Align Probable adenylyltransferase/sulfurtransferase MoeZ; EC 2.7.7.-; EC 2.8.1.- (characterized)
to candidate RR42_RS01815 RR42_RS01815 molybdopterin biosynthesis protein MoeB
Query= SwissProt::P9WMN7 (392 letters) >FitnessBrowser__Cup4G11:RR42_RS01815 Length = 255 Score = 201 bits (510), Expect = 2e-56 Identities = 113/242 (46%), Positives = 152/242 (62%), Gaps = 3/242 (1%) Query: 15 LSREEVARYSRHLIIPDLGVDGQKRLKNARVLVIGAGGLGAPTLLYLAAAGVGTIGIVDF 74 ++ +++ RYSRH+++ +LG++GQ RL + LVIGAGGLGA L YLA+AGVGTI +VD Sbjct: 1 MNDDQLLRYSRHILLDELGIEGQSRLLASHALVIGAGGLGAAALPYLASAGVGTITVVDD 60 Query: 75 DVVDESNLQRQVIHGVADVGRSKAQSARDSIVAINPLIRVRLHELRLAPSNAVDLFKQYD 134 DVVD +NLQRQVIH A+VGR K +SAR+ ++ INP I VRL + R+ + L D Sbjct: 61 DVVDLTNLQRQVIHTTANVGRPKVESAREGMLRINPGIDVRLVQARVGAAELAHLVADAD 120 Query: 135 LILDGTDNFATRYLVNDAAVLAGKPYVWGSIYRFEGQASVFWEDAPDGLGVNYRDLYPEP 194 ++LD DNF TR VN A V P V G+ RF+GQ SVF P Y L+P P Sbjct: 121 VVLDCCDNFDTRQAVNRACVQHSVPLVSGAALRFDGQISVFDHRQPG--APCYACLFP-P 177 Query: 195 PPPGMVPSCAEGGVLGIICASVASVMGTEAIKLITGIGETLLGRLLVYDALEMSYRTITI 254 P +CA GV + V +V EA+KL+ G+G TL GRLL+ DAL M + T+ + Sbjct: 178 SQPAQEVACATMGVFAPLVGMVGTVQAAEALKLLMGVGTTLAGRLLMVDALGMEWTTMRL 237 Query: 255 RK 256 + Sbjct: 238 AR 239 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: 270 Number of extensions: 17 Number of successful extensions: 3 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 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