Align Probable adenylyltransferase/sulfurtransferase MoeZ; EC 2.7.7.-; EC 2.8.1.- (characterized)
to candidate 3609590 Dshi_2974 UBA/THIF-type NAD/FAD binding protein (RefSeq)
Query= SwissProt::P9WMN7 (392 letters) >FitnessBrowser__Dino:3609590 Length = 346 Score = 226 bits (577), Expect = 6e-64 Identities = 124/256 (48%), Positives = 163/256 (63%), Gaps = 3/256 (1%) Query: 6 PPLVEPASALSREEVARYSRHLIIPDLGVDGQKRLKNARVLVIGAGGLGAPTLLYLAAAG 65 P S E+ RY+RH+++ ++G GQKRLK A+VLV+GAGGLG+P LLYLA AG Sbjct: 89 PSETRQTGPFSDVELDRYARHIVMREIGGLGQKRLKEAKVLVVGAGGLGSPVLLYLAGAG 148 Query: 66 VGTIGIVDFDVVDESNLQRQVIHGVADVGRSKAQSARDSIVAINPLIRVRLHELRLAPSN 125 VGTIG++D D V SNLQRQVIH A G K SA ++ A+NP I VR + RL Sbjct: 149 VGTIGVIDHDTVSLSNLQRQVIHTDARSGMPKVFSAEMAMTALNPHITVRPYNRRLTAEI 208 Query: 126 AVDLFKQYDLILDGTDNFATRYLVNDAAVLAGKPYVWGSIYRFEGQASVFWEDAPDGLGV 185 A +LF +YDLILDG DNF TR LVN AAV GKP + G+I ++EGQ S+F D G Sbjct: 209 AEELFAEYDLILDGNDNFETRTLVNKAAVATGKPLISGAIAQWEGQISLF--DPVRGAPC 266 Query: 186 NYRDLYPEPPPPGMVPSCAEGGVLGIICASVASVMGTEAIKLITGIGETLLGRLLVYDAL 245 Y ++PE P G+ PSCAE GV G + + ++M EA+K +T G L GR+++YDAL Sbjct: 267 -YACIFPEAPADGLAPSCAEAGVAGPLPGVIGTMMALEAMKELTDAGTGLSGRMMLYDAL 325 Query: 246 EMSYRTITIRKDPSTP 261 RT+ +++ P Sbjct: 326 NAETRTVKLKRRADCP 341 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: 391 Number of extensions: 27 Number of successful extensions: 2 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: 392 Length of database: 346 Length adjustment: 30 Effective length of query: 362 Effective length of database: 316 Effective search space: 114392 Effective search space used: 114392 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