Align arginosuccinate synthetase (EC 6.3.4.5) (characterized)
to candidate WP_062060233.1 N456_RS18115 argininosuccinate synthase domain-containing protein
Query= reanno::Btheta:353286 (402 letters) >NCBI__GCF_001401755.1:WP_062060233.1 Length = 396 Score = 462 bits (1190), Expect = e-135 Identities = 218/395 (55%), Positives = 294/395 (74%), Gaps = 1/395 (0%) Query: 6 KKVVVAFSGGLDTSFTVMYLAKEKGYEVYAACANTGGFSEEQLKTNEENAYKLGAVKYVT 65 +KVV+A+SGGLDTS+ V YL E+ EV++ NTGGFSE++L E+ AYKLG+ ++ Sbjct: 2 EKVVLAYSGGLDTSYCVKYLIYEQNLEVHSILVNTGGFSEKELDEVEKRAYKLGSSSHIN 61 Query: 66 LDVTQEYYEKSLKYMVFGNVLRNGTYPISVSSERIFQALAIARYANEIGADAIAHGSTGA 125 + ++Y K++KY++FGNVL+N TYP+SVS+ERIFQA+ + YA +IGA IAHGSTGA Sbjct: 62 KTILDDFYNKAIKYLIFGNVLKNNTYPLSVSAERIFQAIEVINYAKKIGAKYIAHGSTGA 121 Query: 126 GNDQIRFDMTFLVLAPNVEIITLTRDMALSRQEEIDYLNKHGFSADFTKLKYSYNVGLWG 185 GNDQIRFD+ F LAP +EIIT RD+ LSR+EE+ YL KHG + K +YS N G+WG Sbjct: 122 GNDQIRFDVIFQTLAPEIEIITPIRDLKLSREEEMAYLQKHGVEYSWEKAQYSINKGIWG 181 Query: 186 TSICGGEILDSAQGLPETAYLKHVEKEGSEQLRLTFEKGELKAVNDETFDDPIQAIQKVE 245 TS+ G E L S LPETAY ++KE E + L F+KGEL +N D P++ IQK+E Sbjct: 182 TSVGGKETLTSHSTLPETAYPSQLQKEEEETITLNFKKGELIGINGHK-DSPVKNIQKLE 240 Query: 246 EIGAAYGIGRDMHVGDTIIGIKGRVGFEAAAPMLIIGAHRFLEKYTLSKWQQYWKDQVAN 305 +I +A+ IGRD+HVGDTIIGIKGRVGFEAAAPM+II AH LEK+ L+KWQQYWK+Q+AN Sbjct: 241 KIASAFAIGRDIHVGDTIIGIKGRVGFEAAAPMIIIKAHHLLEKHVLTKWQQYWKEQLAN 300 Query: 306 WYGMFLHESQYLEPVMRDIEAMLQESQRNVNGTAILELRPLSFSTVGVESEDDLVKTKFG 365 WYGM LHE YL+PVMR+IE ++++Q++V G + L+P F+ G+ES+ D++K+ FG Sbjct: 301 WYGMLLHEGNYLDPVMRNIEVFMEDAQKSVTGDVTVLLKPYHFTLQGIESDYDMMKSDFG 360 Query: 366 EYGEMQKGWTAEDAKGFIKVTSTPLRVYYNNHKDE 400 +YGEM WT++DAKGFIK+ ++Y+N + E Sbjct: 361 QYGEMNNSWTSDDAKGFIKIYGNANKIYHNVNPSE 395 Lambda K H 0.316 0.134 0.385 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: 527 Number of extensions: 26 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: 402 Length of database: 396 Length adjustment: 31 Effective length of query: 371 Effective length of database: 365 Effective search space: 135415 Effective search space used: 135415 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