Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate Dsui_2205 Dsui_2205 aconitate hydratase 2
Query= BRENDA::P36683 (865 letters) >FitnessBrowser__PS:Dsui_2205 Length = 865 Score = 1245 bits (3222), Expect = 0.0 Identities = 626/864 (72%), Positives = 716/864 (82%), Gaps = 6/864 (0%) Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60 MLE YR+HVAERAA GI P PL A Q LV LL+NPP GEE+ L++L+T RVP GVD+A Sbjct: 1 MLEAYRQHVAERAALGIPPLPLSAAQTKDLVALLQNPPKGEEQALVELITYRVPAGVDDA 60 Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120 A VKA FLA +AKGE L++ KA ELLGTM GGYN+ P+ID L DA++ +AA+ L Sbjct: 61 AKVKAEFLAKVAKGELSCALISRAKATELLGTMLGGYNVKPMIDLLGDAEVGAVAAEGLK 120 Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180 TLL+FD F+DV E AK GN AK VMQSWADAEWF +RP + +TVFKVTGETNTD Sbjct: 121 KTLLVFDFFHDVAELAKGGNANAKAVMQSWADAEWFTSRPEVPASQKLTVFKVTGETNTD 180 Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240 DLSPAPDAWSRPDIPLHALAMLKN R GIE D+ G GP+KQ+EAL +KG +AYVGDVV Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKNPRPGIEADKAGERGPVKQLEALAKKGNLIAYVGDVV 240 Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300 GTGSSRKSATNSVLWF G+DIP VPNKR GG+CLG KIAPIFFNTMEDAGALPIE+DV Sbjct: 241 GTGSSRKSATNSVLWFTGEDIPFVPNKRFGGVCLGSKIAPIFFNTMEDAGALPIELDVGQ 300 Query: 301 LNMGDVID--VYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAR 358 ++MGD I+ + +V + G ++A +LKT V++DEVRAGGRIPLIIGRGLTTKAR Sbjct: 301 MDMGDEIELKIDQATAKVTALKNGAVIAESQLKTPVILDEVRAGGRIPLIIGRGLTTKAR 360 Query: 359 EALGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQD 415 EALGL S +FR + + +G+SLAQKMVGRACG+ KGI PG YCEPKMT+VGSQD Sbjct: 361 EALGLAPSTLFRLPQQPNDPGKGYSLAQKMVGRACGLPEGKGILPGTYCEPKMTTVGSQD 420 Query: 416 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPG 475 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPK VDV H LP FI RGGV+LRPG Sbjct: 421 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKLVDVRMHRELPSFISTRGGVALRPG 480 Query: 476 DGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR 535 DGVIHSWLNR+LLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR Sbjct: 481 DGVIHSWLNRLLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR 540 Query: 536 FKGKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFEL 595 FKGKMQPGITLRDLV+AIPLYAIKQGLLTVEKKGKKN+FSGRILEIEGLPDLKVEQAFEL Sbjct: 541 FKGKMQPGITLRDLVNAIPLYAIKQGLLTVEKKGKKNVFSGRILEIEGLPDLKVEQAFEL 600 Query: 596 TDASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANP 655 +DA+AERSAA C I LNKEPI+EYL SNI L+KWMIAEGY D RTL+RRI+ ME+W+AN Sbjct: 601 SDAAAERSAAACAIALNKEPIVEYLRSNITLMKWMIAEGYQDARTLKRRIKAMEEWIANG 660 Query: 656 ELLEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIG 715 LL+AD DA+YAAVI+IDLAD+KEPI+ PNDPDD + LS V G+KIDEVFIGSCMTNIG Sbjct: 661 TLLKADTDAQYAAVIEIDLADVKEPIVACPNDPDDVKVLSEVAGDKIDEVFIGSCMTNIG 720 Query: 716 HFRAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGN 775 HFRAAGK+LD K +PTRLW+APPT+MDA LTEEGYYSV GK+GAR+E+PGCSLCMGN Sbjct: 721 HFRAAGKVLDG-KSDIPTRLWIAPPTKMDALILTEEGYYSVLGKAGARMEMPGCSLCMGN 779 Query: 776 QARVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDK 835 QA++ G+T +STSTRNFPNRLG V+L SAELAA+ +L+GK+PT EY Y+ V+ Sbjct: 780 QAQIRKGSTAMSTSTRNFPNRLGIDTRVYLGSAELAAMCSLLGKIPTVAEYMEYIQVVNA 839 Query: 836 TAVDTYRYLNFNQLSQYTEKADGV 859 A D YRY+NF+Q+ ++ E A+ V Sbjct: 840 KAADIYRYMNFDQIPEFVEVAETV 863 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: 2064 Number of extensions: 83 Number of successful extensions: 4 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: 865 Length adjustment: 42 Effective length of query: 823 Effective length of database: 823 Effective search space: 677329 Effective search space used: 677329 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