Align Probable adenylyltransferase/sulfurtransferase MoeZ; EC 2.7.7.-; EC 2.8.1.- (characterized)
to candidate CA265_RS12640 CA265_RS12640 molybdopterin biosynthesis protein
Query= SwissProt::P9WMN7 (392 letters) >FitnessBrowser__Pedo557:CA265_RS12640 Length = 368 Score = 225 bits (574), Expect = 1e-63 Identities = 139/364 (38%), Positives = 204/364 (56%), Gaps = 15/364 (4%) Query: 22 RYSRHLIIPDLGVDGQKRLKNARVLVIGAGGLGAPTLLYLAAAGVGTIGIVDFDVVDESN 81 RY+R +I+ G + Q++L A+VLVIGAGGLG P L YLAAAG+G IGIVD D + SN Sbjct: 5 RYNRQIILKGFGEEAQQKLLRAKVLVIGAGGLGCPALQYLAAAGIGHIGIVDDDTISLSN 64 Query: 82 LQRQVIHGVADVGRSKAQSARDSIVAINPLIRVRLHELRLAPSNAVDLFKQYDLILDGTD 141 L RQ++ AD+G+ K + A + +N I + H +RL +N +D+ +YD ILDGTD Sbjct: 65 LHRQILFTTADIGKLKVEVAAKRLQEMNTQIGIIRHPIRLQKNNILDIVSRYDYILDGTD 124 Query: 142 NFATRYLVNDAAVLAGKPYVWGSIYRFEGQASVFWEDAPDGL--GVNYRDLYPEPPPPGM 199 NF +RYL+NDA L KP ++ ++ FEGQ ++F +APD L NYRDL+P PP G Sbjct: 125 NFESRYLINDACALLNKPLIFAAVSGFEGQLAIF--NAPDHLTPSTNYRDLFPIPPDKGE 182 Query: 200 VPSCAEGGVLGIICASVASVMGTEAIKLITGIGETLLGRLLVYDALEMSYRTITIRKDP- 258 V +CAE G++G++ + ++ E IKLI IG+ L ++L Y+ L TI I Sbjct: 183 VANCAENGIIGVLPGILGTMAAAETIKLIAKIGQALTNKILSYNLLTQEQYTINISHGGG 242 Query: 259 -STPKITELVDYEQFCGVVADDAAQAAKGSTITPRELRDWLDSGRKLALIDVRDPVEWDI 317 + PK ++F + D ++ +G L LIDVR+ E I Sbjct: 243 YTLPKTV-----DEFLNMDYQDTSEGPQGYIEIDAGELVKLQQLESTILIDVRERHEVPI 297 Query: 318 VHIDGAQLIPKSLINSGEGLAKLPQDRTAVLYCKTGVRSAEALAAV-KKAGFSDAVH-LQ 375 + +P S G ++K + VL C+ G+RS A A+ +K G + ++ L+ Sbjct: 298 LDKQIFTQVPMS--EFGAFMSKEFYQKHVVLICQHGIRSVAAAEAMQEKYGDAKKIYSLK 355 Query: 376 GGIV 379 GGIV Sbjct: 356 GGIV 359 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: 358 Number of extensions: 16 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: 368 Length adjustment: 30 Effective length of query: 362 Effective length of database: 338 Effective search space: 122356 Effective search space used: 122356 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