Align Predicted argE by GapMind curators (no experimental data)
to candidate WP_085641283.1 MGEO_RS18825 amidohydrolase
Query= predicted:W3Y6L2 (394 letters) >NCBI__GCF_002115805.1:WP_085641283.1 Length = 386 Score = 230 bits (587), Expect = 5e-65 Identities = 132/374 (35%), Positives = 203/374 (54%), Gaps = 8/374 (2%) Query: 14 QYKEQVVAWRRHIHSHPELSGEEKETSAFIQSVLTDLGIP-FKADVYKYAVIGEIKGAFD 72 ++ E + WRRH+H HPELS + ET+AF+ L + G+ + + V+ I+G D Sbjct: 9 EFAEDMKTWRRHLHMHPELSLDCHETAAFVVERLKEFGVDEIHEGIAQSGVVALIRGQGD 68 Query: 73 GPVVGLRADMDALPITEVTGLPFTSENPGVMHACGHDSHMAILLGAAAILQSVKDQLHGT 132 GPV GLRADMDALP+ E TG + S PG MHACGHD H +LLGAA L + + GT Sbjct: 69 GPVTGLRADMDALPMDETTGAEWASTIPGKMHACGHDGHTTMLLGAARYLTETR-KFKGT 127 Query: 133 VKLVIQPAEEEALIKGAQGIVDSGVLD--DVDEIYGLHVWPQLPVGTVGLKKGNLMAASD 190 V L+ QPAEE + G + +V+ G+++ D++E+Y +H P G + G +MAA D Sbjct: 128 VALIFQPAEET--VGGGRIMVEEGIMERFDIEEVYAIHTDPFAEEGQLRTTPGPIMAAVD 185 Query: 191 RFLVHIKGKATHGAEPHNGIDAIVAAANWIVNVESMVARETNPMDNLVCTIGVFNSGDRY 250 F + ++G HGA P + D + A ++++V+R T+P+ LV ++ + + G Sbjct: 186 DFHITVRGVGGHGAYPASCKDPMPCALAIGQALQTIVSRNTDPLLPLVVSLTMISGGTAT 245 Query: 251 NVGSGDAYLEGTCRTYDPAKRDYIERRLGESLKALDMMFGTTSTLEYRRGHGATINDADA 310 N+ L GT R++D RD +ERR+ E +G ++Y R + AT+N Sbjct: 246 NIIPETVKLSGTVRSFDADLRDMVERRITEIAVGQAASYGVAVEIDYIRNYPATVNHEAQ 305 Query: 311 IDYVTHIVKTYLGKDAVVHPEFPSMAAEDFSAYLNKIKGAFLWLGTGFEGNPALHNAAFT 370 ++ + + +G + P M AEDFS L GAFL+LG G P+ H+ AF Sbjct: 306 TEFAGRVAQEVVGPAKTITDLRPEMGAEDFSYMLEARPGAFLFLGQGI--GPSCHHPAFD 363 Query: 371 IDESILEPGITMMA 384 ++ + G + A Sbjct: 364 FNDEVATIGASFFA 377 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: 410 Number of extensions: 26 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: 394 Length of database: 386 Length adjustment: 31 Effective length of query: 363 Effective length of database: 355 Effective search space: 128865 Effective search space used: 128865 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