Align Probable adenylyltransferase/sulfurtransferase MoeZ; EC 2.7.7.-; EC 2.8.1.- (characterized)
to candidate GFF891 PGA1_c09040 putative adenylyltransferase ThiF
Query= SwissProt::P9WMN7 (392 letters) >FitnessBrowser__Phaeo:GFF891 Length = 329 Score = 149 bits (377), Expect = 9e-41 Identities = 105/361 (29%), Positives = 173/361 (47%), Gaps = 45/361 (12%) Query: 20 VARYSRHLIIPDLGVDGQKRLKNARVLVIGAGGLGAPTLLYLAAAGVGTIGIVDFDVVDE 79 ++R+ R + +P++G +GQ +L A VLV+GAGGLG+P L YLA AG+G I ++D D V+ Sbjct: 8 MSRFDRQIALPEVGAEGQAKLAAAHVLVVGAGGLGSPVLQYLAGAGIGEITVMDGDSVEA 67 Query: 80 SNLQRQVIHGVADVGRSKAQSARDSIVAINPLIRVRLHELRLAPSNAVDLFKQYDLILDG 139 +NL RQ ++ AD+GR K +AR+ + A+ P +R+ H L P N + DL++D Sbjct: 68 TNLPRQPLYTPADIGRYKVDAARERLCAMAPELRLHPHARDLTPDNVMAAVTPVDLVIDA 127 Query: 140 TDNFATRYLVNDAAVLAGKPYVWGSIYRFEGQASVFWEDAPDGLGVNYRDLYPEPPPPGM 199 D+ A Y ++D G+ + GS G VF G G + R ++P+ PPG Sbjct: 128 ADSHAVSYTLSDCCQRLGRDLISGSALAQSGYVGVFC-----GGGPSLRAVFPD--PPGS 180 Query: 200 VPSCAEGGVLGIICASVASVMGTEAIKLITGIGETLLGRLLVYD--ALEMSYRTITIRKD 257 +CA G++G + + + A+KL+ T GR+ D L+M + ++ Sbjct: 181 AATCATSGIMGPVVGVIGAWQAQLALKLLLNHQPTPRGRIFSVDFAGLQMGGFDFSTARE 240 Query: 258 PSTPKITELVDYEQFCGVVADDAAQAAKGSTITPRELRDWLDSGRKLALIDVRDPVEWDI 317 P+ P F G+ + IT + ++++R E Sbjct: 241 PARPL--------PFIGL-----------NAITDEDY-----------VVELRPEQEAPT 270 Query: 318 VHIDGA-QLIPKSLINSGEGLAKLPQDRTAVLYCKTGVRSAEALAAVKKAGFSDAVHLQG 376 I A +++P++L LP DR VL C +G+R+ A + + V L Sbjct: 271 PAIRTAVRILPEAL-----QARDLPSDRRVVLACHSGLRAWRTAAEIAPDFAGELVLLAA 325 Query: 377 G 377 G Sbjct: 326 G 326 Lambda K H 0.319 0.137 0.404 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: 393 Number of extensions: 25 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 392 Length of database: 329 Length adjustment: 29 Effective length of query: 363 Effective length of database: 300 Effective search space: 108900 Effective search space used: 108900 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 (21.7 bits) S2: 49 (23.5 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