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 BPHYT_RS10160 BPHYT_RS10160 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= SwissProt::Q8ZRS8 (865 letters) >FitnessBrowser__BFirm:BPHYT_RS10160 Length = 861 Score = 1270 bits (3286), Expect = 0.0 Identities = 632/862 (73%), Positives = 724/862 (83%), Gaps = 6/862 (0%) Query: 1 MLEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEA 60 MLE +R H A RA GI P PL A Q A LVELL PP GEE+ LLDL+ NRVP GVDEA Sbjct: 1 MLENFRAHAAARATLGIPPLPLTAQQTAELVELLTNPPAGEEQTLLDLITNRVPAGVDEA 60 Query: 61 AYVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120 A VKAGFLAAVAKG+TT L+S +A ELLGTM GGYNI PLI+ L DA++ +AA+AL Sbjct: 61 ARVKAGFLAAVAKGETTCALISRARATELLGTMLGGYNIQPLIELLSDAEVGTVAAEALK 120 Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFKVTGETNTD 180 TLLMFD F+DV+E A GN AK V+QSWADAEWF SRP + + +T+TVFKVTGETNTD Sbjct: 121 KTLLMFDAFHDVKELADKGNANAKAVLQSWADAEWFTSRPEVPQSLTITVFKVTGETNTD 180 Query: 181 DLSPAPDAWSRPDIPLHAQAMLKNAREGIEPDQPGVVGPIKQIEALQKKGYPLAYVGDVV 240 DLSPAPDA +RPDIP+HA AMLKNAR GI P++ G GPIK I++L++KG+ +AYVGDVV Sbjct: 181 DLSPAPDATTRPDIPMHALAMLKNARPGITPEEDGKRGPIKFIQSLKEKGHLVAYVGDVV 240 Query: 241 GTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300 GTGSSRKSATNSVLWF G+DIP +PNKR GG+CLG KIAPIF+NTMEDAGALPIE+DVS Sbjct: 241 GTGSSRKSATNSVLWFTGEDIPFIPNKRFGGVCLGSKIAPIFYNTMEDAGALPIELDVSQ 300 Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360 + MGDV+++ PY+G+ + G ++A F++K+DVL DEVRAGGRIPLIIGRGLT KAREA Sbjct: 301 MEMGDVVELRPYEGKALKN--GAVIAEFKVKSDVLFDEVRAGGRIPLIIGRGLTAKAREA 358 Query: 361 LGLPHSDVFRQAKDVAESSRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417 LGL S +FR + A+S +GFSLAQKMVGRACG+ +G+RPG YCEPKMTSVGSQDTT Sbjct: 359 LGLAPSTLFRLPQQPADSGKGFSLAQKMVGRACGLPEGQGVRPGTYCEPKMTSVGSQDTT 418 Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDG 477 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPK VDV TH TLPDFI NRGG++LRPGDG Sbjct: 419 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKSVDVKTHRTLPDFISNRGGIALRPGDG 478 Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATG MPLDMPESVLVRFK Sbjct: 479 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGTMPLDMPESVLVRFK 538 Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597 GKMQPG+TLRDLV+AIPLYAIKQG LTV K+GKKNIFSGR+LEIEGLPDLKVEQAFEL+D Sbjct: 539 GKMQPGVTLRDLVNAIPLYAIKQGTLTVAKQGKKNIFSGRVLEIEGLPDLKVEQAFELSD 598 Query: 598 ASAERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADPQL 657 ASAERSAAGCT+ LNKEPI+EYL SN+ LLKWMIA+GY D R+L+RRI+ ME WLADPQL Sbjct: 599 ASAERSAAGCTVHLNKEPIIEYLNSNVTLLKWMIAQGYQDPRSLQRRIKAMEAWLADPQL 658 Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIGHF 717 L DADAEYAAVI+IDLADI EPI+ PNDPDD + LSDV G KIDEVFIGSCMTNIGHF Sbjct: 659 LSPDADAEYAAVIEIDLADIHEPIVACPNDPDDVKTLSDVAGAKIDEVFIGSCMTNIGHF 718 Query: 718 RAAGKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777 RAA KLL+ K +P +LWVAPPT+MD QLTEEG+Y VFG +GAR E+PGCSLCMGNQA Sbjct: 719 RAASKLLEG-KRDIPVKLWVAPPTKMDQKQLTEEGHYGVFGTAGARTEMPGCSLCMGNQA 777 Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837 +V +GATV+STSTRNFPNRLG NV+L SAELAA+ + +GK+PT EEY + + + Sbjct: 778 QVREGATVMSTSTRNFPNRLGKNTNVYLGSAELAAICSRLGKIPTKEEYMADMGVLTASG 837 Query: 838 VDTYRYLNFDQLSQYTEKADGV 859 Y+Y+NFDQ+ + + AD V Sbjct: 838 DKIYQYMNFDQIEDFKDLADTV 859 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: 2048 Number of extensions: 75 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: 861 Length adjustment: 42 Effective length of query: 823 Effective length of database: 819 Effective search space: 674037 Effective search space used: 674037 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 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