Align 4-guanidinobutyramide hydrolase; SubName: Full=Carbon-nitrogen hydrolase (characterized, see rationale)
to candidate PfGW456L13_2675 5-aminopentanamidase (EC 3.5.1.30)
Query= uniprot:A0A291T0X0 (265 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2675 Length = 279 Score = 99.8 bits (247), Expect = 6e-26 Identities = 91/260 (35%), Positives = 127/260 (48%), Gaps = 18/260 (6%) Query: 16 GDPAGNLKVLDEAAARAAADGAGLLVTAEMFLTGYAIGGGVR--DLAEPADGPSGRAVAD 73 GD A N + + A +AA GA ++V E+ +GY LAE DGP+ + Sbjct: 19 GDLAYNRTLTERAIRQAAFQGAQVVVLPELVQSGYLFADRFEALGLAETVDGPTLQLWQT 78 Query: 74 IAAAHGLAILYGYPER-HAGAVHNSARLVGADGTELANYRKTHLYGCFERASFTPGETP- 131 +A L I+ G+ ER A + NSA ++ A+G A YRK HL+ E+ FT G+ P Sbjct: 79 LARELNLVIVGGFCERLPADELANSAAMIDANGLR-AVYRKAHLWDA-EKDIFTAGDAPP 136 Query: 132 -VVQATVGELTVGILVCYDVEFPENVRAHALAGTDLLLVPT----AQMHPFEFVAESL-I 185 VV+ G L G+L+CYD+EFPE VR ALAG +LL P E AE L + Sbjct: 137 PVVETLHGRL--GMLICYDLEFPEWVRLAALAGAELLCAPVNWPDGPRPQTERPAEVLRV 194 Query: 186 PVRAFESQMYIAYVNRSGPEGEFDFVGLSCLAGPDGATCLRAGR--GEELLLGDVDPKLL 243 A ++M+IA +R G E +V S + DG GE++LL ++ Sbjct: 195 QANASVNRMFIAACDRYGHERGVGWVQGSVIVDADGYPLAGPAEQGGEQMLLATLNLAEA 254 Query: 244 TTSR--RINPYLRDRRPGLY 261 R N +DRRP LY Sbjct: 255 RNKRISARNDLHQDRRPQLY 274 Lambda K H 0.319 0.138 0.414 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: 177 Number of extensions: 11 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: 265 Length of database: 279 Length adjustment: 25 Effective length of query: 240 Effective length of database: 254 Effective search space: 60960 Effective search space used: 60960 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: 47 (22.7 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