Align Probable adenylyltransferase/sulfurtransferase MoeZ; EC 2.7.7.-; EC 2.8.1.- (characterized)
to candidate HSERO_RS00835 HSERO_RS00835 molybdopterin biosynthesis protein MoeB
Query= SwissProt::P9WMN7 (392 letters) >FitnessBrowser__HerbieS:HSERO_RS00835 Length = 254 Score = 193 bits (490), Expect = 5e-54 Identities = 106/244 (43%), Positives = 148/244 (60%), Gaps = 3/244 (1%) Query: 18 EEVARYSRHLIIPDLGVDGQKRLKNARVLVIGAGGLGAPTLLYLAAAGVGTIGIVDFDVV 77 +++ RYSRH+++ ++ +DGQ RL LVIGAGGLG+P +YLA+AGVG I +VD D V Sbjct: 4 QQLLRYSRHILLDEIDIDGQTRLLQGHALVIGAGGLGSPAAMYLASAGVGRITLVDHDTV 63 Query: 78 DESNLQRQVIHGVADVGRSKAQSARDSIVAINPLIRVRLHELRLAPSNAVDLFKQYDLIL 137 D +NLQRQ++H A VG+ K +S R ++ INP ++V R+ L Q D++L Sbjct: 64 DLTNLQRQIMHTTARVGQPKVESGRQALEQINPGVQVTALAERVEAERLHALVAQADVVL 123 Query: 138 DGTDNFATRYLVNDAAVLAGKPYVWGSIYRFEGQASVFWEDAPDGLGVNYRDLYPEPPPP 197 D +DNFATR+ VN A V AG P V G+ RF+GQ SVF D Y L+P P Sbjct: 124 DCSDNFATRHAVNRACVAAGVPLVSGAAIRFDGQVSVF--DPRQDASPCYACLFP-PERE 180 Query: 198 GMVPSCAEGGVLGIICASVASVMGTEAIKLITGIGETLLGRLLVYDALEMSYRTITIRKD 257 C+ GV + + ++ EAIKL+ GIG +L GRLL+ DA EM + +IT+ +D Sbjct: 181 FEEVQCSTMGVFSPLVGIIGTMQAAEAIKLLAGIGRSLAGRLLILDAREMEWTSITVGRD 240 Query: 258 PSTP 261 P Sbjct: 241 RQCP 244 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: 256 Number of extensions: 10 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: 254 Length adjustment: 27 Effective length of query: 365 Effective length of database: 227 Effective search space: 82855 Effective search space used: 82855 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