Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate GFF2120 HP15_2074 carbon-nitrogen hydrolase family protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1170 (264 letters) >FitnessBrowser__Marino:GFF2120 Length = 307 Score = 103 bits (257), Expect = 4e-27 Identities = 88/284 (30%), Positives = 133/284 (46%), Gaps = 36/284 (12%) Query: 14 DVAGNLQRLQQLALEA--KGADLLVLPEMFLTGYNIGVDAVSV--LAEVYNGESAQQVAR 69 D A +L ++L EA GA+L++L E+ T Y + SV LAE G ++++++ Sbjct: 22 DKAASLATTEKLVREAVASGANLVILQELHATLYFCQTEETSVFELAEPIPGPTSKRLSD 81 Query: 70 IAKAAGIAILYGYPERTEDGQIYNAVQLIDSDGERVCNYRKTHLFGDLDH---------- 119 +A+ GI ++ ER +G +N + + DG YRK H+ D Sbjct: 82 LARELGIVLVGSIFERRMNGVYHNTAVVFEKDGSLAGLYRKMHIPDDPGFYEKFYFTPGD 141 Query: 120 SMFSAGSDEFPIVELNGWKLGFLICYDLEFPENARRLALAGAELILVPTANMIPFDFVAD 179 + F+ G F ++ + +LG L+C+D +PE AR +ALAGAE+++ PTA I +D D Sbjct: 142 AQFNDGRSGFTPIDTSVGRLGVLVCWDQWYPEAARLMALAGAEILIYPTA--IGWDVTDD 199 Query: 180 -----------VTV-RARAFENQCYVAYANYCGHEGD-------IHYCGQSSIAAPDGSR 220 VTV R A N V N G E D I + G S I P G Sbjct: 200 PDEQARQLDAWVTVQRGHAVANNLPVVAPNRVGTEPDPSGHSDGIRFWGNSFICGPQGEL 259 Query: 221 IAQA-GLDESLIVGELDRQLMVDSRAANRYLLDRRPELYGELNK 263 +A+ E ++ LDR R YL DRR + YG++ K Sbjct: 260 LARGDDSSECILAVTLDRSRSESVRRIWPYLRDRRIDAYGDILK 303 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: 179 Number of extensions: 12 Number of successful extensions: 4 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: 307 Length adjustment: 26 Effective length of query: 238 Effective length of database: 281 Effective search space: 66878 Effective search space used: 66878 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