Align Probable adenylyltransferase/sulfurtransferase MoeZ; EC 2.7.7.-; EC 2.8.1.- (characterized)
to candidate Echvi_1891 Echvi_1891 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2
Query= SwissProt::P9WMN7 (392 letters) >FitnessBrowser__Cola:Echvi_1891 Length = 360 Score = 205 bits (521), Expect = 2e-57 Identities = 128/363 (35%), Positives = 196/363 (53%), Gaps = 18/363 (4%) Query: 22 RYSRHLIIPDLGVDGQKRLKNARVLVIGAGGLGAPTLLYLAAAGVGTIGIVDFDVVDESN 81 RY + + + G Q +L ++ VL+IGAGGLG P YL GVGT+ I+D D V ESN Sbjct: 5 RYQKQIRLKSFGKQSQDKLASSSVLIIGAGGLGTPVAQYLNGVGVGTLAIMDQDTVAESN 64 Query: 82 LQRQVIHGVADVGRSKAQSARDSIVAINPLIR-VRLHELRLAPSNAVDLFKQYDLILDGT 140 L RQ + DVG+ K + NP R + + E L P NA+ YDLI+D + Sbjct: 65 LARQTLFTPEDVGKHKTDVLIQYLRRQNPSTRFINVREF-LTPVNALQELADYDLIVDAS 123 Query: 141 DNFATRYLVNDAAVLAGKPYVWGSIYRFEGQASVF-WEDAPDGLGVNYRDLYPEPPPPGM 199 DNF TRYLVNDA V+ KP+++G+++ FEGQ SV +++ P YR L+PE P Sbjct: 124 DNFGTRYLVNDACVMLDKPFIYGALHEFEGQVSVMNYQNGP-----TYRCLFPEVGDPSA 178 Query: 200 VPSCAEGGVLGIICASVASVMGTEAIKLITGIGETLLGRLLVYDALEMSYRTITIRKDPS 259 + +C E GVLGI+ + + EA+K++TGIGE L G+LL+ D L ++ + + P Sbjct: 179 ILNCDENGVLGILPGLIGTYQALEAVKVLTGIGEPLAGKLLIIDTLAQTHLKVGLTSVPE 238 Query: 260 TPKITELVD-YEQFCGVVADDAAQAAKGSTITPRELRDWLDSGRKLALIDVRDPVEWDIV 318 I +L + Y Q + +++T E + + +IDVR+ E+D Sbjct: 239 NQSIRKLQENYGQ------PMCSTDLPVTSLTCEEFWSKREGDSQHQIIDVRNEGEFDSG 292 Query: 319 HIDGAQLIPKSLINSGEGLAKLPQDRTAVLYCKTGVRSAEALAAVKKAGFSDAVH-LQGG 377 H+D AQ IP S + E ++ + +L C++G RS +A ++ ++ L+GG Sbjct: 293 HLDSAQNIPLSQLT--ERHQEINEKAPVILICQSGKRSLQAAQLLQSLHPEQIIYNLEGG 350 Query: 378 IVA 380 + A Sbjct: 351 MNA 353 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: 356 Number of extensions: 22 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: 360 Length adjustment: 30 Effective length of query: 362 Effective length of database: 330 Effective search space: 119460 Effective search space used: 119460 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