Align Probable adenylyltransferase/sulfurtransferase MoeZ; EC 2.7.7.-; EC 2.8.1.- (characterized)
to candidate 201587 SO2443 thiF protein, putative (NCBI ptt file)
Query= SwissProt::P9WMN7 (392 letters) >FitnessBrowser__MR1:201587 Length = 300 Score = 115 bits (288), Expect = 2e-30 Identities = 86/273 (31%), Positives = 135/273 (49%), Gaps = 28/273 (10%) Query: 10 EPASALSREEVARYSRHLIIPDLGVDGQKRLKNARVLVIGAGGLGAPTLLYLAAAGVGTI 69 + +S+L+ ++ RYSR + +P++G G +LK V++IG GGLG YLA AG+G+I Sbjct: 6 QKSSSLNDKDFIRYSRQIFLPEVGEAGLLQLKQCHVVIIGCGGLGQLAAQYLACAGIGSI 65 Query: 70 GIVDFDVVDESNLQRQVIHGVADVGRSKAQSARDSIVAINPLIRVRLHELRLAPSNAVDL 129 +VD D V+ SNL RQ++ AD+G+ KA A+ + + P ++ L +A L Sbjct: 66 TLVDDDRVELSNLPRQLLFNEADIGQYKAWVAKQKLAVLAPDCQLFAFVQMLTLDSAESL 125 Query: 130 F--------KQYDLILDGTDNFATRYLVNDAAVLAGKPYVWGSIYRFEGQA-SVFWEDAP 180 +Q L+LD TDN A R+ +N + P V SI F GQ +V + P Sbjct: 126 LAHVATANRQQSALLLDCTDNLAARHCINQLCIEHALPLVSASIAAFNGQLFAVDQQRFP 185 Query: 181 DGLGVNYRDLYPEPPPPGMVPSCAEGGVLGIICASVASVMGTEAIKLI------------ 228 G Y ++P +C+ GVLG +AS+ AI+L+ Sbjct: 186 --AGGCYHCVFPADTYAPQ--NCSNQGVLGPSVGVMASMQALLAIQLLLTATVPNLEHST 241 Query: 229 --TGIG-ETLLGRLLVYDALEMSYRTITIRKDP 258 +G E LLGR +DA + + + + +DP Sbjct: 242 KPQAVGAEHLLGRFWRFDAKSLQWHSARLTRDP 274 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: 241 Number of extensions: 10 Number of successful extensions: 4 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: 300 Length adjustment: 29 Effective length of query: 363 Effective length of database: 271 Effective search space: 98373 Effective search space used: 98373 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: 49 (23.5 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