Align Arginine deiminase; ADI; EC 3.5.3.6; Arginine dihydrolase; AD (uncharacterized)
to candidate CA265_RS10470 CA265_RS10470 amidinotransferase
Query= curated2:Q0TUR5 (413 letters) >FitnessBrowser__Pedo557:CA265_RS10470 Length = 481 Score = 142 bits (358), Expect = 2e-38 Identities = 141/493 (28%), Positives = 216/493 (43%), Gaps = 107/493 (21%) Query: 7 LNVTSEIGRLKTVLLHRPGEEIENLTPDLLDRLLFDDIPYLKVARE-EHDAFAQTLREAG 65 ++V +EIGRL+ +L+H P + + P LF+DI +L R+ E+D + + L Sbjct: 10 VSVNTEIGRLRKLLIHSPDSGLGKVVPSKAQDWLFEDIVHLDTIRKGEYDYYIKLL---- 65 Query: 66 VEVLYLEVLAAEAIETSDEVKQQFISEFIDEAGVESE--------RLKEALIEYFNSFSD 117 + +L+ D++K + +S+ EA + +++IE N S+ Sbjct: 66 --MYFLD---------PDKIKGK-LSDIDSEASNRNFYKPNHPDFHNSKSVIEIQNLLSE 113 Query: 118 ---NKAMVDKMMAGVRKEELKDYHRESLYD-----QVNNVY--------PFVCDPMPNLY 161 N+++ K++A V E Y + Q+ ++ + P+PNL Sbjct: 114 MLENESIRKKLVAAVCAIEGCTYKVQLALTNTDPKQLAEIFISGTLADDTMIFAPIPNLI 173 Query: 162 FTRDPFATIGHGITLNHMRTDTRNRETIFAKYIFRHHPRFEG--------KDIPFWFNRN 213 FTRD TI + I LN R RET+ +YIF +HP FE D+ F R Sbjct: 174 FTRDVGTTINNHILLNKPAKKARVRETLLMRYIFFNHPLFEDYRNNILEIPDVTMHFLRP 233 Query: 214 D-----KTSLEGGDELILSKEILAVGISQRTDSASVEKLAKKLLYYPDTSFKTVLAFKIP 268 T+LEGGD +++S + +G S+RT + A KLL+ D K V KIP Sbjct: 234 GDEPAFSTTLEGGDVMMVSPNHVLIGCSERTSEHGANE-AIKLLFDQDVVEK-VTVVKIP 291 Query: 269 VSRAFMHLDTVFTQVDYDKFTV-----HPGIVGPLEVYALTKDPENDGQLLVTEEVD--- 320 R +MHLDTVFTQV + + + H P E K+PE +L T + Sbjct: 292 SKRDYMHLDTVFTQVKRNTWVILNSIAHSPKYNPYEPINFLKEPE---KLEATTAIQFTK 348 Query: 321 ----------TLENILKKYLDRDIK------LIKCGGGDEIIAAREQWNDGSNTLAIAPG 364 +E +L D+K +I G +REQW D N LAI G Sbjct: 349 ANPSEPKHFKHVEALLNDISQNDLKSTEPTQIIYSGNNQFPYDSREQWTDSCNLLAIKDG 408 Query: 365 EVVVYSRNYVTNEILEKEGI------------------------KLHVIPSSELSRGRGG 400 V+ Y RN T E + G L ++PS+ELSR RGG Sbjct: 409 VVLGYDRNDKTVEAFKTAGFDVVDVKDLIQDLESGKVNVETITDTLILMPSAELSRARGG 468 Query: 401 PRCMSMPLIREDL 413 CMS+P++R+++ Sbjct: 469 FHCMSLPILRDNI 481 Lambda K H 0.319 0.138 0.396 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: 478 Number of extensions: 32 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 413 Length of database: 481 Length adjustment: 32 Effective length of query: 381 Effective length of database: 449 Effective search space: 171069 Effective search space used: 171069 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 Sep 17 2021. The underlying query database was built on Sep 17 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