Align Probable adenylyltransferase/sulfurtransferase MoeZ; EC 2.7.7.-; EC 2.8.1.- (characterized)
to candidate N515DRAFT_2678 N515DRAFT_2678 Molybdopterin or thiamine biosynthesis adenylyltransferase
Query= SwissProt::P9WMN7 (392 letters) >FitnessBrowser__Dyella79:N515DRAFT_2678 Length = 388 Score = 227 bits (579), Expect = 4e-64 Identities = 123/251 (49%), Positives = 161/251 (64%), Gaps = 8/251 (3%) Query: 14 ALSREEVARYSRHLIIPDLGVDGQKRLKNARVLVIGAGGLGAPTLLYLAAAGVGTIGIVD 73 AL + RYSR L +P +G GQ +L AR++++GAGGLGAP LYLAAAGVG I ++D Sbjct: 122 ALDADAAERYSRQLRLPQVGEAGQAKLGAARIVLLGAGGLGAPAALYLAAAGVGQITLID 181 Query: 74 FDVVDESNLQRQVIHGVADVGRSKAQSARDSIVAINPLIRVRLHELRLAPSNAVDLFKQY 133 D V+ SNL RQVIH A VG +K +SAR ++ A+NP +R+ E RL N L + Sbjct: 182 DDRVERSNLHRQVIHADARVGMAKTESARLALNALNPRVRIETREERLRADNVERLLADH 241 Query: 134 DLILDGTDNFATRYLVNDAAVLAGKPYVWGSIYRFEGQASVF---WEDAPDGLGVNYRDL 190 DL++DG DNF RYLV A+ G P V+G++ RF GQ SVF +DAP YR L Sbjct: 242 DLVIDGADNFPARYLVAAASRRLGLPMVYGAVERFTGQVSVFDPRRDDAP-----CYRCL 296 Query: 191 YPEPPPPGMVPSCAEGGVLGIICASVASVMGTEAIKLITGIGETLLGRLLVYDALEMSYR 250 +PEPP P+C+E GVLG++ + + TEA+KLI +GETL GRLL DAL M +R Sbjct: 297 FPEPPSAAEAPNCSEAGVLGVLPGLIGLLQATEALKLILELGETLSGRLLHVDALTMRFR 356 Query: 251 TITIRKDPSTP 261 +R+DPS P Sbjct: 357 ETRLRRDPSCP 367 Score = 29.6 bits (65), Expect = 2e-04 Identities = 21/82 (25%), Positives = 35/82 (42%) Query: 306 LIDVRDPVEWDIVHIDGAQLIPKSLINSGEGLAKLPQDRTAVLYCKTGVRSAEALAAVKK 365 LIDVR+ E GA + + + + +DR + C +G RS A A+++ Sbjct: 36 LIDVREDHERADGTPAGALGLSRGFLELRIEQTEANRDRPILALCGSGQRSLLAAEALQR 95 Query: 366 AGFSDAVHLQGGIVAWAKQMQP 387 G+ + GG W + P Sbjct: 96 MGYRQVSSVAGGFNRWKAEGLP 117 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: 441 Number of extensions: 25 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 392 Length of database: 388 Length adjustment: 31 Effective length of query: 361 Effective length of database: 357 Effective search space: 128877 Effective search space used: 128877 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