Align Predicted argE by GapMind curators (no experimental data)
to candidate WP_085635731.1 MGEO_RS05575 amidohydrolase
Query= predicted:W3Y6L2 (394 letters) >NCBI__GCF_002115805.1:WP_085635731.1 Length = 387 Score = 222 bits (566), Expect = 1e-62 Identities = 128/385 (33%), Positives = 207/385 (53%), Gaps = 14/385 (3%) Query: 8 IKQYASQYKEQVVAWRRHIHSHPELSGEEKETSAFIQSVLTDLGIP-FKADVYKYAVIGE 66 +K ++ ++++ AWRR H +PE+ E TSA + L + G + + V+G Sbjct: 3 VKNRFAELQDEITAWRRDFHENPEILFETHRTSALVAERLKEFGCDEIVTGIGRTGVVGV 62 Query: 67 IKGAFD--GPVVGLRADMDALPITEVTGLPFTSENPGVMHACGHDSHMAILLGAAAILQS 124 IKG D G V+GLRADMDALPI E TGL + S+ G MHACGHD H A+LLGAA L Sbjct: 63 IKGKSDTSGKVIGLRADMDALPIHEQTGLEYKSKTDGAMHACGHDGHTAMLLGAAKYLSE 122 Query: 125 VKDQLHGTVKLVIQPAEEEALIKGAQGIVDSGVLD--DVDEIYGLHVWPQLPVGTVGLKK 182 ++ GTV ++ QPAEE G + + + G+++ + E+YG+H WP PVG+ ++ Sbjct: 123 TRN-FDGTVVVIFQPAEEGG--GGGREMCEDGMMERWGIQEVYGMHNWPGKPVGSFAIRP 179 Query: 183 GNLMAASDRFLVHIKGKATHGAEPHNGIDAIVAAANWIVNVESMVARETNPMDNLVCTIG 242 G AA+D+F + +G+ H A+P +D V AA ++ ++++ +R +P+D +V ++ Sbjct: 180 GAFFAATDQFDITFEGRGGHAAKPQETVDTTVMAAQAVLALQTIASRNADPIDQVVVSVT 239 Query: 243 VFNSGDR-YNVGSGDAYLEGTCRTYDPAKRDYIERRLGESLKALDMMFGTTSTLEYRRGH 301 F + + +NV L+GT RT RD E R+ + + FG T + Y RG+ Sbjct: 240 SFETSSKAFNVIPQRVQLKGTVRTMSKDMRDLAETRIKDICAGIAATFGGTVDVTYHRGY 299 Query: 302 GATINDADAIDYVTHIVKTYLGKDAVVHPEFPSMAAEDFSAYLNKIKGAFLWLGTGFEGN 361 +N + D+ + K G D P M EDF+ L + GA++ +G G + Sbjct: 300 PVMVNHEEQTDFAAEVAKAVSG-DCEEAPLV--MGGEDFAFMLEERPGAYILVGNG--DS 354 Query: 362 PALHNAAFTIDESILEPGITMMAGI 386 A+H+ + ++ + G + A I Sbjct: 355 AAVHHPEYNFNDEAIPAGCSWWAEI 379 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: 383 Number of extensions: 15 Number of successful extensions: 6 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: 387 Length adjustment: 31 Effective length of query: 363 Effective length of database: 356 Effective search space: 129228 Effective search space used: 129228 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