Align Probable adenylyltransferase/sulfurtransferase MoeZ; EC 2.7.7.-; EC 2.8.1.- (characterized)
to candidate Synpcc7942_0158 Synpcc7942_0158 hypothetical protein
Query= SwissProt::P9WMN7 (392 letters) >FitnessBrowser__SynE:Synpcc7942_0158 Length = 391 Score = 389 bits (998), Expect = e-112 Identities = 204/387 (52%), Positives = 277/387 (71%), Gaps = 15/387 (3%) Query: 15 LSREEVARYSRHLIIPDLGVDGQKRLKNARVLVIGAGGLGAPTLLYLAAAGVGTIGIVDF 74 L++++ ARYSRHLI+P++G++GQKRLK A+VL IG GGLG+P LLYLAAAG+G IGIVDF Sbjct: 11 LTQDDYARYSRHLILPEVGLEGQKRLKAAKVLCIGTGGLGSPLLLYLAAAGIGRIGIVDF 70 Query: 75 DVVDESNLQRQVIHGVADVGRSKAQSARDSIVAINPLIRVRLHELRLAPSNAVDLFKQYD 134 D+VD SNLQRQVIHG + VG+ K +SA++ I INP +V L+E L+ NA+ + + YD Sbjct: 71 DIVDHSNLQRQVIHGTSWVGKPKIESAKNRIHEINPYCQVDLYETALSSENALSILEPYD 130 Query: 135 LILDGTDNFATRYLVNDAAVLAGKPYVWGSIYRFEGQASVF-WEDAPDGLGVNYRDLYPE 193 +I+DGTDNF TRYLVNDA VL GKP V+GSI+RFEGQA+VF +ED P NYRDLYPE Sbjct: 131 VIVDGTDNFPTRYLVNDACVLLGKPNVYGSIFRFEGQATVFNYEDGP-----NYRDLYPE 185 Query: 194 PPPPGMVPSCAEGGVLGIICASVASVMGTEAIKLITGIGETLLGRLLVYDALEMSYRTIT 253 PPPPGMVPSCAEGGVLGI+ + + TE +K+I G G+TL GRLL+Y+AL+M +R + Sbjct: 186 PPPPGMVPSCAEGGVLGILPGIIGVIQATETVKIILGQGQTLSGRLLLYNALDMKFRELK 245 Query: 254 IRKDPSTPKITELVDYEQFCGVVADDAAQAAKGST---ITPRELRDWLD-SGRKLALIDV 309 +R +P P I L+DY++FCG+ AA+AA + I+ EL+ LD ++ LIDV Sbjct: 246 LRPNPERPVIDRLIDYQEFCGIPQAQAAEAAATDSIPEISVTELKAILDRQDPEVLLIDV 305 Query: 310 RDPVEWDIVHIDGAQLIPKSLINSGEGLAKLPQ----DRTAVLYCKTGVRSAEALAAVKK 365 R+P E +I I GA L+P I +G G+ + + R +++CK G RSA+AL +K+ Sbjct: 306 RNPHEAEIATIPGAILVPLPDIEAGAGVETVRELLNGKRELIVHCKMGGRSAKALGILKE 365 Query: 366 AGFSDAVHLQGGIVAWAKQMQPDMVMY 392 AG + ++ GGI AW++ + P + Y Sbjct: 366 AGIT-GTNVAGGINAWSQDVDPSVPQY 391 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: 526 Number of extensions: 37 Number of successful extensions: 5 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: 391 Length adjustment: 31 Effective length of query: 361 Effective length of database: 360 Effective search space: 129960 Effective search space used: 129960 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: 50 (23.9 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