Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate GFF1236 Psest_1269 Predicted amidohydrolase
Query= reanno::pseudo1_N1B4:Pf1N1B4_2504 (264 letters) >FitnessBrowser__psRCH2:GFF1236 Length = 264 Score = 94.7 bits (234), Expect = 2e-24 Identities = 82/224 (36%), Positives = 113/224 (50%), Gaps = 27/224 (12%) Query: 1 MRVALYQCPPLPLDVAGNLQRLHQLALEAKGADLLVLPEMFLTGYNIGIDAVSVLAEVHN 60 + +AL Q + D A N +R L +A GADL+VLPEMF TG+++ S LAE Sbjct: 10 LELALVQTSLIWQDAAANHERFATLLDQASGADLIVLPEMFTTGFSM---ESSALAEPEE 66 Query: 61 GES----AQQIARI-AKTTGIAILYGYPERTEDGQIYNAVQLIDANGERLCNYRKTHLFG 115 G + Q AR+ A TG I+ DG N + +GE L +Y K HLF Sbjct: 67 GATYAWLRTQAARLEAVITGSVII-----EAADGSHRNRLLWARPDGEVL-HYDKRHLFR 120 Query: 116 DL-DHSMFSPGPDEFPLVELNGWKLGFLICYDLEFPENARRLALAGAELILV----PTAN 170 +H ++PG + L ELNGW++ LICYDL FP +R G +L+L P A Sbjct: 121 MAGEHKHYTPGQQQ-ALFELNGWRVRPLICYDLRFPVWSR--DPHGTDLLLYTANWPAAR 177 Query: 171 MIPYDFIADVTVRARAFENQCYVAYANYCGHEGE-IQYCGQSSI 213 ++ + + ARA EN CYVA N G +G+ Y G S + Sbjct: 178 RDAWNRL----LPARAIENLCYVAAVNRVGEDGKGYPYSGDSQV 217 Lambda K H 0.322 0.140 0.420 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: 205 Number of extensions: 16 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: 264 Length adjustment: 25 Effective length of query: 239 Effective length of database: 239 Effective search space: 57121 Effective search space used: 57121 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 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