Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate GFF1856 PGA1_c18830 aconitate hydratase AcnA
Query= SwissProt::P70920 (906 letters) >FitnessBrowser__Phaeo:GFF1856 Length = 895 Score = 1095 bits (2831), Expect = 0.0 Identities = 549/903 (60%), Positives = 690/903 (76%), Gaps = 19/903 (2%) Query: 5 DSFKCKKTLKVGAKTYVYYSLPTAEKNGLKGISKLPYSMKVLLENLLRNEDGR-SVKKAD 63 D+ K ++ L G K+ YYS+P A + GL +KLP ++KV+LEN+LR EDG SV D Sbjct: 8 DNAKTRRKLSAGGKSISYYSIPAATEAGLGDFAKLPAALKVVLENMLRFEDGGFSVSTDD 67 Query: 64 IVAVSKWLRKKSLE-HEIAFRPARVLMQDFTGVPAVVDLAAMRNAMQKLGGDAEKINPLV 122 I A ++W EIA+RPARVLMQDFTGVPAVVDLAAMR+ ++ LGGDA+KINPL Sbjct: 68 IKAFAEWGANGGKNPREIAYRPARVLMQDFTGVPAVVDLAAMRDGIKALGGDAQKINPLN 127 Query: 123 PVDLVIDHSVIVNFFGDNKAFAKNVTEEYKQNQERYEFLKWGQAAFSNFSVVPPGTGICH 182 PVDLVIDHSV+++ FG+ +AF NV EY++N ERY+FLKWGQ AF+NF VVPPGTGICH Sbjct: 128 PVDLVIDHSVMIDEFGNPRAFQMNVDREYERNMERYQFLKWGQGAFNNFRVVPPGTGICH 187 Query: 183 QVNLEYLSQTVWTKKEKMTVGKKTGTFEVAYPDSLVGTDSHTTMVNGLAVLGWGVGGIEA 242 QVNLEYL+QT+W+ +++ G VAYPD+LVGTDSHTTMVNG AVLGWGVGGIEA Sbjct: 188 QVNLEYLAQTIWSDEDQ------NGDM-VAYPDTLVGTDSHTTMVNGAAVLGWGVGGIEA 240 Query: 243 EACMLGQPLSMLLPNVVGFKLKGAMKEGVTATDLVLTVTQMLRKLGVVGKFVEFFGPGLD 302 EA MLGQP+SML+P V+GF+L GAM EG T TDLVL V +MLR GVVGKFVEF+G GLD Sbjct: 241 EAAMLGQPISMLIPEVIGFELTGAMVEGTTGTDLVLKVVEMLRAKGVVGKFVEFYGKGLD 300 Query: 303 HLSVADKATIANMAPEYGATCGFFPVDAAAIDYLKTSGRAAPRVALVQAYAKAQGLFRTA 362 L +AD+ATIANMAPEYGATCGFFP+D I YL+ +GR R+ALV+AYAK G +R A Sbjct: 301 TLPLADRATIANMAPEYGATCGFFPIDDETIRYLRNTGRDEDRIALVEAYAKENGFWRDA 360 Query: 363 KSADPVFTETLTLDLADVVPSMAGPKRPEGRIALPSVAEGFSVALANEYKKTEEPAKRFA 422 A P++T+TL+LD+ +VP+++GPKRP+ +AL F + +K+ K A Sbjct: 361 DYA-PIYTDTLSLDMGTIVPAISGPKRPQDYVALTGAKAAFQKEMEETFKRPM--GKEIA 417 Query: 423 VEGKKYEIGHGDVVIAAITSCTNTSNPSVLIGAGLLARNAAAKGLKAKPWVKTSLAPGSQ 482 V+G+ Y + G VVIA+ITSCTNTSNP V+IGAGL+AR AAA GL KPWVKTSLAPGSQ Sbjct: 418 VKGEDYTMESGKVVIASITSCTNTSNPYVMIGAGLVARKAAALGLDRKPWVKTSLAPGSQ 477 Query: 483 VVAAYLADSGLQAHLDKVGFNLVGFGCTTCIGNSGPLPEEISKSINDNGIVAAAVLSGNR 542 VV+AYL + LQ LDK+GFNLVG+GCTTCIGNSGP+ +E+S +I + +VA +VLSGNR Sbjct: 478 VVSAYLEAANLQEDLDKIGFNLVGYGCTTCIGNSGPIQQELSDAIAEGDLVATSVLSGNR 537 Query: 543 NFEGRVSPDVQANYLASPPLVVAHALAGSVTKNLAVEPLGEGKDGKPVYLKDIWPTSKEI 602 NFEGR+SPDV+ANYLASPPLVVA+ALAG++ +LA +P+ + KDG VYLKDIWP+ KEI Sbjct: 538 NFEGRISPDVRANYLASPPLVVAYALAGTMDIDLATDPIAQDKDGNDVYLKDIWPSQKEI 597 Query: 603 NAFMKKFVTASIFKKKYADVFKGDTNWRKIKTVESETYRWNMSSTYVQNPPYFEGMKKEP 662 ++ VT F KYADVFKGD W+ ++T ++ETY W +STY+QNPPYF+GM EP Sbjct: 598 ADLVEATVTREAFLSKYADVFKGDEKWQAVETTDAETYDWPAASTYIQNPPYFQGMGTEP 657 Query: 663 EPVTDIVEARILAMFGDKITTDHISPAGSIKLTSPAGKYLSEHQVRPADFNQYGTRRGNH 722 +++I +A+ L + GD +TTDHISPAGS T+PAG+YL + QV+P +FN YG+RRGNH Sbjct: 658 GTISNIKDAKPLLILGDMVTTDHISPAGSFATTTPAGQYLLDRQVQPREFNSYGSRRGNH 717 Query: 723 EVMMRGTFANIRIKNFMLKGADGNIPEGGLTKHWPDGEQMSIYDAAMKYQQEQVPLVVFA 782 E+MMRGTFANIRIKN ML G EGG TK PDGEQ S+Y+A+M YQ++ +PLVVF Sbjct: 718 EIMMRGTFANIRIKNEMLDGV-----EGGYTK-GPDGEQTSVYEASMAYQEQGIPLVVFG 771 Query: 783 GAEYGNGSSRDWAAKGTRLLGVRAVICQSFERIHRSNLVGMGVLPLTFEEGTSWSSLGLK 842 G +YG GSSRDWAAKGT LLGV+AVI +SFERIHRSNLVGMGV+P F G + SL L Sbjct: 772 GEQYGAGSSRDWAAKGTALLGVKAVIAESFERIHRSNLVGMGVIPFEFTGGDTRKSLNLT 831 Query: 843 GDEKVTLRGLVGDLKPRQKLTAEIVSGDGSLQRVSLLCRIDTLDELDYYRNGGILHYVLR 902 GDE V++ GL +KP+++++ +I GDG+ + ++L CRIDT E++Y +GG+LHYVLR Sbjct: 832 GDETVSIHGL-DTIKPQEEVSCDITYGDGTTKTITLKCRIDTAPEIEYIEHGGVLHYVLR 890 Query: 903 KLA 905 LA Sbjct: 891 NLA 893 Lambda K H 0.317 0.134 0.393 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: 2161 Number of extensions: 112 Number of successful extensions: 8 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: 906 Length of database: 895 Length adjustment: 43 Effective length of query: 863 Effective length of database: 852 Effective search space: 735276 Effective search space used: 735276 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: 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