Align Probable adenylyltransferase/sulfurtransferase MoeZ; EC 2.7.7.-; EC 2.8.1.- (characterized)
to candidate 3607497 Dshi_0910 UBA/THIF-type NAD/FAD binding protein (RefSeq)
Query= SwissProt::P9WMN7 (392 letters) >FitnessBrowser__Dino:3607497 Length = 321 Score = 126 bits (317), Expect = 8e-34 Identities = 80/238 (33%), Positives = 122/238 (51%), Gaps = 11/238 (4%) Query: 20 VARYSRHLIIPDLGVDGQKRLKNARVLVIGAGGLGAPTLLYLAAAGVGTIGIVDFDVVDE 79 + RY+R + +P +G +GQ RL A VLVIGAGGL AP L YLA AGVG I ++D D V Sbjct: 1 MTRYARQVQLPQVGAEGQARLAAAHVLVIGAGGLAAPALSYLAGAGVGRITVMDADRVSL 60 Query: 80 SNLQRQVIHGVADVGRSKAQSARDSIVAINPLIRVRLHELRLAPSNAVDLFKQYDLILDG 139 SNL RQ + + D+G KA++A + A NP + + P+N DL+LD Sbjct: 61 SNLHRQTLFTMDDIGAPKAEAAAARLRAQNPEVTITALCEAFTPANGAARLAGVDLVLDC 120 Query: 140 TDNFATRYLVNDAAVLAGKPYVWGSIYRFEGQASVFWEDAPDGLGVNYRDLYPEPPPPGM 199 D++A Y +D + P + S+ G + AP + R L+P+ PP Sbjct: 121 ADSYAASYTASD--LCGPVPLITASVLGASGYVAGCCGGAP-----SLRALFPD--PPDS 171 Query: 200 VPSCAEGGVLGIICASVASVMGTEAIKLITGIGETLLGRLLVYDALEMSYRTITIRKD 257 SCA GV G + ++ ++ A+ + G+ + LG+ + D ++R + R D Sbjct: 172 AASCATAGVFGPVVGALGALQAQMALGALLGLKPSSLGQAITLDT--ATWRMASFRFD 227 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: 331 Number of extensions: 19 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: 321 Length adjustment: 29 Effective length of query: 363 Effective length of database: 292 Effective search space: 105996 Effective search space used: 105996 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