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 WP_097031410.1 CRO07_RS14595 aconitate hydratase AcnA
Query= SwissProt::P70920 (906 letters) >NCBI__GCF_900207575.1:WP_097031410.1 Length = 894 Score = 1129 bits (2921), Expect = 0.0 Identities = 575/902 (63%), Positives = 685/902 (75%), Gaps = 18/902 (1%) Query: 5 DSFKCKKTLKVGAKTYVYYSLPTAEKNGLKGISKLPYSMKVLLENLLRNEDGRSVKKADI 64 DS +KTL VG +Y YYS+P AE GL S+LP ++KV+LEN+LR EDG++V DI Sbjct: 8 DSQNTRKTLNVGGASYAYYSIPAAEAAGLGQFSRLPAALKVVLENMLRFEDGKTVSVDDI 67 Query: 65 VAVSKWLRKKSLE-HEIAFRPARVLMQDFTGVPAVVDLAAMRNAMQKLGGDAEKINPLVP 123 A S+W EIA+RPARVLMQDFTGVPAVVDLAAMR+ + LGGDA+KINPL P Sbjct: 68 RAFSEWGANGGKNPREIAYRPARVLMQDFTGVPAVVDLAAMRDGILGLGGDAQKINPLNP 127 Query: 124 VDLVIDHSVIVNFFGDNKAFAKNVTEEYKQNQERYEFLKWGQAAFSNFSVVPPGTGICHQ 183 VDLVIDHSV+++ FG+ +AF NV EY++N ERY FLKWGQ AF+NF VVPPGTGICHQ Sbjct: 128 VDLVIDHSVMIDEFGNPRAFQMNVDREYERNMERYTFLKWGQKAFNNFRVVPPGTGICHQ 187 Query: 184 VNLEYLSQTVWTKKEKMTVGKKTGTFEVAYPDSLVGTDSHTTMVNGLAVLGWGVGGIEAE 243 VNLEYL+QTVWT +++ EVAYPD+LVGTDSHTTMVNGLAVLGWGVGGIEAE Sbjct: 188 VNLEYLAQTVWTDRDQ-------DGLEVAYPDTLVGTDSHTTMVNGLAVLGWGVGGIEAE 240 Query: 244 ACMLGQPLSMLLPNVVGFKLKGAMKEGVTATDLVLTVTQMLRKLGVVGKFVEFFGPGLDH 303 A MLGQP+SML+P VVGFKL G M EG TATDLVL V QMLRK GVVGKFVEF+G GLDH Sbjct: 241 AAMLGQPVSMLIPEVVGFKLTGQMVEGTTATDLVLKVVQMLRKKGVVGKFVEFYGEGLDH 300 Query: 304 LSVADKATIANMAPEYGATCGFFPVDAAAIDYLKTSGRAAPRVALVQAYAKAQGLFRTAK 363 L +AD+ATIANMAPEYGATCGFFP+DA + YL+ +GR R+ALV+AYAKA G++R Sbjct: 301 LPLADRATIANMAPEYGATCGFFPIDAETLRYLRQTGRDEARIALVEAYAKANGMWRDEG 360 Query: 364 SADPVFTETLTLDLADVVPSMAGPKRPEGRIALPSVAEGFSVALANEYKKTEEPAKRFAV 423 A P++T+TL LD++++VP+++GPKRP+ + L F+ + +K+ + K V Sbjct: 361 YA-PIYTDTLHLDMSEIVPAISGPKRPQDYLPLTEAKASFAKEMEATFKRPQ--GKEVPV 417 Query: 424 EGKKYEIGHGDVVIAAITSCTNTSNPSVLIGAGLLARNAAAKGLKAKPWVKTSLAPGSQV 483 +G+ Y + G VVIA+ITSCTNTSNP VLIGAGL+AR A A GL KPWVKTSLAPGSQV Sbjct: 418 KGEDYTMSSGKVVIASITSCTNTSNPYVLIGAGLVARKARALGLNRKPWVKTSLAPGSQV 477 Query: 484 VAAYLADSGLQAHLDKVGFNLVGFGCTTCIGNSGPLPEEISKSINDNGIVAAAVLSGNRN 543 V+ YL +GLQ LD +GFNLVG+GCTTCIGNSGPL EIS +I + +VA AVLSGNRN Sbjct: 478 VSEYLEAAGLQEDLDAIGFNLVGYGCTTCIGNSGPLQPEISAAIAEGDLVATAVLSGNRN 537 Query: 544 FEGRVSPDVQANYLASPPLVVAHALAGSVTKNLAVEPLGEGKDGKPVYLKDIWPTSKEIN 603 FEGR+SPDV+ANYLASPPLVVA+ALAG + +L EP+G G +G PVYLKDIWPT+ EI Sbjct: 538 FEGRISPDVRANYLASPPLVVAYALAGDMNIDLTSEPIGMGTNG-PVYLKDIWPTNAEIA 596 Query: 604 AFMKKFVTASIFKKKYADVFKGDTNWRKIKTVESETYRWNMSSTYVQNPPYFEGMKKEPE 663 + + VT F KKYADVFKGD W+ ++T +SETY W SSTY+QNPPYF M K+P Sbjct: 597 ELVDRCVTREAFLKKYADVFKGDAKWQAVETTDSETYDWPPSSTYIQNPPYFRNMSKKPG 656 Query: 664 PVTDIVEARILAMFGDKITTDHISPAGSIKLTSPAGKYLSEHQVRPADFNQYGTRRGNHE 723 +T+I AR+LA+ GD ITTDHISPAGS K T+PAGKYL + V P +FN YG RRGNHE Sbjct: 657 VITNITGARVLALLGDMITTDHISPAGSFKDTTPAGKYLVDRGVAPREFNSYGARRGNHE 716 Query: 724 VMMRGTFANIRIKNFMLKGADGNIPEGGLTKHWPDGEQMSIYDAAMKYQQEQVPLVVFAG 783 VMMRGTFANIRIKN ML G +G G PDG Q SIYDA+M YQ PLV+F G Sbjct: 717 VMMRGTFANIRIKNEMLDGVEGGYTLG------PDGVQTSIYDASMAYQAAGTPLVIFGG 770 Query: 784 AEYGNGSSRDWAAKGTRLLGVRAVICQSFERIHRSNLVGMGVLPLTFEEGTSWSSLGLKG 843 EYG GSSRDWAAKGT LLGV+AVI +SFERIHRSNLVGMGV+P F EG + SLGLKG Sbjct: 771 IEYGAGSSRDWAAKGTALLGVKAVIAESFERIHRSNLVGMGVIPFEFTEGQTRKSLGLKG 830 Query: 844 DEKVTLRGLVGDLKPRQKLTAEIVSGDGSLQRVSLLCRIDTLDELDYYRNGGILHYVLRK 903 DE VT+ GL GDLKP + I GDG+++ + L CRIDT E++Y +GG+LHYVLR Sbjct: 831 DEVVTIEGLDGDLKPLSLVPCTITYGDGTVKAIQLKCRIDTEIEIEYVEHGGVLHYVLRD 890 Query: 904 LA 905 LA Sbjct: 891 LA 892 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: 2146 Number of extensions: 93 Number of successful extensions: 7 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: 894 Length adjustment: 43 Effective length of query: 863 Effective length of database: 851 Effective search space: 734413 Effective search space used: 734413 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 24 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