Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate Ac3H11_1292 Enoyl-[acyl-carrier-protein] reductase [NADPH] (EC 1.3.1.10)
Query= reanno::BFirm:BPHYT_RS16920 (266 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1292 Length = 259 Score = 129 bits (325), Expect = 5e-35 Identities = 87/248 (35%), Positives = 126/248 (50%), Gaps = 6/248 (2%) Query: 22 LVDRTVLITGGATGIGASFVEHFAAQGARVAF-FDIDASAGEALADELGDSKHKPLFLSC 80 L + L+TGGA GIGA+ V A GA VAF + A+ +AL + + K L L Sbjct: 14 LAGKVALVTGGARGIGAAIVRRLARDGAAVAFTYSSSAAPAQALVAAIESAGGKALALRA 73 Query: 81 DLTDIDALQKAIADVKAALGPIQVLVNNAANDKRHTIGEVTRESFDAGIAVNIRHQFFAA 140 D D AL +A+ LG + +LVNNA + + FD + VN+R F A Sbjct: 74 DSADAAALTQAVDHAARTLGRLDILVNNAGVAVAGVLDSFSLADFDHTLNVNVRAVFVAT 133 Query: 141 QAVMEDMKAANS-GSIINLGSI-SWMLKNGGYPVYVMSKSAVQGLTRGLARDLGHFNIRV 198 QA + M + G +I +GS S + G+ VY MSK+A+ GLT+GLARDLG I V Sbjct: 134 QAAVRHMGQGGAYGRVITIGSTNSDRVPWPGFSVYGMSKAAIVGLTKGLARDLGPRGITV 193 Query: 199 NTLVPGWVMTEKQKRLWLDDAGRRSIKEGQCIDAELEPADLARMALFLAADDSRMITAQD 258 N + PG V T+ D + ++ P ++A M +LA +S M+T Sbjct: 194 NNVQPGPVNTDMNP---ADGPMAGDMHGLMALNRHAHPDEIAGMVAYLAGPESGMVTGAS 250 Query: 259 IVVDGGWA 266 +++DGG+A Sbjct: 251 LLIDGGFA 258 Lambda K H 0.320 0.134 0.388 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: 176 Number of extensions: 10 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: 266 Length of database: 259 Length adjustment: 25 Effective length of query: 241 Effective length of database: 234 Effective search space: 56394 Effective search space used: 56394 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 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