Align Probable adenylyltransferase/sulfurtransferase MoeZ; EC 2.7.7.-; EC 2.8.1.- (characterized)
to candidate 199334 SO0137 molybdopterin biosynthesis MoeB protein (NCBI ptt file)
Query= SwissProt::P9WMN7 (392 letters) >FitnessBrowser__MR1:199334 Length = 253 Score = 164 bits (414), Expect = 3e-45 Identities = 94/247 (38%), Positives = 138/247 (55%), Gaps = 5/247 (2%) Query: 10 EPASALSREEVARYSRHLIIPDLGVDGQKRLKNARVLVIGAGGLGAPTLLYLAAAGVGTI 69 E LS E+ RYSR + I + +DGQ+RLK A+VL+IGAGGLG YL AG+G + Sbjct: 3 EQVDILSDSELTRYSRQISIKAMDIDGQERLKLAKVLMIGAGGLGCAAGQYLTVAGIGEL 62 Query: 70 GIVDFDVVDESNLQRQVIHGVADVGRSKAQSARDSIVAINPLIRVRLHELRLAPSNAVDL 129 +VDFD V+ SNLQRQV+H A++G+ K +SA+ S+ +NP +++ L L Sbjct: 63 TLVDFDTVELSNLQRQVLHQDANIGQPKVESAKQSLNQLNPHVKINPINAVLDDHEIDAL 122 Query: 130 FKQYDLILDGTDNFATRYLVNDAAVLAGKPYVWGSIYRFEGQASVFWEDAPDGLGVNYRD 189 + +++D TDN + R +N + P V + R EG +VF A + Sbjct: 123 VASHSIVVDCTDNVSVREQLNQSCFKHKVPLVSAAAIRMEGMVTVFDYQAQTPCYHCFSS 182 Query: 190 LYPEPPPPGMVPSCAEGGVLGIICASVASVMGTEAIKLITGIGETLLGRLLVYDALEMSY 249 L+ E SC E G+L + V + EAIK+ITGIG+TL GR+L+ DA+ M + Sbjct: 183 LFGE-----QQLSCVESGILAPVVGMVGCLQAVEAIKVITGIGKTLAGRILMIDAMTMEF 237 Query: 250 RTITIRK 256 R + + K Sbjct: 238 REMKLPK 244 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: 210 Number of extensions: 10 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: 253 Length adjustment: 27 Effective length of query: 365 Effective length of database: 226 Effective search space: 82490 Effective search space used: 82490 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