Align Probable adenylyltransferase/sulfurtransferase MoeZ; EC 2.7.7.-; EC 2.8.1.- (characterized)
to candidate GFF735 HP15_714 molybdopterin synthase sulfurylase MoeB
Query= SwissProt::P9WMN7 (392 letters) >FitnessBrowser__Marino:GFF735 Length = 252 Score = 187 bits (476), Expect = 2e-52 Identities = 108/250 (43%), Positives = 153/250 (61%), Gaps = 10/250 (4%) Query: 15 LSREEVARYSRHLIIPDLGVDGQKRLKNARVLVIGAGGLGAPTLLYLAAAGVGTIGIVDF 74 LS +E+ RYSR +++P + GQ++L++ARVLVIGAGGLG P LYL AAGVGT+ +VD Sbjct: 6 LSDDELLRYSRQILMPRFDIAGQEKLQSARVLVIGAGGLGCPVALYLGAAGVGTLTLVDD 65 Query: 75 DVVDESNLQRQVIHGVADVGRSKAQSARDSIVAINPLIRVRLHELRLAPSNAVDLFKQYD 134 D ++ +NLQRQ+ + +G SKA+S D I INPL+ V RL + Sbjct: 66 DNIELANLQRQIGFETSLLGESKAESLADRIRRINPLVSVIALNQRLEGEALTRTVTEAT 125 Query: 135 LILDGTDNFATRYLVNDAAVLAGKPYVWGSIYRFEGQASVF---WEDAPDGLGVNYRDLY 191 L++D TDNF TR+ +N A V + P V G+ R EGQ SV+ ED+P Y LY Sbjct: 126 LVVDCTDNFNTRFALNRACVASKVPLVSGAAIRGEGQVSVYDSRREDSP-----CYHCLY 180 Query: 192 PEPPPPGMVPSCAEGGVLGIICASVASVMGTEAIKLITGIGETLLGRLLVYDALEMSYRT 251 PE + +C+E GV+ + + + EAIK+I+G+G L+GRLL+ DA EM +R Sbjct: 181 PEQGNEDL--TCSEAGVIAPLVGMIGATQAMEAIKVISGVGSPLVGRLLILDAWEMQWRE 238 Query: 252 ITIRKDPSTP 261 + + +DPS P Sbjct: 239 MKLARDPSCP 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: 236 Number of extensions: 9 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: 252 Length adjustment: 27 Effective length of query: 365 Effective length of database: 225 Effective search space: 82125 Effective search space used: 82125 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