Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate WP_011339275.1 RSPH17029_RS15335 carbon-nitrogen hydrolase family protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1170 (264 letters) >NCBI__GCF_000015985.1:WP_011339275.1 Length = 267 Score = 73.6 bits (179), Expect = 4e-18 Identities = 76/252 (30%), Positives = 106/252 (42%), Gaps = 20/252 (7%) Query: 1 MRVALYQCPPLP-----LDVAGNLQRLQQLALEAKGADLLVLPEMFLTGYNIGVDAVSVL 55 MRV+L Q LDVA + R A+ + DL+VLPE F G +AV Sbjct: 1 MRVSLIQMNSAENKERNLDVAEEMIRK---AVGVEKPDLVVLPEYFAF-LGEGREAVHGN 56 Query: 56 AEVY-NGESAQQVARIAKAAGIAILYGYPERTEDGQIYNAVQLIDSDGERVCNYRKTHLF 114 E + G + ++ + +A G+ + G YN + DG + YRK HLF Sbjct: 57 GEAFPEGPTYRRFSALASELGVTLHLGSMVEKAGNGHYNTTLVFGPDGAEIARYRKMHLF 116 Query: 115 G-DLDHSMFSAGSD------EFPIVELNGWKLGFLICYDLEFPENARRLALAGAELILVP 167 D+ M SD E + +G ICYD+ FPE R L GAE+I++P Sbjct: 117 DIDVPGGMSYRESDTISRGEEVVTYRVGETTVGCAICYDIRFPELFRALRDKGAEVIVLP 176 Query: 168 TA-NMIPFDFVADVTVRARAFENQCYVAYANYCG-HEGDIHYC-GQSSIAAPDGSRIAQA 224 A ++ +V RARA E Q Y G H +C G + P G +AQ Sbjct: 177 AAFTLMTGKDHWEVLARARAIETQTYFLAVGQTGSHAEGRKWCWGHTMAIDPWGHVVAQC 236 Query: 225 GLDESLIVGELD 236 E L +D Sbjct: 237 SDGEGLTTAVVD 248 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: 166 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: 264 Length of database: 267 Length adjustment: 25 Effective length of query: 239 Effective length of database: 242 Effective search space: 57838 Effective search space used: 57838 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 Apr 10 2024. 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