Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate CA265_RS08135 CA265_RS08135 amidohydrolase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1170 (264 letters) >FitnessBrowser__Pedo557:CA265_RS08135 Length = 259 Score = 93.6 bits (231), Expect = 4e-24 Identities = 73/224 (32%), Positives = 110/224 (49%), Gaps = 13/224 (5%) Query: 33 DLLVLPEMFLTGYNIGVDAVSVLAEVYNGESAQQVARIAKAAGIAILYGYPERTEDGQIY 92 D++VLPEMF TG+++ +A LAE G++ Q + ++A ++ G E+ Q + Sbjct: 38 DIIVLPEMFNTGFSMNSEA---LAEEMGGKTMQWMQKMAHQYN-CVVTGSIIIKENNQYF 93 Query: 93 NAVQLIDSDGERVCNYRKTHLFGDLDHSMFSAGSDEFPIVELNGWKLGFLICYDLEFPEN 152 N + ++ DG+ +Y K HLFG D + E IVEL GWK+ ICYDL FP Sbjct: 94 NRLIWMEPDGKNQ-HYDKRHLFGMGDEDEHFSPGKEKLIVELKGWKIRLAICYDLRFPVW 152 Query: 153 ARRLALAGAELILV---PTANMIPFDFVADVTVRARAFENQCYVAYANYCGHEGD-IHYC 208 R + L+LV P + + ARA ENQ YV N GH+G+ I++ Sbjct: 153 LRNVDQEYDILLLVANWPDKRSAHW----KALIPARAIENQSYVIAVNRVGHDGNQIYHS 208 Query: 209 GQSSIAAPDGSRIAQAGLDESLIVGELDRQLMVDSRAANRYLLD 252 G S P G+ + DE L ++ + +V R +L D Sbjct: 209 GLSMCLDPYGNTVYYKPEDEDLYTFSINYEELVKVRRQFPFLKD 252 Lambda K H 0.321 0.139 0.411 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: 151 Number of extensions: 9 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: 264 Length of database: 259 Length adjustment: 25 Effective length of query: 239 Effective length of database: 234 Effective search space: 55926 Effective search space used: 55926 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: 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