Align Probable adenylyltransferase/sulfurtransferase MoeZ; EC 2.7.7.-; EC 2.8.1.- (characterized)
to candidate 5207513 Shew_0047 molybdopterin biosynthesis protein MoeB (RefSeq)
Query= SwissProt::P9WMN7 (392 letters) >FitnessBrowser__PV4:5207513 Length = 255 Score = 169 bits (429), Expect = 6e-47 Identities = 95/244 (38%), Positives = 139/244 (56%), Gaps = 5/244 (2%) Query: 15 LSREEVARYSRHLIIPDLGVDGQKRLKNARVLVIGAGGLGAPTLLYLAAAGVGTIGIVDF 74 LS E+ RYSRH+ I + +GQ+RLK A+VLVIGAGGLG + YLA AGVG + +VDF Sbjct: 10 LSDAEILRYSRHISIKAMDFEGQERLKQAKVLVIGAGGLGCASTQYLAVAGVGQLTLVDF 69 Query: 75 DVVDESNLQRQVIHGVADVGRSKAQSARDSIVAINPLIRVRLHELRLAPSNAVDLFKQYD 134 D V+ SNLQRQV+H A +G+ K +SA+ S++ +NP +RV L + L ++D Sbjct: 70 DTVELSNLQRQVLHHDATIGQPKVESAKTSLMQLNPHLRVETINAVLDDEQILALVAEHD 129 Query: 135 LILDGTDNFATRYLVNDAAVLAGKPYVWGSIYRFEGQASVFWEDAPDGLGVNYRDLYPEP 194 L++D TDN R +N A P V + R EG +VF Y L+ + Sbjct: 130 LVMDCTDNIVVREQLNQACFQHKVPLVSAAAIRMEGTVTVFDYGEQSPCYHCYSKLFGD- 188 Query: 195 PPPGMVPSCAEGGVLGIICASVASVMGTEAIKLITGIGETLLGRLLVYDALEMSYRTITI 254 +C E G+L + + + EAIK++ +G+TL GR+L+ DA+ M +R + + Sbjct: 189 ----QQLTCVESGILAPVVGMIGCLQAVEAIKVLAKMGKTLSGRILMIDAMTMEFREMKL 244 Query: 255 RKDP 258 K P Sbjct: 245 PKQP 248 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: 211 Number of extensions: 8 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: 255 Length adjustment: 27 Effective length of query: 365 Effective length of database: 228 Effective search space: 83220 Effective search space used: 83220 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: 48 (23.1 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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