Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate AO353_28740 AO353_28740 N-carbamoylputrescine amidase
Query= reanno::pseudo1_N1B4:Pf1N1B4_2504 (264 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28740 Length = 302 Score = 105 bits (262), Expect = 1e-27 Identities = 85/276 (30%), Positives = 135/276 (48%), Gaps = 26/276 (9%) Query: 10 PLPLDVAGNLQRLHQLALEA--KGADLLVLPEMFLTGYNIGIDA----VSVLAEVHNGES 63 P D+ NL + QL EA KGA +++L E+F + Y I+ +++ E + Sbjct: 12 PCTWDLKHNLDQAEQLVREAAAKGAQVILLQELFASPY-FCIEQHHKHLALAEEYQHSAV 70 Query: 64 AQQIARIAKTTGIAILYGYPERTEDGQIYNAVQLIDANGERLCNYRKTHL---FGDLDHS 120 ++ A +A+ G+ + + E+ + +N++ + DA+G+ L YRKTH+ G + Sbjct: 71 LKRFAALARELGVVLPLSWFEKAGNAY-FNSLSVADADGQLLGVYRKTHIPNAIGYQEKE 129 Query: 121 MFSPGPDEFPLVELNGWKLGFLICYDLEFPENARRLALAGAELILVPTANMIPYDFIA-- 178 FSPG F + + ++G IC+D FPE AR LAL GAE++L PTA +A Sbjct: 130 YFSPGDTGFRVWDTAFGRIGVGICWDQWFPETARCLALMGAEVLLFPTAIGSEPGCVALD 189 Query: 179 -----DVTVRARAFENQCYVAYANYCGHEG-------EIQYCGQSSIAAPDGSRIAQAGL 226 +T+R A N V AN G E ++ + G S I G +A+A Sbjct: 190 SRDHWQMTMRGHAAANLLPVVAANRIGREVATTDPTLQVNFYGSSFICNHKGKLLAEADR 249 Query: 227 DE-ALIVGELDRQLMIDSRAANRYFLDRRPELYGEL 261 D ++V LD M + R + DRRP++YG L Sbjct: 250 DSTGVLVHSLDLSAMREERLTWGIYRDRRPDMYGAL 285 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: 182 Number of extensions: 13 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: 302 Length adjustment: 26 Effective length of query: 238 Effective length of database: 276 Effective search space: 65688 Effective search space used: 65688 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