Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate N515DRAFT_1420 N515DRAFT_1420 aconitase
Query= BRENDA::P36683 (865 letters) >FitnessBrowser__Dyella79:N515DRAFT_1420 Length = 863 Score = 1260 bits (3261), Expect = 0.0 Identities = 627/864 (72%), Positives = 734/864 (84%), Gaps = 8/864 (0%) Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60 ML YR+HVAERAA GI PL A Q A L+ELLKNPPAGEE FL+DL++NRVP GVD+A Sbjct: 1 MLNAYRQHVAERAALGIPALPLTAQQTADLIELLKNPPAGEEAFLVDLISNRVPAGVDDA 60 Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120 A VKA +LAA+A G+ PLL+ KA ELLGTM GGYNIHPLI+ LDDA++ IAA AL Sbjct: 61 AKVKASYLAAVAFGKEPCPLLSRAKATELLGTMLGGYNIHPLIELLDDAQVGGIAADALK 120 Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180 TLLMFD+F+DV+EKA GN AK V+QSWADAEWF +RP + LT+TVFKV GETNTD Sbjct: 121 KTLLMFDSFHDVKEKADKGNANAKAVLQSWADAEWFTSRPEVPASLTITVFKVPGETNTD 180 Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREG--IEPDQPGVVGPIKQIEALQQKGFPLAYVGD 238 DLSPAPDA +RPDIPLHALAMLKN REG +P++ G GPI+QI+ L ++G +AYVGD Sbjct: 181 DLSPAPDATTRPDIPLHALAMLKNKREGAPFQPEEDGKRGPIQQIQDLARQGHLVAYVGD 240 Query: 239 VVGTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDV 298 VVGTGSSRKSATNSVLW+ G+DIP +PNKR GG+CLG KIAPIF+NTMEDAGALPIE+DV Sbjct: 241 VVGTGSSRKSATNSVLWWTGEDIPFIPNKRFGGVCLGSKIAPIFYNTMEDAGALPIELDV 300 Query: 299 SNLNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAR 358 S ++MGDV+++ PY+G+ + GE++A F++K+DVL DEVRAGGRIPLIIGRGLT KAR Sbjct: 301 SQMDMGDVVELRPYEGKALKN--GEVIAEFQVKSDVLFDEVRAGGRIPLIIGRGLTAKAR 358 Query: 359 EALGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQD 415 EALGL S +FR ++ A++ +G++LAQKMVGRACG+ +G+RPG YCEPKMTSVGSQD Sbjct: 359 EALGLAPSTLFRLPQNPADTGKGYTLAQKMVGRACGLAEGEGVRPGTYCEPKMTSVGSQD 418 Query: 416 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPG 475 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDV THH LP FI RGG+SLRPG Sbjct: 419 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVKTHHELPAFISTRGGISLRPG 478 Query: 476 DGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR 535 DGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR Sbjct: 479 DGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR 538 Query: 536 FKGKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFEL 595 FKG++QPG+TLRDLV+AIPLYAIKQGLLTV K+GK+NIFSGRILEIEGLP+LKVEQAFEL Sbjct: 539 FKGELQPGVTLRDLVNAIPLYAIKQGLLTVAKQGKQNIFSGRILEIEGLPNLKVEQAFEL 598 Query: 596 TDASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANP 655 +DASAERSAAGCT++L++ PIIEYLNSNI LLK+MIA+GY D R+L RRI+ ME+WLANP Sbjct: 599 SDASAERSAAGCTVRLDQAPIIEYLNSNITLLKYMIAQGYQDARSLSRRIKKMEEWLANP 658 Query: 656 ELLEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIG 715 +LLE DADAEYAAVI+IDLAD+ EPI+ PNDPDD + LS V G KIDEVFIGSCMTNIG Sbjct: 659 QLLEPDADAEYAAVIEIDLADVHEPIVACPNDPDDVKSLSDVAGAKIDEVFIGSCMTNIG 718 Query: 716 HFRAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGN 775 HFRAA KLL+ K +PTRLWVAPPT+MD QLTEEG+Y V G +GAR+E+PGCSLCMGN Sbjct: 719 HFRAASKLLEG-KRDIPTRLWVAPPTKMDQQQLTEEGHYGVLGTAGARMEMPGCSLCMGN 777 Query: 776 QARVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDK 835 QA+V +GATV+STSTRNFPNRLG NV+L SAELAA+ + +G++PT EEY + ++ Sbjct: 778 QAQVREGATVMSTSTRNFPNRLGKNTNVYLGSAELAAICSRLGRIPTKEEYMADIGVINA 837 Query: 836 TAVDTYRYLNFNQLSQYTEKADGV 859 YRY+NF+Q++ + + AD V Sbjct: 838 NGEKIYRYMNFDQIADFKQVADTV 861 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: 2066 Number of extensions: 79 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 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