Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate WP_110805530.1 C8J30_RS09125 carbon-nitrogen hydrolase family protein
Query= reanno::pseudo3_N2E3:AO353_07425 (264 letters) >NCBI__GCF_003217355.1:WP_110805530.1 Length = 300 Score = 61.6 bits (148), Expect = 2e-14 Identities = 66/236 (27%), Positives = 96/236 (40%), Gaps = 23/236 (9%) Query: 30 KGADLLVFPE---MFLTGYNIGAEAVGALAEAQDGTCAQYIASIAKASGIAIVYGYPERA 86 K ADLLVFPE M L GA L A + A G+AI +G A Sbjct: 36 KQADLLVFPEYGAMELAALG-GAAVAADLTLAVEEVLRHRAAMERHFEGLAIEFGLYILA 94 Query: 87 EDGQIYNAVQL-----IDSRGQRLANYRKTHLFGELDHSMFSVGPDE-FPLVELNGWKLG 140 G + ++L + R+ + K + + +++GP L + K+G Sbjct: 95 PSGPAQDGLELRNRAVLFGPSGRIGHQDKA-IMTRFEREDWNIGPGRGLTLFDTGIGKIG 153 Query: 141 FLICYDLEFPENARRLALAGAELILVPTANMIPYDF-IADVTVRSRAFENQCYVAYANYC 199 +ICYD EFP +R L AGAE++L P+ + + ++RA ENQC A Sbjct: 154 IVICYDSEFPLLSRGLCEAGAEILLAPSCTDAAAGYNRVRIGSQARALENQCVTVQAPVV 213 Query: 200 G----------HEGEIHYCGQSSIAAPDGSRIAQAGLDE-ALIVGTLDRQLMVDSR 244 G + G G PD IA+ DE +V T+D + SR Sbjct: 214 GLAPWCPAVDENHGAAGIYGPPDEGWPDDGVIAKGVYDEPGWVVATVDLDRVTHSR 269 Lambda K H 0.322 0.139 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: 184 Number of extensions: 12 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: 264 Length of database: 300 Length adjustment: 26 Effective length of query: 238 Effective length of database: 274 Effective search space: 65212 Effective search space used: 65212 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 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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