Align 4-guanidinobutyramide hydrolase; SubName: Full=Carbon-nitrogen hydrolase (characterized, see rationale)
to candidate Pf1N1B4_2504 5-aminopentanamidase (EC 3.5.1.30)
Query= uniprot:A0A291T0X0 (265 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2504 Length = 264 Score = 229 bits (583), Expect = 6e-65 Identities = 129/265 (48%), Positives = 170/265 (64%), Gaps = 8/265 (3%) Query: 4 LRTALLQNSGHPGDPAGNLKVLDEAAARAAADGAGLLVTAEMFLTGYAIG-GGVRDLAEP 62 +R AL Q P D AGNL+ L + A A GA LLV EMFLTGY IG V LAE Sbjct: 1 MRVALYQCPPLPLDVAGNLQRLHQLALEAK--GADLLVLPEMFLTGYNIGIDAVSVLAEV 58 Query: 63 ADGPSGRAVADIAAAHGLAILYGYPER-HAGAVHNSARLVGADGTELANYRKTHLYGCFE 121 +G S + +A IA G+AILYGYPER G ++N+ +L+ A+G L NYRKTHL+G + Sbjct: 59 HNGESAQQIARIAKTTGIAILYGYPERTEDGQIYNAVQLIDANGERLCNYRKTHLFGDLD 118 Query: 122 RASFTPG--ETPVVQATVGELTVGILVCYDVEFPENVRAHALAGTDLLLVPTAQMHPFEF 179 + F+PG E P+V+ +L G L+CYD+EFPEN R ALAG +L+LVPTA M P++F Sbjct: 119 HSMFSPGPDEFPLVELNGWKL--GFLICYDLEFPENARRLALAGAELILVPTANMIPYDF 176 Query: 180 VAESLIPVRAFESQMYIAYVNRSGPEGEFDFVGLSCLAGPDGATCLRAGRGEELLLGDVD 239 +A+ + RAFE+Q Y+AY N G EGE + G S +A PDG+ +AG E L++G++D Sbjct: 177 IADVTVRARAFENQCYVAYANYCGHEGEIQYCGQSSIAAPDGSRIAQAGLDEALIVGELD 236 Query: 240 PKLLTTSRRINPYLRDRRPGLYTSL 264 +L+ SR N Y DRRP LY L Sbjct: 237 RQLMIDSRAANRYFLDRRPELYGEL 261 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: 216 Number of extensions: 12 Number of successful extensions: 3 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: 264 Length adjustment: 25 Effective length of query: 240 Effective length of database: 239 Effective search space: 57360 Effective search space used: 57360 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