Align Predicted argE by GapMind curators (no experimental data)
to candidate WP_101443903.1 BD749_RS08100 amidohydrolase
Query= predicted:W3Y6L2 (394 letters) >NCBI__GCF_002846395.1:WP_101443903.1 Length = 443 Score = 226 bits (575), Expect = 1e-63 Identities = 143/403 (35%), Positives = 214/403 (53%), Gaps = 21/403 (5%) Query: 12 ASQYKEQVVAWRRHIHSHPELSGEEKETSAFIQSVLTDLGIPFKADVYKYAVIGEIKGAF 71 A + + +V+ WRR H +PEL E +T+ I + L LG+ + V V+G +KG Sbjct: 39 ADKLEPKVIEWRRDFHQYPELGNRETKTAEKIAAHLRKLGMEVQTGVAHTGVVGILKGGK 98 Query: 72 DGPVVGLRADMDALPITEVTGLPFTS--------ENPGVMHACGHDSHMAILLGAAAILQ 123 GPVV LRAD+D LP+TE LPF S + GVMHACGHD+H+A+L+GAA IL Sbjct: 99 PGPVVALRADIDGLPVTERVDLPFASKERSTYNGQEVGVMHACGHDTHIAMLMGAAEILA 158 Query: 124 SVKDQLHGTVKLVIQPAEEEALI---KGAQGIVDSGVL---DDVDEIYGLHVWPQLPVGT 177 +K+ L GTVK + QPAEE + I GA +V GVL + I+GLH+ Q VGT Sbjct: 159 GMKNDLKGTVKFIFQPAEEGSPIGEEGGAALMVKEGVLGKGPKPEVIFGLHINSQTEVGT 218 Query: 178 VGLKKGNLMAASDRFLVHIKGKATHGAEPHNGIDAIVAAANWIVNVESMVARETN-PMDN 236 + G MA++D F + +KGK +HGA P +GID IV +A I ++++++R+T P Sbjct: 219 IKYTPGGTMASADIFRIKVKGKQSHGAYPWSGIDPIVVSAQIINGLQTIISRQTQLPEGA 278 Query: 237 LVCTIGVFNSGDRYNVGSGDAYLEGTCRTYDPAKRDYIERRLGESLKALDMMFGTTSTLE 296 V T+G + G R N+ + +EGT R D + + ++ + + G + + Sbjct: 279 AVITVGSIHGGVRNNIIPEEVLMEGTIRALDVEMQKKLHEKINLTATKIAESSGAVAEVV 338 Query: 297 YRRGHGATINDADAIDYVTHIVKTYLGKDAVVHPEFPSMAAEDFSAYLNKIKGAFLWLGT 356 T ND + + + T G+D VV + + AEDF+ Y KI G FL++G Sbjct: 339 IIPQTPVTYNDPALTERMLPTLHTVAGRDKVVLAKAVT-GAEDFAFYQEKIPGLFLFVGG 397 Query: 357 GFEGN-----PALHNAAFTIDESILEPGITMMAGIAAELLQEK 394 +G H F IDES L+ G+ + + ++ K Sbjct: 398 MSKGKKPEEVAPHHTPDFFIDESGLKLGVKTLTSLTLNYMEGK 440 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: 442 Number of extensions: 26 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: 443 Length adjustment: 32 Effective length of query: 362 Effective length of database: 411 Effective search space: 148782 Effective search space used: 148782 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