Align Probable adenylyltransferase/sulfurtransferase MoeZ; EC 2.7.7.-; EC 2.8.1.- (characterized)
to candidate GFF4107 PS417_21040 sulfurylase
Query= SwissProt::P9WMN7 (392 letters) >FitnessBrowser__WCS417:GFF4107 Length = 620 Score = 305 bits (780), Expect = 3e-87 Identities = 167/384 (43%), Positives = 233/384 (60%), Gaps = 11/384 (2%) Query: 14 ALSREEVARYSRHLIIPDLGVDGQKRLKNARVLVIGAGGLGAPTLLYLAAAGVGTIGIVD 73 ALS EEV RY RH+ +P +G +GQ LK A+VL+IG GGLG+P LYLAAAGVGT+G+VD Sbjct: 243 ALSNEEVQRYVRHITLPGVGREGQLNLKKAKVLIIGTGGLGSPISLYLAAAGVGTLGLVD 302 Query: 74 FDVVDESNLQRQVIHGVADVGRSKAQSARDSIVAINPLIRVRLHELRLAPSNAVDLFKQY 133 FDVV+ SNLQRQ++HG + +G K +SAR + +N I++ H+ L NA++L Y Sbjct: 303 FDVVESSNLQRQIVHGNSTLGMPKVESARQRLQDLNRHIQINAHDTALNADNALELVGAY 362 Query: 134 DLILDGTDNFATRYLVNDAAVLAGKPYVWGSIYRFEGQASVFWEDAPDGLGVNYRDLYPE 193 DL++DGTDNF TRYLVNDA V GKP V+G+IYRF+GQ SV G YR L+P Sbjct: 363 DLVIDGTDNFDTRYLVNDACVQLGKPLVYGAIYRFDGQISVLNYKG----GPCYRCLFPS 418 Query: 194 PPPPGMVPSCAEGGVLGIICASVASVMGTEAIKLITGIGETLLGRLLVYDALEMSYRTIT 253 PP + P+C+ GGV+G++ V + TEAIKL+ GIGE L GRL+ +DAL M + I Sbjct: 419 APPAELAPNCSAGGVIGVLPGVVGMIQATEAIKLLIGIGEPLSGRLMRFDALAMKFSEIR 478 Query: 254 IRKDPSTPKITELVDYE----QFCGVVADDAAQAAKGSTITPRELRDWLDSGRKL-ALID 308 ++ P +EL E C A+ I P+ L+ L+ L+D Sbjct: 479 FKRRADCPCCSELRHSETRAPAACADTMPSPPSLAEERYIKPQVLKQVLEHHSSADVLLD 538 Query: 309 VRDPVEWDIVHIDGAQLIPKSLINSGEGLAKLPQDRTAVLYCKTGVRSAEALAAVKKAGF 368 VRD E ++ + G IP + ++ L +L +D T L C G R+ +A + + AGF Sbjct: 539 VRDASELEVCKLPGVVHIPLAELDG--HLDRLSRDNTHYLICYAGTRAEQAASTLLAAGF 596 Query: 369 SDAVHLQGGIVAWAKQMQPDMVMY 392 ++ LQGG+ W + ++PDM +Y Sbjct: 597 ANTKVLQGGMKHWVRDVEPDMPLY 620 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: 656 Number of extensions: 30 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: 620 Length adjustment: 34 Effective length of query: 358 Effective length of database: 586 Effective search space: 209788 Effective search space used: 209788 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: 52 (24.6 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