Align Predicted argE by GapMind curators (no experimental data)
to candidate WP_101443608.1 BD749_RS04195 amidohydrolase
Query= predicted:W3Y6L2 (394 letters) >NCBI__GCF_002846395.1:WP_101443608.1 Length = 371 Score = 251 bits (642), Expect = 2e-71 Identities = 151/376 (40%), Positives = 211/376 (56%), Gaps = 7/376 (1%) Query: 20 VAWRRHIHSHPELSGEEKETSAFIQSVLTDLGIPFKADVYKYAVIGEIKGAFDGPVVGLR 79 + WRRHIH HPE+S EE++TS +++ VL+ L K ++IG +KGA G V R Sbjct: 1 MTWRRHIHQHPEVSFEEEQTSKYVEEVLSKLPNVEVIKPAKTSLIGVLKGAKPGRTVAFR 60 Query: 80 ADMDALPITEVTGLPFTSENPGVMHACGHDSHMAILLGAAAILQSVKDQLHGTVKLVIQP 139 ADMDALPI E TGLP+ S+ V HACGHD+H A+LL AA L ++ +L GTV + Q Sbjct: 61 ADMDALPIQEETGLPYASKEKNVSHACGHDAHTAMLLATAATLSKMQQELKGTVYFIFQH 120 Query: 140 AEEEALIKGAQGIVDSGVLDDVDEIYGLHVWPQLPVGTVG-LKKGNLMAASDRFLVHIKG 198 AEE+ GA IV+SG L V+ +G+HV P P G VG L G A D F ++I G Sbjct: 121 AEEQP-PGGAIDIVESGELKGVEAFFGMHVLPNFPAGHVGILPDGAASTAQDIFNLNIIG 179 Query: 199 KATHGAEPHNGIDAIVAAANWIVNVESMVARETNPMDNLVCTIGVFNSGDRYNVGSGDAY 258 K +HG+ PH GID IV A + ++++V+R P + V TIG F SGD +NV + A Sbjct: 180 KGSHGSMPHLGIDPIVVGAAIVSALQTVVSRNVEPGEMTVVTIGKFQSGDAFNVIADRAE 239 Query: 259 LEGTCRTYDPAKRDYIERRLGESLKALDMMFGTTSTLEYRRGHGATINDADAIDYVTHIV 318 L + RT R +E+R+ E ++++ +G T L+Y + A ND V Sbjct: 240 LAASIRTTSDKTRKQVEQRVKEIIESITKAYGATYELDYINTYPAIQNDKALNAQVRKSA 299 Query: 319 KTYLGKDAVVHPEFPSM-AAEDFSAYLNKIKGAFLWLGTGFEGNPALHNAAFTIDESILE 377 LGK+ V + P M A+EDF+ Y +F+ LG G PA HN F +DES L+ Sbjct: 300 AAILGKEQVF--DAPMMTASEDFAYYRKIAPVSFMTLGIG--DGPANHNPGFKVDESALQ 355 Query: 378 PGITMMAGIAAELLQE 393 G+ + + L + Sbjct: 356 NGVKAQVQLILDYLNK 371 Lambda K H 0.318 0.136 0.401 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: 392 Number of extensions: 17 Number of successful extensions: 5 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: 394 Length of database: 371 Length adjustment: 30 Effective length of query: 364 Effective length of database: 341 Effective search space: 124124 Effective search space used: 124124 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 Jul 26 2024. The underlying query database was built on Jul 25 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