Align Guanidinobutyrase; EC 3.5.3.7 (characterized)
to candidate PfGW456L13_2689 Agmatinase (EC 3.5.3.11)
Query= SwissProt::Q9I3S3 (319 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2689 Length = 333 Score = 157 bits (397), Expect = 3e-43 Identities = 97/284 (34%), Positives = 153/284 (53%), Gaps = 19/284 (6%) Query: 36 DALDA--AFVGVPLDIGTSLRSGTRFGPREIRAESVMIRPYNMATGAAPFD-------SL 86 DALDA A +GVP D+GT RSG RFGPR IR S + + D + Sbjct: 31 DALDADVAVLGVPNDMGTQWRSGARFGPRGIREASTLFSFGHAGAYDHEDDVMYLTASDV 90 Query: 87 NVADIGDVAINTFNLLEAVRIIEQEYDRILGHGILPLTLGGDHTITLPILRAIKKKHGKV 146 + D+GD I ++ + + E +IL G++P+ LGGDH++ P+++A + + G + Sbjct: 91 RMVDVGDADIVHTDMATSNKNTEYAVRKILDAGVMPVVLGGDHSVHAPVIKAFEGR-GPI 149 Query: 147 GLVHVDAHADVNDHMFGEKIAHGTTFRRAVEEDLLDCDRVVQIGLR-AQGYTAEDFNWSR 205 ++H DAH D D G + HG RRA E + + + Q+G+R +D+ + Sbjct: 150 HIIHFDAHLDFVDERHGVRYGHGNPLRRASEMNHIV--GMTQMGIRNVSSSNRDDYEAAH 207 Query: 206 KQGFRVVQAEECWHKSLEPLMAEVREKVGGGPVYLSFDIDGIDPAWAPGTGTPEIGGLTT 265 + G +++ + +E ++A + + + Y++ DIDG DP+ APGTGTP GG Sbjct: 208 EAGSKILSVRDVRRLGVEGVLALIPQNIN---YYITIDIDGFDPSIAPGTGTPSHGGFLY 264 Query: 266 IQAMEIIRGCQGL---DLIGCDLVEVSPPYDTTGNTSLLGANLL 306 + +EII+ +++G DLVEV+P YD TG TS+L A LL Sbjct: 265 YEVLEIIQALAKRSKGNIVGMDLVEVAPVYDPTGMTSILAAQLL 308 Lambda K H 0.321 0.141 0.428 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: 283 Number of extensions: 18 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: 319 Length of database: 333 Length adjustment: 28 Effective length of query: 291 Effective length of database: 305 Effective search space: 88755 Effective search space used: 88755 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 (21.8 bits) S2: 48 (23.1 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