH Sbjct: 122 PVDLVVDHSVQIDHFREKNALDLNMKLEFQRNNERYQFMKWGMQAFDTFKVVPPGVGIVH 181 Query: 193 QVNLEYLARGVHKRKDG---VFYPDTLVGTDSHTTMINGIGVVGWGVGGIEAEAAMLGQP 249 QVNLEYLARGVHK+ +G V+YPD+LVGTDSHTTMINGIGVVGWGVGGIEAEA MLGQP Sbjct: 182 QVNLEYLARGVHKKAEGADTVYYPDSLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQP 241 Query: 250 VYFLTPDVVGFEMTGRLREGVTATDLVLTVTELLRKHKVVGKFVEFFGEGTRTLALPDRA 309 VYFLTPDVVG E+ G+LREG+TATDLVLTVTELLRK KVVGKFVEFFGEGT++L+LPDRA Sbjct: 242 VYFLTPDVVGVELKGKLREGLTATDLVLTVTELLRKEKVVGKFVEFFGEGTKSLSLPDRA 301 Query: 310 TIGNMAPEYGATMGFFPVDEKTIDYFQGTGRTKAEIEAFEAYFKAQGLFGVPLAGEVDYS 369 TIGNMAPEYGATMGFFPVDEKTI+YF+GTGRT AEI AFE YFKAQGLFG+P AG++DY+ Sbjct: 302 TIGNMAPEYGATMGFFPVDEKTIEYFKGTGRTDAEISAFENYFKAQGLFGIPKAGQIDYT 361 Query: 370 QVVTLDLGSVTPSLAGPKRPQDRIELGQVSRQFADLFSQPAAHNGFNRPAELLHTRFHIH 429 +VVTLDLG+VTPSLAGPKRPQDRIE+G V F+DLFS+P A NGF + A Sbjct: 362 KVVTLDLGTVTPSLAGPKRPQDRIEIGHVKSTFSDLFSKPVAENGFAKKA---------- 411 Query: 430 RAAEVVADVTPDGKPTPAGAPRSVVEMEANKPALATAHAEARSATLPARGADPTVGNGDV 489 A EA+ T + G D V NGD+ Sbjct: 412 ------------------------------------ADLEAQYTT--SNGVD--VKNGDI 431 Query: 490 LIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLKVQPHIKTSLAPGSRIVTEYLSETGLLP 549 LIAAITSCTNTSNPSVLLAAGLLAKKAVEAGL V PHIKTSLAPGSRIVTEYL++T L+ Sbjct: 432 LIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLTVAPHIKTSLAPGSRIVTEYLTKTDLMK 491 Query: 550 YLEKLGFSIAGYGCTTCIGNAGDLTPELNEAITQNDLVCAAVLSGNRNFEARIHPNLKAN 609 YL+KLGF++A YGCTTCIGNAGDLTPELNEAIT+ND+V AAVLSGNRNFEARIHPN++AN Sbjct: 492 YLDKLGFTLAAYGCTTCIGNAGDLTPELNEAITKNDIVAAAVLSGNRNFEARIHPNIRAN 551 Query: 610 FLASPPLVVAYAIAGTVLKDLMTEPVGQGKGGKDIYLGDIWPSSDEVHALLKFAMKGKAF 669 FLASPPLVVAYAIAG + +DLMTEPVG+GKGGKDIYLGDIWP+S+EV+ LLKFA+ AF Sbjct: 552 FLASPPLVVAYAIAGNITRDLMTEPVGKGKGGKDIYLGDIWPTSEEVNELLKFALDADAF 611 Query: 670 RDNYAKVATDPGKLWEKIQGVSGTAYTWPASTYIAEPPFFAQFALEKGANKASGTRGEGQ 729 R NY+ + T G LW KI+G G Y WP STYIAEPPFF G Q Sbjct: 612 RKNYSAL-TKKGDLWSKIEGEEGQVYDWPKSTYIAEPPFF-------------GKDFSMQ 657 Query: 730 KDAQLPSVMGARIMALFGDSITTDHISPAGSIKESSPAGQWLLQHGVQKADFNSYGARRG 789 + +V AR + +FGDS+TTDHISPAGSIKE SPAG+WL ++GVQKADFNSYG+RRG Sbjct: 658 PADSIAAVKDARALGIFGDSVTTDHISPAGSIKEDSPAGKWLKENGVQKADFNSYGSRRG 717 Query: 790 NHDVMVRGTFANVRIKNLMIPPTADGSREEGGVTVFQNEGALQGEKMFIFDAAMQYMAQG 849 NHDVM+RGTFANVRIKNLMIP ADG+R EGG+T+ Q GE++ I+DAAM+Y+ G Sbjct: 718 NHDVMMRGTFANVRIKNLMIPAKADGTRVEGGLTIHQP----SGEQLSIYDAAMKYIDAG 773 Query: 850 TPTVVFAGEEYGTGSSRDWAAKGTQLLGIKAVVARSFERIHRSNLVGMGVLPLQFKAGDS 909 TPTVVFAGEEYGTGSSRDWAAKGTQLLG+K VVARSFERIHRSNLVGMGVLPLQFK DS Sbjct: 774 TPTVVFAGEEYGTGSSRDWAAKGTQLLGVKVVVARSFERIHRSNLVGMGVLPLQFKGSDS 833 Query: 910 WETLGLTGNEVIDVLPDPA-LTPQSDARLVIRRADGTVREVVVTLRIDTPIEVDYYRAGG 968 ++LG+TG E D+ A PQ + LVIR +G + V V LRIDTPIEVDYY+ GG Sbjct: 834 VQSLGITGEETYDIEGLGADFKPQQEVTLVIRDKEGKEKRVQVLLRIDTPIEVDYYKHGG 893 Query: 969 ILPFVLRQLL 978 ILPFVLR LL Sbjct: 894 ILPFVLRSLL 903 Lambda K H 0.318 0.136 0.399 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: 2504 Number of extensions: 100 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 980 Length of database: 905 Length adjustment: 44 Effective length of query: 936 Effective length of database: 861 Effective search space: 805896 Effective search space used: 805896 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: 57 (26.6 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