Align Agmatine deiminase; Agmatine iminohydrolase; Protein EMBRYO DEFECTIVE 1873; EC 3.5.3.12 (characterized)
to candidate Pf1N1B4_4325 Agmatine deiminase (EC 3.5.3.12)
Query= SwissProt::Q8GWW7 (383 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4325 Length = 350 Score = 251 bits (640), Expect = 3e-71 Identities = 150/376 (39%), Positives = 202/376 (53%), Gaps = 50/376 (13%) Query: 12 GYYMPAEWDSHAQTWIGWPERQ----DNWRHNALPAQRVFADVAKAISKFEPVTVCASPA 67 G+ MPAEW HA TW+ WP Q W Q FA VA AI++FEPV + P+ Sbjct: 10 GWVMPAEWVRHAATWMVWPHNQALWESGWGVTLALVQEDFARVANAIARFEPVKMVVDPS 69 Query: 68 QWENARKQLPEDIRVVEMSMNDSWFRDSGPTFIVRKRPVKLSSLNRNIAGIDWNFNAWGG 127 +A +I ++E+++NDSW RDSGP+F+ ++ + +AG+ W FNAWGG Sbjct: 70 AVSSAHALCGPNIELIELAVNDSWCRDSGPSFVCHRQ--------QGLAGVSWRFNAWGG 121 Query: 128 ANDGCYNDWSHDL--LVSRKILALERIPRFQHSMILEGGSIHVDGEGTCLVTEECLLNKN 185 + +HDL ++R+ L + F + EGG+IHVDGEGT + TE LLN N Sbjct: 122 KS-------AHDLDESLARRALNHLGVQCFGTPLSNEGGAIHVDGEGTLITTESVLLNPN 174 Query: 186 RNPHMSKEQIEEELKKYLGVQSFIWLPRGLYGDED------TNGHIDNMCCFARPGVVLL 239 RNP M+K ++EE + LGV+ IWLP GD D T+GH+D +C FARPGV+L+ Sbjct: 175 RNPGMNKAEMEEIFTRLLGVKKTIWLP----GDPDHVTGDMTDGHVDGVCAFARPGVLLV 230 Query: 240 SWTDDETDPQYERSVEALSVLSNSIDARGRKIQVIKLYIPEPLYMTEEESSGITQDGEAI 299 T D+ E E L + DA+GRK ++I+LY E S + E Sbjct: 231 DATHDKHSVYAEVVRENRRALELATDAQGRKFELIELY---------EASDAVDAGAEV- 280 Query: 300 PRLAGTRLAASYVNFYIANGGIIAPQFGDPIRDKEAIRVLSDTFPHHSVVGIENAREIVL 359 ASY NFYIAN II P +G D A +VL+ FP H VV + + Sbjct: 281 -------FCASYTNFYIANNAIIMPAYGID-ADHAAAKVLAQAFPDHEVVPV-RINHLAH 331 Query: 360 AGGNIHCITQQQPAEP 375 GG +HCITQQQPA P Sbjct: 332 GGGGVHCITQQQPAWP 347 Lambda K H 0.317 0.134 0.420 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: 423 Number of extensions: 25 Number of successful extensions: 8 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: 383 Length of database: 350 Length adjustment: 30 Effective length of query: 353 Effective length of database: 320 Effective search space: 112960 Effective search space used: 112960 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: 49 (23.5 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