Align Probable adenylyltransferase/sulfurtransferase MoeZ; EC 2.7.7.-; EC 2.8.1.- (characterized)
to candidate PP_0735 PP_0735 molybdopterin-synthase adenylyltransferase
Query= SwissProt::P9WMN7 (392 letters) >FitnessBrowser__Putida:PP_0735 Length = 251 Score = 199 bits (507), Expect = 5e-56 Identities = 112/245 (45%), Positives = 149/245 (60%), Gaps = 4/245 (1%) Query: 15 LSREEVARYSRHLIIPDLGVDGQKRLKNARVLVIGAGGLGAPTLLYLAAAGVGTIGIVDF 74 LS +E+ RYSR +++ + +DGQ RLK ++ L+IG GGLG+P LYLAAAGVG + + DF Sbjct: 2 LSDQELLRYSRQVLLSQIDIDGQLRLKQSKALIIGLGGLGSPVALYLAAAGVGELHLADF 61 Query: 75 DVVDESNLQRQVIHGVADVGRSKAQSARDSIVAINPLIRVRLHELRLAPSNAVDLFKQYD 134 D VD +NLQRQVIH A VG SK SA + AINP + + H L + V D Sbjct: 62 DTVDLTNLQRQVIHDSASVGMSKVDSALQRLQAINPEVSLVAHRQALDEDSLVAAVAAVD 121 Query: 135 LILDGTDNFATRYLVNDAAVLAGKPYVWGSIYRFEGQASVFWEDAPDGLGVNYRDLYPEP 194 L+LD +DNF+TR VN A V AGKP V G+ R EGQ SVF D Y LY Sbjct: 122 LVLDCSDNFSTREAVNAACVAAGKPLVSGAAIRLEGQLSVF--DPRRDYSPCYHCLYGHG 179 Query: 195 PPPGMVPSCAEGGVLGIICASVASVMGTEAIKLITGIGETLLGRLLVYDALEMSYRTITI 254 + +C+E GV+G + V S+ EA+KL+ G GE L+GRLL+ DAL R + + Sbjct: 180 SEAEL--TCSEAGVIGPLVGLVGSLQALEAMKLLAGFGEPLVGRLLLIDALGTRIRELRV 237 Query: 255 RKDPS 259 ++DP+ Sbjct: 238 KRDPA 242 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: 245 Number of extensions: 7 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: 251 Length adjustment: 27 Effective length of query: 365 Effective length of database: 224 Effective search space: 81760 Effective search space used: 81760 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 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