Align methanogen homoaconitase (EC 4.2.1.114) (characterized)
to candidate Echvi_2531 Echvi_2531 aconitate hydratase, mitochondrial
Query= BRENDA::Q58409 (420 letters) >FitnessBrowser__Cola:Echvi_2531 Length = 757 Score = 172 bits (435), Expect = 4e-47 Identities = 118/352 (33%), Positives = 173/352 (49%), Gaps = 24/352 (6%) Query: 84 RFGIKNFHKGGEGICHQILAENYVLPNMFVAGGDSHTCTHGAFGAFATGFGATDMAYIYA 143 ++GI F K G GI HQ++ ENY P + G DSHT G G A G G D + A Sbjct: 128 KYGI-GFWKPGAGIIHQVVLENYAFPGGMMIGTDSHTVNAGGLGMVAIGVGGADAVDVMA 186 Query: 144 TGETW-IKVPKTIRVDIVGK-NENVSAKDIVLRVCKEIGRRGATYMAIEYGGEVVKNMDM 201 G W +K PK I V + GK N SAKD++L+V + +G T +EY GE K++ Sbjct: 187 -GMPWELKFPKLIGVKLTGKMNGWTSAKDVILKVAGILTVKGGTGCIVEYFGEGAKSLSA 245 Query: 202 DGRLTLCNMAIEMGGKTGVIEADEITYDYLKKERGLSDEDIAKLKKERIT----VNRDEA 257 G+ T+CNM E+G T DE YL+ D+A KE +T V + Sbjct: 246 TGKGTICNMGAEIGATTSTFGYDESMERYLRSTDRADVADLANEVKEHLTGDDEVYANPE 305 Query: 258 NYYKE-IEIDITDMEEQVAVPHHPDNVKPISDVEG--------TEINQVFIGSCTNGRLS 308 Y+ + IEID++ +E + P PD P+S + T++ IGSCTN Sbjct: 306 QYFDQVIEIDLSTLEPHINGPFTPDRATPVSQIRAEAEKNGWPTKVEWGLIGSCTNSSYE 365 Query: 309 DLREA---AKYLKGREVHKDVKLIVIPASKKVFLQALKEGIIDIFVKAGAMICTPGCGPC 365 DL A A+ +++ + P S++V A ++G++ IF A I T CGPC Sbjct: 366 DLSRASSIAQQAVDKQLKTKADFGINPGSEQVRFTAERDGMLKIFEDLDATIFTNACGPC 425 Query: 366 LG--AHQGV-LAEGEICLSTTNRNFKGRM-GHINSYIYLASPKIAAISAVKG 413 +G A G E + + NRNF R G+ N++ ++ SP++ A A+ G Sbjct: 426 IGQWARTGADKQEKNTIVHSFNRNFSKRADGNPNTHAFVTSPEMVAAIAISG 477 Lambda K H 0.318 0.136 0.399 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: 695 Number of extensions: 40 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: 420 Length of database: 757 Length adjustment: 36 Effective length of query: 384 Effective length of database: 721 Effective search space: 276864 Effective search space used: 276864 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: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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