Align Arginine biosynthesis bifunctional protein ArgJ; EC 2.3.1.35; EC 2.3.1.1 (characterized)
to candidate 642683833 Cphamn1_1336 N-acetylglutamate synthase (EC 2.3.1.1)/glutamate N-acetyltransferase (EC 2.3.1.35)
Query= SwissProt::Q9Z4S1 (397 letters) >IMG__ChlphaBS1_FD:642683833 Length = 426 Score = 318 bits (815), Expect = 2e-91 Identities = 186/400 (46%), Positives = 250/400 (62%), Gaps = 12/400 (3%) Query: 2 FVPRGFSYAGVHCRIKRKRKDLGIIFSEVPCTAAGVFTTNVVKAAPVIYDMEILGKNPSG 61 F P+G++ IK ++DL +I +E P +AA VFT N+ AAPV E L + S Sbjct: 35 FWPQGYAAGTASAGIKSGKRDLMVIAAEKPASAAAVFTRNLCSAAPVFLSKEHLAQASSS 94 Query: 62 IRAITVNSGVANACTGEQGMINARRMAEKTAKELNIPVESVLVSSTGVIGVQLPMEKVES 121 +RAI NSG AN+ TG++G+ +AR MAEKTA+ L I VLVSSTGVIGV LP EK++ Sbjct: 95 MRAIVCNSGNANSATGDKGLRDARFMAEKTAEVLGIEPHEVLVSSTGVIGVPLPAEKIKG 154 Query: 122 GIEEAVKNLSKDP-VPFAEAIMTTDTKIKIHSKKVTIEGKEITVLGIAKGSGMIHPNMAT 180 ++ + +D AEAIMTTDT K + V++ + + GIAKGSGMI P+MAT Sbjct: 155 ALDSFSAVVLEDSCAKAAEAIMTTDTFPKFFALDVSLSSSVVRICGIAKGSGMICPDMAT 214 Query: 181 MLSFITTDANVSEDALKKLLKISVDDSYNMIDVDGDTSTNDMVIILANGLAGNAPIQEET 240 ML+F+ TDAN+S+ L+ +L + ++S+N I VDGDTSTNDM I LAGN QE Sbjct: 215 MLAFMVTDANISQTLLQDMLSKANENSFNTITVDGDTSTNDMAAI----LAGNGDAQEIL 270 Query: 241 DGFWK---LYEAVHEVNQVLAEKIVEDGEGATKVIEVEVRNAPDRNSARLIARAIVSSNL 297 G Y A+ + LA IV DGEGATK++ + V AP + A AR I +S+L Sbjct: 271 PGSRDAEIFYSALESLMTFLARLIVRDGEGATKLVAIHVEGAPSVSDAHKAARTIANSSL 330 Query: 298 VKTAIYGEDANWGRVIAAAGYSGAQFDPDRLDLFFESAAGRIKVAENGQGVDFDEDTAKK 357 VKTA++GEDANWGR+IAAAG SGA+F+P+ + + F+ + + E G DF E AKK Sbjct: 331 VKTALHGEDANWGRLIAAAGRSGAEFNPENVSVRFDD----LVILEPGYVSDFSEKEAKK 386 Query: 358 ILSEKKVKIILDMKQGKELARAWGCDLTEKYVEINGRYRT 397 ILS + I L + +G A CDL+++YV ING YRT Sbjct: 387 ILSRDEYTITLTLGKGPGKAVVHTCDLSKEYVTINGSYRT 426 Lambda K H 0.315 0.133 0.371 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: 424 Number of extensions: 16 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: 397 Length of database: 426 Length adjustment: 31 Effective length of query: 366 Effective length of database: 395 Effective search space: 144570 Effective search space used: 144570 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 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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