Align Probable adenylyltransferase/sulfurtransferase MoeZ; EC 2.7.7.-; EC 2.8.1.- (characterized)
to candidate BWI76_RS01545 BWI76_RS01545 thiamine biosynthesis protein ThiS
Query= SwissProt::P9WMN7 (392 letters) >FitnessBrowser__Koxy:BWI76_RS01545 Length = 251 Score = 151 bits (382), Expect = 2e-41 Identities = 89/247 (36%), Positives = 136/247 (55%), Gaps = 6/247 (2%) Query: 15 LSREEVARYSRHLIIPDLGVDGQKRLKNARVLVIGAGGLGAPTLLYLAAAGVGTIGIVDF 74 ++ + RYSR L++ D+ ++GQ++L +RVL++G GGLG+P LYLA AGVGT+ + D Sbjct: 1 MNDSDFMRYSRQLLLEDIAIEGQQKLLASRVLLVGLGGLGSPAALYLAGAGVGTLVLADD 60 Query: 75 DVVDESNLQRQVIHGVADVGRSKAQSARDSIVAINPLIRVRLHELRLAPSNAVDLFKQYD 134 D V SNLQRQ++ D+ RSKA +AR + +NP I + + RL D + D Sbjct: 61 DDVHVSNLQRQILFTSDDISRSKAAAARARLARLNPQIELIALKQRLGGEALQDEVAKAD 120 Query: 135 LILDGTDNFATRYLVNDAAVLAGKPYVWGSIYRFEGQASVFWEDAPDGLGVNYRDLYPEP 194 ++LD TDN ATR +N A V P + S GQ V G YR L+P+ Sbjct: 121 VVLDCTDNMATRQAINAACVALQTPLITASAVGLGGQLMVLTPPWDQGC---YRCLWPDA 177 Query: 195 PPPGMVPSCAEGGVLGIICASVASVMGTEAIKLITGIGETLLGRLLVYDALEMSYRTITI 254 P +C G++G + + ++ EAIKL+ G+ T L ++DA S+RT+ + Sbjct: 178 NEPER--NCRTAGIIGPVVGMMGTLQALEAIKLLAGMA-TPRNALRLFDARTSSWRTLAL 234 Query: 255 RKDPSTP 261 ++ P Sbjct: 235 QRAQGCP 241 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: 232 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