Align Arginine biosynthesis bifunctional protein ArgJ; EC 2.3.1.35; EC 2.3.1.1 (characterized)
to candidate 206250 DVU0823 arginine biosynthesis bifunctional protein ArgJ
Query= SwissProt::Q9Z4S1 (397 letters) >MicrobesOnline__882:206250 Length = 393 Score = 283 bits (725), Expect = 5e-81 Identities = 171/397 (43%), Positives = 236/397 (59%), Gaps = 11/397 (2%) Query: 4 PRGFSYAGVHCRIKRK-RKDLGIIFSEVPCTAAGVFTTNVVKAAPVIYDMEILGKNPSGI 62 P+GF +A V +++ R DL +I S+ P TAAGVFTTN +AAPV+ E L P Sbjct: 5 PKGFRFATVSAGFRKEARPDLALIVSDTPATAAGVFTTNRFQAAPVVVARENLSARPVA- 63 Query: 63 RAITVNSGVANACTGEQGMINARRMAEKTAKELNIPVESVLVSSTGVIGVQLPMEKVESG 122 RA+ +NSG ANACTG++GM N R + K IP VL +STGVIG QL M+K Sbjct: 64 RAVVINSGQANACTGDEGMTNCRTTLDLVGKACGIPAAEVLPASTGVIGAQLHMDKWREA 123 Query: 123 IEEAVKNLSKDPV-PFAEAIMTTDTKIKIHSKKVTIEGKEITVLGIAKGSGMIHPNMATM 181 L ++ FA AIMTTD K+ +++ I G + ++G+AKG+GMI PNMATM Sbjct: 124 APRLAAALGQNTHHDFARAIMTTDAFPKVAERELAIAGTTVRLVGMAKGAGMICPNMATM 183 Query: 182 LSFITTDANVSEDALKKLLKISVDDSYNMIDVDGDTSTNDMVIILANGLAGNAPIQEETD 241 LS + DA V+ +A ++L +VD ++N + VDGDTSTND V LANG +G + E + Sbjct: 184 LSVVLCDAAVTPEAWQRLFLDAVDRTFNRVTVDGDTSTNDTVFGLANGASG---VTVEGE 240 Query: 242 GFWKLYEAVHEVNQVLAEKIVEDGEGATKVIEVEVRNAPDRNSARLIARAIVSSNLVKTA 301 KL EA+ +V LA +V+DGEGATKV+ V+V A D A +AR + S LVKTA Sbjct: 241 DLAKLGEALTDVLARLAYMLVQDGEGATKVMRVKVSGAVDDAEAEAVARTVGHSQLVKTA 300 Query: 302 IYGEDANWGRVIAAAGYSGAQFDPDRLDLFFESAAGRIKVAENGQGVDFDEDT-AKKILS 360 +YG DANWGR++AA G SGA F + + + + G +++ NGQ D D DT ++ L Sbjct: 301 MYGRDANWGRIVAAVGRSGASFKAEDVVV---TLCG-VELFRNGQPTDLDFDTLLREPLK 356 Query: 361 EKKVKIILDMKQGKELARAWGCDLTEKYVEINGRYRT 397 + V + +++ G DLT YV N YR+ Sbjct: 357 GRDVTVDIELGAGTGHYELLASDLTHDYVNCNADYRS 393 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: 371 Number of extensions: 19 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: 397 Length of database: 393 Length adjustment: 31 Effective length of query: 366 Effective length of database: 362 Effective search space: 132492 Effective search space used: 132492 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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