Align Probable adenylyltransferase/sulfurtransferase MoeZ; EC 2.7.7.-; EC 2.8.1.- (characterized)
to candidate CCNA_03842 CCNA_03842 molybdopterin biosynthesis protein MoeB
Query= SwissProt::P9WMN7 (392 letters) >FitnessBrowser__Caulo:CCNA_03842 Length = 245 Score = 227 bits (579), Expect = 2e-64 Identities = 124/248 (50%), Positives = 162/248 (65%), Gaps = 8/248 (3%) Query: 14 ALSREEVARYSRHLIIPDLGVDGQKRLKNARVLVIGAGGLGAPTLLYLAAAGVGTIGIVD 73 + S EV RY+RHL++ ++G GQ++LK ARVLV+GAGGLGAP LYLAAAGVGTIG+VD Sbjct: 2 SFSDGEVERYARHLVLREVGGPGQQKLKAARVLVVGAGGLGAPAALYLAAAGVGTIGLVD 61 Query: 74 FDVVDESNLQRQVIHGVADVGRSKAQSARDSIVAINPLIRVRLHELRLAPSNAVDLFKQY 133 D+V SNLQRQV++ DVGR K ++A + + +NP V H + L SNA + Y Sbjct: 62 PDIVSLSNLQRQVLYATGDVGRPKVEAASEHLRTLNPNTSVETHPVWLDASNAQAVVSGY 121 Query: 134 DLILDGTDNFATRYLVNDAAVLAGKPYVWGSIYRFEGQASVFWEDAPDGLGVNYRDLYPE 193 DL+LDGTD+FATR+ V+DA V+ GK V G++ R+ GQ VF YR L P+ Sbjct: 122 DLVLDGTDDFATRFAVSDACVVQGKALVSGALGRWTGQVGVFHGQP------CYRCLVPD 175 Query: 194 PPPPGMVPSCAEGGVLGIICASVASVMGTEAIKLITGIGETLLGRLLVYDALEMSYRTIT 253 PP +CA GV+G + + S+M EA+KLITG GE L GRLL+YD L RT+ Sbjct: 176 IPPD--AETCALVGVVGALAGVIGSMMALEAVKLITGAGEPLSGRLLIYDGLAGETRTVR 233 Query: 254 IRKDPSTP 261 I +DP P Sbjct: 234 IGRDPQCP 241 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: 316 Number of extensions: 16 Number of successful extensions: 2 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: 245 Length adjustment: 27 Effective length of query: 365 Effective length of database: 218 Effective search space: 79570 Effective search space used: 79570 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