Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_057687251.1 ABB28_RS15375 acetylglutamate kinase
Query= BRENDA::A0A0H2X8L7 (447 letters) >NCBI__GCF_001431535.1:WP_057687251.1 Length = 442 Score = 743 bits (1919), Expect = 0.0 Identities = 382/447 (85%), Positives = 407/447 (91%), Gaps = 5/447 (1%) Query: 1 MSLPAQPHKQTRQTIVRLLSSMASAKEISQYLKRFSQLDAKRFAVVKVGGAVLRDDLEAL 60 MS QPH+QTRQTIVRLLSSMASAKEISQYLKRFSQLDAKRFAVVKVGGAVLRDDLEAL Sbjct: 1 MSPALQPHRQTRQTIVRLLSSMASAKEISQYLKRFSQLDAKRFAVVKVGGAVLRDDLEAL 60 Query: 61 TSSLSFLQEVGLTPIVLHGAGPQLDAELSAAGIEKQTVNGLRVTSPHALAIVRKVFQASN 120 TSSLSFLQEVGLTPIVLHGAGPQLD EL+AAGIEKQTVNGLRVTSP ALAIVR+VFQ SN Sbjct: 61 TSSLSFLQEVGLTPIVLHGAGPQLDTELAAAGIEKQTVNGLRVTSPEALAIVRQVFQQSN 120 Query: 121 LKLVEALQQNGARATSITGGVFEAEYLNRDTYGLVGEVKAVNLAPIEASLQAGSIPVITS 180 L+LVEALQQNGARATSITGGVFEAEY+++ TYGLVGEVK VNLAPIEASL+AGSIPVITS Sbjct: 121 LRLVEALQQNGARATSITGGVFEAEYMDQATYGLVGEVKKVNLAPIEASLRAGSIPVITS 180 Query: 181 LGETPSGQILNVNADFAANELVQELQPYKIIFLTGTGGLLDAEGKLIDSINLSTEYDHLM 240 LGET SGQILNVNADFAANELVQELQPYKIIFLTGTGGLLD EGK+IDSINLSTEY+HLM Sbjct: 181 LGETRSGQILNVNADFAANELVQELQPYKIIFLTGTGGLLDEEGKVIDSINLSTEYEHLM 240 Query: 241 QQPWINGGMRVKIEQIKDLLDRLPLESSVSITRPADLAKELFTHKGSGTLVRRGERVLRA 300 QPWI+GGM+VKIEQIK LLDRLPLESSVSITRPADLAKELFTHKGSGTLVR+GERVLRA Sbjct: 241 TQPWIHGGMKVKIEQIKSLLDRLPLESSVSITRPADLAKELFTHKGSGTLVRKGERVLRA 300 Query: 301 TSWDELDLPRLTSLIESSFGRTLVPDYFSNTKLLRAYVSENYRAAVILTDEGMLGASALI 360 TSWDELDLPRL LIESSFGR LVPDYF T+LLRAYVSENYR AVILTDE + + Sbjct: 301 TSWDELDLPRLRGLIESSFGRVLVPDYFDKTRLLRAYVSENYRTAVILTDE-----AEGV 355 Query: 361 YLDKFAVLDDAQGEGLGRAVWNVMREETPQLFWRSRHNNQVNIFYYAESDGCIKQEKWKV 420 YLDKFAVLDDAQGEGLGRAVWNVM +ETPQLFWRSR+ N +N FYYAESDGC KQ WK Sbjct: 356 YLDKFAVLDDAQGEGLGRAVWNVMLDETPQLFWRSRNGNPINHFYYAESDGCYKQGTWKT 415 Query: 421 FWYGLENFEQIQHCVAHCATRQPTLLG 447 FW+G + F++I+ V HCA R P+LLG Sbjct: 416 FWFGADGFDRIKAYVDHCAQRAPSLLG 442 Lambda K H 0.318 0.134 0.383 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: 709 Number of extensions: 13 Number of successful extensions: 2 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: 447 Length of database: 442 Length adjustment: 32 Effective length of query: 415 Effective length of database: 410 Effective search space: 170150 Effective search space used: 170150 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: 51 (24.3 bits)
This GapMind analysis is from Apr 10 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