Align Probable adenylyltransferase/sulfurtransferase MoeZ; EC 2.7.7.-; EC 2.8.1.- (characterized)
to candidate CA265_RS20190 CA265_RS20190 thiamine biosynthesis protein ThiF
Query= SwissProt::P9WMN7 (392 letters) >FitnessBrowser__Pedo557:CA265_RS20190 Length = 345 Score = 258 bits (659), Expect = 2e-73 Identities = 152/352 (43%), Positives = 213/352 (60%), Gaps = 32/352 (9%) Query: 15 LSREEVARYSRHLIIPDLGVDGQKRLKNARVLVIGAGGLGAPTLLYLAAAGVGTIGIVDF 74 L +EE++RY+R +I+P+LG+ GQ++LK A+VLVIGAGGLG P L YLAAAGVG IGI+D Sbjct: 2 LVKEELSRYNRQMILPELGLAGQEKLKAAKVLVIGAGGLGCPILQYLAAAGVGEIGIIDD 61 Query: 75 DVVDESNLQRQVIHGVADVGRSKAQSARDSIVAINPLIRVRLHELRLAPSNAVDLFKQYD 134 DVV+ SNL RQ+++ D+G+ KA+ A + + +NP IR++++ R ++A + + YD Sbjct: 62 DVVELSNLHRQILYNHTDIGQPKAKVAAEKLAVLNPNIRLKVYHERFTAASAAKICRDYD 121 Query: 135 LILDGTDNFATRYLVNDAAVLAGKPYVWGSIYRFEGQASVFWEDAPDGLGVNYRDLYPEP 194 LI+D +DNF+TRYLVND V GK ++GSI +FEGQ +VF NYRDLYP P Sbjct: 122 LIIDCSDNFSTRYLVNDTCVALGKILLFGSILQFEGQVAVFNYQG----SANYRDLYPTP 177 Query: 195 PPPGMVPSCAEGGVLGIICASVASVMGTEAIKLITGIGETLLGRLLVYDALEMSYRTITI 254 P + +CAEGGV+GI+ V M EA+KLI GIGETL G+L+ +AL + I Sbjct: 178 PTENL--NCAEGGVIGILPGIVGLYMANEALKLICGIGETLSGKLMTINALNNTVLVFKI 235 Query: 255 RKDPSTPKITELVDYEQFCGVVADDAAQAAKGS-----TITPRELRDWLDS-GRKLALID 308 + S AD A AA + I L +WL++ + LID Sbjct: 236 AAEKS-----------------ADPAKPAATKNDKAIPEINKTTLNNWLETQADDVFLID 278 Query: 309 VRDPVEWDIVHIDGAQLIPKSLINSGEGLAKLPQDRTAVLYCKTGVRSAEAL 360 VR+ E + +I G L L E LA +P+++ V YC+TG RS A+ Sbjct: 279 VRESYEHEEDNIGGINL---PLYELTESLAAIPKNKNVVFYCQTGQRSKMAV 327 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: 365 Number of extensions: 20 Number of successful extensions: 4 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: 345 Length adjustment: 30 Effective length of query: 362 Effective length of database: 315 Effective search space: 114030 Effective search space used: 114030 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: 49 (23.5 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